US20040141975A1 - Nucleic acid and corresponding protein entitled 98P4B6 useful in treatment and detection of cancer - Google Patents

Abstract

A novel gene 098P4B6 (also designated STEAP-2) and its encoded protein, and variants thereof, are described wherein 98P4B6 exhibits tissue specific expression in normal adult tissue, and is aberrantly expressed in the cancers listed in Table I. Consequently, 98P4B6 provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 98P4B6 gene or fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response; antibodies or T cells reactive with 98P4B6 can be used in active or passive immunization.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS
• This application is a continuation-in-part of pending U.S. patent application Ser. No. 09/455,486, filed 6 Dec. 1999, and claims priority from U.S. patent application Ser. No. 09/323,873, now U.S. Pat. No. 6,329, 503 filed 1 Jun. 1999, and this application claims priority from U.S. provisional application U.S. Ser. No. not yet assigned, filed 20 Dec. 2002 and U.S. provisional patent application No. 60/317,840, filed Sep. 6, 2001 and U.S. provisional patent application No. 60/370,387 filed Apr. 5, 2002. This application relates to U.S. provisional patent application No. 60/087,520, filed Jun. 1, 1998 and U.S. provisional patent application No. 60/091,183, filed Jun. 30, 1998 and U.S. patent application Ser. No. 10/01 1,095, filed Dec. 6, 2001 and U.S. patent application Ser. No. 10/010,667, filed Dec. 6, 2001 and U.S. provisional patent application No. 60/296,656, filed Jun. 6, 2001, and U.S. patent application Ser. No. 10/165,044, filed Jun. 6, 2002. The contents of the applications listed in this paragraph are fully incorporated by reference herein.[0001]
STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH
• Not applicable. [0002]
FIELD OF THE INVENTION
• The invention described herein relates to genes and their encoded proteins, termed 98P4B6 or STEAP-2, expressed in certain cancers, and to diagnostic and therapeutic methods and compositions useful in the management of cancers that express 98P4B6. [0003]
BACKGROUND OF THE INVENTION
• Cancer is the second leading cause of human death next to coronary disease. Worldwide, millions of people die from cancer every year. In the United States alone, as reported by the American Cancer Society, cancer causes the death of well over a half-million people annually, with over 1.2 million new cases diagnosed per year. While deaths from heart disease have been declining significantly, those resulting from cancer generally are on the rise. In the early part of the next century, cancer is predicted to become the leading cause of death. [0004]
• Worldwide, several cancers stand out as the leading killers. In particular, carcinomas of the lung, prostate, breast, colon, pancreas, and ovary represent the primary causes of cancer death. These and virtually all other carcinomas share a common lethal feature. With very few exceptions, metastatic disease from a carcinoma is fatal. Moreover, even for those cancer patients who initially survive their primary cancers, common experience has shown that their lives are dramatically altered. Many cancer patients experience strong anxieties driven by the awareness of the potential for recurrence or treatment failure. Many cancer patients experience physical debilitations following treatment. Furthermore, many cancer patients experience a recurrence. [0005]
• Worldwide, prostate cancer is the fourth most prevalent cancer in men. In North America and Northern Europe, it is by far the most common cancer in males and is the second leading cause of cancer death in men. In the United States alone, well over 30,000 men die annually of this disease—second only to lung cancer. Despite the magnitude of these figures, there is still no effective treatment for metastatic prostate cancer. Surgical prostatectomy, radiation therapy, hormone ablation therapy, surgical castration and chemotherapy continue to be the main treatment modalities. Unfortunately, these treatments are ineffective for many and are often associated with undesirable consequences. [0006]
• On the diagnostic front, the lack of a prostate tumor marker that can accurately detect early-stage, localized tumors remains a significant limitation in the diagnosis and management of this disease. Although the serum prostate specific antigen (PSA) assay has been a very useful tool, however its specificity and general utility is widely regarded as lacking in several important respects. [0007]
• Progress in identifying additional specific markers for prostate cancer has been improved by the generation of prostate cancer xenografts that can recapitulate different stages of the disease in mice. The LAPC ([0008] Los Angeles Prostate Cancer) xenografts are prostate cancer xenografts that have survived passage in severe combined immune deficient (SCID) mice and have exhibited the capacity to mimic the transition from androgen dependence to androgen independence (Klein et al, 1997, Nat. Med. 3:402). More recently identified prostate cancer markers include PCTA-1 (Su et al., 1996, Proc. Natl. Acad. Sci. USA 93: 7252), prostate-specific membrane (PSM) antigen (Pinto et al., Clin Cancer Res 1996 Sep. 2 (9): 1445-51), STEAP (Hubert, et al., Proc Natl Acad Sci U S A. 1999 Dec. 7; 96(25): 14523-8) and prostate stem cell antigen (PSCA) (Reiter et al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).
• While previously identified markers such as PSA, PSM, PCTA and PSCA have facilitated efforts to diagnose and treat prostate cancer, there is need for the identification of additional markers and therapeutic targets for prostate and related cancers in order to further improve diagnosis and therapy. [0009]
• Renal cell carcinoma (RCC) accounts for approximately 3 percent of adult malignancies. Once adenomas reach a diameter of 2 to 3 cm, malignant potential exists. In the adult, the two principal malignant renal tumors are renal cell adenocarcinoma and transitional cell carcinoma of the renal pelvis or ureter. The incidence of renal cell adenocarcinoma is estimated at more than 29,000 cases in the United States, and more than 11,600 patients died of this disease in 1998. Transitional cell carcinoma is less frequent, with an incidence of approximately 500 cases per year in the United States. [0010]
• Surgery has been the primary therapy for renal cell adenocarcinoma for many decades. Until recently, metastatic disease has been refractory to any systemic therapy. With recent developments in systemic therapies, particularly immunotherapies, metastatic renal cell carcinoma may be approached aggressively in appropriate patients with a possibility of durable responses. Nevertheless, there is a remaining need for effective therapies for these patients. [0011]
• Of all new cases of cancer in the United States, bladder cancer represents approximately 5 percent in men (fifth most common neoplasm) and 3 percent in women (eighth most common neoplasm). The incidence is increasing slowly, concurrent with an increasing older population. In 1998, there was an estimated 54,500 cases, including 39,500 in men and 15,000 in women. The age-adjusted incidence in the United States is 32 per 100,000 for men and eight per 100,000 in women. The historic male/female ratio of 3:1 may be decreasing related to smoking patterns in women. There were an estimated 11,000 deaths from bladder cancer in 1998 (7,800 in men and 3,900 in women). Bladder cancer incidence and mortality strongly increase with age and will be an increasing problem as the population becomes more elderly. [0012]
• Most bladder cancers recur in the bladder. Bladder cancer is managed with a combination of transurethral resection of the bladder (TUR) and intravesical chemotherapy or immunotherapy. The multifocal and recurrent nature of bladder cancer points out the limitations of TUR. Most muscle-invasive cancers are not cured by TUR alone. Radical cystectomy and urinary diversion is the most effective means to eliminate the cancer but carry an undeniable impact on urinary and sexual function. There continues to be a significant need for treatment modalities that are beneficial for bladder cancer patients. [0013]
• An estimated 130,200 cases of colorectal cancer occurred in 2000 in the United States, including 93,800 cases of colon cancer and 36,400 of rectal cancer. Colorectal cancers are the third most common cancers in men and women. Incidence rates declined significantly during 1992-1996 (−2.1% per year). Research suggests that these declines have been due to increased screening and polyp removal, preventing progression of polyps to invasive cancers. There were an estimated 56,300 deaths (47,700 from colon cancer, 8,600 from rectal cancer) in 2000, accounting for about 11% of all U.S. cancer deaths. [0014]
• At present, surgery is the most common form of therapy for colorectal cancer, and for cancers that have not spread, it is frequently curative. Chemotherapy, or chemotherapy plus radiation, is given before or after surgery to most patients whose cancer has deeply perforated the bowel wall or has spread to the lymph nodes. A permanent colostomy (creation of an abdominal opening for elimination of body wastes) is occasionally needed for colon cancer and is infrequently required for rectal cancer. There continues to be a need for effective diagnostic and treatment modalities for colorectal cancer. [0015]
• There were an estimated 164,100 new cases of lung and bronchial cancer in 2000, accounting for 14% of all U.S. cancer diagnoses. The incidence rate of lung and bronchial cancer is declining significantly in men, from a high of 86.5 per 100,000 in 1984 to 70.0 in 1996. In the 1990s, the rate of increase among women began to slow. In 1996, the incidence rate in women was 42.3 per 100,000. [0016]
• Lung and bronchial cancer caused an estimated 156,900 deaths in 2000, accounting for 28% of all cancer deaths. During 1992-1996, mortality from lung cancer declined significantly among men (−1.7% per year) while rates for women were still significantly increasing (0.9% per year). Since 1987, more women have died each year of lung cancer than breast cancer, which, for over 40 years, was the major cause of cancer death in women. Decreasing lung cancer incidence and mortality rates most likely resulted from decreased smoking rates over the previous 30 years; however, decreasing smoking patterns among women lag behind those of men. Of concern, although the declines in adult tobacco use have slowed, tobacco use in youth is increasing again. [0017]
• Treatment options for lung and bronchial cancer are determined by the type and stage of the cancer and include surgery, radiation therapy, and chemotherapy. For many localized cancers, surgery is usually the treatment of choice. Because the disease has usually spread by the time it is discovered, radiation therapy and chemotherapy are often needed in combination with surgery. Chemotherapy alone or combined with radiation is the treatment of choice for small cell lung cancer; on this regimen, a large percentage of patients experience remission, which in some cases is long lasting. There is however, an ongoing need for effective treatment and diagnostic approaches for lung and bronchial cancers. [0018]
• An estimated 182,800 new invasive cases of breast cancer were expected to occur among women in the United States during 2000. Additionally, about 1,400 new cases of breast cancer were expected to be diagnosed in men in 2000. After increasing about 4% per year in the 1980s, breast cancer incidence rates in women have leveled off in the 1990s to about 110.6 cases per 100,000. [0019]
• In the U.S. alone, there were an estimated 41,200 deaths (40,800 women, 400 men) in 2000 due to breast cancer. Breast cancer ranks second among cancer deaths in women. According to the most recent data, mortality rates declined significantly during 1992-1996 with the largest decreases in younger women, both white and black. These decreases were probably the result of earlier detection and improved treatment. [0020]
• Taking into account the medical circumstances and the patient's preferences, treatment of breast cancer may involve lumpectomy (local removal of the tumor) and removal of the lymph nodes under the arm; mastectomy (surgical removal of the breast) and removal of the lymph nodes under the arm; radiation therapy; chemotherapy; or hormone therapy. Often, two or more methods are used in combination. Numerous studies have shown that, for early stage disease, long-term survival rates after lumpectomy plus radiotherapy are similar to survival rates after modified radical mastectomy. Significant advances in reconstruction techniques provide several options for breast reconstruction after mastectomy. Recently, such reconstruction has been done at the same time as the mastectomy. [0021]
• Local excision of ductal carcinoma in situ (DCIS) with adequate amounts of surrounding normal breast tissue may prevent the local recurrence of the DCIS. Radiation to the breast and/or tamoxifen may reduce the chance of DCIS occurring in the remaining breast tissue. This is important because DCIS, if left untreated, may develop into invasive breast cancer. Nevertheless, there are serious side effects or sequelae to these treatments. There is, therefore, a need for efficacious breast cancer treatments. [0022]
• There were an estimated 23,100 new cases of ovarian cancer in the United States in 2000. It accounts for 4% of all cancers among women and ranks second among gynecologic cancers. During 1992-1996, ovarian cancer incidence rates were significantly declining. Consequent to ovarian cancer, there were an estimated 14,000 deaths in 2000. Ovarian cancer causes more deaths than any other cancer of the female reproductive system. [0023]
• Surgery, radiation therapy, and chemotherapy are treatment options for ovarian cancer. Surgery usually includes the removal of one or both ovaries, the fallopian tubes (salpingo-oophorectomy), and the uterus (hysterectomy). In some very early tumors, only the involved ovary will be removed, especially in young women who wish to have children. In advanced disease, an attempt is made to remove all intra-abdominal disease to enhance the effect of chemotherapy. There continues to be an important need for effective treatment options for ovarian cancer. [0024]
• There were an estimated 28,300 new cases of pancreatic cancer in the United States in 2000. Over the past 20 years, rates of pancreatic cancer have declined in men. Rates among women have remained approximately constant but may be beginning to decline. Pancreatic cancer caused an estimated 28,200 deaths in 2000 in the United States. Over the past 20 years, there has been a slight but significant decrease in mortality rates among men (about −0.9% per year) while rates have increased slightly among women. [0025]
• Surgery, radiation therapy, and chemotherapy are treatment options for pancreatic cancer. These treatment options can extend survival and/or relieve symptoms in many patients but are not likely to produce a cure for most. There is a significant need for additional therapeutic and diagnostic options for pancreatic cancer. [0026]
SUMMARY OF THE INVENTION
• The present invention relates to a gene, designated 98P4B6, that has now been found to be over-expressed in the cancer(s) listed in Table I. Northern blot expression analysis of 98P4B6 gene expression in normal tissues shows a restricted expression pattern in adult tissues. The nucleotide (FIG. 2) and amino acid (FIG. 2, and FIG. 3) sequences of 98P4B6 are provided. The tissue-related profile of 98P4B6 in normal adult tissues, combined with the over-expression observed in the tissues listed in Table I, shows that 98P4B6 is aberrantly over-expressed in at least some cancers, and thus serves as a useful diagnostic, prophylactic, prognostic, and/or therapeutic target for cancers of the tissue(s) such as those listed in Table I. [0027]
• The invention provides polynucleotides corresponding or complementary to all or part of the 98P4B6 genes, mRNAs, and/or coding sequences, preferably in isolated form, including polynucleotides encoding 98P4B6-related proteins and fragments of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 contiguous amino acids; at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more than 100 contiguous amino acids of a 98P4B6-related protein, as well as the peptides/proteins themselves; DNA, RNA, DNA/RNA hybrids, and related molecules, polynucleotides or oligonucleotides complementary or having at least a 90% homology to the 98P4B6 genes or mRNA sequences or parts thereof, and polynucleotides or oligonucleotides that hybridize to the 98P4B6 genes, mRNAs, or to 98P4B6-encoding polynucleotides. Also provided are means for isolating cDNAs and the genes encoding 98P4B6. Recombinant DNA molecules containing 98P4B6 polynucleotides, cells transformed or transduced with such molecules, and host-vector systems for the expression of 98P4B6 gene products are also provided. The invention further provides antibodies that bind to 98P4B6 proteins and polypeptide fragments thereof, including polyclonal and monoclonal antibodies, murine and other mammalian antibodies, chimeric antibodies, humanized and fully human antibodies, and antibodies labeled with a detectable marker or therapeutic agent. In certain embodiments, there is a proviso that the entire nucleic acid sequence of FIG. 2 is not encoded and/or the entire amino acid sequence of FIG. 2 is not prepared. In certain embodiments, the entire nucleic acid sequence of FIG. 2 is encoded and/or the entire amino acid sequence of FIG. 2 is prepared, either of which are in respective human unit dose forms. [0028]
• The invention further provides methods for detecting the presence and status of 98P4B6 polynucleotides and proteins in various biological samples, as well as methods for identifying cells that express 98P4B6. A typical embodiment of this invention provides methods for monitoring 98P4B6 gene products in a tissue or hematology sample having or suspected of having some form of growth dysregulation such as cancer. [0029]
• The invention further provides various immunogenic or therapeutic compositions and strategies for treating cancers that express 98P4B6 such as cancers of tissues listed in Table I, including therapies aimed at inhibiting the transcription, translation, processing or function of 98P4B6 as well as cancer vaccines. In one aspect, the invention provides compositions, and methods comprising them, for treating a cancer that expresses 98P4B6 in a human subject wherein the composition comprises a carrier suitable for human use and a human unit dose of one or more than one agent that inhibits the production or function of 98P4B6. Preferably, the carrier is a uniquely human carrier. In another aspect of the invention, the agent is a moiety that is immunoreactive with 98P4B6 protein. Non-limiting examples of such moieties include, but are not limited to, antibodies (such as single chain, monoclonal, polyclonal, humanized, chimeric, or human antibodies), functional equivalents thereof (whether naturally occurring or synthetic), and combinations thereof. The antibodies can be conjugated to a diagnostic or therapeutic moiety. In another aspect, the agent is a small molecule as defined herein. [0030]
• In another aspect, the agent comprises one or more than one peptide which comprises a cytotoxic T lymphocyte (CTL) epitope that binds an HLA class I molecule in a human to elicit a CTL response to 98P4B6 and/or one or more than one peptide which comprises a helper T lymphocyte (HTL) epitope which binds an HLA class II molecule in a human to elicit an HTL response. The peptides of the invention may be on the same or on one or more separate polypeptide molecules. In a further aspect of the invention, the agent comprises one or more than one nucleic acid molecule that expresses one or more than one of the CTL or HTL response stimulating peptides as described above. In yet another aspect of the invention, the one or more than one nucleic acid molecule may express a moiety that is immunologically reactive with 98P4B6 as described above. The one or more than one nucleic acid molecule may also be, or encodes, a molecule that inhibits production of 98P4B6. Non-limiting examples of such molecules include, but are not limited to, those complementary to a nucleotide sequence essential for production of 98P4B6 (e.g. antisense sequences or molecules that form a triple helix with a nucleotide double helix essential for 98P4B6 production) or a ribozyme effective to lyse 98P4B6 mRNA. [0031]
• Note that to determine the starting position of any peptide set forth in Tables VIII-XXI and XXII to XLIX (collectively HLA Peptide Tables) respective to its parental protein, e.g., [0032] variant 1, variant 2, etc., reference is made to three factors: the particular variant, the length of the peptide in an HLA Peptide Table, and the Search Peptides in Table VII. Generally, a unique Search Peptide is used to obtain HLA peptides of a particular for a particular variant. The position of each Search Peptide relative to its respective parent molecule is listed in Table VII. Accordingly, if a Search Peptide begins at position “X”, one must add the value “X−1” to each position in Tables VIII-XXI and XXII to XLIX to obtain the actual position of the HLA peptides in their parental molecule. For example, if a particular Search Peptide begins at position 150 of its parental molecule, one must add 150−1, i.e., 149 to each HLA peptide amino acid position to calculate the position of that amino acid in the parent molecule.
• One embodiment of the invention comprises an HLA peptide, that occurs at least twice in Tables VIII-XXI and XXII to XLIX collectively, or an oligonucleotide that encodes the HLA peptide. Another embodiment of the invention comprises an HLA peptide that occurs at least once in Tables VIII-XXI and at least once in tables XXII to XLIX, or an oligonucleotide that encodes the HLA peptide. [0033]
• Another embodiment of the invention is antibody epitopes, which comprise a peptide regions, or an oligonucleotide encoding the peptide region, that has one two, three, four, or five of the following characteristics: [0034]
• i) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Hydrophilicity profile of FIG. 5; [0035]
• ii) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or less than 0.5, 0.4, 0.3, 0.2, 0.1, or having a value equal to 0.0, in the Hydropathicity profile of FIG. 6; [0036]
• iii) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Percent Accessible Residues profile of FIG. 7; [0037]
• iv) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Average Flexibility profile of FIG. 8; or [0038]
• v) a peptide region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Beta-turn profile of FIG. 9.[0039]
BRIEF DESCRIPTION OF THE FIGURES
• FIG. 1. The 98P4B6 SSH sequence of 183 nucleotides. [0040]
• FIG. 2. A) The cDNA and amino acid sequence of 98P4B6 variant 1 (also called “98P4B6 v.1” or “[0041] 98P4B6 variant 1”) is shown in FIG. 2A. The start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon.
• B) The cDNA and amino acid sequence of 98P4B6 variant 2 (also called “98P4B6 v.2”) is shown in FIG. 2B. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 4-138 including the stop codon. [0042]
• C) The cDNA and amino acid sequence of 98P4B6 variant 3 (also called “98P4B6 v.3”) is shown in FIG. 2C. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 188-1552 including the stop codon. [0043]
• D) The cDNA and amino acid sequence of 98P4B6 variant 4 (also called “98P4B6 v.4”) is shown in FIG. 2D. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 318-1682 including the stop codon. [0044]
• E) The cDNA and amino acid sequence of 98P4B6 variant 5 (also called “98P4B6 v.5”) is shown in FIG. 2E. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 318-1577 including the stop codon. [0045]
• F) The cDNA and amino acid sequence of 98P4B6 variant 6 (also called “98P4B6 v.6”) is shown in FIG. 2F. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 318-1790 including the stop codon. [0046]
• G) The cDNA and amino acid sequence of 98P4B6 variant 7 (also called “98P4B6 v.7”) is shown in FIG. 2G. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 295-2025 including the stop codon. [0047]
• H) The cDNA and amino acid sequence of 98P4B6 variant 8 (also called “98P4B6 v.8”) is shown in FIG. 2H. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0048]
• I) The cDNA and amino acid sequence of 98P4B6 variant 9 (also called “98P4B6 v.9”) is shown in FIG. 21. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0049]
• J) The cDNA and amino acid sequence of 98P4B6 variant 10 (also called “98P4B6v.10”)is shown in FIG. 2J. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0050]
• K) The cDNA and amino acid sequence of 98P4B6 variant 11 (also called “98P4B6 v.11”) is shown in FIG. 2K. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0051]
• L) The cDNA and amino acid sequence of 98P4B6 variant 12 (also called “98P4B6 v.12”) is shown in FIG. 2L. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0052]
• M) The cDNA and amino acid sequence of 98P4B6 variant 13 (also called “98P4B6 v.13”) is shown in FIG. 2M. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0053]
• N) The cDNA and amino acid sequence of 98P4B6 variant 14 (also called “98P4B6 v.14”) is shown in FIG. 2N. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0054]
• O) The cDNA and amino acid sequence of 98P4B6 variant 15 (also called “98P4B6 v.15”) is shown in FIG. 20. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0055]
• P) The cDNA and amino acid sequence of 98P4B6 variant 16 (also called “98P4B6 v.16”) is shown in FIG. 2P. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0056]
• Q) The cDNA and amino acid sequence of 98P4B6 variant 17 (also called “98P4B6 v.17”) is shown in FIG. 2Q. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0057]
• R) The cDNA and amino acid sequence of 98P4B6 variant 18 (also called “98P4B6 v.18”) is shown in FIG. 2R. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0058]
• S) The cDNA and amino acid sequence of 98P4B6 variant 19 (also called “98P4B6 v.19”) is shown in FIG. 2S. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 355-1719 including the stop codon. [0059]
• T) The cDNA and amino acid sequence of 98P4B6 variant 20 (also called “98P4B6 v.20”) is shown in FIG. 2T. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 295-2025 including the stop codon. [0060]
• U) The cDNA and amino acid sequence of 98P4B6 variant 21 (also called “98P4B6 v.21”) is shown in FIG. 2U. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 295-2025 including the stop codon. [0061]
• V) The cDNA and amino acid sequence of 98P4B6 variant 22 (also called “98P4B6 v.22”) is shown in FIG. 2V. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 295-2025 including the stop codon. [0062]
• W) The cDNA and amino acid sequence of 98P4B6 variant 23 (also called “98P4B6 v.23”) is shown in FIG. 2W. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 295-2025 including the stop codon. [0063]
• X) The cDNA and amino acid sequence of 98P4B6 variant 24 (also called “98P4B6 v.24”) is shown in FIG. 2X. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 295-2025 including the stop codon. [0064]
• Y) The cDNA and amino acid sequence of 98P4B6 variant 25 (also called “98P4B6 v.25”) is shown in FIG. 2Y. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0065]
• Z) The cDNA and amino acid sequence of 98P4B6 variant 26 (also called “98P4B6 v.26”) is shown in FIG. 2. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0066]
• AA) The cDNA and amino acid sequence of 98P4B6 variant 27 (also called “98P4B6 v.27”) is shown in FIG. 2AA. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0067]
• AB) The cDNA and amino acid sequence of 98P4B6 variant 28 (also called “98P4B6 v.28”) is shown in FIG. 2AB. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0068]
• AC) The cDNA and amino acid sequence of 98P4B6 variant 29 (also called “98P4B6 v.29”) is shown in FIG. 2AC. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0069]
• AD) The cDNA and amino acid sequence of 98P4B6 variant 30 (also called “98P4B6 v.30”) is shown in FIG. 2AD. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0070]
• AE) The cDNA and amino acid sequence of 98P4B6 variant 31 (also called “98P4B6 v.31”) is shown in FIG. 2AE. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0071]
• AF) The cDNA and amino acid sequence of 98P4B6 variant 32 (also called “98P4B6 v.32”) is shown in FIG. 2AF. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0072]
• AG) The cDNA and amino acid sequence of 98P4B6 variant 33 (also called “98P4B6 v.33”) is shown in FIG. 2AG. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0073]
• AH) The cDNA and amino acid sequence of 98P4B6 variant 34 (also called “98P4B6 v.34”) is shown in FIG. 2AH. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0074]
• AI) The cDNA and amino acid sequence of 98P4B6 variant 35 (also called “98P4B6 v.35”) is shown in FIG. 2AI. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0075]
• AJ) The cDNA and amino acid sequence of 98P4B6 variant 36 (also called “98P4B6 v.36”) is shown in FIG. 2AJ. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0076]
• AK) The cDNA and amino acid sequence of 98P4B6 variant 37 (also called “98P4B6 v.37”) is shown in FIG. 2AK. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0077]
• AL) The cDNA and amino acid sequence of 98P4B6 variant 38 (also called “98P4B6 v.38”) is shown in FIG. 2AL. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 394-1866 including the stop codon. [0078]
• FIG. 3. [0079]
• A) The amino acid sequence of 98P4B6 v.1 is shown in FIG. 3A; it has 454 amino acids. [0080]
• B) The amino acid sequence of 98P4B6 v.2 is shown in FIG. 3B; it has 45 amino acids. [0081]
• C) The amino acid sequence of 98P4B6 v.5 is shown in FIG. 3C; it has 419 amino acids. [0082]
• D) The amino acid sequence of 98P4B6 v.6 is shown in FIG. 3D; it has 490 amino acids. [0083]
• E) The amino acid sequence of 98P4B6 v.7 is shown in FIG. 3E; it has 576 amino acids. [0084]
• F) The amino acid sequence of 98P4B6 v.8 is shown in FIG. 3F; it has 490 amino acids. [0085]
• G) The amino acid sequence of 98P4B6 v.13 is shown in FIG. 3G; it has 454 amino acids. [0086]
• H) The amino acid sequence of 98P4B6 v.14 is shown in FIG. 3H; it has 454 amino acids. [0087]
• I) The amino acid sequence of 98P4B6 v.21 is shown in FIG. 31; it has 576 amino acids. [0088]
• J) The amino acid sequence of 98P4B6 v.25 is shown in FIG. 3J; it has 490 amino acids. [0089]
• As used herein, a reference to 98P4B6 includes all variants thereof, including those shown in FIGS. 2, 3, [0090] 10, and 11, unless the context clearly indicates otherwise.
• FIG. 4. Comparison of 98P4B6 with known genes: Human STAMP1, human six transmembrane epithelial antigen of [0091] prostate 2 and mouse six transmembrane epithelial antigen of prostate 2. FIG. 4(A) Alignment of 98P4B6 variant 1 to human STAMP1 (gi 15418732). FIG. 4(B) Alignment of 98P4B6 variant 1 with human STEAP2 (gi:23308593). FIG. 4(C) Alignment of 98P4B6 variant 1 with mouse STEAP2 (gi 28501136). FIG. 4(D): Clustal Alignment of the three 98P4B6 variants, depicting that 98P4B6 V1B contains an additional 62 aa at its N-terminus relative to V1, and that 98P4B6 V2 carries a I to T point mutation at aa 225 relative to V1.
• FIG. 5. Hydrophilicity amino acid profile of 98P4B6v.1, v.2, v.5, v.6, and v.7 determined by computer algorithm sequence analysis using the method of Hopp and Woods (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828) accessed on the Protscale website located on the World Wide Web at (expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server. [0092]
• FIG. 6. Hydropathicity amino acid profile of 98P4B6v.1, v.2, v.5, v.6, and v.7 determined by computer algorithm sequence analysis using the method of Kyte and Doolittle (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132) accessed on the ProtScale website located on the World Wide Web at (.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server. [0093]
• FIG. 7. Percent accessible residues amino acid profile of 98P4B6v.1, v.2, v.5, v.6, and v.7 determined by computer algorithm sequence analysis using the method of Janin (Janin J., 1979 Nature 277:491-492) accessed on the ProtScale website located on the World Wide Web at (.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server. [0094]
• FIG. 8. Average flexibility amino acid profile of 98P4B6v.1, v.2, v.5, v.6, and v.7 determined by computer algorithm sequence analysis using the method of Bhaskaran and Ponnuswamy (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255) accessed on the ProtScale website located on the World Wide Web at (.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server. [0095]
• FIG. 9. Beta-turn amino acid profile of 98P4B6v.1, v.2, v.5, v.6, and v.7 determined by computer algorithm sequence analysis using the method of Deleage and Roux (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294) accessed on the ProtScale website located on the World Wide Web at (.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular biology server. [0096]
• FIG. 10. FIG. 10([0097] a): Schematic alignment of SNP variants of 98P4B6 v.1. Variants 98P4B6 v.9 through v.19 were variants with single nucleotide difference from v.1. Though these SNP variants were shown separately, they could also occur in any combinations and in any transcript variants, as shown in FIG. 12, that contains the bases. SNP in regions of other transcript variants, such as v.2, v.6 and v.8, not common with v.1 were not shown here. Numbers correspond to those of 98P4B6 v.1. Black box shows the same sequence as 98P4B6 v.1. SNPs are indicated above the box. FIG. 10(b): Schematic alignment of SNP variants of 98P4B6 v.7. Variants 98P4B6 v.20 through v.24 were variants with single nucleotide difference from v.7. Though these SNP variants were shown separately, they could also occur in any combinations and in any transcript variants, as shown in FIG. 12, that contains the bases. Those SNP in regions common with v.1 were not shown here. Numbers correspond to those of 98P4B6 v.7. Black box shows the same sequence as 98P4B6 v.7. SNPs are indicated above the box. FIG. 10(c): Schematic alignment of SNP variants of 98P4B6 v.8. Variants 98P4B6 v.25 through v.38 were variants with single nucleotide difference from v.8. Though these SNP variants were shown separately, they could also occur in any combinations and in any transcript variants, as shown in FIG. 12, that contains the bases. Those SNP in regions of common with v.1 were not shown here. Numbers correspond to those of 98P4B6 v.8. Black box shows the same sequence as 98P4B6 v.8. SNPs are indicated above the box.
• FIG. 11. Schematic alignment of protein variants of 98P4B6. Protein variants corresponded to nucleotide variants. Nucleotide variants 98P4B6 v.3, v.4, v.9 through v.12, and v.15 through v.19 coded for the same protein as v.1. Nucleotide variants 98P4B6 v.6 and v.8 coded the same protein except for single amino acid at 475, which is an “M” in v.8. Variants v.25 was translated from v.25, a SNP variant of v.8, with one amino acid difference at 565. Similarly, v.21 differed from v.7 by one amino acid at 565. Single amino acid differences were indicated above the boxes. Black boxes represent the same sequence as 98P4B6 v.1. Numbers underneath the box correspond to 98P4B6 v.1. [0098]
• FIG. 12. Structure of transcript variants of 98P4B6. Variant 98P4B6 v.2 through v.8 were transcript variants of v.1. Variant v.2 was a single exon transcript whose 3′ portion was the same as the last exon of v.1. The first two exons of v.3 were in [0099] intron 1 of v. 1. Variants v.4, v.5 and v.6 spliced out 224-334 in the first exon of v.1. In addition, v.5 spliced out exon 5 while v.6 spliced out exon 6 but extended exon 5 of v.1. Variant v.7 used alternative transcription start and different 3′ exons. Variant v.8 extended 5′ end and kept the whole intron 5 of v.1. The first 35 bases of v.1 were not in the nearby 5′ region of v.1 on the current assembly of the human genome. Ends of exons in the transcripts are marked above the boxes. Potential exons of this gene are shown in order as on the human genome. Poly A tails and single nucleotide differences are not shown in the figure. Numbers in “()” underneath the boxes correspond to those of 98P4B6 v.1. Lengths of introns and exons are not proportional.
• FIG. 13. Secondary structure and transmembrane domains prediction for 98P4B6 protein variants. [0100] 13(A), 13(B), 13(C), 13(D), 13(E): The secondary structure of 98P4B6 protein variant 1 (SEQ ID NO: 193), Variant 2 (SEQ ID NO: 194), Variant 5 (SEQ ID NO: 195), Variant 6 (SEQ ID NO: 196), and Variant 7 (SEQ ID NO: 197) were predicted using the HNN—Hierarchical Neural Network method (Guermeur, 1997, located on the World Wide Web at .pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html, accessed from the ExPasy molecular biology server located on the World Wide Web at .expasy.ch/tools. This method predicts the presence and location of alpha helices, extended strands, and random coils from the primary protein sequence. The percent of the protein in a given secondary structure is also listed.
• [0101] 13(F), 13(H), 13(J), 13(L), and 13(N): Schematic representations of the probability of existence of transmembrane regions and orientation of 98P4B6 variants 1, 2, 5-7, respectively, based on the TMpred algorithm of Hofmann and Stoffel which utilizes TMBASE (K. Hofmann, W. Stoffel. TMBASE—A database of membrane spanning protein segments Biol. Chem. Hoppe-Seyler 374:166,1993). 13(G), 13(I), 13(K), 13(M), and 13(O): Schematic representations of the probability of the existence of transmembrane regions and the extracellular and intracellular orientation of 98P4B6 variants 1, 2, 5-7, respectively, based on the TMHMM algorithm of Sonnhammer, von Heijne, and Krogh (Erik L. L. Sonnhammer, Gunnar von Heijne, and Anders Krogh: A hidden Markov model for predicting transmembrane helices in protein sequences. In Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, p 175-182 Ed J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen Menlo Park, Calif.: AAAI Press, 1998). The TMpred and TMHMM algorithms are accessed from the ExPasy molecular biology server located on the World Wide Web at .expasy.ch/tools/.
• FIG. 14. 98P4B6 Expression in Human Normal and Patient Cancer Tissues. First strand cDNA was generated from normal stomach, normal brain, normal heart, normal liver, normal skeletal muscle, normal testis, normal prostate, normal bladder, normal kidney, normal colon, normal lung, normal pancreas, and a pool of cancer specimens from prostate cancer patients, bladder cancer patients, kidney cancer patients, colon cancer patients, lung cancer patients, pancreas cancer patients, and a pool of 2 patient prostate metastasis to lymph node. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers directed to 98P4B6 v.1, v.13, and v.14 (A), or directed specifically to the splice variants 98P4B6 v.6 and v.8 (B), was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Results show strong expression of 98P4B6 v.1, v.13, and v.14 and its splice variants v.6 and v.8 in normal prostate and in prostate cancer. Expression was also detected in bladder cancer, kidney cancer, colon cancer, lung cancer, pancreas cancer, breast cancer, cancer metastasis as well as in the prostate cancer metastasis to lymph node specimens, compared to all normal tissues tested. [0102]
• FIG. 15. 98P4B6 Expression in lung, ovary, prostate, bladder, cervix, uterus and pancreas patient cancer specimens. First strand cDNA was prepared from a panel of patient cancer specimens. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 98P4B6 v.1, v.13, and v.14, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Expression was recorded as absent, low, medium or strong. Results show expression of 98P4B6 in the majority of all patient cancer specimens tested. [0103]
• FIG. 16. Expression of 98P4B6 in stomach cancer patient specimens. (A) RNA was extracted from normal stomach (N) and from 10 different stomach cancer patient specimens (T). Northern blot with 10 μg of total RNA/lane was probed with 98P4B6 sequence. Results show strong expression of 98P4B6 in the stomach tumor tissues and lower expression in normal stomach. The lower panel represents ethidium bromide staining of the blot showing quality of the RNA samples. (B) Expression of 98P4B6 was assayed in a panel of human stomach cancers (T) and their respective matched normal tissues (N) on RNA dot blots. 98P4B6 was detected in 7 out of 8 stomach tumors but not in the matched normal tissue. [0104]
• FIG. 17. Detection of 98P4B6 expression with polyclonal antibody. 293T cells were transfected with 98P4B6.GFP.pcDNA3.1/mychis construct clone A12 or clone B12. STEAP1.GFP vector was used as a positive control. And as a negative control an empty vector was used. Forty hours later, cell Iysates were collected. Samples were run on an SDS-PAGE acrylamide gel, blotted and stained with either anti-GFP antibody (A), anti-98P4B6 antibody generated against amino acids 198-389 (B), or anti-98P4B6 antibody generated against amino acids 153-165. The blot was developed using the ECL chemiluminescence kit and visualized by autoradiography. Results show expression of the expected 98P4B6.GFP fusion protein as detected by the anti-GFP antibody. Also, we were able to raise 2 different polyclonal antibodies that recognized the 98P4B6.GFP fusion proteins as shown in B and C. [0105]
• FIG. 18. Detection of 98P4B6 expression with polyclonal antibody. 293T cells were transfected with 98P4B6.GFP.pcDNA3.1/mychis construct clone A12 or clone B12. Expression of the 98P4B6.GFP fusion protein was detected by flow cytometry (A) and by flurorescent microscopy (B). Results show strong green fluorescence in the majority of the cells. The fusion protein localized to the perinuclear area and to the cell membrane. [0106]
• FIG. 19. STEAP-2 Characteristics. The expression of STEAP-2 in normal tissues is predominantly restricted to the prostate. STEAP-2 is expressed in several cancerous tissues. In patient-derived prostate, colon, and lung cancer specimens; and Multiple cancer cell lines, including prostate, colon, Ewing's sarcoma, lung, kidney, pancreas and testis. By ISH, STEAP-2 expression appears to be primarily limited to ductal epithelial cells. [0107]
• FIG. 20. STEAP-2 Induces Tyrosine Phosphorylation in PC3 Cells. STEAP-2 induces the tyrosine phosphorylation of proteins at 140-150, 120, 75-80, 62 and 40 kDa. [0108]
• FIG. 21. STEAP-2 Enhances Tyrosine Phosphorylation in NIH 3T3 Cells. STEAP-2 enhances the phosphorylation of p135-140, p78-75 by STEAP-2 in NIH 3T3 cells. STEAP-2 C-Flag enhances the phosphorylation of p180, and induces the de-phosphorylation of p132, p82 and p75. [0109]
• FIG. 22. STEAP-2 Induces ERK Phosphorylation. STEAP-2 Induces ERK phosphorylation in PC3 and 3T3 cells in 0.5 and 10% FBS. Lack or ERK phosphorylation in 3T3-STEAP-2-cflag cells. Potential role as dominant negative. [0110]
• FIG. 23. STEAP Enhances Calcium Flux in PC3 cells. PC-STEAP-1 and PC3-STEAP-2 exhibit enhanced calcium flux in response to LPA. PC3-STEAP-1 demonstrates susceptibility to the L type calcium channel inhibitor, conotoxin. PC3-STEAP-2 shown susceptibility to the PQ type calcium channel inhibitor, agatoxin. NDGA and TEA had no effect on the proliferation of PC3-STEAP-2 cells. [0111]
• FIG. 24. STEAP-2 Alters the Effect of Paclitaxel on PC3 Cells. Other Chemotherapeutics Tested without yielding a differential response between STEAP-expressing and control cells were Flutamide, Genistein, Rapamycin. STEAP-2 confers partial resistance to Paclitaxel in PC3 cells. Over 8 fold increase in percent survival of PC3-STEAP-2 relative to PC3-Neo cells. [0112]
• FIG. 25. Inhibition of Apoptosis by STEAP-2. PC3 cells were treated with paclitaxel for 60 hours and analyzed for apoptosis by annexinV-PI staining. Expression of STEAP-2 partially inhibits apoptosis by paclitaxel. [0113]
• FIG. 26. STEAP-2 Attenuates Paclitaxel Mediated Apoptosis. PC3 cells were treated with paclitaxel for 68 hours and analyzed for apoptosis. Expression of STEAP-2, but not STEAP-2CFlag, partially inhibits apoptosis by paclitaxel.[0114]
DETAILED DESCRIPTION OF THE INVENTION
• Outline of Sections [0115]
• I.) Definitions [0116]
• II.) 98P4B6 Polynucleotides [0117]
• II.A.) Uses of 98P4B6 Polynucleotides [0118]
• II.A.1.) Monitoring of Genetic Abnormalities [0119]
• II.A.2.) Antisense Embodiments [0120]
• II.A.3.) Primers and Primer Pairs [0121]
• II.A.4.) Isolation of 98P4B6-Encoding Nucleic Acid Molecules [0122]
• II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems [0123]
• III) 98P4B6-related Proteins [0124]
• III.A.) Motif-bearing Protein Embodiments [0125]
• III.B.) Expression of 98P4B6-related Proteins [0126]
• III.C.) Modifications of 98P4B6-related Proteins [0127]
• III.D.) Uses of 98P4B6-related Proteins [0128]
• IV.) 98P4B6 Antibodies [0129]
• V.) 98P4B6 Cellular Immune Responses [0130]
• VI.) 98P4B6 Transgenic Animals [0131]
• VII.) Methods for the Detection of 98P4B6 [0132]
• VIII.) Methods for Monitoring the Status of 98P4B6-related Genes and Their Products [0133]
• IX.) Identification of Molecules That Interact With 98P4B6 [0134]
• X.) Therapeutic Methods and Compositions [0135]
• X.A.) Anti-Cancer Vaccines [0136]
• X.B.) 98P4B6 as a Target for Antibody-Based Therapy [0137]
• X.C.) 98P4B6 as a Target for Cellular Immune Responses [0138]
• X.C.1. Minigene Vaccines [0139]
• X.C.2. Combinations of CTL Peptides with Helper Peptides [0140]
• X.C.3. Combinations of CTL Peptides with T Cell Priming Agents [0141]
• X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides [0142]
• X.D.) Adoptive Immunotherapy [0143]
• X.E.) Administration of Vaccines for Therapeutic or Prophylactic Purposes [0144]
• XI.) Diagnostic and Prognostic Embodiments of 98P4B6. [0145]
• XII.) Inhibition of 98P4B6 Protein Function [0146]
• XII.A.) Inhibition of 98P4B6 With Intracellular Antibodies [0147]
• XII.B.) Inhibition of 98P4B6 with Recombinant Proteins [0148]
• XII.C.) Inhibition of 98P4B6 Transcription or Translation [0149]
• XII.D.) General Considerations for Therapeutic Strategies [0150]
• XIII.) Identification, Characterization and Use of Modulators of 98P4B6 [0151]
• XIV.) KITS/Articles of Manufacture [0152]
• I.) Definitions: [0153]
• Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. Many of the techniques and procedures described or referenced herein are well understood and commonly employed using conventional methodology by those skilled in the art, such as, for example, the widely utilized molecular cloning methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd. edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted. [0154]
• The terms “advanced prostate cancer”, “locally advanced prostate cancer”, “advanced disease” and “locally advanced disease” mean prostate cancers that have extended through the prostate capsule, and are meant to include stage C disease under the American Urological Association (AUA) system, stage C1-C2 disease under the Whitmore-Jewett system, and stage T3-T4 and N+ disease under the TNM (tumor, node, metastasis) system. In general, surgery is not recommended for patients with locally advanced disease, and these patients have substantially less favorable outcomes compared to patients having clinically localized (organ-confined) prostate cancer. Locally advanced disease is clinically identified by, palpable evidence of induration beyond the lateral border of the prostate, or asymmetry or induration above the prostate base. Locally advanced prostate cancer is presently diagnosed pathologically following radical prostatectomy if the tumor invades or penetrates the prostatic capsule, extends into the surgical margin, or invades the seminal vesicles. [0155]
• “Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence 98P4B6 (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence 98P4B6. In addition, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present. [0156]
• The term “analog” refers to a molecule which is structurally similar or shares similar or corresponding attributes with another molecule (e.g. a 98P4B6-related protein). For example, an analog of a 98P4B6 protein can be specifically bound by an antibody or T cell that specifically binds to 98P4B6. [0157]
• The term “antibody” is used in the broadest sense. Therefore, an “antibody” can be naturally occurring or man-made such as monoclonal antibodies produced by conventional hybridoma technology. Anti-98P4B6 antibodies comprise monoclonal and polyclonal antibodies as well as fragments containing the antigen-binding domain and/or one or more complementarity determining regions of these antibodies. [0158]
• An “antibody fragment” is defined as at least a portion of the variable region of the immunoglobulin molecule that binds to its target, i.e., the antigen-binding region. In one embodiment it specifically covers single anti-98P4B6 antibodies and clones thereof (including agonist, antagonist and neutralizing antibodies) and anti-98P4B6 antibody compositions with polyepitopic specificity. [0159]
• The term “codon optimized sequences” refers to nucleotide sequences that have been optimized for a particular host species by replacing any codons having a usage frequency of less than about 20%. Nucleotide sequences that have been optimized for expression in a given host species by elimination of spurious polyadenylation sequences, elimination of exon/intron splicing signals, elimination of transposon-like repeats and/or optimization of GC content in addition to codon optimization are referred to herein as an “expression enhanced sequences.”[0160]
• A “combinatorial library” is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical “building blocks” such as reagents. For example, a linear combinatorial chemical library, such as a polypeptide (e.g., mutein) library, is formed by combining a set of chemical building blocks called amino acids in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Numerous chemical compounds are synthesized through such combinatorial mixing of chemical building blocks (Gallop et al., J. Med. Chem. 37(9): 1233-1251 (1994)). [0161]
• Preparation and screening of combinatorial libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Pat. No. 5,010,175, Furka, Pept. Prot. Res. 37:487-493 (1991), Houghton et al., Nature, 354:84-88 (1991)), peptoids (PCT Publication No WO 91/19735), encoded peptides (PCT Publication WO 93/20242), random bio-oligomers (PCT Publication WO 92/00091), benzodiazepines (U.S. Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc. Nat. Acad. Sci. USA 90:6909-6913 (1993)), vinylogous polypeptides (Hagihara et al., J. Amer. Chem. Soc. 114:6568 (1992)), nonpeptidal peptidomimetics with a Beta-D-Glucose scaffolding (Hirschmann et al., J. Amer. Chem. Soc. 114:9217-9218 (1992)), analogous organic syntheses of small compound libraries (Chen et al., J. Amer. Chem. Soc. 116:2661 (1994)), oligocarbamates (Cho, et al., Science 261:1303 (1993)), and/or peptidyl phosphonates (Campbell et al., J. Org. Chem. 59:658 (1994)). See, generally, Gordon et al., J. Med. Chem. 37:1385 (1994), nucleic acid libraries (see, e.g., Stratagene, Corp.), peptide nucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083), antibody libraries (see, e.g., Vaughn et al., Nature Biotechnology 14(3): 309-314 (1996), and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang et al., Science 274:1520-1522 (1996), and U.S. Pat. No. 5,593,853), and small organic molecule libraries (see, e.g., benzodiazepines, Baum, C&EN, January 18, page 33 (1993); isoprenoids, U.S. Pat. No. 5,569,588; thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No. 5,506, 337; benzodiazepines, U.S. Pat. No. 5,288,514; and the like). [0162]
• Devices for the preparation of combinatorial libraries are commercially available (see, e.g., 357 NIPS, 390 NIPS, Advanced Chem Tech, Louisville Ky.; Symphony, Rainin, Woburn, Mass.; 433A, Applied Biosystems, Foster City, Calif.; 9050, Plus, Millipore, Bedford, NIA). A number of well-known robotic systems have also been developed for solution phase chemistries. These systems include automated workstations such as the automated synthesis apparatus developed by Takeda Chemical Industries, LTD. (Osaka, Japan) and many robotic systems utilizing robotic arms (Zymate H, Zymark Corporation, Hopkinton, Mass.; Orca, Hewlett-Packard, Palo Alto, Calif.), which mimic the manual synthetic operations performed by a chemist. Any of the above devices are suitable for use with the present invention. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein will be apparent to persons skilled in the relevant art. In addition, numerous combinatorial libraries are themselves commercially available (see, e.g., ComGenex, Princeton, N.J.; Asinex, Moscow, RU; Tripos, Inc., St. Louis, Mo.; ChemStar, Ltd, Moscow, RU; 3D Pharmaceuticals, Exton, Pa.; Martek Biosciences, Columbia, Md.; etc.). [0163]
• The term “cytotoxic agent” refers to a substance that inhibits or prevents the expression activity of cells, function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes chemotherapeutic agents, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof. Examples of cytotoxic agents include, but are not limited to auristatins, auromycins, maytansinoids, yttrium, bismuth, ricin, ricin A-chain, combrestatin, duocarmycins, dolostatins, doxorubicin, daunorubicin, taxol, cisplatin, cc1065, ethidium bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, actinomycin, diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin, retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin, [0164] Sapaonaria officinalis inhibitor, and glucocorticoid and other chemotherapeutic agents, as well as radioisotopes such as At²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi^212or213, P³² and radioactive isotopes of Lu including Lu¹⁷⁷. Antibodies may also be conjugated to an anti-cancer pro-drug activating enzyme capable of converting the pro-drug to its active form.
• The “gene product” is sometimes referred to herein as a protein or mRNA. For example, a “gene product of the invention” is sometimes referred to herein as a “cancer amino acid sequence”, “cancer protein”, “protein of a cancer listed in Table I”, a “cancer mRNA”, “mRNA of a cancer listed in Table I”, etc. In one embodiment, the cancer protein is encoded by a nucleic acid of FIG. 2. The cancer protein can be a fragment, or alternatively, be the full-length protein to the fragment encoded by the nucleic acids of FIG. 2. In one embodiment, a cancer amino acid sequence is used to determine sequence identity or similarity. In another embodiment, the sequences are naturally occurring allelic variants of a protein encoded by a nucleic acid of FIG. 2. In another embodiment, the sequences are sequence variants as further described herein. [0165]
• “High throughput screening” assays for the presence, absence, quantification, or other properties of particular nucleic acids or protein products are well known to those of skill in the art. Similarly, binding assays and reporter gene assays are similarly well known. Thus, e.g., U.S. Pat. No. 5,559,410 discloses high throughput screening methods for proteins; U.S. Pat. No. 5,585,639 discloses high throughput screening methods for nucleic acid binding (i.e., in arrays); while U.S. Pat. Nos. 5,576,220 and 5,541,061 disclose high throughput methods of screening for ligand/antibody binding. [0166]
• In addition, high throughput screening systems are commercially available (see, e.g., Amersham Biosciences, Piscataway, N.J.; Zymark Corp., Hopkinton, Mass.; Air Technical Industries, Mentor, Ohio; Beckman Instruments, Inc. Fullerton, Calif.; Precision Systems, Inc., Natick, Mass.; etc.). These systems typically automate entire procedures, including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detector(s) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. The manufacturers of such systems provide detailed protocols for various high throughput systems. Thus, e.g., Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like. [0167]
• The term “homolog” refers to a molecule which exhibits homology to another molecule, by for example, having sequences of chemical residues that are the same or similar at corresponding positions. [0168]
• “Human Leukocyte Antigen” or “HLA” is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, et al., I[0169] MMUNOLOGY, 8^TH ED., Lange Publishing, Los Altos, Calif. (1994).
• The terms “hybridize”, “hybridizing”, “hybridizes” and the like, used in the context of polynucleotides, are meant to refer to conventional hybridization conditions, preferably such as hybridization in 50% formamide/6×SSC/0.1% SDS/100 μg/ml ssDNA, in which temperatures for hybridization are above 37 degrees C. and temperatures for washing in 0.1×SSC/0.1% SDS are above 55 degrees C. [0170]
• The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment. For example, a polynucleotide is said to be “isolated” when it is substantially separated from contaminant polynudeotides that correspond or are complementary to genes other than the 98P4B6 genes or that encode polypeptides other than 98P4B6 gene product or fragments thereof. A skilled artisan can readily employ nucleic acid isolation procedures to obtain an isolated 98P4B6 polynucleotide. A protein is said to be “isolated,” for example, when physical, mechanical or chemical methods are employed to remove the 98P4B6 proteins from cellular constituents that are normally associated with the protein. A skilled artisan can readily employ standard purification methods to obtain an isolated 98P4B6 protein. Alternatively, an isolated protein can be prepared by chemical means. [0171]
• The term “mammal” refers to any organism classified as a mammal, including mice, rats, rabbits, dogs, cats, cows, horses and humans. In one embodiment of the invention, the mammal is a mouse. In another embodiment of the invention, the mammal is a human. [0172]
• The terms “metastatic prostate cancer” and “metastatic disease” mean prostate cancers that have spread to regional lymph nodes or to distant sites, and are meant to include stage D disease under the AUA system and stage T×N×M+ under the TNM system. As is the case with locally advanced prostate cancer, surgery is generally not indicated for patients with metastatic disease, and hormonal (androgen ablation) therapy is a preferred treatment modality. Patients with metastatic prostate cancer eventually develop an androgen-refractory state within 12 to 18 months of treatment initiation. Approximately half of these androgen-refractory patients die within 6 months after developing that status. The most common site for prostate cancer metastasis is bone. Prostate cancer bone metastases are often osteoblastic rather than osteolytic (i.e., resulting in net bone formation). Bone metastases are found most frequently in the spine, followed by the femur, pelvis, rib cage, skull and humerus. Other common sites for metastasis include lymph nodes, lung, liver and brain. Metastatic prostate cancer is typically diagnosed by open or laparoscopic pelvic lymphadenectomy, whole body radionuclide scans, skeletal radiography, and/or bone lesion biopsy. [0173]
• The term “modulator” or “test compound” or “drug candidate” or grammatical equivalents as used herein describe any molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., to be tested for the capacity to directly or indirectly alter the cancer phenotype or the expression of a cancer sequence, e.g., a nucleic acid or protein sequences, or effects of cancer sequences (e.g., signaling, gene expression, protein interaction, etc.) In one aspect, a modulator will neutralize the effect of a cancer protein of the invention. By “neutralize” is meant that an activity of a protein is inhibited or blocked, along with the consequent effect on the cell. In another aspect, a modulator will neutralize the effect of a gene, and its corresponding protein, of the invention by normalizing levels of said protein. In preferred embodiments, modulators alter expression profiles, or expression profile nucleic acids or proteins provided herein, or downstream effector pathways. In one embodiment, the modulator suppresses a cancer phenotype, e.g. to a normal tissue fingerprint. In another embodiment, a modulator induced a cancer phenotype. Generally, a plurality of assay mixtures is run in parallel with different agent concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection. [0174]
• Modulators, drug candidates or test compounds encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 100 and less than about 2,500 Daltons. Preferred small molecules are less than 2000, or less than 1500 or less than 1000 or less than 500 D. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, tarbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Modulators also comprise biomolecules such as peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof. Particularly preferred are peptides. One class of modulators are peptides, for example of from about five to about 35 amino acids, with from about five to about 20 amino acids being preferred, and from about 7 to about 15 being particularly preferred. Preferably, the cancer modulatory protein is soluble, includes a non-transmembrane region, and/or, has an N-terminal Cys to aid in solubility. In one embodiment, the C-terminus of the fragment is kept as a free acid and the N-terminus is a free amine to aid in coupling, i.e., to cysteine. In one embodiment, a cancer protein of the invention is conjugated to an immunogenic agent as discussed herein. In one embodiment, the cancer protein is conjugated to BSA. The peptides of the invention, e.g., of preferred lengths, can be linked to each other or to other amino acids to create a longer peptide/protein. The modulatory peptides can be digests of naturally occurring proteins as is outlined above, random peptides, or “biased” random peptides. In a preferred embodiment, peptide/protein-based modulators are antibodies, and fragments thereof, as defined herein. [0175]
• Modulators of cancer can also be nucleic acids. Nucleic acid modulating agents can be naturally occurring nucleic acids, random nucleic acids, or “biased” random nucleic acids. For example, digests of prokaryotic or eukaryotic genomes can be used in an approach analogous to that outlined above for proteins. [0176]
• The term “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the antibodies comprising the population are identical except for possible naturally occurring mutations that are present in minor amounts. [0177]
• A “motif”, as in biological motif of a 98P4B6-related protein, refers to any pattern of amino acids forming part of the primary sequence of a protein, that is associated with a particular function (e.g. protein-protein interaction, protein-DNA interaction, etc) or modification (e.g. that is phosphorylated, glycosylated or amidated), or localization (e.g. secretory sequence, nuclear localization sequence, etc.) or a sequence that is correlated with being immunogenic, either humorally or cellularly. A motif can be either contiguous or capable of being aligned to certain positions that are generally correlated with a certain function or property. In the context of HLA motifs, “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs for HLA binding are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues. [0178]
• A “pharmaceutical excipient” comprises a material such as an adjuvant, a carrier, pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservative, and the like. [0179]
• “Pharmaceutically acceptable” refers to a non-toxic, inert, and/or composition that is physiologically compatible with humans or other mammals. [0180]
• The term “polynucleotide” means a polymeric form of nucleotides of at least 10 bases or base pairs in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide, and is meant to include single and double stranded forms of DNA and/or RNA. In the art, this term if often used interchangeably with “oligonucleotide”. A polynucleotide can comprise a nucleotide sequence disclosed herein wherein thymidine (T), as shown for example in FIG. 2, can also be uracil (U); this definition pertains to the differences between the chemical structures of DNA and RNA, in particular the observation that one of the four major bases in RNA is uracil (U) instead of thymidine (T). [0181]
• The term “polypeptide” means a polymer of at least about 4, 5, 6, 7, or 8 amino acids. Throughout the specification, standard three letter or single letter designations for amino acids are used. In the art, this term is often used interchangeably with “peptide” or “protein”. [0182]
• An HLA “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding groove of an HLA molecule, with their side chains buried in specific pockets of the binding groove. In one embodiment, for example, the primary anchor residues for an HLA class I molecule are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 8, 9, 10, 11, or 12 residue peptide epitope in accordance with the invention. Alternatively, in another embodiment, the primary anchor residues of a peptide binds an HLA class II molecule are spaced relative to each other, rather than to the termini of a peptide, where the peptide is generally of at least 9 amino acids in length. The primary anchor positions for each motif and supermotif are set forth in Table IV. For example, analog peptides can be created by altering the presence or absence of particular residues in the primary and/or secondary anchor positions shown in Table IV. Such analogs are used to modulate the binding affinity and/or population coverage of a peptide comprising a particular HLA motif or supermotif. [0183]
• “Radioisotopes” include, but are not limited to the following (non-limiting exemplary uses are also set forth): [0184]
• Examples of Medical Isotopes: [0185]
• Isotope [0186]
• Description of use [0187]
• Actinium-225 [0188]
• (AC-225) [0189]
• See Thorium-229 (Th-229) [0190]
• Actinium-227 [0191]
• (AC-227) [0192]
• Parent of Radium-223 (Ra-223) which is an alpha emitter used to treat metastases in the skeleton resulting from cancer (i.e., breast and prostate cancers), and cancer radioimmunotherapy [0193]
• Bismuth-212 [0194]
• (Bi-212) [0195]
• See Thorium-228 (Th-228) [0196]
• Bismuth-213 [0197]
• (Bi-213) [0198]
• See Thorium-229 (Th-229) [0199]
• Cadmium-109 [0200]
• (Cd-109) [0201]
• Cancer detection [0202]
• Cobalt-60 [0203]
• (Co-60) [0204]
• Radiation source for radiotherapy of cancer, for food irradiators, and for sterilization of medical supplies [0205]
• Copper-64 [0206]
• (Cu-64) [0207]
• A positron emitter used for cancer therapy and SPECT imaging [0208]
• Copper-67 [0209]
• (Cu-67) [0210]
• Beta/gamma emitter used in cancer radioimmunotherapy and diagnostic studies (i.e., breast and colon cancers, and lymphoma) [0211]
• Dysprosium-166 [0212]
• (Dy-166) [0213]
• Cancer radioimmunotherapy [0214]
• Erbium-169 [0215]
• (Er-169) [0216]
• Rheumatoid arthritis treatment, particularly for the small joints associated with fingers and toes [0217]
• Europium-152 [0218]
• (Eu-152) [0219]
• Radiation source for food irradiation and for sterilization of medical supplies [0220]
• Europium-154 [0221]
• (Eu-154) [0222]
• Radiation source for food irradiation and for sterilization of medical supplies [0223]
• Gadolinium-153 [0224]
• (Gd-153) [0225]
• Osteoporosis detection and nuclear medical quality assurance devices [0226]
• Gold-198 [0227]
• (Au-198) [0228]
• Implant and intracavity therapy of ovarian, prostate, and brain cancers [0229]
• Holmium-166 [0230]
• (Ho-166) [0231]
• Multiple myeloma treatment in targeted skeletal therapy, cancer radioimmunotherapy, bone marrow ablation, and rheumatoid arthritis treatment [0232]
• Iodine-125 [0233]
• (I-125) [0234]
• Osteoporosis detection, diagnostic imaging, tracer drugs, brain cancer treatment, radiolabeling, tumor imaging, mapping of receptors in the brain, interstitial radiation therapy, brachytherapy for treatment of prostate cancer, determination of glomerular filtration rate (GFR), determination of plasma volume, detection of deep vein thrombosis of the legs [0235]
• Iodine-131 [0236]
• (1-131) [0237]
• Thyroid function evaluation, thyroid disease detection, treatment of thyroid cancer as well as other non-malignant thyroid diseases (i.e., Graves disease, goiters, and hyperthyroidism), treatment of leukemia, lymphoma, and other forms of cancer (e.g., breast cancer) using radioimmunotherapy [0238]
• Iridium-192 [0239]
• (Ir-192) [0240]
• Brachytherapy, brain and spinal cord tumor treatment, treatment of blocked arteries (i.e., arteriosclerosis and restenosis), and implants for breast and prostate tumors [0241]
• Lutetium-177 [0242]
• (Lu-177) [0243]
• Cancer radioimmunotherapy and treatment of blocked arteries (i.e., arteriosclerosis and restenosis) [0244]
• Molybdenum-99 [0245]
• (Mo-99) [0246]
• Parent of Technetium-99 m (Tc-99 m) which is used for imaging the brain, liver, lungs, heart, and other organs. Currently, Tc-99 m is the most widely used radioisotope used for diagnostic imaging of various cancers and diseases involving the brain, heart, liver, lungs; also used in detection of deep vein thrombosis of the legs [0247]
• Osmium-194 [0248]
• (Os-194) [0249]
• Cancer radioimmunotherapy [0250]
• Palladium-103 [0251]
• (Pd-103) [0252]
• Prostate cancer treatment [0253]
• Platinum-195 m [0254]
• (Pt-195 m) [0255]
• Studies on biodistribution and metabolism of cisplatin, a chemotherapeutic drug [0256]
• Phosphorus-32 [0257]
• (P-32) [0258]
• Polycythemia rubra vera (blood cell disease) and leukemia treatment, bone cancer diagnosis/treatment; colon, pancreatic, and liver cancer treatment; radiolabeling nucleic acids for in vitro research, diagnosis of superficial tumors, treatment of blocked arteries (i.e., arteriosclerosis and restenosis), and intracavity therapy [0259]
• Phosphorus-33 [0260]
• (P-33) [0261]
• Leukemia treatment, bone disease diagnosis/treatment, radiolabeling, and treatment of blocked arteries (i.e., arteriosclerosis and restenosis) [0262]
• Radium-223 [0263]
• (Ra-223) [0264]
• See Actinium-227 (Ac-227) [0265]
• Rhenium-186 [0266]
• (Re-186) [0267]
• Bone cancer pain relief, rheumatoid arthritis treatment, and diagnosis and treatment of lymphoma and bone, breast, colon, and liver cancers using radioimmunotherapy [0268]
• Rhenium-188 [0269]
• (Re-188) [0270]
• Cancer diagnosis and treatment using radioimmunotherapy, bone cancer pain relief, treatment of rheumatoid arthritis, and treatment of prostate cancer [0271]
• Rhodium-105 [0272]
• (Rh-105) [0273]
• Cancer radioimmunotherapy [0274]
• Samarium-145 [0275]
• (Sm-145) [0276]
• Ocular cancer treatment [0277]
• Samarium-153 [0278]
• (Sm-153) [0279]
• Cancer radioimmunotherapy and bone cancer pain relief [0280]
• Scandium-47 [0281]
• (Sc-47) [0282]
• Cancer radioimmunotherapy and bone cancer pain relief [0283]
• Selenium-75 [0284]
• (Se-75) [0285]
• Radiotracer used in brain studies, imaging of adrenal cortex by gamma-scintigraphy, lateral locations of steroid secreting tumors, pancreatic scanning, detection of hyperactive parathyroid glands, measure rate of bile acid loss from the endogenous pool [0286]
• Strontium-85 [0287]
• (Sr-85) [0288]
• Bone cancer detection and brain scans [0289]
• Strontium-89 [0290]
• (Sr-89) [0291]
• Bone cancer pain relief, multiple myeloma treatment, and osteoblastic therapy [0292]
• Technetium-99m [0293]
• (Tc-99m) [0294]
• See Molybdenum-99 (Mo-99) [0295]
• Thorium-228 [0296]
• (Th-228) [0297]
• Parent of Bismuth-212 (Bi-212) which is an alpha emitter used in cancer radioimmunotherapy [0298]
• Thorium-229 [0299]
• (Th-229) [0300]
• Parent of Actinium-225 (Ac-225) and grandparent of Bismuth-213 (Bi-213) which are alpha emitters used in cancer radioimmunotherapy [0301]
• Thulium-170 [0302]
• (Tm-170) [0303]
• Gamma source for blood irradiators, energy source for implanted medical devices [0304]
• Tin-117 m [0305]
• (Sn-117 m) [0306]
• Cancer immunotherapy and bone cancer pain relief [0307]
• Tungsten-188 [0308]
• (W-188) [0309]
• Parent for Rhenium-188 (Re-188) which is used for cancer diagnostics/treatment, bone cancer pain relief, rheumatoid arthritis treatment, and treatment of blocked arteries (i.e., arteriosclerosis and restenosis) [0310]
• Xenon-127 [0311]
• (Xe-127) [0312]
• Neuroimaging of brain disorders, high resolution SPECT studies, pulmonary function tests, and cerebral blood flow studies [0313]
• Ytterbium-175 [0314]
• (Yb-175) [0315]
• Cancer radioimmunotherapy [0316]
• Yttrium-90 [0317]
• (Y-90) [0318]
• Microseeds obtained from irradiating Yttrum-89 (Y-89) for liver cancer treatment [0319]
• Yttrium-91 [0320]
• (Y-91) [0321]
• A gamma-emitting label for Yttrium-90 (Y-90) which is used for cancer radioimmunotherapy (i.e., lymphoma, breast, colon, kidney, lung, ovarian, prostate, pancreatic, and inoperable liver cancers) [0322]
• By “randomized” or grammatical equivalents as herein applied to nucleic acids and proteins is meant that each nucleic acid and peptide consists of essentially random nucleotides and amino acids, respectively. These random peptides (or nucleic acids, discussed herein) can incorporate any nucleotide or amino acid at any position. The synthetic process can be designed to generate randomized proteins or nucleic acids, to allow the formation of all or most of the possible combinations over the length of the sequence, thus forming a library of randomized candidate bioactive proteinaceous agents. [0323]
• In one embodiment, a library is “fully randomized,” with no sequence preferences or constants at any position. In another embodiment, the library is a “biased random” library. That is, some positions within the sequence either are held constant, or are selected from a limited number of possibilities. For example, the nucleotides or amino acid residues are randomized within a defined class, e.g., of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of nucleic acid binding domains, the creation of cysteines, for cross-linking, prolines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, etc., or to purines, etc. [0324]
• A “recombinant” DNA or RNA molecule is a DNA or RNA molecule that has been subjected to molecular manipulation in vitro. [0325]
• Non-limiting examples of small molecules include compounds that bind or interact with 98P4B6, ligands including hormones, neuropeptides, chemokines, odorants, phospholipids, and functional equivalents thereof that bind and preferably inhibit 98P4B6 protein function. Such non-limiting small molecules preferably have a molecular weight of less than about 10 kDa, more preferably below about 9, about 8, about 7, about 6, about 5 or about 4 kDa. In certain embodiments, small molecules physically associate with, or bind, 98P4B6 protein; are not found in naturally occurring metabolic pathways; and/or are more soluble in aqueous than non-aqueous solutions [0326]
• “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured nucleic acid sequences to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995). [0327]
• “Stringent conditions” or “high stringency conditions”, as defined herein, are identified by, but not limited to, those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodium. citrate) and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C. “Moderately stringent conditions” are described by, but not limited to, those in Sambrook et al., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and % SDS) less stringent than those described above. An example of moderately stringent conditions is overnight incubation at 37° C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like. [0328]
• An HLA “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles. Overall phenotypic frequencies of HLA-supertypes in different ethnic populations are set forth in Table IV (F). The non-limiting constituents of various supetypes are as follows: [0329]
• [0330] A2: A*0201, A*0202, A*0203, A*0204, A* 0205, A*0206, A*6802, A*6901, A*0207
• [0331] A3: A3, A11, A31, A*3301, A*6801, A*0301, A*1101, A*3101
• [0332] B7: B7, B*3501-03, B*51, B*5301, B*5401, B*5501, B*5502, B*5601, B*6701, B*7801, B*0702, B*5101, B*5602
• [0333] B44: B*3701, B*4402, B*4403, B*60 (B*4001), B61 (B*4006)
• [0334] A1: A*0102, A*2604, A*3601, A*4301, A*8001
• [0335] A24: A*24, A*30, A*2403, A*2404, A*3002, A*3003
• [0336] B27: B*1401-02, B*1503, B*1509, B*1510, B*1518, B*3801-02, B*3901, B*3902, B*3903-04, B*4801-02, B*7301, B*2701-08
• [0337] B58: B*1516, B*1517, B*5701, B*5702, B58
• [0338] B62: B*4601, B52, B*1501 (B62), B*1502 (B75), B*1513 (B77)
• Calculated population coverage afforded by different HLA-supertype combinations are set forth in Table IV (G). [0339]
• As used herein “to treat” or “therapeutic” and grammatically related terms, refer to any improvement of any consequence of disease, such as prolonged survival, less morbidity, and/or a lessening of side effects which are the byproducts of an alternative therapeutic modality; full eradication of disease is not required. [0340]
• A “transgenic animal” (e.g., a mouse or rat) is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A “transgene” is a DNA that is integrated into the genome of a cell from which a transgenic animal develops. [0341]
• As used herein, an HLA or cellular immune response “vaccine” is a composition that contains or encodes one or more peptides of the invention. There are numerous embodiments of such vaccines, such as a cocktail of one or more individual peptides; one or more peptides of the invention comprised by a polyepitopic peptide; or nucleic acids that encode such individual peptides or polypeptides, e.g., a minigene that encodes a polyepitopic peptide. The “one or more peptides” can include any whole unit integer from 1-150 or more, e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42,43,44, 45,46,47,48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 or more peptides of the invention. The peptides or polypeptides can optionally be modified, such as by lipidation, addition of targeting or other sequences. HLA class I peptides of the invention can be admixed with, or linked to, HLA class II peptides, to facilitate activation of both cytotoxic T lymphocytes and helper T lymphocytes. HLA vaccines can also comprise peptide-pulsed antigen presenting cells, e.g., dendritic cells. [0342]
• The term “variant” refers to a molecule that exhibits a variation from a described type or norm, such as a protein that has one or more different amino acid residues in the corresponding position(s) of a specifically described protein (e.g. the 98P4B6 protein shown in FIG. 2 or FIG. 3. An analog is an example of a variant protein. Splice isoforms and single nudeotides polymorphisms (SNPs) are further examples of variants. [0343]
• The “98P4B6-related proteins” of the invention include those specifically identified herein, as well as allelic variants, conservative substitution variants, analogs and homologs that can be isolated/generated and characterized without undue experimentation following the methods outlined herein or readily available in the art. Fusion proteins that combine parts of different 98P4B6 proteins or fragments thereof, as well as fusion proteins of a 98P4B6 protein and a heterologous polypeptide are also included. Such 98P4B6 proteins are collectively referred to as the 98P4B6-related proteins, the proteins of the invention, or 98P4B6. The term “98P4B6-related protein” refers to a polypeptide fragment or a 98P4B6 protein sequence of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25amino acids; or, at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, or 576 or more amino acids. [0344]
• II.) 98P4B6 Polynucleotides [0345]
• One aspect of the invention provides polynucleotides corresponding or complementary to all or part of a 98P486 gene, mRNA, and/or coding sequence, preferably in isolated form, including polynucleotides encoding a 98P4B6-related protein and fragments thereof, DNA, RNA, DNA/RNA hybrid, and related molecules, polynucleotides or oligonucleotides complementary to a 98P4B6 gene or mRNA sequence or a part thereof, and polynucleotides or oligonucleotides that hybridize to a 98P4B6 gene, mRNA, or to a 98P4B6 encoding polynucleotide (collectively, “98P4B6 polynucleotides”). In all instances when referred to in this section, T can also be U in FIG. 2. [0346]
• Embodiments of a 98P4B6 polynucleotide include: a 98P4B6 polynucleotide having the sequence shown in FIG. 2, the nucleotide sequence of 98P4B6 as shown in FIG. 2 wherein T is U; at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2; or, at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in FIG. 2 where T is U. For example, embodiments of 98P4B6 nucleotides comprise, without limitation: [0347]
• (I) a polynucleotide comprising, consisting essentially of, or consisting of a sequence as shown in FIG. 2, wherein T can also be U; [0348]
• (II) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2A, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0349]
• (III) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2B, from nucleotide residue number 4 through nucleotide residue number 138, including the stop codon, wherein T can also be U; [0350]
• (IV) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2C, from nucleotide residue number 188 through nucleotide residue number 1552, including the a stop codon, wherein T can also be U; [0351]
• (V) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2D, from nucleotide residue number 318 through nucleotide residue number 1682, including the stop codon, wherein T can also be U; [0352]
• (VI) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2E, from nucleotide residue number 318 through nucleotide residue number 1577, including the stop codon, wherein T can also be U; [0353]
• (VII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2F, from nudeotide residue number 318 through nucleotide residue number 1790, including the stop codon, wherein T can also be U; [0354]
• (VII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2G, from nucleotide residue number 295 through nucleotide residue number 2025, including the stop codon, wherein T can also be U; [0355]
• (IX) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2H, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0356]
• (X) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2I, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0357]
• (XI) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2J, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0358]
• (XII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2K, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0359]
• (XIII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2L, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0360]
• (XIV) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2M, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0361]
• (XV) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2N, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0362]
• (XVI) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 20, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0363]
• (XVII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2P, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0364]
• (XVIII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2Q, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0365]
• (XIX) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2R, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0366]
• (XX) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2S, from nucleotide residue number 355 through nucleotide residue number 1719, including the stop codon, wherein T can also be U; [0367]
• (XXI) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2T, from nucleotide residue number 295 through nucleotide residue number 2025, including the stop codon, wherein T can also be U; [0368]
• (XXII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2U, from nucleotide residue number 295 through nucleotide residue number 2025, including the stop codon, wherein T can also be U; [0369]
• (XXIII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2V, from nucleotide residue number 295 through nucleotide residue number 2025, including the stop codon, wherein T can also be U; [0370]
• (XXIV) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2W, from nucleotide residue number 295 through nucleotide residue number 2025, including the stop codon, wherein T can also be U; [0371]
• (XXV) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2X, from nucleotide residue number 295 through nucleotide residue number 2025, including the stop codon, wherein T can also be U; [0372]
• (XXVI) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2Y, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0373]
• (XXVII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2Z, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0374]
• (XXVIII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2A, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0375]
• (XXIX) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AB, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0376]
• (XXX) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AC, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0377]
• (XXXI) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AD, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0378]
• (XXXII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AE, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0379]
• (XXXIII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AF, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0380]
• (XXIV) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2G, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0381]
• (XXXV) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AH, from nucleotide residue number 394 through nudeotide residue number 1866, including the stop codon, wherein T can also be U; [0382]
• (XXXVI) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AI, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0383]
• (XXXVII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AJ, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0384]
• (XXXVIII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AK, from nudeotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0385]
• (XXXIX) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in FIG. 2AL, from nucleotide residue number 394 through nucleotide residue number 1866, including the stop codon, wherein T can also be U; [0386]
• (XL) a polynucleotide that encodes a 98P4B6-related protein that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% homologous to an entire amino acid sequence shown in FIG. 2A-AL; [0387]
• (XLI) a polynucleotide that encodes a 98P4B6-related protein that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identical to an entire amino acid sequence shown in FIG. 2A-AL; [0388]
• (XLII) a polynucleotide that encodes at least one peptide set forth in Tables VIII-XXI and XXII-XLIX; [0389]
• (XLIII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3A, 3G, and [0390] 3H in any whole number increment up to 454 that includes at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5;
• (XLIV) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3A, 3G, and [0391] 3H in any whole number increment up to 454 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of FIG. 6;
• (XLV) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3A, 3G, and [0392] 3H in any whole number increment up to 454 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7;
• (XLVI) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3A, 3G, and [0393] 3H in any whole number increment up to 454 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Average Flexibility profile of FIG. 8;
• (XLVII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3A, 3G, and [0394] 3H in any whole number increment up to 454 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of FIG. 9;
• (XLVIII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3B in any whole number increment up to 45 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5; [0395]
• (XLIX) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3B in any whole number increment up to 45 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of FIG. 6; [0396]
• (L) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3B in any whole number increment up to 45 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7; [0397]
• (LI) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3B in any whole number increment up to 45 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Average Flexibility profile of FIG. 8; [0398]
• (LII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3B in any whole number increment up to 45 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of FIG. 9 [0399]
• (LII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3C in any whole number increment up to 419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5; [0400]
• (LIV) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3C in any whole number increment up to 419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of FIG. 6; [0401]
• (LV) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3C in any whole number increment up to 419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7; [0402]
• (LVI) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3C in any whole number increment up to 419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid positon(s) having a value greater than 0.5 in the Average Flexibility profile of FIG. 8; [0403]
• (LVII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIG. 3C in any whole number increment up to 419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of FIG. 9 [0404]
• (LVIII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3D, 3F, and [0405] 3J in any whole number increment up to 490 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5;
• (LIX) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3D, 3F, and [0406] 3J in any whole number increment up to 490 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of FIG. 6;
• (LX) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3D, 3F, and [0407] 3J in any whole number increment up to 490 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7;
• (LXI) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3D, 3F, and [0408] 3J in any whole number increment up to 490 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Average Flexibility profile of FIG. 8;
• (LXII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3D, 3F, and [0409] 3J in any whole number increment up to 490 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of FIG. 9
• (LXIII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3E and 3I in any whole number increment up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5; [0410]
• (LXIV) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3E and 3I in any-whole number increment up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of FIG. 6; [0411]
• (LXV) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3E and 3I in any whole number increment up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7; [0412]
• (LXVI) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3E and 3I in any whole number increment up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Average Flexibility profile of FIG. 8; [0413]
• (LXVII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of FIGS. 3E and 3I in any whole number increment up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of FIG. 9 [0414]
• (LXVIII) a polynucleotide that is fully complementary to a polynucleotide of any one of (I)-(LXVII). [0415]
• (LXIX) a peptide that is encoded by any of (I) to (LXVIII); and [0416]
• (LXX) a composition comprising a polynucleotide of any of (I)-(LXVIII) or peptide of (LXIX) together with a pharmaceutical excipient and/or in a human unit dose form. [0417]
• (LXXI) a method of using a polynucleotide of any (I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a method to modulate a cell expressing 98P4B6, [0418]
• (LXXII) a method of using a polynucleotide of any (I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a method to diagnose, prophylax, prognose, or treat an individual who bears a cell expressing 98P4B6 [0419]
• (LXXIII) a method of using a polynucleotide of any (I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a method to diagnose, prophylax, prognose, or treat an individual who bears a cell expressing 98P4B6, said cell from a cancer of a tissue listed in Table I; [0420]
• (LXXIV) a method of using a polynucleotide of any (I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a method to diagnose, prophylax, prognose, or treat a a cancer; [0421]
• (LXXV) a method of using a polynucleotide of any (I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a method to diagnose, prophylax, prognose, or treat a a cancer of a tissue listed in Table I; and, [0422]
• (LXXVI) a method of using a polynucleotide of any (I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a method to identify or characterize a modulator of a cell; expressing 98P4B6. [0423]
• As used herein, a range is understood to disclose specifically all whole unit positions thereof. [0424]
• Typical embodiments of the invention disclosed herein include 98P4B6 polynucleotides that encode specific portions of 98P4B6 mRNA sequences (and those which are complementary to such sequences) such as those that encode the proteins and/or fragments thereof, for example: [0425]
• (a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 410, 420, 430, 440, 450 or 454 or more contiguous amino acids of [0426] 98P4B6 variant 1; the maximal lengths relevant for other variants are: variant 2, 44 amino acids; variant 5, 419 amino acids, variant 6, 490 amino acids, variant 7, 576 amino acids, variant 8, 490 amino acids, variant 13, 454 amino acids, variant 14, 454 amino acids, variant 21, 576 amino acids, and variant 25, 490 amino acids.
• For example, representative embodiments of the invention disclosed herein include: polynucleotides and their encoded peptides themselves encoding about amino acid 1 to about amino acid 10 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 10 to about amino acid 20 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 20 to about amino acid 30 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 30 to about amino acid 40 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 40 to about amino acid 50 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 50 to about amino acid 60 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 60 to about amino acid 70 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 70 to about amino acid 80 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 80 to about amino acid 90 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 90 to about amino acid 100 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, in increments of about 10 amino acids, ending at the carboxyl terminal amino acid set forth in FIG. 2 or FIG. 3. Accordingly, polynucleotides encoding portions of the amino acid sequence (of about 10 amino acids), of amino acids, 100 through the carboxyl terminal amino acid of the 98P4B6 protein are embodiments of the invention. Wherein it is understood that each particular amino acid position discloses that position plus or minus five amino acid residues. [0427]
• Polynucleotides encoding relatively long portions of a 98P4B6 protein are also within the scope of the invention. For example, polynucleotides encoding from about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of the 98P4B6 protein “or variant” shown in FIG. 2 or FIG. 3 can be generated by a variety of techniques well known in the art. These polynucleotide fragments can include any portion of the 98P4B6 sequence as shown in FIG. 2. [0428]
• Additional illustrative embodiments of the invention disclosed herein include 98P4B6 polynucleotide fragments encoding one or more of the biological motifs contained within a 98P4B6 protein “or variant” sequence, including one or more of the motif-bearing subsequences of a 98P4B6 protein “or variants” set forth in Tables VIII-XXI and XXII-XLIX. In another embodiment, typical polynucleotide fragments of the invention encode one or more of the regions of 98P4B6 protein or variant that exhibit homology to a known molecule. In another embodiment of the invention, typical polynucleotide fragments can encode one or more of the 98P4B6 protein or variant N-glycosylation sites, cAMP and cGMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites or N-myristoylation site and amidation sites. [0429]
• Note that to determine the starting position of any peptide set forth in Tables VIII-XXI and Tables XXII to XLIX (collectively HLA Peptide Tables) respective to its parental protein, e.g., [0430] variant 1, variant 2, etc., reference is made to three factors: the particular variant, the length of the peptide in an HLA Peptide Table, and the Search Peptides listed in Table VII. Generally, a unique Search Peptide is used to obtain HLA peptides for a particular variant. The position of each Search Peptide relative to its respective parent molecule is listed in Table VII. Accordingly, if a Search Peptide begins at position “X”, one must add the value “X minus 1” to each position in Tables VIII-XXI and Tables XXII-IL to obtain the actual position of the HLA peptides in their parental molecule. For example if a particular Search Peptide begins at position 150 of its parental molecule, one must add 150−1, i.e., 149 to each HLA peptide amino acid position to calculate the position of that amino acid in the parent molecule.
• II.A.) Uses of 98P4B6 Polynucleotides [0431]
• II.A.1.) Monitoring of Genetic Abnormalities [0432]
• The polynucleotides of the preceding paragraphs have a number of different specific uses. The human 98P4B6 gene maps to the chromosomal location set forth in the Example entitled “Chromosomal Mapping of 98P4B6.” For example, because the 98P4B6 gene maps to this chromosome, polynucleotides that encode different regions of the 98P4B6 proteins are used to characterize cytogenetic abnormalities of this chromosomal locale, such as abnormalities that are identified as being associated with various cancers. In certain genes, a variety of chromosomal abnormalities including rearrangements have been identified as frequent cytogenetic abnormalities in a number of different cancers (see e.g. Krajinovic et al., Mutat. Res. 382(3-4): 81-83(1998); Johansson et al., Blood 86(10): 3905-3914(1995) and Finger et al., P.N.A.S. 85(23): 9158-9162 (1988)). Thus, polynucleotides encoding specific regions of the 98P4B6 proteins provide new tools that can be used to delineate, with greater precision than previously possible, cytogenetic abnormalities in the chromosomal region that encodes 98P4B6 that may contribute to the malignant phenotype. In this context, these polynucleotides satisfy a need in the art for expanding the sensitivity of chromosomal screening in order to identify more subtle and less common chromosomal abnormalities (see e.g. Evans et al., Am. J. Obstet. Gynecol 171(4): 1055-1057 (1994)). [0433]
• Furthermore, as 98P4B6 was shown to be highly expressed in prostate and other cancers, 98P4B6 polynucleotides are used in methods assessing the status of 98P4B6 gene products in normal versus cancerous tissues. Typically, polynucleotides that encode specific regions of the 98P4B6 proteins are used to assess the presence of perturbations (such as deletions, insertions, point mutations, or alterations resulting in a loss of an antigen etc.) in specific regions of the 98P4B6 gene, such as regions containing one or more motifs. Exemplary assays include both RT-PCR assays as well as single-strand conformation polymorphism (SSCP) analysis (see, e.g., Marrogi et al., J. Cutan. Pathol. 26(8): 369-378 (1999), both of which utilize polynucleotides encoding specific regions of a protein to examine these regions within the protein. [0434]
• II.A.2.) Antisense Embodiments [0435]
• Other specifically contemplated nucleic acid related embodiments of the invention disclosed herein are genomic DNA, cDNAs, ribozymes, and antisense molecules, as well as nucleic acid molecules based on an alternative backbone, or including alternative bases, whether derived from natural sources or synthesized, and include molecules capable of inhibiting the RNA or protein expression of 98P4B6. For example, antisense molecules can be RNAs or other molecules, including peptide nucleic acids (PNAs) or non-nucleic acid molecules such as phosphorothioate derivatives that specifically bind DNA or RNA in a base pair-dependent manner. A skilled artisan can readily obtain these classes of nucleic acid molecules using the 98P4B6 polynucleotides and polynucleotide sequences disclosed herein. [0436]
• Antisense technology entails the administration of exogenous oligonucleotides that bind to a target polynucleotide located within the cells. The term “antisense” refers to the fact that such oligonucleotides are complementary to their intracellular targets, e.g., 98P4B6. See for example, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1:1-5 (1988). The 98P4B6 antisense oligonucleotides of the present invention include derivatives such as S-oligonucleotides (phosphorothioate derivatives or S-oligos, see, Jack Cohen, supra), which exhibit enhanced cancer cell growth inhibitory action. S-oligos (nucleoside phosphorothioates) are isoelectronic analogs of an oligonucleotide (O-oligo) in which a nonbridging oxygen atom of the phosphate group is replaced by a sulfur atom. The S-oligos of the present invention can be prepared by treatment of the corresponding O-oligos with 3H-1,2-benzodithiol-3-one-1,1-dioxide, which is a sulfur transfer reagent. See, e.g., lyer, R. P. et al., J. Org. Chem. 55:4693-4698 (1990); and lyer, R. P. et al., J. Am. Chem. Soc. 112:1253-1254 (1990). Additional 98P4B6 antisense oligonucleotides of the present invention include morpholino antisense oligonucleotides known in the art (see, e.g., Partridge et al., 1996, Antisense & Nucleic Acid Drug Development 6: 169-175). [0437]
• The 98P4B6 antisense oligonucleotides of the present invention typically can be RNA or DNA that is complementary to and stably hybridizes with the first 100 5′ codons or last 100 3′ codons of a 98P4B6 genomic sequence or the corresponding mRNA. Absolute complementarity is not required, although high degrees of complementarity are preferred. Use of an oligonucleotide complementary to this region allows for the selective hybridization to 98P4B6 mRNA and not to mRNA specifying other regulatory subunits of protein kinase. In one embodiment, 98P4B6 antisense oligonucleotides of the present invention are 15 to 30-mer fragments of the antisense DNA molecule that have a sequence that hybridizes to 98P4B6 mRNA. Optionally, 98P4B6 antisense oligonucleotide is a 30-mer oligonucleotide that is complementary to a region in the first 10 5′ codons or last 10 3′ codons of 98P4B6. Alternatively, the antisense molecules are modified to employ ribozymes in the inhibition of 98P4B6 expression, see, e.g., L. A. Couture & D. T. Stinchcomb; [0438] Trends Genet 12: 510-515 (1996).
• II.A.3.) Primers and Primer Pairs [0439]
• Further specific embodiments of these nucleotides of the invention include primers and primer pairs, which allow the specific amplification of polynucleotides of the invention or of any specific parts thereof, and probes that selectively or specifically hybridize to nucleic acid molecules of the invention or to any part thereof. Probes can be labeled with a detectable marker, such as, for example, a radioisotope, fluorescent compound, bioluminescent compound, a chemiluminescent compound, metal chelator or enzyme. Such probes and primers are used to detect the presence of a 98P4B6 polynucleotide in a sample and as a means for detecting a cell expressing a 98P4B6 protein. [0440]
• Examples of such probes include polypeptides comprising all or part of the human 98P4B6 cDNA sequence shown in FIG. 2. Examples of primer pairs capable of specifically amplifying 98P4B6 mRNAs are also described in the Examples. As will be understood by the skilled artisan, a great many different primers and probes can be prepared based on the sequences provided herein and used effectively to amplify and/or detect a 98P4B6 mRNA. [0441]
• The 98P4B6 polynucleotides of the invention are useful for a variety of purposes, including but not limited to their use as probes and primers for the amplification and/or detection of the 98P4B6 gene(s), mRNA(s), or fragments thereof; as reagents for the diagnosis and/or prognosis of prostate cancer and other cancers; as coding sequences capable of directing the expression of 98P4B6 polypeptides; as tools for modulating or inhibiting the expression of the 98P4B6 gene(s) and/or translation of the 98P4B6 transcript(s); and as therapeutic agents. [0442]
• The present invention includes the use of any probe as described herein to identify and isolate a 98P4B6 or 98P4B6 related nucleic acid sequence from a naturally occurring source, such as humans or other mammals, as well as the isolated nucleic acid sequence per se, which would comprise all or most of the sequences found in the probe used. [0443]
• II.A.4.) Isolation of 98P4B6-Encoding Nucleic Acid Molecules [0444]
• The 98P4B6 cDNA sequences described herein enable the isolation of other polynucleotides encoding 98P4B6 gene product(s), as well as the isolation of polynucleotides encoding 98P4B6 gene product homologs, alternatively spliced isoforms, allelic variants, and mutant forms of a 98P4B6 gene product as well as polynucleotides that encode analogs of 98P4B6-related proteins. Various molecular cloning methods that can be employed to isolate full length cDNAs encoding a 98P4B6 gene are well known (see, for example, Sambrook, J. et al., Molecular Cloning: A Laboratory Manual, 2d edition, Cold Spring Harbor Press, New York, 1989; Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley and Sons, 1995). For example, lambda phage cloning methodologies can be conveniently employed, using commercially available cloning systems (e.g., Lambda ZAP Express, Stratagene). Phage clones containing 98P4B6 gene cDNAs can be identified by probing with a labeled 98P4B6 cDNA or a fragment thereof. For example, in one embodiment, a 98P4B6 cDNA (e.g., FIG. 2) or a portion thereof can be synthesized and used as a probe to retrieve overlapping and full-length cDNAs corresponding to a 98P4B6 gene. A 98P4B6 gene itself can be isolated by screening genomic DNA libraries, bacterial artificial chromosome libraries (BACs), yeast artificial chromosome libraries (YACs), and the like, with 98P4B6 DNA probes or primers. [0445]
• II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems [0446]
• The invention also provides recombinant DNA or RNA molecules containing a 98P4B6 polynucleotide, a fragment, analog or homologue thereof, including but not limited to phages, plasmids, phagemids, cosmids, YACs, BACs, as well as various viral and non-viral vectors well known in the art, and cells transformed or transfected with such recombinant DNA or RNA molecules. Methods for generating such molecules are well known (see, for example, Sambrook et al., 1989, supra). [0447]
• The invention further provides a host-vector system comprising a recombinant DNA molecule containing a 98P4B6 polynucleotide, fragment, analog or homologue thereof within a suitable prokaryotic or eukaryotic host cell. Examples of suitable eukaryotic host cells include a yeast cell, a plant cell, or an animal cell, such as a mammalian cell or an insect cell (e.g., a baculovirus-infectible cell such as an Sf9 or HighFive cell). Examples of suitable mammalian cells include various prostate cancer cell lines such as DU145 and TsuPr1, other transfectable or transducible prostate cancer cell lines, primary cells (PrEC), as well as a number of mammalian cells routinely used for the expression of recombinant proteins (e.g., COS, CHO, 293, 293T cells). More particularly, a polynucleotide comprising the coding sequence of 98P4B6 or a fragment, analog or homolog thereof can be used to generate 98P4B6 proteins or fragments thereof using any number of host-vector systems routinely used and widely known in the art. [0448]
• A wide range of host-vector systems suitable for the expression of 98P4B6 proteins or fragments thereof are available, see for example, Sambrook et al.,1989, supra; Current Protocols in Molecular Biology, 1995, supra). Preferred vectors for mammalian expression include but are not limited to pcDNA 3.1 myc-His-tag (Invitrogen) and the retroviral vector pSRαtkneo (Muller et al., 1991, MCB 11:1785). Using these expression vectors, 98P4B6 can be expressed in several prostate cancer and non-prostate cell lines, including for example 293, 293T, rat-1, NIH 3T3 and TsuPr1. The host-vector systems of the invention are useful for the production of a 98P4B6 protein or fragment thereof. Such host-vector systems can be employed to study the functional properties of 98P4B6 and 98P4B6 mutations or analogs. [0449]
• Recombinant human 98P4B6 protein or an analog or homolog or fragment thereof can be produced by mammalian cells transfected with a construct encoding a 98P4B6-related nucleotide. For example, 293T cells can be transfected with an expression plasmid encoding 98P4B6 or fragment, analog or homolog thereof, a 98P4B6-related protein is expressed in the 293T cells, and the recombinant 98P4B6 protein is isolated using standard purification methods (e.g., affinity purification using anti-98P4B6 antibodies). In another embodiment, a 98P4B6 coding sequence is subcloned into the retroviral vector pSRαMSVtkneo and used to infect various mammalian cell lines, such as NIH 3T3, TsuPr1, 293 and rat-1 in order to establish 98P4B6 expressing cell lines. Various other expression systems well known in the art can also be employed. Expression constructs encoding a leader peptide joined in frame to a 98P4B6 coding sequence can be used for the generation of a secreted form of recombinant 98P4B6 protein. [0450]
• As discussed herein, redundancy in the genetic code permits variation in 98P4B6 gene sequences. In particular, it is known in the art that specific host species often have specific codon preferences, and thus one can adapt the disclosed sequence as preferred for a desired host. For example, preferred analog codon sequences typically have rare codons (i.e., codons having a usage frequency of less than about 20% in known sequences of the desired host) replaced with higher frequency codons. Codon preferences for a specific species are calculated, for example, by utilizing codon usage tables available on the INTERNET such as at URL dna.affrc.go.jp/˜nakamura/codon.html. [0451]
• Additional sequence modifications are known to enhance protein expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon/intron splice site signals, transposon-like repeats, and/or other such well-characterized sequences that are deleterious to gene expression. The GC content of the sequence is adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. Where possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures. Other useful modifications include the addition of a translational initiation consensus sequence at the start of the open reading frame, as described in Kozak, [0452] Mol. Cell Biol., 9:5073-5080 (1989). Skilled artisans understand that the general rule that eukaryotic ribosomes initiate translation exclusively at the 5′ proximal AUG codon is abrogated only under rare conditions (see, e.g., Kozak PNAS 92(7): 2662-2666, (1995) and Kozak NAR 15(20): 8125-8148 (1987)).
• III.) 98P4B6-Related Proteins [0453]
• Another aspect of the present invention provides 98P4B6-related proteins. Specific embodiments of 98P4B6 proteins comprise a polypeptide having all or part of the amino acid sequence of human 98P4B6 as shown in FIG. 2 or FIG. 3. Alternatively, embodiments of 98P4B6 proteins comprise variant, homolog or analog polypeptides that have alterations in the amino acid sequence of 98P4B6 shown in FIG. 2 or FIG. 3. [0454]
• Embodiments of a 98P4B6 polypeptide include: a 98P4B6 polypeptide having a sequence shown in FIG. 2, a peptide sequence of a 98P4B6 as shown in FIG. 2 wherein T is U; at least 10 contiguous nucleotides of a polypeptide having the sequence as shown in FIG. 2; or, at least 10 contiguous peptides of a polypeptide having the sequence as shown in FIG. 2 where T is U. For example, embodiments of 98P4B6 peptides comprise, without limitation: [0455]
• (I) a protein comprising, consisting essentially of, or consisting of an amino acid sequence as shown in FIG. 2A-AL or FIG. 3A-J; [0456]
• (II) a 98P4B6-related protein that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% homologous to an entire amino acid sequence shown in FIG. 2A-AL; [0457]
• (III) a 98P4B6-related protein that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identical to an entire amino acid sequence shown in FIG. 2A-AL or [0458] 3A-J;
• (IV) a protein that comprises at least one peptide set forth in Tables VIII to XLIX, optionally with a proviso that it is not an entire protein of FIG. 2; [0459]
• (V) a protein that comprises at least one peptide set forth in Tables VIII-XXI, collectively, which peptide is also set forth in Tables XXII to XLIX, collectively, optionally with a proviso that it is not an entire protein of FIG. 2; [0460]
• (VI) a protein that comprises at least two peptides selected from the peptides set forth in Tables VIII-XLIX, optionally with a proviso that it is not an entire protein of FIG. 2; [0461]
• (VII) a protein that comprises at least two peptides selected from the peptides set forth in Tables VIII to XLIX collectively, with a proviso that the protein is not a contiguous sequence from an amino acid sequence of FIG. 2; [0462]
• (VIII) a protein that comprises at least one peptide selected from the peptides set forth in Tables VIII-XXI; and at least one peptide selected from the peptides set forth in Tables XXII to XLIX, with a proviso that the protein is not a contiguous sequence from an amino acid sequence of FIG. 2; [0463]
• (IX) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIGS. 3A, 3B, [0464] 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number increment up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490 respectively that includes at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5;
• (X) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIGS. 3A, 3B, [0465] 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number increment up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490 respectively that includes at least at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of FIG. 6;
• (XI) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIGS. 3A, 3B, [0466] 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number increment up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490 respectively that includes at least at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7;
• (XII) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIGS. 3A, 3B, [0467] 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number increment up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490 respectively that includes at least at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Average Flexibility profile of FIG. 8;
• (XIII) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, amino acids of a protein of FIGS. 3A, 3B, [0468] 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number increment up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490 respectively that includes at least at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of FIG. 9;
• (XIV) a peptide that occurs at least twice in Tables VIII-XXI and XXII to XLIX, collectively; [0469]
• (XV) a peptide that occurs at least three times in Tables VIII-XXI and XXII to XLIX, collectively; [0470]
• (XVI) a peptide that occurs at least four times in Tables VIII-XXI and XXII to XLIX, collectively; [0471]
• (XVII) a peptide that occurs at least five times in Tables VIII-XXI and XXII to XLIX, collectively; [0472]
• (XVIII) a peptide that occurs at least once in Tables VIII-XXI, and at least once in tables XXII to XLIX; [0473]
• (XIX) a peptide that occurs at least once in Tables VIII-XXI, and at least twice in tables XXII to XLIX; [0474]
• (XX) a peptide that occurs at least twice in Tables VIII-XXI, and at least once in tables XXII to XLIX; [0475]
• (XXI) a peptide that occurs at least twice in Tables VIII-XXI, and at least twice in tables XXII to XLIX; [0476]
• (XXII) a peptide which comprises one two, three, four, or five of the following characteristics, or an oligonucleotide encoding such peptide: [0477]
• i) a region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Hydrophilicity profile of FIG. 5; [0478]
• ii) a region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or less than 0.5, 0.4, 0.3, 0.2, 0.1, or having a value equal to 0.0, in the Hydropathicity profile of FIG. 6; [0479]
• iii) a region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Percent Accessible Residues profile of FIG. 7; [0480]
• iv) a region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Average Flexibility profile of FIG. 8; or, [0481]
• v) a region of at least 5 amino acids of a particular peptide of FIG. 3, in any whole number increment up to the full length of that protein in FIG. 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Beta-turn profile of FIG. 9; [0482]
• (XXIII) a composition comprising a peptide of (I)-(XXII) or an antibody or binding region thereof together with a pharmaceutical excipient and/or in a human unit dose form. [0483]
• (XXIV) a method of using a peptide of (I)-(XXII), or an antibody or binding region thereof or a composition of (XXIII) in a method to modulate a cell expressing 98P4B6, [0484]
• (XXV) a method of using a peptide of (I)-(XXII) or an antibody or binding region thereof or a composition of (XXIII) in a method to diagnose, prophylax, prognose, or treat an individual who bears a cell expressing 98P4B6 [0485]
• (XXVI) a method of using a peptide of (I)-(XXII) or an antibody or binding region thereof or a composition (XXIII) in a method to diagnose, prophylax, prognose, or treat an individual who bears a cell expressing 98P4B6, said cell from a cancer of a tissue listed in Table I; [0486]
• (XXVII) a method of using a peptide of (I)-(XXII) or an antibody or binding region thereof or a composition of (XXIII) in a method to diagnose, prophylax, prognose, or treat a a cancer; [0487]
• (XXVIII) a method of using a peptide of (I)-(XXII) or an antibody or binding region thereof or a composition of (XXIII) in a method to diagnose, prophylax, prognose, or treat a a cancer of a tissue listed in Table I; and, [0488]
• (XXIX) a method of using a a peptide of (I)-(XXII) or an antibody or binding region thereof or a composition (XXIII) in a method to identify or characterize a modulator of a cell expressing 98P4B6. [0489]
• As used herein, a range is understood to specifically disclose all whole unit positions thereof. [0490]
• Typical embodiments of the invention disclosed herein include 98P4B6 polynucleotides that encode specific portions of 98P4B6 mRNA sequences (and those which are complementary to such sequences) such as those that encode the proteins and/or fragments thereof, for example: [0491]
• (a)4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 410, 420, 430, 440, 450, or 454 more contiguous amino acids of [0492] 98P4B6 variant 1; the maximal lengths relevant for other variants are: variant 52, 45 amino acids; variant 5, 419 amino acids, variant 6, 490, variant 7, 576 amino acids, variant 8, 490 amino acids, variant 13, 454, variant 14, 454 amino acids, variant 21, 576 amino acids, and variant 25, 490 amino acids.
• In general, naturally occurring allelic variants of human 98P4B6 share a high degree of structural identity and homology (e.g., 90% or more homology). Typically, allelic variants of a 98P4B6 protein contain conservative amino acid substitutions within the 98P4B6 sequences described herein or contain a substitution of an amino acid from a corresponding position in a homologue of 98P4B6. One class of 98P4B6 allelic variants are proteins that share a high degree of homology with at least a small region of a particular 98P4B6 amino acid sequence, but further contain a radical departure from the sequence, such as a non-conservative substitution, truncation, insertion or frame shift. In comparisons of protein sequences, the terms, similarity, identity, and homology each have a distinct meaning as appreciated in the field of genetics. Moreover, orthology and paralogy can be important concepts describing the relationship of members of a given protein family in one organism to the members of the same family in other organisms. [0493]
• Amino acid abbreviations are provided in Table II. Conservative amino acid substitutions can frequently be made in a protein without altering either the conformation or the function of the protein. Proteins of the invention can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 conservative substitutions. Such changes include substituting any of isoleucine (I), valine (V), and leucine (L) for any other of these hydrophobic amino acids; aspartic acid (D) for glutamic acid (E) and vice versa; glutamine (Q) for asparagine (N) and vice versa; and serine (S) for threonine (T) and vice versa. Other substitutions can also be considered conservative, depending on the environment of the particular amino acid and its role in the three-dimensional structure of the protein. For example, glycine (G) and alanine (A) can frequently be interchangeable, as can alanine (A) and valine (V). Methionine (M), which is relatively hydrophobic, can frequently be interchanged with leucine and isoleucine, and sometimes with valine. Lysine (K) and arginine (R) are frequently interchangeable in locations in which the significant feature of the amino acid residue is its charge and the differing pK's of these two amino acid residues are not significant. Still other changes can be considered “conservative” in particular environments (see, e.g. Table III herein; pages 13-15 “Biochemistry” 2[0494] ^nd ED. Lubert Stryer ed (Stanford University); Henikoff et al., PNAS 1992 Vol 89 10915-10919; Lei et al., J Biol Chem 1995 May 19; 270(20):11882-6).
• Embodiments of the invention disclosed herein include a wide variety of art-accepted variants or analogs of 98P4B6 proteins such as polypeptides having amino acid insertions, deletions and substitutions. 98P4B6 variants can be made using methods known in the art such as site-directed mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Carter et al., [0495] Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)), cassette mutagenesis (Wells et al., Gene, 34:315 (1985)), restriction selection mutagenesis (Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)) or other known techniques can be performed on the cloned DNA to produce the 98P4B6 variant DNA.
• Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence that is involved in a specific biological activity such as a protein-protein interaction. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions (Creighton, [0496] The Proteins, (W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does not yield adequate amounts of variant, an isosteric amino acid can be used.
• As defined herein, 98P4B6 variants, analogs or homologs, have the distinguishing attribute of having at least one epitope that is “cross reactive” with a 98P4B6 protein having an amino acid sequence of FIG. 3. As used in this sentence, “cross reactive” means that an antibody or T cell that specifically binds to a 98P4B6 variant also specifically binds to a 98P4B6 protein having an amino acid sequence set forth in FIG. 3. A polypeptide ceases to be a variant of a protein shown in FIG. 3, when it no longer contains any epitope capable of being recognized by an antibody or T cell that specifically binds to the starting 98P4B6 protein. Those skilled in the art understand that antibodies that recognize proteins bind to epitopes of varying size, and a grouping of the order of about four or five amino acids, contiguous or not, is regarded as a typical number of amino acids in a minimal epitope. See, e.g., Nair et al., J. Immunol 2000 165(12): 6949-6955; Hebbes et al., Mol Immunol (1989) 26(9):865-73; Schwartz et al., J Immunol (1985) 135(4):2598-608. [0497]
• Other classes of 98P4B6-related protein variants share 70%, 75%, 80%, 85% or 90% or more similarity with an amino acid sequence of FIG. 3, or a fragment thereof. Another specific class of 98P4B6 protein variants or analogs comprises one or more of the 98P4B6 biological motifs described herein or presently known in the art. Thus, encompassed by the present invention are analogs of 98P4B6 fragments (nucleic or amino acid) that have altered functional (e.g. immunogenic) properties relative to the starting fragment. It is to be appreciated that motifs now or which become part of the art are to be applied to the nucleic or amino acid-sequences of FIG. 2 or FIG. 3. [0498]
• As discussed herein, embodiments of the claimed invention include polypeptides containing less than the full amino acid sequence of a 98P4B6 protein shown in FIG. 2 or FIG. 3. For example, representative embodiments of the invention comprise peptides/proteins having any 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids of a 98P4B6 protein shown in FIG. 2 or FIG. 3. [0499]
• Moreover, representative embodiments of the invention disclosed herein include polypeptides consisting of about amino acid 1 to about amino acid 10 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 10 to about amino acid 20 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 20 to about amino acid 30 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 30 to about amino acid 40 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 40 to about amino acid 50 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 50 to about amino acid 60 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 60 to about amino acid 70 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 70 to about amino acid 80 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 80 to about amino acid 90 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 90 to about amino acid 100 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, etc. throughout the entirety of a 98P4B6 amino acid sequence. Moreover, polypeptides consisting of about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 130, or 140 or 150 etc.) of a 98P4B6 protein shown in FIG. 2 or FIG. 3 are embodiments of the invention. It is to be appreciated that the starting and stopping positions in this paragraph refer to the specified position as well as that position plus or minus 5 residues. [0500]
• 98P4B6-related proteins are generated using standard peptide synthesis technology or using chemical cleavage methods well known in the art. Alternatively, recombinant methods can be used to generate nucleic acid molecules that encode a 98P4B6-related protein. In one embodiment, nucleic acid molecules provide a means to generate defined fragments of a 98P4B6 protein (or variants, homologs or analogs thereof). [0501]
• III.A.) Motif-Bearing Protein Embodiments [0502]
• Additional illustrative embodiments of the invention disclosed herein include 98P4B6 polypeptides comprising the amino acid residues of one or more of the biological motifs contained within a 98P4B6 polypeptide sequence set forth in FIG. 2 or FIG. 3. Various motifs are known in the art, and a protein can be evaluated for the presence of such motifs by a number of publicly available Internet sites (see, e.g., URL addresses: pfam.wustl.edu/; searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html; psort.ims.u-tokyo.ac.jp/; cbs.dtu.dk/; ebi.ac.uk/interpro/scan.html; expasy.ch/tools/scnpsit1.html; Epimatrix™ and Epimer™, Brown University, brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html; and BIMAS, bimas.dcrt.nih.gov/.). [0503]
• Motif bearing subsequences of all 98P4B6 variant proteins are set forth and identified in Tables VIII-XXI and XXII-XLIX. [0504]
• Table V sets forth several frequently occurring motifs based on pfam searches (see URL address pfam.wustl.edu/). The columns of Table V list (1) motif name abbreviation, (2) percent identity found amongst the different member of the motif family, (3) motif name or description and (4) most common function; location information is included if the motif is relevant for location. [0505]
• Polypeptides comprising one or more of the 98P4B6 motifs discussed above are useful in elucidating the specific characteristics of a malignant phenotype in view of the observation that the 98P4B6 motifs discussed above are associated with growth dysregulation and because 98P4B6 is overexpressed in certain cancers (See, e.g., Table I). Casein kinase II, cAMP and camp-dependent protein kinase, and Protein Kinase C, for example, are enzymes known to be associated with the development of the malignant phenotype (see e.g. Chen et al., Lab Invest., 78(2): 165-174 (1998); Gaiddon et al., Endocrinology 136(10): 4331-4338 (1995); Hall et al., Nucleic Acids Research 24(6): 1119-1126 (1996); Peterziel et al., Oncogene 18(46): 6322-6329 (1999) and O'Brian, Oncol. Rep. 5(2): 305-309 (1998)). Moreover, both glycosylation and myristoylation are protein modifications also associated with cancer and cancer progression (see e.g. Dennis et al., Biochem. Biophys. Acta 1473(1):21-34 (1999); Raju et al., Exp. Cell Res. 235(1): 145-154 (1997)). Amidation is another protein modification also associated with cancer and cancer progression (see e.g. Treston et al., J. Natl. Cancer Inst. Monogr. (13): 169-175 (1992)). [0506]
• In another embodiment, proteins of the invention comprise one or more of the immunoreactive epitopes identified in accordance with art-accepted methods, such as the peptides set forth in Tables VIII-XXI and XXII-XLIX. CTL epitopes can be determined using specific algorithms to identify peptides within a 98P4B6 protein that are capable of optimally binding to specified HLA alleles (e.g., Table IV; Epimatrix™ and Epimer™, Brown University, URL brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html; and BIMAS, URL bimas.dcrt.nih.gov/.) Moreover, processes for identifying peptides that have sufficient binding affinity for HLA molecules and which are correlated with being immunogenic epitopes, are well known in the art, and are carried out without undue experimentation. In addition, processes for identifying peptides that are immunogenic epitopes, are well known in the art, and are carried out without undue experimentation either in vitro or in vivo. [0507]
• Also known in the art are principles for creating analogs of such epitopes in order to modulate immunogenicity. For example, one begins with an epitope that bears a CTL or HTL motif (see, e.g., the HLA Class I and HLA Class II motifs/supermotifs of Table IV). The epitope is analoged by substituting out an amino acid at one of the specified positions, and replacing it with another amino acid specified for that position. For example, on the basis of residues defined in Table IV, one can substitute out a deleterious residue in favor of any other residue, such as a preferred residue; substitute a less-preferred residue with a preferred residue; or substitute an originally-occurring preferred residue with another preferred residue. Substitutions can occur at primary anchor positions or at other positions in a peptide; see, e.g., Table IV. [0508]
• A variety of references reflect the art regarding the identification and generation of epitopes in a protein of interest as well as analogs thereof. See, for example, WO 97/33602 to Chesnut et al.; Sette, Immunogenetics 1999 50(3-4): 201-212; Sette et al., J. Immunol. 2001 166(2): 1389-1397; Sidney et al., Hum. Immunol. 1997 58(1): 12-20; Kondo et al., Immunogenetics 1997 45(4): 249-258; Sidney et al., J. Immunol. 1996 157(8): 3480-90; and Falk et al., Nature 351: 290-6 (1991); Hunt et a., Science 255:1261-3 (1992); Parker et al., J. Immunol. 149:3580-7 (1992); Parker et al., J. Immunol. 152:163-75 (1994)); Kast et al., 1994 152(8): 3904-12; Borras-Cuesta et al., Hum. Immunol. 2000 61(3): 266-278; Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., PMID: 7895164, UI: 95202582; O'Sullivan et al., J. Immunol. 1991 147(8): 2663-2669; Alexander et al., Immunity 1994 1(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92. [0509]
• Related embodiments of the invention include polypeptides comprising combinations of the different motifs set forth in Table VI, and/or, one or more of the predicted CTL epitopes of Tables VIII-XXI and XXII-XLIX, and/or, one or more of the predicted HTL epitopes of Tables XLVI-XLIX, and/or, one or more of the T cell binding motifs known in the art. Preferred embodiments contain no insertions, deletions or substitutions either within the motifs or within the intervening sequences of the polypeptides, In addition, embodiments which include a number of either N-terminal and/or C-terminal amino acid residues on either side of these motifs may be desirable (to, for example, include a greater portion of the polypeptide architecture in which the motif is located). Typically, the number of N-terminal and/or C-terminal amino acid residues on either side of a motif is between about 1 to about 100 amino acid residues, preferably 5 to about 50 amino acid residues. [0510]
• 98P4B6-related proteins are embodied in many forms, preferably in isolated form. A purified 98P4B6 protein molecule will be substantially free of other proteins or molecules that impair the binding of 98P4B6 to antibody, T cell or other ligand. The nature and degree of isolation and purification will depend on the intended use. Embodiments of a 98P4B6-related proteins include purified 98P4B6-related proteins and functional, soluble 98P4B6-related proteins. In one embodiment, a functional, soluble 98P4B6 protein or fragment thereof retains the ability to be bound by antibody, T cell or other ligand. [0511]
• The invention also provides 98P4B6 proteins comprising biologically active fragments of a 98P4B6 amino acid sequence shown in FIG. 2 or FIG. 3. Such proteins exhibit properties of the starting 98P4B6 protein, such as the ability to elicit the generation of antibodies that specifically bind an epitope associated with the starting 98P4B6 protein; to be bound by such antibodies; to elicit the activation of HTL or CTL; and/or, to be recognized by HTL or CTL that also specifically bind to the starting protein. [0512]
• 98P4B6-related polypeptides that contain particularly interesting structures can be predicted and/or identified using various analytical techniques well known in the art, including, for example, the methods of Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis, or based on immunogenicity. Fragments that contain such structures are particularly useful in generating subunit-specific anti-98P4B6 antibodies or T cells or in identifying cellular factors that bind to 98P4B6. For example, hydrophilicity profiles can be generated, and immunogenic peptide fragments identified, using the method of Hopp, T. P. and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828. Hydropathicity profiles can be generated, and immunogenic peptide fragments identified, using the method of Kyte, J. and Doolitte, R. F., 1982, J. Mol. Biol. 157:105-132. Percent (%) Accessible Residues profiles can be generated, and immunogenic peptide fragments identified, using the method of Janin J., 1979, Nature 277:491-492. Average Flexibility profiles can be generated, and immunogenic peptide fragments identified, using the method of Bhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. Protein Res. 32:242-255. Beta-turn profiles can be generated, and immunogenic peptide fragments identified, using the method of Deleage, G., Roux B., 1987, Protein Engineering 1:289-294. [0513]
• CTL epitopes can be determined using specific algorithms to identify peptides within a 98P4B6 protein that are capable of optimally binding to specified HLA alleles (e.g., by using the SYFPEITHI site at World Wide Web URL syfpeithi.bmi-heidelberg.com/; the listings in Table IV(A)-(E); Epimatrix™ and Epimer™, Brown University, URL (brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html); and BIMAS, URL bimas.dcrt.nih.gov/). Illustrating this, peptide epitopes from 98P4B6 that are presented in the context of human MHC Class I molecules, e.g., HLA-A1, A2, A3, A11, A24, B7 and B35 were predicted (see, e.g., Tables VIII-XXI, XXII-XLIX). Specifically, the complete amino acid sequence of the 98P4B6 protein and relevant portions of other variants, i.e., for HLA Class I predictions 9 flanking residues on either side of a point mutation or exon juction, and for HLA Class II predictions 14 flanking residues on either side of a point mutation or exon junction corresponding to that variant, were entered into the HLA Peptide Motif Search algorithm found in the Bioinformatics and Molecular Analysis Section (BIMAS) web site listed above; in addition to the site SYFPEITHI, at URL syfpeithi.bmi-heidelberg.com/. [0514]
• The HLA peptide motif search algorithm was developed by Dr. Ken Parker based on binding of specific peptide sequences in the groove of HLA Class I molecules, in particular HLA-A2 (see, e.g., Falk et al., Nature 351: 290-6 (1991); Hunt et al., Science 255:1261-3(1992); Parker et al., J. Immunol. 149:3580-7(1992); Parker et al., J. Immunol. 152:163-75 (1994)). This algorithm allows location and ranking of 8-mer, 9-mer, and 10-mer peptides from a complete protein sequence for predicted binding to HLA-A2 as well as numerous other HLA Class I molecules. Many HLA class I binding peptides are 8-, 9-, 10 or 11-mers. For example, for Class I HLA-A2, the epitopes preferably contain a leucine (L) or methionine (M) at [0515] position 2 and a valine (V) or leucine (L) at the C-terminus (see, e.g., Parker et al., J. Immunol. 149:3580-7 (1992)). Selected results of 98P4B6 predicted binding peptides are shown in Tables VIII-XXI and XXII-XLIX herein. In Tables VIII-XXI and XXII-XLVII, selected candidates, 9-mers and 10-mers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. In Tables XLVI-XLIX, selected candidates, 15-mers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. The binding score corresponds to the estimated half time of dissociation of complexes containing the peptide at 37° C. at pH 6.5. Peptides with the highest binding score are predicted to be the most tightly bound to HLA Class I on the cell surface for the greatest period of time and thus represent the best immunogenic targets for T-cell recognition.
• Actual binding of peptides to an HLA allele can be evaluated by stabilization of HLA expression on the antigen-processing defective cell line T2 (see, e.g., Xue et al., Prostate 30:73-8 (1997) and Peshwa et al., Prostate 36:129-38 (1998)). Immunogenicity of specific peptides can be evaluated in vitro by stimulation of CD8+ cytotoxic T lymphocytes (CTL) in the presence of antigen presenting cells such as dendritic cells. [0516]
• It is to be appreciated that every epitope predicted by the BIMAS site, Epimer™ and Epimatrix™ sites, or specified by the HLA class I or class II motifs available in the art or which become part of the art such as set forth in Table IV (or determined using World Wide Web site URL syfpeithi.bmi-heidelberg.com/, or BIMAS, bimas.dcrt.nih.gov/) are to be “applied” to a 98P4B6 protein in accordance with the invention. As used in this context “applied” means that a 98P4B6 protein is evaluated, e.g., visually or by computer-based patterns finding methods, as appreciated by those of skill in the relevant art. Every subsequence of a 98P4B6 protein of 8, 9, 10, or 11 amino acid residues that bears an HLA Class I motif, or a subsequence of 9 or more amino acid residues that bear an HLA Class II motif are within the scope of the invention. [0517]
• III.B.) Expression of 98P4B6-Related Proteins [0518]
• In an embodiment described in the examples that follow, 98P4B6 can be conveniently expressed in cells (such as 293T cells) transfected with a commercially available expression vector such as a CMV-driven expression vector encoding 98P4B6 with a C-terminal 6×His and MYC tag (pcDNA3.1/mycHIS, Invitrogen or Tag5, GenHunter Corporation, Nashville Tenn.). The Tag5 vector provides an IgGK secretion signal that can be used to facilitate the production of a secreted 98P4B6 protein in transfected cells. The secreted HIS-tagged 98P4B6 in the culture media can be purified, e.g., using a nickel column using standard techniques. [0519]
• III.C.) Modifications of 98P4B6-Related Proteins [0520]
• Modifications of 98P4B6-related proteins such as covalent modifications are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a 98P4B6 polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of a 98P4B6 protein. Another type of covalent modification of a 98P4B6 polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of a protein of the invention. Another type of covalent modification of 98P4B6 comprises linking a 98P4B6 polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337. [0521]
• The 98P4B6-related proteins of the present invention can also be modified to form a chimeric molecule comprising 98P4B6 fused to another, heterologous polypeptide or amino acid sequence. Such a chimeric molecule can be synthesized chemically or recombinantly. A chimeric molecule can have a protein of the invention fused to another tumor-associated antigen or fragment thereof. Alternatively, a protein in accordance with the invention can comprise a fusion of fragments of a 98P4B6 sequence (amino or nucleic acid) such that a molecule is created that is not, through its length, directly homologous to the amino or nucleic acid sequences shown in FIG. 2 or FIG. 3. Such a chimeric molecule can comprise multiples of the same subsequence of 98P4B6. A chimeric molecule can comprise a fusion of a 98P4B6-related protein with a polyhistidine epitope tag, which provides an epitope to which immobilized nickel can selectively bind, with cytokines or with growth factors. The epitope tag is generally placed at the amino- or carboxyl-terminus of a 98P4B6 protein. In an alternative embodiment, the chimeric molecule can comprise a fusion of a 98P4B6-related protein with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule (also referred to as an “immunoadhesin”), such a fusion could be to the Fc region of an IgG molecule. The Ig fusions preferably include the substitution of a soluble (transmembrane domain deleted or inactivated) form of a 98P4B6 polypeptide in place of at least one variable region within an Ig molecule. In a preferred embodiment, the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CH1, CH2 and CH3 regions of an IgGI molecule. For the production of immunoglobulin fusions see, e.g., U.S. Pat. No. 5,428,130 issued Jun. 27, 1995. [0522]
• III.D.) Uses of 98P4B6-Related Proteins [0523]
• The proteins of the invention have a number of different specific uses. As 98P4B6 is highly expressed in prostate and other cancers, 98P4B6-related proteins are used in methods that assess the status of 98P4B6 gene products in normal versus cancerous tissues, thereby elucidating the malignant phenotype. Typically, polypeptides from specific regions of a 98P4B6 protein are used to assess the presence of perturbations (such as deletions, insertions, point mutations etc.) in those regions (such as regions containing one or more motifs). Exemplary assays utilize antibodies or T cells targeting 98P4B6-related proteins comprising the amino acid residues of one or more of the biological motifs contained within a 98P4B6 polypeptide sequence in order to evaluate the characteristics of this region in normal versus cancerous tissues or to elicit an immune response to the epitope. Alternatively, 98P4B6-related proteins that contain the amino acid residues of one or more of the biological motifs in a 98P4B6 protein are used to screen for factors that interact with that region of 98P4B6. [0524]
• 98P4B6 protein fragments/subsequences are particularly useful in generating and characterizing domain-specific antibodies (e.g., antibodies recognizing an extracellular or intracellular epitope of a 98P4B6 protein), for identifying agents or cellular factors that bind to 98P4B6 or a particular structural domain thereof, and in various therapeutic and diagnostic contexts, including but not limited to diagnostic assays, cancer vaccines and methods of preparing such vaccines. [0525]
• Proteins encoded by the 98P4B6 genes, or by analogs, homologs or fragments thereof, have a variety of uses, including but not limited to generating antibodies and in methods for identifying ligands and other agents and cellular constituents that bind to a 98P4B6 gene product Antibodies raised against a 98P4B6 protein or fragment thereof are useful in diagnostic and prognostic assays, and imaging methodologies in the management of human cancers characterized by expression of 98P4B6 protein, such as those listed in Table I. Such antibodies can be expressed intracellularly and used in methods of treating patients with such cancers. 98P4B6-related nucleic acids or proteins are also used in generating HTL or CTL responses. [0526]
• Various immunological assays useful for the detection of 98P4B6 proteins are used, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), immunocytochemical methods, and the like. Antibodies can be labeled and used as immunological imaging reagents capable of detecting 98P4B6-expressing cells (e.g., in radioscintigraphic imaging methods). 98P4B6 proteins are also particularly useful in generating cancer vaccines, as further described herein. [0527]
• IV.) 98P4B6 Antibodies [0528]
• Another aspect of the invention provides antibodies that bind to 98P4B6-related proteins. Preferred antibodies specifically bind to a 98P4B6-related protein and do not bind (or bind weakly) to peptides or proteins that are not 98P4B6-related proteins under physiological conditions. In this context, examples of physiological conditions include: 1) phosphate buffered saline; 2) Tris-buffered saline containing 25 mM Tris and 150 mM NaCl; or normal saline (0.9% NaCl); 4) animal serum such as human serum; or, 5) a combination of any of 1) through 4); these reactions preferably taking place at pH 7.5, alternatively in a range of pH 7.0 to 8.0, or alternatively in a range of pH 6.5 to 8.5; also, these reactions taking place at a temperature between 4° C. to 37° C. For example, antibodies that bind 98P4B6 can bind 98P4B6-related proteins such as the homologs or analogs thereof. [0529]
• 98P4B6 antibodies of the invention are particularly useful in cancer (see, e.g., Table I) diagnostic and prognostic assays, and imaging methodologies. Similarly, such antibodies are useful in the treatment, diagnosis, and/or prognosis of other cancers, to the extent 98P4B6 is also expressed or overexpressed in these other cancers. Moreover, intracellularly expressed antibodies (e.g., single chain antibodies) are therapeutically useful in treating cancers in which the expression of 98P4B6 is involved, such as advanced or metastatic prostate cancers. [0530]
• The invention also provides various immunological assays useful for the detection and quantification of 98P4B6 and mutant 98P4B6-related proteins. Such assays can comprise one or more 98P4B6 antibodies capable of recognizing and binding a 98P4B6-related protein, as appropriate. These assays are performed within various immunological assay formats well known in the art, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), and the like. [0531]
• Immunological non-antibody assays of the invention also comprise T cell immunogenicity assays (inhibitory or stimulatory) as well as major histocompatibility complex (MHC) binding assays. [0532]
• In addition, immunological imaging methods capable of detecting prostate cancer and other cancers expressing 98P4B6 are also provided by the invention, including but not limited to radioscintigraphic imaging methods using labeled 98P4B6 antibodies. Such assays are clinically useful in the detection, monitoring, and prognosis of 98P4B6 expressing cancers such as prostate cancer. [0533]
• 98P4B6 antibodies are also used in methods for purifying a 98P4B6-related protein and for isolating 98P4B6 homologues and related molecules. For example, a method of purifying a 98P4B6-related protein comprises incubating a 98P4B6 antibody, which has been coupled to a solid matrix, with a lysate or other solution containing a 98P4B6-related protein under conditions that permit the 98P4B6 antibody to bind to the 98P4B6-related protein; washing the solid matrix to eliminate impurities; and eluting the 98P4B6-related protein from the coupled antibody. Other uses of 98P4B6 antibodies in accordance with the invention include generating anti-idiotypic antibodies that mimic a 98P4B6 protein. [0534]
• Various methods for the preparation of antibodies are well known in the art. For example, antibodies can be prepared by immunizing a suitable mammalian host using a 98P4B6-related protein, peptide, or fragment, in isolated or immunoconjugated form (Antibodies: A Laboratory Manual, CSH Press, Eds., Harlow, and Lane (1988); Harlow, Antibodies, Cold Spring Harbor Press, NY (1989)). In addition, fusion proteins of 98P4B6 can also be used, such as a 98P4B6 GST-fusion protein. In a particular embodiment, a GST fusion protein comprising all or most of the amino acid sequence of FIG. 2 or FIG. 3 is produced, then used as an immunogen to generate appropriate antibodies. In another embodiment, a 98P4B6-related protein is synthesized and used as an immunogen. [0535]
• In addition, naked DNA immunization techniques known in the art are used (with or without purified 98P4B6-related protein or 98P4B6 expressing cells) to generate an immune response to the encoded immunogen (for review, see Donnelly et al., 1997, Ann. Rev. Immunol. 15: 617-648). [0536]
• The amino acid sequence of a 98P4B6 protein as shown in FIG. 2 or FIG. 3 can be analyzed to select specific regions of the 98P4B6 protein for generating antibodies. For example, hydrophobicity and hydrophilicity analyses of a 98P4B6 amino acid sequence are used to identify hydrophilic regions in the 98P4B6 structure. Regions of a 98P4B6 protein that show immunogenic structure, as well as other regions and domains, can readily be identified using various other methods known in the art, such as Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis. Hydrophilicity profiles can be generated using the method of Hopp, T. P. and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828. Hydropathicity profiles can be generated using the method of Kyte, J. and Doolittle, R. F., 1982, J. Mol. Biol. 157:105-132. Percent (%) Accessible Residues profiles can be generated using the method of Janin J., 1979, Nature 277:491-492. Average Flexibility profiles can be generated using the method of Bhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. Protein Res. 32:242-255. Beta-turn profiles can be generated using the method of Deleage, G., Roux B., 1987, Protein Engineering 1:289-294. Thus, each region identified by any of these programs or methods is within the scope of the present invention. Methods for the generation of 98P4B6 antibodies are further illustrated by way of the examples provided herein. Methods for preparing a protein or polypeptide for use as an immunogen are well known in the art. Also well known in the art are methods for preparing immunogenic conjugates of a protein with a carrier, such as BSA, KLH or other carrier protein. In some circumstances, direct conjugation using, for example, carbodiimide reagents are used; in other instances linking reagents such as those supplied by Pierce Chemical Co., Rockford, Ill., are effective. Administration of a 98P4B6 immunogen is often conducted by injection over a suitable time period and with use of a suitable adjuvant, as is understood in the art. During the immunization schedule, titers of antibodies can be taken to determine adequacy of antibody formation. [0537]
• 98P4B6 monoclonal antibodies can be produced by various means well known in the art. For example, immortalized cell lines that secrete a desired monoclonal antibody are prepared using the standard hybridoma technology of Kohler and Milstein or modifications that immortalize antibody-producing B cells, as is generally known. Immortalized cell lines that secrete the desired antibodies are screened by immunoassay in which the antigen is a 98P4B6-related protein. When the appropriate immortalized cell culture is identified, the cells can be expanded and antibodies produced either from in vitro cultures or from ascites fluid. [0538]
• The antibodies or fragments of the invention can also be produced, by recombinant means. Regions that bind specifically to the desired regions of a 98P4B6 protein can also be produced in the context of chimeric or complementarity-determining region (CDR) grafted antibodies of multiple species origin. Humanized or human 98P4B6 antibodies can also be produced, and are preferred for use in therapeutic contexts. Methods for humanizing murine and other non-human antibodies, by substituting one or more of the non-human antibody CDRs for corresponding human antibody sequences, are well known (see for example, Jones et al., 1986, Nature 321: 522-525; Riechmann et al., 1988, Nature 332: 323-327; Verhoeyen et al., 1988, Science 239: 1534-1536). See also, Carter et al., 1993, Proc. Natl. Acad. Sci. USA 89:4285 and Sims et al., 1993, J. Immunol. 151: 2296. [0539]
• Methods for producing fully human monoclonal antibodies include phage display and transgenic methods (for review, see Vaughan et al., 1998, Nature Biotechnology 16: 535-539). Fully human 98P4B6 monoclonal antibodies can be generated using cloning technologies employing large human Ig gene combinatorial libraries (i.e., phage display) (Griffiths and Hoogenboom, Building an in vitro immune system: human antibodies from phage display libraries. In: Protein Engineering of Antibody Molecules for Prophylactic and Therapeutic Applications in Man, Clark, M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and Barbas, Human Antibodies from combinatorial libraries. Id., pp 65-82). Fully human 98P4B6 monoclonal antibodies can also be produced using transgenic mice engineered to contain human immunoglobulin gene loci as described in PCT Patent Application WO98/24893, Kucherlapati and Jakobovits et al., published Dec. 3, 1997 (see also, Jakobovits, 1998, Exp. Opin. Invest. Drugs 7(4): 607-614; U.S. Pat. No. 6,162,963 issued 19 Dec. 2000; U.S. Pat. No. 6,150,584 issued 12 Nov. 2000; and, U.S. Pat. No. 6,114,598 issued 5 Sep. 2000). This method avoids the in vitro manipulation required with phage display technology and efficiently produces high affinity authentic human antibodies. [0540]
• Reactivity of 98P4B6 antibodies with a 98P4B6-related protein can be established by a number of well known means, including Western blot, immunoprecipitation, ELISA, and FACS analyses using, as appropriate, 98P4B6-related proteins, 98P4B6-expressing cells or extracts thereof. A 98P4B6 antibody or fragment thereof can be labeled with a detectable marker or conjugated to a second molecule. Suitable detectable markers include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, chemiluminescent compound, a metal chelator or an enzyme. Further, bi-specific antibodies specific for two or more 98P4B6 epitopes are generated using methods generally known in the art. Homodimeric antibodies can also be generated by cross-linking techniques known in the art (e.g., Wolff et al., Cancer Res. 53: 2560-2565). [0541]
• V.) 98P4B6 Cellular Immune Responses [0542]
• The mechanism by which T cells recognize antigens has been delineated. Efficacious peptide epitope vaccine compositions of the invention induce a therapeutic or prophylactic immune responses in very broad segments of the world-wide population. For an understanding of the value and efficacy of compositions of the invention that induce cellular immune responses, a brief review of immunology-related technology is provided. [0543]
• A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., [0544] Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are set forth in Table IV (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via World Wide Web at URL (134.2.96.221/scripts.hlaserver.dll/home.htm); Sette, A. and Sidney, J. Curr. Opin. Immunol. 10:478,1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13,1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics 1999 November; 50(3-4):201-12, Review).
• Furthermore, x-ray crystallographic analyses of HLA-peptide complexes have revealed pockets within the peptide binding cleft/groove of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. [0545] Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A. , Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991.)
• Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that are correlated with binding to particular HLA antigen(s). [0546]
• Thus, by a process of HLA motif identification, candidates for epitope-based vaccines have been identified; such candidates can be further evaluated by HLA-peptide binding assays to determine binding affinity and/or the time period of association of the epitope and its corresponding HLA molecule. Additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, and/or immunogenicity. [0547]
• Various strategies can be utilized to evaluate cellular immunogenicity, including: [0548]
• 1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., [0549] Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol 59:1, 1998). This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a lymphokine- or ⁵¹Cr-release assay involving peptide sensitized target cells.
• 2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. et al., [0550] J. Immunol 26:97, 1996; Wentworth, P. A. et al., Int. Immunol 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997). For example, in such methods peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a ⁵¹Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.
• 3) Demonstration of recall T cell responses from immune individuals who have been either effectively vaccinated and/or from chronically ill patients (see, e.g., Rehermann, B. et al., [0551] J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). Accordingly, recall responses are detected by culturing PBL from subjects that have been exposed to the antigen due to disease and thus have generated an immune response “naturally”, or from patients who were vaccinated against the antigen. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays including ⁵¹Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.
• VI.) 98P4B6 Transgenic Animals [0552]
• Nucleic acids that encode a 98P4B6-related protein can also be used to generate either transgenic animals or “knock out” animals that, in turn, are useful in the development and screening of therapeutically useful reagents. In accordance with established techniques, cDNA encoding 98P4B6 can be used to clone genomic DNA that encodes 98P4B6. The cloned genomic sequences can then be used to generate transgenic animals containing cells that express DNA that encode 98P4B6. Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Pat. No. 4,736,866 issued 12 Apr. 1988, and U.S. Pat. No. 4,870,009 issued 26 Sep. 1989. Typically, particular cells would be targeted for 98P4B6 transgene incorporation with tissue-specific enhancers. [0553]
• Transgenic animals that include a copy of a transgene encoding 98P4B6 can be used to examine the effect of increased expression of DNA that encodes 98P4B6. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. In accordance with this aspect of the invention, an animal is treated with a reagent and a reduced incidence of a pathological condition, compared to untreated animals that bear the transgene, would indicate a potential therapeutic intervention for the pathological condition. [0554]
• Alternatively, non-human homologues of 98P4B6 can be used to construct a 98P4B6 “knock out” animal that has a defective or altered gene encoding 98P4B6 as a result of homologous recombination between the endogenous gene encoding 98P4B6 and altered genomic DNA encoding 98P4B6 introduced into an embryonic cell of the animal. For example, cDNA that encodes 98P4B6 can be used to clone genomic DNA encoding 98P4B6 in accordance with established techniques. A portion of the genomic DNA encoding 98P4B6 can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5′ and 3′ ends) are included in the vector (see, e.g., Thomas and Capecchi, [0555] Cell, 51:503 (1987) for a description of homologous recombination vectors). The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected (see, e.g., Li et at., Cell, 69:915 (1992)). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras (see, e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152). A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal, and the embryo brought to term to create a “knock out” animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knock out animals can be characterized, for example, for their ability to defend against certain pathological conditions or for their development of pathological conditions due to absence of a 98P4B6 polypeptide.
• VII.) Methods for the Detection of 98P4B6 [0556]
• Another aspect of the present invention relates to methods for detecting 98P4B6 polynucleotides and 98P4B6-related proteins, as well as methods for identifying a cell that expresses 98P4B6. The expression profile of 98P4B6 makes it a diagnostic marker for metastasized disease. Accordingly, the status of 98P4B6 gene products provides information useful for predicting a variety of factors including susceptibility to advanced stage disease, rate of progression, and/or tumor aggressiveness. As discussed in detail herein, the status of 98P4B6 gene products in patient samples can be analyzed by a variety protocols that are well known in the art including immunohistochemical analysis, the variety of Northern blotting techniques including in situ hybridization, RT-PCR analysis (for example on laser capture micro-dissected samples), Western blot analysis and issue array analysis. [0557]
• More particularly, the invention provides assays for the detection of 98P4B6 polynucleotides in a biological sample, such as serum, bone, prostate, and other tissues, urine, semen, cell preparations, and the like. Detectable 98P4B6 polynucleotides include, for example, a 98P4B6 gene or fragment thereof, 98P4B6 mRNA, alternative splice variant 98P4B6 mRNAs, and recombinant DNA or RNA molecules that contain a 98P4B6 polynucleotide. A number of methods for amplifying and/or detecting the presence of 98P4B6 polynucleotides are well known in the art and can be employed in the practice of this aspect of the invention. [0558]
• In one embodiment, a method for detecting a 98P4B6 mRNA in a biological sample comprises producing cDNA from the sample by reverse transcription using at least one primer; amplifying the cDNA so produced using a 98P4B6 polynucleotides as sense and antisense primers to amplify 98P4B6 cDNAs therein; and detecting the presence of the amplified 98P4B6 cDNA. Optionally, the sequence of the amplified 98P4B6 cDNA can be determined. [0559]
• In another embodiment, a method of detecting a 98P4B6 gene in a biological sample comprises first isolating genomic DNA from the sample; amplifying the isolated genomic DNA using 98P4B6 polynucleotides as sense and antisense primers; and detecting the presence of the amplified 98P4B6 gene. Any number of appropriate sense and antisense probe combinations can be designed from a 98P4B6 nucleotide sequence (see, e.g., FIG. 2) and used for this purpose. [0560]
• The invention also provides assays for detecting the presence of a 98P4B6 protein in a tissue or other biological sample such as serum, semen, bone, prostate, urine, cell preparations, and the like. Methods for detecting a 98P4B6-related protein are also well known and include, for example, immunoprecipitation, immunohistochemical analysis, Western blot analysis, molecular binding assays, ELISA, ELIFA and the like. For example, a method of detecting the presence of a 98P4B6-related protein in a biological sample comprises first contacting the sample with a 98P4B6 antibody, a 98P4B6-reactive fragment thereof, or a recombinant protein containing an antigen-binding region of a 98P4B6 antibody; and then detecting the binding of 98P4B6-related protein in the sample. [0561]
• Methods for identifying a cell that expresses 98P4B6 are also within the scope of the invention. In one embodiment, an assay for identifying a cell that expresses a 98P4B6 gene comprises detecting the presence of 98P4B6 mRNA in the cell. Methods for the detection of particular mRNAs in cells are well known and include, for example, hybridization assays using complementary DNA probes (such as in situ hybridization using labeled 98P4B6 riboprobes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR using complementary primers specific for 98P4B6, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like). Alternatively, an assay for identifying a cell that expresses a 98P4B6 gene comprises detecting the presence of 98P4B6-related protein in the cell or secreted by the cell. Various methods for the detection of proteins are well known in the art and are employed for the detection of 98P4B6-related proteins and cells that express 98P4B6-related proteins. [0562]
• 98P4B6 expression analysis is also useful as a tool for identifying and evaluating agents that modulate 98P4B6 gene expression. For example, 98P4B6 expression is significantly upregulated in prostate cancer, and is expressed in cancers of the tissues listed in Table I. Identification of a molecule or biological agent that inhibits 98P4B6 expression or over-expression in cancer cells is of therapeutic value. For example, such an agent can be identified by using a screen that quantifies 98P4B6 expression by RT-PCR, nucleic acid hybridization or antibody binding. [0563]
• VIII.) Methods for Monitoring the Status of 98P4B6-Related Genes and Their Products [0564]
• Oncogenesis is known to be a multistep process where cellular growth becomes progressively dysregulated and cells progress from a normal physiological state to precancerous and then cancerous states (see, e.g., Alers et al., Lab Invest. 77(5): 437-438 (1997) and Isaacs et al., Cancer Surv. 23: 19-32 (1995)). In this context, examining a biological sample for evidence of dysregulated cell growth (such as aberrant 98P4B6 expression in cancers) allows for early detection of such aberrant physiology, before a pathologic state such as cancer has progressed to a stage that therapeutic options are more limited and or the prognosis is worse. In such examinations, the status of 98P4B6 in a biological sample of interest can be compared, for example, to the status of 98P4B6 in a corresponding normal sample (e.g. a sample from that individual or alternatively another individual that is not affected by a pathology). An alteration in the status of 98P4B6 in the biological sample (as compared to the normal sample) provides evidence of dysregulated cellular growth. In addition to using a biological sample that is not affected by a pathology as a normal sample, one can also use a predetermined normative value such as a predetermined normal level of mRNA expression (see, e.g., Grever et al., J. Comp. Neurol. 1996 Dec. 9; 376(2): 306-14 and U.S. Pat. No. 5,837,501) to compare 98P4B6 status in a sample. [0565]
• The term “status” in this context is used according to its art accepted meaning and refers to the condition or state of a gene and its products. Typically, skilled artisans use a number of parameters to evaluate the condition or state of a gene and its products. These include, but are not limited to the location of expressed gene products (including the location of 98P4B6 expressing cells) as well as the level, and biological activity of expressed gene products (such as 98P4B6 mRNA, polynucleotides and polypeptides). Typically, an alteration in the status of 98P4B6 comprises a change in the location of 98P4B6 and/or 98P4B6 expressing cells and/or an increase in 98P4B6 mRNA and/or protein expression. [0566]
• 98P4B6 status in a sample can be analyzed by a number of means well known in the art, including without limitation, immunohistochemical analysis, in situ hybridization, RT-PCR analysis on laser capture micro-dissected samples, Western blot analysis, and tissue array analysis. Typical protocols for evaluating the status of a 98P4B6 gene and gene products are found, for example in Ausubel et al. eds., 1995, Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4 (Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Thus, the status of 98P4B6 in a biological sample is evaluated by various methods utilized by skilled artisans including, but not limited to genomic Southern analysis (to examine, for example perturbations in a 98P4B6 gene), Northern analysis and/or PCR analysis of 98P4B6 mRNA (to examine, for example alterations in the polynucleotide sequences or expression levels of 98P4B6 mRNAs), and, Western and/or immunohistochemical analysis (to examine, for example alterations in polypeptide sequences, alterations in polypeptide localization within a sample, alterations in expression levels of 98P4B6 proteins and/or associations of 98P4B6 proteins with polypeptide binding partners). Detectable 98P4B6 polynucleotides include, for example, a 98P4B6 gene or fragment thereof, 98P4B6 mRNA, alternative splice variants, 98P4B6 mRNAs, and recombinant DNA or RNA molecules containing a 98P4B6 polynucleotide. [0567]
• The expression profile of 98P4B6 makes it a diagnostic marker for local and/or metastasized disease, and provides information on the growth or oncogenic potential of a biological sample. In particular, the status of 98P4B6 provides information useful for predicting susceptibility to particular disease stages, progression, and/or tumor aggressiveness. The invention provides methods and assays for determining 98P4B6 status and diagnosing cancers that express 98P4B6, such as cancers of the tissues listed in Table I. For example, because 98P4B6 mRNA is so highly expressed in prostate and other cancers relative to normal prostate tissue, assays that evaluate the levels of 98P4B6 mRNA transcripts or proteins in a biological sample can be used to diagnose a disease associated with 98P4B6 dysregulation, and can provide prognostic information useful in defining appropriate therapeutic options. [0568]
• The expression status of 98P4B6 provides information including the presence, stage and location of dysplastic, precancerous and cancerous cells, predicting susceptibility to various stages of disease, and/or for gauging tumor aggressiveness. Moreover, the expression profile makes it useful as an imaging reagent for metastasized disease. Consequently, an aspect of the invention is directed to the various molecular prognostic and diagnostic methods for examining the status of 98P4B6 in biological samples such as those from individuals suffering from, or suspected of suffering from a pathology characterized by dysregulated cellular growth, such as cancer. [0569]
• As described above, the status of 98P4B6 in a biological sample can be examined by a number of well-known procedures in the art. For example, the status of 98P4B6 in a biological sample taken from a specific location in the body can be examined by evaluating the sample for the presence or absence of 98P4B6 expressing cells (e.g. those that express 98P4B6 mRNAs or proteins). This examination can provide evidence of dysregulated cellular growth, for example, when 98P4B6-expressing cells are found in a biological sample that does not normally contain such cells (such as a lymph node), because such alterations in the status of 98P4B6 in a biological sample are often associated with dysregulated cellular growth. Specifically, one indicator of dysregulated cellular growth is the metastases of cancer cells from an organ of origin (such as the prostate) to a different area of the body (such as a lymph node). In this context, evidence of dysregulated cellular growth is important for example because occult lymph node metastases can be detected in a substantial proportion of patients with prostate cancer, and such metastases are associated with known predictors of disease progression (see, e.g., Murphy et al., Prostate 42(4): 315-317 (2000);Su et al., Semin. Surg. Oncol. 18(1): 17-28 (2000) and Freeman et al., J Urol 1995 August 154(2 Pt 1):474-8). [0570]
• In one aspect, the invention provides methods for monitoring 98P4B6 gene products by determining the status of 98P4B6 gene products expressed by cells from an individual suspected of having a disease associated with dysregulated cell growth (such as hyperplasia or cancer) and then comparing the status so determined to the status of 98P4B6 gene products in a corresponding normal sample. The presence of aberrant 98P4B6 gene products in the test sample relative to the normal sample provides an indication of the presence of dysregulated cell growth within the cells of the individual. [0571]
• In another aspect, the invention provides assays useful in determining the presence of cancer in an individual, comprising detecting a significant increase in 98P4B6 mRNA or protein expression in a test cell or tissue sample relative to expression levels in the corresponding normal cell or tissue. The presence of 98P4B6 mRNA can, for example, be evaluated in tissues including but not limited to those listed in Table I. The presence of significant 98P4B6 expression in any of these tissues is useful to indicate the emergence, presence and/or severity of a cancer, since the corresponding normal tissues do not express 98P4B6 mRNA or express it at lower levels. [0572]
• In a related embodiment, 98P4B6 status is determined at the protein level rather than at the nucleic acid level. For example, such a method comprises determining the level of 98P4B6 protein expressed by cells in a test tissue sample and comparing the level so determined to the level of 98P4B6 expressed in a corresponding normal sample. In one embodiment, the presence of 98P4B6 protein is evaluated, for example, using immunohistochemical methods. 98P4B6 antibodies or binding partners capable of detecting 98P4B6 protein expression are used in a variety of assay formats well known in the art for this purpose. [0573]
• In a further embodiment, one can evaluate the status of 98P4B6 nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules. These perturbations can include insertions, deletions, substitutions and the like. Such evaluations are useful because perturbations in the nucleotide and amino acid sequences are observed in a large number of proteins associated with a growth dysregulated phenotype (see, e.g., Marrogi et al., 1999, J. Cutan. Pathol. 26(8):369-378). For example, a mutation in the sequence of 98P4B6 may be indicative of the presence or promotion of a tumor. Such assays therefore have diagnostic and predictive value where a mutation in 98P4B6 indicates a potential loss of function or increase in tumor growth. [0574]
• A wide variety of assays for observing perturbations in nucleotide and amino acid sequences are well known in the art. For example, the size and structure of nucleic acid or amino acid sequences of 98P4B6 gene products are observed by the Northern, Southern, Western, PCR and DNA sequencing protocols discussed herein. In addition, other methods for observing perturbations in nucleotide and amino acid sequences such as single strand conformation polymorphism analysis are well known in the art (see, e.g., U.S. Pat. No. 5,382,510 issued 7 Sep. 1999, and U.S. Pat. No. 5,952,170 issued 17 Jan. 1995). [0575]
• Additionally, one can examine the methylation status of a 98P4B6 gene in a biological sample. Aberrant demethylation and/or hypermethylation of CpG islands in gene 5′ regulatory regions frequently occurs in immortalized and transformed cells, and can result in altered expression of various genes. For example, promoter hypermethylation of the pi-class glutathione S-transferase (a protein expressed in normal prostate but not expressed in >90% of prostate carcinomas) appears to permanently silence transcription of this gene and is the most frequently detected genomic alteration in prostate carcinomas (De Marzo et al., Am. J. Pathol. 155(6): 1985-1992 (1999)). In addition, this alteration is present in at least 70% of cases of high-grade prostatic intraepithelial neoplasia (PIN) (Brooks et al., Cancer Epidemiol. Biomarkers Prev., 1998, 7:531-536). In another example, expression of the LAGE-I tumor specific gene (which is not expressed in normal prostate but is expressed in 25-50% of prostate cancers) is induced by deoxy-azacytidine in lymphoblastoid cells, suggesting that tumoral expression is due to demethylation (Lethe et al., Int. J. Cancer 76(6): 903-908 (1998)). A variety of assays for examining methylation status of a gene are well known in the art. For example, one can utilize, in Southern hybridization approaches, methylation-sensitive restriction enzymes that cannot cleave sequences that contain methylated CpG sites to assess the methylation status of CpG islands. In addition, MSP (methylation specific PCR) can rapidly profile the methylation status of all the CpG sites present in a CpG island of a given gene. This procedure involves initial modification of DNA by sodium bisulfite (which will convert all unmethylated cytosines to uracil) followed by amplification using primers specific for methylated versus unmethylated DNA. Protocols involving methylation interference can also be found for example in Current Protocols In Molecular Biology, Unit 12, Frederick M. Ausubel et al. eds., 1995. [0576]
• Gene amplification is an additional method for assessing the status of 98P4B6. Gene amplification is measured in a sample directly, for example, by conventional Southern blotting or Northern blotting to quantitate the transcription of mRNA (Thomas, 1980, Proc. Natl. Acad. Sci. USA, 77:5201-5205), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies are employed that recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn are labeled and the assay carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected. [0577]
• Biopsied tissue or peripheral blood can be conveniently assayed for the presence of cancer cells using for example, Northern, dot blot or RT-PCR analysis to detect 98P4B6 expression. The presence of RT-PCR amplifiable 98P4B6 mRNA provides an indication of the presence of cancer. RT-PCR assays are well known in the art RT-PCR detection assays for tumor cells in peripheral blood are currently being evaluated for use in the diagnosis and management of a number of human solid tumors. In the prostate cancer field, these include RT-PCR assays for the detection of cells expressing PSA and PSM (Verkaik et al., 1997, Urol. Res. 25:373-384; Ghossein et al., 1995, J. Clin. Oncol. 13:1195-2000; Heston et al., 1995, Clin. Chem. 41:1687-1688). [0578]
• A further aspect of the invention is an assessment of the susceptibility that an individual has for developing cancer. In one embodiment, a method for predicting susceptibility to cancer comprises detecting 98P4B6 mRNA or 98P4B6 protein in a tissue sample, its presence indicating susceptibility to cancer, wherein the degree of 98P4B6 mRNA expression correlates to the degree of susceptibility. In a specific embodiment, the presence of 98P4B6 in prostate or other tissue is examined, with the presence of 98P4B6 in the sample providing an indication of prostate cancer susceptibility (or the emergence or existence of a prostate tumor). Similarly, one can evaluate the integrity 98P4B6 nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations in 98P4B6 gene products in the sample is an indication of cancer susceptibility (or the emergence or existence of a tumor). [0579]
• The invention also comprises methods for gauging tumor aggressiveness. In one embodiment, a method for gauging aggressiveness of a tumor comprises determining the level of 98P4B6 mRNA or 98P4B6 protein expressed by tumor cells, comparing the level so determined to the level of 98P4B6 mRNA or 98P4B6 protein expressed in a corresponding normal tissue taken from the same individual or a normal tissue reference sample, wherein the degree of 98P4B6 mRNA or 98P4B6 protein expression in the tumor sample relative to the normal sample indicates the degree of aggressiveness. In a specific embodiment, aggressiveness of a tumor is evaluated by determining the extent to which 98P4B6 is expressed in the tumor cells, with higher expression levels indicating more aggressive tumors. Another embodiment is the evaluation of the integrity of 98P4B6 nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations indicates more aggressive tumors. [0580]
• Another embodiment of the invention is directed to methods for observing the progression of a malignancy in an individual over time. In one embodiment, methods for observing the progression of a malignancy in an individual over time comprise determining the level of 98P4B6 mRNA or 98P4B6 protein expressed by cells in a sample of the tumor, comparing the level so determined to the level of 98P4B6 mRNA or 98P4B6 protein expressed in an equivalent tissue sample taken from the same individual at a different time, wherein the degree of 98P4B6 mRNA or 98P4B6 protein expression in the tumor sample over time provides information on the progression of the cancer. In a specific embodiment, the progression of a cancer is evaluated by determining 98P4B6 expression in the tumor cells over time, where increased expression over time indicates a progression of the cancer. Also, one can evaluate the integrity 98P4B6 nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like, where the presence of one or more perturbations indicates a progression of the cancer. [0581]
• The above diagnostic approaches can be combined with any one of a wide variety of prognostic and diagnostic protocols known in the art. For example, another embodiment of the invention is directed to methods for observing a coincidence between the expression of 98P4B6 gene and 98P4B6 gene products (or perturbations in 98P4B6 gene and 98P4B6 gene products) and a factor that is associated with malignancy, as a means for diagnosing and prognosticating the status of a tissue sample. A wide variety of factors associated with malignancy can be utilized, such as the expression of genes associated with malignancy (e.g. PSA, PSCA and PSM expression for prostate cancer etc.) as well as gross cytological observations (see, e.g., Bocking et al., 1984, Anal. Quant. Cytol. 6(2):74-88; Epstein, 1995, Hum. Pathol. 26(2):223-9; Thorson et al., 1998, Mod. Pathol. 11(6):543-51; Baisden et al., 1999, Am. J. Surg. Pathol. 23(8):918-24). Methods for observing a coincidence between the expression of 98P4B6 gene and 98P4B6 gene products (or perturbations in 98P4B6 gene and 98P4B6 gene products) and another factor that is associated with malignancy are useful, for example, because the presence of a set of specific factors that coincide with disease provides information crucial for diagnosing and prognosticating the status of a tissue sample. [0582]
• In one embodiment, methods for observing a coincidence between the expression of 98P4B6 gene and 98P4B6 gene products (or perturbations in 98P4B6 gene and 98P4B6 gene products) and another factor associated with malignancy entails detecting the overexpression of 98P4B6 mRNA or protein in a tissue sample, detecting the overexpression of PSA mRNA or protein in a tissue sample (or PSCA or PSM expression), and observing a coincidence of 98P4B6 mRNA or protein and PSA mRNA or protein overexpression (or PSCA or PSM expression). In a specific embodiment, the expression of 98P4B6 and PSA mRNA in prostate tissue is examined, where the coincidence of 98P4B6 and PSA mRNA overexpression in the sample indicates the existence of prostate cancer, prostate cancer susceptibility or the emergence or status of a prostate tumor. [0583]
• Methods for detecting and quantifying the expression of 98P4B6 mRNA or protein are described herein, and standard nucleic acid and protein detection and quantification technologies are well known in the art. Standard methods for the detection and quantification of 98P4B6 mRNA include in situ hybridization using labeled 98P4B6 riboprobes, Northern blot and related techniques using 98P4B6 polynucleotide probes, RT-PCR analysis using primers specific for 98P4B6, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like. In a specific embodiment, semi-quantitative RT-PCR is used to detect and quantify 98P4B6 mRNA expression. Any number of primers capable of amplifying 98P4B6 can be used for this purpose, including but not limited to the various primer sets specifically described herein. In a specific embodiment, polyclonal or monoclonal antibodies specifically reactive with the wild-type 98P4B6 protein can be used in an immunohistochemical assay of biopsied tissue. [0584]
• IX.) Identification of Molecules that Interact with 98P4B6 [0585]
• The 98P4B6 protein and nucleic acid sequences disclosed herein allow a skilled artisan to identify proteins, small molecules and other agents that interact with 98P4B6, as well as pathways activated by 98P4B6 via any one of a variety of art accepted protocols. For example, one can utilize one of the so-called interaction trap systems (also referred to as the “two-hybrid assay”). In such systems, molecules interact and reconstitute a transcription factor which directs expression of a reporter gene, whereupon the expression of the reporter gene is assayed. Other systems identify protein-protein interactions in vivo through reconstitution of a eukaryotic transcriptional activator, see, e.g., U.S. Pat. No. 5,955,280 issued 21 Sep. 1999, U.S. Pat. No. 5,925,523 issued 20 Jul. 1999, U.S. Pat. No. 5,846,722 issued 8 Dec. 1998 and U.S. Pat. No. 6,004,746 issued 21 Dec. 1999. Algorithms are also available in the art for genome-based predictions of protein function (see, e.g., Marcotte, et al., Nature 402: 4 Nov. 1999, 83-86). [0586]
• Alternatively one can screen peptide libraries to identify molecules that interact with 98P4B6 protein sequences. In such methods, peptides that bind to 98P4B6 are identified by screening libraries that encode a random or controlled collection of amino acids. Peptides encoded by the libraries are expressed as fusion proteins of bacteriophage coat proteins, the bacteriophage particles are then screened against the 98P4B6 protein(s). [0587]
• Accordingly, peptides having a wide variety of uses, such as therapeutic, prognostic or diagnostic reagents, are thus identified without any prior information on the structure of the expected ligand or receptor molecule. Typical peptide libraries and screening methods that can be used to identify molecules that interact with 98P4B6 protein sequences are disclosed for example in U.S. Pat. No. 5,723,286 issued 3 Mar. 1998 and U.S. Pat. No. 5,733,731 issued 31 Mar. 1998. [0588]
• Alternatively, cell lines that express 98P4B6 are used to identify protein-protein interactions mediated by 98P4B6. Such interactions can be examined using immunoprecipitation techniques (see, e.g., Hamilton B. J., et al. Biochem. Biophys. Res. Commun. 1999, 261:646-51). 98P4B6 protein can be immunoprecipitated from 98P4B6-expressing cell lines using anti-98P4B6 antibodies. Alternatively, antibodies against His-tag can be used in a cell line engineered to express fusions of 98P4B6 and a His-tag (vectors mentioned above). The immunoprecipitated complex can be examined for protein association by procedures such as Western blotting, [0589] ³⁵S-methionine labeling of proteins, protein microsequencing, silver staining and two-dimensional gel electrophoresis.
• Small molecules and ligands that interact with 98P4B6 can be identified through related embodiments of such screening assays. For example, small molecules can be identified that interfere with protein function, including molecules that interfere with 98P4B6's ability to mediate phosphorylation and de-phosphorylation, interaction with DNA or RNA molecules as an indication of regulation of cell cycles, second messenger signaling or tumorigenesis. Similarly, small molecules that modulate 98P4B6-related ion channel, protein pump, or cell communication functions are identified and used to treat patients that have a cancer that expresses 98P4B6 (see, e.g., Hille, B., Ionic Channels of [0590] Excitable Membranes 2^nd Ed., Sinauer Assoc., Sunderland, Mass., 1992). Moreover, ligands that regulate 98P4B6 function can be identified based on their ability to bind 98P4B6 and activate a reporter construct. Typical methods are discussed for example in U.S. Pat. No. 5,928,868 issued 27 Jul. 1999, and include methods for forming hybrid ligands in which at least one ligand is a small molecule. In an illustrative embodiment, cells engineered to express a fusion protein of 98P4B6 and a DNA-binding protein are used to co-express a fusion protein of a hybrid ligand/small molecule and a cDNA library transcriptional activator protein. The cells further contain a reporter gene, the expression of which is conditioned on the proximity of the first and second fusion proteins to each other, an event that occurs only if the hybrid ligand binds to target sites on both hybrid proteins. Those cells that express the reporter gene are selected and the unknown small molecule or the unknown ligand is identified. This method provides a means of identifying modulators, which activate or inhibit 98P4B6.
• An embodiment of this invention comprises a method of screening for a molecule that interacts with a 98P4B6 amino acid sequence shown in FIG. 2 or FIG. 3, comprising the steps of contacting a population of molecules with a 98P4B6 amino acid sequence, allowing the population of molecules and the 98P4B6 amino acid sequence to interact under conditions that facilitate an interaction, determining the presence of a molecule that interacts with the 98P4B6 amino acid sequence, and then separating molecules that do not interact with the 98P4B6 amino acid sequence from molecules that do. In a specific embodiment, the method further comprises purifying, characterizing and identifying a molecule that interacts with the 98P4B6 amino acid sequence. The identified molecule can be used to modulate a function performed by 98P4B6. In a preferred embodiment, the 98P4B6 amino acid sequence is contacted with a library of peptides. [0591]
• X.) Therapeutic Methods and Compositions [0592]
• The identification of 98P4B6 as a protein that is normally expressed in a restricted set of tissues, but which is also expressed in prostate and other cancers, opens a number of therapeutic approaches to the treatment of such cancers. As contemplated herein, 98P4B6 functions as a transcription factor involved in activating tumor-promoting genes or repressing genes that block tumorigenesis. [0593]
• Accordingly, therapeutic approaches that inhibit the activity of a 98P4B6 protein are useful for patients suffering from a cancer that expresses 98P4B6. These therapeutic approaches generally fall into two classes. One class comprises various methods for inhibiting the binding or association of a 98P4B6 protein with its binding partner or with other proteins. Another class comprises a variety of methods for inhibiting the transcription of a 98P4B6 gene or translation of 98P4B6 mRNA. [0594]
• X.A.) Anti-Cancer Vaccines [0595]
• The invention provides cancer vaccines comprising a 98P4B6-related protein or 98P4B6-related nucleic acid. In view of the expression of 98P4B6, cancer vaccines prevent and/or treat 98P4B6-expressing cancers with minimal or no effects on non-target tissues. The use of a tumor antigen in a vaccine that generates humoral and/or cell-mediated immune responses as anti-cancer therapy is well known in the art and has been employed in prostate cancer using human PSMA and rodent PAP immunogens (Hodge et al., 1995, Int. J. Cancer 63:231-237; Fong et al., 1997, J. Immunol. 159:3113-3117). [0596]
• Such methods can be readily practiced by employing a 98P4B6-related protein, or a 98P4B6-encoding nucleic acid molecule and recombinant vectors capable of expressing and presenting the 98P4B6 immunogen (which typically comprises a number of antibody or T cell epitopes). Skilled artisans understand that a wide variety of vaccine systems for delivery of immunoreactive epitopes are known in the art (see, e.g., Heryln et al., Ann Med 1999 Feb. 31(1):66-78; Maruyama et al., Cancer Immunol Immunother 2000 June 49(3):123-32) Briefly, such methods of generating an immune response (e.g. humoral and/or cell-mediated) in a mammal, comprise the steps of: exposing the mammal's immune system to an immunoreactive epitope (e.g. an epitope present in a 98P4B6 protein shown in FIG. 3 or analog or homolog thereof) so that the mammal generates an immune response that is specific for that epitope (e.g. generates antibodies that specifically recognize that epitope). In a preferred method, a 98P4B6 immunogen contains a biological motif, see e.g., Tables VIII-XXI and XXII-XLIX, or a peptide of a size range from 98P4B6 indicated in FIG. 5, FIG. 6, FIG. 7, FIG. 8, and FIG. 9. [0597]
• The entire 98P4B6 protein, immunogenic regions or epitopes thereof can be combined and delivered by various means. Such vaccine compositions can include, for example, lipopeptides (e.g.,Vitiello, A. et al., [0598] J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413,1988; Tam, J. P., J. Immunol Methods 196:17-32,1996), peptides formulated as multivalent peptides; peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.
• In patients with 98P4B6-associated cancer, the vaccine compositions of the invention can also be used in conjunction with other treatments used for cancer, e.g., surgery, chemotherapy, drug therapies, radiation therapies, etc. including use in combination with immune adjuvants such as IL-2, IL-12, GM-CSF, and the like. [0599]
• Cellular Vaccines: [0600]
• CTL epitopes can be determined using specific algorithms to identify peptides within 98P4B6 protein that bind corresponding HLA alleles (see e.g., Table IV; Epimer™ and Epimatrix™, Brown University (URL brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html); and, BIMAS, (URL bimas.dcrt.nih.gov/; SYFPEITHI at URL syfpeithi.bmi-heidelberg.com/). In a preferred embodiment, a 98P4B6 immunogen contains one or more amino acid sequences identified using techniques well known in the art, such as the sequences shown in Tables VIII-XXI and XXII-XLIX or a peptide of 8, 9, 10 or 11 amino acids specified by an HLA Class I motif/supermotif (e.g., Table IV (A), Table IV (D), or Table IV (E)) and/or a peptide of at least 9 amino acids that comprises an HLA Class II motif/supermotif (e.g., Table IV (B) or Table IV (C)). As is appreciated in the art, the HLA Class I binding groove is essentially closed ended so that peptides of only a particular size range can fit into the groove and be bound, generally HLA Class I epitopes are 8, 9, 10, or 11 amino acids long. In contrast, the HLA Class II binding groove is essentially open ended; therefore a peptide of about 9 or more amino acids can be bound by an HLA Class II molecule. Due to the binding groove differences between HLA Class I and II, HLA Class I motifs are length specific, i.e., position two of a Class I motif is the second amino acid in an amino to carboxyl direction of the peptide. The amino acid positions in a Class II motif are relative only to each other, not the overall peptide, i.e., additional amino acids can be attached to the amino and/or carboxyl termini of a motif-bearing sequence. HLA Class II epitopes are often 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids long, or longer than 25 amino acids. [0601]
• Antibody-Based Vaccines [0602]
• A wide variety of methods for generating an immune response in a mammal are known in the art (for example as the first step in the generation of hybridomas). Methods of generating an immune response in a mammal comprise exposing the mammal's immune system to an immunogenic epitope on a protein (e.g. a 98P4B6 protein) so that an immune response is generated. A typical embodiment consists of a method for generating an immune response to 98P4B6 in a host, by contacting the host with a sufficient amount of at least one 98P4B6 B cell or cytotoxic T-cell epitope or analog thereof; and at least one periodic interval thereafter re-contacting the host with the 98P4B6 B cell or cytotoxic T-cell epitope or analog thereof. A specific embodiment consists of a method of generating an immune response against a 98P4B6-related protein or a man-made multiepitopic peptide comprising: administering 98P4B6 immunogen (e.g. a 98P4B6 protein or a peptide fragment thereof, a 98P4B6 fusion protein or analog etc.) in a vaccine preparation to a human or another mammal. Typically, such vaccine preparations further contain a suitable adjuvant (see, e.g., U.S. Pat. No. 6,146,635) or a universal helper epitope such as a PADRE™ peptide (Epimmune Inc., San Diego, Calif.; see, e.g., Alexander et al., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., Immunity 1994 1(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92). An alternative method comprises generating an immune response in an individual against a 98P4B6 immunogen by: administering in vivo to muscle or skin of the individual's body a DNA molecule that comprises a DNA sequence that encodes a 98P4B6 immunogen, the DNA sequence operatively linked to regulatory sequences which control the expression of the DNA sequence; wherein the DNA molecule is taken up by cells, the DNA sequence is expressed in the cells and an immune response is generated against the immunogen (see, e.g., U.S. Pat. No. 5,962,428). Optionally a genetic vaccine facilitator such as anionic lipids; saponins; lectins; estrogenic compounds; hydroxylated lower alkyls; dimethyl sulfoxide; and urea is also administered. In addition, an antiidiotypic antibody can be administered that mimics 98P4B6, in order to generate a response to the target antigen. [0603]
• Nucleic Acid Vaccines: [0604]
• Vaccine compositions of the invention include nucleic acid-mediated modalities. DNA or RNA that encode protein(s) of the invention can be administered to a patient. Genetic immunization methods can be employed to generate prophylactic or therapeutic humoral and cellular immune responses directed against cancer cells expressing 98P4B6. Constructs comprising DNA encoding a 98P4B6-related protein/immunogen and appropriate regulatory sequences can be injected directly into muscle or skin of an individual, such that the cells of the muscle or skin take-up the construct and express the encoded 98P4B6 protein/immunogen. Alternatively, a vaccine comprises a 98P4B6-related protein. Expression of the 98P4B6-related protein immunogen results in the generation of prophylactic or therapeutic humoral and cellular immunity against cells that bear a 98P4B6 protein. Various prophylactic and therapeutic genetic immunization techniques known in the art can be used (for review, see information and references published at Internet address genweb.com). Nucleic acid-based delivery is described, for instance, in Wolff et. al, [0605] Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).
• For therapeutic or prophylactic immunization purposes, proteins of the invention can be expressed via viral or bacterial vectors. Various viral gene delivery systems that can be used in the practice of the invention include, but are not limited to, vaccinia, fowlpox, canarypox, adenovirus, influenza, poliovirus, adeno-associated virus, lentivirus, and sindbis virus (see, e.g., Restifo, 1996, Curr. Opin. Immunol. 8:658-663; Tsang et al. [0606] J. Nat. Cancer Inst. 87:982-990 (1995)). Non-viral delivery systems can also be employed by introducing naked DNA encoding a 98P4B6-related protein into the patient (e.g., intramuscularly or intradermally) to induce an anti-tumor response.
• Vaccinia virus is used, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into a host, the recombinant vaccinia virus expresses the protein immunogenic peptide, and thereby elicits a host immune response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., [0607] Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.
• Thus, gene delivery systems are used to deliver a 98P4B6-related nucleic acid molecule. In one embodiment, the full-length human 98P4B6 cDNA is employed. In another embodiment, 98P4B6 nucleic acid molecules encoding specific cytotoxic T lymphocyte (CTL) and/or antibody epitopes are employed. [0608]
• Ex Vivo Vaccines [0609]
• Various ex vivo strategies can also be employed to generate an immune response. One approach involves the use of antigen presenting cells (APCs) such as dendritic cells (DC) to present 98P4B6 antigen to a patient's immune system. Dendritic cells express MHC class I and II molecules, B7 co-stimulator, and IL-12, and are thus highly specialized antigen presenting cells. In prostate cancer, autologous dendritic cells pulsed with peptides of the prostate-specific membrane antigen (PSMA) are being used in a Phase I clinical trial to stimulate prostate cancer patients' immune systems (Tjoa et al., 1996, Prostate 28:65-69; Murphy et al., 1996, Prostate 29:371-380). Thus, dendritic cells can be used to present 98P4B6 peptides to T cells in the context of MHC class I or II molecules. In one embodiment, autologous dendritic cells are pulsed with 98P4B6 peptides capable of binding to MHC class I and/or class II molecules. In another embodiment, dendritic cells are pulsed with the complete 98P4B6 protein. Yet another embodiment involves engineering the overexpression of a 98P4B6 gene in dendritic cells using various implementing vectors known in the art, such as adenovirus (Arthur et al., 1997, Cancer Gene Ther. 4:17-25), retrovirus (Henderson et al., 1996, Cancer Res. 56:3763-3770), lentivirus, adeno-associated virus, DNA transfection (Ribas et al., 1997, Cancer Res. 57:2865-2869), or tumor-derived RNA transfection (Ashley et al., 1997, J. Exp. Med. 186:1177-1182). Cells that express 98P4B6 can also be engineered to express immune modulators, such as GM-CSF, and used as immunizing agents. [0610]
• X.B.) 98P4B6 as a Target for Antibody-Based Therapy [0611]
• 98P4B6 is an attractive target for antibody-based therapeutic strategies. A number of antibody strategies are known in the art for targeting both extracellular and intracellular molecules (see, e.g., complement and ADCC mediated killing as well as the use of intrabodies). Because 98P4B6 is expressed by cancer cells of various lineages relative to corresponding normal cells, systemic administration of 98P4B6-immunoreactive compositions are prepared that exhibit excellent sensitivity without toxic, non-specific and/or non-target effects caused by binding of the immunoreactive composition to non-target organs and tissues. Antibodies specifically reactive with domains of 98P4B6 are useful to treat 98P4B6-expressing cancers systemically, either as conjugates with a toxin or therapeutic agent, or as naked antibodies capable of inhibiting cell proliferation or function. [0612]
• 98P4B6 antibodies can be introduced into a patient such that the antibody binds to 98P4B6 and modulates a function, such as an interaction with a binding partner, and consequently mediates destruction of the tumor cells and/or inhibits the growth of the tumor cells. Mechanisms by which such antibodies exert a therapeutic effect can include complement-mediated cytolysis, antibody-dependent cellular cytotoxicity, modulation of the physiological function of 98P4B6, inhibition of ligand binding or signal transduction pathways, modulation of tumor cell differentiation, alteration of tumor angiogenesis factor profiles, and/or apoptosis. [0613]
• Those skilled in the art understand that antibodies can be used to specifically target and bind immunogenic molecules such as an immunogenic region of a 98P4B6 sequence shown in FIG. 2 or FIG. 3. In addition, skilled artisans understand that it is routine to conjugate antibodies to cytotoxic agents (see, e.g., Slevers et al. [0614] Blood 93:11 3678-3684 (Jun. 1, 1999)). When cytotoxic and/or therapeutic agents are delivered directly to cells, such as by conjugating them to antibodies specific for a molecule expressed by that cell (e.g. 98P4B6), the cytotoxic agent will exert its known biological effect (i.e. cytotoxicity) on those cells.
• A wide variety of compositions and methods for using antibody-cytotoxic agent conjugates to kill cells are known in the art. In the context of cancers, typical methods entail administering to an animal having a tumor a biologically effective amount of a conjugate comprising a selected cytotoxic and/or therapeutic agent linked to a targeting agent (e.g. an anti-98P4B6 antibody) that binds to a marker (e.g. 98P4B6) expressed, accessible to binding or localized on the cell surfaces. A typical embodiment is a method of delivering a cytotoxic and/or therapeutic agent to a cell expressing 98P4B6, comprising conjugating the cytotoxic agent to an antibody that immunospecifically binds to a 98P4B6 epitope, and, exposing the cell to the antibody-agent conjugate. Another illustrative embodiment is a method of treating an individual suspected of suffering from metastasized cancer, comprising a step of administering parenterally to said individual a pharmaceutical composition comprising a therapeutically effective amount of an antibody conjugated to a cytotoxic and/or therapeutic agent. [0615]
• Cancer immunotherapy using anti-98P4B6 antibodies can be done in accordance with various approaches that have been successfully employed in the treatment of other types of cancer, including but not limited to colon cancer (Arlen et al., 1998, Crit. Rev. Immunol. 18:133-138), multiple myeloma (Ozaki et al., 1997, Blood 90:3179-3186, Tsunenari et al., 1997, Blood 90:2437-2444), gastric cancer (Kasprzyk et al., 1992, Cancer Res. 52:2771-2776), B-cell lymphoma (Funakoshi et al., 1996, J. Immunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhong et al., 1996, Leuk. Res. 20:581-589), colorectal cancer (Moun et al., 1994, Cancer Res. 54:6160-6166; Velders et al., 1995, Cancer Res. 55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin. Immunol. 11:117-127). Some therapeutic approaches involve conjugation of naked antibody to a toxin or radioisotope, such as the conjugation of Y[0616] ⁹¹ or I¹³¹ to anti-CD20 antibodies (e.g., Zevalin™, IDEC Pharmaceuticals Corp. or Bexxar™, Coulter Pharmaceuticals), while others involve co-administration of antibodies and other therapeutic agents, such as Herceptin™ (trastuzumab) with paclitaxel (Genentech, Inc.). The antibodies can be conjugated to a therapeutic agent. To treat prostate cancer, for example, 98P4B6 antibodies can be administered in conjunction with radiation, chemotherapy or hormone ablation. Also, antibodies can be conjugated to a toxin such as calicheamicin (e.g., Mylotarg™, Wyeth-Ayerst, Madison, N.J., a recombinant humanized IgG₄ kappa antibody conjugated to antitumor antibiotic calicheamicin) or a maytansinoid (e.g., taxane-based Tumor-Activated Prodrug, TAP, platform, ImmunoGen, Cambridge, Mass., also see e.g., U.S. Pat. No. 5,416,064).
• Although 98P4B6 antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well. Fan et al. (Cancer Res. 53:4637-4642, 1993), Prewett et al. (International J. of Onco. 9:217-224, 1996), and Hancock et al. (Cancer Res. 51:4575-4580, 1991) describe the use of various antibodies together with chemotherapeutic agents. [0617]
• Although 98P4B6 antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well. [0618]
• Cancer patients can be evaluated for the presence and level of 98P4B6 expression, preferably using immunohistochemical assessments of tumor tissue, quantitative 98P4B6 imaging, or other techniques that reliably indicate the presence and degree of 98P4B6 expression. Immunohistochemical analysis of tumor biopsies or surgical specimens is preferred for this purpose. Methods for immunohistochemical analysis of tumor tissues are well known in the art. [0619]
• Anti-98P4B6 monoclonal antibodies that treat prostate and other cancers include those that initiate a potent immune response against the tumor or those that are directly cytotoxic. In this regard, anti-98P4B6 monoclonal antibodies (mAbs) can elicit tumor cell lysis by either complement-mediated or antibody-dependent cell cytotoxicity (ADCC) mechanisms, both of which require an intact Fc portion of the immunoglobulin molecule for interaction with effector cell Fc receptor sites on complement proteins. In addition, anti-98P4B6 mAbs that exert a direct biological effect on tumor growth are useful to treat cancers that express 98P4B6. Mechanisms by which directly cytotoxic mAbs act include: inhibition of cell growth, modulation of cellular differentiation, modulation of tumor angiogenesis factor profiles, and the induction of apoptosis. The mechanism(s) by which a particular anti-98P4B6 mAb exerts an anti-tumor effect is evaluated using any number of in vitro assays that evaluate cell death such as ADCC, ADMMC, complement-mediated cell lysis, and so forth, as is generally known in the art. [0620]
• In some patients, the use of murine or other non-human monoclonal antibodies, or human/mouse chimeric mAbs can induce moderate to strong immune responses against the non-human antibody. This can result in clearance of the antibody from circulation and reduced efficacy. In the most severe cases, such an immune response can lead to the extensive formation of immune complexes which, potentially, can cause renal failure. Accordingly, preferred monoclonal antibodies used in the therapeutic methods of the invention are those that are either fully human or humanized and that bind specifically to the target 98P4B6 antigen with high affinity but exhibit low or no antigenicity in the patient. [0621]
• Therapeutic methods of the invention contemplate the administration of single anti-98P4B6 mAbs as well as combinations, or cocktails, of different mAbs. Such mAb cocktails can have certain advantages inasmuch as they contain mAbs that target different epitopes, exploit different effector mechanisms or combine directly cytotoxic mAbs with mAbs that rely on immune effector functionality. Such mAbs in combination can exhibit synergistic therapeutic effects. In addition, anti-98P4B6 mAbs can be administered concomitantly with other therapeutic modalities, including but not limited to various chemotherapeutic agents, androgen-blockers, immune modulators (e.g., IL-2, GM-CSF), surgery or radiation. The anti-98P4B6 mAbs are administered in their “naked” or unconjugated form, or can have a therapeutic agent(s) conjugated to them. [0622]
• Anti-98P4B6 antibody formulations are administered via any route capable of delivering the antibodies to a tumor cell. Routes of administration include, but are not limited to, intravenous, intraperitoneal, intramuscular, intratumor, intradermal, and the like. Treatment generally involves repeated administration of the anti-98P4B6 antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 mg/kg body weight. In general, doses in the range of 10-1000 mg mAb per week are effective and well tolerated. [0623]
• Based on clinical experience with the Herceptin™ mAb in the treatment of metastatic breast cancer, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-98P4B6 mAb preparation represents an acceptable dosing regimen. Preferably, the initial loading dose is administered as a 90-minute or longer infusion. The periodic maintenance dose is administered as a 30 minute or longer infusion, provided the initial dose was well tolerated. As appreciated by those of skill in the art, various factors can influence the ideal dose regimen in a particular case. Such factors include, for example, the binding affinity and half life of the Ab or mAbs used, the degree of 98P4B6 expression in the patient, the extent of circulating shed 98P4B6 antigen, the desired steady-state antibody concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient. [0624]
• Optionally, patients should be evaluated for the levels of 98P4B6 in a given sample (e.g. the levels of circulating 98P4B6 antigen and/or 98P4B6 expressing cells) in order to assist in the determination of the most effective dosing regimen, etc. Such evaluations are also used for monitoring purposes throughout therapy, and are useful to gauge therapeutic success in combination with the evaluation of other parameters (for example, urine cytology and/or ImmunoCyt levels in bladder cancer therapy, or by analogy, serum PSA levels in prostate cancer therapy). [0625]
• Anti-idiotypic anti-98P4B6 antibodies can also be used in anti-cancer therapy as a vaccine for inducing an immune response to cells expressing a 98P4B6-related protein. In particular, the generation of anti-idiotypic antibodies is well known in the art; this methodology can readily be adapted to generate anti-idiotypic anti-98P4B6 antibodies that mimic an epitope on a 98P4B6-related protein (see, for example, Wagner et al., 1997, Hybridoma 16: 33-40; Foon et al., 1995, J. Clin. Invest. 96:334-342; Herlyn et al., 1996, Cancer Immunol. Immunother. 43:65-76). Such an anti-idiotypic antibody can be used in cancer vaccine strategies. [0626]
• X.C.) 98P4B6 as a Target for Cellular Immune Responses [0627]
• Vaccines and methods of preparing vaccines that contain an immunogenically effective amount of one or more HLA-binding peptides as described herein are further embodiments of the invention. Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptides. A peptide can be present in a vaccine individually. Alternatively, the peptide can exist as a homopolymer comprising multiple copies of the same peptide, or as a heteropolymer of various peptides. Polymers have the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition can be a naturally occurring region of an antigen or can be prepared, e.g., recombinantly or by chemical synthesis. [0628]
• Carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P[0629] ₃CSS). Moreover, an adjuvant such as a synthetic cytosine-phosphorothiolated-guanine-containing (CpG) oligonucleotides has been found to increase CTL responses 10- to 100-fold. (see, e.g. Davila and Celis, J. Immunol. 165:539-547 (2000)) Upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the, host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later development of cells that express or overexpress 98P4B6 antigen, or derives at least some therapeutic benefit when the antigen was tumor-associated.
• In some embodiments, it may be desirable to combine the class I peptide components with components that induce or facilitate neutralizing antibody and or helper T cell responses directed to the target antigen. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a cross reactive HTL epitope such as PADRE™ (Epimmune, San Diego, Calif.) molecule (described e.g., in U.S. Pat. No. 5,736,142). [0630]
• A vaccine of the invention can also include antigen-presenting cells (APC), such as dendritic cells (DC), as a vehicle to present peptides of the invention. Vaccine compositions can be created in vitro, following dendritic cell mobilization and harvesting, whereby loading of dendritic cells occurs in vitro. For example, dendritic cells are transfected, e.g., with a minigene in accordance with the invention, or are pulsed with peptides. The dendritic cell can then be administered to a patient to elicit immune responses in vivo. Vaccine compositions, either DNA- or peptide-based, can also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo. [0631]
• Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. It is preferred that each of the following principles be balanced in order to make the selection. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived. [0632]
• 1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with tumor clearance. For HLA Class I this includes 3-4 epitopes that come from at least one tumor associated antigen (TAA). For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one TAA (see, e.g., Rosenberg et al., [0633] Science 278:1447-1450). Epitopes from one TAA may be used in combination with epitopes from one or more additional TAAs to produce a vaccine that targets tumors with varying expression patterns of frequently-expressed TAAs.
• 2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC[0634] ₅₀ of 500 nM or less, often 200 nM or less; and for Class II an IC₅₀ of 1000 nM or less.
• 3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage. [0635]
• 4.) When selecting epitopes from cancer-related antigens it is often useful to select analogs because the patient may have developed tolerance to the native epitope. [0636]
• 5.) Of particular relevance are epitopes referred to as “nested epitopes”. Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A nested peptide sequence can comprise B cell, HLA class I and/or HLA class II epitopes. When providing nested epitopes, a general objective is to provide the greatest number of epitopes per sequence. Thus, an aspect is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a multi-epitopic sequence, such as a sequence comprising nested epitopes, it is generally important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties. [0637]
• 6.) If a polyepitopic protein is created, or when creating a minigene, an objective is to generate the smallest peptide that encompasses the epitopes of interest. This principle is similar, if not the same as that employed when selecting a peptide comprising nested epitopes. However, with an artificial polyepitopic peptide, the size minimization objective is balanced against the need to integrate any spacer sequences between epitopes in the polyepitopic protein. Spacer amino acid residues can, for example, be introduced to avoid junctional epitopes (an epitope recognized by the immune system, not present in the target antigen, and only created by the man-made juxtaposition of epitopes), or to facilitate cleavage between epitopes and thereby enhance epitope presentation. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed. [0638]
• 7.) Where the sequences of multiple variants of the same target protein are present, potential peptide epitopes can also be selected on the basis of their conservancy. For example, a criterion for conservancy may define that the entire sequence of an HLA class I binding peptide or the entire 9-mer core of a class II binding peptide be conserved in a designated percentage of the sequences evaluated for a specific protein antigen. [0639]
• X.C.1. Minigene Vaccines [0640]
• A number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention. [0641]
• The use of multi-epitope minigenes is described below and in, Ishioka et al., [0642] J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding supermotif- and/or motif-bearing epitopes derived 98P4B6, the PADRE® universal helper T cell epitope or multiple HTL epitopes from 98P4B6 (see e.g., Tables VIII-XXI and XXII to XLIX), and an endoplasmic reticulum-translocating signal sequence can be engineered. A vaccine may also comprise epitopes that are derived from other TAAs.
• The immunogenicity of a multi-epitopic minigene can be confirmed in transgenic mice to evaluate the magnitude of CTL induction responses against the epitopes tested. Further, the immunogenicity of DNA-encoded epitopes in vivo can be correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these experiments can show that the minigene serves to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes. [0643]
• For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, antibody epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention. [0644]
• The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector. [0645]
• Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an [0646] E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.
• Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression. [0647]
• Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate [0648] E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.
• In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity. [0649]
• In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRE™, Epimmune, San Diego, Calif.). Helper (HTL) epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases. [0650]
• Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in [0651] E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well-known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif. If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.
• Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids, glycolipids, and fusogenic liposomes can also be used in the formulation (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, [0652] Bio Techniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In addition, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.
• Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 ([0653] ⁵Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by ⁵¹Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.
• In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (i.p.) for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for one week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, [0654] ⁵¹Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is confirmed in transgenic mice in an analogous manner.
• Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles. [0655]
• Minigenes can also be delivered using other bacterial or viral delivery systems well known in the art, e.g., an expression construct encoding epitopes of the invention can be incorporated into a viral vector such as vaccinia. [0656]
• X.C.2. Combinations of CTL Peptides with Helper Peptides [0657]
• Vaccine compositions comprising CTL peptides of the invention can be modified, e.g., analoged, to provide desired attributes, such as improved serum half life, broadened population coverage or enhanced immunogenicity. [0658]
• For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Although a CTL peptide can be directly linked to a T helper peptide, often CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues and sometimes 10 or more residues. The CTL peptide epitope can be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated. [0659]
• In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in a majority of a genetically diverse population. This can be accomplished by selecting peptides that bind to many, most, or all of the HLA class II molecules. Examples of such amino acid bind many HLA Class II molecules include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO: 97), [0660] Plasmodium falciparum circumsporozoite (CS) protein at positions 378-398 (DIEKKIAKMEKASSVFNWNS; SEQ ID NO: 98), and Streptococcus 18 kD protein at positions 116-131 (GAVDSILGGVATYGAA; SEQ ID NO: 99). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.
• Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego, Calif.) are designed, most preferably, to bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: XKXVAAWTLKAAX (SEQ ID NO: 100), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope. [0661]
• HTL peptide epitopes can also be modified to alter their biological properties. For example, they can be modified to include D-amino acids to increase their resistance to proteases and thus extend their serum half life, or they can be conjugated to other molecules such as lipids, proteins, carbohydrates, and the like to increase their biological activity. For example, a T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini. [0662]
• X.C.3. Combinations of CTL Peptides with T Cell Priming Agents [0663]
• In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes B lymphocytes or T lymphocytes. Lipids have been identified as agents capable of priming CTL in vivo. For example, palmitic acid residues can be attached to the ε- and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic composition comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide. [0664]
• As another example of lipid priming of CTL responses, [0665] E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide (see, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P₃CSS, for example, and the lipopeptide administered to an individual to prime specifically an immune response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P₃CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses.
• X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL andlor HTL Peptides [0666]
• An embodiment of a vaccine composition in accordance with the invention comprises ex vivo administration of a cocktail of epitope-bearing peptides to PBMC, or isolated DC therefrom, from the patient's blood. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Pharmacia-Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides and prior to reinfusion into patients, the DC are washed to remove unbound peptides. In this embodiment, a vaccine comprises peptide-pulsed DCs which present the pulsed peptide epitopes complexed with HLA molecules on their surfaces. [0667]
• The DC can be pulsed ex vivo with a cocktail of peptides, some of which stimulate CTL responses to 98P4B6. Optionally, a helper T cell (HTL) peptide, such as a natural or artificial loosely restricted HLA Class II peptide, can be included to facilitate the CTL response. Thus, a vaccine in accordance with the invention is used to treat a cancer which expresses or overexpresses 98P4B6. [0668]
• X.D. Adoptive Immunotherapy [0669]
• Antigenic 98P4B6-related peptides are used to elicit a CTL and/or HTL response ex vivo, as well. The resulting CTL or HTL cells, can be used to treat tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (e.g., a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells. [0670]
• X.E. Administration of Vaccines for Therapeutic or Prophylactic Purposes [0671]
• Pharmaceutical and vaccine compositions of the invention are typically used to treat and/or prevent a cancer that expresses or overexpresses 98P4B6. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective B cell, CTL and/or HTL response to the antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician. [0672]
• For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual already bearing a tumor that expresses 98P4B6. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences. Patients can be treated with the immunogenic peptides separately or in conjunction with other treatments, such as surgery, as appropriate. [0673]
• For therapeutic use, administration should generally begin at the first diagnosis of 98P4B6-associated cancer. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. The embodiment of the vaccine composition (i.e., including, but not limited to embodiments such as peptide cocktails, polyepitopic polypeptides, minigenes, or TAA-specific CTLs or pulsed dendritic cells) delivered to the patient may vary according to the stage of the disease or the patient's health status. For example, in a patient with a tumor that expresses 98P4B6, a vaccine comprising 98P4B6-specific CTL may be more efficacious in killing tumor cells in patient with advanced disease than alternative embodiments. [0674]
• It is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to stimulate effectively a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention. [0675]
• The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1,000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50,000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. Administration should continue until at least clinical symptoms or laboratory tests indicate that the neoplasia, has been eliminated or reduced and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art. [0676]
• In certain embodiments, the peptides and compositions of the present invention are employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts. [0677]
• The vaccine compositions of the invention can also be used purely as prophylactic agents. Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 μg to about 50,000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine can be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood. [0678]
• The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, nasal, intrathecal, or local (e.g. as a cream or topical ointment) administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier. [0679]
• A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well-known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. [0680]
• The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, welting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc. [0681]
• The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected. [0682]
• A human unit dose form of a composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, in one embodiment an aqueous carrier, and is administered in a volume/quantity that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17[0683] ^th Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985). For example a peptide dose for initial immunization can be from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. For example, for nucleic acids an initial immunization may be performed using an expression vector in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-10⁷ to 5×10⁹ pfu.
• For antibodies, a treatment generally involves repeated administration of the anti-98P4B6 antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1 to about 10 mg/kg body weight. In general, doses in the range of 10-500 mg mAb per week are effective and well tolerated. Moreover, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-98P4B6 mAb preparation represents an acceptable dosing regimen. As appreciated by those of skill in the art, various factors can influence the ideal dose in a particular case. Such factors include, for example, half life of a composition, the binding affinity of an Ab, the immunogenicity of a substance, the degree of 98P4B6 expression in the patient, the extent of circulating shed 98P4B6 antigen, the desired steady-state concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient. Non-limiting preferred human unit doses are, for example, 500 μg-1 mg, 1 mg-50 mg, 50 mg-100 mg, 100 mg-200 mg, 200 mg-300 mg, 400 mg-500 mg, 500 mg-600 mg, 600 mg-700 mg, 700 mg-800 mg, 800 mg-900 mg, 900 mg-1 g, or 1 mg-700 mg. In certain embodiments, the dose is in a range of 2-5 mg/kg body weight, e.g., with follow on weekly doses of 1-3 mg/kg; 0.5 mg, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 mg/kg body weight followed, e.g., in two, three or four weeks by weekly doses; 0.5-10 mg/kg body weight, e.g., followed in two, three or four weeks by weekly doses; 225, 250, 275, 300, 325, 350, 375, 400 mg m[0684] ² of body area weekly; 1-600 mg m² of body area weekly; 225-400 mg m² of body area weekly; these does can be followed by weekly doses for 2, 3, 4, 5, 6, 7, 8, 9, 19, 11, 12 or more weeks.
• In one embodiment, human unit dose forms of polynucleotides comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art a therapeutic effect depends on a number of factors, including the sequence of the polynucleotide, molecular weight of the polynucleotide and route of administration. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. Generally, for a polynucleotide of about 20 bases, a dosage range may be selected from, for example, an independently selected lower limit such as about 0.1, 0.25, 0.5, 1, 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400 or 500 mg/kg up to an independently selected upper limit, greater than the lower limit, of about 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For example, a dose may be about any of the following: 0.1 to 100 mg/kg, 0.1 to 50 mg/kg, 0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500 mg/kg, 100 to 400 mg/kg, 200 to 300 mg/kg, 1 to 100 mg/kg, 100 to 200 mg/kg, 300 to 400 mg/kg, 400 to 500 mg/kg, 500 to 1000 mg/kg, 500 to 5000 mg/kg, or 500 to 10,000 mg/kg. Generally, parenteral routes of administration may require higher doses of polynucleotide compared to more direct application to the nucleotide to diseased tissue, as do polynucleotides of increasing length. [0685]
• In one embodiment, human unit dose forms of T-cells comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art, a therapeutic effect depends on a number of factors. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. A dose may be about 10[0686] ⁴ cells to about 10⁶ cells, about 10⁶ cells to about 10⁸ cells, about 10⁸ to about 10¹¹ cells, or about 10⁸ to about 5×10¹⁰ cells. A dose may also about 10⁶ cells/m² to about 10¹⁰ cells/m², or about 10⁶ cells/m² to about 10⁸ cells/m².
• Proteins(s) of the invention, and/or nucleic acids encoding the protein(s), can also be administered via liposomes, which may also serve to: 1) target the proteins(s) to a particular tissue, such as lymphoid tissue; 2) to target selectively to diseases cells; or, 3) to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., [0687] Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.
• For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated. [0688]
• For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%. [0689]
• For aerosol administration, immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are about 0.01%-20% by weight, preferably about 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from about 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute about 0.1%-20% by weight of the composition, preferably about 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery. [0690]
• XI.) Diagnostic and Prognostic Embodiments of 98P4B6. [0691]
• As disclosed herein, 98P4B6 polynucleotides, polypeptides, reactive cytotoxic T cells (CTL), reactive helper T cells (HTL) and anti-polypeptide antibodies are used in well known diagnostic, prognostic and therapeutic assays that examine conditions associated with dysregulated cell growth such as cancer, in particular the cancers listed in Table I (see, e.g., both its specific pattern of tissue expression as well as its overexpression in certain cancers as described for example in the Example entitled “Expression analysis of 98P4B6 in normal tissues, and patient specimens”). [0692]
• 98P4B6 can be analogized to a prostate associated antigen PSA, the archetypal marker that has been used by medical practitioners for years to identify and monitor the presence of prostate cancer (see, e.g., Merrill et al., J. Urol. 163(2):503-5120 (2000); Polascik et al., J. Urol. August; 162(2):293-306(1999) and Fortier et al., J. Nat. Cancer Inst. 91(19): 1635-1640(1999)). A variety of other diagnostic markers are also used in similar contexts including p53 and K-ras (see, e.g., Tulchinsky et al., Int J Mol Med 1999 July 4(1):99-102 and Minimoto et al., Cancer Detect Prev 2000;24(1):1-12). Therefore, this disclosure of 98P4B6 polynucleotides and polypeptides (as well as 98P4B6 polynucleotide probes and anti-98P4B6 antibodies used to identify the presence of these molecules) and their properties allows skilled artisans to utilize these molecules in methods that are analogous to those used, for example, in a variety of diagnostic assays directed to examining conditions associated with cancer. [0693]
• Typical embodiments of diagnostic methods which utilize the 98P4B6 polynucleotides, polypeptides, reactive T cells and antibodies are analogous to those methods from well-established diagnostic assays, which employ, e.g., PSA polynucleotides, polypeptides, reactive T cells and antibodies. For example, just as PSA polynucleotides are used as probes (for example in Northern analysis, see, e.g., Sharief et al., Biochem. Mol. Biol. Int. 33(3):567-74(1994)) and primers (for example in PCR analysis, see, e.g., Okegawa et al., J. Urol. 163(4): 1189-1190 (2000)) to observe the presence and/or the level of PSA mRNAs in methods of monitoring PSA overexpression or the metastasis of prostate cancers, the 98P4B6 polynucleotides described herein can be utilized in the same way to detect 98P4B6 overexpression or the metastasis of prostate and other cancers expressing this gene. Alternatively, just as PSA polypeptides are used to generate antibodies specific for PSA which can then be used to observe the presence and/or the level of PSA proteins in methods to monitor PSA protein overexpression (see, e.g., Stephan et al., Urology 55(4):560-3 (2000)) or the metastasis of prostate cells (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3):233-7 (1996)), the 98P4B6 polypeptides described herein can be utilized to generate antibodies for use in detecting 98P4B6 overexpression or the metastasis of prostate cells and cells of other cancers expressing this gene. [0694]
• Specifically, because metastases involves the movement of cancer cells from an organ of origin (such as the lung or prostate gland etc.) to a different area of the body (such as a lymph node), assays which examine a biological sample for the presence of cells expressing 98P4B6 polynucleotides and/or polypeptides can be used to provide evidence of metastasis. For example, when a biological sample from tissue that does not normally contain 98P4B6-expressing cells (lymph node) is found to contain 98P4B6-expressing cells such as the 98P4B6 expression seen in LAPC4 and LAPC9, xenografts isolated from lymph node and bone metastasis, respectively, this finding is indicative of metastasis. [0695]
• Alternatively 98P4B6 polynucleotides and/or polypeptides can be used to provide evidence of cancer, for example, when cells in a biological sample that do not normally express 98P4B6 or express 98P4B6 at a different level are found to express 98P4B6 or have an increased expression of 98P4B6 (see, e.g., the 98P4B6 expression in the cancers listed in Table I and in patient samples etc. shown in the accompanying Figures). In such assays, artisans may further wish to generate supplementary evidence of metastasis by testing the biological sample for the presence of a second tissue restricted marker (in addition to 98P4B6) such as PSA, PSCA etc. (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233-237 (1996)). [0696]
• Just as PSA polynucleotide fragments and polynucleotide variants are employed by skilled artisans for use in methods of monitoring PSA, 98P4B6 polynucleotide fragments and polynucleotide variants are used in an analogous manner. In particular, typical PSA polynucleotides used in methods of monitoring PSA are probes or primers which consist of fragments of the PSA cDNA sequence. Illustrating this, primers used to PCR amplify a PSA polynucleotide must include less than the whole PSA sequence to function in the polymerase chain reaction. In the context of such PCR reactions, skilled artisans generally create a variety of different polynucleotide fragments that can be used as primers in order to amplify different portions of a polynucleotide of interest or to optimize amplification reactions (see, e.g., Caetano-Anolles, G. Biotechniques 25(3): 472-476, 478-480 (1998); Robertson et al., Methods Mol. Biol. 98:121-154 (1998)). An additional illustration of the use of such fragments is provided in the Example entitled “Expression analysis of 98P4B6 in normal tissues, and patient specimens,” where a 98P4B6 polynucleotide fragment is used as a probe to show the expression of 98P4B6 RNAs in cancer cells. In addition, variant polynucleotide sequences are typically used as primers and probes for the corresponding mRNAs in PCR and Northern analyses (see, e.g., Sawai et al., Fetal Diagn. Ther. 1996 November-December 11(6):407-13 and Current Protocols In Molecular Biology, [0697] Volume 2, Unit 2, Frederick M. Ausubel et al. eds., 1995)). Polynucleotide fragments and variants are useful in this context where they are capable of binding to a target polynucleotide sequence (e.g., a 98P4B6 polynucleotide shown in FIG. 2 or variant thereof) under conditions of high stringency.
• Furthermore, PSA polypeptides which contain an epitope that can be recognized by an antibody or T cell that specifically binds to that epitope are used in methods of monitoring PSA. 98P4B6 polypeptide fragments and polypeptide analogs or variants can also be used in an analogous manner. This practice of using polypeptide fragments or polypeptide variants to generate antibodies (such as anti-PSA antibodies or T cells) is typical in the art with a wide variety of systems such as fusion proteins being used by practitioners (see, e.g., Current Protocols In Molecular Biology, [0698] Volume 2, Unit 16, Frederick M. Ausubel et al. eds., 1995). In this context, each epitope(s) functions to provide the architecture with which an antibody or T cell is reactive. Typically, skilled artisans create a variety of different polypeptide fragments that can be used in order to generate immune responses specific for different portions of a polypeptide of interest (see, e.g., U.S. Pat. No. 5,840,501 and U.S. Pat. No. 5,939,533). For example it may be preferable to utilize a polypeptide comprising one of the 98P4B6 biological motifs discussed herein or a motif-bearing subsequence which is readily identified by one of skill in the art based on motifs available in the art. Polypeptide fragments, variants or analogs are typically useful in this context as long as they comprise an epitope capable of generating an antibody or T cell specific for a target polypeptide sequence (e.g. a 98P4B6 polypeptide shown in FIG. 3).
• As shown herein, the 98P4B6 polynucleotides and polypeptides (as well as the 98P4B6 polynucleotide probes and anti-98P4B6 antibodies or T cells used to identify the presence of these molecules) exhibit specific properties that make them useful in diagnosing cancers such as those listed in Table I. Diagnostic assays that measure the presence of 98P4B6 gene products, in order to evaluate the presence or onset of a disease condition described herein, such as prostate cancer, are used to identify patients for preventive measures or further monitoring, as has been done so successfully with PSA. Moreover, these materials satisfy a need in the art for molecules having similar or complementary characteristics to PSA in situations where, for example, a definite diagnosis of metastasis of prostatic origin cannot be made on the basis of a test for PSA alone (see, e.g., Alanen et al., Pathol. Res. Pract. 192(3):233-237 (1996)), and consequently, materials such as 98P4B6 polynucleotides and polypeptides (as well as the 98P4B6 polynucleotide probes and anti-98P4B6 antibodies used to identify the presence of these molecules) need to be employed to confirm a metastases of prostatic origin. [0699]
• Finally, in addition to their use in diagnostic assays, the 98P4B6 polynucleotides disclosed herein have a number of other utilities such as their use in the identification of oncogenetic associated chromosomal abnormalities in the chromosomal region to which the 98P4B6 gene maps (see the Example entitled “Chromosomal Mapping of 98P4B6” below). Moreover, in addition to their use in diagnostic assays, the 98P4B6-related proteins and polynucleotides disclosed herein have other utilities such as their use in the forensic analysis of tissues of unknown origin (see, e.g., Takahama K Forensic Sci Int 1996 June 28;80(1-2): 63-9). [0700]
• Additionally, 98P4B6-related proteins or polynucleotides of the invention can be used to treat a pathologic condition characterized by the over-expression of 98P4B6. For example, the amino acid or nucleic acid sequence of FIG. 2 or FIG. 3, or fragments of either, can be used to generate an immune response to a 98P4B6 antigen. Antibodies or other molecules that react with 98P4B6 can be used to modulate the function of this molecule, and thereby provide a therapeutic benefit. [0701]
• XII.) Inhibition of 98P4B6 Protein Function [0702]
• The invention includes various methods and compositions for inhibiting the binding of 98P4B6 to its binding partner or its association with other protein(s) as well as methods for inhibiting 98P4B6 function. [0703]
• XII.A.) Inhibition of 98P4B6 with Intracellular Antibodies [0704]
• In one approach, a recombinant vector that encodes single chain antibodies that specifically bind to 98P4B6 are introduced into 98P4B6 expressing cells via gene transfer technologies. Accordingly, the encoded single chain anti-98P4B6 antibody is expressed intracellularly, binds to 98P4B6 protein, and thereby inhibits its function. Methods for engineering such intracellular single chain antibodies are well known. Such intracellular antibodies, also known as “intrabodies”, are specifically targeted to a particular compartment within the cell, providing control over where the inhibitory activity of the treatment is focused. This technology has been successfully applied in the art (for review, see Richardson and Marasco, 1995, TIBTECH vol. 13). Intrabodies have been shown to virtually eliminate the expression of otherwise abundant cell surface receptors (see, e.g., Richardson et al., 1995, Proc. Natl. Acad. Sci. USA 92: 3137-3141; Beerli et al., 1994, J. Biol. Chem. 289: 23931-23936; Deshane et al., 1994, Gene Ther. 1: 332-337). [0705]
• Single chain antibodies comprise the variable domains of the heavy and light chain joined by a flexible linker polypeptide, and are expressed as a single polypeptide. Optionally, single chain antibodies are expressed as a single chain variable region fragment joined to the light chain constant region. Well-known intracellular trafficking signals are engineered into recombinant polynucleotide vectors encoding such single chain antibodies in order to target precisely the intrabody to the desired intracellular compartment. For example, intrabodies targeted to the endoplasmic reticulum (ER) are engineered to incorporate a leader peptide and, optionally, a C-terminal ER retention signal, such as the KDEL amino acid motif. Intrabodies intended to exert activity in the nucleus are engineered to include a nuclear localization signal. Lipid moieties are joined to intrabodies in order to tether the intrabody to the cytosolic side of the plasma membrane. Intrabodies can also be targeted to exert function in the cytosol. For example, cytosolic intrabodies are used to sequester factors within the cytosol, thereby preventing them from being transported to their natural cellular destination. [0706]
• In one embodiment, intrabodies are used to capture 98P4B6 in the nucleus, thereby preventing its activity within the nucleus. Nuclear targeting signals are engineered into such 98P4B6 intrabodies in order to achieve the desired targeting. Such 98P4B6 intrabodies are designed to bind specifically to a particular 98P4B6 domain. In another embodiment, cytosolic intrabodies that specifically bind to a 98P4B6 protein are used to prevent 98P4B6 from gaining access to the nucleus, thereby preventing it from exerting any biological activity within the nucleus (e.g., preventing 98P4B6 from forming transcription complexes with other factors). [0707]
• In order to specifically direct the expression of such intrabodies to particular cells, the transcription of the intrabody is placed under the regulatory control of an appropriate tumor-specific promoter and/or enhancer. In order to target intrabody expression specifically to prostate, for example, the PSA promoter and/or promoter/enhancer can be utilized (See, for example, U.S. Pat. No. 5,919,652 issued 6 Jul. 1999). [0708]
• XII.B.) Inhibition of 98P4B6 with Recombinant Proteins [0709]
• In another approach, recombinant molecules bind to 98P4B6 and thereby inhibit 98P4B6 function. For example, these recombinant molecules prevent or inhibit 98P4B6 from accessing/binding to its binding partner(s) or associating with other protein(s). Such recombinant molecules can, for example, contain the reactive part(s) of a 98P4B6 specific antibody molecule. In a particular embodiment, the 98P4B6 binding domain of a 98P4B6 binding partner is engineered into a dimeric fusion protein, whereby the fusion protein comprises two 98P4B6 ligand binding domains linked to the Fc portion of a human IgG, such as human IgG1. Such IgG portion can contain, for example, the [0710] C _H2 and C _H3 domains and the hinge region, but not the C _H1 domain. Such dimeric fusion proteins are administered in soluble form to patients suffering from a cancer associated with the expression of 98P4B6, whereby the dimeric fusion protein specifically binds to 98P4B6 and blocks 98P4B6 interaction with a binding partner. Such dimeric fusion proteins are further combined into multimeric proteins using known antibody linking technologies.
• XII.C.) Inhibition of 98P4B6 Transcription or Translation [0711]
• The present invention also comprises various methods and compositions for inhibiting the transcription of the 98P4B6 gene. Similarly, the invention also provides methods and compositions for inhibiting the translation of 98P4B6 mRNA into protein. [0712]
• In one approach, a method of inhibiting the transcription of the 98P4B6 gene comprises contacting the 98P4B6 gene with a 98P4B6 antisense polynucleotide. In another approach, a method of inhibiting 98P4B6 mRNA translation comprises contacting a 98P4B6 mRNA with an antisense polynucleotide. In another approach, a 98P4B6 specific ribozyme is used to cleave a 98P4B6 message, thereby inhibiting translation. Such antisense and ribozyme based methods can also be directed to the regulatory regions of the 98P4B6 gene, such as 98P4B6 promoter and/or enhancer elements. Similarly, proteins capable of inhibiting a 98P4B6 gene transcription factor are used to inhibit 98P4B6 mRNA transcription. The various polynucleotides and compositions useful in the aforementioned methods have been described above. The use of antisense and ribozyme molecules to inhibit transcription and translation is well known in the art. [0713]
• Other factors that inhibit the transcription of 98P4B6 by interfering with 98P4B6 transcriptional activation are also useful to treat cancers expressing 98P4B6. Similarly, factors that interfere with 98P4B6 processing are useful to treat cancers that express 98P4B6. Cancer treatment methods utilizing such factors are also within the scope of the invention. [0714]
• XII.D.) General Considerations for Therapeutic Strategies [0715]
• Gene transfer and gene therapy technologies can be used to deliver therapeutic polynudeotide molecules to tumor cells synthesizing 98P4B6 (i.e., antisense, ribozyme, polynudeotdes encoding intrabodies and other 98P4B6 inhibitory molecules). A number of gene therapy approaches are known in the art. Recombinant vectors encoding 98P4B6 antisense polynudeotides, ribozymes, factors capable of interfering with 98P4B6 transcription, and so forth, can be delivered to target tumor cells using such gene therapy approaches. [0716]
• The above therapeutic approaches can be combined with any one of a wide variety of surgical, chemotherapy or radiation therapy regimens. The therapeutic approaches of the invention can enable the use of reduced dosages of chemotherapy (or other therapies) and/or less frequent administration, an advantage for all patients and particularly for those that do not tolerate the toxicity of the chemotherapeutic agent well. [0717]
• The anti-tumor activity of a particular composition (e.g., antisense, ribozyme, intrabody), or a combination of such compositions, can be evaluated using various in vitro and in vivo assay systems. In vitro assays that evaluate therapeutic activity include cell growth assays, soft agar assays and other assays indicative of tumor promoting activity, binding assays capable of determining the extent to which a therapeutic composition will inhibit the binding of 98P4B6 to a binding partner, etc. [0718]
• In vivo, the effect of a 98P4B6 therapeutic composition can be evaluated in a suitable animal model. For example, xenogenic prostate cancer models can be used, wherein human prostate cancer explants or passaged xenograft tissues are introduced into immune compromised animals, such as nude or SCID mice (Klein et al., 1997, Nature Medicine 3: 402-408). For example, PCT Patent Applicaton WO98/16628 and U.S. Pat. No. 6,107,540 describe various xenograft models of human prostate cancer capable of recapitulating the development of primary tumors, micrometastasis, and the formation of osteoblastic metastases characteristic of late stage disease. Efficacy can be predicted using assays that measure inhibition of tumor formation, tumor regression or metastasis, and the like. [0719]
• In vivo assays that evaluate the promotion of apoptosis are useful in evaluating therapeutic compositions. In one embodiment, xenografts from tumor bearing mice treated with the therapeutic composition can be examined for the presence of apoptotic foci and compared to untreated control xenograft-bearing mice. The extent to which apoptotic foci are found in the tumors of the treated mice provides an indication of the therapeutic efficacy of the composition. [0720]
• The therapeutic compositions used in the practice of the foregoing methods can be formulated into pharmaceutical compositions comprising a carrier suitable for the desired delivery method. Suitable carriers include any material that when combined with the therapeutic composition retains the anti-tumor function of the therapeutic composition and is generally non-reactive with the patient's immune system. Examples include, but are not limited to, any of a number of standard pharmaceutical carriers such as sterile phosphate buffered saline solutions, bacteriostatic water, and the like (see, generally, Remington's [0721] Pharmaceutical Sciences 16^th Edition, A. Osal., Ed., 1980).
• Therapeutic formulations can be solubilized and administered via any route capable of delivering the therapeutic composition to the tumor site. Potentially effective routes of administration include, but are not limited to, intravenous, parenteral, intraperitoneal, intramuscular, intratumor, intradermal, intraorgan, orthotopic, and the like. A preferred formulation for intravenous injection comprises the therapeutic composition in a solution of preserved bacteriostatic water, sterile unpreserved water, and/or diluted in polyvinylchloride or polyethylene bags containing 0.9% sterile Sodium Chloride for Injection, USP. Therapeutic protein preparations can be lyophilized and stored as sterile powders, preferably under vacuum, and then reconstituted in bacteriostatic water (containing for example, benzyl alcohol preservative) or in sterile water prior to injection. [0722]
• Dosages and administration protocols for the treatment of cancers using the foregoing methods will vary with the method and the target cancer, and will generally depend on a number of other factors appreciated in the art. [0723]
• XIII.) Identification, Characterization and Use of Modulators of 98P4B6 [0724]
• Methods to Identify and Use Modulators [0725]
• In one embodiment, screening is performed to identify modulators that induce or suppress a particular expression profile, suppress or induce specific pathways, preferably generating the associated phenotype thereby. In another embodiment, having identified differentially expressed genes important in a particular state; screens are performed to identify modulators that alter expression of individual genes, either increase or decrease. In another embodiment, screening is performed to identify modulators that alter a biological function of the expression product of a differentially expressed gene. Again, having identified the importance of a gene in a particular state, screens are performed to identify agents that bind and/or modulate the biological activity of the gene product. [0726]
• In addition, screens are done for genes that are induced in response to a candidate agent. After identifying a modulator (one that suppresses a cancer expression pattern leading to a normal expression pattern, or a modulator of a cancer gene that leads to expression of the gene as in normal tissue) a screen is performed to identify genes that are specifically modulated in response to the agent. Comparing expression profiles between normal tissue and agent-treated cancer tissue reveals genes that are not expressed in normal tissue or cancer tissue, but are expressed in agent treated tissue, and vice versa. These agent-specific sequences are identified and used by methods described herein for cancer genes or proteins. In particular these sequences and the proteins they encode are used in marking or identifying agent-treated cells. In addition, antibodies are raised against the agent-induced proteins and used to target novel therapeutics to the treated cancer tissue sample. [0727]
• Modulator-Related Identification and Screening Assays: [0728]
• Gene Expression-Related Assays [0729]
• Proteins, nucleic acids, and antibodies of the invention are used in screening assays. The cancer-associated proteins, antibodies, nucleic acids, modified proteins and cells containing these sequences are used in screening assays, such as evaluating the effect of drug candidates on a “gene expression profile,” expression profile of polypeptides or alteration of biological function. In one embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after treatment with a candidate agent (e.g., Davis, G F, et al., J Biol Screen 7:69 (2002); Zlokarnik, et al., Science 279:84-8 (1998); Heid, Genome Res 6:986-94, 1996). [0730]
• The cancer proteins, antibodies, nucleic acids, modified proteins and cells containing the native or modified cancer proteins or genes are used in screening assays. That is, the present invention comprises methods for screening for compositions which modulate the cancer phenotype or a physiological function of a cancer protein of the invention. This is done on a gene itself or by evaluating the effect of drug candidates on a “gene expression profile” or biological function. In one embodiment, expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring after treatment with a candidate agent, see Zlokamik, supra. [0731]
• A variety of assays are executed directed to the genes and proteins of the invention. Assays are run on an individual nucleic acid or protein level. That is, having identified a particular gene as up regulated in cancer, test compounds are screened for the ability to modulate gene expression or for binding to the cancer protein of the invention. “Modulation” in this context includes an increase or a decrease in gene expression. The preferred amount of modulation will depend on the original change of the gene expression in normal versus tissue undergoing cancer, with changes of at least 10%, preferably 50%, more preferably 100-300%, and in some embodiments 300-1000% or greater. Thus, if a gene exhibits a 4-fold increase in cancer tissue compared to normal tissue, a decrease of about four-fold is often desired; similarly, a 10-fold decrease in cancer tissue compared to normal tissue a target value of a 10-fold increase in expression by the test compound is often desired. Modulators that exacerbate the type of gene expression seen in cancer are also useful, e.g., as an upregulated target in further analyses. [0732]
• The amount of gene expression is monitored using nucleic acid probes and the quantification of gene expression levels, or, alternatively, a gene product itself is monitored, e.g., through the use of antibodies to the cancer protein and standard immunoassays. Proteomics and separation techniques also allow for quantification of expression. [0733]
• Expression Monitoring to Identify Compounds that Modify Gene Expression [0734]
• In one embodiment, gene expression monitoring, i.e., an expression profile, is monitored simultaneously for a number of entities. Such profiles will typically involve one or more of the genes of FIG. 2. In this embodiment, e.g., cancer nucleic acid probes are attached to biochips to detect and quantify cancer sequences in a particular cell. Alternatively, PCR can be used. Thus, a series, e.g., wells of a microtiter plate, can be used with dispensed primers in desired wells. A PCR reaction can then be performed and analyzed for each well. [0735]
• Expression monitoring is performed to identify compounds that modify the expression of one or more cancer-associated sequences, e.g., a polynucleotide sequence set out in FIG. 2. Generally, a test modulator is added to the cells prior to analysis. Moreover, screens are also provided to identify agents that modulate cancer, modulate cancer proteins of the invention, bind to a cancer protein of the invention, or interfere with the binding of a cancer protein of the invention and an antibody or other binding partner. [0736]
• In one embodiment, high throughput screening methods involve providing a library containing a large number of potential therapeutic compounds (candidate compounds). Such “combinatorial chemical libraries” are then screened in one or more assays to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional “lead compounds,” as compounds for screening, or as therapeutics. [0737]
• In certain embodiments, combinatorial libraries of potential modulators are screened for an ability to bind to a cancer polypeptide or to modulate activity. Conventionally, new chemical entities with useful properties are generated by identifying a chemical compound (called a “lead compound”) with some desirable property or activity, e.g., inhibiting activity, creating variants of the lead compound, and evaluating the property and activity of those variant compounds. Often, high throughput screening (HTS) methods are employed for such an analysis. [0738]
• As noted above, gene expression monitoring is conveniently used to test candidate modulators (e.g., protein, nucleic acid or small molecule). After the candidate agent has been added and the cells allowed to incubate for a period, the sample containing a target sequence to be analyzed is, e.g., added to a biochip. [0739]
• If required, the target sequence is prepared using known techniques. For example, a sample is treated to lyse the cells, using known lysis buffers, electroporation, etc., with purification and/or amplification such as PCR performed as appropriate. For example, an in vitro transcription with labels covalently attached to the nucleotides is performed. Generally, the nucleic acids are labeled with biotin-FITC or PE, or with cy3 or cy5. [0740]
• The target sequence can be labeled with, e.g., a fluorescent, a chemiluminescent, a chemical, or a radioactive signal, to provide a means of detecting the target sequence's specific binding to a probe. The label also can be an enzyme, such as alkaline phosphatase or horseradish peroxidase, which when provided with an appropriate substrate produces a product that is detected. Alternatively, the label is a labeled compound or small molecule, such as an enzyme inhibitor, that binds but is not catalyzed or altered by the enzyme. The label also can be a moiety or compound, such as, an epitope tag or biotin which specifically binds to streptavidin. For the example of biotin, the streptavidin is labeled as described above, thereby, providing a detectable signal for the bound target sequence. Unbound labeled streptavidin is typically removed prior to analysis. [0741]
• As will be appreciated by those in the art, these assays can be direct hybridization assays or can comprise “sandwich assays”, which include the use of multiple probes, as is generally outlined in U.S. Pat. Nos. 5,681,702; 5,597,909; 5,545,730; 5,594,117; 5,591,584; 5,571,670; 5,580,731; 5,571,670; 5,591,584; 5,624,802; 5,635,352; 5,594,118; 5,359,100; 5,124,246; and 5,681,697. In this embodiment, in general, the target nucleic acid is prepared as outlined above, and then added to the biochip comprising a plurality of nucleic acid probes, under conditions that allow the formation of a hybridization complex. [0742]
• A variety of hybridization conditions are used in the present invention, including high, moderate and low stringency conditions as outlined above. The assays are generally run under stringency conditions which allow formation of the label probe hybridization complex only in the presence of target. Stringency can be controlled by altering a step parameter that is a thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt concentration, chaotropic salt concentration pH, organic solvent concentration, etc. These parameters may also be used to control non-specific binding, as is generally outlined in U.S. Pat. No. 5,681,697. Thus, it can be desirable to perform certain steps at higher stringency conditions to reduce non-specific binding. [0743]
• The reactions outlined herein can be accomplished in a variety of ways. Components of the reaction can be added simultaneously, or sequentially, in different orders, with preferred embodiments outlined below. In addition, the reaction may include a variety of other reagents. These include salts, buffers, neutral proteins, e.g. albumin, detergents, etc. which can be used to facilitate optimal hybridization and detection, and/or reduce nonspecific or background interactions. Reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may also be used as appropriate, depending on the sample preparation methods and purity of the target. The assay data are analyzed to determine the expression levels of individual genes, and changes in expression levels as between states, forming a gene expression profile. [0744]
• Biological Activity-Related Assays [0745]
• The invention provides methods identify or screen for a compound that modulates the activity of a cancer-related gene or protein of the invention. The methods comprise adding a test compound, as defined above, to a cell comprising a cancer protein of the invention. The cells contain a recombinant nucleic acid that encodes a cancer protein of the invention. In another embodiment, a library of candidate agents is tested on a plurality of cells. [0746]
• In one aspect, the assays are evaluated in the presence or absence or previous or subsequent exposure of physiological signals, e.g. hormones, antibodies, peptides, antigens, cytokines, growth factors, action potentials, pharmacological agents including chemotherapeutics, radiation, carcinogenics, or other cells (i.e., cell-cell contacts). In another example, the determinations are made at different stages of the cell cycle process. In this way, compounds that modulate genes or proteins of the invention are identified. Compounds with pharmacological activity are able to enhance or interfere with the activity of the cancer protein of the invention. Once identified, similar structures are evaluated to identify critical structural features of the compound. [0747]
• In one embodiment, a method of modulating (e.g., inhibiting) cancer cell division is provided; the method comprises administration of a cancer modulator. In another embodiment, a method of modulating (e.g., inhibiting) cancer is provided; the method comprises administration of a cancer modulator. In a further embodiment, methods of treating cells or individuals with cancer are provided; the method comprises administration of a cancer modulator. [0748]
• In one embodiment, a method for modulating the status of a cell that expresses a gene of the invention is provided. As used herein status comprises such art-accepted parameters such as growth, proliferation, survival, function, apoptosis, senescence, location, enzymatic activity, signal transduction, etc. of a cell. In one embodiment, a cancer inhibitor is an antibody as discussed above. In another embodiment, the cancer inhibitor is an antisense molecule. A variety of cell growth, proliferation, and metastasis assays are known to those of skill in the art, as described herein. [0749]
• High Throughput Screening to Identify Modulators [0750]
• The assays to identify suitable modulators are amenable to high throughput screening. Preferred assays thus detect enhancement or inhibition of cancer gene transcription, inhibition or enhancement of polypeptide expression, and inhibition or enhancement of polypeptide activity. [0751]
• In one embodiment, modulators evaluated in high throughput screening methods are proteins, often naturally occurring proteins or fragments of naturally occurring proteins. Thus, e.g., cellular extracts containing proteins, or random or directed digests of proteinaceous cellular extracts, are used. In this way, libraries of proteins are made for screening in the methods of the invention. Particularly preferred in this embodiment are libraries of bacterial, fungal, viral, and mammalian proteins, with the latter being preferred, and human proteins being especially preferred. Particularly useful test compound will be directed to the class of proteins to which the target belongs, e.g., substrates for enzymes, or ligands and receptors. [0752]
• Use of Soft Agar Growth and Colony Formation to Identify and Characterize Modulators [0753]
• Normal cells require a solid substrate to attach and grow. When cells are transformed, they lose this phenotype and grow detached from the substrate. For example, transformed cells can grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft agar. The transformed cells, when transfected with tumor suppressor genes, can regenerate normal phenotype and once again require a solid substrate to attach to and grow. Soft agar growth or colony formation in assays are used to identify modulators of cancer sequences, which when expressed in host cells, inhibit abnormal cellular proliferation and transformation. A modulator reduces or eliminates the host cells' ability to grow suspended in solid or semisolid media, such as agar. [0754]
• Techniques for soft agar growth or colony formation in suspension assays are described in Freshney, Culture of Animal Cells a Manual of Basic Technique (3rd ed., 1994). See also, the methods section of Garkavtsev et al. (1996), supra. [0755]
• Evaluation of Contact Inhibition and Growth Density Limitation to Identify and Characterize Modulators [0756]
• Normal cells typically grow in a flat and organized pattern in cell culture until they touch other cells. When the cells touch one another, they are contact inhibited and stop growing. Transformed cells, however, are not contact inhibited and continue to grow to high densities in disorganized foci. Thus, transformed cells grow to a higher saturation density than corresponding normal cells. This is detected morphologically by the formation of a disoriented monolayer of cells or cells in foci. Alternatively, labeling index with ([0757] ³H)-thymidine at saturation density is used to measure density limitation of growth, similarly an MTT or Alamar blue assay will reveal proliferation capacity of cells and the the ability of modulators to affect same. See Freshney (1994), supra. Transformed cells, when transfected with tumor suppressor genes, can regenerate a normal phenotype and become contact inhibited and would grow to a lower density.
• In this assay, labeling index with [0758] ³H)-thymidine at saturation density is a preferred method of measuring density limitation of growth. Transformed host cells are transfected with a cancer-associated sequence and are grown for 24 hours at saturation density in non-limiting medium conditions. The percentage of cells labeling with (³H)-thymidine is determined by incorporated cpm.
• Contact independent growth is used to identify modulators of cancer sequences, which had led to abnormal cellular proliferation and transformation. A modulator reduces or eliminates contact independent growth, and returns the cells to a normal phenotype. [0759]
• Evaluation of Growth Factor or Serum Dependence to Identify and Characterize Modulators [0760]
• Transformed cells have lower serum dependence than their normal counterparts (see, e.g., Temin, J. Natl. Cancer Inst. 37:167-175 (1966); Eagle et al., J. Exp. Med 131:836-879 (1970)); Freshney, supra. This is in part due to release of various growth factors by the transformed cells. The degree of growth factor or serum dependence of transformed host cells can be compared with that of control. For example, growth factor or serum dependence of a cell is monitored in methods to, identify and characterize compounds that modulate cancer-associated sequences of the invention. [0761]
• Use of Tumor-Specific Marker Levels to Identify and Characterize Modulators [0762]
• Tumor cells release an increased amount of certain factors (hereinafter “tumor specific markers”) than their normal counterparts. For example, plasminogen activator (PA) is released from human glioma at a higher level than from normal brain cells (see, e.g., Gullino, Angiogenesis, Tumor Vascularization, and Potential Interference with Tumor Growth, in Biological Responses in Cancer, pp. 178-184 (Mihich (ed.) 1985)). Similarly, Tumor Angiogenesis Factor (TAF) is released at a higher level in tumor cells than their normal counterparts. See, e.g., Folkman, Angiogenesis and Cancer, Sem Cancer Biol. (1992)), while bFGF is released from endothelial tumors (Ensoli, B et al). [0763]
• Various techniques which measure the release of these factors are described in Freshney (1994), supra. Also, see, Unkless et al., J. Biol. Chem. 249:4295-4305 (1974); Strickland & Beers, J. Biol. Chem. 251:5694-5702 (1976); Whur et al., Br. J. Cancer 42:305 312 (1980); Gullino, Angiogenesis, Tumor Vascularization, and Potential Interference with Tumor Growth, in Biological Responses in Cancer, pp. 178-184 (Mihich (ed.) 1985); Freshney, Anticancer Res. 5:111-130 (1985). For example, tumor specific marker levels are monitored in methods to identify and characterize compounds that modulate cancer-associated sequences of the invention. [0764]
• Invasiveness into Matrigel to Identify and Characterize Modulators [0765]
• The degree of invasiveness into Matrigel or an extracellular matrix constituent can be used as an assay to identify and characterize compounds that modulate cancer associated sequences. Tumor cells exhibit a positive correlation between malignancy and invasiveness of cells into Matrigel or some other extracellular matrix constituent. In this assay, tumorigenic cells are typically used as host cells. Expression of a tumor suppressor gene in these host cells would decrease invasiveness of the host cells. Techniques described in Cancer Res. 1999; 59:6010; Freshney (1994), supra, can be used. Briefly, the level of invasion of host cells is measured by using filters coated with Matrigel or some other extracellular matrix constituent. Penetration into the gel, or through to the distal side of the filter, is rated as invasiveness, and rated histologically by number of cells and distance moved, or by prelabeling the cells with [0766] ¹²⁵1 and counting the radioactivity on the distal side of the filter or bottom of the dish. See, e.g., Freshney (1984), supra.
• Evaluation of Tumor Growth in Vivo to Identify and Characterize Modulators [0767]
• Effects of cancer-associated sequences on cell growth are tested in transgenic or immune-suppressed organisms. Transgenic organisms are prepared in a variety of art-accepted ways. For example, knock-out transgenic organisms, e.g., mammals such as mice, are made, in which a cancer gene is disrupted or in which a cancer gene is inserted. Knock-out transgenic mice are made by insertion of a marker gene or other heterologous gene into the endogenous cancer gene site in the mouse genome via homologous recombination. Such mice can also be made by substituting the endogenous cancer gene with a mutated version of the cancer gene, or by mutating the endogenous cancer gene, e.g., by exposure to carcinogens. [0768]
• To prepare transgenic chimeric animals, e.g., mice, a DNA construct is introduced into the nuclei of embryonic stem cells. Cells containing the newly engineered genetic lesion are injected into a host mouse embryo, which is re-implanted into a recipient female. Some of these embryos develop into chimeric mice that possess germ cells some of which are derived from the mutant cell line. Therefore, by breeding the chimeric mice it is possible to obtain a new line of mice containing the introduced genetic lesion (see, e.g., Capecchi et al., Science 244:1288 (1989)). Chimeric mice can be derived according to U.S. Pat. No. 6,365,797, issued 2 Apr. 2002; U.S. Pat. No. 6,107,540 issued 22 Aug. 2000; Hogan et al., Manipulating the Mouse Embryo: A laboratory Manual, Cold Spring Harbor Laboratory (1988) and Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, ed., IRL Press, Washington, D.C., (1987). [0769]
• Alternatively, various immune-suppressed or immune-deficient host animals can be used. For example, a genetically athymic “nude” mouse (see, e.g., Giovanella et al., J. Natl. Cancer Inst. 52:921 (1974)), a SCID mouse, a thymectornized mouse, or an irradiated mouse (see, e.g., Bradley et al., Br. J. Cancer 38:263 (1978); Selby et al., Br. J. Cancer 41:52 (1980)) can be used as a host. Transplantable tumor cells (typically about 10[0770] ⁶ cells) injected into isogenic hosts produce invasive tumors in a high proportion of cases, while normal cells of similar origin will not. In hosts which developed invasive tumors, cells expressing cancer-assodated sequences are injected subcutaneously or orthotopically. Mice are then separated into groups, including control groups and treated experimental groups) e.g. treated with a modulator). After a suitable length of time, preferably 4-8 weeks, tumor growth is measured (e.g., by volume or by its two largest dimensions, or weight) and compared to the control. Tumors that have statistically significant reduction (using, e.g., Student's T test) are said to have inhibited growth.
• In Vitro Assays to Identify and Characterize Modulators [0771]
• Assays to identify compounds with modulating activity can be performed in vitro. For example, a cancer polypeptide is first contacted with a potential modulator and incubated for a suitable amount of time, e.g., from 0.5 to 48 hours. In one embodiment, the cancer polypeptide levels are determined in vitro by measuring the level of protein or mRNA. The level of protein is measured using immunoassays such as Western blotting, ELISA and the like with an antibody that selectively binds to the cancer polypeptide or a fragment thereof. For measurement of mRNA, amplification, e.g., using PCR, LCR, or hybridization assays, e. g., Northern hybridization, RNAse protection, dot blotting, are preferred. The level of protein or mRNA is detected using directly or indirectly labeled detection agents, e.g., fluorescently or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein. [0772]
• Alternatively, a reporter gene system can be devised using a cancer protein promoter operably linked to a reporter gene such as luciferase, green fluorescent protein, CAT, or P-gal. The reporter construct is typically transfected into a cell. After treatment with a potential modulator, the amount of reporter gene transcription, translation, or activity is measured according to standard techniques known to those of skill in the art (Davis G F, supra; Gonzalez, J. & Negulescu, P. Curr. Opin. Biotechnol. 1998: 9:624). [0773]
• As outlined above, in vitro screens are done on individual genes and gene products. That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of the expression of the gene or the gene product itself is performed. [0774]
• In one embodiment, screening for modulators of expression of specific gene(s) is performed. Typically, the expression of only one or a few genes is evaluated. In another embodiment, screens are designed to first find compounds that bind to differentially expressed proteins. These compounds are then evaluated for the ability to modulate differentially expressed activity. Moreover, once initial candidate compounds are identified, variants can be further screened to better evaluate structure activity relationships. [0775]
• Binding Assays to Identify and Characterize Modulators [0776]
• In binding assays in accordance with the invention, a purified or isolated gene product of the invention is generally used. For example, antibodies are generated to a protein of the invention, and immunoassays are run to determine the amount and/or location of protein. Alternatively, cells comprising the cancer proteins are used in the assays. [0777]
• Thus, the methods comprise combining a cancer protein of the invention and a candidate compound such as a ligand, and determining the binding of the compound to the cancer protein of the invention. Preferred embodiments utilize the human cancer protein; animal models of human disease of can also be developed and used. Also, other analogous mammalian proteins also can be used as appreciated by those of skill in the art. Moreover, in some embodiments variant or derivative cancer proteins are used. [0778]
• Generally, the cancer protein of the invention, or the ligand, is non-diffusibly bound to an insoluble support. The support can, e.g., be one having isolated sample receiving areas (a microtiter plate, an array, etc.). The insoluble supports can be made of any composition to which the compositions can be bound, is readily separated from soluble material, and is otherwise compatible with the overall method of screening. The surface of such supports can be solid or porous and of any convenient shape. [0779]
• Examples of suitable insoluble supports include microtiter plates, arrays, membranes and beads. These are typically made of glass, plastic (e.g., polystyrene), polysaccharide, nylon, nitrocellulose, or Teflon™, etc. Microtiter plates and arrays are especially convenient because a large number of assays can be carried out simultaneously, using small amounts of reagents and samples. The particular manner of binding of the composition to the support is not crucial so long as it is compatible with the reagents and overall methods of the invention, maintains the activity of the composition and is nondiffusable. Preferred methods of binding include the use of antibodies which do not sterically block either the ligand binding site or activation sequence when attaching the protein to the support, direct binding to “sticky” or ionic supports, chemical crosslinking, the synthesis of the protein or agent on the surface, etc. Following binding of the protein or ligand/binding agent to the support, excess unbound material is removed by washing. The sample receiving areas may then be blocked through incubation with bovine serum albumin (BSA), casein or other innocuous protein or other moiety. [0780]
• Once a cancer protein of the invention is bound to the support, and a test compound is added to the assay. Alternatively, the candidate binding agent is bound to the support and the cancer protein of the invention is then added. Binding agents include specific antibodies, non-natural binding agents identified in screens of chemical libraries, peptide analogs, etc. [0781]
• Of particular interest are assays to identify agents that have a low toxicity for human cells. A wide variety of assays can be used for this purpose, including proliferation assays, cAMP assays, labeled in vitro protein-protein binding assays, electrophoretic mobility shift assays, immunoassays for protein binding, functional assays (phosphorylation assays, etc.) and the like. [0782]
• A determination of binding of the test compound (ligand, binding agent, modulator, etc.) to a cancer protein of the invention can be done in a number of ways. The test compound can be labeled, and binding determined directly, e.g., by attaching all or a portion of the cancer protein of the invention to a solid support, adding a labeled candidate compound (e.g., a fluorescent label), washing off excess reagent, and determining whether the label is present on the solid support. Various blocking and washing steps can be utilized as appropriate. [0783]
• In certain embodiments, only one of the components is labeled, e.g., a protein of the invention or ligands labeled. Alternatively, more than one component is labeled with different labels, e.g., I[0784] ¹²⁵, for the proteins and a fluorophor for the compound. Proximity reagents, e.g., quenching or energy transfer reagents are also useful.
• Competitive Binding to Identify and Characterize Modulators [0785]
• In one embodiment, the binding of the “test compound” is determined by competitive binding assay with a “competitor.” The competitor is a binding moiety that binds to the target molecule (e.g., a cancer protein of the invention). Competitors include compounds such as antibodies, peptides, binding partners, ligands, etc. Under certain circumstances, the competitive binding between the test compound and the competitor displaces the test compound. In one embodiment, the test compound is labeled. Either the test compound, the competitor, or both, is added to the protein for a time sufficient to allow binding. Incubations are performed at a temperature that facilitates optimal activity, typically between four and 40° C. Incubation periods are typically optimized, e.g., to facilitate rapid high throughput screening; typically between zero and one hour will be sufficient. Excess reagent is generally removed or washed away. The second component is then added, and the presence or absence of the labeled component is followed, to indicate binding. [0786]
• In one embodiment, the competitor is added first, followed by the test compound. Displacement of the competitor is an indication that the test compound is binding to the cancer protein and thus is capable of binding to, and potentially modulating, the activity of the cancer protein. In this embodiment, either component can be labeled. Thus, e.g., if the competitor is labeled, the presence of label in the post-test compound wash solution indicates displacement by the test compound. Alternatively, if the test compound is labeled, the presence of the label on the support indicates displacement. [0787]
• In an alternative embodiment, the test compound is added first, with incubation and washing, followed by the competitor. The absence of binding by the competitor indicates that the test compound binds to the cancer protein with higher affinity than the competitor. Thus, if the test compound is labeled, the presence of the label on the support, coupled with a lack of competitor binding, indicates that the test compound binds to and thus potentially modulates the cancer protein of the invention. [0788]
• Accordingly, the competitive binding methods comprise differential screening to identity agents that are capable of modulating the activity of the cancer proteins of the invention. In this embodiment, the methods comprise combining a cancer protein and a competitor in a first sample. A second sample comprises a test compound, the cancer protein, and a competitor. The binding of the competitor is determined for both samples, and a change, or difference in binding between the two samples indicates the presence of an agent capable of binding to the cancer protein and potentially modulating its activity. That is, if the binding of the competitor is different in the second sample relative to the first sample, the agent is capable of binding to the cancer protein. [0789]
• Alternatively, differential screening is used to identify drug candidates that bind to the native cancer protein, but cannot bind to modified cancer proteins. For example the structure of the cancer protein is modeled and used in rational drug design to synthesize agents that interact with that site, agents which generally do not bind to site-modified proteins. Moreover, such drug candidates that affect the activity of a native cancer protein are also identified by screening drugs for the ability to either enhance or reduce the activity of such proteins. [0790]
• Positive controls and negative controls can be used in the assays. Preferably control and test samples are performed in at least triplicate to obtain statistically significant results. Incubation of all samples occurs for a time sufficient to allow for the binding of the agent to the protein. Following incubation, samples are washed free of non-specifically bound material and the amount of bound, generally labeled agent determined. For example, where a radiolabel is employed, the samples can be counted in a scintillation counter to determine the amount of bound compound. [0791]
• A variety of other reagents can be included in the screening assays. These include reagents like salts, neutral proteins, e.g. albumin, detergents, etc. which are used to facilitate optimal protein-protein binding and/or reduce non-specific or background interactions. Also reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., can be used. The mixture of components is added in an order that provides for the requisite binding. [0792]
• Use of Polynucleotides to Down-Regulate or Inhibit a Protein of the Invention. [0793]
• Polynucleotide modulators of cancer can be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand-binding molecule, as described in WO 91/04753. Suitable ligand-binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors. Preferably, conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell. Alternatively, a polynucleotide modulator of cancer can be introduced into a cell containing the target nucleic acid sequence, e.g., by formation of a polynucleotide-lipid complex, as described in WO 90/10448. It is understood that the use of antisense molecules or knock out and knock in models may also be used in screening assays as discussed above, in addition to methods of treatment. [0794]
• Inhibitory and Antisense Nucleotides [0795]
• In certain embodiments, the activity of a cancer-associated protein is down-regulated, or entirely inhibited, by the use of antisense polynucleotide or inhibitory small nuclear RNA (snRNA), i.e., a nucleic acid complementary to, and which can preferably hybridize specifically to, a coding mRNA nucleic acid sequence, e.g., a cancer protein of the invention, mRNA, or a subsequence thereof. Binding of the antisense polynucleotide to the mRNA reduces the translation and/or stability of the mRNA. [0796]
• In the context of this invention, antisense polynucleotides can comprise naturally occurring nucleotides, or synthetic species formed from naturally occurring subunits or their close homologs. Antisense polynucleotides may also have altered sugar moieties or inter-sugar linkages. Exemplary among these are the phosphorothioate and other sulfur containing species which are known for use in the art. Analogs are comprised by this invention so long as they function effectively to hybridize with nucleotides of the invention. See, e.g., Isis Pharmaceuticals, Carlsbad, Calif.; Sequitor, Inc., Natick, Mass. [0797]
• Such antisense polynucleotides can readily be synthesized using recombinant means, or can be synthesized in vitro. Equipment for such synthesis is sold by several vendors, including Applied Biosystems. The preparation of other oligonucleotides such as phosphorothioates and alkylated derivatives is also well known to those of skill in the art. [0798]
• Antisense molecules as used herein include antisense or sense oligonucleotides. Sense oligonucleotides can, e.g., be employed to block transcription by binding to the anti-sense strand. The antisense and sense oligonucleotide comprise a single stranded nucleic acid sequence (either RNA or DNA) capable of binding to target mRNA (sense) or DNA (antisense) sequences for cancer molecules. Antisense or sense oligonucleotides, according to the present invention, comprise a fragment generally at least about 12 nucleotides, preferably from about 12 to 30 nucleotides. The ability to derive an antisense or a sense oligonucleotide, based upon a cDNA sequence encoding a given protein is described in, e.g., Stein & Cohen (Cancer Res. 48:2659 (1988 and van der Krol et al. (BioTechniques 6:958 (1988)). [0799]
• Ribozymes [0800]
• In addition to antisense polynucleotides, ribozymes can be used to target and inhibit transcription of cancer-associated nucleotide sequences. A ribozyme is an RNA molecule that catalytically cleaves other RNA molecules. Different kinds of ribozymes have been described, including group I ribozymes, hammerhead ribozymes, hairpin ribozymes, RNase P, and axhead ribozymes (see, e.g., Castanotto et al., Adv. in Pharmacology 25: 289-317 (1994) for a general review of the properties of different ribozymes). [0801]
• The general features of hairpin ribozymes are described, e.g., in Hampel et al., Nucl. Acids Res. 18:299-304 (1990); European Patent Publication No. 0360257; U.S. Pat. No. 5,254,678. Methods of preparing are well known to those of skill in the art (see, e.g., WO 94/26877; Ojwang et al., Proc. Natl. Acad. Sci. USA 90:6340-6344 (1993); Yamada et al., Human Gene Therapy 1:39-45 (1994); Leavitt et al., Proc. Natl. Acad Sci. USA 92:699-703 (1995); Leavitt et al., Human Gene Therapy 5: 1151-120 (1994); and Yamada et al., Virology 205: 121-126 (1994)). [0802]
• Use of Modulators in Phenotypic Screening [0803]
• In one embodiment, a test compound is administered to a population of cancer cells, which have an associated cancer expression profile. By “administration” or “contacting” herein is meant that the modulator is added to the cells in such a manner as to allow the modulator to act upon the cell, whether by uptake and intracellular action, or by action at the cell surface. In some embodiments, a nucleic acid encoding a proteinaceous agent (i.e., a peptide) is put into a viral construct such as an adenoviral or retroviral construct, and added to the cell, such that expression of the peptide agent is accomplished, e.g., PCT US97/01019. Regulatable gene therapy systems can also be used. Once the modulator has been administered to the cells, the cells are washed if desired and are allowed to incubate under preferably physiological conditions for some period. The cells are then harvested and a new gene expression profile is generated. Thus, e.g., cancer tissue is screened for agents that modulate, e.g., induce or suppress, the cancer phenotype. A change in at least one gene, preferably many, of the expression profile indicates that the agent has an effect on cancer activity. Similarly, altering a biological function or a signaling pathway is indicative of modulator activity. By defining such a signature for the cancer phenotype, screens for new drugs that alter the phenotype are devised. With this approach, the drug target need not be known and need not be represented in the original gene/protein expression screening platform, nor does the level of transcript for the target protein need to change. The modulator inhibiting function will serve as a surrogate marker [0804]
• As outlined above, screens are done to assess genes or gene products. That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of either the expression of the gene or the gene product itself is performed. [0805]
• Use of Modulators to Affect Peptides of the Invention [0806]
• Measurements of cancer polypeptide activity, or of the cancer phenotype are performed using a variety of assays. For example, the effects of modulators upon the function of a cancer polypeptide(s) are measured by examining parameters described above. A physiological change that affects activity is used to assess the influence of a test compound on the polypeptides of this invention. When the functional outcomes are determined using intact cells or animals, a variety of effects can be assesses such as, in the case of a cancer associated with solid tumors, tumor growth, tumor metastasis, neovascularization, hormone release, transcriptional changes to both known and uncharacterized genetic markers (e.g., by Northern blots), changes in cell metabolism such as cell growth or pH changes, and changes in intracellular second messengers such as cGNIP. [0807]
• Methods of Identifyinq Characterizing Cancer-Associated Sequences [0808]
• Expression of various gene sequences is correlated with cancer. Accordingly, disorders based on mutant or variant cancer genes are determined. In one embodiment, the invention provides methods for identifying cells containing variant cancer genes, e.g., determining the presence of, all or part, the sequence of at least one endogenous cancer gene in a cell. This is accomplished using any number of sequencing techniques. The invention comprises methods of identifying the cancer genotype of an individual, e.g., determining all or part of the sequence of at least one gene of the invention in the individual. This is generally done in at least one tissue of the individual, e.g., a tissue set forth in Table I, and may include the evaluation of a number of tissues or different samples of the same tissue. The method may include comparing the sequence of the sequenced gene to a known cancer gene, i.e., a wild-type gene to determine the presence of family members, homologies, mutations or variants. The sequence of all or part of the gene can then be compared to the sequence of a known cancer gene to determine if any differences exist. This is done using any number of known homology programs, such as BLAST, Bestfit, etc. The presence of a difference in the sequence between the cancer gene of the patient and the known cancer gene correlates with a disease state or a propensity for a disease state, as outlined herein. [0809]
• In a preferred embodiment, the cancer genes are used as probes to determine the number of copies of the cancer gene in the genome. The cancer genes are used as probes to determine the chromosomal localization of the cancer genes. Information such as chromosomal localization finds use in providing a diagnosis or prognosis in particular when chromosomal abnormalities such as translocations, and the like are identified in the cancer gene locus. [0810]
• XIV.) Kits/Articles of Manufacture [0811]
• For use in the diagnostic and therapeutic applications described herein, kits are also within the scope of the invention. Such kits can comprise a carrier, package or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in the method. For example, the container(s) can comprise a probe that is or can be detectably labeled. Such probe can be an antibody or polynucleotide specific for a FIG. 2-related protein or a FIG. 2 gene or message, respectively. Where the method utilizes nucleic acid hybridization to detect the target nucleic acid, the kit can also have containers containing nucleotide(s) for amplification of the target nucleic acid sequence and/or a container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, florescent, or radioisotope label. The kit can include all or part of the amino acid sequences in FIG. 2 or FIG. 3 or analogs thereof, or a nucleic acid molecules that encodes such amino acid sequences. [0812]
• The kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes; carrier, package, container, vial and/or tube labels listing contents and/or instructions for use, and package inserts with instructions for use. [0813]
• A label can be present on the container to indicate that the composition is used for a specific therapy or non-therapeutic application, such as a diagnostic or laboratory application, and can also indicate directions for either in vivo or in vitro use, such as those described herein. Directions and or other information can also be included on an insert(s) or label(s) which is included with or on the kit. [0814]
• The terms “kit” and “article of manufacture” can be used as synonyms. [0815]
• In another embodiment of the invention, an article(s) of manufacture containing compositions, such as amino acid sequence(s), small molecule(s), nucleic acid sequence(s), and/or antibody(s), e.g., materials useful for the diagnosis, prognosis, prophylaxis and/or treatment of neoplasias of tissues such as those set forth in Table I is provided. The article of manufacture typically comprises at least one container and at least one label. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers can be formed from a variety of materials such as glass or plastic. The container can hold amino acid sequence(s), small molecule(s), nucleic acid sequence(s), and/or antibody(s), in one embodiment the container holds a polynucleotide for use in examining the mRNA expression profile of a cell, together with reagents used for this purpose. [0816]
• The container can alternatively hold a composition which is effective for treating, diagnosis, prognosing or prophylaxing a condition and can have a sterile access port (for example the container can be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The active agents in the composition can be an antibody capable of specifically binding 98P4B6 and modulating the function of 98P4B6. [0817]
• The label can be on or associated with the container. A label a can be on a container when letters, numbers or other characters forming the label are molded or etched into the container itself; a label can be associated with a container when it is present within a receptacle or carrier that also holds the container, e.g., as a package insert. The label can indicate that the composition is used for diagnosing, treating, prophylaxing or prognosing a condition, such as a neoplasia of a tissue set forth in Table I. The article of manufacture can further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringer's solution and/ordextrose solution. It can further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, stirrers, needles, syringes, and/or package inserts with indications and/or instructions for use. [0818]
EXAMPLES
• Various aspects of the invention are further described and illustrated by way of the several examples that follow, none of which are intended to limit the scope of the invention. [0819]
Example 1 SSH-Generated Isolation of cDNA Fragment of the 98P4B6 Gene
• To isolate genes that are over-expressed in prostate cancer we used the Suppression Subtractive Hybridization (SSH) procedure using cDNA derived from prostate tissues. The 98P4B6 SSH cDNA sequence was derived from normal prostate minus LAPC-4AD prostate xenograft cDNAs. The 98P4B6 cDNA was identified as highly expressed in prostate cancer. [0820]
• Materials and Methods [0821]
• Human Tissues: [0822]
• The patient cancer and normal tissues were purchased from different sources such as the NDRI (Philadelphia, Pa.). mRNA for some normal tissues were purchased from Clontech, Palo Alto, Calif. [0823]
• RNA Isolation: [0824]
• Tissues were homogenized in Trizol reagent (Life Technologies, Gibco BRL) using 10 ml/g tissue isolate total RNA. Poly A RNA was purified from total RNA using Qiagen's Oligotex mRNA Mini and Midi kits. Total and mRNA were quantified by spectrophotometric analysis (O.D. 260/280 nm) and analyzed by gel electrophoresis. [0825]
• Oligonucleotides: [0826]
• The following HPLC purified oligonucleotides were used. [0827]
• DPNCDN (cDNA Synthesis Primer): [0828]
• 5′[0829] TTTTGATCAAGCTT ₃₀3′ (SEQ ID NO: 101)
• Adaptor 1: [0830]

  5′CTAATACGACTCACTATAGGGCTCGAGCGGC	(SEQ ID NO: 102)
  CGCCCGGGCAG3′
  3′GGCCCGTCCTAG5′	(SEQ ID NO: 103)

• Adaptor 2: [0831]

  5′GTAATACGACTCACTATAGGGCAGCGTGGTC	(SEQ ID NO: 104)
  GCGGCCGAG3′
  3′CGGCTCCTAG5′	(SEQ ID NO: 105)

• PCR Primer 1: [0832]
• 5′CTAATACGACTCACTATAGGGC3′ (SEQ ID NO: 106) [0833]
• Nested Primer (NP)1: [0834]
• 5′TCGAGCGGCCGCCCGGGCAGGA3′ (SEQ ID NO: 107) [0835]
• Nested Primer (NP)2: [0836]
• 5′AGCGTGGTCGCGGCCGAGGA3′ (SEQ ID NO: 108) [0837]
• Suppression Subtractive Hybridization: [0838]
• Suppression Subtractive Hybridization (SSH) was used to identify cDNAs corresponding to genes that may be differentially expressed in prostate cancer. The SSH reaction utilized cDNA from prostate cancer xenograft and normal tissues. [0839]
• The gene 98P4B6 sequence was derived from normal prostate tissue minus prostate cancer xenograft LAPC-4AD cDNA subtraction. The SSH DNA sequence (FIG. 1) was identified. [0840]
• The cDNA derived from LAPC-4AD was used as the source of the “driver” cDNA, while the cDNA from normal prostate was used as the source of the “tester” cDNA. Double stranded cDNAs corresponding to tester and driver cDNAs were synthesized from 2 μg of poly(A)[0841] ⁺ RNA isolated from the relevant tissue, as described above, using CLONTECH's PCR-Select cDNA Subtraction Kit and 1 ng of oligonucleotide DPNCDN as primer. First- and second-strand synthesis were carried out as described in the Kit's user manual protocol (CLONTECH Protocol No. PT 1117-1, Catalog No. K1804-1). The resulting cDNA was digested with Dpn II for 3 hrs at 370° C. Digested cDNA was extracted with phenol/chloroform (1:1) and ethanol precipitated.
• Driver cDNA was generated by combining in a 1:1 ratio Dpn II digested cDNA from the relevant tissue source (see above) with digested cDNAs derived from normal tissue. [0842]
• Tester cDNA was generated by diluting 1 μl of Dpn II digested cDNA from the relevant tissue source (see above) (400 ng) in 5 μl of water. The diluted cDNA (2 μl, 160 ng) was then ligated to 2 μl of [0843] Adaptor 1 and Adaptor 2 (10 μM), in separate ligation reactions, in a total volume of 10 μl at 16° C. overnight, using 400 u of T4 DNA ligase (CLONTECH). Ligation was terminated with 1 μl of 0.2 M EDTA and heating at 72° C. for 5 min.
• The first hybridization was performed by adding 1.5 μl (600 ng) of driver cDNA to each of two tubes containing 1.5 μl (20 ng) Adaptor 1- and Adaptor 2-ligated tester cDNA. In a final volume of 4 μl, the samples were overlaid with mineral oil, denatured in an MJ Research thermal cycler at 98° C. for 1.5 minutes, and then were allowed to hybridize for 8 hrs at 68° C. The two hybridizations were then mixed together with an additional 1 μl of fresh denatured driver cDNA and were allowed to hybridize overnight at 68° C. The second hybridization was then diluted in 200 μl of 20 mM Hepes, pH 8.3, 50 mM NaCl, 0.2 mM EDTA, heated at 70° C. for 7 min. and stored at −20° C. [0844]
• PCR Amplification, Cloning and Sequencing of Gene Fragments Generated from SSH: [0845]
• To amplify gene fragments resulting from SSH reactions, two PCR amplifications were performed. In the [0846] primary PCR reaction 1 μl of the diluted final hybridization mix was added to 1 μ of PCR primer 1 (10 μM), 0.5 μl dNTP mix (10 μM), 2.5 μl 10×reaction buffer (CLONTECH) and 0.5 μl 50×Advantage cDNA polymerase Mix (CLONTECH) in a final volume of 25 μl. PCR 1 was conducted using the following conditions: 75° C. for 5 min., 94° C. for 25 sec., then 27 cycles of 94° C. for 10 sec, 66° C. for 30 sec, 72° C. for 1.5 min. Five separate primary PCR reactions were performed for each experiment. The products were pooled and diluted 1:10 with water. For the secondary PCR reaction, 1 μl from the pooled and diluted primary PCR reaction was added to the same reaction mix as used for PCR 1, except that primers NP1 and NP2 (10 μM) were used instead of PCR primer 1. PCR 2 was performed using 10-12 cycles of 94° C. for 10 sec, 68° C. for 30 sec, and 72° C. for 1.5 minutes. The PCR products were analyzed using 2% agarose gel electrophoresis.
• The PCR products were inserted into pCR2.1 using the T/A vector cloning kit (Invitrogen). Transformed [0847] E. coli were subjected to blue/white and ampicillin selection. White colonies were picked and arrayed into 96 well plates and were grown in liquid culture overnight. To identify inserts, PCR amplification was performed on 1 ul of bacterial culture using the conditions of PCR1 and NP1 and NP2 as primers. PCR products were analyzed using 2% agarose gel electrophoresis.
• Bacterial clones were stored in 20% glycerol in a 96 well format. Plasmid DNA was prepared, sequenced, and subjected to nucleic acid homology searches of the GenBank, dBest, and NCI-CGAP databases. [0848]
• RT-PCR Expression Analysis: [0849]
• First strand cDNAs can be generated from 1 μg of mRNA with oligo (dT)12-18 priming using the Gibco-BRL Superscript Preamplification system. The manufacturer's protocol was used which included an incubation for 50 min at 42° C. with reverse transcriptase followed by RNAse H treatment at 37° C. for 20 min. After completing the reaction, the volume can be increased to 200 μl with water prior to normalization. First strand cDNAs from 16 different normal human tissues can be obtained from Clontech. [0850]
• Normalization of the first strand cDNAs from multiple tissues was performed by using the primers 5′atatcgccgcgctcgtcgtcgacaa3′ (SEQ ID NO: 109) and 5′[0851] agccacacgcagctcattgtagaagg 3′ (SEQ ID NO: 110) to amplify β-actin. First strand cDNA (5 μl) were amplified in a total volume of 50 μl containing 0.4 μM primers, 0.2 μM each dNTPs, 1×PCR buffer (Clontech, 10 mM Tris-HCL, 1.5 mM MgCl₂, 50 mM KCl, pH8.3) and 1×Klentaq DNA polymerase (Clontech). Five μl of the PCR reaction can be removed at 18, 20, and 22 cycles and used for agarose gel electrophoresis. PCR was performed using an MJ Research thermal cycler under the following conditions: Initial denaturation can be at 94° C. for 15 sec, followed by a 18, 20, and 22 cycles of 94° C. for 15, 65° C. for 2 min, 72° C. for 5 sec. A final extension at 72° C. was carried out for 2 min. After agarose gel electrophoresis, the band intensities of the 283 bp β-actin bands from multiple tissues were compared by visual inspection. Dilution factors for the first strand cDNAs were calculated to result in equal β-actin band intensities in all tissues after 22 cycles of PCR. Three rounds of normalization can be required to achieve equal band intensities in all tissues after 22 cycles of PCR.
• To determine expression levels of the 98P4B6 gene, 5 μl of normalized first strand cDNA were analyzed by PCR using 26, and 30 cycles of amplification. Semi-quantitative expression analysis can be achieved by comparing the PCR products at cycle numbers that give light band intensities. The primers used for RT-PCR were designed using the 98P4B6 SSH sequence and are listed below: [0852]
• 98P4B6.1 [0853]
• 5′-GACTGAGCTGGAACTGGAATTTGT-3′ (SEQ ID NO: 111) [0854]
• 98P4B6.2 [0855]
• 5′-TTTGAGGAGACTTCATCTCACTGG-3′ (SEQ ID NO: 112) [0856]
Example 2 Isolation of Full Length 98P4B6 Encoding cDNA
• The 98P4B6 SSH cDNA sequence was derived from a substraction consisting of normal prostate minus prostate cancer xenograft. The SSH cDNA sequence (FIG. 1) was designated 98P4B6. [0857]
• The 98P4B6 SSH DNA sequence of 183 bp is shown in FIG. 1. Full-length 98P4B6 v.1 (clone GTD3) of 2453 bp was cloned from prostate cDNA library, revealing an ORF of 454 amino acids (FIG. 2 and FIG. 3). 98P4B6 v.6 was also cloned from normal prostate library. Other variants of 98P4B6 were also identified and these are listed in FIGS. 2 and 3. [0858]
• 98P4B6 v.2, v.3, v.4, v.5, v.6, v.7 and v.8 are splice variants of 98P4B6 v.1. 98P4B6 v.9 through v.19 are SNP variants and differ from v.1 by one amino acid. 98P4B6 v.20 through v.24 are SNP variants of v.7. 98P4B6 v.25 through v.38 are SNP variants of v.8. Though these SNP variants were shown separately, they could also occur in any combinations and in any transcript variants. [0859]
Example 3 Chromosomal Mapping of 98P4B6
• Chromosomal localization can implicate genes in disease pathogenesis. Several chromosome mapping approaches are available including fluorescent in situ hybridization (FISH), human/hamster radiation hybrid (RH) panels (Walter et al., 1994; Nature Genetics 7:22; Research Genetics, Huntsville Ala.), human-rodent somatic cell hybrid panels such as is available from the Cornell Institute (Camden, N.J.), and genomic viewers utilizing BLAST homologies to sequenced and mapped genomic clones (NCBI, Bethesda, Md.). [0860]
• 98P4B6 maps to chromosome 7q21 using 98P4B6 sequence and the NCBI BLAST tool: located on the World Wide Web at .ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsBlast.html&&ORG=Hs). [0861]
Example 4 Expression Analysis of 98P4B6
• Expression analysis by RT-PCR demonstrated that 98P4B6 is strongly expressed in prostate cancer patient specimens (FIG. 14). First strand cDNA was generated from normal stomach, normal brain, normal heart, normal liver, normal skeletal muscle, normal testis, normal prostate, normal bladder, normal kidney, normal colon, normal lung, normal pancreas, and a pool of cancer specimens from prostate cancer patients, bladder cancer patients, kidney cancer patients, colon cancer patients, lung cancer patients, pancreas cancer patients, and a pool of 2 patient prostate metastasis to lymph node. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers directed to 98P4B6 v.1, v.13, or/and v.14 (A), or directed specifically to the splice variants 98P4B6 v.6 and v.8 (B), was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Results show strong expression of 98P4B6 and its splice variants v.6 and v.8 in normal prostate and in prostate cancer. Expression was also detected in bladder cancer, kidney cancer, colon cancer, lung cancer, pancreas cancer, breast cancer, cancer metastasis as well as in the prostate cancer metastasis to lymph node specimens, compared to all normal tissues tested. As noted below, e.g., in Example 6, as 98P4B6 v.1 is in expressed in cancer tissues such as those listed in Table 1, the other protein-encoding 98P4B6 variants are expressed in these tissues as well; this principle is corroborated by data in (FIG. 14) for the proteins herein designated 98P4B6 v.6 or v.8 is found, e.g., in prostate, lung, ovary, bladder, breast, colon, kidney and pancreas, cancers, as well as in the literature (Porkka et al., Lab Invest, 2002 and Korkmaz et al., JBC, 2002) where the protein 98P4B6 v.8 is identified in normal prostate and prostate cancer. [0862]
• When the genomic region to which a gene maps is modulated in a particular cancer, the alternative transcripts or splice variants of the gene are modulated as well. Disclosed herein is that 98P4B6 has a particular expression profile related to cancer. Alternative transcripts and splice variants of 98P4B6 are also involved in cancers in the same or additional tissues, thus serving as tumor-associated markers/antigens. [0863]
• Expression of 98P4B6 v.1, v.13, and/or v.14 was detected in prostate, lung, ovary, bladder, cervix, uterus and pancreas cancer patient specimens (FIG. 15). First strand cDNA was prepared from a panel of patient cancer specimens. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 98P4B6, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Expression was recorded as absent, low, medium or strong. Results show expression of 98P4B6 in the majority of all patient cancer specimens tested. [0864]
• FIG. 16 shows that 98P4B6 is expressed in stomach cancer patient specimens. (A) RNA was extracted from normal stomach (N) and from 10 different stomach cancer patient specimens (T). Northern blot with 10 μg of total RNA/lane was probed with 98P4B6 sequence. Results show strong expression of 98P4B6 in the stomach tumor tissues and lower expression in normal stomach. The lower panel represents ethidium bromide staining of the blot showing quality of the RNA samples. (B) Expression of 98P4B6 was assayed in a panel of human stomach cancers (T) and their respective matched normal tissues (N) on RNA dot blots. 98P4B6 was detected in 7 out of 8 stomach tumors but not in the matched normal tissues. [0865]
Example 5 Transcript Variants of 98P4B6
• Transcript variants are variants of mature mRNA from the same gene which arise by alternative transcription or alternative splicing. Alternative transcripts are transcripts from the same gene but start transcription at different points. Splice variants are mRNA variants spliced differently from the same transcript. In eukaryotes, when a multi-exon gene is transcribed from genomic DNA, the initial RNA is spliced to produce functional mRNA, which has only exons and is used for translation into an amino acid sequence. Accordingly, a given gene can have zero to many alternative transcripts and each transcript can have zero to many splice variants. Each transcript variant has a unique exon makeup, and can have different coding and/or non-coding (5′ or 3′ end) portions, from the original transcript. Transcript variants can code for similar or different proteins with the same or a similar function or can encode proteins with different functions, and can be expressed in the same tissue at the same time or in different tissues at the same time or in the same tissue at different times or in different tissues at different times. Proteins encoded by transcript variants can have similar or different cellular or extracellular localizations, e.g., secreted versus intracellular. [0866]
• Transcript variants are identified by a variety of art-accepted methods. For example, alternative transcripts and splice variants are identified by full-length cloning experiment, or by use of full-length transcript and EST sequences. First, all human ESTs were grouped into clusters which show direct or indirect identity with each other. Second, ESTs in the same duster were further grouped into sub-clusters and assembled into a consensus sequence. The original gene sequence is compared to the consensus sequence(s) or other full-length sequences. Each consensus sequence is a potential splice variant for that gene. Even when a variant is identified that is not a full-length clone, that portion of the variant is very useful for antigen generation and for further cloning of the full-length splice variant, using techniques known in the art. [0867]
• Moreover, computer programs are available in the art that identify transcript variants based on genomic sequences. Genomic-based transcript variant identification programs include FgenesH (A. Salamov and V. Solovyev, “Ab initio gene finding in Drosophila genomic DNA,” Genome Research. 2000 April;10(4):516-22); Grail (URL compbio.ornl.gov/Grail-bin/EmptyGrailForm) and GenScan (URL genes.mit.edu/GENSCAN.html). For a general discussion of splice variant identification protocols see., e.g., Southan, C., A genomic perspective on human proteases, FEBS Lett. 2001 Jun. 8; 498(2-3):214-8; de Souza, S. J., et al., Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags, Proc. Natl Acad Sci U S A. 2000 Nov. 7; 97(23):12690-3. [0868]
• To further confirm the parameters of a transcript variant, a variety of techniques are available in the art, such as full-length cloning, proteomic validation, PCR-based validation, and 5′ RACE validation, etc. (see e.g., Proteomic Validation: Brennan, S. O., et al., Albumin banks peninsula: a new termination variant characterized by electrospray mass spectrometry, Biochem Biophys Acta. 1999 Aug. 17;1433(1-2):321-6; Ferranti P, et al., Differential splicing of pre-messenger RNA produces multiple forms of mature caprine alpha(s1)-casein, Eur J Biochem. 1997 Oct. 1;249(1):1-7. For PCR-based Validation: Wellmann S, et al., Specific reverse transcription-PCR quantification of vascular endothelial growth factor (VEGF) splice variants by LightCycler technology, Clin Chem. 2001 April ;47(4):654-60; Jia, H. P., et al., Discovery of new human beta-defensins using a genomics-based approach, Gene. 2001 Jan. 24; 263(1-2):211-8. For PCR-based and 5′ RACE Valdation: Brigle, K. E., et al., Organization of the murine reduced folate carrier gene and identification of variant splice forms, Biochem Biophys Acta. 1997 Aug. 7; 1353(2): 191-8). [0869]
• It is known in the art that genomic regions are modulated in cancers. Recently, Porkka et al. (2002) reported that transcript variants of STEAP2 were expressed and were found in both normal and malignant prostate tissue (Porkka, K. P., et al. Cloning and characterization of a novel six-transmembrane protein STEAP2, expressed in normal and malignant prostate. Laboratory Investigation 2002 November; 82(11):1573-1582). Another group of scientists also reported that transcript variants of STEAP2 (98P4B6 v.6 herein) also were expressed significantly higher in prostate cancer than normal prostate (Korkmaz, K. S., et al. Molecular cloning and characterization of STAMP1, a highly prostate-specific six transmembrane protein that is overexpressed in prostate cancer. The Journal of Biological Chemistry. 2002 September 277(39):36689-36696.). When the genomic region to which a gene maps is modulated in a particular cancer, the alternative transcripts or splice variants of the gene are modulated as well. Disclosed herein is that 98P4B6 has a particular expression profile related to cancer. Alternative transcripts and splice variants of 98P4B6 are also involved in cancers in the same or additional tissues, thus serving as tumor-associated markers/antigens. [0870]
• Using the full-length gene and EST sequences, seven transcript variants were identified, designated as 98P4B6 v.2, v.3, v.4, v.5, v.6, v.7 and v.8, as shown in FIG. 12. The boundaries of exons in the original transcript, 98P4B6 v.1 were shown in Table LI. The first 22 bases of v.1 were not in the nearby 5′ region of v.1 on the current assembly of the human genome. Compared with 98P4B6 v.1, variant v.2 was a single exon transcript whose 3′ portion was the same as the last exon of v.1. The first two exons of v.3 were in [0871] intron 1 of v. 1. Variants v.4, v.5, and v.6 spliced out 224-334 in the first exon of v.1. In addition, v.5 spliced out exon 5 while v.6 spliced out exon 6 but extended exon 5 of v.1. Variant v.7 used alternative transcription start and different 3′ exons. Variant v.8 extended 5′ end and kept the whole intron 5 of v.1. Theoretically, each different combination of exons in spatial order, e.g. exons 2 and 3, is a potential splice variant.
• Tables LII through LV are set forth on a variant-by-variant basis. Tables LII(a)-(g) show the nucleotide sequence of the transcript variant. Tables LII (a)-(g) show the alignment of the transcript variant with the nucleic acid sequence of 98P4B6 v.1. Tables LIV(a)-(g) lay out the amino acid translation of the transcript variant for the identified reading frame orientation. Tables LV(a)-(g) display alignments of the amino acid sequence encoded by the splice variant with that of 98P4B6 v.1. Additionally, single nucleotide polymorphisms (SNP) are noted in the alignment. [0872]
Example 6 Single Nucleotide Polymorphisms of 98P4B6
• A Single Nucleotide Polymorphism (SNP) is a single base pair variation in a nucleotide sequence at a specific location. At any given point of the genome, there are four possible nucleotide base pairs: A/T, C/G, G/C and T/A. Genotype refers to the specific base pair sequence of one or more locations in the genome of an individual. Haplotype refers to the base pair sequence of more than one location on the same DNA molecule (or the same chromosome in higher organisms), often in the context of one gene or in the context of several tightly linked genes. SNP that occurs on a cDNA is called cSNP. This cSNP may change amino acids of the protein encoded by the gene and thus change the functions of the protein. Some SNP cause inherited diseases; others contribute to quantitative variations in phenotype and reactions to environmental factors including diet and drugs among individuals. Therefore, SNP and/or combinations of alleles (called haplotypes) have many applications, including diagnosis of inherited diseases, determination of drug reactions and dosage, identification of genes responsible for diseases, andlanalysis of the genetic relationship between individuals (P. Nowotny, J. M. Kwon and A. M. Goate, “SNP analysis to dissect human traits,” Curr. Opin. Neurobiol. 2001 October; 11 (5):637-641; M. Pirmohamed and B. K. Park, “Genetic susceptibility to adverse drug reactions,” Trends Pharmacol. Sci. 2001 June; 22(6):298-305; J. H. Riley, C. J. Allan, E. Lai and A. Roses, “The use of single nucleotide polymorphisms in the isolation of common disease genes,” Pharmacogenomics. 2000 February ; 1(1):39-47; R. Judson, J. C. Stephens and A. Windemuth, “The predictive power of haplotypes in clinical response,” Pharmacogenomics. 2000 February; 1(1):15-26). [0873]
• SNP are identified by a variety of art-accepted methods (P. Bean, “The promising voyage of SNP target discovery,” Am. Clin. Lab. 2001 October-November; 20(9):18-20; K. M. Weiss, “In search of human variation,” Genome Res. 1998 July; 8(7):691-697; M. M. She, “Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies,” Clin. Chem. 2001 February; 47(2):164-172). For example, SNP can be identified by sequencing DNA fragments that show polymorphism by gel-based methods such as restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE). They can also be discovered by direct sequencing of DNA samples pooled from different individuals or by comparing sequences from different DNA samples. With the rapid accumulation of sequence data in public and private databases, one can discover SNP by comparing sequences using computer programs (Z. Gu, L. Hillier and P. Y. Kwok, “Single nucleotide polymorphism hunting in cyberspace,” Hum. Mutat. 1998; 12(4):221-225). SNP can be verified and genotype or haplotype of an individual can be determined by a variety of methods including direct sequencing and high throughput microarrays (P. Y. Kwok, “Methods for genotyping single nucleotide polymorphisms,” Annu. Rev. Genomics Hum. Genet. 2001; 2:235-258; M. Kokoris, K. Dix, K. Moynihan, J. Mathis, B. Erwin, P. Grass, B. Hines and A. Duesterhoeft, “High-throughput SNP genotyping with the Masscode system,” Mol. Diagn. 2000 December; 5(4):329-340). [0874]
• Using the methods described above, eleven SNP were identified in the original transcript, 98P4B6 v.1, at positions 46 (A/G), 179 (C/T), 180 (A/G), 269 (A/G), 404 (G/T), 985 (C/T), 1170 (T/C), 1497 (A/G), 1746 (T/G), 2046 (T/G) and 2103 (T/C). The transcripts or proteins with alternative allele were designated as variant 98P4B6 v.9 through v.19, as shown in FIG. 10[0875] a. FIG. 11 shows the schematic alignment of protein variants, corresponding to nucleotide variants. Nucleotide variants that code for the same amino acid sequence as v.1 are not shown in FIG. 11. These alleles of the SNP, though shown separately here, can occur in different combinations (haplotypes) and in any one of the transcript variants (such as 98P4B6 v.5) that contains the site of the SNP. In addition, there were SNP in other transcript variants in regions not shared with v.1. For example, there were fourteen SNP in the fifth intron of v.1, which was part of transcript variants v.2, v.6 and v.8. These SNP are shown in FIG. 10c and listed as following (numbers relative v.8): 1760 (G/A), 1818 (G/T), 1870 (C/T), 2612 (T/C), 2926 (T/A), 4241 (TIA), 4337 (A/G), 4338 (A/C), 4501 (A/G), 4506 (C/T), 5434 (C/A), 5434 (C/G), 5434 (C/T) and 5589 (C/A). FIG. 10b shows the SNP in the unique regions of transcript variant v.7: 1956 (A/C), 1987 (T/A), 2010 (G/C), 2010 (G/T) and 2059 (G/A) (numbers correspond to nucleotide sequence of v.7).
Example 7 Production of Recombinant 98P4B6 in Prokaryotic Systems
• To express recombinant 98P4B6 and 98P4B6 variants in prokaryotic cells, the full or partial length 98P4B6 and 98P4B6 variant cDNA sequences are cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 98P4B6 variants are expressed: the full length sequence presented in FIGS. 2 and 3, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 98P4B6, variants, or analogs thereof. [0876]
• A. In Vitro Transcription and Translation Constructs: [0877]
• pCRII: [0878]
• To generate 98P4B6 sense and anti-sense RNA probes for RNA in situ investigations, pCRII constructs (Invitrogen, Carlsbad Calif.) are generated encoding either all or fragments of the 98P4B6 cDNA. The pCRII vector has Sp6 and T7 promoters flanking the insert to drive the transcription of 98P4B6 RNA for use as probes in RNA in situ hybridization experiments. These probes are used to analyze the cell and tissue expression of 98P4B6 at the RNA level. Transcribed 98P4B6 RNA representing the cDNA amino acid coding region of the 98P4B6 gene is used in in vitro translation systems such as the TnT™ Coupled Reticulolysate System (Promega, Corp., Madison, Wis.) to synthesize 98P4B6 protein. [0879]
• B. Bacterial Constructs: [0880]
• pGEX Constructs: [0881]
• To generate recombinant 98P4B6 proteins in bacteria that are fused to the Glutathione S-transferase (GST) protein, all or parts of the 98P4B6 cDNA protein coding sequence are cloned into the pGEX family of GST-fusion vectors (Amersham Pharmacia Biotech, Piscataway, N.J.). These constructs allow controlled expression of recombinant 98P4B6 protein sequences with GST fused at the amino-terminus and a six histidine epitope (6×His) at the carboxyl-terminus. The GST and 6×His tags permit purification of the recombinant fusion protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-GST and anti-His antibodies. The 6×His tag is generated by adding 6 histidine codons to the cloning primer at the 3′ end, e.g., of the open reading frame (ORF). A proteolytic cleavage site, such as the PreScission™ recognition site in pGEX-6P-1, may be employed such that it permits cleavage of the GST tag from 98P4B6-related protein. The ampicillin resistance gene and pBR322 origin permits selection and maintenance of the pGEX plasmids in [0882] E. coli. A glutathione-S-transferase (GST) fusion protein encompassing amino acids 2-204 of the STEAP-2 protein sequence was generated in the pGEX vector. The recombinant GST-STEAP-2 fusion protein was purified from induced bacteria by glutathione-sepaharose affinity chromatography and used as immunogen for generation of a polyclonal antibody.
• pMAL Constructs: [0883]
• To generate, in bacteria, recombinant 98P4B6 proteins that are fused to maltose-binding protein (MBP), all or parts of the 98P4B6 cDNA protein coding sequence are fused to the MBP gene by cloning into the pMAL-c2X and pMAL-p2X vectors (New England Biolabs, Beverly, Mass.). These constructs allow controlled expression of recombinant 98P4B6 protein sequences with MBP fused at the amino-terminus and a 6×His epitope tag at the carboxyl-terminus. The MBP and 6×His tags permit purification of the recombinant protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-MBP and anti-His antibodies. The 6×His epitope tag is generated by adding 6 histidine codons to the 3′ cloning primer. A Factor Xa recognition site permits cleavage of the pMAL tag from 98P4B6. The pMAL-c2X and pMAL-p2X vectors are optimized to express the recombinant protein in the cytoplasm or periplasm respectively. Periplasm expression enhances folding of proteins with disulfide bonds. [0884]
• pET Constructs: [0885]
• To express 98P4B6 in bacterial cells, all or parts of the 98P4B6 cDNA protein coding sequence are cloned into the pET family of vectors (Novagen, Madison, Wis.). These vectors allow tightly controlled expression of recombinant 98P4B6 protein in bacteria with and without fusion to proteins that enhance solubility, such as NusA and thioredoxin (Trx), and epitope tags, such as 6×His and S-Tag™ that aid purification and detection of the recombinant protein. For example, constructs are made utilizing pET NusA fusion system 43.1 such that regions of the 98P4B6 protein are expressed as amino-terminal fusions to NusA. [0886]
• C. Yeast Constructs: [0887]
• pESC Constructs: [0888]
• To express 98P4B6 in the yeast species [0889] Saccharomyces cerevisiae for generation of recombinant protein and functional studies, all or parts of the 98P4B6 cDNA protein coding sequence are cloned into the pESC family of vectors each of which contain 1 of 4 selectable markers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La Jolla, Calif.). These vectors allow controlled expression from the same plasmid of up to 2 different genes or cloned sequences containing either Flag™ or Myc epitope tags in the same yeast cell. This system is useful to confirm protein-protein interactions of 98P4B6. In addition, expression in yeast yields similar post-translational modifications, such as glycosylations and phosphorylations, that are found when expressed in eukaryotic cells.
• pESP Constructs: [0890]
• To express 98P4B6 in the yeast species [0891] Saccharomyces pombe, all or parts of the 98P4B6 cDNA protein coding sequence are cloned into the pESP family of vectors. These vectors allow controlled high level of expression of a 98P4B6 protein sequence that is fused at either the amino terminus or at the carboxyl terminus to GST which aids purification of the recombinant protein. A Flag™ epitope tag allows detection of the recombinant protein with anti-Flag™ antibody.
Example 8 Production of Recombinant 98P4B6 in Higher Eukaryotic Systems
• A. Mammalian Constructs: [0892]
• To express recombinant 98P4B6 in eukaryotic cells, the full or partial length 98P4B6 cDNA sequences can be cloned into any one of a variety of expression vectors known in the art. One or more of the following regions of 98P4B6 are expressed in these constructs, [0893] amino acids 1 to 255, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 98P4B6 v.1 through v.11; amino acids 1 to 1266, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 98P4B6 v.12 and v.13, variants, or analogs thereof.
• The constructs can be transfected into any one of a wide variety of mammalian cells such as 293T cells. Transfected 293T cell lysates can be probed with the anti-98P4B6 polyclonal serum, described herein. [0894]
• pcDNA4/HisMax Constructs: [0895]
• To express 98P4B6 in mammalian cells, a 98P4B6 ORF, or portions thereof, of 98P4B6 are cloned into pcDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter and the SP16 translational enhancer. The recombinant protein has Xpress™ and six histidine (6×His) epitopes fused to the amino-terminus. The pcDNA4/HisMax vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColEl origin permits selection and maintenance of the plasmid in [0896] E. coli.
• pcDNA3.11MycHis Constructs: [0897]
• To express 98P4B6 in mammalian cells, a 98P4B6 ORF, or portions thereof, of 98P4B6 with a consensus Kozak translation initiation site was cloned into pcDNA3.1/MycHis Version A (Invitrogen, Carlsbad, Calif.). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the myc epitope and 6×His epitope fused to the carboxyl-terminus. The pcDNA3.1/MycHis vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability, along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene can be used, as it allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in [0898] E. coli.
• pcDNA3.1IGFP Construct: [0899]
• To express 98P4B6 in mammalian cells and to allow detection of the recombinant proteins using fluorescence, the 98P4B6 ORF sequence was codon optimized according to Mirzabekov et al. (1999), and was cloned into pcDNA3.1/GFP vector to generate 98P4B6.GFP.pcDNA3.1 construct. Protein expression was driven from the cytomegalovirus (CMV) promoter. The recombinant protein had the Green Fluorescent Protein (GFP) fused to the carboxyl-terminus facilitating non-invasive, in vivo detection and cell biology studies. The pcDNA3.1/GFP vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in [0900] E coli.
• Transfection of 98P4B6.GFP.pcDNA3.1 into 293T cells was performed as shown in FIGS. 17 and 18. Results show strong expression of the fusion protein by western blot analysis (FIG. 17), flow cytometry (FIG. 18A) and fluorescent microscopy (FIG. 18B). [0901]
• Additional constructs with an amino-terminal GFP fusion are made in pcDNA3.1/NT-GFP-TOPO spanning the entire length of a 98P4B6 protein. [0902]
• PAPtag: [0903]
• A 98P4B6 ORF, or portions thereof, is cloned into pAPtag-5 (GenHunter Corp. Nashville, Tenn.). This construct generates an alkaline phosphatase fusion at the carboxyl-terminus of a 98P4B6 protein while fusing the IgG[0904] _K signal sequence to the amino-terminus. Constructs are also generated in which alkaline phosphatase with an amino-terminal IgG_K signal sequence is fused to the amino-terminus of a 98P4B6 protein. The resulting recombinant 98P4B6 proteins are optimized for secretion into the media of transfected mammalian cells and can be used to identify proteins such as ligands or receptors that interact with 98P4B6 proteins. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and 6×His epitopes fused at the carboxyl-terminus that facilitates detection and purification. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the recombinant protein and the ampicillin resistance gene permits selection of the plasmid in E. coli.
• pTag5: [0905]
• A 98P4B6 ORF, or portions thereof, is cloned into pTag-5. This vector is similar to pAPtag but without the alkaline phosphatase fusion. This construct generates 98P4B6 protein with an amino-terminal IgG[0906] _K signal sequence and myc and 6×His epitope tags at the carboxyl-terminus that facilitate detection and affinity purification. The resulting recombinant 98P4B6 protein is optimized for secretion into the media of transfected mammalian cells, and is used as immunogen or ligand to identify proteins such as ligands or receptors that interact with the 98P4B6 proteins. Protein expression is driven from the CMV promoter. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the protein, and the ampicillin resistance gene permits selection of the plasmid in E. coli.
• PsecFc: [0907]
• A 98P4B6 ORF, or portions thereof, is also cloned into psecFc. The psecFc vector was assembled by cloning the human immunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen, California). This construct generates an IgG1 Fc fusion at the carboxyl-terminus of the 98P4B6 proteins, while fusing the IgGK signal sequence to N-terminus. 98P4B6 fusions utilizing the murine IgG1 Fc region are also used. The resulting recombinant 98P4B6 proteins are optimized for secretion into the media of transfected mammalian cells, and can be used as immunogens or to identify proteins such as ligands or receptors that interact with 98P4B6 protein. Protein expression is driven from the CMV promoter. The hygromycin resistance gene present in the vector allows for selection of mammalian cells that express the recombinant protein, and the ampicillin resistance gene permits selection of the plasmid in [0908] E coli.
• pSRα Constructs: [0909]
• To generate mammalian cell lines that express 98P4B6 constitutively, 98P4B6 ORF, or portions thereof, of 98P4B6 were cloned into pSRα constructs. Amphotropic and ecotropic retroviruses were generated by transfection of pSRα constructs into the 293T-10A1 packaging line or co-transfection of pSRα and a helper plasmid (containing deleted packaging sequences) into the 293 cells, respectively. The retrovirus is used to infect a variety of mammalian cell lines, resulting in the integration of the cloned gene, 98P4B6, into the host cell-lines. Protein expression is driven from a long terminal repeat (LTR). The Neomycin resistance gene present in the vector allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permit selection and maintenance of the plasmid in [0910] E. coli. The retroviral vectors can thereafter be used for infection and generation of various cell lines using, for example, PC3, NIH 3T3, TsuPr1, 293 or rat-1 cells.
• Additional pSRα constructs are made that fuse an epitope tag such as the FLAG™ tag to the carboxyl-terminus of 98P4B6 sequences to allow detection using anti-Flag antibodies. For example, the FLAG™ sequence 5′ gat tac aag gat gac gac gat aag 3′ (SEQ ID NO: 113) is added to cloning primer at the 3′ end of the ORF. Additional pSRα constructs are made to produce both amino-terminal and carboxyl-terminal GFP and myc/6×His fusion proteins of the full-length 98P4B6 proteins. [0911]
• Additional Viral Vectors: [0912]
• Additional constructs are made for viral-mediated delivery and expression of 98P4B6. High virus titer leading to high level expression of 98P4B6 is achieved in viral delivery systems such as adenoviral vectors and herpes amplicon vectors. A 98P4B6 coding sequences or fragments thereof are amplified by PCR and subcloned into the AdEasy shuttle vector (Stratagene). Recombination and virus packaging are performed according to the manufacturer's instructions to generate adenoviral vectors. Alternatively, 98P4B6 coding sequences or fragments thereof are cloned into the HSV-1 vector (Imgenex) to generate herpes viral vectors. The viral vectors are thereafter used for infection of various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells. [0913]
• Regulated Expression Systems: [0914]
• To control expression of 98P4B6 in mammalian cells, coding sequences of 98P4B6, or portions thereof, are cloned into regulated mammalian expression systems such as the T-Rex System (Invitrogen), the GeneSwitch System (Invitrogen) and the tightly-regulated Ecdysone System (Sratagene). These systems allow the study of the temporal and concentration dependent effects of recombinant 98P4B6. These vectors are thereafter used to control expression of 98P4B6 in various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells. [0915]
• B. Baculovirus Expression Systems [0916]
• To generate recombinant 98P4B6 proteins in a baculovirus expression system, 98P4B6 ORF, or portions thereof, are cloned into the baculovirus transfer vector pBlueBac 4.5 (Invitrogen), which provides a His-tag at the N-terminus. Specifically, pBlueBac-98P4B6 is co-transfected with helper plasmid pBac-N-Blue (Invitrogen) into SF9 ([0917] Spodoptera frugiperda) insect cells to generate recombinant baculovirus (see Invitrogen instruction manual for details). Baculovirus is then collected from cell supernatant and purified by plaque assay.
• Recombinant 98P4B6 protein is then generated by infection of HighFive insect cells (Invitrogen) with purified baculovirus. Recombinant 98P4B6 protein can be detected using anti-98P4B6 or anti-His-tag antibody. 98P4B6 protein can be purified and used in various cell-based assays or as immunogen to generate polyclonal and monoclonal antibodies specific for 98P4B6. [0918]
Example 9 Antigenicity Profiles and Secondary Structure
• FIGS. [0919] 5(A-E), FIGS. 6(A-E), FIGS. 7(A-E), FIGS. 8(A-E), and FIGS. 9(A-E) depict graphically five amino acid profiles of 98P4B6 variants 1, 2, 5-7, each assessment available by accessing the ProtScale website located on the World Wide Web at .expasy.ch/cgi-bin/protscale.pl) on the ExPasy molecular biology server.
• These profiles: FIG. 5, Hydrophilicity, (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828); FIG. 6, Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol. 157:105-132); FIG. 7, Percentage Accessible Residues (Janin J., 1979 Nature 277:491-492); FIG. 8, Average Flexibility, (Bhaskaran R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255); FIG. 9, Beta-turn (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294); and optionally others available in the art, such as on the ProtScale website, were used to identify antigenic regions of each of the 98P4B6 variant proteins. Each of the above amino acid profiles of 98P4B6 variants were generated using the following ProtScale parameters for analysis: 1) A window size of 9; 2) 100% weight of the window edges compared to the window center; and, 3) amino acid profile values normalized to lie between 0 and 1. [0920]
• Hydrophilicity (FIG. 5), Hydropathicity (FIG. 6) and Percentage Accessible Residues (FIG. 7) profiles were used to determine stretches of hydrophilic amino acids (i.e., values greater than 0.5 on the Hydrophilicity and Percentage Accessible Residues profile, and values less than 0.5 on the Hydropathicity profile). Such regions are likely to be exposed to the aqueous environment, be present on the surface of the protein, and thus available for immune recognition, such as by antibodies. [0921]
• Average Flexibility (FIG. 8) and Beta-turn (FIG. 9) profiles determine stretches of amino acids (i.e., values greater than 0.5 on the Beta-turn profile and the Average Flexibility profile) that are not constrained in secondary structures such as beta sheets and alpha helices. Such regions are also more likely to be exposed on the protein and thus accessible to immune recognition, such as by antibodies. [0922]
• Antigenic sequences of the 98P4B6 variant proteins indicated, e.g., by the profiles set forth in FIGS. [0923] 5(A-E), FIGS. 6(A-E), FIGS. 7(A-E), FIGS. 8(A-E), and/or FIGS. 9(A-E) are used to prepare immunogens, either peptides or nucleic acids that encode them, to generate therapeutic and diagnostic anti-98P4B6 antibodies. The immunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more than 50 contiguous amino acids, or the corresponding nucleic acids that encode them, from the 98P4B6 protein variants 1, 2, 5-7 listed in FIGS. 2 and 3. In particular, peptide immunogens of the invention can comprise, a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profiles of FIG. 5; a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIGS. 6; a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profiles of FIG. 7; a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profiles on FIG. 8; and, a peptide region of at least 5 amino acids of FIGS. 2 and 3 in any whole number increment that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIGS. 9 . Peptide immunogens of the invention can also comprise nucleic acids that encode any of the forgoing.
• All immunogens of the invention, peptide or nucleic acid, can be embodied in human unit dose form, or comprised by a composition that includes a pharmaceutical excipient compatible with human physiology. [0924]
• The secondary structure of [0925] 98P4B6 protein variants 1, 2, 5-7, namely the predicted presence and location of alpha helices, extended strands, and random coils, is predicted from the primary amino acid sequence using the HNN—Hierarchical Neural Network method (Guermeur, 1997, htp:https://pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html), accessed from the ExPasy molecular biology server (located on the World Wide Web at .expasy.ch/tools/). The analysis indicates that 98P4B6 variant 1 is composed of 54.41% alpha helix, 12.33% extended strand, and 33.26% random coil (FIG. 13A). Variant 2 is composed of 17.78% alpha helix, 6.67% extended strand, and 75.56% random coil (FIG. 13B). Variant 5 is composed of 51.55% alpha helix, 13.13% extended strand, and 35.32% random coil (FIG. 13C). Variant 6 is composed of 54.49% alpha helix, 11.84% extended strand, and 33.67% random coil (FIG. 13D). Variant 7 is composed of 48.26% alpha helix, 15.28% extended strand, and 36.46% random coil (FIG. 13E).
• Analysis for the potential presence of transmembrane domains in the 98P4B6 variant proteins was carried out using a variety of transmembrane prediction algorithms accessed from the ExPasy molecular biology server (located on the World Wide Web at .expasy.ch/tools/). Shown graphically in FIGS. 13F and 13G are the results of analysis of [0926] variant 1 depicting the presence and location of 6 transmembrane domains using the TMpred program (FIG. 13F) and 5 transmembrane domains using the TMHMM program (FIG. 13G). Shown graphically in FIGS. 13H and 13I are the results of analysis of variant 2 depicting the presence and location of 1 transmembrane domains using the TMpred program (FIG. 13H) and no transmembrane domains using the TMHMM program (FIG. 13I). Shown graphically in FIGS. 13J and 13K are the results of analysis of variant 5 depicting the presence and location of 6 transmembrane domains using the TMpred program (FIG. 13J) and 4 transmembrane domains using the TMHMM program (FIG. 13K). Shown graphically in FIGS. 13L and 13M are the results of analysis of variant 6 depicting the presence and location of 6 transmembrane domains using the TMpred program (FIG. 13L) and 6 transmembrane domains using the TMHMM program (FIG. 13M). Shown graphically in FIGS. 13N and 13O are the results of analysis of variant 7 depicting the presence and location of 6 transmembrane domains using the TMpred program (FIG. 13N) and 4 transmembrane domains using the TMHMM program (FIG. 13O). The results of each program, namely the amino acids encoding the transmembrane domains are summarized in Table VI.
Example 10 Generation of 98P4B6 Polyclonal Antibodies
• Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. In addition to immunizing with a full length 98P4B6 protein variant, computer algorithms are employed in design of immunogens that, based on amino acid sequence analysis contain characteristics of being antigenic and available for recognition by the immune system of the immunized host (see Example 9 entitled “Antigenicity Profiles and Secondary Structure”). Such regions would be predicted to be hydrophilic, flexible, in beta-turn conformations, and be exposed on the surface of the protein (see, e.g., FIGS. [0927] 5(A-E), FIGS. 6(A & B), FIGS. 7(A-E), FIGS. 8(A -E), or FIGS. 9(A-E) for amino acid profiles that indicate such regions of 98P4B6 protein variants).
• For example, recombinant bacterial fusion proteins or peptides containing hydrophilic, flexible, beta-turn regions of 98P4B6 protein variants are used as antigens to generate polyclonal antibodies in New Zealand White rabbits or monoclonal antibodies as described in Example 11. For example, in [0928] 98P4B6 variant 1, such regions include, but are not limited to, amino acids 153-165, amino acids 240-260, and amino acids 345-358. In sequence specific for variant 2, such regions include, but are not limited to, amino acids 26-38. In sequence specific for variant 5, such regions include, but are not limited to, amino acids 400-410. In sequence specific for variant 6, such regions include, but are not limited to, amino acids 455-490. In sequence specific for variant 7, such regions include, but are not limited to, amino acids 451-465 and amino acids 472-498. It is useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin (KLH), serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. In one embodiment, a peptide encoding amino acids 153-165 of 98P4B6 variant 1 was conjugated to KLH and used to immunize a rabbit. Alternatively the immunizing agent may include all or portions of the 98P4B6 variant proteins, analogs or fusion proteins thereof. For example, the 98P4B6 variant 1 amino acid sequence can be fused using recombinant DNA techniques to any one of a variety of fusion protein partners that are well known in the art, such as glutathione-S-transferase (GST) and HIS tagged fusion proteins. In another embodiment, amino acids 2-204 of 98P4B6 variant 1 was fused to GST using recombinant techniques and the pGEX expression vector, expressed, purified and used to immunize a rabbit. Such fusion proteins are purified from induced bacteria using the appropriate affinity matrix.
• Other recombinant bacterial fusion proteins that may be employed include maltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulin constant region (see the section entitled “Production of 98P4B6 in Prokaryotic Systems” and Current Protocols In Molecular Biology, [0929] Volume 2, Unit 16, Frederick M. Ausubul et al. eds., 1995; Linsley, P. S., Brady, W., Urnes, M., Grosmaire, L., Damle, N., and Ledbetter, L.(1991) J. Exp. Med. 174, 561-566).
• In addition to bacterial derived fusion proteins, mammalian expressed protein antigens are also used. These antigens are expressed from mammalian expression vectors such as the Tag5 and Fc-fusion vectors (see the section entitled “Production of Recombinant 98P4B6 in Eukaryotic Systems”), and retain post-translational modifications such as glycosylations found in native protein. In one embodiment, amino acids 324-359 of [0930] variant 1, encoding an extracellular loop between transmembrane domains, is cloned into the Tag5 mammalian secretion vector. The recombinant protein is purified by metal chelate chromatography from tissue culture supernatants of 293T cells stably expressing the recombinant vector. The purified Tag5 98P4B6 protein is then used as immunogen.
• During the immunization protocol, it is useful to mix or emulsify the antigen in adjuvants that enhance the immune response of the host animal. Examples of adjuvants include, but are not limited to, complete Freund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). [0931]
• In a typical protocol, rabbits are initially immunized subcutaneously with up to 200 μg, typically 100-200 μg, of fusion protein or peptide conjugated to KLH mixed in complete Freund's adjuvant (CFA). Rabbits are then injected subcutaneously every two weeks with up to 200 μg, typically 100-200 μg, of the immunogen in incomplete Freund's adjuvant (IFA). Test bleeds are taken approximately 7-10 days following each immunization and used to monitor the titer of the antiserum by ELISA. [0932]
• To test reactivity and specificity of immune serum, such as the rabbit serum derived from immunization with the Tag5-[0933] 98P4B6 variant 1 protein, the full-length 98P4B6 variant 1 cDNA is cloned into pCDNA 3.1 myc-his expression vector (Invitrogen, see the Example entitled “Production of Recombinant 98P4B6 in Eukaryotic Systems”). After transfection of the constructs into 293T cells, cell lysates are probed with the anti-98P4B6 serum and with anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.) to determine specific reactivity to denatured 98P4B6 protein using the Western blot technique. Detection of 98P4B6 variant 1 protein expressed in 293T with polyclonal antibodies raised to a GST-fusion protein and peptide is shown in FIGS. 17B and 17C, respectively. In addition, the immune serum is tested by fluorescence microscopy, flow cytometry and immunoprecipitation against 293T and other recombinant 98P4B6-expressing cells to determine specific recognition of native protein. Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometric techniques using cells that endogenously express 98P4B6 are also carried out to test reactivity and specificity.
• Anti-serum from rabbits immunized with 98P4B6 variant fusion proteins, such as GST and MBP fusion proteins, are purified by depletion of antibodies reactive to the fusion partner sequence by passage over an affinity column containing the fusion partner either alone or in the context of an irrelevant fusion protein. For example, antiserum derived from a GST-[0934] 98P4B6 variant 1 fusion protein was first purified by passage over a column of GST protein covalently coupled to AffiGel matrix (BioRad, Hercules, Calif.). The antiserum is then affinity purified by passage over a column composed of a MBP-98P4B6 fusion protein covalently coupled to Affigel matrix. The serum is then further purified by protein G affinity chromatography to isolate the IgG fraction. Sera from other His-tagged antigens and peptide immunized rabbits as well as fusion partner depleted sera are affinity purified by passage over a column matrix composed of the original protein immunogen or free peptide, such as the anti-peptide polyclonal antibody used in FIG. 17C.
Example 11 Generation of 98P4B6 Monoclonal Antibodies (mAbs)
• In one embodiment, therapeutic mAbs to 98P4B6 variants comprise those that react with epitopes specific for each variant protein or specific to sequences in common between the variants that would disrupt or modulate the biological function of the 98P4B6 variants, for example those that would disrupt the interaction with ligands and binding partners. Immunogens for generation of such mAbs include those designed to encode or contain the entire 98P4B6 protein variant sequence, regions of the 98P4B6 protein variants predicted to be antigenic from computer analysis of the amino acid sequence (see, e.g., FIGS. [0935] 5(A-E), FIGS. 6(A-E), FIGS. 7(A-E), FIGS. 8(A-E), or FIGS. 9(A-E), and Example 9 entitled “Antigenicity Profiles and Secondary Structure”). Immunogens include peptides, recombinant bacterial proteins, and mammalian expressed Tag 5 proteins and human and murine IgG FC fusion proteins. In addition, cells engineered to express high levels of a respective 98P4B6 variant, such as 293T-98P4B6 variant 1 or 300.19-98P4B6 variant 1 murine Pre-B cells, are used to immunize mice.
• To generate mAbs to a 98P4B6 variant, mice are first immunized intraperitoneally (IP) with, typically, 10-50 μg of protein immunogen or 10[0936] ⁷ 98P4B6-expressing cells mixed in complete Freund's adjuvant. Mice are then subsequently immunized IP every 2-4 weeks with, typically, 10-50 μg of protein immunogen or 10⁷ cells mixed in incomplete Freund's adjuvant. Alternatively, MPL-TDM adjuvant is used in immunizations. In addition to the above protein and cell-based immunization strategies, a DNA-based immunization protocol is employed in which a mammalian expression vector encoding a 98P4B6 variant sequence is used to immunize mice by direct injection of the plasmid DNA. For example, amino acids 324-359 is cloned into the Tag5 mammalian secretion vector and the recombinant vector is used as immunogen. In another example the same amino acids are cloned into an Fc-fusion secretion vector in which the 98P4B6 variant 1 sequence is fused at the amino-terminus to an IgK leader sequence and at the carboxyl-terminus to the coding sequence of the human or murine IgG Fc region. This recombinant vector is then used as immunogen. The plasmid immunization protocols are used in combination with purified proteins expressed from the same vector and with cells expressing the respective 98P4B6 variant.
• During the immunization protocol, test bleeds are taken 7-10 days following an injection to monitor titer and specificity of the immune response. Once appropriate reactivity and specificity is obtained as determined by ELISA, Western blotting, immunoprecipitation, fluorescence microscopy, and flow cytometric analyses, fusion and hybridoma generation is then carried out with established procedures well known in the art (see, e.g., Harlow and Lane, 1988). [0937]
• In one embodiment for generating 98P4B6 monoclonal antibodies, a Tag5-[0938] 98P4B6 variant 1 antigen encoding amino acids 324-359, is expressed and purified from stably transfected 293T cells. Balb C mice are initially immunized intraperitoneally with 25 μg of the Tag5-98P4B6 variant 1 protein mixed in complete Freund's adjuvant. Mice are subsequently immunized every two weeks with 25 μg of the antigen mixed in incomplete Freund's adjuvant for a total of three immunizations. ELISA using the Tag5 antigen determines the titer of serum from immunized mice. Reactivity and specificity of serum to full length 98P4B6 variant 1 protein is monitored by Western blotting, immunoprecipitation and flow cytometry using 293T cells transfected with an expression vector encoding the 98P4B6 variant 1 cDNA (see e.g., the Example entitled “Production of Recombinant 98P4B6 in Eukaryotic Systems” and FIG. 20). Other recombinant 98P4B6 variant 1-expressing cells or cells endogenously expressing 98P4B6 variant 1 are also used. Mice showing the strongest reactivity are rested and given a final injection of Tag5 antigen in PBS and then sacrificed four days later. The spleens of the sacrificed mice are harvested and fused to SPO/2 myeloma cells using standard procedures (Harlow and Lane, 1988). Supernatants from HAT selected growth wells are screened by ELISA, Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometry to identify 98P4B6 specific antibody-producing clones.
• To generate monoclonal antibodies that are specific for each 98P4B6 variant protein, immunogens are designed to encode sequences unique for each variant. In one embodiment, a Tag5 antigen encoding the full sequence of 98P4B6 variant 2 (AA1-45) is produced, purified and used as immunogen to derive monoclonal antibodies specific to [0939] 98P4B6 variant 2. In another embodiment, an antigenic peptide composed of amino acids 400-410 of 98P4B6 variant 5 is coupled to KLH and used as immunogen. In another embodiment, a GST fusion protein encoding amino acids 455-490 of 98P4B6 of variant 6 is used as immunogen to derive variant 6 specific monoclonal antibodies. In another embodiment, a peptide composed of amino acids 472-498 of variant 7 is coupled to KLH and used as immunogen to generate variant 7 specific monoclonal antibodies. Hybridoma supernatants are then screened on the respective antigen and then further screened on cells expressing the specific variant and cross-screened on cells expressing the other variants to derive variant-specific monoclonal antibodies.
• The binding affinity of a 98P4B6 variant monoclonal antibody is determined using standard technologies. Affinity measurements quantify the strength of antibody to epitope binding and are used to help define which 98P4B6 variant monoclonal antibodies preferred for diagnostic or therapeutic use, as appreciated by one of skill in the art. The BlAcore system (Uppsala, Sweden) is a preferred method for determining binding affinity. The BlAcore system uses surface plasmon resonance (SPR, Welford K. 1991, Opt. Quant. Elect. 23:1; Morton and Myszka, 1998, Methods in Enzymology 295: 268) to monitor biomolecular interactions in real time. BlAcore analysis conveniently generates association rate constants, dissociation rate constants, equilibrium dissociation constants, and affinity constants. [0940]
Example 12 HLA Class I and Class II Binding Assays
• HLA class I and class II binding assays using purified HLA molecules are performed in accordance with disclosed protocols (e.g., PCT publications WO 94/20127 and WO 94/03205; Sidney et al., [0941] Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, purified MHC molecules (5 to 500 nM) are incubated with various unlabeled peptide inhibitors and 1-10 nM ¹²⁵I-radiolabeled probe peptides as described. Following incubation, MHC-peptide complexes are separated from free peptide by gel filtration and the fraction of peptide bound is determined. Typically, in preliminary experiments, each MHC preparation is titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays are performed using these HLA concentrations.
• Since under these conditions [label]<[HLA] and IC[0942] ₅₀≧[HLA], the measured IC₅₀ values are reasonable approximations of the true K_D values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC₅₀ of a positive control for inhibition by the IC₅₀ for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC₅₀ nM values by dividing the IC₅₀ nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation is accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.
• Binding assays as outlined above may be used to analyze HLA supermotif and/or HLA motif-bearing peptides (see Table IV). [0943]
Example 13 Identification of HLA Supermotif- and Motif-Bearing CTL Candidate Epitopes
• HLA vaccine compositions of the invention can include multiple epitopes. The multiple epitopes can comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification and confirmation of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Calculation of population coverage is performed using the strategy described below. [0944]
• Computer Searches and Algorithms for Identification of Supermotif and/or Motif-Bearing Epitopes [0945]
• The searches performed to identify the motif-bearing peptide sequences in the Example entitled “Antigenicity Profiles” and Tables VIII-XXI and XXII-XLIX employ the protein sequence data from the gene product of 98P4B6 set forth in FIGS. 2 and 3, the specific search peptides used to generate the tables are listed in Table VII. [0946]
• Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs are performed as follows. All translated 98P4B6 protein sequences are analyzed using a text string search software program to identify potential peptide sequences containing appropriate HLA binding motifs; such programs are readily produced in accordance with information in the art in view of known motif/supermotif disclosures. Furthermore, such calculations can be made mentally. [0947]
• Identified A2-, A3-, and DR-supermotif sequences are scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms account for the impact of different amino acids at different positions, and are essentially based on the premise that the overall affinity (or ΔG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type: [0948]
• “ΔG”=a _1i ×a _2i ×a _3i . . . ×a _ni
• where a[0949] _ji is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount ji to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide.
• The method of derivation of specific algorithm coefficients has been described in Gulukota et al., [0950] J. Mol. Biol. 267:1258-126, 1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al., J. Immunol 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate of j_i. For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.
• Selection of HLA-A2 Supertype Cross-Reactive Peptides [0951]
• Protein sequences from 98P4B6 are scanned utilizing motif identification software, to identify 8-, 9- 10- and 11-mer sequences containing the HLA-A2-supermotif main anchor specificity. Typically, these sequences are then scored using the protocol described above and the peptides corresponding to the positive-scoring sequences are synthesized and tested for their capacity to bind purified HLA-A*0201 molecules in vitro (HLA-A*0201 is considered a prototype A2 supertype molecule). [0952]
• These peptides are then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). Peptides that bind to at least three of the five A2-supertype alleles tested are typically deemed A2-supertype cross-reactive binders. Preferred peptides bind at an affinity equal to or less than 500 nM to three or more HLA-A2 supertype molecules. [0953]
• Selection of HLA-A3 Supermotif-Bearing Epitopes [0954]
• The 98P4B6 protein sequence(s) scanned above is also examined for the presence of peptides with the HLA-A3-supermotif primary anchors. Peptides corresponding to the HLA A3 supermotif-bearing sequences are then synthesized and tested for binding to HLA-A*0301 and HLA-A*1101 molecules, the molecules encoded by the two most prevalent A3-supertype alleles. The peptides that bind at least one of the two alleles with binding affinities of ≦500 nM, often ≦200 nM, are then tested for binding cross-reactivity to the other common A3-supertype alleles (e.g., A*3101, A*3301, and A*6801) to identify those that can bind at least three of the five HLA-A3-supertype molecules tested. [0955]
• Selection of HLA-B7 Supermotif Bearing Epitopes [0956]
• The 98P4B6 protein(s) scanned above is also analyzed for the presence of 8-, 9- 10-, or 11-mer peptides with the HLA-B7-supermotif. Corresponding peptides are synthesized and tested for binding to HLA-B*0702, the molecule encoded by the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Peptides binding B*0702 with IC[0957] ₅₀ of ≦500 nM are identified using standard methods. These peptides are then tested for binding to other common B7-supertype molecules (e.g., B*3501, B*5101, B*5301, and B*5401). Peptides capable of binding to three or more of the five B7-supertype alleles tested are thereby identified.
• Selection of A1 and A24 Motif-Bearing Epitopes [0958]
• To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into vaccine compositions. An analysis of the 98P4B6 protein can also be performed to identify HLA-A1- and A24-motif-containing sequences. [0959]
• High affinity and/or cross-reactive binding epitopes that bear other motif and/or supermotifs are identified using analogous methodology. [0960]
Example 14 Confirmation of Immunogenicity
• Cross-reactive candidate CTL A2-supermotif-bearing peptides that are identified as described herein are selected to confirm in vitro immunogenicity. Confirmation is performed using the following methodology: [0961]
• Target Cell Lines for Cellular Screening: [0962]
• The .221A2.1 cell line, produced by transferring the HLA-A2.1 gene into the HLA-A, -B, -C null mutant human B-lymphoblastoid cell line 721.221, is used as the peptide-loaded target to measure activity of HLA-A2.1-restricted CTL. This cell line is grown in RPMI-1640 medium supplemented with antibiotics, sodium pyruvate, nonessential amino acids and 10% (v/v) heat inactivated FCS. Cells that express an antigen of interest, or transfectants comprising the gene encoding the antigen of interest, can be used as target cells to confirm the ability of peptide-specific CTLs to recognize endogenous antigen. [0963]
• Primary CTL Induction Cultures: [0964]
• Generation of Dendritic Cells (DC): [0965]
• PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed twice and resuspended in complete medium (RPMI-1640 plus 5% AB human serum, non-essential amino acids, sodium pyruvate, L-glutamine and penicillin/streptomycin). The monocytes are purified by plating 10×10[0966] ⁶ PBMC/well in a 6-well plate. After 2 hours at 37° C., the non-adherent cells are removed by gently shaking the plates and aspirating the supernatants. The wells are washed a total of three times with 3 ml RPMI to remove most of the non-adherent and loosely adherent cells. Three ml of complete medium containing 50 ng/ml of GM-CSF and 1,000 U/ml of IL-4 are then added to each well. TNFα is added to the DCs on day 6 at 75 ng/ml and the cells are used for CTL induction cultures on day 7.
• Induction of CTL with DC and Peptide: [0967]
• CD8+ T-cells are isolated by positive selection with Dynal immunomagnetic beads (Dynabeads® M450) and the detacha-bead® reagent. Typically about 200-250×10[0968] ⁶ PBMC are processed to obtain 24×10⁶ CD8⁺ T-cells (enough for a 48-well plate culture). Briefly, the PBMCs are thawed in RPMI with 30 μg/ml DNAse, washed once with PBS containing 1% human AB serum and resuspended in PBS/1% AB serum at a concentration of 20×10⁶ cells/ml. The magnetic beads are washed 3 times with PBS/AB serum, added to the cells (140 μl beads/20×10⁶ cells) and incubated for 1 hour at 4° C. with continuous mixing. The beads and cells are washed 4× with PBS/AB serum to remove the nonadherent cells and resuspended at 100×10⁶ cells/ml (based on the original cell number) in PBS/AB serum containing 100 μl/ml detacha-bead® reagent and 30 μg/ml DNAse. The mixture is incubated for 1 hour at room temperature with continuous mixing. The beads are washed again with PBS/AB/DNAse to collect the CD8+ T-cells. The DC are collected and centrifuged at 1300 rpm for 5-7 minutes, washed once with PBS with 1% BSA, counted and pulsed with 40 μg/ml of peptide at a cell concentration of 1-2×10⁶/ml in the presence of 3 μg/ml β₂-microglobulin for 4 hours at 20° C. The DC are then irradiated (4,200 rads), washed 1 time with medium and counted again.
• Setting Up Induction Cultures: [0969]
• 0.25 ml cytokine-generated DC (at 1×10[0970] ⁵ cells/ml) are co-cultured with 0.25 ml of CD8+ T-cells (at 2×10⁶ cell/ml) in each well of a 48-well plate in the presence of 10 ng/ml of IL-7. Recombinant human IL-10 is added the next day at a final concentration of 10 ng/ml and rhuman IL-2 is added 48 hours later at 10 IU/ml.
• Restimulation of the Induction Cultures with Peptide-Pulsed Adherent Cells: [0971]
• Seven and fourteen days after the primary induction, the cells are restimulated with peptide-pulsed adherent cells. The PBMCs are thawed and washed twice with RPMI and DNAse. The cells are resuspended at 5×10[0972] ⁶ cells/ml and irradiated at ˜4200 rads. The PBMCs are plated at 2×10⁶ in 0.5 ml complete medium per well and incubated for 2 hours at 37° C. The plates are washed twice with RPMI by tapping the plate gently to remove the nonadherent cells and the adherent cells pulsed with 10 μg/ml of peptide in the presence of 3 μg/ml β₂ microglobulin in 0.25 ml RPMI/5%AB per well for 2 hours at 37° C. Peptide solution from each well is aspirated and the wells are washed once with RPMI. Most of the media is aspirated from the induction cultures (CD8+ cells) and brought to 0.5 ml with fresh media. The cells are then transferred to the wells containing the peptide-pulsed adherent cells. Twenty four hours later recombinant human IL-10 is added at a final concentration of 10 ng/ml and recombinant human IL2 is added the next day and again 2-3 days later at 50 IU/ml (Tsai et al., Critical Reviews in Immunology 18(1-2):65-75, 1998). Seven days later, the cultures are assayed for CTL activity in a ⁵¹Cr release assay. In some experiments the cultures are assayed for peptide-specific recognition in the in situ IFNγ ELISA at the time of the second restimulation followed by assay of endogenous recognition 7 days later. After expansion, activity is measured in both assays for a side-by-side comparison.
• Measurement of CTL Lytic Activity by [0973] ⁵¹Cr Release.
• Seven days after the second restimulation, cytotoxicity is determined in a standard (5 hr) [0974] ⁵¹Cr release assay by assaying individual wells at a single E:T. Peptide-pulsed targets are prepared by incubating the cells with 10 μg/ml peptide overnight at 37° C.
• Adherent target cells are removed from culture flasks with trypsin-EDTA. Target cells are labeled with 200 μCi of [0975] ⁵¹Cr sodium chromate (Dupont, Wilmington, Del.) for 1 hour at 37° C. Labeled target cells are resuspended at 10⁶ per ml and diluted 1:10 with K562 cells at a concentration of 3.3×10⁶/ml (an NK-sensitive erythroblastoma cell line used to reduce non-specific lysis). Target cells (100 μl) and effectors (100 μl) are plated in 96 well round-bottom plates and incubated for 5 hours at 37° C. At that time, 100 μl of supernatant are collected from each well and percent lysis is determined according to the formula:
• [(cpm of the test sample−cpm of the spontaneous ⁵¹Cr release sample)/(cpm of the maximal ⁵¹Cr release sample−cpm of the spontaneous ⁵¹Cr release sample)]×100.
• Maximum and spontaneous release are determined by incubating the labeled targets with 1% Triton X-100 and media alone, respectively. A positive culture is defined as one in which the specific lysis (sample-background) is 10% or higher in the case of individual wells and is 15% or more at the two highest E:T ratios when expanded cultures are assayed. [0976]
• In situ Measurement of Human IFNγ Production as an Indicator of Peptide-specific and Endogenous Recognition [0977]
• [0978] Immulon 2 plates are coated with mouse anti-human IFNγ monoclonal antibody (4 μg/ml 0.1M NaHCO₃, pH8.2) overnight at 4° C. The plates are washed with Ca²⁺, Mg²⁺-free PBS/0.05% Tween 20 and blocked with PBS/10% FCS for two hours, after which the CTLs (100 μl/well) and targets (100 μl/well) are added to each well, leaving empty wells for the standards and blanks (which received media only). The target cells, either peptide-pulsed or endogenous targets, are used at a concentration of 1×10⁶ cells/ml. The plates are incubated for 48 hours at 37° C. with 5% CO₂.
• Recombinant human IFN-gamma is added to the standard wells starting at 400 pg or 1200 pg/100 microliter/well and the plate incubated for two hours at 37° C. The plates are washed and 100 μl of biotinylated mouse anti-human IFN-gamma monoclonal antibody (2 microgram/ml in PBS/3%FCS/0.05% Tween 20) are added and incubated for 2 hours at room temperature. After washing again, 100 microliter HRP-streptavidin (1:4000) are added and the plates incubated for one hour at room temperature. The plates are then washed 6× with wash buffer, 100 microliter/well developing solution (TMB 1:1) are added, and the plates allowed to develop for 5-15 minutes. The reaction is stopped with 50 microliter/well 1 M H[0979] ₃PO₄ and read at OD450. A culture is considered positive if it measured at least 50 pg of IFN-gamma/well above background and is twice the background level of expression.
• CTL Expansion. [0980]
• Those cultures that demonstrate specific lytic activity against peptide-pulsed targets and/or tumor targets are expanded over a two week period with anti-CD3. Briefly, 5×10[0981] ⁴ CD8+ cells are added to a T25 flask containing the following: 1×10⁶ irradiated (4,200 rad) PBMC (autologous or allogeneic) per ml, 2×10⁵ irradiated (8,000 rad) EBV-transformed cells per ml, and OKT3 (anti-CD3) at 30 ng per ml in RPMI-1640 containing 10% (v/v) human AB serum, non-essential amino acids, sodium pyruvate, 25 μM 2-mercaptoethanol, L-glutamine and penicillin/streptomycin. Recombinant human IL2 is added 24 hours later at a final concentration of 200 IU/ml and every three days thereafter with fresh media at 50 IU/ml. The cells are split if the cell concentration exceeds 1×10⁶/ml and the cultures are assayed between days 13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the ⁵¹Cr release assay or at 1×10⁶/ml in the in situ IFNγ assay using the same targets as before the expansion.
• Cultures are expanded in the absence of anti-CD3+ as follows. Those cultures that demonstrate specific lytic activity against peptide and endogenous targets are selected and 5×10[0982] ⁴ CD8⁺ cells are added to a T25 flask containing the following: 1×10⁶ autologous PBMC per ml which have been peptide-pulsed with 10 μg/ml peptide for two hours at 37° C. and irradiated (4,200 rad); 2×10⁵ irradiated (8,000 rad) EBV-transformed cells per ml RPMI-1640 containing 10%(v/v) human AB serum, non-essential M, sodium pyruvate, 25 mM 2-ME, L-glutamine and gentamicin.
• Immunogenicity of A2 Supermotif-Bearing Peptides [0983]
• A2-supermotif cross-reactive binding peptides are tested in the cellular assay for the ability to induce peptide-specific CTL in normal individuals. In this analysis, a peptide is typically considered to be an epitope if it induces peptide-specific CTLs in at least individuals, and preferably, also recognizes the endogenously expressed peptide. [0984]
• Immunogenicity can also be confirmed using PBMCs isolated from patients bearing a tumor that expresses 98P4B6. Briefly, PBMCs are isolated from patients, re-stimulated with peptide-pulsed monocytes and assayed for the ability to recognize peptide-pulsed target cells as well as transfected cells endogenously expressing the antigen. [0985]
• Evaluation of A*03/A11 Immunogenicity [0986]
• HLA-A3 supermotif-bearing cross-reactive binding peptides are also evaluated for immunogenicity using methodology analogous for that used to evaluate the immunogenicity of the HLA-A2 supermotif peptides. [0987]
• Evaluation of B7 Immunogenicity [0988]
• Immunogenicity screening of the B7-supertype cross-reactive binding peptides identified as set forth herein are confirmed in a manner analogous to the confirmation of A2- and A3-supermotif-bearing peptides. [0989]
• Peptides bearing other supermotifs/motifs, e.g., HLA-A1, HLA-A24 etc. are also confirmed using similar methodology [0990]
Example 15 Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs
• HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analoged to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analoging peptides to exhibit modulated binding affinity are set forth in this example. [0991]
• Analoging at Primary Anchor Residues [0992]
• Peptide engineering strategies are implemented to further increase the cross-reactivity of the epitopes. For example, the main anchors of A2-supermotif-bearing peptides are altered, for example, to introduce a preferred L, I, V, or M at [0993] position 2, and I or V at the C-terminus.
• To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A2 supertype allele A*0201, then, if A*0201 binding capacity is maintained, for A2-supertype cross-reactivity. [0994]
• Alternatively, a peptide is confirmed as binding one or all supertype members and then analoged to modulate binding affinity to any one (or more) of the supertype members to add population coverage. [0995]
• The selection of analogs for immunogenicity in a cellular screening analysis is typically further restricted by the capacity of the parent wild type (WT) peptide to bind at least weakly, i.e., bind at an IC[0996] ₅₀ of 5000 nM or less, to three of more A2 supertype alleles. The rationale for this requirement is that the WT peptides must be present endogenously in sufficient quantity to be biologically relevant. Analoged peptides have been shown to have increased immunogenicity and cross-reactivity by T cells specific for the parent epitope (see, e.g., Parkhurst et al., J. Immunol. 157:2539, 1996; and Pogue et al., Proc. Natl. Acad. Sci. USA 92:8166,1995).
• In the cellular screening of these peptide analogs, it is important to confirm that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, target cells that endogenously express the epitope. [0997]
• Analoging of HLA-A3 and B7-Supermotif-Bearing Peptides [0998]
• Analogs of HLA-A3 supermotif-bearing epitopes are generated using strategies similar to those employed in analoging HLA-A2 supermotif-bearing peptides. For example, peptides binding to ⅗ of the A3-supertype molecules are engineered at primary anchor residues to possess a preferred residue (V, S, M, or A) at [0999] position 2.
• The analog peptides are then tested for the ability to bind A*03 and A*11 (prototype A3 supertype alleles). Those peptides that demonstrate ≦500 nM binding capacity are then confirmed as having A3-supertype cross-reactivity. [1000]
• Similarly to the A2- and A3-motif bearing peptides, peptides binding 3 or more B7-supertype alleles can be improved, where possible, to achieve increased cross-reactive binding or greater binding affinity or binding half life. B7 supermotif-bearing peptides are, for example, engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney et al. ([1001] J. Immunol. 157:3480-3490, 1996).
• Analoging at primary anchor residues of other motif and/or supermotif-bearing epitopes is performed in a like manner. [1002]
• The analog peptides are then be confirmed for immunogenicity, typically in a cellular screening assay. Again, it is generally important to demonstrate that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, targets that endogenously express the epitope. [1003]
• Analoging at Secondary Anchor Residues [1004]
• Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of a B7 supermotif-bearing peptide with an F residue at [1005] position 1 is analyzed. The peptide is then analoged to, for example, substitute L for F at position 1. The analoged peptide is evaluated for increased binding affinity, binding half life and/or increased cross-reactivity. Such a procedure identifies analoged peptides with enhanced properties.
• Engineered analogs with sufficiently improved binding capacity or cross-reactivity can also be tested for immunogenicity in HLA-B7-transgenic mice, following for example, IFA immunization or lipopeptide immunization. Analoged peptides are additionally tested for the ability to stimulate a recall response using PBMC from patients with 98P4B6-expressing tumors. [1006]
• Other Analoging Strategies [1007]
• Another form of peptide analoging, unrelated to anchor positions, involves the substitution of a cysteine with α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substitution of α-amino butyric acid for cysteine not only alleviates this problem, but has been shown to improve binding and crossbinding capabilities in some instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999). [1008]
• Thus, by the use of single amino acid substitutions, the binding properties and/or cross-reactivity of peptide ligands for HLA supertype molecules can be modulated. [1009]
Example 16 Identification and Confirmation of 98P4B6-Derived Sequences with HLA-DR Binding Motifs
• Peptide epitopes bearing an HLA class II supermotif or motif are identified and confirmed as outlined below using methodology similar to that described for HLA Class I peptides. [1010]
• Selection of HLA-DR-Supermotif-Bearing Epitopes. [1011]
• To identify 98P4B6-derived, HLA class II HTL epitopes, a 98P4B6 antigen is analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences are selected comprising a DR-supermotif, comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total). [1012]
• Protocols for predicting peptide binding to DR molecules have been developed (Southwood et al., [1013] J. Immunol. 160:3363-3373, 1998). These protocols, specific for individual DR molecules, allow the scoring, and ranking, of 9-mer core regions. Each protocol not only scores peptide sequences for the presence of DR-supermotif primary anchors (i.e., at position 1 and position 6) within a 9-mer core, but additionally evaluates sequences for the presence of secondary anchors. Using allele-specific selection tables (see, e.g., Southwood et al., ibid.), it has been found that these protocols efficiently select peptide sequences with a high probability of binding a particular DR molecule. Additionally, it has been found that performing these protocols in tandem, specifically those for DR1, DR4w4, and DR7, can efficiently select DR cross-reactive peptides.
• The 98P4B6-derived peptides identified above are tested for their binding capacity for various common HLA-DR molecules. All peptides are initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least two of these three DR molecules are then tested for binding to DR2w2 β1, DR2w2 β2, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least two of the four secondary panel DR molecules, and thus cumulatively at least four of seven different DR molecules, are screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least seven of the ten DR molecules comprising the primary, secondary, and tertiary screening assays are considered cross-reactive DR binders. 98P4B6-derived peptides found to bind common HLA-DR alleles are of particular interest. [1014]
• Selection of DR3 Motif Peptides [1015]
• Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is a relevant criterion in the selection of HTL epitopes. Thus, peptides shown to be candidates may also be assayed for their DR3 binding capacity. However, in view of the binding specificity of the DR3 motif, peptides binding only to DR3 can also be considered as candidates for inclusion in a vaccine formulation. [1016]
• To efficiently identify peptides that bind DR3, target 98P4B6 antigens are analyzed for sequences carrying one of the two DR3-specific binding motifs reported by Geluk et al. ([1017] J. Immunol. 152:5742-5748, 1994). The corresponding peptides are then synthesized and confirmed as having the ability to bind DR3 with an affinity of 1 μM or better, i.e., less than 1 μM. Peptides are found that meet this binding criterion and qualify as HLA class II high affinity binders.
• DR3 binding epitopes identified in this manner are included in vaccine compositions with DR supermotif-bearing peptide epitopes. [1018]
• Similarly to the case of HLA class I motif-bearing peptides, the class II motif-bearing peptides are analoged to improve affinity or cross-reactivity. For example, aspartic acid at position 4 of the 9-mer core sequence is an optimal residue for DR3 binding, and substitution for that residue often improves [1019] DR 3 binding.
Example 17 Immunogenicity of 98P4B6-Derived HTL Epitopes
• This example determines immunogenic DR supermotif- and DR3 motif-bearing epitopes among those identified using the methodology set forth herein. [1020]
• Immunogenicity of HTL epitopes are confirmed in a manner analogous to the determination of immunogenicity of CTL epitopes, by assessing the ability to stimulate HTL responses and/or by using appropriate transgenic mouse models. Immunogenicity is determined by screening for: 1.) in vitro primary induction using normal PBMC or 2.) recall responses from patients who have 98P4B6-expressing tumors. [1021]
Example 18 Calculation of Phenotypic Frequencies of HLA-Supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage
• This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs. [1022]
• In order to analyze population coverage, gene frequencies of HLA alleles are determined. Gene frequencies for each HLA allele are calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., [1023] Human Immunol 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies are calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1−(1−Cgf)²].
• Where frequency data is not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies is assumed. To obtain total potential supertype population coverage no linkage disequilibrium is assumed, and only alleles confirmed to belong to each of the supertypes are included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations are made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3, A11, A31, A*3301, and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, and B*5602). [1024]
• Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups. Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, A1 is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%, see, e.g., Table IV (G). An analogous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes. [1025]
• Immunogenicity studies in humans (e.g., Bertoni et al., [1026] J. Clin. Invest. 100:503, 1997; Doolan et al., Immunity 7:97, 1997; and Threlkeld et al., J. Immunol. 159:1648, 1997) have shown that highly cross-reactive binding peptides are almost always recognized as epitopes. The use of highly cross-reactive binding peptides is an important selection criterion in identifying candidate epitopes for inclusion in a vaccine that is immunogenic in a diverse population.
• With a sufficient number of epitopes (as disclosed herein and from the art), an average population coverage is predicted to be greater than 95% in each of five major ethnic populations. The game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994), can be used to estimate what percentage of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize the vaccine epitopes described herein. A preferred .percentage is 90%. A more preferred percentage is 95%. [1027]
Example 19 CTL Recognition of Endogenously Processed Antigens after Priming
• This example confirms that CTL induced by native or analoged peptide epitopes identified and selected as described herein recognize endogenously synthesized, i.e., native antigens. [1028]
• Effector cells isolated from transgenic mice that are immunized with peptide epitopes, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on [1029] ⁵¹Cr labeled Jurkat-A2.1/K^b target cells in the absence or presence of peptide, and also tested on ⁵¹Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with 98P4B6 expression vectors.
• The results demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized 98P4B6 antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that are being evaluated. In addition to HLA-A*0201/K[1030] ^b transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.
Example 20 Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice
• This example illustrates the induction of CTLs and HTLs in transgenic mice, by use of a 98P4B6-derived CTL and HTL peptide vaccine compositions. The vaccine composition used herein comprise peptides to be administered to a patient with a 98P4B6-expressing tumor. The peptide composition can comprise multiple CTL and/or HTL epitopes. The epitopes are identified using methodology as described herein. This example also illustrates that enhanced immunogenicity can be achieved by inclusion of one or more HTL epitopes in a CTL vaccine composition; such a peptide composition can comprise an HTL epitope conjugated to a CTL epitope. The CTL epitope can be one that binds to multiple HLA family members at an affinity of 500 nM or less, or analogs of that epitope. The peptides may be lipidated, if desired. [1031]
• Immunization Procedures: [1032]
• Immunization of transgenic mice is performed as described (Alexander et al., [1033] J. Immunol. 159:4753-4761, 1997). For example, A2/K^b mice, which are transgenic for the human HLA A2.1 allele and are used to confirm the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, and are primed subcutaneously (base of the tail) with a 0.1 ml of peptide in Incomplete Freund's Adjuvant, or if the peptide composition is a lipidated CTL/HTL conjugate, in DMSO/saline, or if the peptide composition is a polypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.
• Cell Lines: [1034]
• Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/K[1035] ^b chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991)
• In Vitro CTL Activation: [1036]
• One week after priming, spleen cells (30×10[1037] ⁶ cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×10⁶ cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.
• Assay for cytotoxic activity: Target cells (1.0 to 1.5×10[1038] ⁶) are incubated at 37° C. in the presence of 200 μl of ⁵¹Cr. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/mi. For the assay, 10^{4 51}Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a six hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % ⁵¹Cr release data is expressed as lytic units/10⁶ cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a six hour ⁵¹Cr release assay. To obtain specific lytic units/10⁶, the lytic units/10⁶ obtained in the absence of peptide is subtracted from the lytic units/10⁶ obtained in the presence of peptide. For example, if 30% ⁵¹Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×10⁵ effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×10⁴ effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [(1150,000)−(1/500,000)]×10⁶=18 LU.
• The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using, for example, CTL epitopes as outlined above in the Example entitled “Confirmation of Immunogenicity.” Analyses similar to this may be performed to confirm the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures, it is found that a CTL response is induced, and concomitantly that an HTL response is induced upon administration of such compositions. [1039]
Example 21 Selection of CTL and HTL Epitopes for Inclusion in a 98P4B6-Specific Vaccine
• This example illustrates a procedure for selecting peptide epitopes for vaccine compositions of the invention. The peptides in the composition can be in the form of a nucleic acid sequence, either single or one or more sequences (ie., minigene) that encodes peptide(s), or can be single and/or polyepitopic peptides. [1040]
• The following principles are utilized when selecting a plurality of epitopes for inclusion in a vaccine composition. Each of the following principles is balanced in order to make the selection. [1041]
• Epitopes are selected which, upon administration, mimic immune responses that are correlated with 98P4B6 clearance. The number of epitopes used depends on observations of patients who spontaneously clear 98P4B6. For example, if it has been observed that patients who spontaneously clear 98P4B6-expressing cells generate an immune response to at least three (3) epitopes from 98P4B6 antigen, then at least three epitopes should be included for HLA class I. A similar rationale is used to determine HLA class II epitopes. [1042]
• Epitopes are often selected that have a binding affinity of an IC[1043] ₅₀ of 500 nM or less for an HLA class I molecule, or for class II, an IC₅₀ of 1000 nM or less; or HLA Class I peptides with high binding scores from the BIMAS web site, at URL bimas.dcrt.nih.gov/.
• In order to achieve broad coverage of the vaccine through out a diverse population, sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. In one embodiment, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess breadth, or redundancy, of population coverage. [1044]
• When creating polyepitopic compositions, or a minigene that encodes same, it is typically desirable to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same, as those employed when selecting a peptide comprising nested epitopes. For example, a protein sequence for the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. Epitopes may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. A multi-epitopic, peptide can be generated synthetically, recombinantiy, or via cleavage from the native source. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes. This embodiment provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent the creating of any analogs) directs the immune response to multiple peptide sequences that are actually present in 98P4B6, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions. Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length. [1045]
• A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude to an immune response that controls or clears cells that bear or overexpress 98P4B6. [1046]
Example 22 Construction of “Minigene” Multi-Epitope DNA Plasmids
• This example discusses the construction of a minigene expression plasmid. Minigene plasmids may, of course, contain various configurations of B cell, CTL and/or HTL epitopes or epitope analogs as described herein. [1047]
• A minigene expression plasmid typically includes multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. HLA class I supermotif or motif-bearing peptide epitopes derived 98P4B6, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from 98P4B6 to provide broad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector. [1048]
• Such a construct may additionally include sequences that direct the HTL epitopes to the endoplasmic reticulum. For example, the Ii protein may be fused to one or more HTL epitopes as described in the art, wherein the CLIP sequence of the li protein is removed and replaced with an HLA class II epitope sequence so that HLA class II epitope is directed to the endoplasmic reticulum, where the epitope binds to an HLA class II molecules. [1049]
• This example illustrates the methods to be used for construction of a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art. [1050]
• The minigene DNA plasmid of this example contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector. [1051]
• Overlapping oligonucleotides that can, for example, average about 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min. [1052]
• For example, a minigene is prepared as follows. For a first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: In an example using eight oligonucleotides, i.e., four pairs of primers, [1053] oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)₂SO₄, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO₄, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.
Example 23 The Plasmid Construct and the Degree to Which it Induces Immunogenicity
• The degree to which a plasmid construct, for example a plasmid constructed in accordance with the previous Example, is able to induce immunogenicity is confirmed in vitro by determining epitope presentation by APC following transduction or transfection of the APC with an epitope-expressing nucleic acid construct. Such a study determines “antigenicity” and allows the use of human APC. The assay determines the ability of the epitope to be presented by the APC in a context that is recognized by a T cell by quantifying the density of epitope-HLA class I complexes on the cell surface. Quantitation can be performed by directly measuring the amount of peptide eluted from the APC (see, e.g., Sijts et al., [1054] J. Immunol. 156:683-692, 1996; Demotz et al., Nature 342:682-684, 1989); or the number of peptide-HLA class I complexes can be estimated by measuring the amount of lysis or lymphokine release induced by diseased or transfected target cells, and then determining the concentration of peptide necessary to obtain equivalent levels of lysis or lymphokine release (see, e.g., Kageyama et al., J. Immunol. 154:567-576, 1995).
• Alternatively, immunogenicity is confirmed through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analyzed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in Alexander et al., [1055] Immunity 1:751-761, 1994.
• For example, to confirm the capacity of a DNA minigene construct containing at least one HLA-A2 supermotif peptide to induce CTLs in vivo, HLA-A2.1/K[1056] ^b transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.
• Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a [1057] ⁵¹Cr release assay. The results indicate the magnitude of the CTL response directed against the A2-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine.
• It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A2 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A3 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes, whereby it is also found that the minigene elicits appropriate immune responses directed toward the provided epitopes. [1058]
• To confirm the capacity of a class II epitope-encoding minigene to induce HTLs in vivo, DR transgenic mice, or for those epitopes that cross react with the appropriate mouse MHC molecule, I-A[1059] ^b-restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant. CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a ³H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al. Immunity 1:751-761, 1994). The results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.
• DNA minigenes, constructed as described in the previous Example, can also be confirmed as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent can consist of recombinant protein (e.g., Barnett et al., [1060] Aids Res. and Human Retroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA 95:7648-53, 1998; Hanke and McMichael, Immunol. Letters 66:177-181, 1999; and Robinson et al., Nature Med. 5:526-34, 1999).
• For example, the efficacy of the DNA minigene used in a prime boost protocol is initially evaluated in transgenic mice. In this example, A2.1/K[1061] ^b transgenic mice are immunized IM with 100 μg of a DNA minigene encoding the immunogenic peptides including at least one HLA-A2 supermotif-bearing peptide. After an incubation period (ranging from 3-9 weeks), the mice are boosted IP with 10⁷ pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 μg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an alpha, beta and/or gamma IFN ELISA.
• It is found that the minigene utilized in a prime-boost protocol elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis can also be performed using HLA-A11 or HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 or HLA-B7 motif or supermotif epitopes. The use of prime boost protocols in humans is described below in the Example entitled “Induction of CTL Responses Using a Prime Boost Protocol.”[1062]
Example 24 Peptide Compositions for Prophylactic Uses
• Vaccine compositions of the present invention can be used to prevent 98P4B6 expression in persons who are at risk for tumors that bear this antigen. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in the above Examples, which are also selected to target greater than 80% of the population, is administered to individuals at risk for a 98P4B6-associated tumor. [1063]
• For example, a peptide-based composition is provided as a single polypeptide that encompasses multiple epitopes. The vaccine is typically administered in a physiological solution that comprises an adjuvant, such as Incomplete Freunds Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against 98P4B6-associated disease. [1064]
• Alternatively, a composition typically comprising transfecting agents is used for the administration of a nucleic acid-based vaccine in accordance with methodologies known in the art and disclosed herein. [1065]
Example 25 Polyepitopic Vaccine Compositions Derived from Native 98P4B6 Sequences
• A native 98P4B6 polyprotein sequence is analyzed, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes. The “relatively short” regions are preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct or overlapping, “nested” epitopes can be used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes. [1066]
• The vaccine composition will include, for example, multiple CTL epitopes from 98P4B6 antigen and at least one HTL epitope. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide. [1067]
• The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally, such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup(s) that is presently unknown. Furthermore, this embodiment (excluding an analoged embodiment) directs the immune response to multiple peptide sequences that are actually present in native 98P4B6, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing peptide or nucleic acid vaccine compositions. [1068]
• Related to this embodiment, computer programs are available in the art which can be used to identify in a target sequence, the greatest number of epitopes per sequence length. [1069]
Example 26 Polyepitopic Vaccine Compositions from Multiple Antigens
• The 98P4B6 peptide epitopes of the present invention are used in conjunction with epitopes from other target tumor-associated antigens, to create a vaccine composition that is useful for the prevention or treatment of cancer that expresses 98P4B6 and such other antigens. For example, a vaccine composition can be provided as a single polypeptide that incorporates multiple epitopes from 98P4B6 as well as tumor-associated antigens that are often expressed with a target cancer associated with 98P4B6 expression, or can be administered as a composition comprising a cocktail of one or more discrete epitopes. Alternatively, the vaccine can be administered as a minigene construct or as dendritic cells which have been loaded with the peptide epitopes in vitro. [1070]
Example 27 Use of Peptides to Evaluate an Immune Response
• Peptides of the invention may be used to analyze an immune response for the presence of specific antibodies, CTL or HTL directed to 98P4B6. Such an analysis can be performed in a manner described by Ogg et al., [1071] Science 279:2103-2106, 1998. In this Example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.
• In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, 98P4B6 HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of disease or following immunization comprising a 98P4B6 peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., [1072] N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′ triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.
• For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive non-diseased donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the 98P4B6 epitope, and thus the status of exposure to 98P4B6, or exposure to a vaccine that elicits a protective or therapeutic response. [1073]
Example 28 Use of Peptide Epitopes to Evaluate Recall Responses
• The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from 98P4B6-associated disease or who have been vaccinated with a 98P4B6 vaccine. [1074]
• For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any 98P4B6 vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type. [1075]
• PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128-140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation. [1076]
• In the microculture format, 4×10[1077] ⁵ PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 μl of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 10⁵ irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific ⁵¹Cr release, based on comparison with non-diseased control subjects as previously described (Rehermann, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).
• Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. [1078] J. Virol. 66:2670-2678, 1992).
• Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of [1079] ⁵¹Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.
• Cytolytic activity is determined in a standard 4-h, split well [1080] ⁵¹Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (EIT) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100×[(experimental release-spontaneous release)/maximum release-spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.
• The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to 98P4B6 or a 98P4B6 vaccine. [1081]
• Similarly, Class II restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×10[1082] ⁵ cells/well and are stimulated with 10 μg/ml synthetic peptide of the invention, whole 98P4B6 antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 μCi ³H-thymidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for ³H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of 3H-thymidine incorporation in the presence of antigen divided by the ³H-thymidine incorporation in the absence of antigen.
Example 29 Induction of Specific CTL Response in Humans
• A human clinical trial for an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial. Such a trial is designed, for example, as follows: [1083]
• A total of about 27 individuals are enrolled and divided into 3 groups: [1084]
• Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition; [1085]
• Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition; [1086]
• Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition. [1087]
• After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage. [1088]
• The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints. [1089]
• Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility. [1090]
• Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity. [1091]
• The vaccine is found to be both safe and efficacious. [1092]
Example 30 Phase II Trials in Patients Expressing 98P4B6
• Phase II trials are performed to study the effect of administering the CTL-HTL peptide compositions to patients having cancer that expresses 98P4B6. The main objectives of the trial are to determine an effective dose and regimen for inducing CTLs in cancer patients that express 98P4B6, to establish the safety of inducing a CTL and HTL response in these patients, and to see to what extent activation of CTLs improves the clinical picture of these patients, as manifested, e.g., by the reduction and/or shrinking of lesions. Such a study is designed, for example, as follows: [1093]
• The studies are performed in multiple centers. The trial design is an open-label, uncontrolled, dose escalation protocol wherein the peptide composition is administered as a single dose followed six weeks later by a single booster shot of the same dose. The dosages are 50, 500 and 5,000 micrograms per injection. Drug-associated adverse effects (severity and reversibility) are recorded. [1094]
• There are three patient groupings. The first group is injected with 50 micrograms of the peptide composition and the second and third groups with 500 and 5,000 micrograms of peptide composition, respectively. The patients within each group range in age from 21-65 and represent diverse ethnic backgrounds. All of them have a tumor that expresses 98P4B6. [1095]
• Clinical manifestations or antigen-specific T-cell responses are monitored to assess the effects of administering the peptide compositions. The vaccine composition is found to be both safe and efficacious in the treatment of 98P4B6-associated disease. [1096]
Example 31 Induction of CTL Responses Using a Prime Boost Protocol
• A prime boost protocol similar in its underlying principle to that used to confirm the efficacy of a DNA vaccine in transgenic mice, such as described above in the Example entitled “The Plasmid Construct and the Degree to Which It Induces Immunogenicity,” can also be used for the administration of the vaccine to humans. Such a vaccine regimen can include an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptide mixture administered in an adjuvant. [1097]
• For example, the initial immunization may be performed using an expression vector, such as that constructed in the Example entitled “Construction of “Minigene” Multi-Epitope DNA Plasmids” in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-10[1098] ⁷ to 5×10⁹ pfu. An alternative recombinant virus, such as an MVA, canarypox, adenovirus, or adeno-associated virus, can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples are obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.
• Analysis of the results indicates that a magnitude of response sufficient to achieve a therapeutic or protective immunity against 98P4B6 is generated. [1099]
Example 32 Administration of Vaccine Compositions Using Dendritic Cells (DC)
• Vaccines comprising peptide epitopes of the invention can be administered using APCs, or “professional” APCs such as DC. In this example, peptide-pulsed DC are administered to a patient to stimulate a CTL response in vivo. In this method, dendritic cells are isolated, expanded, and pulsed with a vaccine comprising peptide CTL and HTL epitopes of the invention. The dendritic cells are infused back into the patient to elicit CTL and HTL responses in vivo. The induced CTL and HTL then destroy or facilitate destruction, respectively, of the target cells that bear the 98P4B6 protein from which the epitopes in the vaccine are derived. [1100]
• For example, a cocktail of epitope-comprising peptides is administered ex vivo to PBMC, or isolated DC therefrom. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides, and prior to reinfusion into patients, the DC are washed to remove unbound peptides. [1101]
• As appreciated clinically, and readily determined by one of skill based on clinical outcomes, the number of DC reinfused into the patient can vary (see, e.g., [1102] Nature Med. 4:328, 1998; Nature Med. 2:52, 1996 and Prostate 32:272, 1997). Although 2-50×10⁶ DC per patient are typically administered, larger number of DC, such as 10⁷ or 10⁸ can also be provided. Such cell populations typically contain between 50-90% DC.
• In some embodiments, peptide-loaded PBMC are injected into patients without purification of the DC. For example, PBMC generated after treatment with an agent such as Progenipoietin™ are injected into patients without purification of the DC. The total number of PBMC that are administered often ranges from 10[1103] ⁸ to 10¹⁰. Generally, the cell doses injected into patients is based on the percentage of DC in the blood of each patient, as determined, for example, by immunofluorescence analysis with specific anti-DC antibodies. Thus, for example, if Progenipoietin™ mobilizes 2% DC in the peripheral blood of a given patient, and that patient is to receive 5×10⁶ DC, then the patient will be injected with a total of 2.5×10⁸ peptide-loaded PBMC. The percent DC mobilized by an agent such as Progenipoietin™ is typically estimated to be between 2-10%, but can vary as appreciated by one of skill in the art.
• Ex Vivo Activation of CTL/HTL responses [1104]
• Alternatively, ex vivo CTL or HTL responses to 98P4B6 antigens can be induced by incubating, in tissue culture, the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of APC, such as DC, and immunogenic peptides. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, i.e., tumor cells. [1105]
Example 33 An Alternative Method of Identifying and Confirming Motif-Bearing Peptides
• Another method of identifying and confirming motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can be transfected with nucleic acids that express the antigen of interest, e.g. 98P4B6. Peptides produced by endogenous antigen processing of peptides produced as a result of transfection will then bind to HLA molecules within the cell and be transported and displayed on the cell's surface. Peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., [1106] J. Immunol. 152:3913, 1994). Because the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.
• Alternatively, cell lines that do not express endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells can then be used as described, i.e., they can then be transfected with nucleic acids that encode 98P4B6 to isolate peptides corresponding to 98P4B6 that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell. [1107]
• As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell. [1108]
Example 34 Complementary Polynucleotides
• Sequences complementary to the 98P4B6-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring 98P4B6. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using, e.g., OLIGO 4.06 software (National Biosciences) and the coding sequence of 98P4B6. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to a 98P4B6-encoding transcript. [1109]
Example 35 Purification of Naturally-Occurring or Recombinant 98P4B6 Using 98P4B6-Specific Antibodies
• Naturally occurring or recombinant 98P4B6 is substantially purified by immunoaffinity chromatography using antibodies specific for 98P4B6. An immunoaffinity column is constructed by covalently coupling anti-98P4B6 antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturers instructions. [1110]
• Media containing 98P4B6 are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of 98P4B6 (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/98P4B6 binding (e.g., a buffer of [1111] pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and GCR.P is collected.
Example 36 Identification of Molecules which Interact with 98P4B6
• 98P4B6, or biologically active fragments thereof, are labeled with 121 1 Bolton-Hunter reagent. (See, e.g., Bolton et al. (1973) Biochem. J. 133:529.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled 98P4B6, washed, and any wells with labeled 98P4B6 complex are assayed. Data obtained using different concentrations of 98P4B6 are used to calculate values for the number, affinity, and association of 98P4B6 with the candidate molecules. [1112]
Example 37 In Vivo Assay for 98P4B6 Tumor Growth Promotion
• The effect of the 98P4B6 protein on tumor cell growth is evaluated in vivo by gene overexpression in tumor-bearing mice. For example, prostate (PC3), lung (A427), stomach, ovarian (PA1) and uterus cell lines are engineered to express 98P4B6. SCID mice are injected subcutaneously on each flank with 1×10[1113] ⁶ of PC3, A427, PA1, or NIH-3T3 cells containing tkNeo empty vector or 98P4B6. At least two strategies may be used: (1) Constitutive 98P4B6 expression under regulation of a promoter such as a constitutive promoter obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published 5 Jul. 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus, and Simian Virus 40 (SV40), or from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, provided such promoters are compatible with the host cell systems, and (2) Regulated expression under control of an inducible vector system, such as ecdysone, tet, etc., provided such promoters are compatible with the host cell systems. Tumor volume is then monitored at the appearance of palpable tumors and followed over time to determine if 98P4B6-expressing cells grow at a faster rate and whether tumors produced by 98P4B6-expressing cells demonstrate characteristics of altered aggressiveness (e.g. enhanced metastasis, vascularization, reduced responsiveness to chemotherapeutic drugs).
• Additionally, mice can be implanted with 1×10[1114] ⁵ of the same cells orthotopically to determine if 98P4B6 has an effect on local growth in the prostate or on the ability of the cells to metastasize, specifically to lungs, lymph nodes, and bone marrow.
• The assay is also useful to determine the 98P4B6 inhibitory effect of candidate therapeutic compositions, such as for example, 98P4B6 intrabodies, 98P4B6 antisense molecules and ribozymes. [1115]
Example 38 98P4B6 Monoclonal Antibody-Mediated Inhibition of Tumors in Vivo
• The significant expression of 98P4B6 in prostate, lung, stomach, ovary, and uterus cancer tissues, its restrictive expression in normal tissues, together with its expected cell surface expression makes 98P4B6 an excellent target for antibody therapy. Similarly, 98P4B6 is a target for T-cell based immunotherapy. Thus, the therapeutic efficacy of anti-98P4B6 mAbs in human prostate cancer xenograft mouse models is evaluated by using androgen-independent LAPC-4 and LAPC-9 xenografts (Craft, N., et al., Cancer Res, 1999. 59(19): p. 5030-6) and the androgen independent recombinant cell line PC3-98P4B6 (see, e.g., Kaighn, M. E., et al., Invest Urol, 1979. 17(1): p. 16-23). Similar approaches using patient derived xenografts or xenograft cell lines are used for cancers listed in Table I. [1116]
• Antibody efficacy on tumor growth and metastasis formation is studied, e.g., in a mouse orthotopic prostate cancer xenograft models and mouse lung, uterus, or stomach xenograft models. The antibodies can be unconjugated, as discussed in this Example, or can be conjugated to a therapeutic modality, as appreciated in the art. Anti-98P4B6 mAbs inhibit formation of both the androgen-dependent LAPC-9 and androgen-independent PC3-98P4B6 tumor xenografts. Anti-98P4B6 mAbs also retard the growth of established orthotopic tumors and prolonged survival of tumor-bearing mice. These results indicate the utility of anti-98P4B6 mAbs in the treatment of local and advanced stages of cancer. (See, e.g., (Saffran, D., et al., PNAS 10:1073-1078 or URL located on the World Wide Web at .pnas.org/cgi/doi/10.1073/pnas.051624698). [1117]
• Administration of the anti-98P4B6 mAbs can lead to retardation of established orthotopic tumor growth and inhibition of metastasis to distant sites, resulting in a significant prolongation in the survival of tumor-bearing mice. These studies indicate that 98P4B6 is an attractive target for immunotherapy and demonstrate the therapeutic potential of anti-98P4B6 mAbs for the treatment of local and metastatic cancer. This example demonstrates that unconjugated 98P4B6 monoclonal antibodies are effective to inhibit the growth of human prostate tumor xenografts, as well as lung, uterus, or stomach xenograft grown in SCID mice; accordingly a combination of such efficacious monoclonal antibodies is also effective. [1118]
• Tumor Inhibition Using Multiple Unconjugated 98P4B6 mAbs [1119]
• Materials and Methods [1120]
• 98P4B6 Monoclonal Antibodies: [1121]
• Monoclonal antibodies are raised against 98P4B6 as described in Example 11 entitled “Generation of 98P4B6 Monoclonal Antibodies (mAbs).” The antibodies are characterized by ELISA, Western blot, FACS, and immunoprecipitation for their capacity to bind 98P4B6. Epitope mapping data for the anti-98P4B6 mAbs, as determined by ELISA and Western analysis, recognize epitopes on the 98P4B6 protein. Immunohistochemical analysis of cancer tissues and cells with these antibodies is performed. [1122]
• The monoclonal antibodies are purified from ascites or hybridoma tissue culture supernatants by Protein-G Sepharose chromatography, dialyzed against PBS, filter sterilized, and stored at −20° C. Protein determinations are performed by a Bradford assay (Bio-Rad, Hercules, Calif.). A therapeutic monoclonal antibody or a cocktail comprising a mixture of individual monoclonal antibodies is prepared and used for the treatment of mice receiving subcutaneous or orthotopic injections of LAPC-9 tumor xenografts. [1123]
• Cancer Xenografts and Cell Lines [1124]
• The LAPC-9 xenograft, which expresses a wild-type androgen receptor and produces prostate-specific antigen (PSA), is passaged in 6- to 8-week-old male ICR-severe combined immunodeficient (SCID) mice (Taconic Farms) by s.c. trocar implant (Craft, N., et at., supra). The prostate (PC3), lung (A427), ovarian (PA1) carcinoma cell lines (American Type Culture Collection) are maintained in RPMI or DMEM supplemented with L-glutamine and 10% FBS. [1125]
• PC3-98P4B6, A427-98P4B6, PA1-98P4B6 and 3T3-98P4B6 cell populations are generated by retroviral gene transfer as described in Hubert, R. S., et al., STEAP: a prostate-specific cell-surface antigen highly expressed in human prostate tumors. Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-8. Anti-98P4B6 staining is detected by using an FITC-conjugated goat anti-mouse antibody (Southern Biotechnology Associates) followed by analysis on a Coulter Epics-XL f low cytometer. [1126]
• Xenograft Mouse Models. [1127]
• Subcutaneous (s.c.) tumors are generated by injection of 1×10[1128] ⁶ LAPC-9, PC3, PC3-98P4B6, A427, A427-98P4B6, PA1, PA1-98P4B6, 3T3 or 3T3-98P4B6 cells mixed at a 1:1 dilution with Matrigel (Collaborative Research) in the right flank of male SCID mice. To test antibody efficacy on tumor formation, i.p. antibody injections are started on the same day as tumor-cell injections. As a control, mice are injected with either purified mouse IgG (ICN) or PBS; or a purified monoclonal antibody that recognizes an irrelevant antigen not expressed in human cells. In preliminary studies, no difference is found between mouse IgG or PBS on tumor growth. Tumor sizes are determined by vernier caliper measurements, and the tumor volume is calculated as length×width×height. Mice with s.c. tumors greater than 1.5 cm in diameter are sacrificed. PSA levels are determined by using a PSA ELISA kit (Anogen, Mississauga, Ontario). Circulating levels of anti-98P4B6 mAbs are determined by a capture ELISA kit (Bethyl Laboratories, Montgomery, Tex.). (See, e.g., (Saffran, D., et al., PNAS 10:1073-1078 or URL located on the World Wide Web at .pnas.org/cgi/doi/10.1073/pnas.051624698)
• Orthotopic injections are performed under anesthesia by using ketamine/xylazine. For prostate orthotopic studies, an incision is made through the abdominal muscles to expose the bladder and seminal vesicles, which then are delivered through the incision to expose the dorsal prostate. LAPC-9 or PC3 cells (5×10[1129] ⁵) mixed with Matrigel are injected into each dorsal lobe in a 10-μl volume. To monitor tumor growth, mice are bled on a weekly basis for determination of PSA levels. The mice are segregated into groups for the appropriate treatments, with anti-98P4B6 or control mAbs being injected i.p.
• Anti-98P4B6 mAbs Inhibit Growth of 98P4B6-Expressing Xenograft-Cancer Tumors [1130]
• The effect of anti-98P4B6 mAbs on tumor formation is tested by using LAPC-9 and PC3-98P4B6 orthotopic models. As compared with the s.c. tumor model, the orthotopic model, which requires injection of tumor cells directly in the mouse prostate, lung, or ovary, respectively, results in a local tumor growth, development of metastasis in distal sites, deterioration of mouse health, and subsequent death (Saffran, D., et al., PNAS supra; Fu, X., et al., Int J Cancer, 1992. 52(6): p. 987-90; Kubota, T., J Cell Biochem, 1994. 56(1): p. 4-8). The features make the orthotopic model more representative of human disease progression and allowed us to follow the therapeutic effect of mAbs on clinically relevant end points. [1131]
• Accordingly, tumor cells are injected into the mouse prostate, lung, or ovary, and 2 days later, the mice are segregated into two groups and treated with either: a) 200-500 μg, of anti-98P4B6 Ab, or b) PBS three times per week for two to five weeks. [1132]
• A major advantage of the orthotopic cancer model is the ability to study the development of metastases. Formation of metastasis in mice bearing established orthotopic tumors is studies by IHC analysis on lung sections using an antibody against a prostate-specific cell-surface protein STEAP expressed at high levels in LAPC-9 xenografts (Hubert, R. S., et al., Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-8). [1133]
• Mice bearing established orthotopic LAPC-9 or PC3-98P4B6 tumors are administered 1000 μg injections of either anti-98P4B6 mAb or PBS over a 4-week period. Mice in both groups are allowed to establish a high tumor burden (PSA levels greater than 300 ng/ml for IAPC-9), to ensure a high frequency of metastasis formation in mouse lungs. Mice then are killed and their prostate and lungs are analyzed for the presence of tumor cells by IHC analysis. [1134]
• These studies demonstrate a broad anti-tumor efficacy of anti-98P4B6 antibodies on initiation and progression of prostate cancer in xenograft mouse models. Anti-98P4B6 antibodies inhibit tumor formation of both androgen-dependent and androgen-independent tumors as well as retarding the growth of already established tumors and prolong the survival of treated mice. Moreover, anti-98P4B6 mAbs demonstrate a dramatic inhibitory effect on the spread of local prostate tumor to distal sites, even in the presence of a large tumor burden. Thus, anti-98P4B6 mAbs are efficacious on major clinically relevant end points (tumor growth), prolongation of survival, and health. [1135]
Example 39 Therapeutic and Diagnostic Use of Anti-98P4B6 Antibodies in Humans
• Anti-98P4B6 monoclonal antibodies are safely and effectively used for diagnostic, prophylactic, prognostic and/or therapeutic purposes in humans. Western blot and immunohistochemical analysis of cancer tissues and cancer xenografts with anti-98P4B6 mAb show strong extensive staining in carcinoma but significantly lower or undetectable levels in normal tissues. Detection of 98P4B6 in carcinoma and in metastatic disease demonstrates the usefulness of the mAb as a diagnostic and/or prognostic indicator. Anti-98P4B6 antibodies are therefore used in diagnostic applications such as immunohistochemistry of kidney biopsy specimens to detect cancer from suspect patients. [1136]
• As determined by flow cytometry, anti-98P4B6 mAb specifically binds to carcinoma cells. Thus, anti-98P4B6 antibodies are used in diagnostic whole body imaging applications, such as radioimmunoscintigraphy and radioimmunotherapy, (see, e.g., Potamianos S., et. al. Anticancer Res 20(2A):925-948 (2000)) for the detection of localized and metastatic cancers that exhibit expression of 98P4B6. Shedding or release of an extracellular domain of 98P4B6 into the extracellular milieu, such as that seen for alkaline phosphodiesterase B10 (Meerson, N. R., Hepatology 27:563-568 (1998)), allows diagnostic detection of 98P4B6 by anti-98P4B6 antibodies in serum and/or urine samples from suspect patients. [1137]
• Anti-98P4B6 antibodies that specifically bind 98P4B6 are used in therapeutic applications for the treatment of cancers that express 98P4B6. Anti-98P4B6 antibodies are used as an unconjugated modality and as conjugated form in which the antibodies are attached to one of various therapeutic or imaging modalities well known in the art, such as a prodrugs, enzymes or radioisotopes. In preclinical studies, unconjugated and conjugated anti-98P4B6 antibodies are tested for efficacy of tumor prevention and growth inhibition in the SCID mouse cancer xenograft models, e.g., kidney cancer models AGS-K3 and AGS-K6, (see, e.g., the Example entitled “98P4B6 Monoclonal Antibody-mediated Inhibition of Bladder and Lung Tumors In Vivo”). Either conjugated and unconjugated anti-98P4B6 antibodies are used as a therapeutic modality in human clinical trials either alone or in combination with other treatments as described in following Examples. [1138]
Example 40 Human Clinical Trials for the Treatment and Diagnosis of Human Carcinomas Through use of Human Anti-98P4B6 Antibodies In Vivo
• Antibodies are used in accordance with the present invention which recognize an epitope on 98P4B6, and are used in the treatment of certain tumors such as those listed in Table I. Based upon a number of factors, including 98P4B6 expression levels, tumors such as those listed in Table I are presently preferred indications. In connection with each of these indications, three clinical approaches are successfully pursued. [1139]
• I.) Adjunctive Therapy: [1140]
• In adjunctive therapy, patients are treated with anti-98P4B6 antibodies in combination with a chemotherapeutic or antineoplastic agent and/or radiation therapy. Primary cancer targets, such as those listed in Table I, are treated under standard protocols by the addition anti-98P4B6 antibodies to standard first and second line therapy. Protocol designs address effectiveness as assessed by reduction in tumor mass as well as the ability to reduce usual doses of standard chemotherapy. These dosage reductions allow additional and/or prolonged therapy by reducing dose-related toxicity of the chemotherapeutic agent. Anti-98P4B6 antibodies are utilized in several adjunctive clinical trials in combination with the chemotherapeutic or antineoplastic agents adriamycin (advanced prostrate carcinoma), cisplatin (advanced head and neck and lung carcinomas), taxol (breast cancer), and doxorubicin (preclinical). [1141]
• II.) Monotherapy: [1142]
• In connection with the use of the anti-98P4B6 antibodies in monotherapy of tumors, the antibodies are administered to patients without a chemotherapeutic or antineoplastic agent. In one embodiment, monotherapy is conducted clinically in end stage cancer patients with extensive metastatic disease. Patients show some disease stabilization. Trials demonstrate an effect in refractory patients with cancerous tumors. [1143]
• III.) Imaging Agent: [1144]
• Through binding a radionuclide (e.g., iodine or yttrium (I[1145] ¹³¹, Y⁹⁰) to anti-98P4B6 antibodies, the radiolabeled antibodies are utilized as a diagnostic and/or imaging agent. In such a role, the labeled antibodies localize to both solid tumors, as well as, metastatic lesions of cells expressing 98P4B6. In connection with the use of the anti-98P4B6 antibodies as imaging agents, the antibodies are used as an adjunct to surgical treatment of solid tumors, as both a pre-surgical screen as well as a post-operative follow-up to determine what tumor remains and/or returns. In one embodiment, a (¹¹¹In)-98P4B6 antibody is used as an imaging agent in a Phase I human clinical trial in patients having a carcinoma that expresses 98P4B6 (by analogy see, e.g., Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991)). Patients are followed with standard anterior and posterior gamma camera. The results indicate that primary lesions and metastatic lesions are identified
• Dose and Route of Administration [1146]
• As appreciated by those of ordinary skill in the art, dosing considerations can be determined through comparison with the analogous products that are in the clinic. Thus, anti-98P4B6 antibodies can be administered with doses in the range of 5 to 400 Mg/m[1147] ², with the lower doses used, e.g., in connection with safety studies. The affinity of anti-98P4B6 antibodies relative to the affinity of a known antibody for its target is one parameter used by those of skill in the art for determining analogous dose regimens. Further, anti-98P4B6 antibodies that are fully human antibodies, as compared to the chimeric antibody, have slower clearance; accordingly, dosing in patients with such fully human anti-98P4B6 antibodies can be lower, perhaps in the range of 50 to 300 mg/m², and still remain efficacious. Dosing in mg/m², as opposed to the conventional measurement of dose in mg/kg, is a measurement based on surface area and is a convenient dosing measurement that is designed to include patients of all sizes from infants to adults.
• Three distinct delivery approaches are useful for delivery of anti-98P4B6 antibodies. Conventional intravenous delivery is one standard delivery technique for many tumors. However, in connection with tumors in the peritoneal cavity, such as tumors of the ovaries, biliary duct, other ducts, and the like, intraperitoneal administration may prove favorable for obtaining high dose of antibody at the tumor and to also minimize antibody clearance. In a similar manner, certain solid tumors possess vasculature that is appropriate for regional perfusion. Regional perfusion allows for a high dose of antibody at the site of a tumor and minimizes short term clearance of the antibody. [1148]
• Clinical Development Plan (CDP) [1149]
• Overview: [1150]
• The CDP follows and develops treatments of anti-98P4B6 antibodies in connection with adjunctive therapy, monotherapy, and as an imaging agent. Trials initially demonstrate safety and thereafter confirm efficacy in repeat doses. Trails are open label comparing standard chemotherapy with standard therapy plus anti-98P4B6 antibodies. As will be appreciated, one criteria that can be utilized in connection with enrollment of patients is 98P4B6 expression levels in their tumors as determined by biopsy. [1151]
• As with any protein or antibody infusion-based therapeutic, safety concerns are related primarily to (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 98P4B6. Standard tests and follow-up are utilized to monitor each of these safety concerns. Anti-98P4B6 antibodies are found to be safe upon human administration. [1152]
Example 41 Human Clinical Trial Adjunctive Therapy with Human Anti-98P4B6 Antibody and Chemotherapeutic Agent
• A phase I human clinical trial is initiated to assess the safety of six intravenous doses of a human anti-98P4B6 antibody in connection with the treatment of a solid tumor, e.g., a cancer of a tissue listed in Table I. In the study, the safety of single doses of anti-98P4B6 antibodies when utilized as an adjunctive therapy to an antineoplastic or chemotherapeutic agent as defined herein, such as, without limitation: cisplafin, topotecan, doxorubicin, adriamycin, taxol, or the like, is assessed. The trial design includes delivery of six single doses of an anti-98P4B6 antibody with dosage of antibody escalating from approximately about 25 mg/m[1153] ² to about 275 mg/m² over the course of the treatment in accordance with the following schedule:

  	Day 0	Day 7	Day 14	Day 21	Day 28	Day 35
  mAb Dose	25	75	125	175	225	275
  	mg/m2	mg/m2	mg/m2	mg/m2	mg/m2	mg/m2
  Chemotherapy	+	+	+	+	+	+
  (standard dose)

• Patients are closely followed for one-week following each administration of antibody and chemotherapy. In particular, patients are assessed for the safety concerns mentioned above: (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the human antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 98P4B6. Standard tests and follow-up are utilized to monitor each of these safety concerns. Patients are also assessed for clinical outcome, and particularly reduction in tumor mass as evidenced by MRI or other imaging. [1154]
• The anti-98P4B6 antibodies are demonstrated to be safe and efficacious, Phase II trials confirm the efficacy and refine optimum dosing. [1155]
Example 42 Human Clinical Trial: Monotherapy with Human Anti-98P4B6 Antibody
• Anti-98P4B6 antibodies are safe in connection with the above-discussed adjunctive trial, a Phase II human clinical trial confirms the efficacy and optimum dosing for monotherapy. Such trial is accomplished, and entails the same safety and outcome analyses, to the above-described adjunctive trial with the exception being that patients do not receive chemotherapy concurrently with the receipt of doses of anti-98P4B6 antibodies. [1156]
Example 43 Human Clinical Trial: Diagnostic Imaging with Anti-98P4B6 Antibody
• Once again, as the adjunctive therapy discussed above is safe within the safety criteria discussed above, a human clinical trial is conducted concerning the use of anti-98P4B6 antibodies as a diagnostic imaging agent. The protocol is designed in a substantially similar manner to those described in the art, such as in Divgi et al. [1157] J. Natl. Cancer Inst. 83:97-104 (1991). The antibodies are found to be both safe and efficacious when used as a diagnostic modality.
Example 44 Homology Comparison of 98P4B6 to Known Sequences
• The 98P4B6 gene is homologous to a cloned and sequenced gene, namely human STAMP1 (gi 15418732) (Korkmaz, K. S et al., J. Biol. Chem. 2002, 277: 36689), showing 99% identity and 99% homology to that gene (FIG. 4). The 98P4B6 protein also shows 99% identity and 99% homology to another human six transmembrane epithelial antigen of prostate 2 (gi 23308593) (Walker, M. G et al., Genome Res. 1999, 9: 1198; Porkka, K. P., Helenius, M. A. and Visakorpi, T, Lab. Invest. 2002, 82: 1573). The closest mouse homolog to 98P4B6is six transmembrane epithelial antigen of prostate 2 (gi 28501136), with 97% identity and 99% homology. We have identified several variants of the 98P4B6 protein, including 4 splice variants and 3 SNPs (FIG. 11). The 98P4B6 v.1 protein consists of 454 amino acids, with calculated molecular weight of 52 kDa, and pl of 8.7. It is a 6 transmembrane protein that can localize to the cell surface or possibly to the endoplasmic reticulum (Table VI). Several 98P4B6 variants, including v.1, v.5-8, v.13, v.14, v.21, v.25 share similar features, such protein motifs with functional significance, as well as structural commonalities such as multiple transmembrane domains. The 98P4B6 v.2 is a short protein with no known motifs. [1158]
• Motif analysis revealed the presence of several known motifs, including oxido-reductase, homocysteine hydrolase and dudulin motifs. Variant v.7 and SNPs of this variant also carry an Ets motif, often associated with transcriptional activity. [1159]
• Several oxidoreductases have been identified in mammalian cells, including the NADH/quinone oxidoreductase. This protein associate with the cell membrane and function as a proton/Na+ pump, which regulates the protein degradation of the tumor suppressor p53, and protects mammalian cells from oxidative stress, cytotoxicity, and mutages (Asher G, et al., Proc Natl Acad Sci U S A. 2002, 99:13125; Jaiswal A K, Arch Biochem Biophys 2000, 375:62 Yano T, Mol Aspects Med 2002, 23:345). Homocysteine hydrolase is an enzyme known to catalyze the breakdown of S-adenosylhomocysteine to homocysteine and adenosine, ultimately regulating trans-methylation, therby regulating protein expression, cell cycle and proliferation (Turner MAet al. Cell Biochem Biophys 2000;33:101;Zhang et al., J Biol Chem. 2001; 276:35867) [1160]
• This information indicates that 98P4B6 plays a role in the cell growth of mammalian cells, regulate gene transcription and transport of electrons and small molecules. Accordingly, when 98P4B6 functions as a regulator of cell growth, tumor formation, or as a modulator of transcription involved in activating genes associated with inflammation, tumorigenesis, or proliferation, 98P4B6 is used for therapeutic, diagnostic, prognostic and/or preventative purposes. In addition, when a molecule, such as a variant or polymorphism of 98P4B6 is expressed in cancerous tissues, it is used for therapeutic, diagnostic, prognostic and/or preventative purposes. [1161]
Example 45 Phenotypic Effects of STEAP-2 Expression
• Experiments regarding the expression of STEAP-2 protein having the amino acid sequence shown in FIG. 2 and encoded by a cDNA insert in a plasmid deposited with the American Type Culture Collection on 2 Jul. 1999 and assigned as ATCC Accession No. PTA-311. As deduced from the coding sequence, the open reading frame encodes 454 amino acids with 6 transmembrane domains. A summary of the characteristics associated with STEAP-2 protein is shown on FIG. 19. [1162]
• The data set forth in the present patent application provide an expression profile of the STEAP-2 protein that is predominantly specific for the prostate among normal tissues, for certain types of prostate tumors as well as other tumors. This evidence is based on detecting messenger RNA using Northern blotting. In keeping with standard practice in this industry, Northern blots are routinely used to assess gene expression, as it does not require the time consuming process of synthesizing the relevant protein, raising antibodies, assuring the specificity of the antibodies, required for Western blotting of proteins and the histological examination of tissues. Northern blotting offers a credible and efficient method of assessing RNA expression and expression levels. [1163]
• This Example demonstrates that STEAP-2 protein is, indeed, produced. In summary, the experiments show that PC-3 cells and 3T3 cells which were modified to contain an expression system for STEAP-2 showed enhanced levels of tyrosine phosphorylation in general, and of phosphorylation of ERK protein in particular. The data also show that PC-3 cells that contain an expression system for STEAP-2 showed modified calcium flux, a modified response to paclitaxel, and a general inhibition of drug-induced apoptosis. These are effects exhibited at the protein level, thus these data alone are probative that the STEAP-2 protein exists. [1164]
• Furthermore, although such phenotypic effects are protein-mediated, further evidence indicates that the STEAP-2 protein itself is the mediator of the effects. This evidence is obtained by utilizing a modified STEAP-2 protein. An expression system is stably introduced into PC3 and 3T3 cells which allows the expression of a modified form of STEAP-2, designated STEAP-2CFl, where “Fl” stands for flag. STEAP-2CFl is a STEAP-2 protein having a peptide extension, i.e., a Flag epitope that alters the physical conformation of this protein. The Flag epitope is a string 8 amino acids, often introduced at either the amino or carboxy termini of protein as a means of identifying and following a recombinant protein in engineered cells (Slootstra J W et al., Mol Divers 1997, 2:156). In most cases, the introduction of the Flag epitope at either termini of a protein has little effect on the natural function and location of that protein (Molloy S S et al., EMBO J 1994, 13:18). However, this is dependent on the characteristics of the protein being Flag tagged. Recent studies have shown that a Flag tag affects the function and conformation of select proteins such as the CLN3 protein (see, e.g., Haskell R E, et al. Mol Genet Metab 1999, 66:253). As with CLN3, introducing a Flag epitope tag to the C-terminus of STEAP-2 alters the physical conformation and properties of this protein. Altering the STEAP-2 protein with the C-Flag epitope resulted in a significant decrease in the effects otherwise observed, including phosphorylation of ERK and resistance to drug-induced cell death. The data indicate that it is the STEAP-2 protein that mediated these phenotypic effects. Finally, in vitro translation studies using rabbit reticulocyte lysate, showed that the STEAP-2 protein is translated and exhibits the expected molecular weight. [1165]
• FIGS. 20 and 21 show the results obtained when PC-3 and 3T3 cells, respectively, were modified to contain the retroviral expression system pSR[1166]

  

  encoding the indicated proteins, including STEAP-1, STEAP-2 and STEAP-2CFl, respectively. Gene-specific protein expression was driven from a long terminal repeat (LTR), and the Neomycin resistance gene was used for selection of mammalian cells that stably express the protein. PC-3 and 3T3 cells were transduced with the retrovirus, selected in the presence of G418 and cultured under conditions which permit expression of the STEAP-2 coding sequence. The cells were grown overnight in low concentrations of FBS (0.5-1% FBS) and were then stimulated with 10% FBS. The cells were lysed in RIPA buffer and quantitated for protein concentration. Whole cell lysates were separated by SDS-PAGE and analyzed by Western blotting using anti-phospho-ERK (Cell Signaling Inc.) or anti-phosphotyrosine (UBI) antibodies (FIGS. 20, 21, and 22). As shown on FIG. 20, as compared to untransformed PC-3 cells, cells modified to contain STEAP-2 contain enhanced amounts of phosphorylated tyrosine. Similar results from an analogous experiment on 3T3 cells are shown on page 3. In this latter experiment, the STEAP-2CFl expression system was also transfected into 3T3 cells, which cells were used as a control. As shown on FIG. 21, the enhanced phosphorylation found in the presence of native STEAP-2 was significantly reduced when the conformation of the protein was altered. These results thus show conclusively that the STEAP-2 protein was produced and mediated the above-described phenotypic effects.
• FIG. 22 shows similar results, both in PC-3 and 3T3 cells where phosphorylation of ERK, specifically, is detected. The protocol is similar to that set forth in paragraph 5 above, except that rather than probing the gels with antibodies specific for phosphotyrosine the gels were probed both the anti-ERK and anti-phospho-ERK antibodies. As shown on FIG. 22, in the presence of 10% FBS, both PC-3 cells and 3T3 cells modified to express STEAP-2 showed phosphorylation of ERK which was not detectable in cells transformed to contain STEAP-2CFl. In contrast to control PC-3 cells which exhibit no background ERK phosphorylation, control 3T3-neo cells show low levels of endogenous ERK phosphorylation. Treatment with 10% FBS enhanced phosphorylation of ERK protein in cells expressing STEAP-2 relative to 3T3-neo cells, while no increase in ERK phosphorylation was observed in 3T3 cells expressing modified STEAP-2, i.e. STEAP-2 CFl. [1167]
• Other effects on cellular metabolism in cells modified to contain a STEAP-2 expression system were also shown in our data. FIG. 23 shows that when cells with and without expression systems for STEAP-2 were measured for calcium flux in the presence of LPA, calcium flux was enhanced in the STEAP-2 containing cells. Using FACS analysis and commercially available indicators (Molecular Probes), parental cells and cells expressing STEAP-2 were compared for their ability to transport calcium. PC3-neo and PC3-STEAP-2 cells were loaded with calcium responsive indicators Fluo4 and Fura red, incubated in the presence or absence of calcium and LPA, and analyzed by flow cytometry. PC3 cells expressing a known calcium transporter, PC3-83P3H3 pCaT were used as positive control (Biochem Biophys Res Commun. 2001, 282:729). The table on FIG. 23 shows that STEAP-2 mediates calcium flux in response to LPA, and that the magnitude of calcium flux is comparable to that produced by a known calcium channel. [1168]
• In addition, STEAP-2 expressing PC3 cells demonstrated increased sensitivity to agatoxin, a calcium channel blocker as compared to PC3-neo cells. These results indicate that STEAP-2 expression renders PC3 cells sensitive to treatment with the Ca++ channel inhibitors. Information derived from the above experiments provides a mechanism by which cancer cells are regulated. This is particularly relevant in the case of calcium, as calcium channel inhibitors have been reported to induce the death of certain cancer cells, including prostate cancer cell lines (see, e.g., Batra S, Popper L D, Hartley-Asp B. Prostate. 1991, 19:299). [1169]
• FIG. 24 shows that cells transfected with a STEAP-2 expression system have enhanced ability to survive exposure to paclitaxel. In order to determine the effect of STEAP-2 on survival, PC3 cells lacking or expressing STEAP-2 were treated with chemotherapeutic agents currently used in the clinic. Effect of treatment was evaluated by measuring cell proliferation using the Alamare blue assay (FIG. 23). While only 5.2% of PC3-neo cells were able to metabolize Alamare Blue and proliferate in the presence of 5 μM paclitaxel, 44.8% of PC3-STEAP-2 cells survived under the same conditions. These results indicate that expression of STEAP-2 imparts resistance to paclitaxel. These findings have significant in vivo implications, as they indicate that STEAP-2 provides a growth advantage for prostate tumor cells in patients treated with common therapeutic agents. [1170]
• A more detailed form of these results is shown on FIGS. 25 and 26. Results in these two pages demonstrate the mode of action by which STEAP-2 supports the survival of PC3 cells. In these studies, PC3 cells expressing or lacking STEAP-2 were treated with paclitaxel for 60 hours, and assayed for apoptosis using annexin V conjugated to FITC and propidium iodide staining. In apoptotic cells, the membrane phospholipid phosphatidylserine (PS) is translocated from the inner to the outer leaflet of the membrane, thereby exposing PS to the external cellular environment. PS is recognized by and binds to annexin V, providing scientists with a reliable means of identifying cells undergoing programmed cell death. Staining with propidium iodide identifies dead cells. FIG. 25 show that expression of STEAP-2 inhibits paclitaxel-mediated apoptosis by 45% relative to paclitaxel-treated PC3-neo cells. The protective effect of STEAP-2 is inhibited when STEAP-2 is modified by the presence of Flag at its C-terminus FIG. 26. [1171]
• The publicly available literature contains several examples of prostate and other cancers that exhibit similar phenotypic characteristics as those observed in PC3 cells that express STEAP-2. In particular, clinical studies have reported transient tumor regression and/or only partial responses in patients treated with paclitaxel. For instance, only around 50% of prostate cancer patients entered in a single agent clinical trial of paclitaxel showed reduced PSA levels when treated with doses of paclitaxel that induced [1172] grade 3 and grade 4 toxicity; a much higher level of response would have been expected based on this dose level, thus this data indicates the development of paclitaxel resistance in prostate cancer patients (Beer T M et al., Ann Oncol 2001, 12:1273). A similar phenomenon of reduced responsiveness and progressive tumor recurrence was observed in other studies (see, e.g., Obasaju C, and Hudes G R. Hematol Oncol Clin North Am 2001,15:525). In addition, inhibition of calcium flux in cells that endogenously express STEAP-2, such as LNCaP cells, induces their cell death (Skryma R et al., J Physiol. 2000, 527:71).
• Thus, STEAP-2 protein is produced not only in the cells tested, but also in unmodified tumor cells or unmodified prostate cells where the presence of mRNA has been shown. The Northern blot data in the specification clearly show that the messenger RNA encoding STEAP-2 is produced in certain prostate and tumor cells. The 3T3 and PC-3 cells, which are themselves tumor cell lines, are clearly able to translate the messenger RNA into protein. Because it has been shown that there is no barrier to translation of the message in cells similar to those tumor and prostate cells in which the mRNA has been shown to be produced, it can properly be concluded that the protein itself can be detected in the unmodified tumor or prostate cells, given the fact that it is shown that mRNA is produced. This conclusion is also supported by the patterns of phenotypic changes seen in cells specifically modified to express STEAP-2, these changes comport with changes seen in cancer cells. Based on the above data, it is scientifically concluded that cells and tissues which produce mRNA encoding STEAP-2 also produce the protein itself. [1173]
Example 46 Identification and Confirmation of Potential Signal Transduction Pathways
• Many mammalian proteins have been reported to interact with signaling molecules and to participate in regulating signaling pathways (J Neurochem. 2001; 76:217-223. Using immunoprecipitation and Western blotting techniques, proteins are identified that associate with 98P4B6 and mediate signaling events. Several pathways known to play a role in cancer biology can be regulated by 98P4B6, including phospholipid pathways such as P13K, AKT, etc, adhesion and migration pathways, including FAK, Rho, Rac-1, etc, as well as mitogenic/survival cascades such as ERK, p38, etc (Cell Growth Differ. 2000,11:279; J Biol Chem. 1999, 274:801; Oncogene. 2000,19:3003, J. Cell Biol. 1997, 138:913.). [1174]
• To confirm that 98P4B6 directly or indirectly activates known signal transduction pathways in cells, luciferase (luc) based transcriptional reporter assays are carried out in cells expressing individual genes. These transcriptional reporters contain consensus-binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways. The reporters and examples of these associated transcription factors, signal transduction pathways, and activation stimuli are listed below. [1175]
• 1. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK; growth/apoptosis/stress [1176]
• 2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation [1177]
• 3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress [1178]
• 4. ARE-luc, androgen receptor; steroids/MAPK; growth/differentiation/apoptosis [1179]
• 5. p53-luc, p53; SAPK; growth/differentiation/apoptosis [1180]
• 6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress [1181]
• Gene-mediated effects can be assayed in cells showing mRNA expression. Luciferase reporter plasmids can be introduced by lipid-mediated transfection (TFX-50, Promega). Luciferase activity, an indicator of relative transcriptional activity, is measured by incubation of cell extracts with luciferin substrate and luminescence of the reaction is monitored in a luminometer. [1182]
• Signaling pathways activated by 98P4B6 are mapped and used for the identification and validation of therapeutic targets. When 98P4B6 is involved in cell signaling, it is used as target for diagnostic, prognostic, preventative and/or therapeutic purposes. [1183]
Example 47 98P4B6 Functions as a Proton or Small Molecule Transporter
• Sequence and homology analysis of 98P4B6 indicate that the 98P4B6 may function as a transporter. To confirm that STEAP-1 functions as an ion channel, FACS analysis and fluorescent microscopy techniques are used (Gergely L, et al., Clin Diagn Lab Immunol. 1997; 4:70; Skryma R, et al., J Physiol. 2000, 527: 71). Using FACS analysis and commercially available indicators (Molecular Probes), parental cells and cells expressing 98P4B6 are compared for their ability to transport electrons, sodium, calcium; as well as other small molecules in cancer and normal cell lines. For example, PC3 and PC3-98P4B6 cells were loaded with calcium responsive indicators Fluo4 and Fura red, incubated in the presence or absence of calcium and lipophosphatidic acid (LPA), and analyzed by flow cytometry. Ion flux represents an important mechanism by which cancer cells are regulated. This is particularly true in the case of calcium, as calcium channel inhibitors have been reported to induce the death of certain cancer cells, including prostate cancer cell lines (Batra S, Popper L D, Hartley-Asp B. Prostate. 1991, 19: 299). Similar studies are conducted using sodium, potassium, pH, etc indicators. [1184]
• Due to its homology to an oxidoreductase, 98P4B6 can participate in imparting drug resistance by mobilizing and transporting small molecules. The effect of 98P4B6 on small molecule transport is investigated using a modified MDR assay. Control and 98P4B6 expressing cells are loaded with a fluorescent small molecule such as calcein AM. Extrusion of calcein from the cell is measured by examining the supernatants for fluorescent compound. MDR-like activity is confirmed using MDR inhibitors. [1185]
• When 98P4B6 functions as a transporter, it is used as target for diagnostic, prognostic, preventative and/or therapeutic purposes. [1186]
Example 48 Involvement in Tumor Progression
• The 98P4B6 gene can contribute to the growth of cancer cells. The role of 98P4B6 in tumor growth is confirmed in a variety of primary and transfected cell lines including prostate as well as NIH 3T3 cells engineered to stably express 98P4B6. Parental cells lacking 98P4B6 and cells expressing 98P4B6 are evaluated for cell growth using a well-documented proliferation assay (Fraser S P, Grimes J A, Djamgoz M B. Prostate. 2000;44:61, Johnson D E, Ochieng J, Evans S L. Anticancer Drugs. 1996, 7:288). [1187]
• To confirm the role of 98P4B6 in the transformation process, its effect in colony forming assays is investigated. Parental NIH-3T3 cells lacking 98P4B6 are compared to NIH-3T3 cells expressing 98P4B6, using a soft agar assay under stringent and more permissive conditions (Song Z. et al. Cancer Res. 2000;60:6730). [1188]
• To confirm the role of 98P4B6 in invasion and metastasis of cancer cells, a well-established assay is used, e.g., a Transwell Insert System assay (Becton Dickinson) (Cancer Res. 1999; 59:6010). Control cells, including prostate and fibroblast cell lines lacking 98P4B6 are compared to cells expressing 98P4B6. Cells are loaded with the fluorescent dye, calcein, and plated in the top well of the Transwell insert coated with a basement membrane analog. Invasion is determined by fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population. [1189]
• 98P4B6 can also play a role in cell cycle and apoptosis. Parental cells and cells expressing 98P4B6 are compared for differences in cell cycle regulation using a well-established BrdU assay (Abdel-Malek Z A. J Cell Physiol. 1988, 136:247). In short, cells are grown under both optimal (full serum) and limiting (low serum) conditions are labeled with BrdU and stained with anti-BrdU Ab and propidium iodide. Cells are analyzed for entry into the G1, S, and G2M phases of the cell cycle. Alternatively, the effect of stress on apoptosis is evaluated in control parental cells and cells expressing 98P4B6, including normal and tumor prostate cells. Engineered and parental cells are treated with various chemotherapeutic agents, such as etoposide, flutamide, etc, and protein synthesis inhibitors, such as cycloheximide. Cells are stained with annexin V-FITC and cell death is measured by FACS analysis. The modulation of cell death by 98P4B6 can play a critical role in regulating tumor progression and tumor load. [1190]
• When 98P4B6 plays a role in cell growth, transformation, invasion or apoptosis, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes. [1191]
Example 49 Involvement in Angiogenesis
• Angiogenesis or new capillary blood vessel formation is necessary for tumor growth (Hanahan D, Folkman J. Cell. 1996, 86:353; Folkman J. Endocrinology. 1998 139:441). Based on the effect of phsophodieseterase inhibitors on endothelial cells, 98P4B6 plays a role in angiogenesis (DeFouw L et al., Microvasc Res 2001, 62:263). Several assays have been developed to measure angiogenesis in vitro and in vivo, such as the tissue culture assays endothelial cell tube formation and endothelial cell proliferation. Using these assays as well as in vitro neo-vascularization, the role of 98P4B6 in angiogenesis, enhancement or inhibition, is confirmed. [1192]
• For example, endothelial cells engineered to express 98P4B6 are evaluated using tube formation and proliferation assays. The effect of 98P4B6 is also confirmed in animal models in vivo. For example, cells either expressing or lacking 98P4B6 are implanted subcutaneously in immunocompromised mice. Endothelial cell migration and angiogenesis are evaluated 5-15 days later using immunohistochemistry techniques. 98P4B6 affects angiogenesis, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes. [1193]
Example 50 Regulation of Transcription
• The localization of 98P4B6 and its similarity to hydrolases as well as its Ets motif (v.7) indicate that 98P4B6 is effectively used as a modulator of the transcriptional regulation of eukaryotic genes. Regulation of gene expression is confirmed, e.g., by studying gene expression in cells expressing or lacking 98P4B6. For this purpose, two types of experiments are performed. [1194]
• In the first set of experiments, RNA from parental and 98P4B6-expressing cells are extracted and hybridized to commercially available gene arrays (Clontech) (Smid-Koopman E et al. Br J Cancer. 2000. 83:246). Resting cells as well as cells treated with FBS or androgen are compared. Differentially expressed genes are identified in accordance with procedures known in the art. The differentially expressed genes are then mapped to biological pathways (Chen K et al. Thyroid. 2001. 11:41.). [1195]
• In the second set of experiments, specific transcriptional pathway activation is evaluated using commercially available (Stratagene) luciferase reporter constructs including: NFkB-luc, SRE-luc, ELK1-luc, ARE-luc, p53-luc, and CRE-luc. These transcriptional reporters contain consensus binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways, and represent a good tool to ascertain pathway activation and screen for positive and negative modulators of pathway activation. [1196]
• Thus, 98P4B6 plays a role in gene regulation. When 98P4B6 is involved in gene regulation it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes. [1197]
Example 51 Protein-Protein Association
• Several 6TM proteins have been shown to interact with other proteins, thereby regulating signal transduction, gene transcription, transformation, and cell adhesion. Using immunoprecipitation techniques as well as two yeast hybrid systems, proteins are identified that associate with 98P4B6. Immunoprecipitates from cells expressing 98P4B6 and cells lacking 98P4B6 are compared for specific protein-protein associations. [1198]
• Studies are performed to confirm the extent of association of 98P4B6 with effector molecules, such as nuclear proteins, transcription factors, kinases, phsophates etc. Studies comparing 98P4B6 positive and 98P4B6 negative cells as well as studies comparing unstimulated/resting cells and cells treated with epithelial cell activators, such as cytokines, growth factors, androgen and anti-integrin Ab reveal unique interactions. [1199]
• In addition, protein-protein interactions are confirmed using two yeast hybrid methodology (Curr Opin Chem Biol. 1999, 3:64). A vector carrying a library of proteins fused to the activation domain of a transcription factor is introduced into yeast expressing a 98P4B6-DNA-binding domain fusion protein and a reporter construct. Protein-protein interaction is detected by colorimetric reporter activity. Specific association with effector molecules and transcription factors directs one of skill to the mode of action of 98P4B6, and thus identifies therapeutic, prognostic, preventative and/or diagnostic targets for cancer. This and similar assays are also used to identify and screen for small molecules that interact with 98P4B6. [1200]
• Thus it is found that 98P4B6 associates with proteins and small molecules. Accordingly, 98P4B6and these proteins and small molecules are used for diagnostic, prognostic, preventative and/or therapeutic purposes. [1201]
• Throughout this application, various website data content, publications, patent applications and patents are referenced. (Websites are referenced by their Uniform Resource Locator, or URL, addresses on the World Wide Web.) The disclosures of each of these references are hereby incorporated by reference herein in their entireties. [1202]
• The present invention is not to be limited in scope by the embodiments disclosed herein, which are intended as single illustrations of individual aspects of the invention, and any that are functionally equivalent are within the scope of the invention. Various modifications to the models and methods of the invention, in addition to those described herein, will become apparent to those skilled in the art from the foregoing description and teachings, and are similarly intended to fall within the scope of the invention. Such modifications or other embodiments can be practiced without departing from the true scope and spirit of the invention. [1203]

  TABLE I
  Tissues that Express 98P4B6:
  a. Malignant Tissues

  a	Bladder
  b.	Breast
  c.	Cervix
  d.	Colon
  e.	Kidney
  f.	Lung
  g.	Ovary
  h.	Pancreas
  i.	Prostate
  j.	Stomach
  k.	Uterus

• [1204]

  TABLE II
  Amino Acid Abbreviations

  	SINGLE LETTER	THREE LETTER	FULL NAME
  	F	Phe	phenylalanine
  	L	Leu	leucine
  	S	Ser	serine
  	Y	Tyr	tyrosine
  	C	Cys	cysteine
  	W	Trp	tryptophan
  	P	Pro	proline
  	H	His	histidine
  	Q	Gln	glutamine
  	R	Arg	arginine
  	I	Ile	isoleucine
  	M	Met	methionine
  	T	Thr	threonine
  	N	Asn	asparagine
  	K	Lys	lysine
  	V	Val	valine
  	A	Ala	alanine
  	D	Asp	aspartic acid
  	E	Glu	glutamic acid
  	G	Gly	glycine

• [1205]

  TABLE III
  Amino Acid Substitution Matrix
  Adapted from the GCG Software 9.0 BLOSUM62 amino acid substitution matrix
  (block substitution matrix). The higher the value, the more likely a substitution is
  found in related, natural proteins.
  (See world wide web URL ikp.unibe.ch/manual/blosum62.html)

  A

  C

  D

  E

  F

  G

  H

  I

  K

  L

  M

  N

  P

  Q

  R

  S

  T

  V

  W

  Y

  .

  4

  0

  −2

  −1

  −2

  0

  −2

  −1

  −1

  −1

  −1

  −2

  −1

  −1

  −1

  1

  0

  0

  −3

  −2

  A

  9

  −3

  −4

  −2

  −3

  −3

  −1

  −3

  −1

  −1

  −3

  −3

  −3

  −3

  −1

  −1

  −1

  −2

  −2

  C

  6

  2

  −3

  −1

  −1

  −3

  −1

  −4

  −3

  1

  −1

  0

  −2

  0

  −1

  −3

  −4

  −3

  D

  5

  −3

  −2

  0

  −3

  1

  −3

  −2

  0

  −1

  2

  0

  0

  −1

  −2

  −3

  −2

  E

  6

  −3

  −1

  0

  −3

  0

  0

  −3

  −4

  −3

  −3

  −2

  −2

  −1

  1

  3

  F

  6

  −2

  −4

  −2

  −4

  −3

  0

  −2

  −2

  −2

  0

  −2

  −3

  −2

  −3

  G

  8

  −3

  −1

  −3

  −2

  1

  −2

  0

  0

  −1

  −2

  −3

  −2

  2

  H

  4

  −3

  2

  1

  −3

  −3

  −3

  −3

  −2

  −1

  3

  −3

  −1

  I

  5

  −2

  −1

  0

  −1

  1

  2

  0

  −1

  −2

  −3

  −2

  K

  4

  2

  −3

  −3

  −2

  −2

  −2

  −1

  1

  −2

  −1

  L

  5

  −2

  −2

  0

  −1

  −1

  −1

  1

  −1

  −1

  M

  6

  −2

  0

  0

  1

  0

  −3

  −4

  −2

  N

  7

  −1

  −2

  −1

  −1

  −2

  −4

  −3

  P

  5

  1

  0

  −1

  −2

  −2

  −1

  Q

  5

  −1

  −1

  −3

  −3

  −2

  R

  4

  1

  −2

  −3

  −2

  S

  5

  0

  −2

  −2

  T

  4

  −3

  −1

  V

  11

  2

  W

  7

  Y

• [1206]

  TABLE IV
  HLA Class I/II Motifs/Supermotifs

• [1207]

  TABLE IV (A)
  HLA Class I Supermotifs/Motifs

  		POSITION	POSITION
  	POSITION	3 (Primary	C Terminus
  	2 (Primary Anchor)	Anchor)	(Primary Anchor)
  SUPERMOTIF
  A1	TI LVMS		FWY
  A2	LIVM ATQ		IV MATL
  A3	VSMA TLI		RK
  A24	YF WIVLMT		FI YWLM
  B7	P		VILF MWYA
  B27	RHK		FYL WMIVA
  B44	E D		FWYLIMVA
  B58	ATS		FWY LIVMA
  B62	QL IVMP		FWY MIVLA
  MOTIFS
  A1	TSM		Y
  A1		DE AS	Y
  A2.1	LM VQIAT		V LIMAT
  A3	LMVISATF CGD		KYR HFA
  A11	VTMLISAGN CDF		K RYH
  A24	YFWM		FLIW
  A*3101	MVT ALIS		R K
  A*3301	MVALF IST		RK
  A*6801	AVT MSLI		RK
  B*0702	P		LMF WYAIV
  B*3501	P		LMFWY IVA
  B51	P		LIVF WYAM
  B*5301	P		IMFWY ALV
  B*5401	P		ATIV LMFWY

• [1208]

  TABLE IV (B)
  HLA Class II Supermotif

  1	6	9
  W, F, Y, V, I, L	A, V, I, L, P, C, S, T	A, V, I, L, C, S, T, M, Y

• [1209]

  TABLE IV (C)
  HLA Class II Motifs

  MOTIFS

  		1° anchor 1	2	3	4	5	1° anchor 6	7	8	9
  DR4	preferred	FMYLIVW	M	T		I	VSTCPALIM	MH		MH
  	deleterious				W			R		WDE
  DR1	preferred	MFLIVWY			PAMQ		VMATSPLIC	M		AVM
  	deleterious		C	CH	FD	CWD		GDE	D
  DR7	preferred	MFLIVWY	M	W	A		IVMSACTPL	M		IV
  	deleterious		C		G			GRD	N	G

  DR3

  MOTIFS

  	1° anchor 1	2	3	1° anchor 4	5	1° anchor 6
  Motif a preferred		LIVMFY			D
  Motif b preferred		LIVMFAY			DNQEST		KRH
  DR Supermotif		MFLIVWY					VMSTACPLI

• [1210]

  TABLE IV (D)
  HLA Class I Supermotifs

  SUPER-

  POSITION:

  MOTIFS		1	2	3	4	5	6	7	8	C-terminus
  A1			1° Anchor							1° Anchor
  			TILVMS							FWY
  A2			1° Anchor							1° Anchor
  			{overscore (LIVMATQ)}							LIVMAT
  A3	Preferred		1° Anchor	YFW			YFW	YFW	P	1° Anchor
  			VSMATLI	(4/5)			(3/5)	(4/5)	(4/5)	RK
  	deleterious	DE(3/5);		DE
  		P(5/5)		(4/5)
  A24			1° Anchor							1° Anchor
  			{overscore (YFWIVLMT)}							FIYWLM
  B7	Preferred	FWY(5/5)	1° Anchor	FWY					FWY	1° Anchor
  		LIVM(3/5)	P	(4/5)					(3/5)	{overscore (VILFMWYA)}
  	deleterious	DE(3/5);				DE	G	QN	DE
  		P(5/5);				(3/5)	(4/5)	(4/5)	(4/5)
  		G(4/5);
  		A(3/5);
  		QN(3/5)
  B27			1° Anchor							1° Anchor
  			RHK							{overscore (FYLWMIVA)}
  B44			1° Anchor							1° Anchor
  			ED							{overscore (FWYLIMVA)}
  B58			1° Anchor							1° Anchor
  			ATS							{overscore (FWYLIVMA)}
  B62			1° Anchor							1° Anchor
  			QLIVMP							{overscore (FWYMIVLA)}

• [1211]

  TABLE IV (E)
  HLA Class I Motifs

  POSITION

  										9 or C-	C-
  		1	2	3	4	5	6	7	8	terminus	terminus
  A1	preferred	GFYW	1° Anchor	DEA	YFW		P	DEQN	YFW	1° Anchor
  9-mer			STM							Y
  	deleterious	DE		RHKLIVMP	A	G	A
  A1	preferred	GRHK	ASTCLIVM	1° Anchor	GSTC		ASTC	LIVM	DE	1° Anchor
  9-mer				DEAS						Y
  	deleterious	A	RHKDEPYFW		DE	PQN	RHK	PG	GP
  A1	preferred	YFW	1° Anchor	DEAQN	A	YFWQN		PASTC	GDE	P	1° Anchor
  10-mer			STM								Y
  	deleterious	GP		RHKGLIVM	DE	RHK	QNA	RHKYFW	RHK	A
  A1	preferred	YFW	STCLIVM	1° Anchor	A	YFW		PG	G	YFW	1° Anchor
  10-mer				DEAS							Y
  	deleterious	RHK	RHKDEPYFW			P	G		PRHK	QN
  A2.1	preferred	YFW	1° Anchor	YFW	STC	YFW		A	P	1° Anchor
  9-mer			LMIVQAT							VLIMAT
  	deleterious	DEP		DERKH			RKH	DERKH

  POSITION:

  C-

  		1	2	3	4	5	6	7	8	9	terminus
  A2.1	pre-	AYFW	1° Anchor	LVIM	G		G		FYWLVIM		1° Anchor
  10-mer	ferred		LMIVQAT								VLIMAT
  	dele-	DEP		DE	RKHA	P		RKH	DERKH	RKH
  	te-
  	rious
  A3	pre-	RHK	1° Anchor	YFW	PRHKYFW	A	YFW		P	1° Anchor
  	ferred		{overscore (LMVISATFCGD)}							KYRHFA
  	dele-	DEP		DE
  	te-
  	rious
  A11	pre-	A	1° Anchor	YFW	YFW	A	YFW	YFW	P	1° Anchor
  	ferred		{overscore (VTLMISAGNCDF)}							KRYH
  	dele-	DEP						A	G
  	te-
  	rious
  A24	pre-	YFWRHK	1° Anchor		STC			YFW	YFW	1° Anchor
  9-mer	ferred		YFWM							FLIW
  	dele-	DEG		DE	G	QNP	DERHK	G	AQN
  	te-
  	rious
  A24	Pre-		1° Anchor		P	YFWP		P			1° Anchor
  10-mer	ferred		YFWM								FLIW
  	Dele-			GDE	QN	RHK	DE	A	QN	DEA
  	te-
  	rious
  A3101	Pre-	RHK	1° Anchor	YFW	P		YFW	YFW	AP	1° Anchor
  	ferred		MVTALIS							RK
  	Dele-	DEP		DE		ADE	DE	DE	DE
  	te-
  	rious
  A3301	Pre-		1° Anchor	YFW				AYFW		1° Anchor
  	ferred		{overscore (MVALFIST)}							RK
  	Dele-	GP		DE
  	te-
  	rious
  A6801	Pre-	YFWSTC	1° Anchor			YFW		YFW	P	1° Anchor
  	ferred		AVTMSLI			LIVM				RK
  	Dele-	GP		DEG		RHK			A
  	te-
  	rious
  B0702	Pre-	RHKFWY	1° Anchor	RHK		RHK	RHK	RHK	PA	1° Anchor
  	ferred		P							{overscore (LMFWY)}
  										AIV
  	Dele-	DEQNP		DEP	DE	DE	GDE	QN	DE
  	te-
  	rious
  B3501	Pre-	FWYLIVM	1° Anchor	FWY				FWY		1° Anchor
  	ferred		P							{overscore (LMFWYIVA)}
  	dele-	AGP				G	G
  	te-
  	rious

  POSITION:

  										9 or C-	C-
  		1	2	3	4	5	6	7	8	terminus	terminus
  A1	pre-	GFYW	1° Anchor	DEA	YFW		P	DEQN	YFW	1° Anchor
  9-mer	ferred		STM							Y
  	dele-	DE		RHKLIVMP	A	G	A
  	te-
  	rious
  A1	pre-	GRHK	ASTCLIVM	1° Anchor	GSTC		A	LIVM	DE	1° Anchor
  9-mer	ferred			DEAS			STC			Y
  	dele-	A	RHKDEP		DE	PQN	RHK	PG	GP
  	te-		YFW
  	rious
  	dele-	AGP				G	G
  	te-
  	rious
  B51	Pre-	LIVMFWY	1° Anchor	FWY	STC	FWY		G	FWY	1° Anchor
  	ferred		P							{overscore (LIVFWYAM)}
  	dele-	AGPDERHKSTC				DE	G	DEQN	GDE
  	te-
  	rious
  B5301	pre-	LIVMFWY	1° Anchor	FWY	STC	FWY		LIVM	FWY	1° Anchor
  	ferred		P					FWY		{overscore (IMFWYALV)}
  	dele-	AGPQN					G	RHKQN	DE
  	te-
  	rious
  B5401	pre-	FWY	1° Anchor	FWYLIVM		LIVM		ALIVM	FWYAP	1° Anchor
  	ferred		P							{overscore (ATIVLMFWY)}
  	dele-	GPQNDE		GDESTC		RHKDE	DE	QNDGE	DE
  	te-
  	rious

• [1212]

  TABLE IV (F)
  Summary of HLA-supertypes
  Overall phenotypic frequencies of HLA-supertypes in different ethnic populations

  Specificity

  Phenotypic frequency

  Supertype	Position 2	C-Terminus	Caucasian	N.A. Black	Japanese	Chinese	Hispanic	Average

  B7	P	AILMVFWY	43.2	55.1	57.1	43.0	49.3	49.5
  A3	AILMVST	RK	37.5	42.1	45.8	52.7	43.1	44.2
  A2	AILMVT	AILMVT	45.8	39.0	42.4	45.9	43.0	42.2
  A24	YF (WIVLMT)	FI (YWLM)	23.9	38.9	58.6	40.1	38.3	40.0
  B44	E (D)	FWYLIMVA	43.0	21.2	42.9	39.1	39.0	37.0
  A1	TI (LVMS)	FWY	47.1	16.1	21.8	14.7	26.3	25.2
  B27	RHK	FYL (WMI)	28.4	26.1	13.3	13.9	35.3	23.4
  B62	QL (IVMP)	FWY (MIV)	12.6	4.8	36.5	25.4	11.1	18.1
  B58	ATS	FWY (LIV)	10.0	25.1	1.6	9.0	5.9	10.3

• [1213]

  TABLE IV (G)
  Calculated population coverage afforded by different HLA-supertype combinations

  Phenotypic frequency

  HLA-supertypes	Caucasian	N.A Blacks	Japanese	Chinese	Hispanic	Average

  A2, A3 and B7	83.0	86.1	87.5	88.4	86.3	86.2
  A2, A3, B7, A24, B44	99.5	98.1	100.0	99.5	99.4	99.3
  and A1	99.9	99.6	100.0	99.8	99.9	99.8
  A2, A3, B7, A24
  B44, A1, B27, B62,
  and B58

• [1214]

  TABLE V
  Frequently Occurring Motifs

  	avrg. %
  Name	identity	Description	Potential Function
  zf-C2H2	34%	Zinc finger, C2H2 type	Nucleic acid-binding protein functions as
  			transcription factor, nuclear location
  			probable
  cytochrome_b_N	68%	Cytochrome b(N-	membrane bound oxidase, generate
  		terminal)/b6/petB	superoxide
  lg	19%	Immunoglobulin domain	domains are one hundred amino acids
  			long and include a conserved
  			intradomain disulfide bond.
  WD40	18%	WD domain, G-beta repeat	tandem repeats of about 40 residues,
  			each containing a Trp-Asp motif.
  			Function in signal transduction and
  			protein interaction
  PDZ
  	23%	PDZ domain	may function in targeting signaling
  			molecules to sub-membranous sites
  LRR	28%	Leucine Rich Repeat	short sequence motifs involved in
  			protein-protein interactions
  Pkinase	23%	Protein kinase domain	conserved catalytic core common to
  			both serine/threonine and tyrosine
  			protein kinases containing an ATP
  			binding site and a catalytic site
  PH
  	16%	PH domain	pleckstrin homology involved in
  			intracellular signaling or as constituents
  			of the cytoskeleton
  EGF	34%	EGF-like domain	30-40 amino-acid long found in the
  			extracellular domain of membrane-
  			bound proteins or in secreted proteins
  Rvt	49%	Reverse transcriptase
  		(RNA-dependent DNA
  		polymerase)
  Ank	25%	Ank repeat	Cytoplasmic protein, associates integral
  			membrane proteins to the cytoskeleton
  Oxidored_q1	32%	NADH-	membrane associated. Involved in
  		Ubiquinone/plastoquinone	proton translocation across the
  		(complex I), various chains	membrane
  Efhand	24%	EF hand	calcium-binding domain, consists of a12
  			residue loop flanked on both sides by a
  			12 residue alpha-helical domain
  Rvp	79%	Retroviral aspartyl	Aspartyl or acid proteases, centered on
  		protease	a catalytic aspartyl residue
  Collagen	42%	Collagen triple helix repeat	extracellular structural proteins involved
  		(20 copies)	in formation of connective tissue. The
  			sequence consists of the G-X-Y and the
  			polypeptide chains forms a triple helix.
  Fn3	20%	Fibronectin type III domain	Located in the extracellular ligand-
  			binding region of receptors and is about
  			200 amino acid residues long with two
  			pairs of cysteines involved in disulfide
  			bonds
  7tm_1	19%	7 transmembrane receptor	seven hydrophobic transmembrane
  		(rhodopsin family)	regions, with the N-terminus located
  			extracellularly while the C-terminus is
  			cytoplasmic. Signal through G proteins

• [1215]

  TABLE VI
  Motifs and Post-translational
  Modifications of 98P4B6
  cAMP- and cGMP-dependent
  protein kinase phosphorylation site.

  	176-179	RKET	(SEQ ID NO: 114)

  Protein kinase C phosphorylation site.

  	235-237	SVK

  Casein kinase II phosphorylation site.

  	9-12	SATD	(SEQ ID NO: 115)
  	50-53	TVME	(SEQ ID NO: 116)
  	130-133	SCTD	(SEQ ID NO: 117)
  	172-175	SPEE	(SEQ ID NO: 118)

  N-myristoylation site.

  	14-19	GLSIST	(SEQ ID NO: 119)

  G-protein coupled receptors family 1 signature.

  	52-68	MESSVLLAMAFDRFVAV	(SEQ ID NO: 120)

• [1216]

  TABLE VII
  Search Peptides

  v.1 aa1-454 (SEQ ID NO: 121)
  9-mers, 10-mers and 15-mers
  MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD FAKSLTIRLI RCGYHVVIGS
  RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS LWDLRHLLVG KILIDVSNNM
  RINQYPESNA EYLASLFPDS LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE
  LARQLNFIPI DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA
  RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ
  CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN EEEVWRIEMY
  ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY VALLISTFHV LIYGWKRAFE
  EEYYRFYTPP NFVLALVLPS IVILDLLQLC RYPD
  v.2 aa1-45 (SEQ ID NO: 122)
  9-mers, 10-mers, 15-mers
  SGSPGLQALSL SLSSGFTPFS CLSLPSSWDY RCPPPCPADF FLYF
  v.5, (one aa diff at 211 and different c-terminal)
  Part A
  9-mers: aa203-219

  NLPLRLFTFWRGPVVVA	(SEQ ID NO: 123)
  10-mers: aa202-220
  ENLPLRLFTFWRGPVVVAI	(SEQ ID NO: 124)
  15-mers: aa197-225
  SAREIENLPLRLFTFWRGPVVVAISLATF	(SEQ ID NO: 125)
  Part B
  9-mers: aa388-419
  WREFSFIQIFCSFADTQTELELEFVFLLTLLL	(SEQ ID NO: 126)
  10-mers: aa387-419
  NWREFSFIQIFCSFADTQTELELEFVFLLTLLL	(SEQ ID NO: 127)
  15-mers: aa382-419
  VSNALNWREFSFIQIFCSFADTQTELELEFVFLLTLLL	(SEQ ID NO: 128)

  v.6, (different from our original in 445-490)
  9-mers; aa447-490 (SEQ ID NO: 129)
  VLPSIVILGKIILFLPCISRKLKRIKKGWEKSQFLEEGIGGTIPHVSPERVTVM
  10-mers: aa446-490 (SEQ ID NO: 130)
  LVLPSIVILGKIILFLPCISRKLKRIKKGWEKSQFLEEGIGGTIPHVSPERVTVM
  15-mers: aa441-490 (SEQ ID NO: 131)
  NFVLALVLPSIVILGKIILFLPCISRKLKRIKKGWEKSQFLEEGIGGTIPHVSPERVTVM
  v.7, (deleting our original 340-394, 392-576 is different)
  Part A
  9-mers: aa334-350

  FLNMAYQQSTLGYVALL	(SEQ ID NO: 132)
  10-mers: aa333-351
  LFLNMAYQQSTLGYVALLI	(SEQ ID NO: 133)
  15-mers: aa328-355
  RSERYLFLNMAYQQSTLGYVALLISTFHV	(SEQ ID NO: 134)
  Part B

  9-mers: aa384-576 (SEQ ID NO: 135)
  PSIVILDLSVEVLASPAAAWKCLGANILRGGLSEIVLPIEWQQDRKIPPLSTPPPPAMWTEEAGA
  TAEAQESGIRNKSSSSSQIPVVGVVTEDDEAQDSIDPPESPDRALKAANSWRNPVLPHTNGVGPL
  WEFLLRLLKSQAASGTLSLAFTSWSLGEFLGSGTWMKLETIILSKLT QEQKSKHCMF SLISGS
  10-mers: aa383-576 (SEQ ID NO: 136)
  LPSIVILDLSVEVLASPAAAWKCLGANILRGGLSEIVLPIEWQQDRKIPPLSTPPPPAMWTEEAG
  ATAEAQESGIRNKSSSSSQIPVVGVVTEDDEAQDSIDPPESPDRALKAANSWRNPVLPHTNGVGP
  LWEFLLRLLKSQAASGTLSLAFTSWSLG EFLGSGTWMK LETIILSKLT QEQKSKHCMF
  SLISGS
  15-mers: aa378-576 (SEQ ID NO: 137)
  VLALVLPSIVILDLSVEVLASPAAAWKCLGANILRGGLSEIVLPIEWQQDRKIPPLSTPPPPAMW
  TEEAGATAEAQESGIRNKSSSSSQIPVVGVVTEDDEAQDSIDPPESPDRALKAANSWRNPVLPHT
  NGVGPLWEFLLRLLKSQAASGTLSLAFTSWSLG EFLGSGTWMK LETIILSKLT
  QEQKSKHCMF SLISGS
  v.8, SNP variant of v.6, one aa different at 475
  9-mers: aa466-482

  KSQFLEEGMGGTIPHVS	(SEQ ID NO: 138)
  10-mers: aa465-483
  EKSQFLEEGMGGTIPHVSP	(SEQ ID NO: 139)
  15-mers: aa460-489
  IKKGWEKSQFLEEGMGGTIPHVSPERVTV	(SEQ ID NO: 140)
  V13
  9-mers: aa9-25
  SPKSLSETFLPNGINGI	(SEQ ID NO: 141)
  10-mers: aa8-26
  GSPKSLSETFLPNGINGIK	(SEQ ID NO: 142)
  15-mers: aa3-31
  SISMMGSPKSLSETFLPNGINGIKDARKV	(SEQ ID NO: 143)
  v.14
  9-mers: aa203-219
  NLPLRLFTFWRGPVVVA	(SEQ ID NO: 144)
  10-mers: aa202-220
  ENLPLRLFTFWRGPVVVAI	(SEQ ID NO: 145)
  15-mers: aa197-225
  SAREIENLPLRLFTFWRGPVVVAISLATF	(SEQ ID NO: 146)
  V.21
  9-mers 557-572
  SKLTQEQKTKHCMFSLI	(SEQ ID NO: 147)
  10-mers 556-573
  LSKLTQEQKTKHCMFSLIS	(SEQ ID NO: 148)
  15-mers 551-576
  LETIILSKLTQEQKTKHCMFSLISGS	(SEQ ID NO: 149)
  V.25
  9-mers aa 447-463
  ILFLPCISQKLKRIKKG	(SEQ ID NO: 150)
  10-mers aa 446-464
  IILFLPCISQKLKRIKKGW	(SEQ ID NO: 151)
  15-mers aa440-468
  VILGKIILFLPCISQKLKRIKKGWEKSQF	(SEQ ID NO: 152)

• [1217]

  TABLE VIII
  Start	Subsequence	Score

  V1-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  443	ILDLLQLCR	25.000
  129	NAEYLASLF	9.000
  294	WLETWLQCR	9.000
  113	LIDVSNNMR	5.000
  200	EIENLPLRL	4.500
  244	QSDFYKIPI	3.750
  405	ISTFHVLIY	3.750
  13	LSETCLPNG	2.700
  221	SLATFFFLY	2.500
  263	AITLLSLVY	2.500
  276	LAAAYQLYY	2.500
  419	FEEEYYRFY	2.250
  155	QLGPKDASR	2.000
  66	ASEFFPHVV	1.350
  272	LAGLLAAAY	1.000
  35	VIGSGDFAK	1.000
  178	VIELARQLN	0.900
  356	RIEMYISFG	0.900
  418	AFEEEYYRF	0.900
  319	YSLCLPMRR	0.750
  43	KSLTIRLIR	0.750
  327	RSERYLFLN	0.675
  427	YTPPNFVLA	0.500
  304	QLGLLSFFF	0.500
  257	KTLPIVAIT	0.500
  135	SLFPDSLIV	0.500
  223	ATFFFLYSF	0.500
  275	LLAAAYQLY	0.500
  385	ALNWREFSF	0.500
  219	AISLATFFF	0.500
  16	TCLPNGING	0.500
  90	FVAIHREHY	0.500
  87	NIIFVAIHR	0.500
  249	KIPIEIVNK	0.400
  137	FPDSLIVKG	0.250
  189	PIDLGSLSS	0.250
  241	RNQQSDFYK	0.250
  351	EEEVWRIEM	0.225
  349	WNEEEVWRI	0.225
  125	YPESNAEYL	0.225
  420	EEEYYRFYT	0.225
  388	WREFSFIQS	0.225
  198	AREIENLPL	0.225
  57	VIGSRNPKF	0.200
  56	VVIGSRNPK	0.200
  217	VVAISLATF	0.200
  3	SISMMGSPK	0.200
  417	RAFEEEYYR	0.200
  436	LVLPSIVIL	0.200
  377	TSIPSVSNA	1.150
  158	PKDASRQVY	0.125
  101	LWDLRHLLV	0.125
  117	SNNMRINQY	0.125
  392	SFIQSTLGY	0.125
  202	ENLPLRLFT	0.125
  330	RYLFLNMAY	0.125
  38	SGDFAKSLT	0.125
  98	YTSLWDLRH	0.125
  406	STFHVLIYG	0.125
  218	VAISLATFF	0.100
  167	ICSNNIQAR	0.100
  400	YVALLISTF	0.100
  235	VIHPYARNQ	0.100
  381	SVSNALNWR	0.100
  22	INGIKDARK	0.100
  21	GINGIKDAR	0.100
  281	QLYYGTKYR	0.100
  322	CLPMRRSER	0.100
  411	LIYGWKRAF	0.100
  191	DLGSLSSAR	0.100
  409	HVLIYGWKR	0.100
  344	NIENSWNEE	0.090
  251	PIEIVNKTL	0.090
  308	LSFFFAMVH	0.075
  195	LSSAREIEN	0.075
  116	VSNNMRINQ	0.075
  280	YQLYYGTKY	0.075
  220	ISLATFFFL	0.075
  175	RQQVIELAR	0.075
  127	ESNAEYLAS	0.075
  432	FVLALVLPS	0.050
  12	SLSETCLPN	0.050
  106	HLLVGKILI	0.050
  311	FFAMVHVAY	0.050
  269	LVYLAGLLA	0.050
  216	VVVAISLAT	0.050
  124	QYPESNAEY	0.050
  166	YICSNNIQA	0.050
  258	TLPIVAITL	0.050
  18	LPNGINGIK	0.050
  435	ALVLPSIVI	0.050
  25	IKDARKVTV	0.050
  73	VVDVTHHED	0.050
  222	LATFFFLYS	0.050
  184	QLNFIPIDL	0.050
  367	SLGLLSLLA	0.050
  46	TIRLIRCGY	0.050
  306	GLLSFFFAM	0.050
  261	IVAITLLSL	0.050
  203	NLPLRLFTL	0.050

  V2-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  23	LSLPSSWDY	7.500
  33	CPPPCPADF	0.500
  36	PCPADFFLY	0.250
  9	LSLSLSSGF	0.150
  37	CPADFFLYF	0.125
  17	FTPFSCLSL	0.125
  24	SLPSSWDYR	0.100
  12	SLSSGFTPF	0.100
  14	SSFGTPGSC	0.075
  5	GLQALSLSL	0.050
  7	QALSLSLSS	0.050
  13	LSSGFTPFS	0.030
  2	GSPGLQALS	0.030
  20	FSCLSLPSS	0.030
  1	SGSPGLQAL	0.025
  32	RCPPPCPAD	0.020
  35	PPCPADFFL	0.013
  3	SPGLQALSL	0.013
  21	SCLSLPSSW	0.010
  8	ALSLSLSSG	0.010
  10	SLSLSSGFT	0.010
  11	LSLSSGFTP	0.007
  25	LPSSWDYRC	0.005
  16	GFTPFSCLS	0.005
  28	SWDYRCPPP	0.005
  31	YRCPPPCPA	0.005
  15	SGFTPFSCL	0.003
  34	PPPCPADFF	0.003
  6	LQALSLSLS	0.002
  22	CLSLPSSWD	0.001
  19	PFSCLSLPS	0.000
  18	TPFSCLSLP	0.000
  4	PGLQALSLS	0.000
  27	SSWDYRCPP	0.000
  26	PSSWDYRCP	0.000
  29	WDYRCPPPC	0.000
  30	DYRCPPPCP	0.000

  V5A-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  1	NLPLRLFTF	0.500
  7	FTFWRGPVV	0.050
  3	PLRLFTFWR	0.005
  5	RLFTFWRGP	0.001
  6	LFTFWRGPV	0.001
  4	LRLFTFWRG	0.001
  2	LPLRLFTFW	0.000
  9	FWRGPVVVA	0.000
  8	TFWRGPVVV	0.000

  V5B-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position for
  each peptide is the start position plus eight.

  21	ELEFVFLLT	4.500
  17	QTELELEFV	2.250
  19	ELELEFVFL	1.800
  1	WREFSFIQI	0.225
  16	TQTELELEF	0.075
  4	FSFIQIFCS	0.075
  24	FVFLLTLLL	0.050
  13	FADTQTELE	0.050
  18	TELELEFVF	0.025
  8	QIFCSFADT	0.020
  10	FCSFADTQT	0.010
  6	FIQIFCSFA	0.010
  2	REFSFIQIF	0.005
  5	SFIQIFCSF	0.005
  15	DTQTELELE	0.003
  20	LELEFVFLL	0.003
  22	LEFVFLLTL	0.003
  14	ADTQTELEL	0.003
  3	EFSFIQIFC	0.003
  11	CSFADTQTE	0.002
  7	IQIFCSFAD	0.001
  23	EFVFLLTLL	0.001
  12	SFADTQTEL	0.001
  9	IFCSFADTQ	0.001

  V6-HLA-A1-9MERS-98P4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  34	FLEEGIGGT	0.900
  12	ILFLPCISR	0.500
  6	VILGKIILF	0.500
  2	LPSIVILGK	0.250
  42	TIPHVSPER	0.200
  45	HVSPERVTV	0.200
  13	LFLPCISRK	0.100
  16	PCISRKLKR	0.050
  1	VLPSIVILG	0.050
  15	LPCISRKLK	0.050
  5	IVILGKIIL	0.050
  35	LEEGIGGTI	0.045
  41	GTIPHVSPE	0.025
  38	GIGGTIPHV	0.020
  10	KILLFLPCI	0.020
  31	KSQFLEEGI	0.015
  46	VSPERVTVM	0.015
  37	EGIGGTIPH	0.013
  4	SIVILGKII	0.010
  14	FLPCISRKL	0.010
  11	IILFLPCIS	0.010
  19	SRKLKRIKK	0.005
  7	ILGKIILFL	0.005
  26	KKGWEKSQF	0.005
  18	ISRKLKRIK	0.003
  33	QFLEEGIGG	0.003
  43	IPHVSPERV	0.003
  9	GKIILFLPC	0.003
  39	IGGTIPHVS	0.003
  28	GWEKSQFLE	0.002
  3	PSIVILGKI	0.002
  32	SQFLEEGIG	0.002
  23	KRIKKGWEK	0.001
  17	CISRKLKRI	0.001
  40	GGTIPHVSP	0.001
  30	EKSQFLEEG	0.001
  27	KGWEKSQFL	0.000
  8	LGKIILFLP	0.000
  24	RIKKGWEKS	0.000
  21	KLKRIKKGW	0.000
  36	EEGIGGTIP	0.000
  44	PHVSPERVT	0.000
  20	RKLKRIKKG	0.000
  25	IKKGWEKSQ	0.000
  29	WEKSQFLEE	0.000
  22	LKRIKKGWE	0.000

  V7A-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position os specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  5	LSETFLPNG	2.700
  4	SLSETFLPN	0.050
  7	ETFLPNGIN	0.025
  8	TFLPNGING	0.025
  9	FLPNGINGI	0.010
  3	KSLSETFLP	0.007
  1	SPKSLSETF	0.003
  6	SETFLPNGI	0.001
  2	PKSLSETFL	0.000

  V7B-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  5	AYQQSTLGY	0.125
  9	STLGYVALL	0.050
  8	QSTLGYVAL	0.030
  1	FLNMAYQQS	0.010
  4	MAYQQSTLG	0.010
  3	NMAYQQSTL	0.005
  7	QQSTLGYVA	0.003
  2	LNMAYQQST	0.003
  6	YQQSTLGYV	0.002

  V7C-HLA-A1-9mers-98P4B6

  Each peptide is a portion of SEQ ID NO: 15;

  each start position is specified, the length of

  peptide is 9 amino acids, and the end position

  for each peptide is the start position plus eight.

  167	KLETIILSK	90.00
  59	WTEEAGATA	4.500
  13	LASPAAAWK	4.000
  69	AQESGIRNK	2.700
  38	PIEWQQDRK	1.800
  66	TAEAQESGI	0.900
  9	SVEVLASPA	0.900
  143	ASGTLSLAF	0.750
  99	SIDPPESPD	0.500
  51	STPPPPAMW	0.500
  5	ILDLSVEVL	0.500
  21	KCLGANILR	0.500
  90	VTEDDEAQD	0.450
  50	LSTPPPPAM	0.300
  32	LSEIVLPIE	0.270
  151	FTSWSLGEF	0.250
  156	LGEFLGSGT	0.225
  175	KLTQEQKSK	0.200
  159	FLGSGTWMK	0.200
  177	TQEQKSKHC	0.135
  128	GPLWEFLLR	0.125
  145	GTLSLAFTS	0.125
  52	TPPPPAMWT	0.125
  126	GVGPLWELF	0.100
  35	IVLPIEWQQ	0.100
  100	IDPPESPDR	0.100
  104	ESPDRALKA	0.075
  78	SSSSSQIPV	0.075
  154	WSLGEFLGS	0.075
  131	WEFLLRLLK	0.050
  22	CLGANILRG	0.050
  68	EAQESGIRN	0.050
  184	HCMFSLISG	0.050
  7	DLSVEVLAS	0.050
  170	TIILSKLTQ	0.050
  2	SIVILDLSV	0.050
  17	AAAWKCLGA	0.050
  141	QAASGTLSL	0.050
  123	HTNGVGPLW	0.050
  31	GLSEIVLPI	0.050
  130	LWEFLLRLL	0.045
  173	LSKLTQEQK	0.030
  80	SSSQIPVVG	0.030
  81	SSQIPVVGV	0.030

  V7C-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  79	SSSSQIPVV	0.030
  125	NGVGPLWEF	0.025
  65	ATAEAQESG	0.025
  37	LPIEWQQDR	0.025
  92	EDDEAQDSI	0.025
  169	ETIILSKLT	0.025
  176	LTQEQKSKH	0.025
  91	TEDDEAQDS	0.025
  102	PPESPDRAL	0.022
  103	PESPDRALK	0.020
  11	EVLASPAAA	0.020
  83	QIPVVGVVT	0.020
  4	VILDLSVEV	0.020
  12	VLASPAAAW	0.020
  42	QQDRKIPPL	0.015
  71	ESGIRNKSS	0.015
  96	AQDSIDPPE	0.015
  14	ASPAAAWKC	0.015
  82	SQIPVVGVV	0.015
  139	KSQAASGTL	0.015
  147	LSLAFTSWS	0.015
  29	RGGLSEIVL	0.013
  105	SPDRALKAA	0.013
  162	SGTWMKLET	0.013
  160	LGSGTWMKL	0.013
  127	VGPLWEFLL	0.013
  146	TLSLAFTSW	0.010
  88	GVVTEDDEA	0.010
  142	AASGTLSLA	0.010
  64	GATAEAQES	0.010
  119	PVLPHTNGV	0.010
  46	KIPPLSTPP	0.010
  62	EAGATAEAQ	0.010
  109	ALKAANSWR	0.010
  148	SLAFTSWSL	0.010
  112	AANSWRNPV	0.010
  149	LAFTSWSLG	0.010
  34	EIVLPIEWQ	0.010
  116	WRNPVLPHT	0.010
  24	GANILRGGL	0.010
  89	VVTEDDEAQ	0.010
  155	SLGEFLGSG	0.010
  120	VLPHTNGVG	0.010
  181	KSKHCMFSL	0.008
  113	ANSWRNPVL	0.005
  67	AEAQESGIR	0.005
  185	CMGSLISGS	0.005
  144	SGTLSLAFT	0.005
  93	DDEAQDSID	0.005
  60	TEEAGATAE	0.005
  8	LSVEVLASP	0.003
  183	KHCMFSLIS	0.003
  25	ANILRGGLS	0.003
  165	WMKLETIIL	0.003
  101	DPPESPDRA	0.003
  15	SPAAAWKCL	0.003

• [1218]

  TABLE IX
  Start	Subsequence	Score

  V1-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  178	VIELARQLNF	45.000
  443	ILDLLQLCRY	25.000
  294	WLETWLQCRK	18.000
  135	SLFPDSLIVK	10.000
  200	EIENLPLRLF	9.000
  356	RIEMYISFGI	4.500
  220	ISLATFFFLY	3.750
  391	FSFIQSTLGY	3.750
  76	VTHHEDALTK	2.500
  404	LISTFHVLIY	2.500
  262	VAITLLSLVY	2.500
  275	LLAAAYQLYY	2.500
  113	LIDVSNNMRI	2.500
  351	EEEVWRIEMY	2.250
  418	AFEEEYYRFY	2.250
  123	NQYPESNAEY	1.500
  13	LSETCLPNGI	1.350
  137	FPDSLIVKGF	1.250
  427	YTPPNFVLAL	1.250
  257	KTLPIVAITL	1.250
  271	YLAGLLAAAY	1.000
  34	GVIGSGDFAK	1.000
  321	LCLPMRRSER	1.000
  198	AREIENLPLR	0.900
  116	VSNNMRINQY	0.750
  327	RSERYLFLNM	0.675
  38	SGDFAKSLTI	0.625
  384	NALNWREFSF	0.500
  218	VAISLATFFF	0.500
  274	GLLAAAYQLY	0.500
  81	DALTKTNIIF	0.500
  322	CLPMRRSERY	0.500
  73	VVDVTHHEDA	0.500
  232	VRDVIHPYAR	0.500
  442	VILDLLQLCR	0.500
  125	YPESNAEYLA	0.450
  129	NAEYLASLFP	0.450
  21	GINGIKDARK	0.400
  2	ESISMMGSPK	0.300
  66	ASEFFPHVVD	0.270
  419	FEEEYYRFYT	0.225
  350	NEEEVWRIEM	0.225
  222	LATFFFLYSF	0.200
  56	VVIGSRNPKF	0.200
  281	QLYYGTKYRR	0.200
  55	HVVIGSRNPK	0.200
  278	AAYQLYYGTK	0.200
  417	RAFEEEYYRF	0.200
  216	VVVAISLATF	0.200
  248	YKIPIEIVNK	0.200
  317	VAYSLCLPMR	0.200
  17	CLPNGINGIK	0.200
  244	QSDFYKIPIE	0.150
  377	TSIPSVSNAL	0.150
  382	VSNALNWREF	0.150
  202	ENLPLRLFTL	0.125
  101	LWDLRHLLVG	0.125
  329	ERYLFLNMAY	0.125
  15	ETCLPNGING	0.125
  396	STLGYVALLI	0.125
  45	LTIRLIRCGY	0.125
  86	TNIIFVAIHR	0.125
  32	TVGVIGSGDF	0.100
  235	VIHPYARNQQ	0.100
  410	VLIYGWKRAF	0.100
  112	ILIDVSNNMR	0.100
  166	YICSNNIQAR	0.100
  16	TCLPNGINGI	0.100
  217	VVAISLATFF	0.100
  155	QLGPKDASRQ	0.100
  344	NIENSWNEEE	0.090
  139	DSLIVKGFNV	0.075
  405	ISTFHVLIYG	0.075
  366	MSLGLLSLLA	0.075
  11	KSLSETCLPN	0.075
  134	ASLFPDSLIV	0.075
  43	KSLTIRLIRC	0.075
  303	KQLGLLSFFF	0.075
  361	ISFGIMSLGL	0.075
  304	QLGLLSFFFA	0.050
  107	LLVGKILIDV	0.050
  60	SRNPKFASEF	0.050
  269	LVYLAGLLAA	0.050
  434	LALVLPSIVI	0.050
  397	TLFYVALLIS	0.050
  364	GIMSLGLLSL	0.050
  401	VALLISTFHV	0.050
  147	NVVSAWALQL	0.050
  189	PIDLGSLSSA	0.050
  264	ITLLSLVYLA	0.050
  307	LLSFFFAMVH	0.050
  310	FFFAMVHVAY	0.050
  209	FTLWRGPVVV	0.050
  194	SLSSAREIEN	0.050
  240	ARNQQSDFYK	0.050
  298	WLQCRKQLG	0.050
  440	SIVILDLLQL	0.050
  221	SLATFFFLYS	0.050
  436	LVLPSIVILD	0.050
  406	STFHVLIYGW	0.050

  V2-HLA-A1-10mers-98PB6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  32	RCPPPCPADF	2.000
  23	LSLPSSWDYR	1.500
  35	PPCPADFFLY	0.625
  22	CLSLPSSWDY	0.500
  33	CPPPCPADFF	0.250
  11	LSLSSGFTPF	0.150
  8	ALSLSLSSGF	0.100
  13	LSSGFTPFSC	0.075
  2	GSPGLQALSL	0.075
  28	SWDYRCPPPC	0.050
  1	SGSPGLQALS	0.050
  36	PCPADFFLYF	0.050
  16	GFTPFSCLSL	0.025
  12	SLSSGFTPFS	0.020
  24	SLPSSWDYRC	0.020
  20	FSCLSLPSSW	0.015
  14	SSGFTPFSCL	0.015
  9	LSLSLSSGFT	0.015
  18	TPFSCLSLPS	0.013
  7	QALSLSLSSG	0.010
  5	GLQALSLSLS	0.010
  6	LQALSLSLSS	0.007
  10	SLSLSSGFTP	0.005
  15	SGFTPFSCLS	0.003
  3	SPGLQALSLS	0.003
  17	FTPFSCLSLP	0.003
  34	PPPCPADFFL	0.001
  4	PGLQALSLSL	0.001
  31	YRCPPPCPAD	0.001
  21	SCLSLPSSWD	0.001
  27	SSWDYRCPPP	0.000
  25	LPSSWDYRCP	0.000
  26	PSSWDYRCPP	0.000
  19	PFSCLSLPSS	0.000
  30	DYRCPPPCPA	0.000
  29	WDYRCPPPCP	0.000

  V5A-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  1	ENLPLRLFTF	1.250
  8	FTFWRGPVVV	0.050
  3	LPLRLFTFWR	0.013
  2	NLPLRLFTFW	0.010
  6	RLFTFWRGPV	0.010
  7	LFTFWRGPVV	0.001
  4	PLRLFTFWRG	0.000
  10	FWRGPVVVAI	0.000
  5	LRLFTFWRGP	0.000
  9	TFWRGPVVVA	0.000

  V5B-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  18	QTELELEFVF	112.500
  20	ELELEFVFLL	4.500
  22	ELEFVFLLTL	4.500
  14	FADTQTELEL	2.500
  16	DTQTELELEF	1.250
  2	WREFSFIQIF	0.450
  5	FSFIQIFCSF	0.150
  12	CSFADTQTEL	0.015
  9	QIFCSFADTQ	0.010
  7	FIQIFCSFAD	0.005
  8	IQIFCSFADT	0.003
  21	LELEFVFLLT	0.003
  4	EFSFIQIFCS	0.003
  24	EFVFLLTLLL	0.003
  3	REFSFIQIFC	0.003
  17	TQTELELEFV	0.002
  11	FCSFADTQTE	0.001
  19	TELELEFVFL	0.001
  6	SFIQIFCSFA	0.001
  10	IFCSFADTQT	0.001
  23	LEFVFLLTLL	0.001
  1	NWREFSFIQI	0.000
  15	ADTQTELELE	0.000
  13	SFADTQTELE	0.000

  V6-HLA-A1-10mers-98B4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  42	GTIPHVSPER	5.000
  2	VLPSIVILGK	1.000
  35	FLEEGIGGTI	0.900
  1	LVLPSIVLG	0.500
  12	IILFLPCISR	0.500
  6	IVILGKIILF	0.500
  13	ILFLPCISRK	0.200
  15	FLPCISRKLK	0.200
  16	LPCISRKLKR	0.125
  46	KVSPERVTVM	0.100
  7	VILGKIILFL	0.050
  5	SIVILGKIIL	0.050
  18	CISRKLKRIK	0.020
  19	ISRKLKRIKK	0.015
  32	KSQFLEEGIG	0.015
  39	GIGGTIPHVS	0.010
  43	TIPHVSPERV	0.010
  11	KIILFLPCIS	0.010
  33	SQFLEEGIGG	0.007
  38	EGIGGTIPHV	0.005
  14	LFLPCISRKL	0.005
  36	LEEGIGGTIP	0.005
  37	EEGIGGTIPH	0.003
  3	LPSIVILGKI	0.003
  44	IPHVSPERVT	0.003
  29	GWEKSQFLEE	0.002
  4	PSIVILGKII	0.002
  9	LGKIILFLPC	0.001
  23	LKRIKKGWEK	0.001
  17	PCISRKLKRI	0.001
  10	GKIILFLPCI	0.001
  26	IKKGWEKSQF	0.001
  34	QFLEEGIGGT	0.001
  31	EKSQFLEEGI	0.001
  27	KKGWEKSQFL	0.001
  8	ILGKIILFLP	0.001
  40	IGGTIPHVSP	0.001
  41	GGTIPHVSPE	0.000
  28	KGWEKSQFLE	0.000
  25	RIKKGWEKSQ	0.000
  45	PHVSPERVTV	0.000
  21	RKLKRIKKGW	0.000
  20	SRKLKRIKKG	0.000
  30	WEKSQFLEEG	0.000
  24	KRIKKGWEKS	0.000
  22	KLKRIKKGWE	0.000

  V7A-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  6	LSETFLPNGI	1.350
  10	FLPNGINGIK	0.200
  8	KEFLPNGING	0.125
  4	KSLSETFLPN	0.075
  5	SLSETFLPNG	0.020
  1	GSPKSLSETF	0.015
  9	TFLPNGINGI	0.005
  7	SETFLPNGIN	0.001
  2	SPKSLSETFL	0.000
  3	PKSLSETFLP	0.000

  V7B-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  5	MAYQQSTLGY	2.500
  10	STLGYVALLI	0.125
  9	QSTLGYVALL	0.030
  2	FLNMAYQQST	0.010
  4	NMAYQQSTLG	0.005
  7	YQQSTLGYVA	0.003
  8	QQSTLGYVAL	0.003
  3	LNMAYQQSTL	0.003
  6	AYQQSTLGYV	0.001
  1	LFLNMAYQQS	0.001

  V7C-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  100	SIDPPESPDR	100.000
  67	TAEAQESGIR	9.000
  33	LSEIVLPIEW	6.750
  131	LWEFLLRLLK	4.500
  91	VTEDDEAQDS	2.250
  10	SVEVLASPAA	1.800
  52	STPPPPAMWT	1.250
  6	ILDLSVEVLA	1.000
  168	KLETIILSKL	0.900
  103	PPESPDRALK	0.900
  127	GVGPLWEFLL	0.500
  143	AASGTLSLAF	0.500
  13	VLASPAAAWK	0.400
  51	LSTPPPPAMW	0.300
  60	WTEEAGATAE	0.225
  157	LGEFLGSGTW	0.225
  69	EAQESGIRNK	0.200
  97	AQDSIDPPES	0.150
  70	AQESGIRNKS	0.135
  178	TQEQKSKHCM	0.135
  170	ETIILSKLTQ	0.125
  128	VGPLWEFLLR	0.125
  37	VLPIEWQQDR	0.100
  14	LASPAAAWKC	0.100
  61	TEEAGATAEA	0.090
  39	PIEWQQDRKI	0.090
  162	GSGTWMKLET	0.075
  78	KSSSSSQIPV	0.075
  160	FLGSGTWMKL	0.050
  22	KCLGANILRG	0.050
  167	MKLETIILSK	0.050
  38	LPIEWQQDRK	0.050
  80	SSSSQIPVVG	0.030
  79	SSSSSQIPVV	0.030
  83	SQIPVVGVVT	0.030
  144	ASGTLSLAFT	0.030
  81	SSSQIPVVGV	0.030
  146	GTLSLAFTSW	0.025
  66	ATAEAQESGI	0.025
  152	FTSWSLGEFL	0.025
  125	TNGVGPLWEF	0.025
  92	TEDDEAQDSI	0.025
  177	LTQEQKSKHC	0.025
  21	WKCLGANILR	0.025
  106	SPDRALKAAN	0.025
  94	DDEAQDSIDP	0.022
  12	EVLASPAAAW	0.020
  4	IVILDLSVEV	0.020
  173	ILSKLTQEQK	0.020
  47	KIPPLSTPPP	0.020
  113	AANSWRNPVL	0.020
  72	ESGIRNKSSS	0.015
  43	QQDRKIPPLS	0.015
  15	ASPAAAWKCL	0.015
  140	KSQAASGTLS	0.015
  9	LSVEVLASPA	0.015
  82	SSQIPVVGVV	0.015
  155	WSLGEFLGSG	0.015
  105	ESPDRALKAA	0.015
  148	LSLAFTSWSL	0.015
  124	HTNGVGPLWE	0.013
  129	GPLWEFLLRL	0.013
  31	GGLSEIVLPI	0.013
  145	SGTLSLAFTS	0.013
  185	HCMFSLISGS	0.010
  149	SLAFTSWSLG	0.010
  65	GATAEAQESG	0.010
  112	KAANSWRNPV	0.010
  142	QAASGTLSLA	0.010
  25	GANILRGGLS	0.010
  159	EFLGSGTWMK	0.010
  23	CLGANILRGG	0.010
  109	RALKAANSWR	0.010
  176	KLTQEQKSKH	0.010
  35	EIVLPIEWQQ	0.010
  175	SKLTQEQKSK	0.010
  18	AAAWKCLGAN	0.010
  36	IVLPIEWQQD	0.010
  5	VILDLSVEVL	0.010
  172	IILSKLTQEQ	0.010
  156	SLGEFLGSGT	0.010
  120	PVLPHTNGVG	0.010
  147	TLSLAFTSWS	0.010
  89	GVVTEDDEAQ	0.010
  153	TSWSLGEFLG	0.008
  2	PSIVILDLSV	0.008
  141	SQAASGTLSL	0.007
  150	LAFTSWSLGE	0.005
  17	PAAAWKCLGA	0.005
  101	IDPPESPDRA	0.005
  151	AFTSWSLGEF	0.005
  117	WRNPVLPHTN	0.005
  42	WQQDRKIPPL	0.003
  104	PESPDRALKA	0.003
  24	LGANILRGGL	0.003
  119	NPVLPHTNGV	0.003
  118	RNPVLPHTNG	0.003
  102	DPPESPDRAL	0.003
  53	TPPPPAMWTE	0.003
  1	LPSIVILDLS	0.003

• [1219]

  TABLE X
  Start	Subsequence	Score

  V1-HLA-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  227	FLYSFVRDV	1789.612
  402	ALLISTFHV	1492.586
  307	LLSFFFAMV	853.681
  306	GLLSFFFAM	769.748
  100	SLWDLRHLL	726.962
  333	FLNMAYQQV	479.909
  140	SLIVKGFNV	403.402
  203	NLPLRLFTL	284.974
  210	TLWRGPVVV	236.685
  65	FASEFFPHV	131.539
  135	SLFPDSLIV	105.510
  274	GLLAAAYQL	79.041
  393	FIQSTLGYV	72.344
  48	RLIRCGYHV	69.552
  365	IMSLGLLSL	60.325
  5	SMMGSPKSL	57.085
  220	ISLATFFFL	53.163
  271	YLAGLLAAA	52.561
  265	TLLSLVYLA	42.278
  433	VLALVLPSI	40.792
  442	VILDLLQLC	40.518
  112	ILIDVSNNM	34.627
  360	YISFGIMSL	31.077
  403	LLISTFHVL	28.290
  369	GLLSLLAVT	26.001
  17	CLPNGINGI	23.995
  108	LVGKILIDV	23.795
  264	ITLLSLVYL	23.608
  258	TLPIVAITL	21.362
  184	QLNFIPIDL	21.362
  313	AMVHVAYSL	15.428
  410	VLIYGWKRA	14.358
  141	LIVKGFNVV	12.665
  305	LGLLSFFFA	12.364
  44	SLTIRLIRC	11.426
  436	LVLPSIVIL	11.087
  397	TLGYVALLI	10.433
  386	LNWREFSFI	10.042
  180	ELARQLNFI	9.989
  254	IVNKTLPIV	9.756
  404	LISTFHVLI	9.267
  357	IEMYISFGI	7.401
  441	IVILDLLQL	7.309
  261	IVAITLLSL	7.309
  209	FTLWRGPVV	6.741
  368	LGLLSLLAV	6.568
  367	SLGLLSLLA	4.968
  153	ALQLGPKDA	4.968
  146	FNVVSAWAL	4.811
  389	REFSFIQST	4.686
  435	ALVLPSIVI	4.277
  187	FIPIDLGSL	4.040
  374	LAVTSIPSV	3.777
  262	VAITLLSLV	3.777
  299	LQCRKQLGL	3.682
  335	NMAYQQVHA	3.588
  291	FPPWLETWL	3.528
  331	YLFLNMAYQ	3.209
  148	VVSAWALQL	3.178
  166	YICSNNIQA	3.142
  353	EVWRIEMYI	3.125
  221	SLATFFFLY	3.121
  378	SIPSVSNAL	2.937
  164	QVYICSNNI	2.921
  268	SLVYLAGLL	2.777
  396	STLGYVALL	2.525
  434	LALVLPSIV	2.491
  304	QLGLLSFFF	2.377
  269	LVYLAGLLA	2.365
  37	GSGDFAKSL	2.173
  366	MSLGLLSLL	2.017
  267	LSLVYLAGL	2.017
  242	NQQSDFYKI	2.010
  177	QVIELARQL	1.533
  224	TFFFLYSFV	1.474
  349	WNEEEVWRI	1.418
  128	SNAEYLASL	1.315
  106	HLLVGKILI	1.312
  257	KTLPIVAIT	1.264
  303	KQLGLLSFF	1.238
  428	TPPNFVLAL	1.219
  34	GVIGSGDFA	1.172
  216	VVVAISLAT	1.108
  314	MVHVAYSLC	1.108
  371	LSLLAVTSI	0.985
  91	VAIHREHYT	0.968
  85	KTNIIFVAI	0.964
  133	LASLFPDSL	0.939
  425	RFYTPPNFV	0.850
  250	IPIEIVNKT	0.780
  49	LIRCGYHVV	0.760
  83	LTKTNIIFV	0.727
  132	YLASLFPDS	0.651
  427	YTPPNFVLA	0.603
  171	NIQARQQVI	0.588
  259	LPIVAITLL	0.545
  438	LPSIVILDL	0.545
  278	AAYQLYYGT	0.497
  170	NNIQARQQV	0.454
  385	ALNWREFSF	0.432

  V2-HLA-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  5	GLQALSLSL	21.362
  10	SLSLSSGFT	5.328
  17	FTPFSCLSL	1.365
  15	SGFTPFSCL	0.980
  1	SGSPGLQAL	0.321
  14	SSGFTPFSC	0.188
  8	ALSLSLSSG	0.171
  12	SLSSGFTPF	0.142
  3	SPGLQALSL	0.139
  29	WDYRCPPPC	0.102
  35	PPCPADFFL	0.098
  22	CLSLPSSWD	0.082
  37	CPADFFLYF	0.079
  24	SLPSSWDYR	0.068
  25	LPSSWDYRC	0.055
  6	LQALSLSLS	0.030
  23	LSLPSSWDY	0.023
  13	LSSGFTPFS	0.017
  20	FSCLSLPSS	0.005
  7	QALSLSLSS	0.004
  11	LSLSSGFTP	0.004
  27	SSWDYRCPP	0.003
  31	YRCPPPCPA	0.003
  9	LSLSLSSGF	0.003
  21	SCLSLPSSW	0.002
  18	TPFSCLSLP	0.001
  2	GSPGLQALS	0.000
  33	CPPPCPADF	0.000
  16	GFTPFSCLS	0.000
  36	PCPADFFLY	0.000
  32	RCPPPCPAD	0.000
  4	PGLQALSLS	0.000
  34	PPPCPADFF	0.000
  19	PFSCLSLPS	0.000
  28	SWDYRCPPP	0.000
  26	PSSWDYRCP	0.000
  30	DYRCPPPCP	0.000

  V5A-HLA-A0201-9mers-98PB6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  7	FTFWRGPVV	6.741
  1	NLPLRLFTF	0.994
  8	TFWRGPVVV	0.164
  5	RLFTFWRGP	0.071
  2	LPLRLFTFW	0.032
  6	LFTFWRGPV	0.011
  3	PLRLFTFWR	0.003
  4	LRLFTFWRG	0.001
  9	FWRGPVVVA	0.000

  V5B-HLA-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  20	LELEFVFLL	543.025
  6	FIQIFCSFA	65.673
  24	FVFLLTLLL	31.814
  22	LEFVFLLTL	22.835
  8	QIFCSFADT	7.203
  19	ELELEFVFL	1.072
  17	QTELELEFV	0.383
  10	FCSFADTQT	0.224
  4	FSFIQIFCS	0.110
  21	ELEFVFLLT	0.068
  12	SFADTQTEL	0.061
  18	TELELEFVF	0.052
  16	TQTELELEF	0.031
  14	ADTQTELEL	0.030
  2	REFSFIQIF	0.019
  7	IQIFCSFAD	0.015
  23	EFVFLLTLL	0.003
  3	EFSFIQIFC	0.001
  1	WREFSFIQI	0.001
  11	CSFADTQTE	0.000
  13	FADTQTELE	0.000
  5	SFIQIFCSF	0.000
  9	IFCSFADTQ	0.000
  15	DTQTELELE	0.000

  V6-HLA-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  7	ILGKIILFL	459.398
  27	KGWEKSQFL	91.350
  10	KIILFLPCI	43.882
  38	GIGGTIPHV	21.996
  14	FLPCISRKL	19.653
  17	CISRKLKRI	3.299
  34	FLEEGIGGT	2.689
  5	IVILGKIIL	1.303
  4	SIVILGKII	0.588
  43	IPHVSPERV	0.378
  1	VLPSIVILG	0.291
  46	VSPERVTVM	0.213
  45	HVSPERVTV	0.207
  6	VILGKIILF	0.148
  31	KSQFLEEGL	0.117
  12	ILFLPCISR	0.094
  11	IILFLPCIS	0.026
  9	GKIILFLPC	0.013
  21	KLKRIKKGW	0.009
  35	LEEGIGGTI	0.003
  42	TIPHVSPER	0.002
  32	SQFLEEGIG	0.001
  20	RKLKRIKKG	0.001
  33	QFLEEGIGG	0.001
  41	GTIPHVSPE	0.000
  3	PSIVILGKI	0.000
  2	LPSIVILGK	0.000
  26	KKGWEKSQF	0.000
  39	IGGTIPHVS	0.000
  24	RIKKGWEKS	0.000
  15	LPCISRKLK	0.000
  13	LFLPCISRK	0.000
  40	GGTIPHVSP	0.000
  29	WEKSQFLEE	0.000
  8	LGKIILFLP	0.000
  23	KRIKKGWEK	0.000
  37	EGIGGTIPH	0.000
  30	EKSQFLEEG	0.000
  44	PHVSPERVT	0.000
  36	EEGIGGTIP	0.000
  16	PCISRKLKR	0.000
  22	LKRIKKGWE	0.000
  25	IKKGWEKSQ	0.000
  18	ISRKLKRIK	0.000
  28	GWEKSQFLE	0.000
  19	SRKLKRIKK	0.000

  V7A-HLA-A0201-9mers-98PB6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  9	FLPNGINGI	110.379
  4	SLSETFLPN	0.581
  6	SETFLPNGI	0.203
  3	KSLSETFLP	0.007
  2	PKSLSETFL	0.004
  5	LSETFLPNG	0.000
  8	TFLPNGING	0.000
  7	ETFLPNGIN	0.000
  1	SPKSLSETF	0.000

  V7B-HLA-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  6	YQQSTLGYV	53.345
  3	NMAYQQSTL	15.428
  9	STLGYVALL	2.525
  1	FLNMAYQQS	0.514
  2	LNMAYQQST	0.306
  8	QSTLGYVAL	0.209
  7	QQSTLGYVA	0.207
  4	MAYQQSTLG	0.006
  5	AYQQSTLGY	0.000

  V7C-A0201-9mers-98PB6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  4	VILDLSVEV	246.631
  148	SLAFTSWSL	160.218
  129	PLWEFLLRL	139.780
  31	GLSEIVLPI	98.381
  57	AMWTEEAGA	29.780
  2	SIVILDLSV	9.563
  126	GVGPLWEFL	8.564
  5	ILDLSVEVL	6.712
  152	TSWSLGEFL	3.119
  27	ILRGGLSEI	3.100
  42	QQDRKIPPL	1.993
  168	LETIILSKL	1.624
  127	VGPLWEFLL	1.375
  163	GTWMKLETI	1.355
  81	SSQIPVVGV	1.044
  165	WMKLETIIL	1.018
  112	AANSWRNPV	0.966
  82	SQIPVVGVV	0.864
  134	LLRLLKSQA	0.642
  144	SGTLSLAFT	0.615
  133	FLLRLLKSQ	0.583
  39	IEWQQDRKI	0.572
  159	FLGSGTWMK	0.514
  119	PVLPHTNGV	0.495
  185	CMFSLISGS	0.458
  78	SSSSSQIPV	0.454
  79	SSSSQIPVV	0.428
  83	QIPVVGVVT	0.420
  160	LGSGTWMKL	0.403
  155	SLGEFLGSG	0.347
  141	QAASGTLSL	0.297
  136	RLLKSQAAS	0.276
  52	TPPPPAMWT	0.268
  14	ASPAAAWKC	0.243
  15	SPAAAWKCL	0.237
  181	KSKHCMFSL	0.228
  88	GVVTEDDEA	0.213
  22	CLGANILRG	0.171
  10	VEVLASPAA	0.164
  142	AASGTLSLA	0.159
  146	TLSLAFTSW	0.142
  12	VLASPAAAW	0.127
  11	EVLASPAAA	0.121
  49	PLSTPPPPA	0.109
  178	QEQKSKHCM	0.097
  59	WTEEAGATA	0.083
  17	AAAWKCLGA	0.069
  147	LSLAFTSWS	0.064
  139	KSQAASGTL	0.063
  35	IVLPIEWQQ	0.062
  29	RGGLSEIVL	0.057
  113	ANSWRNPVL	0.057
  20	SKCLGANIL	0.056
  50	LSTPPPPAM	0.055
  175	KLTQEQKSK	0.052
  162	SGTWMKLET	0.049
  6	LDLSVEVLA	0.043
  36	VLPIEWQQD	0.043
  24	GANILRGGL	0.039
  177	TQEQKSKHC	0.032
  105	SPDRALKAA	0.030
  171	IILSKLTQE	0.030
  41	WQQDRKIPP	0.028
  9	SVEVLASPA	0.028
  182	SKHCMFSLI	0.028
  172	ILSKLTQEQ	0.025
  145	GTLSLAFTS	0.022
  138	LKSQAASGT	0.018
  154	WSLGEFLGS	0.016
  76	NKSSSSSQI	0.014
  7	DLSVEVLAS	0.013
  149	LAFTSWSLG	0.011
  116	WRNPVLPHT	0.011
  104	ESPDRALKA	0.010
  66	TAEAQESGI	0.009
  125	NVGVPLWEF	0.008
  169	ETIILSKLT	0.008
  167	KLETIILSK	0.008
  26	NILRGGLSE	0.008
  140	SQAASGTLS	0.008
  61	EEAGATAEA	0.007
  176	LTQEQKSKH	0.007
  46	KIPPLSTPP	0.007
  120	VLPHTNGVG	0.007
  166	MKLETIILS	0.006
  156	LGEFLGSGT	0.005
  158	EFLGSGTWM	0.005
  131	WEFLLRLLK	0.005
  101	DPPESPDRA	0.005
  89	VVTEDDEAQ	0.004
  137	LLKSQAASG	0.004
  135	LRLLKSQAA	0.004
  108	RALKAANSW	0.004
  28	LRGGLSEIV	0.003
  109	ALKAANSWR	0.003
  18	AAWKCLGAN	0.003
  91	TEDDEAQDS	0.002
  164	TWMKLETII	0.002
  3	IVILDLSVE	0.002
  65	ATAEAQESG	0.002

• [1220]

  TABLE XI
  Start	Subsequence	Score

  V1-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  100	SLWDLRHLLV	2366.855
  306	GLLSFFFAMV	1585.012
  82	ALTKTNIIFV	879.833
  304	QLGLLSFFFA	301.110
  373	LLAVTSIPSV	271.948
  107	LLVGKILIDV	271.948
  132	YLASLFPDSL	182.973
  219	AISLATFFFL	178.032
  367	SLGLLSLLAV	159.970
  385	ALNWREFSFI	109.023
  298	WLQCRKQLGL	98.267
  437	VLPSIVILDL	83.527
  266	LLSLVYLAGL	83.527
  403	LLISTFHVLI	67.396
  402	ALLISTFHVL	61.573
  365	IMSLGLLSLL	60.325
  140	SLIVKGFNVV	54.181
  258	TLPIVAITLL	49.134
  433	VLALVLPSIV	48.478
  48	RLIRCGYHVV	42.774
  370	LLSLLAVTSI	40.792
  210	TLWRGPVVVA	38.884
  263	AITLLSLVYL	37.157
  432	FVLALVLPSI	35.735
  401	VALLISTFHV	35.242
  207	RLFTLWRGPV	33.455
  227	FLYSFVRDVI	30.852
  223	ATFFFLYSFV	29.487
  65	FASEFFPHVV	28.385
  364	GIMSLGLLSL	24.997
  261	IVAITLLSLV	23.795
  435	ALVLPSIVIL	20.145
  90	FVAIHREHYT	16.497
  179	IELARQLNFI	16.141
  427	YTPPNFVLAL	11.929
  67	SEFFPHVVDV	11.509
  111	KILIDVSNNM	8.846
  305	LGLLSFFFAM	8.542
  172	IQARQQVIEL	8.469
  249	KIPIEIVNKT	8.248
  183	RQLNFIPIDL	8.014
  95	REHYTSLWDL	7.165
  440	SIVILDLLQL	6.756
  209	FTLWRGPVVV	6.741
  308	LSFFFAMVHV	6.568
  57	VIGSRNPKFA	6.387
  419	FEEEYYRFYT	5.579
  394	IQSTLGYVAL	5.523
  269	LVYLAGLLAA	5.439
  313	AMVHVAYSLC	5.382
  312	FAMVHVAYSL	5.050
  268	SLVYLAGLLA	4.968
  92	AIHREHYTSL	4.406
  243	QQSDFYKIPI	4.337
  257	KTLPIVAITL	3.842
  231	FVRDVIHPYA	3.427
  314	MVHVAYSLCL	3.178
  303	KQLGLLSFFF	3.121
  221	SLATFFFLYS	2.959
  144	KGFNVVSAWA	2.310
  286	TKYRRFPPWL	1.984
  147	NVVSAWALQL	1.869
  199	REIENLPLRL	1.703
  441	IVILDLLQLC	1.700
  389	REFSFIQSTL	1.537
  226	FFLYSFVRDV	1.437
  24	GIKDARKVTV	1.372
  201	IENLPLRLFT	1.355
  393	FIQSTLGYVA	1.288
  64	KFASEFFPHV	1.221
  152	WALQLGPKDA	1.174
  345	IENSWNEEEV	1.127
  299	LQCRKQLGLL	1.101
  163	RQVYICSNNI	1.058
  428	TPPNFVLALV	1.044
  264	ITLLSLVYLA	0.998
  113	LIDVSNNMRI	0.975
  250	IPIEIVNKTL	0.972
  43	KSLTIRLIRC	0.966
  323	LPMRRSERYL	0.965
  424	YRFYTPPNFV	0.904
  36	IGSGDFAKSL	0.901
  361	ISFGIMSLGL	0.877
  4	ISMMGSPKSL	0.877
  336	MAYQQVHANI	0.788
  139	DSLIVKGFNV	0.731
  12	SLSETCLPNG	0.703
  275	LLAAAYQLYY	0.697
  134	ASLFPDSLIV	0.689
  121	RINQYPESNA	0.683
  253	EIVNKTLPIV	0.676
  98	YTSLWDLRHL	0.628
  398	LGYVALLIST	0.609
  16	TCLPNGINGI	0.580
  396	STLGYVALLI	0.536
  356	RIEMYISFGI	0.532
  202	ENLPLRLFTL	0.516
  99	TSLWDLRHLL	0.516
  273	AGLLAAAYQL	0.516
  332	LFLNMAYQQV	0.456

  V2-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  24	SLPSSWDYRC	4.968
  12	SLSSGFTPFS	1.557
  22	CLSLPSSWDY	0.559
  13	LSSGFTPFSC	0.320
  14	SSGFTPFSCL	0.265
  9	LSLSLSSGFT	0.219
  5	GLQALSLSLS	0.171
  2	GSPGLQALSL	0.139
  34	PPPCPADFFL	0.098
  10	SLSLSSGFTP	0.086
  8	ALSLSLSSGF	0.075
  16	GFTPFSCLSL	0.015
  6	LQALSLSLSS	0.013
  4	PGLQALSLSL	0.011
  7	QALSLSLSSG	0.009
  15	SGFTPFSCLS	0.007
  11	LSLSSGFTPF	0.006
  27	SSWDYRCPPP	0.003
  23	LSLPSSWDYR	0.003
  20	FSCLSLPSSW	0.002
  17	FTPFSCLSLP	0.002
  21	SCLSLPSSWD	0.002
  18	TPFSCLSLPS	0.002
  33	CPPPCPADFF	0.001
  3	SPGLQALSLS	0.001
  32	RCPPPCPADF	0.000
  1	SGSPGLQALS	0.000
  36	PCPADFFLYF	0.000
  29	WDYRCPPPCP	0.000
  28	SWDYRCPPPC	0.000
  35	PPCPADFFLY	0.000
  25	LPSSWDYRCP	0.000
  31	YRCPPPCPAD	0.000
  30	DYRCPPPCPA	0.000
  19	PFSCLSLPSS	0.000
  26	PSSWDYRCPP	0.000

  V5A-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  6	RLFTFWRGPV	33.455
  8	FTFWRGPVVV	6.741
  2	NLPLRLFTFW	0.779
  3	LPLRLFTFWR	0.074
  7	LFTFWRGPVV	0.034
  9	TFWRGPVVVA	0.027
  1	ENLPLRLFTF	0.002
  4	PLRLFTFWRG	0.002
  10	FWRGPVVVAI	0.001
  5	LRLFTFWRGP	0.000

  V5B-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  17	TQTELELEFV	179.213
  19	TELELEFVFL	65.849
  21	LELEFVFLLT	7.100
  23	LEEVFLLTLL	6.009
  20	ELELEFVFLL	5.198
  8	IQIFCSFADT	2.440
  3	REFSFIQIFC	1.966
  22	ELEFVFLLTL	0.896
  14	FADTQTELEL	0.546
  12	CSFADTQTEL	0.516
  6	SFIQIFCSFA	0.072
  7	FIQIFCSFAD	0.055
  5	FSFIQIFCSF	0.016
  9	QIFCSFADTQ	0.014
  10	IFCSFADTQT	0.009
  24	EFVFLLTLLL	0.001
  1	NWREFSFIQI	0.001
  11	FCSFADTQTE	0.000
  18	QTELELEFVF	0.000
  16	DTWTELELEF	0.000
  4	EFSFIQIFCS	0.000
  15	ADTQTELELE	0.000
  13	SFADTQTELE	0.000
  2	WREFSFIQIF	0.000

  V6-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  7	VILGKIILFL	233.719
  43	TIPHVSPERV	4.686
  35	FLEEGIGGTI	1.637
  5	SIVILGKIIL	1.204
  27	KKGWEKSQFL	0.571
  8	ILGKIILFLP	0.338
  13	ILFLPCISRK	0.216
  10	GKIILFLPCI	0.127
  1	LVLPSIVILG	0.094
  38	EGIGGTIPHV	0.078
  15	FLPCISRKLK	0.069
  28	KGWEKSQFLE	0.067
  2	VLPSIVILGK	0.058
  3	LPSIVILGKI	0.035
  33	SQFLEEGIGG	0.028
  6	IVILGKIILF	0.025
  34	QFLEEGIGGT	0.023
  14	LFLPCISRKL	0.019
  11	KIILFLPCIS	0.015
  46	HVSPERVTVM	0.014
  12	IILFLPCISR	0.013
  44	IPHVSPERVT	0.007
  39	GIGGTIPHVS	0.004
  9	LGKIILFLPC	0.004
  17	PCISRKLKRI	0.003
  22	KLKRIKKGWE	0.001
  45	PHVSPERVTV	0.001
  30	WEKSQFLEEG	0.001
  4	PSIVILGKII	0.001
  31	EKSQFLEEGI	0.001
  21	RKLKRIKKGW	0.000
  41	GGTIPHVSPE	0.000
  42	GTIPHVSPER	0.000
  18	CISRKLKRIK	0.000
  40	IGGTIPHVSP	0.000
  16	LPCISRKLKR	0.000
  37	EEGIGGTIPH	0.000
  32	KSQFLEEGIG	0.000
  25	RIKKGWEKSQ	0.000
  24	KRIKKGWEKS	0.000
  23	LKRIKKGWEK	0.000
  36	LEEGIGGTIP	0.000
  19	ISRKLKRIKK	0.000
  26	IKKGWEKSQF	0.000
  20	SRKLKRIKKG	0.000
  29	GWEKSQFLEE	0.000

  V7A-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  5	SLSETFLPNG	2.670
  9	TFLPNGINGI	0.062
  2	SPKSLSETFL	0.027
  4	KSLSETFLPN	0.012
  6	LSETFLPNGI	0.007
  10	FLPNGINGIK	0.004
  8	ETFLPNGING	0.000
  1	GSPKSLSETF	0.000
  7	SETFLPNGIN	0.000
  3	PKSLSETFLP	0.000

  V7B-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  2	FLNMAYQQST	34.279
  8	QQSTLGYVAL	3.249
  7	YQQSTLGYVA	0.950
  3	LNMAYQQSTL	0.877
  10	STLGYVALLI	0.536
  9	QSTLGYVALL	0.321
  4	NMAYQQSTLG	0.054
  6	AYQQSTLGYV	0.016
  5	MAYQQSTLGY	0.006
  1	LFLNMAYQQS	0.000

  V7C-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  160	FLGSGTWMKL	167.054
  42	WQQDRKIPPL	93.953
  134	FLLRLLKSQA	84.555
  5	VILDLSVEVL	35.002
  156	SLGEFLGSGT	30.553
  27	NILRGGLSEI	12.208
  168	KLETIILSKL	11.006
  127	GVGPLWEFLL	10.841
  4	IVILDLSVEV	10.346
  130	PLWEFLLRLL	7.357
  148	LSLAFTSWSL	6.579
  58	AMWTEEAGAT	5.807
  129	GPLWEFLLRL	4.510
  152	FTSWSLGEFL	3.678
  112	KAANSWRNPV	3.381
  6	ILDLSVEVLA	3.378
  141	SQAASGTLSL	2.166
  158	GEFLGSGTWM	1.966
  28	ILRGGLSEIV	1.805
  78	KSSSSSQIPV	1.589
  147	TLSLAFTSWS	1.557
  19	AAWKCLGANI	1.203
  81	SSSQIPVVGV	1.044
  14	LASPAAAWKC	0.880
  135	LLRLLKSQAA	0.642
  126	NGVGPLWEFL	0.639
  144	ASGTLSLAFT	0.615
  66	ATAEAQESGI	0.594
  31	GGLSEIVLPI	0.580
  52	STPPPPAMWT	0.569
  164	GTWMKLETII	0.493
  177	LTQEQKSKHC	0.481
  119	NPVLPHTNGV	0.454
  138	LLKSQAASGT	0.443
  79	SSSSSQIPVV	0.428
  181	QKSKHCMFSL	0.396
  83	SQIPVVGVVT	0.310
  137	RLLKSQAASG	0.276
  176	KLTQEQKSKH	0.261
  169	LETIILSKLT	0.246
  15	ASPAAAWKCL	0.237
  9	LSVEVLASPA	0.226
  11	VEVLASPAAA	0.164
  92	TEDDEAQDSI	0.163
  142	QAASGTLSLA	0.159
  13	VLASPAAAWK	0.139
  149	SLAFTSWSLG	0.127
  113	AANSWRNPVL	0.122
  50	PLSTPPPPAM	0.109
  163	SGTWMKLETI	0.077
  122	LPHTNGVGPL	0.071
  32	GLSEIVLPIE	0.058
  132	WEFLLRLLKS	0.057
  82	SSQIPVVGVV	0.056
  162	GSGTWMKLET	0.049
  23	CLGANILRGG	0.034
  178	TQEQKSKHCM	0.032
  24	LGANILRGGL	0.031
  10	SVEVLASPAA	0.028
  88	VGVVTEDDEA	0.027
  37	VLPIEWQQDR	0.025
  121	VLPHTNGVGP	0.025
  153	TSWSLGEFLG	0.023
  105	ESPDRALKAA	0.023
  166	WMKLETILLS	0.020
  110	ALKAANSWRN	0.020
  182	KSKHCMFSLI	0.016
  22	KCLGANILRG	0.014
  36	IVLPEIWQQD	0.014
  172	IILSKLTQEQ	0.013
  173	ILSKLTQEQK	0.012
  2	PSIVILDLSV	0.010
  155	WSLGEFLGSG	0.009
  115	NSWRNPVLPH	0.009
  90	VVTEDDEAQD	0.009
  102	DPPESPDRAL	0.009
  125	TNGVGPLWEF	0.008
  146	GTLSLAFTSW	0.007
  47	KIPPLSTPPP	0.007
  139	LKSQAASGTL	0.007
  61	TEEAGATAEA	0.006
  101	IDPPESPDRA	0.006
  57	PAMWTEEAGA	0.006
  59	MWTEEAGATA	0.005
  171	TIILSKLTQE	0.005
  84	QIPVVGVVTE	0.005
  165	TWMKLETIIL	0.005
  109	RALKAANSWR	0.004
  97	AQDSIDPPES	0.003
  43	QQDRKIPPLS	0.003
  145	SGTLSLAFTS	0.003
  49	PPLSTPPPPA	0.003
  8	DLSVEVLASP	0.003
  76	RNKSSSSSQI	0.002
  104	PESPDRALKA	0.002
  29	LRGGLSEIVL	0.002
  3	SIVILDLSVE	0.002
  12	EVLASPAAAW	0.002
  34	SEIVLPIEWQ	0.002
  140	KSQAASGTLS	0.002

• [1221]

  TABLE XII
  Start	Subsequence	Score

  V1-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  221	SLATFFFLY	108.000
  306	GLLSFFFAM	24.300
  294	WLETWLQCR	18.000
  281	QLYYGTKYR	10.000
  249	KIPIEIVNK	9.000
  103	DLRHLLVGK	9.000
  274	GLLAAAYQL	8.100
  443	ILDLLQLCR	8.000
  223	ATFFFLYSF	6.750
  304	QLGLLSFFF	6.000
  155	QLGPKDASR	6.000
  385	ALNWREFSF	6.000
  35	VIGSGDFAK	6.000
  409	HVLIYGWKR	5.400
  56	VVIGSRNPK	4.500
  313	AMVHVAYSL	4.050
  82	ALTKTNIIF	4.000
  322	CLPMRRSER	4.000
  275	LLAAAYQLY	4.000
  135	SLFPDSLIV	3.000
  100	SLWDLRHLL	3.000
  21	GINGIKDAR	2.700
  403	LLISTFHVL	2.700
  265	TLLSLVYLA	2.700
  435	ALVLPSIVI	2.700
  203	NLPLRLFTL	2.700
  205	PLRLFTLWR	2.400
  3	SISMMGSPK	2.000
  258	TLPIVAITL	1.800
  184	QLNFIPIDL	1.800
  397	TLGYVALLI	1.800
  365	IMSLGLLSL	1.800
  307	LLSFFFAMV	1.800
  87	NIIFVAIHR	1.800
  106	HLLVGKILI	1.800
  433	VLALVLPSI	1.350
  191	DLGSLSSAR	1.200
  210	TLWRGPVVV	1.000
  140	SLIVKGFNV	0.900
  17	CLPNGINGI	0.900
  231	FVRDVIHPY	0.900
  48	RLIRCGYHV	0.900
  402	ALLISTFHV	0.900
  227	FLYSFVRDV	0.900
  417	RAFEEEYYR	0.900
  263	AITLLSLVY	0.800
  5	SMMGSPKSL	0.675
  369	GLLSLLAVT	0.675
  396	STLGYVALL	0.608
  303	KQLGLLSFF	0.608
  44	SLTIRLIRC	0.600
  381	SVSNALNWR	0.600
  46	TIRLIRCGY	0.600
  219	AISLATFFF	0.600
  280	YQLYYGTKY	0.540
  411	LIYGWKRAF	0.450
  271	YLAGLLAAA	0.450
  112	ILIDVSNNM	0.450
  85	KTNIIFVAI	0.405
  90	FVAIHREHY	0.400
  367	SLGLLSLLA	0.400
  113	LIDVSNNMR	0.400
  148	VVSAWALQL	0.360
  175	RQQVIELAR	0.360
  217	VVAISLATF	0.300
  164	QVYICSNNI	0.300
  400	YVALLISTF	0.300
  43	KSLTIRLIR	0.270
  441	IVILDLLQL	0.270
  268	SLVYLAGLL	0.270
  180	ELARQLNFI	0.270
  353	EVWRIEMYI	0.270
  358	EMYISFGIM	0.270
  276	LAAAYQLYY	0.240
  436	LVLPSIVIL	0.203
  335	NMAYQQVHA	0.200
  57	VIGSRNPKF	0.200
  269	LVYLAGLLA	0.200
  333	FLNMAYQQV	0.200
  261	IVAITLLSL	0.180
  225	FFFLYSFVR	0.180
  360	YISFGIMSL	0.180
  437	VLPSIVILD	0.180
  404	LISTFHVLI	0.180
  242	NQQSDFYKI	0.162
  257	KTLPIVAIT	0.152
  331	YLFLNMAYQ	0.150
  410	VLIYGWKRA	0.150
  34	GVIGSGDFA	0.135
  18	LPNGINGIK	0.135
  107	LLVGKILID	0.135
  241	RNQQSDFYK	0.120
  405	ISTFHVLIY	0.120
  132	YLASLFPDS	0.120
  428	TPPNFVLAL	0.108
  153	ALQLGPKDA	0.100
  108	LVGKILIDV	0.090
  378	SIPSVSNAL	0.090
  141	LIVKGFNVV	0.090
  282	LYYGTKYRR	0.090

  V2-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  12	SLSSGFTPF	6.000
  24	SLPSSWDYR	4.000
  5	GLQALSLSL	3.600
  37	CPADFFLYF	0.360
  23	LSLPSSWDY	0.135
  17	FTPFSCLSL	0.060
  36	PCPADFFLY	0.036
  8	ALSLSLSSG	0.030
  22	CLSLPSSWD	0.030
  10	SLSLSSGFT	0.030
  33	CPPPCPADF	0.030
  25	LPSSWDYRC	0.018
  9	LSLSLSSGF	0.015
  15	SGFTPFSCL	0.013
  3	SPGLQALSL	0.012
  34	PPPCPADFF	0.003
  14	SSGFTPFSC	0.003
  21	SCLSLPSSW	0.003
  35	PPCPADFFL	0.003
  6	LQALSLSLS	0.002
  18	TPFSCLSLP	0.002
  27	SSWDYRCPP	0.002
  1	SGSPGLQAL	0.001
  7	QALSLSLSS	0.001
  29	WDYRCPPPC	0.001
  13	LSSGFTPFS	0.001
  2	GSPGLQALS	0.001
  16	GFTPFSCLS	0.001
  31	YRCPPPCPA	0.000
  11	LSLSSGFTP	0.000
  32	RCPPPCPAD	0.000
  20	FSCLSLPSS	0.000
  28	SWDYRCPPP	0.000
  4	PGLQALSLS	0.000
  30	DYRCPPPCP	0.000
  19	PFSCLSLPS	0.000
  26	PSSWDYRCP	0.000

  V5A-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  1	NLPLRLFTF	9.000
  3	PLRLFTFWR	3.600
  7	FTFWRGPVV	0.050
  5	RLFTFWRGP	0.030
  2	LPLRLFTFW	0.009
  9	FWRGPVVVA	0.001
  8	TFWRGPVVV	0.001
  4	LRLFTFWRG	0.000
  6	LFTFWRGPV	0.000

  V5B-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  24	FVFLLTLLL	0.600
  19	ELELEFVFL	0.540
  21	ELEFVFLLT	0.270
  16	TQTELELEF	0.180
  8	QIFCSFADT	0.150
  2	REFSFIQIF	0.135
  20	LELEFVFLL	0.109
  22	LEFVFLLTL	0.081
  6	FIQIFCSFA	0.060
  18	TELELEFVF	0.041
  17	QTELELEFV	0.015
  5	SFIQIFCSF	0.013
  4	FSFIQIFCS	0.005
  1	WREFSFIQI	0.004
  7	IQIFCSFAD	0.003
  14	ADTQTELEL	0.001
  10	FCSFADTQT	0.001
  12	SFADTQTEL	0.001
  11	CSFADTQTE	0.001
  15	DTQTELELE	0.000
  23	EFVFLLTLL	0.000
  13	FADTQTELE	0.000
  3	EFSFIQIFC	0.000
  9	IFCSFADTQ	0.000

  V6-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  12	ILFLPCISR	60.000
  7	ILGKIILFL	2.700
  6	VILGKIILF	1.350
  10	KILLFLPCI	1.215
  2	LPSIVILGK	0.900
  42	TIPHVSPER	0.600
  21	KLKRIKKGW	0.450
  23	KRIKKGWEK	0.270
  5	IVILGKIIL	0.180
  1	VLPSIVILG	0.180
  38	GIGGTIPHV	0.135
  15	LPCISRKLK	0.100
  14	FLPCISRKL	0.090
  13	LFLPCISRK	0.068
  34	FLEEGIGGT	0.068
  17	CISRKLKRI	0.045
  4	SIVILGKII	0.045
  19	SRKLKRIKK	0.040
  45	HVSPERVTV	0.030
  41	GTIPHVSPE	0.020
  27	KGWEKSQFL	0.014
  16	PCISRKLKR	0.012
  18	ISRKLKRIK	0.010
  31	KSQFLEEGI	0.009
  26	KKGWEKSQF	0.006
  11	IILFLPCIS	0.006
  9	GKIILFLPC	0.005
  46	VSPERVTVM	0.005
  24	RIKKGWEKS	0.004
  43	IPHVSPERV	0.002
  35	LEEGIGGTI	0.001
  32	SQFLEEGIG	0.001
  29	WEKSQFLEE	0.000
  3	PSIVILGKI	0.000
  37	EFIFFTIPH	0.000
  28	GWEKSQFLE	0.000
  8	LGKIILFLP	0.000
  33	QFLEEGIGG	0.000
  40	GGTIPHVSP	0.000
  39	IGGTIPHVS	0.000
  25	IKKGWEKSQ	0.000
  30	EKSQFLEEG	0.000
  20	RKLKRIKKG	0.000
  36	EEGIGGTIP	0.000
  22	LKRIKKGWE	0.000
  44	PHVSPERVT	0.000

  V7A-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  9	FLPNGINGI	0.900
  4	SLSETFLPN	0.180
  1	SPKSLSETF	0.020
  6	SETFLPNGI	0.002
  3	KSLSETFLP	0.001
  7	ETFLPNGIN	0.001
  5	LSETFLPNG	0.000
  8	TFLPNGING	0.000
  2	PKSLSETFL	0.000

  V7B-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  9	STLGYVALL	0.608
  3	NMAYQQSTL	0.600
  1	FLNMAYQQS	0.040
  7	QQSTLGYVA	0.018
  5	AYQQSTLGY	0.008
  8	QSTLGYVAL	0.003
  6	YQQSTLGYV	0.003
  4	MAYQQSTLG	0.001
  2	LNMAYQQST	0.001

  V7C-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  167	KLETIILSK	270.000
  159	FLGSGTWMK	60.000
  175	KLTQEQKSK	30.000
  31	GLSEIVLPI	24.300
  129	GLSEIVLPI	24.300
  109	ALKAANSWR	4.000
  148	SLAFTWESL	1.800
  5	ILDLSVEVL	1.800
  27	ILRGGLSEI	1.350
  165	WMKLETIIL	1.200
  128	GPLWEFLLR	1.080
  57	AMWTEEAGA	1.000
  163	GTWMKLETI	0.675
  146	TLSLAFTSW	0.600
  131	WEFLLRLLK	0.600
  21	KCLGANILR	0.540
  12	VLASPAAAW	0.300
  185	CMFSLISGS	0.300
  13	LASPAAAWK	0.300
  37	LPIEWQQDR	0.270
  126	GVGPLWEFL	0.270
  38	PIEWQQDRK	0.200
  134	LLRLLKSDA	0.200
  173	LSKLTQEQK	0.100
  88	GVVTEDDEA	0.090
  69	AQESGIRNK	0.090
  7	DLSVEVLAS	0.072
  2	SIVILDLSV	0.060
  136	RLLKSQAAS	0.060
  22	CLGANILRG	0.060
  151	FTWESLGEF	0.045
  155	SLGEFLGSG	0.041
  181	KSKHCMFSL	0.041
  125	NGVGPLWEF	0.030
  49	PLSTPPPPA	0.030
  4	VILDLSVEV	0.030
  145	GTLSLAFTS	0.027
  42	QQDRKIPPL	0.027
  123	HTNGVGPLW	0.022
  51	STPPPPAMW	0.022
  133	FLLRLLKSQ	0.022
  35	IVLPIEWQQ	0.020
  36	VLPIEWQQD	0.020
  172	ILSKLTQEQ	0.020
  143	ASFTLSLAF	0.020
  9	SVEVLASPA	0.020
  137	LLKSQAASG	0.020
  82	SQIPVVGVV	0.018
  179	EQKSKHCMF	0.018
  59	WTEEAGATA	0.015
  83	QIPVVGVVT	0.015
  152	TSWSLGEFL	0.015
  176	LTQEQKSKH	0.015
  73	GIRNKSSSS	0.012
  141	QAASGTLSL	0.012
  46	KIPPLSTPP	0.009
  11	EVLASPAAA	0.009
  103	PESPDRALK	0.009
  100	IDPPESPDR	0.006
  112	AANSWRNPV	0.006
  170	TIILSKLTQ	0.006
  120	VLPHTNGVG	0.006
  66	TAEAQESGI	0.006
  26	NILRGGLSE	0.006
  127	VGPLWEFLL	0.005
  24	GANILRGGL	0.005
  142	AASGTLSLA	0.005
  81	SSQIPVVGV	0.005
  52	TPPPPAMWT	0.005
  3	IVILDLSVE	0.005
  171	IILSKLTQE	0.005
  119	PVLPHTNGV	0.005
  99	SIDPPESPD	0.005
  168	LETIILSKL	0.004
  17	AAAWKCLGA	0.004
  67	AEAQESGIR	0.004
  108	RALKAANSW	0.003
  15	SPAAAWKCL	0.003
  86	VVGVVTEDD	0.003
  177	TQEQKSKHC	0.003
  14	ASPAAAWKC	0.003
  89	VVTEDDEAQ	0.003
  154	WSLGEFLGS	0.003
  139	KSQAASGTL	0.003
  157	GEFLGSGTW	0.003
  50	LSTPPPPAM	0.002
  34	EIVLPIEWQ	0.002
  85	PVVGVVTED	0.002
  78	SSSSSQIPV	0.002
  182	SKHCMFSLI	0.002
  160	LGSGTWMKL	0.002
  115	SWRNPVLPH	0.002
  33	SEIVLPIEW	0.002
  79	SSSSQIPVV	0.002
  105	SPDRALKAA	0.002
  65	ATAEAQESG	0.002
  64	GATAEAQES	0.001
  29	RGGLSEIVL	0.001
  113	ANSWRNPVL	0.001
  140	SQAASGTLS	0.001

• [1222]

  TABLE XIII
  Start	Subsequence	Score

  V1-HLA-A3-10-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  100	SLWDLRHLLV	2.000
  76	VTHHEDALTK	2.000
  370	LLSLLAVTSI	1.800
  132	YLASLFPDSL	1.800
  304	QLGLLSFFFA	1.800
  385	ALNWREFSFI	1.800
  435	ALVLPSIVIL	1.350
  303	KQLGLLSFFF	1.215
  307	LLSFFFAMVH	1.200
  442	VILDLLQLCR	1.200
  298	WLQCRKQLGL	1.200
  365	IMSLGLLSLL	0.900
  410	VLIYGWKRAF	0.900
  140	SLIVKGFNVV	0.900
  207	RLFTLWRGPV	0.900
  258	TLPIVAITLL	0.900
  123	NQYPESNAEY	0.900
  278	AAYQLYYGTK	0.900
  364	GIMSLGLLSL	0.810
  427	YTPPNFVLAL	0.810
  220	ISLATFFFLY	0.810
  221	SLATFFFLYS	0.720
  257	KTLPIVAITL	0.608
  333	FLNMAYQQVH	0.600
  268	SLVYLAGLLA	0.600
  324	PMRRSERYLF	0.600
  82	ALTKTNIIFV	0.600
  367	SLGLLSLLAV	0.600
  203	NLPLRLFTLW	0.600
  166	YICSNNIQAR	0.600
  219	AISLATFFFL	0.540
  147	NVVSAWALQL	0.540
  150	SAWALQLGPK	0.450
  56	VVIGSRNPKF	0.450
  417	RAFEEEYYRF	0.450
  45	LTIRLIRCGY	0.450
  216	VVVAISLATF	0.450
  178	VIELARQLNF	0.400
  204	LPLRLFTLWR	0.360
  358	EMYISFGIMS	0.360
  314	MVHVAYSLCL	0.360
  48	RLIRCGYHVV	0.300
  317	VAYSLCLPMR	0.300
  331	YLFLNMAYQQ	0.300
  313	AMVHVAYSLC	0.300
  373	LLAVTSIPSV	0.300
  269	LVYLAGLLAA	0.300
  440	SIVILDLLQL	0.270
  222	LATFFFLYSF	0.270
  154	LQLGP KDASR	0.270
  85	KTNIIFVAIH	0.270
  356	RIEMYISFGI	0.270
  406	STFHVLIYGW	0.225
  396	STLGYVALLI	0.203
  432	FVLALVLPSI	0.203
  217	VVAISLATFF	0.200
  433	VLALVLPSIV	0.200
  391	FSFIQSTLGY	0.200
  369	GLLSLLAVTS	0.180
  224	TFFFLYSFVR	0.180
  49	LIRCGYHVVI	0.180
  103	DLRHLLVGKI	0.162
  111	KILIDVSNNM	0.135
  249	KIPIEIVNKT	0.135
  264	ITLLSLVYLA	0.135
  5	SMMGSPKSLS	0.135
  113	LIDVSNNMRI	0.120
  262	VAITLLSLVY	0.120
  372	SLLAVTSIPS	0.120
  397	TLGYVALLIS	0.120
  157	GPKDASRQVY	0.120
  172	IQARQQVIEL	0.108
  243	QQSDFYKIPI	0.108
  347	NSWNEEEVWR	0.100
  39	GDFAKSLTIR	0.090
  218	VAISLATFFF	0.090
  384	NALNWREFSF	0.090
  285	GTKYRRFPPW	0.090

  V2-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  22	CLSLPSSWDY	12.000
  8	ALSLSLSSGF	2.000
  24	SLPSSWDYRC	1.800
  5	GLQALSLSLS	0.180
  12	SLSSGFTPFS	0.120
  10	SLSLSSGFTP	0.060
  35	PPCPADFFLY	0.054
  11	LSLSSGFTPF	0.045
  23	LSLPSSWDYR	0.045
  33	CPPPCPADFF	0.045
  36	PCPADFFLYF	0.036
  32	RCPPPCPADF	0.030
  2	GSPGLQALSL	0.027
  14	SSGFTPFSCL	0.013
  16	GFTPFSCLSL	0.005
  13	LSSGFTPFSC	0.005
  18	TPFSCLSLPS	0.004
  6	LQALSLSLSS	0.002
  34	PPPCPADFFL	0.002
  17	FTPFSCLSLP	0.002
  20	FSCLSLPSSW	0.001
  3	SPGLQALSLS	0.001
  15	SGFTPFSCLS	0.001
  27	SSWDYRCPPP	0.001
  21	SCLSLPSSWD	0.000
  7	QALSLSLSSG	0.000
  9	LSLSLSSGFT	0.000
  28	SWDYRCPPPC	0.000
  4	PGLQALSLSL	0.000
  29	WDYRCPPPCP	0.000
  30	DYRCPPPCPA	0.000
  1	SGSPGLQALS	0.000
  31	YRCPPPCPAD	0.000
  26	PSSWDYRCPP	0.000
  25	LPSSWDYRCP	0.000
  19	PFSCLSLPSS	0.000

  V5A-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  6	RLFTFWRGPV	0.900
  2	NLPLRLFTFW	0.600
  3	LPLRLFTFWR	0.540
  8	FTFWRGPVVV	0.050
  4	PLRLFTFWRG	0.018
  1	ENLPLRLFTF	0.012
  9	TFWRGPVVVA	0.005
  10	FWRGPVVVAI	0.004
  7	LFTFWRGPVV	0.000
  5	LRLFTFWRGP	0.000

  V5B-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  20	ELELEFVFLL	4.860
  22	ELEFVFLLTL	1.620
  18	QTELELEFVF	0.300
  5	FSFIQIFCSF	0.225
  16	DTQTELELEF	0.060
  9	QIFCSFADTQ	0.030
  12	CSFADTQTEL	0.015
  8	IQIFCSFADT	0.013
  23	LEFVFLLTLL	0.013
  17	TQTELELEFV	0.013
  19	TELELEFVFL	0.012
  14	FADTQTELEL	0.012
  2	WREFSFIQIF	0.009
  3	REFSFIQIFC	0.009
  21	LELEFVFLLT	0.006
  7	FIQIFCSFAD	0.006
  1	NWREFSFIQI	0.005
  6	SFIQIFCSFA	0.001
  24	EFVFLLTLLL	0.001
  11	FCSFADTQTE	0.000
  10	IFCSFADTQT	0.000
  4	EFSFIQIFCS	0.000
  15	ADTQTELELE	0.000
  13	SFADTQTELE	0.000

  V6-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  13	ILFLPCISRK	150.000
  2	VLPSIVILGK	90.000
  15	FLPCISRKLK	10.000
  42	GTIPHVSPER	2.025
  12	IILFLPCISR	1.800
  6	IVILGKIILF	0.900
  7	VILGKIILFL	0.608
  35	FLEEGIGGTI	0.405
  19	ISRKLKRIKK	0.200
  18	CISRKLKRIK	0.200
  5	SIVILGKIIL	0.180
  8	ILGKIILFLP	0.135
  46	HVSPERVTVM	0.090
  16	LPCISRKLKR	0.080
  23	LKRIKKGWEK	0.060
  1	LVLPSIVILG	0.041
  39	GIGGTIPHVS	0.027
  43	TIPHVSPERV	0.020
  22	KLKRIKKGWE	0.018
  11	KIILFLPCIS	0.018
  10	GKIILFLPCI	0.012
  33	SQFLEEGIGG	0.006
  3	LPSIVILGKI	0.004
  26	IKKGWEKSQF	0.003
  25	RIKKGWEKSQ	0.003
  27	KKGWEKSQFL	0.002
  28	KGWEKSQFLE	0.001
  9	LGKIILFLPC	0.001
  17	PCISRKLKRI	0.001
  29	KWEKSQFLEE	0.000
  37	EEGIGGTIPH	0.000
  30	WEKSQFLEEG	0.000
  21	RKLKRIKKGW	0.000
  4	PSIVILGKII	0.000
  38	EGIGGTIPHV	0.000
  14	LFLPCISRKL	0.000
  41	GGTIPHVSPE	0.000
  24	KRIKKGWEKS	0.000
  31	EKSQFLEEGI	0.000
  44	IPHVSPERVT	0.000
  34	QFLEEGIGGT	0.000
  32	KSQFLEEGIG	0.000
  36	LEEGIGGTIP	0.000
  45	PHVSPERVTV	0.000
  40	IGGTIPHVSP	0.000
  20	SRKLKRIKKG	0.000

  V7A-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  10	FLPNGINGIK	9.000
  5	SLSETFLPNG	0.135
  1	GPSKSLSETF	0.030
  2	SPKSLSETFL	0.006
  6	LSETFLPNGI	0.003
  8	ETFLPNGING	0.003
  4	KSLSETFLPN	0.003
  9	TFLPNGINGI	0.002
  7	SETFLPNGIN	0.000
  3	PKSLSETFLP	0.000

  V7B-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  5	MAYQQSTLGY	0.400
  2	FLNMAYQQST	0.300
  10	STLGYVALLI	0.203
  9	QSTLGYVALL	0.027
  4	NMAYQQSTLG	0.020
  7	YQQSTLGYVA	0.018
  8	QQSTLGYVAL	0.018
  3	LNMAYQQSTL	0.002
  6	AYQQSTLGYV	0.000
  1	LFLNMAYQQS	0.000

  V7C-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  13	VLASPAAAWK	20.000
  173	ILSKLTQEQK	20.000
  37	VLPIEWQQDR	12.000
  168	KLETIILSKL	4.050
  127	GVGPLWEFLL	2.430
  160	FLGSGTWMKL	1.200
  100	SIDPPESPDR	0.600
  176	KLTQEQKSKH	0.600
  38	LPIEWQQDRK	0.450
  164	GTWMKLETII	0.450
  134	FLLRLLKSQA	0.300
  6	ILDLSVEVLA	0.300
  28	ILRGGLSEIV	0.300
  5	VILDLSVEVL	0.270
  129	GPLWEFLLRL	0.243
  167	MKLETIILSK	0.203
  32	GLSEIVLPIE	0.203
  135	LLRLLKSQAA	0.200
  156	SLGEFLGSGT	0.150
  58	AMWTEEAGAT	0.150
  146	GTLSLAFTSW	0.135
  27	NILRGGLSEI	0.135
  166	WMKLETIILS	0.120
  147	TLSLAFTSWS	0.120
  138	LLKSQAASGT	0.100
  130	PLWEFLLRLL	0.068
  143	AASGTLSLAF	0.060
  110	ALKAANSWRN	0.060
  109	RALKAANSWR	0.060
  66	ATAEAQESGI	0.045
  115	NSWRNPVLPH	0.045
  159	EFLGSGTWMK	0.041
  131	LWEFLLRLLK	0.040
  141	SQAASGTLSL	0.036
  152	FTSWSLGEFL	0.030
  50	PLSTPPPPAM	0.030
  137	RLLKSQAASG	0.030
  4	IVILKLSVEV	0.030
  19	AAWKCLGANI	0.030
  125	TNGVGPLWEF	0.027
  42	WQQDRKIPPL	0.027
  182	KSKHCMFSLI	0.027
  31	GGLSEIVLPI	0.024
  128	VGPLWEFLLR	0.024
  52	STPPPPAMWT	0.022
  103	PPESPDRALK	0.020
  10	SVEVLASPAA	0.020
  149	SLAFTSWSLG	0.020
  121	VLPHTNGVGP	0.020
  112	KAANSWRNPV	0.018
  175	SKLTQEQKSK	0.015
  148	LSLAFTSWSL	0.013
  12	EVLASPAAAW	0.013
  8	DLSVEVLASP	0.013
  69	EAQESGIRNK	0.013
  74	GIRNKSSSSS	0.012
  67	TAEAQESGIR	0.012
  83	SQIPVVGVVT	0.010
  89	GVVTEDDEAQ	0.009
  47	KIPPLSTPPP	0.009
  14	LASPAAAWKC	0.009
  158	GEFLGSGTWM	0.009
  21	WKCLGANILR	0.008
  177	LTQEQKSKHC	0.007
  179	QEQKSKHCMF	0.006
  113	AANSWRNPVL	0.006
  84	QIPVVGVVTE	0.006
  178	TQEQKSKHCM	0.006
  150	LAFTSWSLGE	0.006
  78	KSSSSSQIPV	0.006
  122	LPHTNGVGPL	0.005
  3	SIVILDLSVE	0.005
  36	IVLPIEWQQD	0.005
  23	CLGANILRGG	0.005
  171	TIILSKLTQE	0.005
  81	SSSQIPVVGV	0.005
  22	KCLGANILRG	0.004
  35	EIVLPIEWQQ	0.004
  119	NPVLPHTNGV	0.003
  162	GSGTWMKLET	0.003
  142	QAASGTLSLA	0.003
  124	HTNGVGPLWE	0.003
  90	VVTEDDEAQD	0.003
  172	IILSKLTQEQ	0.003
  181	QKSKHCMFSL	0.003
  9	LSVEVLASPA	0.002
  51	LSTPPPPAMW	0.002
  87	VVGVVTEDDE	0.002
  33	LSEIVLPIEW	0.002
  91	VTEDDEAQDS	0.002
  165	TWMKLETIIL	0.002
  29	LRGGLSEIVL	0.002
  70	AWESGIRNKS	0.002
  132	WEFLLRLLKS	0.002
  43	QQDRKIPPLS	0.002
  92	TEDDEAQDSI	0.002
  79	SSSSSQIPVV	0.002
  60	WTEEAGATAE	0.002
  153	TSWSLGEFLG	0.002
  15	ASPAAAWKCL	0.002

• [1223]

  TABLE XIV
  Start	Subsequence	Score

  V1-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  56	VVIGSRNPK	3.000
  409	HVLIYGWKR	1.200
  249	KIPIEIVNK	1.200
  35	VIGSGDFAK	1.200
  175	RQQVIELAR	0.720
  417	RAFEEEYYR	0.480
  3	SISMMGSPK	0.400
  279	AYQLYYGTK	0.400
  136	LFPDSLIVK	0.400
  381	SVSNALNWR	0.400
  241	RNQQSDFYK	0.360
  282	LYYGTKYRR	0.320
  225	FFFLYSFVR	0.240
  21	GINGIKDAR	0.240
  53	GYHVVIGSR	0.240
  87	NIIFVAIHR	0.240
  18	LPNGINGIK	0.200
  443	ILDLLQLCR	0.160
  103	DLRHLLVGK	0.120
  34	GVIGSGDFA	0.090
  322	CLPMRRSER	0.080
  113	LIDVSNNMR	0.080
  155	QLGPKDASR	0.080
  318	AYSLCLPMR	0.080
  269	LVYLAGLLA	0.080
  281	QLYYGTKYR	0.080
  294	WLETWLQCR	0.080
  97	HYTSLWDLR	0.080
  295	LETWLQCRK	0.060
  441	IVILDLLQL	0.060
  306	GLLSFFFAM	0.054
  199	REIENLPLR	0.054
  22	INGIKDARK	0.040
  148	VVSAWALQL	0.040
  77	THHEDALTK	0.040
  108	LVGKILIDV	0.040
  223	ATFFFLYSF	0.040
  261	IVAITLLSL	0.040
  167	ICSNNIQAR	0.040
  164	QVYICSNNI	0.040
  43	KSLTIRLIR	0.036
  233	RDVIHPYAR	0.036
  48	RLIRCGYHV	0.036
  274	GLLAAAYQL	0.036
  330	RYLFLNMAY	0.036
  408	FHVLIYGWK	0.030
  85	KTNIIFVAI	0.030
  436	LVLPSIVIL	0.030
  303	KQLGLLSFF	0.027
  353	EVWRIEMYI	0.024
  191	DLGSLSSAR	0.024
  254	IVNKTLPIV	0.020
  90	FVAIHREHY	0.020
  151	AWALQLGPK	0.020
  83	LTKTNIIFV	0.020
  98	YTSLWDLRH	0.020
  231	FVRDVIHPY	0.020
  400	YVALLISTF	0.020
  217	VVAISLATF	0.020
  402	ALLISTFHV	0.018
  64	KFASEFFPH	0.018
  140	SLIVKGFNV	0.018
  214	GPVVVAISL	0.018
  135	SLFPDSLIV	0.016
  205	PLRLFTLWR	0.016
  209	FRLWRGPVV	0.015
  264	ITLLSLVYL	0.015
  396	STLGYVALL	0.015
  319	YSLCLPMRR	0.012
  394	IQSTLGYVA	0.012
  30	KVTVGVIGS	0.012
  270	VYLAGLLAA	0.012
  203	NLPLRLFTL	0.012
  425	RFYTPPNFV	0.012
  242	NQQSDFYKI	0.012
  287	KYRRFPPWL	0.012
  435	ALVLPSIVI	0.012
  265	TLLSLVYLA	0.012
  299	LQCRKQLGL	0.012
  313	AMVHVAYSL	0.012
  40	DFAKSLTIR	0.012
  106	HLLVGKILI	0.012
  426	FYTPPNFVL	0.012
  385	ALNWREFSF	0.012
  219	AISLATFFF	0.012
  304	QLGLLSFFF	0.012
  221	SLATFFFLY	0.012
  427	YTPPNFVLA	0.010
  285	GTKYRRFPP	0.009
  280	YQLYYGTKY	0.009
  397	TLGYVALLI	0.008
  367	SLGLLSLLA	0.008
  166	YICSNNIQA	0.008
  258	TLPIVAITL	0.008
  317	VAYSLCLPM	0.008
  100	SLWDLRHLL	0.008
  210	TLWRGPVVV	0.008
  365	IMSLGLLSL	0.008
  263	AITLLSLVY	0.008
  360	YISFGIMSL	0.008

  V2-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  24	SLPSSWDYR	0.080
  5	GLQALSLSL	0.024
  17	FTPFSCLSL	0.020
  3	SPGLQALSL	0.004
  12	SLSSGFTPF	0.004
  37	CPADFFLYF	0.004
  21	SCLSLPSSW	0.003
  33	CPPPCPADF	0.002
  23	LSLPSSWDY	0.001
  6	LQALSLSLS	0.001
  16	GFTPFSCLS	0.001
  32	RCPPPCPAD	0.001
  36	PCPADFFLY	0.001
  35	PPCPADFFL	0.001
  7	QALSLSLSS	0.001
  10	SLSLSSGFT	0.000
  15	SGFTPFSCL	0.000
  22	CLSLPSSWD	0.000
  8	ALSLSLSSG	0.000
  18	TPFSCLSLP	0.000
  25	LPSSWDYRC	0.000
  9	LSLSLSSGF	0.000
  1	SGSPGLQAL	0.000
  31	YRCPPPCPA	0.000
  34	PPPCPADFF	0.000
  30	DYRCPPPCP	0.000
  11	LSLSSGFTP	0.000
  14	SSGFTPFSC	0.000
  2	GSPGLQALS	0.000
  19	PFSCLSLPS	0.000
  29	WDYRCPPPC	0.000
  27	SSWDYRCPP	0.000
  13	LSSGFTPFS	0.000
  20	FSCLSLPSS	0.000
  28	SWDYRCPPP	0.000
  4	PGLQALSLS	0.000
  26	PSSWDYRCP	0.000

  V5A-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  3	PLRLFTFWR	0.024
  7	FTFWRGPVV	0.020
  1	NLPLRLFTF	0.012
  8	TFWRGPVVV	0.004
  2	LPLRLFTFW	0.003
  6	LFTFWRGPV	0.002
  5	RLFTFWRGP	0.000
  9	FWRGPVVVA	0.000
  4	LRLFTFWRG	0.000

  V5B-HLA-A11-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  24	FVFLLTLLL	0.080
  16	TQTELELEF	0.012
  17	QTELELEFV	0.010
  6	FIQIFCSFA	0.004
  2	REFSFIQIF	0.004
  5	SFIQIFCSF	0.003
  7	IQIFCSFAD	0.003
  18	TELELEFVF	0.003
  20	LELEFVFLL	0.003
  22	LEFVFLLTL	0.002
  12	SFADTQTEL	0.002
  19	ELELEFVFL	0.001
  23	EFVFLLTLL	0.001
  8	QIFCSFADT	0.001
  14	ADTQTELEL	0.000
  1	WREFSFIQI	0.000
  15	DTQTELELE	0.000
  21	ELEFVFLLT	0.000
  9	IFCSFADTQ	0.000
  13	FADTQTELE	0.000
  10	FCSFADTQT	0.000
  4	FSFIQIFCS	0.000
  3	EFSFIQIFC	0.000
  11	CSFADTQTE	0.000

  V6-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  2	LPSIVILGK	0.400
  12	ILFLPCISR	0.320
  13	LFLPCISRK	0.300
  23	KRIKKGWEK	0.180
  15	LPCISRKLK	0.100
  42	TIPHVSPER	0.080
  5	IVILGKIIL	0.060
  19	SRKLKRIKK	0.040
  45	HVSPERVTV	0.020
  10	KILLFLPCI	0.018
  16	PCISRKLKR	0.012
  6	VILGKIILF	0.012
  38	GIGGTIPHV	0.012
  7	ILGKIILFL	0.008
  21	KLKRIKKGW	0.006
  41	GTIPHVSPE	0.005
  4	SIVILGKII	0.003
  18	ISRKLKRIK	0.002
  17	CISRKLKRI	0.002
  43	IPHVSPERV	0.002
  32	SQFLEEGIG	0.001
  24	RIKKGWEKS	0.001
  27	KGWEKSQFL	0.001
  1	VLPSIVILG	0.001
  26	KKGWEKSQF	0.001
  11	IILFLPCIS	0.001
  33	QFLEEGIGG	0.001
  31	KSQFLEEGI	0.001
  35	LEEGIGGTI	0.001
  14	FLPCISRKL	0.000
  34	FLEEGIGGT	0.000
  46	VSPERVTVM	0.000
  9	GKIILFLPC	0.000
  28	GWEKSQFLE	0.000
  37	EGIGGTIPH	0.000
  29	WEKSQFLEE	0.000
  8	LGKIILFLP	0.000
  40	GGTIPHVSP	0.000
  20	RKLKRIKKG	0.000
  3	PSIVILGKI	0.000
  22	LKRIKKGWE	0.000
  39	IGGTIPHVS	0.000
  36	EEGIGGTIP	0.000
  25	IKKGWEKSQ	0.000
  30	EKSQFLEEG	0.000
  44	PHVSPERVT	0.000

  V7A-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  9	FLPNGINGI	0.004
  1	SPKSLSETF	0.002
  4	SLSETFLPN	0.001
  7	ETFLPNGIN	0.001
  8	TFLPNGING	0.001
  6	SETFLPNGI	0.001
  3	KSLSETFLP	0.000
  2	PKSLSETFL	0.000
  5	LSETFLPNG	0.000

  V7B-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  9	STLGYVALL	0.015
  7	QQSTLGYVA	0.012
  5	AYQQSTLGY	0.008
  6	YQQSTLGYV	0.006
  3	NMAYQQSTL	0.004
  4	MAYQQSTLG	0.000
  1	FLNMAYQQS	0.000
  8	QSTLGYVAL	0.000
  2	LNMAYQQST	0.000

  V7C-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  167	KLETIILSK	2.400
  159	FLGSGTWMK	0.800
  175	KLTQEQKSK	0.600
  21	KCLGANILR	0.360
  128	GPLWEFLLR	0.360
  131	WEFLLRLLK	0.240
  13	LASPAAAWK	0.200
  88	GVVTEDDEA	0.090
  109	ALKAANSWR	0.080
  69	AQESGIRNK	0.060
  163	GTWMKLETI	0.060
  37	LPIEWQQDR	0.060
  126	GVGPLWEFL	0.060
  38	PIEWQQDRK	0.040
  31	GLSEIVLPI	0.024
  173	LSKLTQEQK	0.020
  9	SVEVLASPA	0.020
  145	GTLSLAFTS	0.013
  2	SIVILDLSV	0.012
  67	AEAQESGIR	0.012
  151	FTSWSLGEF	0.010
  176	LTQEQKSKH	0.010
  51	STPPPPAMW	0.010
  59	WTEEAGATA	0.010
  123	HTNGVGPLW	0.010
  11	EVLASPAAA	0.009
  82	SQIPVVGVV	0.009
  108	RALKAANSW	0.009
  57	AMWTEEAGA	0.008
  165	WMKLETIIL	0.008
  148	SLAFTSWSL	0.008
  4	VILDLSVEV	0.006
  103	PESPDRALK	0.006
  42	QQDRKIPPL	0.006
  24	GANILRGGL	0.006
  35	IVLPIEWQQ	0.006
  5	ILDLSVEVL	0.004
  134	LLRLLKSQA	0.004
  100	IDPPESPDR	0.004
  141	QAASGTLSL	0.004
  27	ILRGGLSEI	0.004
  146	TLSLAFTSW	0.004
  12	VLASPAAAW	0.004
  17	AAAWKCLGA	0.004
  157	GEFLGSGTW	0.004
  3	IVILDLSVE	0.003
  119	PVLPHTNGV	0.003
  89	VVTEDDEAQ	0.002
  66	TAEAQESGI	0.002
  86	VVGVVTEDD	0.002
  142	AASGTLSLA	0.002
  112	AANSWRNPV	0.002
  181	KSKHCMFSL	0.002
  136	RLLKSQAAS	0.002
  179	EQKSKHCMF	0.002
  33	SEIVLPIEW	0.002
  129	PLWEFLLRL	0.002
  170	TIILSKLTQ	0.001
  73	GIRNKSSSS	0.001
  29	RGGLSEIVL	0.001
  46	KIPPLSTPP	0.001
  41	WQQDRKIPP	0.001
  26	NILRGGLSE	0.001
  105	SPDRALKAA	0.001
  65	ATAEAQESG	0.001
  15	SPAAAWKCL	0.001
  90	VTEDDEAQD	0.001
  158	EFLGSGTWM	0.001
  10	VEVLASPAA	0.001
  22	CLGANILRG	0.001
  185	CMFSLISGS	0.001
  184	HCMFSLISG	0.001
  127	VGPLWEFLL	0.001
  139	KSQAASGTL	0.001
  125	NGVGPLWEF	0.001
  64	GATAEAQES	0.001
  140	SQAASGTLS	0.001
  171	IILSKLTQE	0.001
  96	AQDSIDPPE	0.001
  168	LETIILSKL	0.001
  178	QEQKSKHCM	0.001
  101	DPPESPDRA	0.001
  164	TWMKLETII	0.000
  49	PLSTPPPPA	0.000
  18	AAWKCLGAN	0.000
  143	ASGTLSLAF	0.000
  150	AFTSWSLGE	0.000
  36	VLPIEWQQD	0.000
  83	QIPVVGVVT	0.000
  160	LGSGTWMKL	0.000
  52	TPPPPAMWT	0.000
  172	ILSKLTQEQ	0.000
  115	SWRNPVLPH	0.000
  99	SIDPPESPD	0.000
  149	LAFTSWSLG	0.000
  113	ANSWRNPVL	0.000
  155	SLGEFLGSG	0.000
  137	LLKSQAASG	0.000
  120	VLPHTNGVG	0.000
  78	SSSSSQIPV	0.000

• [1224]

  TABLE XV
  Start	Subsequence	Score

  V1-HLA-A1101-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  34	GVIGSGDFAK	27.000
  55	HVVIGSRNPK	3.000
  76	VTHHEDALTK	2.000
  135	SLFPDSLIVK	1.600
  21	GINGIKDARK	1.200
  294	WLETWLQCRK	0.400
  278	AAYQLYYGTK	0.400
  150	SAWALQLGPK	0.400
  17	CLPNGINGIK	0.400
  281	QLYYGTKYRR	0.320
  442	VILDLLQLCR	0.240
  224	TFFFLYSFVR	0.240
  407	TFHVLIYGWK	0.200
  154	LQLGPKDASR	0.180
  318	AYSLCLPMRR	0.160
  204	LPLRLFTLWR	0.120
  112	ILIDVSNNMR	0.120
  280	YQLYYGTKYR	0.090
  257	KTLPIVAITL	0.090
  303	KQLGLLSFFF	0.081
  166	YICSNNIQAR	0.080
  269	LVYLAGLLAA	0.080
  317	VAYSLCLPMR	0.080
  240	ARNQQSDFYK	0.060
  321	LCLPMRRSER	0.060
  147	NVVSAWALQL	0.060
  183	RQLNFIPIDL	0.054
  364	GIMSLGLLSL	0.048
  406	STFHVLIYGW	0.040
  254	IVNKTLPIVA	0.040
  314	MVHVAYSLCL	0.040
  316	HVAYSLCLPM	0.040
  356	RIEMYISFGI	0.036
  425	RFYTPPNFVL	0.036
  102	WDRLRHLLVGK	0.030
  248	YKIPIEIVNK	0.030
  56	VVIGSRNPKF	0.030
  285	GTKYRRFPPW	0.030
  216	VVVAISLATF	0.030
  83	LTKTNIIFVA	0.030
  85	KTNIIFVAIH	0.030
  396	STLGYVALLI	0.030
  432	FVLALVLPSI	0.030
  264	ITLLSLVYLA	0.030
  163	RQVYICSNNI	0.027
  416	KRAFEEEYYR	0.024
  86	RNIIFVAIHR	0.024
  39	GDFAKSLTIR	0.024
  417	RAFEEEYYRF	0.024
  207	RLFTLWRGPV	0.024
  217	VVAISLATFF	0.020
  223	ATFFFLYSFV	0.020
  400	YVALLISTFH	0.020
  261	IVAITLLSLV	0.020
  32	TVGVIGSGDF	0.020
  142	IVKGFNVVSA	0.020
  231	FVRDVIHPYA	0.020
  73	VVDVTHHEDA	0.020
  340	QVHANIENSW	0.020
  427	YTPPNFVLAL	0.020
  399	GYVALLISTF	0.018
  111	KILIDVSNNM	0.018
  274	GLLAAAYQLY	0.018
  48	RLIRCGYHVV	0.018
  306	GLLSFFFAMV	0.018
  100	SLWDLRHLLV	0.016
  45	LTIRLIRCGY	0.015
  209	FTLWRGPVVV	0.015
  409	HVLIYGWKRA	0.015
  408	FHVLIYGWKR	0.012
  243	QQSDFYKIPI	0.012
  440	SIVILDLLQL	0.012
  24	GIKDARKVTV	0.012
  304	QLGLLSFFFA	0.012
  145	GFNVVSAWAL	0.012
  359	MYISFGIMSL	0.012
  172	IQARQQVIEL	0.012
  121	RINGYPESNA	0.012
  123	NQYPESNAEY	0.012
  165	VYICSNNIQA	0.012
  107	LLVGKILIDV	0.012
  219	AISLATFFFL	0.012
  268	SLVYLAGLLA	0.012
  376	VTSIPSVSNA	0.010
  2	ESISMMGSPK	0.009
  401	VALLISTFHV	0.009
  214	VPVVVAISLA	0.009
  218	VAISLATFFF	0.009
  384	VALNWREFSF	0.009
  367	SLGLLSLLAV	0.008
  307	LLSFFFAMVH	0.008
  437	VLPSIVILDL	0.008
  227	FLYSFVRDVI	0.008
  42	AKSLTIRLIR	0.008
  113	LIDVSNNMRI	0.008
  210	TLWRGPVVVA	0.008
  178	VIELARQLNF	0.008
  298	WLQCRKQLGL	0.008
  404	LISTFHVLIY	0.008
  82	ALTKTNIIFV	0.008

  V2-HLA-A1101-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  16	GFTPFSCLSL	0.012
  22	CLSLPSSWDY	0.008
  23	LSLPSSWDYR	0.006
  32	RCPPPCPADF	0.006
  8	ALSLSLSSGF	0.004
  33	CPPPCPADFF	0.002
  6	LQALSLSLSS	0.001
  2	GSPGLQALSL	0.001
  5	GLQALSLSLS	0.001
  10	SLSLSSGFTP	0.001
  30	DYRCPPPCPA	0.001
  17	FTPFSCLSLP	0.001
  18	TPFSCLSLPS	0.001
  24	SLPSSWDYRC	0.001
  35	PPCPADFFLY	0.001
  34	PPPCPADFFL	0.001
  36	PCPADFFLYF	0.000
  12	SLSSGFTPFS	0.000
  11	LSLSSGFTPF	0.000
  21	SCLSLPSSWD	0.000
  7	QALSLSLSSG	0.000
  3	SPGLQALSLS	0.000
  20	FSCLSLPSSW	0.000
  14	SSGFTPFSCL	0.000
  4	PGLQALSLSL	0.000
  13	LSSGFTPFSC	0.000
  29	WDYRCPPPCP	0.000
  27	SSWDYRCPPP	0.000
  15	SGFTPFSCLS	0.000
  9	LSLSLSSGFT	0.000
  31	YRCPPPCPAD	0.000
  19	PFSCLSLPSS	0.000
  25	LPSSWDYRCP	0.000
  28	SWDYRCPPPC	0.000
  1	SGSPGLQALS	0.000
  26	PSSWDYRCPP	0.000

  V5A-HLA-A1101-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  3	LPLRLFTFWR	0.180
  6	RLFTFWRGPV	0.024
  8	FTFWRGPVVV	0.020
  9	TFWRGPVVVA	0.004
  2	NLPLRLFTFW	0.004
  7	LFTFWRGPVV	0.002
  1	ENLPLRLFTF	0.001
  10	FWRGPVVVAI	0.000
  4	PLRLFTFWRG	0.000
  5	LRLFTFWRGP	0.000

  V5B-HLA-A1101-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  18	QTELELEFVF	0.030
  16	DTWTELELEF	0.006
  17	TQTELELEFV	0.006
  14	FADTQTELEL	0.004
  20	ELELEFVFLL	0.004
  6	SFIQIFCSFA	0.003
  22	ELEFVFLLTL	0.002
  24	EFVFLLTLLL	0.002
  7	FIQIFCSFAD	0.001
  23	LEFVFLLTLL	0.001
  8	IQIFCSFADT	0.001
  19	TELELEFVFL	0.001
  9	QIFCSFADTQ	0.001
  3	REFSFIQIFC	0.001
  1	NWREFSFIQI	0.000
  12	CSFADTQTEL	0.000
  5	FSFIQIFCSF	0.000
  13	SFADTQTELE	0.000
  2	WREFSFIQIF	0.000
  11	FCSFADTQTE	0.000
  10	IFCSFADTQT	0.000
  4	EFSFIQIFCS	0.000
  21	LELEFVFLLT	0.000
  15	ADTQTELELE	0.000

  V6-HLA-A1101-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  42	GTIPHVSPER	0.900
  2	VLPSIVILGK	0.800
  13	ILFLPCISRK	0.800
  12	IILFLPCISR	0.240
  15	FLPCISRKLK	0.200
  16	LPCISRKLKR	0.080
  6	IVILGKIILF	0.060
  19	ISRKLKRIKK	0.040
  18	CISRKLKRIK	0.040
  23	LKRIKKGWEK	0.040
  46	HVSPERVTVM	0.020
  5	SIVILGKIIL	0.012
  7	VILGKIILFL	0.012
  1	LVLPSIVILG	0.006
  35	FLEEGIGGTI	0.004
  43	TIPHVSPERV	0.004
  33	SQFLEEGIGG	0.002
  3	LPSIVILGKI	0.002
  11	KILLFLPCIS	0.002
  39	GIGGTIPHVS	0.001
  8	ILGKIILFLP	0.001
  22	KLKRIKKGWE	0.001
  10	GKIILFLPCI	0.001
  25	RIKKGWEKSQ	0.001
  27	KKGWEKSQFL	0.001
  21	RKLKRIKKGW	0.000
  28	KGWEKSQFLE	0.000
  37	EEGIGGTIPH	0.000
  14	LFLPCISRKL	0.000
  34	QFLEEGIGGT	0.000
  26	IKKGWEKSQF	0.000
  17	PCISRKLKRI	0.000
  29	GWEKSQFLEE	0.000
  24	KRIKKGWEKS	0.000
  38	EGIGGTIPHV	0.000
  41	GGTIPHVSPE	0.000
  32	KSQFLEEGIG	0.000
  36	LEEGIGGTIP	0.000
  31	EKSQFLEEGI	0.000
  30	WEKSQFLEEG	0.000
  9	LGKIILFLPC	0.000
  45	PHVSPERVTV	0.000
  44	IPHVSPERVT	0.000
  40	IGGTIPHVSP	0.000
  4	PSIVILGKII	0.000
  20	SKRLKRIKKG	0.000

  V7A-HLA-A1101-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  10	FLPNGINGIK	0.400
  9	TFLPNGINGI	0.003
  2	SPKSLSETFL	0.002
  8	ETFLPNGING	0.001
  1	GSPKSLSETF	0.001
  5	SLSETFLPNG	0.000
  6	LSETFLPNGI	0.000
  4	KSLSETFLPN	0.000
  7	SETFLPNGIN	0.000
  3	PKSLSETFLP	0.000

  V7B-HLA-A1101-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  10	STLGYVALLI	0.030
  7	YQQSTLGYVA	0.012
  5	MAYQQSTLGY	0.008
  8	QQSTLGYVAL	0.006
  6	AYQQSTLGYV	0.004
  3	LNMAYQQSTL	0.001
  2	FLNMAYQQST	0.000
  4	NMAYQQSTLG	0.000
  1	LFLNMAYQQS	0.000
  9	QSTLGYVALL	0.000

  V7C-HLA-A1101-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 10 amino acids, and the end position
  for each peptide is the start position plus nine.

  173	ILSKLTQEQK	0.400
  13	VLASPAAAWK	0.400
  38	LPIEWQQDRK	0.300
  109	RALKAANSWR	0.180
  127	GVGPLWEFLL	0.180
  159	EFLGSGTWMK	0.180
  100	SIDPPESPDR	0.080
  37	VLPIEWQQDR	0.080
  167	MKLETIILSK	0.060
  164	GTWMKLETII	0.060
  146	GTLSLAFTSW	0.045
  131	LWEFLLRLLK	0.040
  67	TAEAQESGIR	0.040
  4	IVILDLSVEV	0.030
  103	PPESPDRALK	0.020
  10	SVEVLASPAA	0.020
  129	GPLWEFLLRL	0.018
  175	SKLTQEQKSK	0.015
  176	KLTQEQKSKH	0.012
  141	SQAASGTLSL	0.012
  168	KLETIILSKL	0.012
  66	ATAEAQESGI	0.010
  152	FTSWSLGEFL	0.010
  12	EVLASPAAAW	0.009
  89	GVVTEDDEAQ	0.009
  160	FLGSGTWMKL	0.008
  21	WKCLGANILR	0.008
  128	VGPLWEFLLR	0.008
  5	VILDLSVEVL	0.006
  112	KAANSWRNPV	0.006
  134	FLLRLLKSQA	0.006
  69	EAQESGIRNK	0.006
  27	NILRGGLSEI	0.006
  178	TQEQKSKHCM	0.006
  42	WQQDRKIPPL	0.006
  6	ILDLSVEVLA	0.004
  135	LLRLLKSQAA	0.004
  143	AASGTLSLAF	0.004
  19	AAWKCLGANI	0.004
  28	ILRGGLSEIV	0.004
  158	GEFLGSGTWM	0.004
  36	IVLPIEWQQD	0.003
  119	NPVLPHTNGV	0.003
  124	HTNGVGPLWE	0.002
  113	AANSWRNPVL	0.002
  122	LPHTNGVGPL	0.002
  52	STPPPPAMWT	0.002
  90	VVTEDDEAQD	0.002
  142	QAASGTLSLA	0.002
  87	VVGVVTEDDE	0.002
  151	AFTSWSLGEF	0.002
  31	GGLSEIVLPI	0.002
  137	RLLKSQAASG	0.002
  22	KCLGANILRG	0.002
  74	GIRNKSSSSS	0.001
  47	SIPPLSTPPP	0.001
  32	GLSEIVLPIE	0.001
  76	RNKSSSSSQI	0.001
  78	KSSSSSQIPV	0.001
  60	WTEEAGATAE	0.001
  91	VTEDDEAQDS	0.001
  83	SQIPVVGVVT	0.001
  170	ETIILSKLTQ	0.001
  11	VEVLASPAAA	0.001
  165	TWMKLETIIL	0.001
  125	TNGVGPLWEF	0.001
  110	ALKAANSWRN	0.001
  166	WMKLETIILS	0.001
  115	NSWRNPVLPH	0.001
  150	LAFTSWSLGE	0.001
  58	AMWTEEAGAT	0.001
  3	SIVILDLSVE	0.001
  182	KSKHCMFSLI	0.001
  171	TIILSKLTQE	0.001
  70	AQESGIRNKS	0.001
  181	QKSKHCMFSL	0.001
  172	IILSKLTQEQ	0.001
  148	LSLAFTSWSL	0.001
  65	GATAEAQESG	0.001
  25	GANILRGGLS	0.001
  97	AQDSIDPPES	0.001
  43	QQDRKIPPLS	0.001
  92	TEDDEAQDSI	0.001
  61	TEEAGATAEA	0.001
  179	QEQKSKHCMF	0.001
  177	LTQEQKSKHC	0.001
  147	TLSLAFTSWS	0.000
  121	VLPHTNGVGP	0.000
  17	PAAAWKCLGA	0.000
  138	LLKSQAASGT	0.000
  29	LRGGLSEIVL	0.000
  53	TPPPPAMWTE	0.000
  14	LASPAAAWKC	0.000
  84	QIPVVGVVTE	0.000
  50	PLSTPPPPAM	0.000
  185	HCMFSLISGS	0.000
  57	PAMWTEEAGA	0.000
  149	SLAFTSWSLG	0.000
  33	LSEIVLPIEW	0.000
  156	SLGEFLGSGT	0.000

• [1225]

  TABLE XVI
  Start	Subsequence	Score

  V1-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  287	KYRRFPPWL	400.000
  426	FYTPPNFVL	240.000
  337	AYQQVHANI	105.000
  283	YYGTKYRRF	100.000
  228	LYSFVRDVI	70.000
  390	EFSFIQSTL	28.000
  362	SFGIMSLGL	20.000
  418	AFEEEYYRF	18.000
  330	RYLFLNMAY	18.000
  378	SIPSVSNAL	10.080
  124	QYPESNAEY	9.900
  399	GYVALLIST	9.000
  177	QVIELARQL	8.640
  184	QLNFIPIDL	8.400
  258	TLPIVAITL	8.400
  313	AMVHVAYSL	8.400
  214	GPVVVAISL	8.400
  246	DFYKIPIEI	7.700
  270	VYLAGLLAA	7.500
  359	MYISFGIMS	7.500
  268	SLVYLAGLL	7.200
  291	FPPSLETWL	7.200
  366	MSLGLLSLL	7.200
  220	ISLATFFFL	7.200
  403	LLISTFHVL	7.200
  303	KQLGLLSFF	7.200
  436	LVLPSIVIL	7.200
  200	EIENLPLRL	7.200
  61	RNPKFASEF	6.600
  428	TPPNFVLAL	6.000
  274	GLLAAAYQL	6.000
  125	YPESNAEYL	6.000
  363	FGIMSLGLL	6.000
  264	ITLLSLVYL	6.000
  396	STLGYVALL	6.000
  297	TWLQCRKQL	6.000
  259	LPIVAITLL	6.000
  5	SMMGSPKSL	6.000
  203	NLPLRLFTL	6.000
  441	IVILDLLQL	6.000
  187	FIPIDLGSL	6.000
  146	FNVVSAWAL	6.000
  267	LSLVYLAGL	6.000
  99	TSLWDLRHL	6.000
  100	SLWDLRHLL	5.760
  438	LPSIVILDL	5.600
  85	KTNIIFVAI	5.040
  247	FYKIPIEIV	5.000
  423	YYRFYTPPN	5.000
  128	SNAEYLASL	4.800
  41	FAKSLTIRL	4.800
  37	GSGDFAKSL	4.800
  173	QARQQVIEL	4.400
  300	QCRKQLGLL	4.000
  75	DVTHHEDAL	4.000
  395	QSTLGYVAL	4.000
  299	LQCRKQLGL	4.000
  133	LASLFPDSL	4.000
  365	IMSLGLLSL	4.000
  148	VVSAWALQL	4.000
  360	YISFGIMSL	4.000
  261	IVAITLLSL	4.000
  196	SSAREIENL	4.000
  129	NAEYLASLF	3.600
  218	VAISLATFF	3.600
  385	ALNWREFSF	3.000
  33	VGVIGSGDF	3.000
  400	YVALLISTF	2.400
  304	QLGLLSFFF	2.400
  383	SNALNWREF	2.200
  57	VIGSRNPKF	2.200
  223	ATFFFLYSF	2.000
  411	LIYGWKRAF	2.000
  219	AISLATFFF	2.000
  62	NPKFASEFF	2.000
  82	ALTKTNIIF	2.000
  239	YARNQQSDF	2.000
  217	VVAISLATF	2.000
  242	NQQSDFYKI	1.980
  81	DALTKTNII	1.800
  17	CLPNGINGI	1.800
  349	WNEEEVWRI	1.800
  171	NIQARQQVI	1.800
  290	RFPPWLETW	1.800
  105	RHLLVGKIL	1.680
  193	GSLSSAREI	1.650
  112	ILIDVSNNM	1.512
  435	ALVLPSIVI	1.500
  106	HLLVGKILI	1.500
  134	ASLFPDSLI	1.500
  253	EIVNKTLPI	1.500
  371	LSLLAVTSI	1.500
  353	EVWRIEMYI	1.400
  397	TLGYVALLI	1.400
  433	VLALVLPSI	1.400
  186	NFIPIDLGS	1.260
  164	QVYICSNII	1.200
  180	ELARQLNFI	1.200
  425	RFYTPPNFV	1.200
  386	LNWREFSFI	1.200

  V2-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  5	GLQALSLSL	7.200
  17	FTPFSCLSL	6.000
  1	SGSPGLQAL	5.760
  15	SGFTPFSCL	4.800
  3	SPGLQALSL	4.000
  33	CPPPCPADF	3.600
  9	LSLSLSSGF	3.600
  37	CPADFFLYF	2.880
  12	SLSSGFTPF	2.400
  16	GFTPFSCLS	0.600
  30	DYRCPPPCP	0.500
  35	PPCPADFFL	0.480
  34	PPPCPADFF	0.300
  23	LSLPSSWDY	0.180
  2	GSPGLQALS	0.180
  21	SCLSLPSSW	0.180
  7	QALSLSLSS	0.180
  14	SSGFTPFSC	0.100
  10	SLSLSSGFT	0.100
  6	LQALSLSLS	0.100
  25	LPSSWDYRC	0.100
  13	LSSGFTPFS	0.100
  20	FSCLSLPSS	0.100
  19	PFSCLSLPS	0.060
  32	RCPPPCPAD	0.036
  36	PCPADFFLY	0.018
  24	SLPSSWDYR	0.015
  4	PGLQALSLS	0.015
  11	LSLSSGFTP	0.015
  27	SSWDYRCPP	0.012
  31	YRCPPPCPA	0.012
  18	TPFSCLSLP	0.010
  29	WDYRCPPPC	0.010
  8	ALSLSLSSG	0.010
  28	SWDYRCPPP	0.010
  22	CLSLPSSWD	0.010
  26	PSSWDYRCP	0.001

  V5A-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  1	NLPLRLFTF	3.000
  8	TFWRGPVVV	0.500
  6	LFTFWRGPV	0.500
  2	LPLRLFTFW	0.216
  7	FTFWRGPVV	0.100
  9	FWRGPVVVA	0.100
  5	RLFTFWRGP	0.020
  4	LRLFTFWRG	0.002
  3	PLRLFTFWR	0.001

  V5B-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  23	EFVFLLTLL	36.000
  12	SFADTQTEL	26.400
  5	SFIQIFCSF	25.200
  19	ELELEFVFL	7.200
  24	FVFLLTLLL	4.800
  16	TQTELELEF	3.168
  20	LELEFVFLL	0.720
  3	EFSFIQIFC	0.700
  2	REFSFIQIF	0.480
  14	ADTQTELEL	0.440
  18	TELELEFVF	0.432
  22	LEFVFLLTL	0.400
  21	ELEFVFLLT	0.252
  1	WREFSFIQI	0.180
  6	FIQIFCSFA	0.150
  17	QTELELEFV	0.150
  8	QIFCSFADT	0.120
  10	FCSFADTQT	0.100
  4	FSFIQIFCS	0.100
  9	IFCSFADTQ	0.050
  7	IQIFCSFAD	0.015
  15	DTQTELELE	0.015
  11	CSFADTQTE	0.012
  13	FADTQTELE	0.010

  V6-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  27	KGWEKSQFL	11.520
  14	FLPCISRKL	9.240
  5	IVILGKIIL	6.000
  7	ILGKIILFL	5.600
  31	KSQFLEEGI	3.600
  10	KIILFLPCI	3.000
  6	VILGKIILF	3.000
  4	SIVILGKII	1.800
  17	CISRKLKRI	1.000
  46	VSPERVTVM	0.900
  26	KKGWEKSQF	0.400
  21	KLKRIKKGW	0.280
  3	PSIVILGKI	0.231
  24	RIKKGWEKS	0.220
  35	LEEGIGGTI	0.210
  34	FLEEGIGGT	0.180
  11	IILFLPCIS	0.180
  39	IGGTIPHVS	0.140
  45	HVSPERVTV	0.120
  38	GIGGTIPHV	0.100
  43	IPHVSPERV	0.100
  33	QFLEEGIGG	0.090
  13	LFLPCISRK	0.090
  42	TIPHVSPER	0.023
  9	GKILLFLPC	0.022
  1	VLPSIVILG	0.021
  41	GTIPHVSPE	0.018
  28	GWEKSQFLE	0.015
  37	EGIGGTIPH	0.015
  2	LPSIVILGK	0.014
  8	LKGIILFLP	0.014
  18	ISRKLKRIK	0.012
  32	SQFLEEGIG	0.010
  40	GGTIPHVSP	0.010
  15	LPCISRKLK	0.010
  12	ILFLPCISR	0.010
  23	KRIKKGWEK	0.003
  20	RKLKRIKKG	0.003
  16	PCISRKLKR	0.002
  44	PHVSPERVT	0.002
  29	WEKSQFLEE	0.001
  19	SRKLKRIKK	0.001
  30	EKSQFLEEG	0.001
  22	LKRIKKGWE	0.001
  25	IKKGWEKSQ	0.001
  36	EEGIGGTIP	0.001

  V7A-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  1	SPKSLSETF	2.400
  9	FLPNGINGI	1.800
  4	SLSETFLPN	0.144
  6	SETFLPNGI	0.144
  7	ETFLPNGIN	0.100
  8	TFLPNGING	0.090
  2	PKSLSETFL	0.040
  3	KSLSETFLP	0.030
  5	LSETFLPNG	0.015

  V7B-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  5	AYQQSTLGY	7.500
  9	STLGYVALL	6.000
  8	QSTLGYVAL	4.000
  3	NMAYQQSTL	4.000
  1	FLNMAYQQS	0.180
  2	LNMAYQQST	0.180
  6	YQQSTLGYV	0.150
  7	QQSTLGYVA	0.120
  4	MAYQQSTLG	0.010

  V7C-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length of
  peptide is 9 amino acids, and the end position
  for each peptide is the start position plus eight.

  139	KSQAASGTL	12.000
  29	RGGLSEIVL	8.000
  181	KSKHCMFSL	8.000
  130	LWEFLLRLL	7.200
  24	GANILRGGL	7.200
  127	VGPLWEFLL	6.000
  126	GVGPLWEFL	5.760
  152	TSWSLGEFL	4.800
  160	LGSGTWMKL	4.400
  148	SLAFTSWSL	4.000
  42	QQDRKIPPL	4.000
  15	SPAAAWKCL	4.000
  141	QAASGTLSL	4.000
  5	ILDLSVEVL	4.000
  165	WMKLETIIL	4.000
  113	ANSWRNPVL	4.000
  158	EFLGSGTWM	3.750
  125	NGVGPLWEF	3.300
  143	ASGTLSLAF	2.400
  151	FTSWSLGEF	2.200
  179	EQKSKHCMF	2.000
  164	TWMKLETII	1.800
  31	GLSEIVLPI	1.680
  66	TAEAQESGI	1.500
  19	AWKCLGANI	1.200
  27	ILRGGLSEI	1.100
  163	GTWMKLETI	1.000
  132	EFLLRLLKS	0.825
  168	LETIILSKL	0.616
  102	PPESPDRAL	0.600
  50	LSTPPPPAM	0.600
  129	PLWEFLLRL	0.480
  20	WKCLGANIL	0.480
  108	RALKAANSW	0.360
  117	RNPVLPHTN	0.360
  136	RLLKSQAAS	0.300
  82	SQIPVVGVV	0.252
  4	VILDLSVEV	0.238
  123	HTNGVGPLW	0.210
  83	QIPVVGVVT	0.210
  104	ESPDRALKA	0.198
  51	STPPPPAMW	0.180
  145	GTLSLAFTS	0.180
  154	WSLGEFLGS	0.180
  68	EAQESGIRN	0.180
  9	SVEVLASPA	0.180
  59	WTEEAGATA	0.180
  156	LGEFLGSGT	0.180
  52	TPPPPAMWT	0.180
  112	AANSWRNPV	0.180
  101	DPPESPDRA	0.180
  2	SIVILDLSV	0.180
  169	ETIILSKLT	0.180
  88	GVVTEDDEA	0.165
  14	ASPAAAWKC	0.165
  25	ANILRGGLS	0.150
  72	SGIRNKSSS	0.150
  11	EVLASPAAA	0.150
  81	SSQIPVVGV	0.150
  177	TQEQKSKHC	0.150
  147	LSLAFTSWS	0.150
  64	GATAEAQES	0.132
  134	LLRLLKSQA	0.120
  146	TLSLAFTSW	0.120
  185	CMFSLISGS	0.120
  182	SKHCMFSLI	0.120
  58	MWTEEAGAT	0.120
  92	EDDEAQDSI	0.120
  39	IEWQQDRKI	0.110
  162	SGTWMKLET	0.110
  17	AAAWKCLGA	0.100
  79	SSSSQIPVV	0.100
  140	SQAASGTLS	0.100
  76	NKSSSSSQI	0.100
  142	AASGTLSLA	0.100
  105	SPDRALKAA	0.100
  57	AMWTEEAGA	0.100
  144	SGTLSLAFT	0.100
  18	AAWKCLGAN	0.100
  7	DLSVEVLAS	0.100
  78	SSSSSQIPV	0.100
  12	VLASPAAAW	0.100
  73	GIRNKSSSS	0.100
  71	ESGIRNKSS	0.100
  178	QEQKSKHCM	0.075
  150	AFTWESLGE	0.050
  46	KIPPLSTPP	0.043
  167	KLETIILSK	0.042
  122	PHTNGVGPL	0.040
  21	KCLGANILR	0.030
  116	WRNPVLPHT	0.025
  35	IVLPIEWQQ	0.025
  8	LSVEVLASP	0.025
  77	KSSSSSQIP	0.024
  119	PVLPHTNGV	0.022
  37	LPIEWQQDR	0.022
  1	PSIVILDLS	0.021
  6	LDLSVEVLA	0.021
  32	LSEIVLPIE	0.021
  183	KHCMFSLIS	0.020

• [1226]

  TABLE XVII
  Start	Subsequence	Score

  V1-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  124	QYPESNAEYL	360.000
  359	MYISFGIMSL	300.000
  399	GYVALLISTF	180.000
  282	LYYGTKYRRF	100.000
  423	YYRFYTPPNF	100.000
  290	RFPPWLETWL	86.400
  425	RFYTPPNFVL	40.000
  186	NFIPIDLGSL	36.000
  145	GFNVVSAWAL	30.000
  40	DFAKSLTIRL	24.000
  257	KTLPIVAITL	20.160
  362	SFGIMSLGLL	20.000
  213	RGPVVVAISL	16.800
  377	TSIPSVSNAL	12.096
  131	EYLASLFPDS	10.800
  250	IPIEIVNKTL	10.080
  238	PYARNQQSDF	10.000
  270	VYLAGLLAAA	8.000
  437	VLPSIVILDL	84.00
  312	FAMVHVAYSL	8.400
  279	AYQLYYGTKY	8.250
  165	VYICSNNIQA	7.500
  176	QQVIELARQL	7.200
  202	ENLPLRLFTL	7.200
  99	TLSWDLRHLL	7.200
  427	YTPPNFVLAL	7.200
  303	KQLGLLSFFF	7.200
  267	LSLVYLAGLL	7.200
  426	FYTPPNFVLA	7.200
  402	ALLISTFHVL	7.200
  53	GYHVVIGSRN	7.000
  247	FYKIPIEIVN	7.000
  364	GIMSLGLLSL	6.000
  127	ESNAEYLASL	6.000
  61	RNPKFASEFF	6.000
  298	WLQCRKQLGL	6.000
  4	ISMMGSPKSL	6.000
  273	AGLLAAAYQL	6.000
  323	LPMRRSERYL	6.000
  147	NVVSAWALQL	6.000
  435	ALVLPSIVIL	6.000
  440	SIVILDLLQL	6.000
  258	TLPIVAITLL	6.000
  438	LPSIVILDLL	5.600
  422	EYYRFYTPPN	5.000
  219	AISLATFFFL	4.800
  417	RAFEEEYYRF	4.800
  365	IMSLGLLSLL	4.800
  197	SAREIENLPL	4.800
  172	IQARQQVIEL	4.400
  356	RIEMYISFGI	4.200
  36	IGSGDFAKSL	4.000
  98	YTSLWDLRHL	4.000
  132	YLASLFPDSL	4.000
  296	ETWLQCRKQL	4.000
  266	LLSLVYLAGL	4.000
  195	LSSAREIENL	4.000
  314	MVHVAYSLCL	4.000
  263	AITLLSLVYL	4.000
  299	LQCRKQLGLL	4.000
  92	AIHREHYTSL	4.000
  361	ISFGIMSLGL	4.000
  9	SPKSLSETCL	4.000
  395	QSTLGYVALL	4.000
  394	IQSTLGYVAL	4.000
  241	RNQQSDFYKI	3.960
  163	RQVYICSNNI	3.600
  382	VSNALNWREF	3.300
  56	VVIGSRNPKF	3.300
  384	NALNWREFSF	3.000
  410	VLIYGWKRAF	3.000
  216	VVVAISLATF	3.000
  178	VIELARQLNF	3.000
  218	VAISLATFFF	3.000
  200	EIENLPLRLF	3.000
  81	DALTKTNIIF	3.000
  128	SNAEYLASLF	2.880
  137	FPDSLIVKGF	2.800
  111	KILIDVSNNM	2.520
  217	VVAISLATFF	2.400
  16	TCLPNGINGI	2.160
  327	RSERYLFLNM	2.160
  13	LSETCLPNGI	2.160
  396	STLGYVALLI	2.100
  432	FVLALVLPSI	2.100
  354	VWRIEMYISF	2.000
  222	LATFFFLYSF	2.000
  32	TVGVIGSGDF	2.000
  385	ALNWREFSFI	1.800
  170	NNIQARQQVI	1.800
  348	SWNEEEVWRI	1.800
  199	REIENLPLRL	1.728
  403	LLISTFHVLI	1.500
  330	RYLFLNMAYQ	1.500
  434	LALVLPSIVI	1.500
  211	LWRGPVVVAI	1.400
  336	MAYQQVHANI	1.400
  227	FLYSFVRDVI	1.400
  103	DLRHLLVGKI	1.320

  V2-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified,
  the length of peptide is 10 amino acids,
  and the end position for each peptide is
  the start position plus nine.

  16	GFTPFSCLSL	24.000
  32	RCPPPCPADF	7.200
  2	GSPGLQALSL	6.000
  30	DYRCPPPCPA	5.000
  14	SSGFTPFSCL	4.800
  11	LSLSSGFTPF	3.600
  33	CPPPCPADFF	3.600
  8	ALSLSLSSGF	2.500
  4	PGLQALSLSL	0.720
  34	PPPCPADFFL	0.600
  36	PCPADFFLYF	0.360
  9	LSLSLSSGFT	0.150
  5	GLQALSLSLS	0.150
  24	SLPSSWDYRC	0.150
  1	SGSPGLQALS	0.144
  6	LQALSLSLSS	0.120
  20	FSCLSLPSSW	0.120
  18	TPFSCLSLPS	0.120
  15	SGFTPFSCLS	0.100
  12	SLSSGFTPFS	0.100
  28	SWDYRCPPPC	0.100
  13	LSSGFTPFSC	0.100
  3	SPGLQALSLS	0.100
  22	CLSLPSSWDY	0.100
  19	PFSCLSLPSS	0.050
  23	LSLPSSWDYR	0.018
  7	QALSLSLSSG	0.015
  17	FTPFSCLSLP	0.015
  21	SCLSLPSSWD	0.015
  35	PPCPADFFLY	0.014
  27	SSWDYRCPPP	0.012
  25	LPSSWDYRCP	0.010
  10	SLSLSSGFTP	0.010
  31	YRCPPPCPAD	0.001
  29	WDYRCPPCP	0.001
  26	PSSWDYRCPP	0.001

  V5A-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptide is 10 amino acids,
  and the end position for each peptide is
  the start position plus nine.

  1	ENLPLRLFTF	3.600
  10	FWRGPVVVAI	1.400
  7	LFTFWRGPVV	0.500
  9	TFWRGPVVVA	0.500
  2	NLPLRLFTFW	0.216
  6	RLFTFWRGPV	0.200
  8	FTFWRGPVVV	0.100
  3	LPLRLFTFWR	0.015
  5	LRLFTFWRGP	0.002
  4	PLRLFTFWRG	0.001

  V5B-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptide is 10 amino acids,
  and the end position for each peptide is
  the start position plus nine.

  24	EFVFLLTLLL	36.000
  22	ELEFVFLLTL	6.000
  20	ELELEFVFLL	6.000
  12	CSFADTQTEL	4.400
  14	FADTQTELEL	4.400
  16	DTQTELELEF	3.960
  18	QTELELEFVF	3.600
  5	FSFIQIFCSF	3.360
  1	NWREFSFIQI	1.440
  19	TELELEFVFL	0.864
  6	SFIQIFCSFA	0.750
  4	EFSFIQIFCS	0.500
  10	IFCSFADTQT	0.500
  23	LEFVFLLTLL	0.480
  2	WREFSFIQIF	0.360
  8	IQIFCSFADT	0.180
  17	TQTELELEFV	0.120
  13	SFADTQTELE	0.060
  21	LELEFVFLLT	0.030
  3	REFSFIQIFC	0.028
  7	FIQIFCSFAD	0.015
  11	FCSFADTQTE	0.012
  9	QIFCSFADTQ	0.010
  15	ADTWTELELE	0.001

  V6-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified,
  the length of peptide is 10 amino acids,
  and the end position for each peptide is
  the start position plus nine.

  14	LFLPCISRKL	55.440
  7	VILGKIILFL	8.400
  5	SIVILGKIIL	6.000
  6	IVILGKIILF	3.000
  35	FLEEGIGGTI	2.520
  3	LPSIVILGKI	1.540
  27	KKGWEKSQFL	0.960
  34	QFLEEGIGGT	0.900
  46	HVSPERVTVM	0.600
  11	KIILFLPCIS	0.360
  26	IKKGWEKSQF	0.200
  4	PSIVILGKII	0.180
  38	EGIGGTIPHV	0.150
  17	PCISRKLKRI	0.150
  43	TIPHVSPERV	0.150
  10	GKIILFLPCI	0.150
  9	LGKIILFLPC	0.144
  39	GIGGTIPHVS	0.140
  31	EKSQFLEEGI	0.120
  44	IPHVSPERVT	0.100
  21	RKLKRIKKGW	0.042
  24	KRIKKGWEKS	0.033
  32	KSQFLEEGIS	0.030
  42	GTIPHVSPER	0.028
  1	LVLPSIVILG	0.025
  28	KGWEKSQFLE	0.024
  2	VLPSIVILGK	0.021
  25	RIKKGWEKSQ	0.020
  22	KLKRIKKGWE	0.020
  29	GWEKSQFLEE	0.020
  12	IILFLPCISR	0.015
  15	FLPCISRKLK	0.015
  8	ILGKIILFLP	0.014
  18	CISRKLKRIK	0.012
  16	LPCISRKLKR	0.011
  19	ISRKLKRIKK	0.011
  33	SQFLEEGIGG	0.010
  41	GGTIPHVSPE	0.010
  40	IGGTIPHVSP	0.010
  13	ILFLPCISRK	0.010
  36	LEEGIGGTIP	0.002
  45	PHVSPERVTV	0.002
  20	SRKLKRIKKG	0.001
  30	WEKSQFLEEG	0.001
  23	LKRIKKGWEK	0.001
  37	EEGIGGTIPH	0.001

  V7A-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptide is 10 amino acids,
  and the end position for each peptide is
  the start position plus nine.

  9	TFLPNGINGI	10.800
  2	SPKSLSETFL	4.000
  1	GSPKSLSETF	3.600
  6	LSETFLPNGI	2.160
  4	KSLSETFLPN	0.360
  10	FLPNGINGIK	0.021
  5	SLSETFLPNG	0.012
  7	SETFLPNGIN	0.010
  8	ETFLPNGING	0.010
  3	PKSLSETFLP	0.000

  VtB-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptide is 10 amino acids,
  and the end position for each peptide is
  the start position plus nine.

  6	AYQQSTLGYV	7.500
  3	LNMAYQQSTL	6.000
  8	QQSTLGYVAL	4.000
  9	QSTLGYVALL	4.000
  10	STLGYVALLI	2.100
  1	LFLNMAYQQS	0.900
  7	YQQSTLGYVA	0.180
  2	FLNMAYQQST	0.180
  5	MAYQQSTLGY	0.100
  4	NMAYQQSTLG	0.010

  V7C-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptide is 10 amino acids,
  and the end position for each peptide is
  the start position plus nine.

  168	KLETIILSKL	18.480
  151	AFTSWSLGEF	11.000
  5	VILDLSVEVL	7.200
  42	WQQDRKIPPL	7.200
  126	NGVGPLWEFL	7.200
  102	DPPESPDRAL	7.200
  113	AANSWRNPVL	6.000
  129	GPLWEFLLRL	6.000
  148	LSLAFTSWSL	6.000
  15	ASPAAAWKCL	6.000
  165	TWMKLETIIL	6.000
  24	LGANILRGGL	4.800
  20	AWKCLGANIL	4.800
  127	GVGPLWEFLL	4.800
  152	FTSWSLGEFL	4.800
  160	FLGSGTWMKL	4.400
  122	LPHTNGVGPL	4.000
  141	SQAASGTLSL	4.000
  182	KSKHCMFSLI	2.400
  143	AASGTLSLAF	2.400
  125	TNGVGPLWEF	2.200
  31	GGLSEIVLPI	2.100
  76	RNKSSSSSQI	2.000
  27	NILRGGLSEI	1.650
  164	GTWMKLETII	1.200
  19	AAWKCLGANI	1.200
  66	ATAEAQESGI	1.200
  163	SGTWMKLETI	1.000
  178	TQEQKSKHCM	0.750
  130	PLWEFLLRLL	0.576
  29	LRGGLSEIVL	0.400
  181	QKSKHCMFSL	0.400
  139	LKSQAASGTL	0.400
  179	QEQKSKHCMF	0.300
  140	KSQAASGTLS	0.300
  70	AQESGIRNKS	0.277
  83	SQIPVVGVVT	0.252
  112	KAANSWRNPV	0.240
  91	VTEDDEAQDS	0.216
  9	LSVEVLASPA	0.216
  82	SSQIPVVGVV	0.210
  78	KSSSSSQIPV	0.200
  4	IVILDLSVEV	0.198
  33	LSEIVLPIEW	0.198
  119	NPVLPHTNGV	0.180
  105	ESPDRALKAA	0.180
  52	STPPPPAMWT	0.180
  177	LTQEQKSKHC	0.180
  134	FLLRLLKSQ	0.180
  185	HCMFSLISGS	0.180
  146	GTLSLAFTSW	0.180
  39	PIEWQQDRKI	0.165
  88	VGVVTEDDEA	0.165
  10	SVEVLASPAA	0.150
  73	SGIRNKSSSS	0.150
  25	GANILRGGLS	0.150
  157	LGEFLGSGTW	0.150
  12	EVLASPAAAW	0.150
  156	SLGEFLGSGT	0.144
  1	LPSIVILDLS	0.140
  6	ILDLSVEVLA	0.140
  116	SWRNPVLPHT	0.140
  43	QQDRKIPPLS	0.140
  64	AGATAEAQES	0.132
  14	LASPAAAWKC	0.132
  174	LSKLTQEQKS	0.132
  51	LSTPPPPAMW	0.120
  92	TEDDEAQDSI	0.120
  135	LLRLLKSQAA	0.120
  106	SPDRALKAAN	0.120
  59	MWTEEAGATA	0.120
  28	ILRGGLSEIV	0.120
  154	SWSLGEFLGS	0.120
  145	STGLSLAFTS	0.120
  162	GSGTWMKLET	0.110
  97	AQDSIDPPES	0.110
  147	TLSLAFTSWS	0.100
  180	EQKSKHCMFS	0.100
  79	SSSSSQIPVV	0.100
  152	QAASGTLSLA	0.100
  18	AAAWKCLGAN	0.100
  138	LLKSQAASGT	0.100
  110	ALKAANSWRN	0.100
  144	ASGTLSLAFT	0.100
  74	GIRNKSSSSS	0.100
  81	SSSQIPVVGV	0.100
  166	WMKLETIILS	0.100
  72	ESGIRNKSSS	0.100
  58	AMWTEEAGAT	0.100
  133	EFLLRLLKSQ	0.090
  159	EFLGSGTWMK	0.075
  158	GEFLGSGTWM	0.050
  50	PLSTPPPPAM	0.050
  47	KIPPLSTPPP	0.036
  22	KCLGANILRG	0.030
  118	RNPVLPHTNG	0.030
  109	RALKAANSWR	0.030
  137	RLLKSQAASG	0.030
  96	EAQDSIDPPE	0.025
  172	IILSKLTQEQ	0.024

• [1227]

  TABLE XVIII
  Start	Subsequence	Score

  V1-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  173	QARQQVIEL	120.000
  214	GPVVVAISL	80.000
  259	LPIVAITLL	80.000
  428	TPPNFVLAL	80.000
  438	LPSIVILDL	80.000
  291	FPPWLETWL	80.000
  300	QCRKQLGLL	40.000
  125	YPESNAEYL	24.000
  177	QVIELARQL	20.000
  148	VVSAWALQL	20.000
  251	IVAITLLSL	20.000
  75	DVTHHEDAL	20.000
  441	IVILDLLQL	20.000
  436	LVLPSIVIL	20.000
  41	FAKSLTIRL	12.000
  313	AMVHVAYSL	12.000
  133	LASLFPDSL	12.000
  5	SMMGSPKSL	12.000
  27	DARKVTVGV	6.000
  100	SLWDLRHLL	6.000
  146	FNVVSAWAL	4.000
  220	ISLATFFFL	4.000
  187	FIPIDLGSL	4.000
  128	SNAEYLASL	4.000
  363	FGIMSLGLL	4.000
  274	GLLAAAYQL	4.000
  365	IMSLGLLSL	4.000
  366	MSLGLLSLL	4.000
  184	QLNFIPIDL	4.000
  93	IHREHYTSL	4.000
  324	PMRRSERYL	4.000
  395	QSTLGYVAL	4.000
  267	LSLVYLAGL	4.000
  268	SLVYLAGLL	4.000
  360	YISFGIMSL	4.000
  196	SSAREIENL	4.000
  378	SIPSVSNAL	4.000
  258	TLPIVAITL	4.000
  299	LQCRKQLGL	4.000
  99	TSLWDLRHL	4.000
  403	LLISTFHVL	4.000
  37	GSGDFAKSL	4.000
  203	NLPLRLFTL	4.000
  264	ITLLSLVYL	4.000
  396	STLGYVALL	4.000
  287	KYRRFPPWL	4.000
  157	GPKDASRQV	4.000
  317	VAYSLCLPM	3.000
  9	SPKSLSETC	2.000
  250	IPIEIVNKT	2.000
  353	EVWRIEMYI	2.000
  49	LIRCGYHVV	2.000
  164	QVYICSNNI	2.000
  134	ASLFPDSLI	1.800
  435	ALVLPSIVI	1.800
  200	EIENLPLRL	1.200
  81	DALTKTNII	1.200
  323	LPMRRSERY	1.200
  108	LVGKILIDV	1.000
  358	EMYISFGIM	1.000
  112	ILIDVSNNM	1.000
  254	IVNKTLPIV	1.000
  231	FVRDVIHPY	1.000
  328	SERYLFLNM	1.000
  306	GLLSFFFAM	1.000
  278	AAYQLYYGT	0.800
  402	ALLISTFHV	0.600
  297	TWLQCRKQL	0.600
  262	VAITLLSLV	0.600
  239	YARNQQSDF	0.600
  434	LALVLPSIV	0.600
  65	FASEFFPHV	0.600
  161	ASRQVYICS	0.600
  426	FYTPPNFVL	0.600
  374	LAVTSIPSV	0.600
  314	MVHVAYSLC	0.500
  34	GVIGSGDFA	0.500
  216	VVVAISLAT	0.500
  269	LVYLAGLLA	0.500
  237	HPYARNQQS	0.400
  371	LSLLAVTSI	0.400
  85	KTNIIFVAI	0.400
  390	EFSFIQSTL	0.400
  439	PSIVILDLL	0.400
  397	TLGYVALLI	0.400
  430	PNFVLALVL	0.400
  362	SFGIMSLGL	0.400
  171	NIQARQQVI	0.400
  180	ELARQLNFI	0.400
  193	GSLSSAREI	0.400
  386	LNWREFSFI	0.400
  204	LPLRLFTLW	0.400
  429	PPNFVLALV	0.400
  188	IPIDLGSLS	0.400
  279	IPSVSNALN	0.400
  62	NPKFASEFF	0.400
  326	RRSERYLFL	0.400
  433	VLALVLPSI	0.400
  253	EIVNKTLPI	0.400
  106	HLLVGKILI	0.400

  V2-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  3	SPGLQALSL	80.000
  35	PPCPADFFL	8.000
  15	SGFTPFSCL	6.000
  1	SGSPGLQAL	4.000
  17	FTPFSCLSL	4.000
  5	GLQALSLSL	4.000
  25	LPSSWDYRC	2.000
  37	CPADFFLYF	0.400
  33	CPPPCPADF	0.400
  18	TPFSCLSLP	0.200
  10	SLSLSSGFT	0.100
  14	SSGFTPFSC	0.100
  7	QALSLSLSS	0.060
  34	PPPCPADFF	0.060
  8	ALSLSLSSG	0.030
  23	LSLPSSWDY	0.020
  12	SLSSGFTPF	0.020
  21	SCLSLPSSW	0.020
  6	LQALSLSLS	0.020
  13	LSSGFTPFS	0.020
  2	GSPGLQALS	0.020
  9	LSLSLSSGF	0.020
  20	FSCLSLPSS	0.020
  32	RCPPPCPAD	0.015
  22	CLSLPSSWD	0.015
  31	YRCPPPCPA	0.015
  30	DYRCPPPCP	0.015
  27	SSWDYRCPP	0.015
  29	WDYRCPPPC	0.010
  24	SLPSSWDYR	0.010
  11	LSLSSGFTP	0.010
  36	PCPADFFLY	0.002
  16	GFTPFSCLS	0.002
  4	PGLQALSLS	0.002
  26	PSSWDYRCP	0.001
  28	SWDYRCPPP	0.000
  19	PFSCLSLPS	0.000

  V5A-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  2	LPLRLFTFW	0.400
  7	FTFWRGPVV	0.200
  9	FWRGPVVVA	0.150
  6	LFTFWRGPV	0.030
  8	TFWRGPVVV	0.020
  1	NLPLRLFTF	0.020
  3	PLRLFTFWR	0.010
  5	RLFTFWRGP	0.010
  4	LRLFTFWRG	0.001

  V5B-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  24	FVFLLTLLL	20.000
  14	ADTQTELEL	1.200
  19	ELELEFVFL	1.200
  12	SFADTQTEL	0.400
  23	EFVGLLTLL	0.400
  22	LEFVFLLTL	0.400
  20	LELEFVFLL	0.400
  10	FCSFADTQT	0.100
  8	QIFCSFADT	0.100
  6	FIQIFCSFA	0.100
  17	QTELELEFV	0.060
  21	ELEFVFLLT	0.030
  4	FSFIQIFCS	0.020
  16	TQTELELEF	0.020
  1	WREFSFIQI	0.012
  11	CSFADTQTE	0.010
  3	EFSFIQIFC	0.010
  7	IQIFCSFAD	0.010
  15	DTQTELELE	0.010
  13	FADTQTELE	0.009
  5	SFIQIFCSF	0.002
  2	REFSFIQIF	0.002
  18	TELELFVF	0.002
  9	IFCSFADTQ	0.001

  V6-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  5	IVILGKIIL	20.000
  14	FLPCISRKL	4.000
  43	IPHVSPERV	4.000
  7	ILGKIILFL	4.000
  27	KGWEKSQFL	4.000
  45	HVSPERVTV	1.500
  46	VSPERVTVM	1.000
  31	KSQFLEEGI	0.400
  4	SIVILGKII	0.400
  17	CISRKLKRI	0.400
  10	KIILFLPCI	0.400
  15	LPCISRKLK	0.300
  38	GIGGTIPHV	0.200
  2	LPSIVILGK	0.200
  18	ISRKLKRIK	0.100
  3	PSIVILGKI	0.040
  34	FLEEGIGGT	0.030
  11	IILFLPCIS	0.020
  39	IGGTIPHVS	0.020
  6	VILGKIILF	0.020
  24	RIKKGWEKS	0.020
  21	KLKRIKKGW	0.020
  40	GGTIPHVSP	0.015
  12	ILFLPCISR	0.015
  35	LEEGIGGTI	0.012
  37	EGIGGTIPH	0.010
  22	LKRIKKGWE	0.010
  8	LGKIILFLP	0.010
  32	SQFLEEGIG	0.010
  41	GTIPHVSPE	0.010
  1	VLPSIVILG	0.010
  9	GKIILFLPC	0.010
  42	TIPHVSPER	0.010
  26	KKGWEKSQF	0.002
  19	SRKLKRIKK	0.002
  44	PHVSPERVT	0.002
  36	EEGIGGTIP	0.001
  20	RKLKRIKKG	0.001
  29	WEKSQFLEE	0.001
  13	LFLPCISRK	0.001
  25	IKKGWEKSQ	0.001
  30	EKSQFLEEG	0.001
  33	QFLEEGIGG	0.001
  23	KRIKKGWEK	0.001
  16	PCISRKLKR	0.001
  28	GWEKSQFLE	0.000

  V7A-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  9	FLPNGINGI	0.400
  1	SPKSLSETF	0.400
  5	SETFLPNGI	0.040
  2	PKSLSETFL	0.040
  7	ETFLPNGIN	0.030
  4	SLSETFLPN	0.020
  3	KSLSETFLP	0.010
  5	LSETFLPNG	0.003
  8	TFLPNGING	0.001

  V7B-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  9	STLGYVALL	4.000
  8	QSTLGYVAL	4.000
  3	NMAYQQSTL	4.000
  2	LNMAYQQST	3.000
  6	YQQSTLGYV	0.200
  7	QQSTLGYVA	0.100
  4	MAYQQSTLG	0.030
  1	FLNMAYQQS	0.020
  5	AYQQSTLGY	0.006

  V7C-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  15	SPAAAWKCL	80.000
  126	GVGPLWEFL	20.000
  24	GANILRGGL	18.000
  113	ANSWRNPVL	12.000
  141	QAASGTLSL	12.000
  127	VGPLWEFLL	4.000
  148	SLAFTSWSL	4.000
  181	KSKHCMFSL	4.000
  29	RGGLSEIVL	4.000
  139	KSQAASGTL	4.000
  27	ILRGGLSEI	4.000
  165	WMKLETIIL	4.000
  152	TSWSLGEFL	4.000
  160	LGSGTWMKL	4.000
  102	PPESPDRAL	3.600
  52	TPPPPAMWT	3.000
  112	AANSWRNPV	2.700
  101	DPPESPDRA	2.000
  50	LSTPPPPAM	1.500
  5	ILDLSVEVL	1.200
  42	QQDRKIPPL	1.200
  134	LLRLLKSQA	1.000
  142	AASGTLSLA	0.900
  17	AAAWKCLGA	0.900
  105	SPDRALKAA	0.600
  11	EVLASPAAA	0.500
  88	GVVTEDDEA	0.500
  31	GLSEIVLPI	0.400
  20	WKCLGANIL	0.400
  168	LETIILSKL	0.400
  163	GTWMKLETI	0.400
  129	PLWEFLLRL	0.400
  66	TAEAQESGI	0.360
  81	SSQIPVVGV	0.300
  57	AMWTEEAGA	0.300
  14	ASPAAAWKC	0.300
  118	NPVLPHTNG	0.300
  84	IPVVGVVTE	0.200
  79	SSSSQIPVV	0.200
  55	PPAMWTEEA	0.200
  82	SQIPVVGVV	0.200
  37	LPIEWQQDR	0.200
  78	SSSSSQIPV	0.200
  73	GIRNKSSSS	0.200
  4	VILDLSVEV	0.200
  2	SIVILDLSV	0.200
  47	IPPLSTPPP	0.200
  128	GPLWEFLLR	0.200
  121	LPHTNGVGP	0.200
  18	AAWKCLGAN	0.180
  9	SVEVLASPA	0.150
  164	TWMKLETII	0.120
  19	AWKCLGANI	0.120
  130	LWEFLLRLL	0.120
  104	ESPDRALKA	0.100
  158	EFLGSGTWM	0.100
  162	SGTWMKLET	0.100
  169	ETIILSKLT	0.100
  83	QIPVVGVVT	0.100
  178	QEQKSKHCM	0.100
  144	SGTLSLAFT	0.100
  119	PVLPHTNGV	0.100
  143	ASGTLSLAF	0.060
  64	GATAEAQES	0.060
  68	EAQESGIRN	0.060
  25	ANILRGGLS	0.060
  108	RALKAANSW	0.060
  35	IVLPIEWQQ	0.050
  86	VVGVVTEDD	0.050
  3	IVILDLSVE	0.050
  89	VVTEDDEAQ	0.050
  122	PHTNGVGPL	0.040
  76	NKSSSSSQI	0.040
  182	SKHCMFSLI	0.040
  39	IEWQQDRKI	0.040
  12	VLASPAAAW	0.030
  62	EAGATAEAQ	0.030
  125	NGVGPLWEF	0.030
  13	LASPAAAWK	0.030
  109	ALKAANSWR	0.030
  63	AGATAEAQE	0.030
  95	EAQDSIDPP	0.030
  65	ATAEAQESG	0.030
  149	LAFTSWSLG	0.030
  111	KAANSWRNP	0.030
  51	STPPPPAMW	0.030
  184	HCMFSLISG	0.030
  59	WTEEAGATA	0.030
  156	LGEFLGSGT	0.030
  177	TQEQKSKHC	0.030
  140	SQAASGTLS	0.020
  48	PPLSTPPPP	0.020
  71	ESGIRNKSS	0.020
  123	HTNGVGPLW	0.020
  72	SGIRNKSSS	0.020
  179	EQKSKHCMF	0.020
  185	CMFSLISGS	0.020
  54	PPPAMWTEE	0.020
  147	LSLAFTSWS	0.020
  28	LRGGLSEIV	0.020

• [1228]

  TABLE XIX
  Start	Subsequence	Score

  V1-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  323	LPMRRSERYL	240.000
  197	SAREIENLPL	120.000
  328	LPSIVILDLL	80.000
  9	SPKSLSETCL	80.000
  250	IPIEIVNKTL	80.000
  312	RAMVH VAYSL	36.000
  147	NVVSAWALQL	20.000
  314	MVHV AYSLCL	20.000
  364	GIMSLGLLSL	12.000
  263	AITLLSLVYL	12.000
  219	AISLATFFFL	12.000
  402	ALLISTFHVL	12.000
  435	ALVLPSIVIL	12.000
  273	AGLLAAAYQL	12.000
  4	ISMMGSPKSL	12.000
  92	AIHREHYTSL	12.000
  27	DARKVTVGVI	12.000
  181	LARQLNFIPI	12.000
  429	PPNFVLALVL	8.000
  296	ETWLQCRKQL	6.000
  99	TSLWDLRHLL	6.000
  316	HVA YSLCLPM	5.000
  231	FVRDVIHPYA	5.000
  195	LSSAREIENL	4.000
  257	KTLPIVAITL	4.000
  377	TSIPSVSNAL	4.000
  266	LLSLVYLAGL	4.000
  202	ENLPLRLFTL	4.000
  132	YLASLFPDSL	4.000
  299	LQCRKQLGLL	4.000
  176	QQVIELARQL	4.000
  427	YTPPNFVLAL	4.000
  394	IQSTLGYVAL	4.000
  213	RGPVVVAISL	4.000
  365	IMSLGLLSLL	4.000
  49	LIRCGYHVVI	4.000
  428	TPPNFVLALV	4.000
  103	DLRHLLVGKI	4.000
  36	IGSGDFAKSL	4.000
  98	YTSLWDLRHL	4.000
  298	WLQCRKQLGL	4.000
  325	MRRS ERYLFL	4.000
  361	ISFGIMSLGL	4.000
  258	TLPIVAITLL	4.000
  172	IQARQQVIEL	4.000
  127	ESNAEYLASL	4.000
  440	SIVILDLLQL	4.000
  183	RQLNFIPIDL	4.000
  267	LSLVYLAGLL	4.000
  437	VLPSIVILDL	4.000
  395	QSTLGYVALL	4.000
  173	QARQQVIELA	3.000
  432	FVLALVLPSI	2.000
  214	GPVVVAISLA	2.000
  434	LALVLPSIVI	1.800
  133	LASLFPDSLI	1.800
  385	ALNWREFSFI	1.200
  336	MAYQQVHANI	1.200
  41	FAKSLTIRLI	1.200
  111	KILIDVSNNM	1.000
  261	IVAITLLSLV	1.000
  305	LGLLSFFFAM	1.000
  277	AA AYQLYYGT	0.900
  161	ASRQVYICSN	0.600
  239	YARNQQSDFY	0.600
  255	VNKTLPIVAI	0.600
  401	VALLISTFHV	0.600
  125	YPESNAEYLA	0.600
  157	GPKDASRQVY	0.600
  227	FLYSFVRDVI	0.600
  82	ALTKTNIIFV	0.600
  425	RFYTPPNFVL	0.600
  65	FASEFFPHVV	0.600
  134	ASLFPDSLIV	0.600
  223	ATFFFLYSFV	0.600
  269	LVYLAGLLAA	0.500
  142	IVKGFNVVSA	0.500
  75	DVTHHEDALT	0.500
  441	IVILDLLQLC	0.500
  409	HVLIYGWKRA	0.500
  254	IVNKTLPIVA	0.500
  90	FVAIHREHYT	0.500
  375	AVTSIPSVSN	0.450
  199	REIENLPLRL	0.400
  95	REHYTSLWDL	0.400
  379	IPSVSNALNW	0.400
  259	LPIVAITLLS	0.400
  211	LWRGPVVVAI	0.400
  163	RQVYICSNNI	0.400
  145	GFNVVSAWAL	0.400
  186	NFIPIDLGSL	0.400
  188	IPIDLGSLSS	0.400
  370	LLSLLAVTSI	0.400
  359	MYISFGIMSL	0.400
  16	TCLPNGINGI	0.400
  124	CYP ESNAEYL	0.400
  170	NNIQARQQVI	0.400
  243	QQSDFYKIPI	0.400
  241	RNQQSDFYKI	0.400
  74	VDVTHHEDAL	0.400

  V2-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  34	PPPCPADFFL	8.000
  14	SSGFTPFSCL	6.000
  2	GSPGLQALSL	4.000
  33	CPPPCPADFF	0.600
  18	TPFSCLSLPS	0.400
  16	GFTPFSCLSL	0.400
  3	SPGLQALSLS	0.400
  4	PGLQALSLSL	0.400
  25	LPSSWDYRCP	0.200
  30	DYRCPPPCPA	0.150
  24	SLPSSWDYRC	0.100
  13	LSSGFTPFSC	0.100
  9	LSLSLSSGFT	0.100
  8	ALSLSLSSGF	0.060
  35	PPCPADFFLY	0.040
  7	QALSLSLSSG	0.030
  15	SGFTPFSCLS	0.020
  22	CLSLPSSWDY	0.020
  11	LSLSSGFTPF	0.020
  6	LQALSLSLSS	0.020
  32	RCPPPCPADF	0.020
  1	SGSPGLQALS	0.020
  20	FSCLSLPSSW	0.020
  12	SLSSGFTPFS	0.020
  5	GLQALSLSLS	0.020
  21	SCLSLPSSWD	0.015
  10	SLSLSSGFTP	0.010
  17	FTPFSCLSLP	0.010
  27	SSWDYRCPPP	0.010
  23	LSLPSSWDYR	0.010
  28	SWDYRCPPPC	0.003
  36	PCPADFFLYF	0.002
  26	PSSWDYRCPP	0.002
  31	YRCPPPCPAD	0.002
  29	WDYRCPPPCP	0.002
  19	PFSCLSLPSS	0.000
  8	FTFWRGPVVV	0.200
  3	LPLRLFTFWR	0.200
  2	NLPLRLFTFW	0.020
  7	LFTFWRGPVV	0.020
  1	ENLPLRLFTF	0.020
  9	TFWRGPVVVA	0.015
  4	PLRLFTFWRG	0.010
  5	LRLFTFWRGP	0.001

  V5B-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  12	CSFADTQTEL	4.000
  14	FADTQTELEL	3.600
  20	ELELEFVFLL	1.200
  22	ELEFVFLLTL	1.200
  23	LEFVFLLTLL	0.400
  1	NWREFSFIQI	0.400
  19	TELELEFVFL	0.400
  24	EFVFLLTLLL	0.400
  17	TQTELELEFV	0.200
  8	IQIFCSFADT	0.100
  5	FSFIQIFCSF	0.020
  16	DTQTELELEF	0.020
  10	IFCSFADTQT	0.010
  21	LELEFVFLLT	0.010
  6	SFIQIFCSFA	0.010
  3	REFSFIQIFC	0.010
  9	QIFCSFADTQ	0.010
  7	FIQIFCSFAD	0.010
  11	FCSFADTQTE	0.010
  18	QTELELEFVF	0.006
  15	ADTQTELELE	0.003
  4	EFSFIQIFCS	0.002
  13	SFADTQTELE	0.001
  2	WREFSFIQIF	0.001

  V6-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  3	LPSIVILGKI	8.000
  46	HVSPERVTVM	4.000
  5	SIVILGKIIL	4.000
  7	VILGKIILFL	4.000
  44	IPHVSPERVT	3.000
  14	LFLPCISRKL	0.400
  27	KKGWEKSQFL	0.400
  16	LPCISRKLKR	0.200
  43	TIPHVSPERV	0.200
  38	EGIGGTIPHV	0.200
  19	ISRKLKRIKK	0.140
  35	FLEEGIGGTI	0.120
  9	LGKIILFLPC	0.100
  6	IVILGKIILF	0.100
  1	LVLPSIVILG	0.050
  10	GKIILFLPCI	0.040
  4	PSIVILGKII	0.040
  31	EKSQFLEEGI	0.040
  17	PCISRKLKRI	0.040
  11	KIILFLPCIS	0.020
  39	GIGGTIPHVS	0.020
  15	FLPCISRKLK	0.015
  40	IGGTIPHVSP	0.015
  12	ILLFLPCISR	0.015
  34	QFLEEGIGGT	0.010
  2	VLPSIVILGK	0.010
  33	SQFLEEGIGG	0.010
  25	RIKKGWEKSQ	0.010
  32	KSQFLEEGIG	0.010
  13	ILFLPCISRK	0.010
  22	KLKRIKKGWE	0.010
  8	ILGKIILFLP	0.010
  41	GGTIPHVSPE	0.010
  18	CISRKLKRIK	0.010
  28	KGWEKSQFLE	0.10
  42	GTIPHVSPER	0.010
  23	LKRIKKGWEK	0.010
  45	PHVSPERVTV	0.003
  24	KRIKKGWEKS	0.002
  26	IKKGWEKSQF	0.002
  21	RKLKRIKKGW	0.002
  20	SRKLKRIKKG	0.001
  37	EEGIGGTIPH	0.001
  30	WEKSQFLEEG	0.001
  29	GWEKSQFLEE	0.000
  36	LEEGIGGTIP	0.000

  V7A-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  2	SPKSLSETFL	80.000
  6	LSETFLPNGI	0.120
  9	TFLPNGINGI	0.040
  1	GSPKSLSETF	0.020
  4	KSLSETFLPN	0.020
  10	FLPNGINGIK	0.010
  5	SLSETFLPNG	0.010
  8	ETFLPNGING	0.010
  7	SETFLPNGIN	0.003
  3	PKSLSETFLP	0.000

  V7B-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  3	LNMAYQQSTL	12.000
  8	QQSTLGYVAL	4.000
  9	QSTLGYVALL	4.000
  10	STLGYVALLI	0.400
  7	YQQSTLGYVA	0.100
  2	FLNMAYQQST	0.100
  6	AYQQSTLGYV	0.060
  5	MAYQQSTLGY	0.060
  4	NMAYQQSTLG	0.010
  1	LFLNMAYQQS	0.002

  V7C-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  102	DPPESPDRAL	120.000
  122	LPHTNGVGPL	80.000
  129	GPLWEFLLRL	80.000
  113	AANSWRNPVL	36.000
  127	GVGPLWEFLL	20.000
  15	ASPAAAWKCL	12.000
  24	LGANILRGGL	5.000
  152	FTSWSLGEFL	4.000
  42	WQQDRKIPPL	4.000
  160	FLGSGTWMKL	4.000
  5	VILDLSVEVL	4.000
  126	NGVGPLWEFL	4.000
  141	SQAASGTLSL	4.000
  119	NPVLPHTNGV	4.000
  148	LSLAFTSWSL	4.000
  19	AAWKCLGANI	3.600
  28	ILRGGLSEIV	2.000
  168	KLETIILSKL	1.200
  20	AWKCLGANIL	1.200
  165	TWMKLETIIL	1.200
  66	ATAEAQESGI	1.200
  4	IVILDLSVEV	1.000
  135	LLRLLKSQAA	1.000
  112	KAANSWRNPV	0.900
  164	GTWMKLETII	0.400
  139	LKSQAASGTL	0.400
  181	QKSKHCMFSL	0.400
  76	RNKSSSSSQI	0.400
  29	LRGGLSEIVL	0.400
  1	LPSIVILDLS	0.400
  130	PLWEFLLRLL	0.400
  27	NILRGGLSEI	0.400
  31	GGLSEIVLPI	0.400
  163	SGTWMKLETI	0.400
  182	KSKHCMFSLI	0.400
  144	ASGTLSLAFT	0.300
  49	PPLSTPPPPA	0.300
  81	SSSQIPVVGV	0.300
  142	QAASGTLSLA	0.300
  14	LASPAAAWKC	0.300
  58	AMWTEEAGAT	0.300
  178	TQEQKSKHCM	0.300
  16	SPAAAWKCLG	0.200
  85	IPVVGVVTED	0.200
  82	SSQIPVVGVV	0.200
  48	IPPLSTPPPP	0.200
  55	PPPAMWTEEA	0.200
  78	KSSSSSQIPV	0.200
  79	SSSSSQIPVV	0.200
  74	GIRNKSSSSS	0.200
  53	TPPPPAMWTE	0.200
  38	LPIEWQQDRK	0.200
  18	AAAWKCLGAN	0.180
  143	AASGTLSLAF	0.180
  50	PLSTPPPPAM	0.150
  10	SVEVLASPAA	0.150
  52	STPPPPAMWT	0.150
  44	QDRKIPPLST	0.150
  12	EVLASPAAAW	0.150
  106	SPDRALKAAN	0.120
  158	GEFLGSGTWN	0.100
  156	SLGEFLGSGT	0.100
  162	GSGTWMKLET	0.100
  88	VGVVTEDDEA	0.100
  134	FLLRLLKSQA	0.100
  138	LLKSQAASGT	0.100
  177	LTQEQKSKHC	0.100
  83	AQIPVVGVVT	0.100
  105	ESPDRALKAA	0.100
  116	SWRNPVLPHT	0.100
  9	LSVEVLASPA	0.100
  57	PAMWTEEAGA	0.090
  185	HCMFSLISGS	0.060
  110	ALKAANSWRN	0.060
  25	GANILRGGLS	0.060
  64	AGATAEAQES	0.060
  36	IVLPIEWQQD	0.050
  87	VVGVVTEDDE	0.050
  90	VVTEDDEAQD	0.050
  89	BVVTEDDEAQ	0.050
  90	VVTEDDEAQD	0.050
  89	GVVTEDDEAQ	0.050
  150	LAFTSWSLGE	0.030
  125	TNGVGPLWEF	0.030
  109	RALKAANSWR	0.030
  96	EAQDSIDPPE	0.030
  63	EAGATAEAQE	0.030
  26	ANILRGGLSE	0.030
  51	LSTPPPPAMW	0.030
  69	EAQESGIRNK	0.030
  17	PAAAWKCLGA	0.030
  65	GATAEAQESG	0.030
  114	ANSWRNPVLP	0.030
  6	ILDLSVEVLA	0.030
  70	AQESGIRNKS	0.027
  147	TLSLAAFTSWS	0.020
  146	GTLSLAFTSW	0.020
  140	KSQAASGTLS	0.020
  180	EQKSKHCMFS	0.020
  56	PPAMWTEEAG	0.020
  145	SGTLSLAFTS	0.020
  72	ESBIFNKSSS	0.020

• [1229]

  TABLE XX
  Start	Subsequence	Score

  V1-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  62	NPKFASEFF	60.000
  323	LPMRRSERY	40.000
  157	GPKDASRQV	24.000
  259	LPIVAITLL	20.000
  428	TPPNFVLAL	20.000
  291	FPPWLETWL	20.000
  438	LPSIVILDL	20.000
  214	GPVVAISL	20.000
  231	FVRDVIHPY	12.000
  37	GSGDFAKSL	10.000
  405	ISTFHVLIY	10.000
  204	LPLRLFTLW	10.000
  239	YARNQQSDF	9,000
  41	FAKSLTIRL	9.000
  173	QARQQVIEL	9.000
  99	TSLWDLRHL	7.500
  196	SSAREIENL	7.500
  9	SPKSLSETC	6.000
  317	VAYSLCLPM	6.000
  276	LAAAYQLYY	6.000
  272	LAGLLAAAY	6.000
  125	YPESNAEYL	6.000
  46	TIRLIRCGY	6.000
  267	LSLVYLAGL	5.000
  395	QSTLGYVAL	5.000
  366	MSLGLLSLL	5.000
  220	ISLATFFFL	5.000
  250	IPIEIVNKT	4.000
  112	ILIDVSNNM	4.000
  188	IPIDLGSLS	4.000
  347	NSWNEEEVW	3.750
  133	LASLFPDSL	3.000
  300	QCRKQLGLL	3.000
  218	VAISLATFF	3.000
  177	QVIELARQL	2.000
  303	KQLGLLSFF	2.000
  371	LSLLAVTSI	2.000
  128	SNAEYLASL	2.000
  275	LLAAAYQLY	2.000
  61	RNPKFASEF	2.000
  100	SLWDLRHLL	2.000
  237	HPYARNQQS	2.000
  379	IPSVSNALN	2.000
  117	SNNMRINQY	2.000
  306	GLLSFFFAM	2.000
  134	ASLFPDSLI	2.000
  221	SLATFFFLY	2.000
  193	GSLSSAREI	2.000
  263	AITLLSLVY	2.000
  90	FVAIHREHY	2.000
  280	YQLYYGTKY	2.000
  358	EMYISFGIM	2.000
  27	DARKVTVGV	1.800
  441	IVILDLLQL	1.500
  161	ASRQVYICS	1.500
  59	GSRNPKFAS	1.500
  187	FIPIDLGSL	1.500
  81	DALTKTNII	1.200
  65	FASEFFPHV	1.200
  365	IMSLGLLSL	1.000
  184	QLNFIPIDL	1.000
  385	ALNWREFSF	1.000
  148	VVSAWALQL	1.000
  274	GLLAAAYQL	1.000
  144	KGFNVVSAW	1.000
  146	FNVVSAWAL	1.000
  383	SNALNWREF	1.000
  304	QLGLLSFFF	1.000
  363	FGIMSLGLL	1.000
  217	VVAISLATF	1.000
  57	VIGSRNPKF	1.000
  313	AMVHVAYSL	1.000
  411	LIYGWKRAF	1.000
  378	SIPSVSNAL	1.000
  264	ITLLSLVYL	1.000
  75	DVTHHEDAL	1.000
  436	LVLPSIVIL	1.000
  82	ALTKTNIIF	1.000
  403	LLISTFHVL	1.000
  299	LQCRKQLGL	1.000
  400	YVALLISTF	1.000
  258	TLPIVAITL	1.000
  268	SLVYLAGLL	1.000
  5	SMMGSPKSL	1.000
  223	ATFFFLYSF	1.000
  33	VGVIGSGDF	1.000
  396	STLGYVALL	1.000
  261	IVAITLLSL	1.000
  360	YISFGIMSL	1.000
  219	AISLATFFF	1.000
  203	NLPLRLFTL	1.000
  129	NAEYLASLF	0.900
  85	KTNIIFVAI	0.800
  127	ESNAEYLAS	0.750
  386	LNWREFSFI	0.600
  434	LALVLPSIV	0.600
  416	KRAFEEEYY	0.600
  328	SERYLFLNM	0.600
  287	KYRRFPPWL	0.600
  24	GIKDARKVT	0.600

  V2-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  37	CPADFFLYF	40.000
  33	CPPPCPADF	20.000
  3	SPGLQALSL	20.000
  23	LSLPSSWDY	10.000
  9	LSLSLSSGF	5.000
  35	PPCPADFFL	2.000
  34	PPPCPADFF	2.000
  25	LPSSWDYRC	2.000
  15	SGFTPFSCL	1.000
  1	SGSPGLQAL	1.000
  12	SLSSGFTPF	1.000
  5	GLQALSLSL	1.000
  17	FTPFSCLSL	1.000
  20	FSCLSLPSS	0.500
  2	GSPGLQALS	0.500
  13	LSSGFTPFS	0.500
  14	SSGFTPFSC	0.500
  21	SCLSLPSSW	0.500
  7	QALSLSLSS	0.300
  35	PCPADFFLY	0.300
  18	TPFSCLSLP	0.200
  6	LQALSLSLS	0.100
  10	SLSLSSGFT	0.100
  27	SSWDYRCPP	0.100
  11	LSLSSGFTP	0.050
  32	RCPPPCPAD	0.020
  8	ALSLSLSSG	0.010
  22	CLSLPSSWD	0.010
  29	WDYRCPPPC	0.010
  24	SLPSSWDYR	0.010
  31	YRCPPPCPA	0.010
  4	PGLQALSLS	0.010
  16	GFTPFSCLS	0.010
  26	PSSWDYRCP	0.008
  30	DYRCPPPCP	0.003
  19	PFSCLSLPS	0.001
  28	SWDYRCPPP	0.000

  V5A-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  2	LRLRLFTFW	10.000
  1	NLPLRLFTF	1.000
  7	FTFWRGPVV	0.200
  9	FWRGPVVVA	0.030
  6	LFTFWRGPV	0.020
  5	RLFTFWRGP	0.020
  8	TFWRGPVVV	0.020
  3	PLRLFTFWR	0.003
  4	LRLFTFWRG	0.001

  V5B-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  16	TQTELELEF	2.000
  24	FVFLLTLLL	1.000
  4	FSFIQIFCS	0.500
  19	ELELEFVFL	0.450
  12	SFADTQTEL	0.200
  18	TELELEFVF	0.200
  20	LELEFVFLL	0.200
  2	REFSFIQIF	0.200
  22	LEFVFLLTL	0.100
  10	FCSFADTQT	0.100
  8	QIFCSFADT	0.100
  23	EFVFLLTLL	0.100
  6	FIQIFCSFA	0.100
  14	ADTQTELEL	0.100
  5	SFIQIFCSF	0.100
  17	QTELELEFV	0.090
  11	CSFADTQTE	0.075
  21	ELEFVFLLT	0.030
  15	DTQTELELE	0.015
  1	WREFSFIQI	0.012
  7	IQIFCSFAD	0.010
  3	EFSFIQIFC	0.010
  13	FADTQTELE	0.009
  9	IFCSFADTQ	0.001

  V6-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  46	VSPERVTVM	20.000
  27	KGWEKSQFL	4.000
  43	IPHVSPERV	4.000
  31	KSQFLEEGI	4.000
  21	KLKRIKKGW	3.000
  14	FLPCISRKL	1.000
  6	VILGKIILF	1.000
  5	IVILGKIIL	1.000
  7	ILGKIILFL	1.000
  10	KIILFLPCI	0.800
  24	RIKKGWEKS	0.600
  17	CISRKLKRI	0.400
  4	SIVILGKII	0.400
  45	HVSPERVTV	0.300
  26	KKGWEKSQF	0.300
  2	LPSIVILGK	0.200
  15	LPCISRKLK	0.200
  38	GIGGTIPHV	0.200
  3	PSIVILGKI	0.200
  18	ISRKLKRIK	0.150
  39	IGGTIPHVS	0.100
  11	IILFLPCIS	0.100
  34	FLEEGIGGT	0.060
  8	LGKIILFLP	0.030
  32	SQFLEEGIG	0.015
  35	LEEGIGGTI	0.012
  37	EGIGGTIPH	0.010
  41	GTIPHVSPE	0.010
  40	GGTIPHVSP	0.010
  1	VLPSIVILIG	0.010
  9	GKIILFLPC	0.010
  12	ILFLPCISR	0.010
  42	TIPHVSPER	0.010
  33	QFLEEGIGG	0.003
  29	WEKSQFLEE	0.003
  25	IKKGWEKSQ	0.003
  22	LKRIKKGWE	0.003
  19	SRKLKRIKK	0.003
  20	RKLKRIKKG	0.002
  23	KRIKKGWEK	0.002
  44	PHVSPERVT	0.001
  13	LFLPCISRK	0.001
  30	EKSQFLEEG	0.001
  16	PCISRKLKR	0.001
  36	EEGIGGTIP	0.001
  28	GWEKSQFLE	0.000

  V7A-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  1	SPKSLSETF	60.000
  9	FLPNGINGI	0.400
  4	SLSETFLPN	0.200
  3	KSLSETFLP	0.150
  7	ETFLPNGIN	0.100
  6	SETFLPNGI	0.040
  5	LSETFLPNG	0.015
  2	PKSLSETFL	0.010
  8	TFLPNGING	0.001

  V7B-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	QSTLGYVAL	5.000
  9	STLGYVALL	1.000
  3	NMAYQQSTL	1.000
  6	YQQSTLGYV	0.200
  5	AYQQSTLGY	0.200
  7	QQSTLGYVA	0.100
  1	FLNMAYQQS	0.100
  2	LNMAYQQST	0.100
  4	MAYQQSTLG	0.030

  V7C-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  181	KSKHCMFSL	30.000
  15	SPAAAWKCL	20.000
  139	KSQAASGTL	10.000
  50	LSTPPPPAM	10.000
  152	TSWSLGEFL	5.000
  143	ASGTLSLAF	5.000
  165	WMKLETIIL	4.500
  101	DPPESPDRA	4.000
  179	EQKSKHCMF	3.000
  24	GANILRGGL	3.000
  141	QAASGTLSL	3.000
  108	RALKAANSW	3.000
  29	RGGLSEIVL	2.000
  52	TPPPPAMWT	2.000
  27	ILRGGLSEI	1.200
  78	SSSSSQIPV	1.000
  126	GVGPLWEFL	1.000
  113	ANSWRNPVL	1.000
  104	ESPDRALKA	1.000
  160	LGSGTWMKL	1.000
  127	VGPLWEFLL	1.000
  79	SSSSQIPVV	1.000
  148	SLAFTSWSL	1.000
  151	FTSWSLGEF	1.000
  125	NGVGPLWEF	1.000
  81	SSQIPVVGV	1.000
  31	GLSEIVLPI	0.800
  154	WSLGEFLGS	0.750
  102	PPESPDRAL	0.600
  112	AANSWRNPV	0.600
  105	SPDRALKAA	0.600
  68	EAQESGIRN	0.600
  51	STPPPPAMW	0.500
  147	LSLAFTSWS	0.500
  146	TLSLAFTSW	0.500
  12	VLAPSPAAAW	0.500
  71	ESGIRNKSS	0.500
  123	HTNGVGPLW	0.500
  14	ASPAAAWKC	0.500
  64	GATAEAQES	0.450
  163	GTWMKLETI	0.400
  37	LPIEWQQDR	0.400
  4	VILDLSVEV	0.400
  66	TAEAQESGI	0.360
  134	LLRLLKSQA	0.300
  42	QQDRKIPPL	0.300
  73	GIRNKSSSS	0.300
  17	AAAWKCLGA	0.300
  142	AASGTLSLA	0.300
  128	GPLWEFLLR	0.300
  18	AAWKCLGAN	0.300
  5	ILDLSVEVL	0.300
  136	RLLKSQAAS	0.200
  82	SQIPVVGVV	0.200
  47	IPPLSTPPP	0.200
  55	PPAMWTEEA	0.200
  121	LPHTNGVGP	0.200
  129	PLWEFLLRL	0.200
  178	QEQKSKHCM	0.200
  117	RNPVLPHTN	0.200
  2	SIVILDLSV	0.200
  158	EFLGSGTWM	0.200
  84	IPVVGVVTE	0.200
  118	NPVLPHTNG	0.200
  57	AMWTEEAGA	0.150
  173	LSKLTQEQK	0.150
  7	DLSVEVLAS	0.150
  88	GVVTEDDEA	0.150
  19	AWKCLGANI	0.120
  98	DSIDPPESP	0.100
  145	GTLSLAFTS	0.100
  83	QIPVVGVVT	0.100
  8	LSVEVLASP	0.100
  168	LETIILSKL	0.100
  169	ETIILSKLT	0.100
  162	SGTWMKLET	0.100
  11	EVLASPAAA	0.100
  25	ANILRGGLS	0.100
  72	SGIRNKSSS	0.100
  144	SGTLSLAFT	0.100
  140	SQAASGTLS	0.100
  77	KSSSSSQIP	0.100
  185	CMFSLISGS	0.100
  20	WKCLGANIL	0.100
  95	EAQDSIDPP	0.060
  111	KAANSWRNP	0.060
  75	RNKSSSSSQ	0.060
  59	WTEEAGATA	0.060
  1	PSIVILDLS	0.050
  80	SSSQIPVVG	0.050
  157	GEFLGSGTW	0.050
  33	SEIVLPIEW	0.050
  161	GSGTWMKLE	0.050
  114	NSWRNPVLP	0.050
  76	NKSSSSSQI	0.040
  164	TWMKLETII	0.040
  182	SKHCMFSLI	0.040
  39	IEWQQDRKI	0.040
  58	MWTEEAGAT	0.030
  89	VVTEDDEAQ	0.030

• [1230]

  TABLE XXI
  Start	Subsequence	Score

  V1-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  157	GPKDASRQVY	240.000
  9	SPKSLSETCL	60.000
  250	IPIEIVNKTL	40.000
  197	SAREIENLPL	27.000
  323	LPMRRSERYL	20.000
  438	LPSIVILDLL	20.000
  239	YARNQQSDFY	18.000
  417	RAFEEEYYRF	18.000
  379	IPSVSNALNW	10.000
  116	VSNNMRINQY	10.000
  391	FSFIQSTLGY	10.000
  220	ISLATFFFLY	10.000
  195	LSSAREIENL	7.500
  137	FPDSLIVKGF	6.000
  327	RSERYLFLNM	6.000
  262	VAITLLSLVY	6.000
  361	ISFGIMSLGL	5.000
  395	QSTLGYVALL	5.000
  267	LSLVYLAGLL	5.000
  99	TSLWDLRHLL	5.000
  127	ESNAEYLASL	5.000
  4	ISMMGSPKSL	5.000
  382	VSNALNWREF	5.000
  377	TSIPSVSNAL	5.000
  428	TPPNFVLALV	4.000
  188	IPIDLGSLSS	4.000
  111	KILIDVSNNM	4.000
  181	LARQLNFIPI	3.600
  27	DARKVTVGVI	3.600
  41	FAKSLTIRLI	3.600
  384	NALNWREFSF	3.000
  312	FAMVHVAYSL	3.000
  222	LATFFFLYSF	3.000
  81	DALTKTNIIF	3.000
  218	VAISLATFFF	3.000
  322	CLPMRRSERY	2.000
  429	PPNFVLALVL	2.000
  316	HVAYSLCLPM	2.000
  61	RNPKFASEFF	2.000
  257	KTLPIVAITL	2.000
  259	LPIVAITLLS	2.000
  45	LTIRLIRCGY	2.000
  275	LLAAAYQLYY	2.000
  274	GLLAAAYQLY	2.000
  303	KQLGLLSFFF	2.000
  128	SNAEYLASLF	2.000
  123	NQYPESNAEY	2.000
  305	LGLLSFFFAM	2.000
  404	LISTFHVLIY	2.000
  213	RGPVVVAISL	2.000
  271	YLAGLLAAAY	2.000
  183	RQLNFIPIDL	2.000
  214	GPVVVAISLA	2.000
  134	ASLFPDSLIV	1.500
  440	SIVILDLLQL	1.500
  98	YTSLWDLRHL	1.500
  161	ASRQVYICSN	1.500
  285	GTKYRRFPPW	1.500
  103	DLRHLLVGKI	1.200
  336	MAYQQVHANI	1.200
  255	VNKTLPIVAI	1.200
  65	FASEFFPHVV	1.200
  49	LIRCGYHVVI	1.200
  434	LALVLPSIVI	1.200
  133	LASLFPDSLI	1.200
  24	GIKDARKVTV	1.200
  241	RNQQSDFYKI	1.200
  32	TVGVIGSGDF	1.000
  435	ALVLPSIVIL	1.000
  273	AGLLAAAYQL	1.000
  36	IGSGDFAKSL	1.000
  308	LSFFFAMVHV	1.000
  56	VVIGSRNPKF	1.000
  176	QQVIELARQL	1.000
  296	ETWLQCRKQL	1.000
  43	KSLTIRLIRC	1.000
  202	ENLPLRLFTL	1.000
  147	NVVSAWALQL	1.000
  217	VVAISLATFF	1.000
  216	VVVAISLATF	1.000
  132	YLASLFPDSL	1.000
  364	GIMSLGLLSL	1.000
  365	IMSLGLLSLL	1.000
  92	AIHRHYTSL	1.000
  314	MVHVAYSLCL	1.000
  410	VLIYGWKRAF	1.000
  299	LQCRKQLGLL	1.000
  394	IQSTLGYVAL	1.000
  11	KSLSETCLPN	1.000
  263	AITLLSLVYL	1.000
  172	IQARQQVIEL	1.000
  219	AISLATFFFL	1.000
  298	WLQCRKQLGL	1.000
  37	GSGDFAKSLT	1.000
  402	ALLISTFHVL	1.000
  258	TLPIVAITLL	1.000
  427	YTPPNFVLAL	1.000
  139	DSLIVKGFNV	1.000
  437	VLPSIVILDL	1.000
  266	LLSLVYLAGL	1.000

  V2-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  33	CPPPCPADFF	20.000
  35	PPCPADFFLY	6.000
  14	SSGFTPFSCL	5.000
  11	LSLSSGFTPF	5.000
  2	GSPGLQALSL	5.000
  20	FSCLSLPSSW	2.500
  34	PPPCPADFFL	2.000
  3	SPGLQALSLS	2.000
  22	CLSLPSSWDY	2.000
  32	RCPPPCPADF	2.000
  18	TPFSCLSLPS	2.000
  8	ALSLSLSSGF	1.000
  9	LSLSLSSGFT	0.500
  13	LSSGFTPFSC	0.500
  25	LPSSWDYRCP	0.300
  4	PGLQALSLSL	0.100
  15	SGFTPFSCLS	0.100
  27	SSWDYRCPPP	0.100
  16	GFTPFSCLSL	0.100
  6	LQALSLSLSS	0.100
  1	SGSPGLQALS	0.100
  24	SLPSSWDYRC	0.100
  36	PCPADFFLYF	0.100
  5	GLQALSLSLS	0.100
  12	SLSSGFTPFS	0.100
  23	LSLPSSWDYR	0.050
  7	QALSLSLSSG	0.030
  30	DYRCPPPCPA	0.030
  17	FTPFSCLSLP	0.010
  10	SLSLSSGFTP	0.010
  21	SCLSLPSSWD	0.010
  26	PSSWDYRCPP	0.005
  28	SWDYRCPPPC	0.003
  29	WSYRCPPPCP	0.001
  19	PFSCLSLPSS	0.001
  31	YRCPPPCPAD	0.001

  V5A-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  1	ENLPLRLFTF	1.000
  2	NLPLRLFTFW	0.500
  6	RLFTFWRGPV	0.500
  8	FTFWRGPVVV	0.200
  3	LPLRLFTFWR	0.200
  10	FWRGPVVVAI	0.120
  7	LFTFWRGPVV	0.020
  9	TFWRGPVVVA	0.010
  4	PLRLFTFWRG	0.003
  5	LRLFTFWRGP	0.001

  V5B-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  12	CSFADTQTEL	5.000
  5	FSFIQIFCSF	5.000
  16	DTQTELELEF	1.000
  14	FADTQTELEL	0.900
  17	TQTELELEFV	0.600
  22	ELEFVFLLTL	0.300
  18	QTELELEFVF	0.300
  20	ELELEFVFLL	0.300
  19	TELELEFVFL	0.300
  1	NWREFSFIQI	0.240
  8	IQIFCSFADT	0.100
  23	LEFVFLLTLL	0.100
  24	EFVFLLTLLL	0.100
  2	WREFSFIQIF	0.030
  3	REFSFIQIFC	0.020
  21	LELEFVFLLT	0.020
  11	FCSFADTQTE	0.015
  10	IFCSFADTQT	0.010
  7	FIQIFCSFAD	0.010
  4	EFSFIQIFCS	0.010
  9	QIFCSFADTQ	0.010
  6	SFIQIFCSFA	0.010
  13	SFADTQTELE	0.002
  15	ADTQTELELE	0.002

  V6-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  3	LPSIVILGKI	8.000
  44	IPHVSPERVT	2.000
  46	HVSPERVTVM	2.000
  6	IVILGKIILF	1.000
  7	VILGKIILFL	1.000
  5	SIVILGKIIL	1.000
  26	IKKGWEKSQF	0.450
  9	LGKIILFLPC	0.300
  35	FLEEGIGGTI	0.240
  43	TIPHVSPERV	0.200
  11	KIILFLPCIS	0.200
  27	KKGWEKSQFL	0.200
  38	EGIGGTIPHV	0.200
  16	LPCISRKLKR	0.200
  4	PSIVILGKII	0.200
  32	KSQFLEEGIG	0.150
  19	ISRKLKRIKK	0.150
  39	GIGGTIPHVS	0.100
  14	LFLPCISRKL	0.100
  21	RKLKRIKKGW	0.100
  25	RIKKGWEKSQ	0.060
  22	KLKRIKKGWE	0.060
  10	GKIILFLPCI	0.040
  28	KGWEKSQFLE	0.040
  17	PCISRKLKRI	0.040
  31	EKSQFLEEGI	0.040
  24	KRIKKGWEKS	0.020
  34	QFLEEGIGGT	0.020
  33	SQFLEEGIGG	0.015
  13	ILFLPCISRK	0.010
  18	CISRKLKRIK	0.010
  8	ILGKIILFLP	0.010
  2	VLPSIVILGK	0.010
  40	IGGTIPHVSP	0.010
  15	FLPCISRKLK	0.010
  41	GGTIPHVSPE	0.010
  1	LVLPSIVILG	0.010
  42	GTIPHVSPER	0.010
  12	IILFLPCISR	0.010
  45	PHVSPERVTV	0.003
  20	SRKLKRIKKG	0.003
  30	WEKSQFLEEG	0.003
  23	LKRIKKGWEK	0.003
  37	EEGIGGTIPH	0.001
  36	LEEGIGGTIP	0.000
  29	GWEKSQFLEE	0.000

  V7A-HLA-3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  2	SPKSLSETFL	60.000
  1	GSPKSLSETF	5.000
  4	KSLSETFLPN	1.000
  6	LSETFLPNGI	0.600
  9	TFLPNGINGI	0.040
  5	SLSETFLPNG	0.020
  10	FLPNGINGIK	0.010
  7	SETFLPNGIN	0.010
  8	ETFLPNGING	0.010
  3	PKSLSETFLP	0.000

  V7B-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	MAYQQSTLGY	6.000
  9	QSTLGYVALL	0.500
  3	LNMAYQQSTL	1.000
  8	QQSTLGYVAL	1.000
  10	STLGYVALLI	0.400
  7	YQQSTLGYVA	0.100
  2	FLNMAYQQST	0.100
  6	AYQQSTLGYV	0.020
  4	NMAYQQSTLG	0.010
  1	LFLNMAYQQS	0.010

  V7C-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  100	SIDPPESPDR	100.000
  67	TAEQESGIR	9.000
  33	LSEIVLPIEW	6.750
  131	LWEFLLRLLK	4.500
  91	VTEDDEAQDS	2.250
  10	SVEVLASPAA	1.800
  52	STPPPPAMWT	1.250
  6	ILDLSVEVLA	1.000
  168	KLETIILSKL	0.900
  103	PPESPDRALK	0.900
  127	GVGPLWEFLL	0.500
  143	AASGTLSLAF	0.500
  13	VLASPAAAWK	0.400
  51	LSTPPPPAMW	0.300
  60	WTEEAGATAE	0.225
  157	LGEFLGSGTW	0.225
  69	EAQESGIRNK	0.200
  97	AQDSIDPPES	0.150
  70	AQESGIRNKS	0.135
  178	TQEQKSKHCM	0.135
  170	ETIILSKLTQ	0.125
  128	VGPLWEFLLR	0.125
  37	VLPIEWQQDR	0.100
  14	LASPAAAWKC	0.100
  61	TEEAGATAEA	0.090
  39	PEIWQQDRKI	0.090
  162	GSGTWMKLET	0.075
  78	KSSSSSQIPV	0.075
  160	FLGSGTWMKL	0.050
  22	KCLGANILRG	0.050
  167	MKLETIILSK	0.050
  38	LPIEWQQDRK	0.050
  80	SSSSQIPVVG	0.030
  79	SSSSSQIPVV	0.030
  83	SQIPVVGVVT	0.030
  144	ASGTLSLAFT	0.030
  81	SSSQIPVVGV	0.030
  146	GTLSLAFTSW	0.025
  66	ATAEAQESGI	0.025
  152	FTSWSLGEFL	0.025
  125	TNGVGPLWEF	0.025
  92	TEDDEAQDSI	0.025
  177	LTQEQKSKHC	0.025
  21	WKCLGANILR	0.025
  106	SPDRALKAAN	0.025
  94	DDEAQDSIDP	0.022
  12	EVLASPAAAW	0.020
  4	IVILDLSVEV	0.020
  173	ILSKLTQEQK	0.020
  47	KIPPLSTPPP	0.020
  113	AANSWRNPVL	0.020
  72	ESGIRNKSSS	0.015
  43	QQDRKIPPLS	0.015
  15	ASPAAAWKCL	0.015
  140	KSQAASGTLS	0.015
  9	LSVEVLASPA	0.015
  82	SSQIPVVGVV	0.015
  155	WSLGEFLGSG	0.015
  105	ESPDRALKAA	0.015
  148	LSLAFTSWSL	0.015
  124	HTNGVGPLWE	0.013
  129	GPLWEFLLRL	0.013
  31	GGLSEIVLPI	0.013
  145	SGTLSLAFTS	0.013
  185	HCMFSLISGS	0.010
  149	SLAFTSWSLG	0.010
  65	GATAEAQESG	0.010
  112	KAANSWRNPV	0.010
  142	QAASGTLSLA	0.010
  25	GANILRGGLS	0.010
  159	EFLGSGTWMK	0.010
  23	CLGANILRGG	0.010
  109	RALKAANSWR	0.010
  176	KLTQEQKSKH	0.010
  35	EIVLPIEWQQ	0.010
  175	SKLTQEQKSK	0.010
  18	AAAWKCLGAN	0.010
  36	IVLPIEWQQD	0.010
  5	VILDLSVEVL	0.010
  172	IILSKLTQEQ	0.010
  156	SLGEFLGSGT	0.010
  120	PVLPHTNGVG	0.010
  147	TLSLAFTSWS	0.010
  89	GVVTEDDEAQ	0.010
  153	TSWSLGEFLG	0.008
  2	PSIVILDLSV	0.008
  141	SQAASGTLSL	0.007
  150	LAFTSWSLGE	0.005
  17	PAAAWKCLGA	0.005
  101	IDPPESPDRA	0.005
  151	AFTSWSLGEF	0.005
  117	WRNPVLPHTN	0.005
  42	WQQDRKIPPL	0.003
  104	PESPDRALKA	0.003
  24	LGAINILRGGL	0.003
  119	NPVLPHTNGV	0.003
  118	RNPVLPHTNG	0.003
  102	DPPESPDRAL	0.003
  53	TPPPPAMWTE	0.003
  1	LPSIVILDLS	0.003

• [1231]

  TABLE VIII
  Start	Subsequence	Score

  V8-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  4	FLEEGMGGT	0.900
  5	LEEGMGGTI	0.045
  1	KSQFLEEGM	0.015
  7	EGMGGTIPH	0.013
  8	GMGGTIPHV	0.010
  9	MGGTIPHVS	0.003
  3	QFLEEGMGG	0.003
  2	SQFLEEGMG	0.002
  6	EEGMGGTIP	0.001

  V13-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  5	LSETFLPNG	2.700
  4	SLSETFLPN	0.050
  7	ETFLPNGIN	0.025
  8	TFLPNGING	0.025
  9	FLPNGINGI	0.010
  3	KSLSETFLP	0.007
  1	SPKSLSETF	0.003
  6	SETFLPNGI	0.001
  2	PKSLSETFL	0.000

  V14-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  1	NLPLRLFTF	0.500
  7	FTFWRGPVV	0.050
  3	PLRLFTFWR	0.005
  5	RLFTFWRGP	0.001
  6	LFTFWRGPV	0.001
  4	LRLFTFWRG	0.001
  2	LPLRLFTFW	0.000
  9	FWRGPVVVA	0.000
  8	TFWRGPVVV	0.000

  V21-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  2	KLTQEQKTK	0.200
  4	TQEQKTKHC	0.135
  3	LTQEQKTKH	0.025
  8	KTKHCMFSL	0.013
  6	EQKTKHCMF	0.002
  9	TKHCMFSLI	0.001
  1	SKLTQEQKT	0.001
  7	QKTKHCMFS	0.000
  5	QEQKTKHCM	0.000

  V25-HLA-A1-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  2	LFLPCISQK	0.100
  1	ILFLPCISQ	0.050
  5	PCISQKLKR	0.050
  4	LPCISQKLK	0.050
  7	ISQKLKRIK	0.030
  8	SQKLKRIKK	0.015
  3	FLPCISQKL	0.010
  6	CISQKLKRI	0.010
  9	QKLKRIKKG	0.000

• [1232]

  TABLE IX
  Start	Subsequence	Score

  V8-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	FLEEGMGGTI	0.900
  2	KSQFLEEGMG	0.015
  3	SQFLEEGMGG	0.007
  8	EGMGGTIPHV	0.005
  9	GMGGTIPHVS	0.005
  5	LEEGMGGTIP	0.005
  7	EEGMGGTIPH	0.003
  4	QFLEEGMGGT	0.001
  10	MGGTIPHVSP	0.001
  1	EKSQFLEEGM	0.001

  V13-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  6	LSETFLPNGI	1.350
  10	FLPNGINGIK	0.200
  8	ETFLPNGING	0.125
  4	KSLSETFLPN	0.075
  5	SLSETFLPNG	0.020
  1	GSPKSLSETF	0.015
  9	TFLPNGINGI	0.005
  7	SETFLPNGIN	0.001
  2	SPKSLSETFL	0.000
  3	PKSLSETFLP	0.000

  V14-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  1	ENLPLRLFTF	1.250
  8	FTFWRGPVVV	0.050
  3	LPLRLFTFWR	0.013
  2	NLPLRLFTFW	0.010
  6	RLFTFWRGPV	0.010
  7	LFTFWRGPVV	0.001
  4	PLRLFTFWRG	0.000
  10	FWRGPVVVAI	0.000
  5	LRLFTFWRGP	0.000
  9	TFWRGPVVVA	0.000

  V21-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	TQEQKTKHCM	0.135
  4	LTQEQKTKHC	0.025
  3	KLTQEQKTKH	0.010
  2	SKLTQEQKTK	0.010
  9	KTKHCMFSLI	0.003
  10	TKHCMFSLIS	0.003
  1	LSKLTQEQKT	0.002
  7	EQKTKHCMFS	0.001
  6	QEQKTKHCMF	0.001
  8	QKTKHCMFSL	0.000

  V25-HLA-A1-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  7	CISQKLKRIK	0.200
  4	FLPCISQKLK	0.200
  2	ILFLPCISQK	0.200
  8	ISQKLKRIKK	0.150
  5	LPCISQKLKR	0.125
  1	IILFLPCISQ	0.050
  3	LFLPCISQKL	0.005
  6	PCISQKLKRI	0.001
  9	SQKLKRIKKG	0.000
  10	QKLKRIKKGW	0.000

• [1233]

  TABLE X
  Start	Subsequence	Score

  V8-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	GMGGTIPHV	115.534
  4	FLEEGMGGT	2.689
  1	KSQFLEEGM	0.056
  2	SQFLEEGMG	0.004
  5	LEEGMGGTI	0.003
  3	QFLEEGMGG	0.001
  9	MGGTIPHVS	0.000
  7	EGMGGTIPH	0.000
  6	EEGMGGTIP	0.000

  V13-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  9	FLPNGINGI	110.379
  4	SLSETFLPN	0.581
  6	SETFLPNGI	0.203
  3	KSLSETFLP	0.007
  2	PKSLSETFL	0.004
  5	LSETFLPNG	0.000
  8	TFLPNGING	0.000
  7	ETFLPNGIN	0.000
  1	SPKSLSETF	0.000

  V14-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  7	FTFWRGPVV	6.741
  1	NLPLRLFTF	0.994
  8	TFWRGPVVV	0.164
  5	RLFTFWRGP	0.071
  2	LPLRLFTFW	0.032
  6	LFTFWRGPV	0.011
  3	PLRLFTFWR	0.003
  4	LRLFTFWRG	0.001
  9	FWRGPVVVA	0.000

  V21-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	KTKHCMFSL	0.485
  5	QEQKTKHCM	0.097
  2	KLTQEQKTK	0.052
  1	SKLTQEQKT	0.038
  4	TQEQKTKHC	0.032
  9	TKHCMFSLI	0.028
  3	LTQEQKTKH	0.007
  7	QKTKHCMFS	0.001
  6	EQKTKHCMF	0.000

  V25-A0201-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  3	FLPCISQKL	98.267
  6	CISQKLKRI	3.299
  1	ILFLPCISQ	0.094
  9	QKLKRIKKG	0.001
  4	LPCISQKLK	0.000
  2	LFLPCISQK	0.000
  8	SQKLKRIKK	0.000
  7	ISQKLKRIK	0.000
  5	PCISQKLKR	0.000

  V8-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	FLEEGMGGTI	1.637
  8	EGMGGTIPHV	0.290
  3	SQFLEEGMGG	0.028
  4	QFLEEGMGGT	0.023
  9	GMGGTIPHVS	0.022
  1	EKSQFLEEGM	0.000
  2	KSQFLEEGMG	0.000
  10	MGGTIPHVSP	0.000
  7	EEGMGGTIPH	0.000
  6	LEEGMGGTIP	0.000

  V13-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	SLSETFLPNG	2.670
  9	TFLPNGINGI	0.062
  2	SPKSLSETFL	0.027
  4	KSLSETFLPN	0.012
  6	LSETFLPNGI	0.007
  10	FLPNGINGIK	0.004
  8	ETFLPNGING	0.000
  1	GSPKSLSETF	0.000
  7	SETFLPNGIN	0.000
  3	PKSLSETFLP	0.000

  V14-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  6	RLFTFWRGPV	33.455
  8	FTFWRGPVVV	6.741
  2	NLPLRLFTFW	0.779
  3	LPLRLFTFWR	0.074
  7	LFTFWRGPVV	0.034
  9	TFWRGPVVVA	0.027
  1	ENLPLRLFTF	0.002
  4	PLRLFTFWRG	0.002
  10	FWRGPVVVAI	0.001
  5	LRLFTFWRGP	0.000

  V21-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	TQEQKTKHCM	0.135
  4	LTQEQKTKHC	0.025
  3	KLTQEQKTKH	0.025
  2	SKLTQEQKTK	0.010
  9	KTKHCMFSLI	0.003
  10	TKHCMFSLIS	0.003
  1	LSKLTQEQKT	0.002
  7	EQKTKHCMFS	0.001
  6	QEQKTKHCMF	0.001
  8	QKTKHCMFSL	0.000

  V25-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  2	ILFLPCISQK	0.216
  3	LFLPCISQKL	0.093
  4	FLPCISQKLK	0.069
  1	IILFLPCISQ	0.013
  6	PCISQKLKRI	0.003
  9	SQKLKRIKKG	0.001
  10	QKLKRIKKGW	0.000
  7	CISQKLKRIK	0.000
  8	ISQKLKRIKK	0.000
  5	LPCISQKLKR	0.000

• [1234]

  TABLE XII
  Start	Subsequence	Score

  V8-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	GMGGTIPHV	1.350
  4	FLEEGMGGT	0.068
  1	KSQFLEEGM	0.003
  2	SQFLEEGMG	0.001
  5	LEEGMGGTI	0.001
  7	EGMGGTIPH	0.000
  3	QFLEEGMGG	0.000
  9	MGGTIPHVS	0.000
  6	EEGMGGTIP	0.000

  V13-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  9	FLPNGINGI	0.900
  4	SLSETFLPN	0.180
  1	SPKSLSETF	0.020
  6	SETFLPNGI	0.002
  3	KSLSETFLP	0.001
  7	ETFLPNGIN	0.001
  5	LSETFLPNG	0.000
  8	TFLPNGING	0.000
  2	PKSLSETFL	0.000

  V14-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  	NLPLRLFTF	9.000
  3	PLRLFTFWR	3.600
  7	FTFWRGPVV	0.050
  5	RLFTFWRGP	0.030
  2	LRLRLFTFW	0.009
  9	FWRGPVVVA	0.001
  8	TFWRGPVVV	0.001
  4	LRLFTFWRG	0.000
  6	LFTFWRGPV	0.000

  V21-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  2	KLTQEQKTK	30.000
  8	KTKHCMFLS	0.405
  6	EQKTKHCMF	0.018
  3	LTQEQKTKH	0.015
  4	TQEQKTKHC	0.003
  9	TKHCMFSLI	0.002
  5	QEQKTKHCM	0.001
  1	SKLTQEQKT	0.000
  7	QKTKHCMFS	0.000

  V25-HLA-A3-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	SQKLKRIKK	1.200
  3	FLPCISQKL	0.900
  1	ILFLPCISQ	0.300
  4	LPCISQKLK	0.100
  2	LFLPCISQK	0.068
  6	CISQKLKRI	0.045
  5	PCISQKLKR	0.012
  7	ISQKLKRIK	0.010
  9	QKLKRIKKG	0.000

• [1235]

  TABLE XIII
  Start	Subsequence	Score

  V8-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  9	GMGGTIPHVS	0.270
  5	FLEEGMGGTI	0.270
  3	SQFLEEGMGG	0.006
  7	EEGMGGTIPH	0.000
  8	EGMGGTIPHV	0.000
  4	QFLEEGMGGT	0.000
  5	LEEGMGGTIP	0.000
  2	KSQFLEEGMG	0.000
  1	EKSQFLEEGM	0.000
  10	MGGTIPHVSP	0.000

  V13-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  10	FLPNGINGIK	9.000
  5	SLSETFLPNG	0.135
  1	GSPKSLSETF	0.030
  2	SPKSLSETFL	0.006
  6	LSETFLPNGI	0.003
  8	ETFLPNGING	0.003
  4	KSLSETFLPN	0.003
  9	TFLPNGINGI	0.002
  7	SETFLPNGIN	0.000
  3	PKSLSETFLP	0.000

  V14-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  6	RLFTFWRGPV	0.900
  2	NLPLRLFTFW	0.600
  3	LPLRLFTFWR	0.540
  8	FTFWRGPVVV	0.050
  4	PLRLFTFWRG	0.018
  1	ENLPLRLFTF	0.012
  9	TFWRGPVVVA	0.005
  10	FWRGPVVVAI	0.005
  7	LFTFWRGPVV	0.000
  5	LRLFTFWRGP	0.000

  V21-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  3	KLTQEQKTKH	0.600
  9	KTKHCMFSLI	0.270
  2	SKLTQEQKTK	0.015
  4	LTQEQKTKHC	0.007
  6	QEQKTKHCMF	0.006
  5	TQEQKTKHCM	0.006
  8	QKTKHCMFSL	0.003
  7	EQKTKHCMFS	0.001
  1	LSKLTQEQKT	0.001
  10	TKHCMFSLIS	0.000

  V25-HLA-A3-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  2	ILFLPCISQK	150.000
  4	FLPCISQKLK	10.000
  8	ISQKLKRIKK	0.200
  7	CISQKLKRIK	0.200
  5	LPCISQKLKR	0.080
  1	IILFLPCISQ	0.009
  3	LFLPCISQKL	0.002
  5	PCISQKLKRI	0.001
  9	SQKLKRIKKG	0.000
  10	QKLKRIKKGW	0.000

• [1236]

  TABLE XIV
  Start	Subsequence	Score

  V8-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	GMGGTIPHV	1.350
  4	FLEEGMGGT	0.068
  1	KSQFLEEGM	0.003
  2	SQFLEEGMG	0.001
  5	LEEGMGGTI	0.001
  7	EGMGGTIPH	0.000
  3	QFLEEGMGG	0.000
  9	MGGTIPHVS	0.000
  6	EEGMGGTIP	0.000

  V13-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  9	FLPNGINGI	0.004
  1	SPKSLSETF	0.002
  4	SLSETFLPN	0.001
  7	ETFLPNGIN	0.001
  8	TFLPNGING	0.001
  5	SETFLPNGI	0.001
  3	KSLSETFLP	0.000
  2	PKSLSETFL	0.000
  5	LSETFLPNG	0.000

  V14-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  3	PLRLFTFWR	0.024
  7	FTFWRGPVV	0.020
  1	NLPLRLFTF	0.012
  8	TFWRGPVVV	0.004
  2	LRLRLFTFW	0.003
  6	LFTFWRGPV	0.002
  5	RLFTFWRGP	0.000
  9	FWRGPVVVA	0.000
  4	LRLFTFWRG	0.000

  V21-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  2	KLTQEQKTK	0.600
  8	KTKHCMFSL	0.090
  3	LTQEQKTKH	0.010
  6	EQKTKHCMF	0.002
  5	QEQKTKHCM	0.001
  4	TQEQKTKHC	0.000
  9	TKHCMFSLI	0.000
  7	QKTKHCMFS	0.000
  1	SKLTQEQKT	0.000

  V25-HLA-A1101-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	SQKLKRIKK	1.200
  2	LFLPCISQK	0.300
  4	LPCISQKLK	0.100
  5	PCISQKLKR	0.012
  3	FLPCISQKL	0.004
  7	ISQKLKRIK	0.002
  6	CISQKLKRI	0.002
  1	ILFLPCISQ	0.002
  9	QKLKRIKKG	0.000

• [1237]

  TABLE XV
  Start	Subsequence	Score

  V8-HLA-A11-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	FLEEGMGGTI	0.004
  3	SQFLEEGMGG	0.002
  9	GMGGTIPHVS	0.001
  7	EEGMGGTIPH	0.000
  4	QFLEEGMGGT	0.000
  8	EGMGGTIPHV	0.000
  2	KSQFLEEGMG	0.000
  5	LEEGMGGTIP	0.000
  1	EKSQFLEEGM	0.000
  10	MGGTIPHVSP	0.000

  V13-HLA-A11-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  10	FLPNGINGIK	0.400
  9	TFLPNGINGI	0.003
  2	SPKSLSETFL	0.002
  8	ETFLPNGING	0.001
  1	GSPKSLSETF	0.001
  5	SLSETFLPNG	0.000
  6	LSETFLPNGI	0.000
  4	KSLSETFLPN	0.000
  7	SETFLPNGIN	0.000
  3	PKSLSETFLP	0.000

  V14-HLA-A11-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  3	LPLRLFTFWR	0.180
  6	RLFTFWRGPV	0.024
  8	FTFWRGPVVV	0.020
  9	TFWRGPVVVA	0.004
  2	NLPLRLFTFW	0.004
  7	LFTFWRGPVV	0.002
  1	ENLPLRLFTF	0.001
  10	FWRGPVVVAI	0.000
  4	PLRLFTFWRG	0.000
  5	LRLFTFWRGP	0.000

  V21-HLA-A11-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  9	KTKHCMFSLI	0.030
  2	SKLTQEQKTK	0.015
  3	KLTQEQKTKH	0.012
  5	TQEQKTKHCM	0.006
  8	QKTKHCMFSL	0.001
  6	QEQKTKHCMF	0.001
  4	LTQEQKTKHC	0.001
  7	EQKTKHCMFS	0.000
  10	TKHCMFSLIS	0.000
  1	LSKLTQEQKT	0.000

  V25-HLA-A11-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  2	ILFLPCISQK	0.800
  4	FLPCISQKLK	0.200
  5	LPCISQKLKR	0.080
  8	ISQKLKRIKK	0.040
  7	CISQKLKRIK	0.040
  3	LFLPCISQKL	0.003
  1	IILFLPCISQ	0.001
  9	SQKLKRIKKG	0.000
  10	QKLKRIKKGW	0.000
  6	PCISQKLKRI	0.000

• [1238]

  TABLE XVI
  Start	Subsequence	Score

  V8-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  1	KSQFLEEGM	1.800
  4	FLEEGMGGT	0.180
  5	LEEGMGGTI	0.150
  9	MGGTIPHVS	0.140
  8	GMGGTIPHV	0.100
  3	QFLEEGMGG	0.090
  7	EGMGGTIPH	0.015
  2	SQFLEEGMG	0.010
  6	EEGMGGTIP	0.001

  V13-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  1	SPKSLSETF	2.400
  9	FLPNGINGI	1.800
  4	SLSETFLPN	0.144
  6	SETFLPNGI	0.144
  7	ETFLPNGIN	0.100
  8	TFLPNGING	0.090
  2	PKSLSETFL	0.040
  3	KSLSETFLP	0.030
  5	LSETFLPNG	0.015

  V14-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  1	NLPLRLFTF	3.000
  8	TFWRGPVVV	0.500
  6	LFTFWRGPV	0.500
  2	LPLRLFTFW	0.216
  7	FTFWRGPVV	0.100
  9	FWRGPVVVA	0.100
  5	RLFTFWRGP	0.020
  4	LRLFTFWRG	0.002
  3	PLRLFTFWR	0.001

  V21-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	KTKHCMFSL	8.000
  6	EQKTKHCMF	2.000
  4	TQEQKTKHC	0.150
  9	TKHCMFSLI	0.120
  5	QEQKTKHCM	0.075
  2	KLTQEQKTK	0.020
  1	SLKTQEQKT	0.020
  3	LTQEQKTKH	0.020
  7	QKTKHCMFS	0.010

  V25-HLA-A24-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  3	FLPCISQKL	11.088
  6	CISQKLKRI	1.000
  2	LFLPCISQK	0.090
  7	ISQKLKRIK	0.018
  8	SQKLKRIKK	0.011
  1	ILFLPCISQ	0.010
  4	LPCISQKLK	0.010
  9	QKLKRIKKG	0.002
  5	PCISQKLKR	0.002

• [1239]

  TABLE XVII
  Start	Subsequence	Score

  V8-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	FLEEGMGGTI	1.800
  4	QFLEEGMGGT	0.900
  8	EGMGGTIPHV	0.150
  9	GMGGTIPHVS	0.140
  1	EKSQFLEEGM	0.060
  2	KSQFLEEGMG	0.030
  10	MGGTIPHVSP	0.010
  3	SQFLEEGMGG	0.010
  6	LEEGMGGTIP	0.002
  7	EEGMGGTIPH	0.001

  V13-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  9	TFLPNGINGI	10.800
  2	SPKSLSETFL	4.000
  1	GSPKSLSETF	3.600
  6	LSETFLPNGI	2.160
  4	KSLSETFLPN	0.360
  10	FLPNGINGIK	0.021
  5	SLSETFLPNG	0.012
  7	SETFLPNGIN	0.010
  8	ETFLPNGING	0.010
  3	PKSLSETFLP	0.000

  V14-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  1	ENLPLRLFTF	3.600
  10	FWRGPVVVAI	1.400
  7	LFTFWRGPVV	0.500
  9	TFWRGPVVVA	0.500
  2	NLPLRLFTFW	0.216
  6	RLFTFWRGPV	0.200
  8	FTFWRGPVVV	0.100
  3	LPLRLFTFWR	0.015
  5	LRLFTFWRGP	0.002
  4	PLRLFTFWRG	0.001

  V21-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  9	KTKHCMFSLI	2.400
  5	TQEQKTKHCM	0.750
  8	QKTKHCMFSL	0.400
  6	QEQKTKHCMF	0.300
  4	LTQEQKTKHC	0.180
  1	LSKLTQEQKT	0.132
  7	EQKTKHCMFS	0.100
  3	KLTQEQKTKH	0.022
  10	TKHCMFSLIS	0.010
  2	SKLTQEQKTK	0.002

  V25-HLA-A24-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  3	LFLPCISQKL	66.528
  6	PCISQKLKRI	0.150
  10	QKLKRIKKGW	0.021
  8	ISQKLKRIKK	0.017
  4	FLPCISQKLK	0.015
  1	IILFLPCISQ	0.015
  7	CISQKLKRIK	0.012
  9	SQKLKRIKKG	0.011
  5	LPCISQKLKR	0.011
  2	ILFLPCISQK	0.010

• [1240]

  TABLE XVIII
  Start	Subsequence	Score

  V8-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  1	KSQFLEEGM	1.000
  8	GMGGTIPHV	0.200
  7	EGMGGTIPH	0.030
  4	FLEEGMGGT	0.030
  9	MGGTIPHVS	0.020
  5	LEEGMGGTI	0.012
  2	SQFLEEGMG	0.010
  6	EEGMGGTIP	0.001
  3	QFLEEGMGG	0.001

  V13-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  9	FLPNGINGI	0.400
  1	SPKSLSETF	0.400
  6	SETFLPNGI	0.040
  2	PKSLSETFL	0.040
  7	ETFLPNGIN	0.030
  4	SLSETFLPN	0.020
  3	KSLSETFLP	0.010
  5	LSETFLPNG	0.003
  8	TFLPNGING	0.001

  V14-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  2	LPLRLFTFW	0.400
  7	FTFWRGPVV	0.200
  9	FWRGPVVVA	0.150
  6	LFTFWRGPV	0.030
  8	TFWRGPVVV	0.020
  1	NLPLRLFTF	0.020
  3	PLRLFTFWR	0.010
  5	RLFTFWRGP	0.010
  4	LRLFTFWRG	0.001

  V21-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	KTKHCMFSL	4.000
  5	QEQKTKHCM	0.100
  9	TKHCMFSLI	0.040
  4	TQEQKTKHC	0.030
  6	EQKTKHCMF	0.020
  3	LTQEQKTKH	0.010
  1	SKLTQEQKT	0.010
  2	LKTQEQKTK	0.010
  7	QKTKHCMFS	0.002

  V25-HLA-B7-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  3	FLPCISQKL	4.000
  6	CISQKLKRI	0.400
  4	LPCISQKLK	0.200
  8	SQKLKRIKK	0.015
  1	ILFLPCISQ	0.015
  7	ISQKLKRIK	0.010
  9	QKLKRIKKG	0.001
  2	LFLPCISQK	0.001
  5	PCISQKLKR	0.001

• [1241]

  TABLE XIX
  Start	Subsequence	Score

  V8-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  8	EGMGGTIPHV	0.600
  5	FLEEGMGGTI	0.120
  1	EKSQFLEEGM	0.100
  9	GMGGTIPHVS	0.020
  10	MGGTIPHVSP	0.015
  4	QFLEEGMGGT	0.010
  3	SQFLEEGMGG	0.010
  2	KSQFLEEGMG	0.010
  7	EEGMGGTIPH	0.001
  6	LEEGMGGTIP	0.000

  V13-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  2	SPKSLSETFL	80.000
  6	LSETFLPNGI	0.120
  9	TFLPNGINGI	0.040
  1	GSPKSLSETF	0.020
  4	KSLSETFLPN	0.020
  10	FLPNGINGIK	0.010
  5	SLSETFLPNG	0.010
  8	ETFLPNGING	0.010
  7	SETFLPNGIN	0.003
  3	PKSLSETFLP	0.000

  V14-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  10	FWRGPVVVAI	0.400
  6	RLFTFWRGPV	0.300
  8	FTFWRGPVVV	0.200
  3	LPLRLFTFWR	0.200
  2	NLPLRLFTFW	0.020
  7	LFTFWRGPVV	0.020
  1	ENLPLFLFTF	0.020
  9	TFWRGPVVVA	0.015
  4	PLRLFTFWRG	0.010
  5	LRLFTFWRGP	0.001

  V21-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  9	KTKHCMFSLI	0.400
  8	QKTKHCMFSL	0.400
  5	TQEQKTKHCM	0.300
  1	LSKLTQEQKT	0.100
  4	LTQEQKTKHC	0.100
  7	EQKTKHCMFS	0.020
  3	KLTQEQKTKH	0.010
  10	TKHCMFSLIS	0.002
  6	QEQKTKHCMF	0.002
  2	SKLTQEQKTK	0.001

  V25-HLA-B7-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  3	LFLPCISQKL	0.400
  5	LPCISQKLKR	0.200
  6	PCISQKLKRI	0.040
  8	ISQKLKRIKK	0.015
  1	IILFLPCISQ	0.015
  7	CISQKLKRIK	0.010
  4	FLPCISQKLK	0.010
  9	SQKLKRIKKG	0.010
  2	ILFLPCISQK	0.010
  10	QKLKRIKKGW	0.002

• [1242]

  TABLE XX
  Start	Subsequence	Score

  V8-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  1	KSQFLEEGM	20.000
  8	GMGGTIPHV	0.200
  9	MGGTIPHVS	0.100
  4	FLEEGMGGT	0.060
  2	SQFLEEGMG	0.015
  5	LEEGMGGTI	0.012
  7	EGMGGTIPH	0.010
  3	QFLEEGMGG	0.003
  6	EEGMGGTIP	0.001

  V13-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  1	SPKSLSETF	60.000
  9	FLPNGINGI	0.400
  4	SLSETFLPN	0.200
  3	KSLSETFLP	0.150
  7	ETFLPNGIN	0.100
  6	SETFLPNGI	0.040
  5	LSETFLPNG	0.015
  2	PKSLSETFL	0.010
  8	TFLPNGING	0.001

  V14-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  2	LRLRLFTFW	10.000
  1	NLPLRLFTF	1.000
  7	FTFWRGPVV	0.200
  9	FWRGPVVVA	0.030
  6	LFTFWRGPV	0.020
  5	RLFTFWRGP	0.020
  8	TFWRGPVVV	0.020
  3	PLRLFTFWR	0.003
  4	LRLFTFWRG	0.001

  V21-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  8	KTKHCMFSL	6.000
  6	EQKTKHCMF	3.000
  5	QEQKTKHCM	0.200
  9	TKHCMFSLI	0.040
  2	KLTQEQKTK	0.030
  4	TQEQKTKHC	0.030
  3	LTQEQKTKH	0.020
  7	QKTKHCMFS	0.010
  1	SKLTQEQKT	0.010

  V25-HLA-B3501-9mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 9 amino acids, and the
  end position for each peptide is the start
  position plus eight.

  3	FLPCISQKL	1.000
  6	CISQKLKRI	0.400
  4	LPCISQKLK	0.200
  7	ISQKLKRIK	0.050
  8	SQKLKRIKK	0.030
  1	ILFLPCISQ	0.010
  9	QKLKRIKKG	0.001
  2	LFLPCISQK	0.001
  5	PCISQKLKR	0.001

• [1243]

  TABLE XXI
  Start	Subsequence	Score

  V14-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  1	ENLPLRLFTF	1.000
  2	NLPLRLFTFW	0.500
  6	RLFTFWRGPV	0.400
  8	FTFWRGPVVV	0.200
  3	LPLRLFTFWR	0.200
  10	FWRGPVVVAI	0.120
  7	LFTFWRGPVV	0.020
  9	TFWRGPVVVA	0.010
  4	PLRLFTFWRG	0.003
  5	LRLFTFWRGP	0.001

  V21-HLA-B3501-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  9	KTKHCMFSLI	2.400
  1	LSKLTQEQKT	1.500
  5	TQEQKTKHCM	0.600
  7	EQKTKHCMFS	0.300
  4	LTQEQKTKHC	0.200
  6	QEQKTKHCMF	0.100
  8	QKTKHCMFSL	0.100
  3	KLTQEQKTKH	0.020
  10	TKHCMFSLIS	0.010
  2	SLKTQEQKTK	0.002

  V25-HLA-B35-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified, the
  length of peptide is 10 amino acids, and the
  end position for each peptide is the start
  position plus nine.

  5	LPCISQKLKR	0.200
  3	LFLPCISQKL	0.100
  8	ISQKLKRIKK	0.050
  10	QKLRIKKGW	0.050
  6	PCISQKLKRI	0.040
  9	SQKLKRIKKG	0.030
  4	FLPCISQKLK	0.010
  7	CISQKLKRIK	0.010
  2	ILFLPCISQK	0.010
  1	IILFIPCISQ	0.010

• [1244]

  TABLE XXII
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-A1-9mers-98P4B6

  158	PKDASRQVY	27
  419	FEEEYYRFY	27
  405	ISTFHVLIY	26
  221	SLATFFFLY	23
  263	AITLLSLVY	23
  392	SFIQSTLGY	23
  276	LAAAYQLYY	22
  280	YQLYYGTKY	21
  244	QSDFYKIPI	19
  101	LWDLRHLLV	18
  189	PIDLGSLSS	18
  198	AREIENLPL	18
  231	FVRDVIHPY	18
  240	ARNQQSDFY	18
  275	LLAAAYQLY	18
  311	FFAMTHVAY	18
  90	FVAIHREHY	17
  117	SNNMRINQY	17
  327	RSERYLFLN	17
  388	WREFSFIQS	17
  427	YTPPNFVLA	17
  443	ILDLLQLCR	17
  444	LDLLQLCRY	17
  46	TIRLIRCGY	16
  66	ASEFFPHVV	16
  124	QYPESNAEY	16
  200	EIENLPLRL	16
  330	RYLFLNMAY	16
  352	EEVWRIEMY	16
  272	LAGLLAAAY	15
  323	LPMRRSERY	15
  351	EEEVWRIEM	15
  415	WKRAFEEEY	15
  416	KRAFEEEYY	15
  13	LSETCLPNG	14
  38	SGDFAKSLT	14
  98	YTSLWDLRH	14
  178	VIELARQLN	14
  406	STFHVLIYG	14
  94	HREHYTSLW	13
  135	SLFPDSLIV	13
  137	FPDSLIVKG	13
  251	PIEIVNKTL	13
  396	STLGYVALL	13

  V2-HLA-A1-9mers-98P4B6

  23	LSLPSSWDY	23
  36	PCPADFFLY	20
  17	FTPFSCLSL	13
  28	SWDYRCPPP	12

  Each peptide is a portion of SEQ ID NO; 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-A1-9mers-98P4B6

  7	FTFWRGPVV	9
  9	FWRGPVVVA	5

  V5B-HLA-A1-9mers-98P4B6

  21	ELEFVFLLT	24
  1	WREFSFIQI	17
  17	QTELELEFV	16
  13	FADTQTELE	15
  19	ELELEFVFL	14

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-A1-9mers-98P4B6

  34	FLEEGIGGT	14
  28	GWEKSQFLE	12
  35	LEEGIGGTI	12
  29	WEKSQFLEE	11
  41	GTIPHVSPE	11
  1	VLPSIVILG	9
  9	GKIILFLPC	9
  19	SRKLKRIKK	9
  2	LPSIVILGK	8
  6	VILGKIILF	8
  16	PCISRKLKR	8
  7	ILGKIILFL	7
  37	EGIGGTIPH	7
  46	VSPERVTVM	7
  3	PSIVILGKI	6
  5	IVILGKIIL	6
  12	ILFLPCISR	6

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-A1-9mers-98P4B6

  5	LSETFLPNG	14
  4	SLSETFLPN	12
  8	TFLPNGING	9
  7	ETFLPNGIN	8
  3	KSLSETFLP	6

  V7B-HLA-A1-9mers-98P4B6

  5	AYQQSTLGY	22
  9	STLGYVALL	13

  V7C-HLA-A1-9mers-98P4B6

  59	WTEEAGATA	17
  90	VTEDDEAQD	17
  99	SIDPPESPD	17
  167	KLETIILSK	17
  32	LSEIVLPIE	16
  51	STPPPPAMW	14
  154	WSLGEFLGS	14
  5	ILDLSVEVL	13
  69	AQESGIRNK	13
  9	SVEVLASPA	12
  38	PIEWQQDRK	12
  60	TEEAGATAE	12
  66	TAEAQESGI	12
  93	DDEAQDSID	12
  104	ESPDRALKA	12
  105	SPDRALKAA	12
  123	HTNGVGPLW	12
  130	LWEFLLRLL	12
  96	AQDSIDPPE	11
  102	PPESPDRAL	11
  128	GPLWEFLLR	11
  143	ASGTLSLAF	11
  156	LGEFLGSGT	11
  42	QQDRKIPPL	10
  78	SSSSSQIPV	10
  82	SQIPVVGVV	10
  91	TEDDEAQDS	10
  92	EDDEAQDSI	10
  115	SWRNPVLPH	10
  176	LTEQEQKSKH	10
  177	TQEQKSKHC	10
  26	NILRGGLSE	9
  50	LSTPPPPAM	9
  79	SSSSQIPVV	9
  131	WEFLLRLLK	9
  2	SIVILDLSV	8
  7	DLSVEVLAS	8
  21	KCLGANILR	8
  31	GLSEIVLPI	8
  81	SSQIPVVGV	8
  124	TNGVGPLWE	8
  132	EFLLRLLKS	8
  141	QAASGTLSL	8
  162	SGTWMKLET	8
  169	ETIILSKLT	8

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-A1-9mers-98P4B6

  4	FLEEGMGGT	14
  5	LEEGMGGTI	12
  7	EGMGGTIPH	7

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-A1-9mers-98P4B6

  5	LSETFLPNG	14
  4	SLSETFLPN	12
  8	TFLPNGING	9
  7	ETFLPNGIN	8
  3	KSLSETFLP	6

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-A1-9mers-98P4B6

  7	FTFWRGPVV	9
  9	FWRGPVVVA	5

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-A1-9mers-98P4B6

  3	LTQEQKTKH	10
  4	TQEQKTKHC	10
  1	SKLTQEQKT	6
  8	KTKHCMFSL	6
  9	TKHCMFSLI	5

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-A1-9mers-98P4B6

  5	PCISQKLKR	10
  8	SQKLKRIKK	9
  1	ILFLPCISQ	6
  2	LFLPCISQK	4
  3	FLPCISQKL	4
  7	ISQKLKRIK	4

• [1245]

  TABLE XXIII
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-A0201-9mers-98P4B6

  365	IMSLGLLLSL	29
  271	YLAGLLAAA	28
  433	VLALVLPSI	28
  227	FLYSFVRDV	27
  360	YISFGIMSL	27
  396	STLGYVALL	27
  17	CLPNGINGI	26
  100	SLWDLRHLL	26
  135	SLFPDSLIV	26
  203	NLPRLFTL	26
  402	ALLISTFHV	26
  436	LVLPSIVIL	26
  128	SNAEYLASL	25
  140	SLIVKGFNV	25
  187	FIPIDLGSL	25
  210	TLWRGPVVV	25
  261	IVAITLLSL	25
  403	LLISTFHVL	25
  5	SMMGSPKSL	24
  264	ITLLSLVYL	24
  274	GLLAAAYQL	24
  307	LLSFFFAMV	24
  369	GLLSLLAVT	24
  48	RLIRCGYHV	23
  49	LIRCGYHVV	23
  141	LIVKGFNVV	23
  313	AMVHVAYSL	23
  374	LAVTSIPSV	23
  393	FIQSTLGYV	23
  441	IVILDLLQL	23
  106	HLLVGKILI	22
  180	ELARQLNFI	22
  254	IVNKTLPIV	22
  258	TLPIVAITL	22
  262	VAITLLSLV	22
  265	TLLSLVYLA	22
  267	LSLVYLAGL	22
  268	SLVYLAGLL	22
  333	FLNMAYQQV	22
  378	SIPSVSNAL	22
  404	LISTFHVLI	21
  435	ALVLPSIVI	21
  107	LLVGKILID	20
  108	LVGKILIDV	20
  112	ILIDVSNNM	20
  173	QARQQVIEL	20
  184	QLNFIPIDL	20
  368	LGLLSLLAV	20
  65	FASEFFPHV	19
  83	LTKTNIIFV	19
  133	KLASLFPDSL	19
  177	QVIELARQL	19
  257	KTLPIVAIT	19
  306	GLLSFFFAM	19
  366	MSLGLLSLL	19
  434	LALVLPSIV	19
  27	DARKVTVGV	18
  196	SSAREIENL	18
  209	FTLWRGPVV	18
  259	LPIVAITLL	18
  367	SLGLLSLLA	18
  371	LSLLAVTSI	18
  397	TLGYVALLI	18
  41	FAKSLTIRL	17
  81	DALTKTNII	17
  85	KTNIIFVAI	17
  103	DLRHLLVGK	17
  104	LRHLLVGKI	17
  153	ALQLGPKDA	17
  155	QLGPKDASR	17
  212	WRGPVVVAI	17
  250	IPIEIVNKT	17
  253	EIVNKTLPI	17
  363	FGIMSLGLL	17
  370	LLSLLAVTS	17
  410	VLIYGWKRA	17
  428	TPPNFVLAL	17
  438	LPSIVILDL	17
  442	VILDLLQLC	17
  25	IKDARKVTV	16
  68	EFFPHVVDV	16
  88	IIFVAIHRE	16
  93	IHREHYTSL	16
  99	TSLWDLRHL	16
  132	YLASLFPDS	16
  148	VVSAWALQL	16
  171	NIQARQQVI	16
  190	IDLGSLSSA	16
  200	EIENLPLRL	16
  372	SLLAVTSIP	16
  12	SLSETCLPN	15
  44	SLTIRLIRC	15
  50	IRCGYHVVI	15
  111	KILIDVSNN	15
  211	LWRGPVVVA	15
  217	VVAISLATF	15
  221	SLATFFFLY	15
  247	FYKIPIEIV	15
  249	KIPIEIVNK	15
  251	PIEIVNKTL	15
  256	NKTLPIVAI	15
  270	VYLAGLLAA	15
  299	LQCRKQLGL	15
  324	PMRRSERYL	15
  331	YLFLNMAYQ	15
  335	NMAYQQVHA	15
  385	ALNWREFSF	15
  400	YVALLISTF	15
  437	VLPSIVILD	15
  23	NGIKDARKV	14
  37	GSGDFAKSL	14
  39	GDFAKSLTI	14
  42	AKSLTIRLI	14
  164	QVYICSNNI	14
  166	YICSNNIQA	14
  220	ISLATFFFL	14
  223	ATFFFLYSF	14
  266	LLSLVYLAG	14
  275	LLAAAYQLY	14
  278	AAYQLYYGT	14
  300	QCRKQLGLL	14
  309	SFFFAMVHV	14
  362	SFGIMSLGL	14
  373	LLAVTSIPS	14
  395	QSTLGYVAL	14
  411	LIYGWKRAF	14
  427	YTPPNFVLA	14
  443	ILDLLQLCR	14

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-A0201-9mers-98P4B6

  5	GLQALSLSL	25
  1	SGSPGLQAL	21
  8	ALSLSLSSG	18
  17	FTPFSCLSL	17
  10	SLSLSSGFT	16
  3	SPGLQALSL	15
  12	SLSSGFTPF	14
  15	SGFTPFSCL	14
  24	SLPSSWDYR	12

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-A0201-9mers-98P4B6

  7	FTFWRGPVV	17
  1	NLPLRLFTF	16
  8	TFWRGPVVV	15
  9	FWRGPVVVA	14
  5	RLFTFWRGP	13
  3	PLRLFTFWR	10
  6	LFTFWRGPV	10

  V5B-HLA-A0201-9mers-98P4B6

  20	LELEFVFLL	21
  22	LEFVFLLTL	21
  24	FVFLLTLLL	20
  19	ELELEFVFL	18
  12	SFADTQTEL	17
  17	QTELELEFV	17
  8	QIFCSFADT	15
  6	FIQIFCSFA	14
  14	ADTQTELEL	14
  23	EFVFLLTLL	11
  21	ELEFVFLLT	10

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-A0201-9mers-98P4B6

  7	ILGKIILFL	27
  38	GIGGTIPHV	26
  10	KIILFLPCI	25
  14	FLPCISRKL	23
  34	FLEEGIGGT	23
  5	IVILGKIIL	20
  17	CISRKLKRI	20
  45	HVSPERVTV	20
  4	SIVILGKII	18
  6	VILGKIILF	18
  12	ILFLPCISR	16
  1	VLPSIVILG	15
  27	KGWEKSQFL	15
  3	PSIVILGKI	13
  35	LEEGIGGTI	13
  41	GTIPHVSPE	13

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-A0201-9mers-98P4B6

  9	FLPNGINGI	27
  4	SLSETFLPN	15

  V7B-HLA-A0201-9mers-98P4B6

  9	STLGYVALL	27
  3	NMAYQQSTL	21
  6	YQQSTLGYV	16
  8	QSTLGYVAL	14

  V7C-HLA-A0201-9mers-98P4B6

  27	ILRGGLSEI	30
  4	VILDLSVEV	27
  5	ILDLSVEVL	26
  31	GLSEIVLPI	26
  129	PLWEFLLRL	26
  148	SLAFTSWSL	25
  2	SIVILDLSV	24
  141	QAASGTLSL	23
  155	SLGEFLGSG	21
  163	GTWMKLETI	21
  81	SSQIPVVGV	20
  82	SQIPVVGVV	20
  119	PVLPHTNGV	19
  133	FLLRLLKSQ	19
  165	WMKLETIIL	19
  24	GANILRGGL	18
  57	AMWTEEAGA	18
  112	AANSWRNPV	18
  126	GVGPLWEFL	18
  12	VLASPAAAW	17
  79	SSSSQIPVV	17
  134	LLRLLKSQA	17
  167	KLETILLSK	17
  168	LETIILSKL	17
  171	IILSKLTQE	17
  172	ILSKLTQEQ	17
  42	QQDRKIPPL	16
  142	AASGTLSLA	16
  160	LGSGTWMKL	16
  7	DLSVEVLAS	15
  17	AAAWKCLGA	15
  22	CLGANILRG	15
  26	NILRGGLSE	15
  28	LRGGLSEIV	15
  130	LWEFLLRLL	15
  136	RLLKSQAAS	15
  137	LLKSQAASG	15
  159	FLGSGTWMK	15
  185	CMFSLISGS	15
  83	QIPVVGVVT	14

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-A0201-9mers-98P4B6

  8	GMGGTIPHV	26
  4	FLEEGMGGT	19
  5	LEEGMGGTI	13

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-A0201-9mers-98P4B6

  9	FLPNGINGI	27
  4	SLSETFLPN	15

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-A0201-9mers-98P4B6

  7	FTFWRGPVV	17
  1	NLPLRLFTF	16
  8	TFWRGPVVV	15
  9	FWRGPVVVA	14
  5	RLFTFWRGP	13
  3	PLRLFTFWR	10
  6	LFTFWRGPV	10

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-A0201-9mers-98P4B6

  8	KTKHCMFSL	16
  2	KLTQEQKTK	11
  1	SKLTQEQKT	10
  3	LTQEQKTKH	10
  9	TKHCMFSLI	8

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-A0201-9mers-98P4B6

  3	FLPCISQKL	23
  6	CISQKLKRI	20
  1	ILFLPCISQ	16

• [1246]

  	TABLE XXIV
  	Pos	123456789	score

  V1-HLA-A0203-9mers-98P4B6
  No Results Found.
  V2-HLA-A0203-9mers-98P4B6
  No Results Found.
  V5A-HLA-A0203-9mers-98P4B6
  No Results Found.
  V5B-HLA-A0203-9mers-98P4B6
  No Results Found.
  V6-HLA-A0203-9mers-98P4B6
  No Results Found.
  V7A-HLAA0203-9mers-98P4B6
  No Results Found.
  V7B-HLA-A0203-9mers-98P4B6
  No Results Found.
  V7C-HLA-A0203-9mers-98P4B6
  No Results Found.
  V8-HLA-A0203-9mers-98P4B6
  No Results Found.
  V13-HLA-A0203-9mers-98P4B6
  No Results Found.
  V14-HLA-A0203-9mers-98P4B6
  No Results Found.
  V21-HLA-A0203-9mers-98P4B6
  No Results Found.
  V25-HLA-A0203-9mers-98P4B6
  No Results Found.

• [1247]

  TABLE XXV
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-A3-9mers-98P4B6

  103	DLRHLLVGK	27
  56	VVIGSRNPK	26
  249	KIPIEIVNK	26
  3	SISMMGSPK	25
  155	QLGPKDASR	25
  263	AITLLSLVY	25
  210	TLWRGPVVV	24
  48	RLIRCGYHV	23
  142	IVKGFNVVS	23
  217	VVAISLATF	23
  400	YVALLISTF	23
  177	QVIELARQL	22
  205	PLRLFTLWR	22
  281	QLYYGTKYR	22
  370	LLSLLAVTS	22
  441	IVILDLLQL	22
  35	VIGSGDFAK	21
  77	THHEDALTK	21
  148	VVSAWALQL	21
  231	FVRDVIHPY	21
  269	LVYLAGLLA	21
  375	AVTSIPSVS	21
  385	ALNWREFSF	21
  274	GLLAAAYQL	20
  322	CLPMRRSER	20
  409	HVLIYGWKR	20
  443	ILDLLQLCR	20
  46	TIRLIRCGY	19
  87	NIIFVAIHR	19
  90	FVAIHREHY	19
  258	TLPIVAITL	19
  261	IVAITLLSL	19
  275	LLAAAYQLY	19
  279	AYQLYYGTK	19
  369	GLLSLLAVT	19
  372	SLLAVTSIP	19
  411	LIYGWKRAF	19
  436	LVLPSIVIL	19
  34	GVIGSGDFA	18
  92	AIHREHYTS	18
  140	SLIVKGFNV	18
  191	DLGSLSSAR	18
  221	SLATFFFLY	18
  435	ALVLPSIVI	18
  22	INGIKDARK	17
  49	LIRCGYHVV	17
  82	ALTKTNIIF	17
  111	KILIDVSNN	17
  112	ILIDVSNNM	17
  135	SLFPDSLIV	17
  153	ALQLGPKDA	17
  164	QVYICSNNI	17
  203	NLPLRLFTL	17
  271	YLAGLLAAA	17
  304	QLGLLSFFF	17
  381	SVSNALNWR	17
  397	TLGYVALLI	17
  403	LLISTFHVL	17
  432	FVLALVLPS	17
  32	TVGVIGSGD	16
  107	LLVGKILID	16
  151	AWALQLGPK	16
  171	NIQARQQVI	16
  189	PIDLGSLSS	16
  216	VVVAISLAT	16
  219	AISLATFFF	16
  234	DVIHPYARN	16
  266	LLSLVYLAG	16
  302	RKQLGLLSF	16
  402	ALLISTFHV	16
  12	SLSETCLPN	15
  21	GINGIKDAR	15
  24	GIKDARKVT	15
  30	KVTVGVIGS	15
  121	RINQYPESN	15
  136	LFPDSLIVK	15
  179	IELARQLNF	15
  268	SLVYLAGLL	15
  356	RIEMYISFG	15
  367	SLGLLSLLA	15
  410	VLIYGWKRA	15
  433	VLALVLPSI	15
  25	IKDARKVTV	14
  44	SLTIRLIRC	14
  57	VIGSRNPKF	14
  61	RNPKFASEF	14
  106	HLLVGKILI	14
  141	LIVKGFNVV	14
  180	ELARQLNFI	14
  207	RLFTLWRGP	14
  227	FLYSFVRDV	14
  235	VIHPYARNQ	14
  241	RNQQSDFYK	14
  251	PIEIVNKTL	14
  272	LAGLLAAAY	14
  294	WLETWLQCR	14
  303	KQLGLLSFF	14
  307	LLSFFFAMV	14
  330	RYLFLNMAY	14
  331	YLFLNMAYQ	14
  340	QVHANIENS	14
  353	EVWRIEMYI	14
  364	GIMSLGLLS	14
  17	CLPNGINGI	13
  18	LPNGINGIK	13
  26	KDARKVTVG	13
  43	KSLTIRLIR	13
  55	HVVIGSRNP	13
  70	FPHVVDVTH	13
  100	SLWDLRHLL	13
  113	LIDVSNNMR	13
  147	NVVSAWALQ	13
  158	PKDASRQVY	13
  184	QLNFIPIDL	13
  200	EIENLPLRL	13
  211	LWRGPVVVA	13
  215	PVVVAISLA	13
  253	EIVNKTLPI	13
  260	PIVAITLLS	13
  306	GLLSFFFAM	13
  311	FFAMVHVAY	13
  314	MVHVAYSLC	13
  333	FLNMAYQQV	13
  360	YISFGIMSL	13
  392	SFIQSTLGY	13
  408	FHVLIYGWK	13
  440	SIVILDLLQ	13

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-A3-9mers-98P4B6

  8	ALSLSLSSG	19
  12	SLSSGFTPF	18
  5	GLQALSLSL	17
  22	CLSLPSSWD	15
  24	SLPSSWDYR	15
  10	SLSLSSGFT	13
  23	LSLPSSWDY	11
  33	CPPPCPADF	11
  3	SPGLQALSL	10
  7	QALSLSLSS	9
  9	LSLSLSSGF	9
  11	LSLSSGFTP	9
  21	SCLSLPSSW	9
  37	CPADFFLYF	9

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-A3-9mers-98P4B6

  1	NLPLRLFTF	21
  3	PLRLFTFWR	19
  5	RLFTFWRGP	14
  8	TFWRGPVVV	14
  9	FWRGPVVVA	13

  V5B-HLA-A3-9mers-98P4B6

  19	ELELEFVFL	15
  21	ELEFVFLLT	14
  24	FVFLLTLLL	14
  8	QIFCSFADT	13
  6	FIQIFCSFA	12
  18	TELELEFVF	11
  5	SFIQIFCSF	10
  9	IFCSFADTQ	9
  2	REFSFIQIF	8
  16	TQTELELEF	8
  22	LEFVFLLTL	7

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-A3-9mers-98P4B6

  45	HVSPERVTV	22
  23	KRIKKGWEK	20
  12	ILFLPCISR	19
  5	IVILGKIIL	18
  13	LFLPCISRK	18
  6	VILGKIILF	17
  21	KLKRIKKGW	17
  2	LPSIVILGK	15
  7	ILGKIILFL	15
  10	KIILFLPCI	15
  18	ISRKLKRIK	15
  19	SRKLKRIKK	15
  24	RIKKGWEKS	15
  34	FLEEGIGGT	14
  4	SIVILGKII	13
  11	IILFLPCIS	13
  26	KKGWEKSQF	13
  42	TIPHVSPER	13
  15	LPCISRKLK	12
  16	PCISRKLKR	12
  17	CISRKLKRI	12
  37	EGIGGTIPH	11
  1	VLPSIVILG	10
  14	FLPCISRKL	10
  35	LEEGIGGTI	10
  38	GIGGTIPHV	10

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-A3-9mers-98P4B6

  4	SLSETFLPN	15
  9	FLPNGINGI	13
  1	SPKSLSETF	10
  8	TFLPNGING	8

  V7B-HLA-A3-9mers-98P4B6

  1	FLNMAYQQS	13
  5	AYQQSTLGY	12
  8	QSTLGYVAL	10
  7	QQSTLGYVA	9
  3	NMAYQQSTL	8
  9	STLGYVALL	8
  4	MAYQQSTLG

  V7C-HLA-A3-9mers-98P4B6

  167	KLETIILSK	28
  175	KLTQEQKSK	25
  109	ALKAANSWR	24
  3	IVILDLSVE	23
  26	NILRGGLSE	23
  159	FLGSGTWMK	23
  27	ILRGGLSEI	22
  83	QIPVVGVVT	22
  13	LASPAAAWK	20
  35	IVLPIEWQQ	20
  134	LLRLLKSQA	20
  136	RLLKSQAAS	20
  11	EVLASPAAA	19
  137	LLKSQAASG	19
  170	TIILSKLTQ	19
  12	VLASPAAAW	18
  38	PIEWQQDRK	18
  73	GIRNKSSSS	18
  5	ILDLSVEVL	17
  9	SVEVLASPA	17
  45	RKIPPLSTP	17
  103	PESPDRALK	17
  133	FLLRLLKSQ	17
  171	IILSKLTQE	17
  2	SIVILDLSV	15
  4	VILDLSVEV	15
  22	CLGANILRG	15
  46	KIPPLSTPP	15
  69	AQESGIRNK	15
  99	SIDPPESPD	15
  119	PVLPHTNGV	15
  120	VLPHTNGVG	15
  131	WEFLLRLLK	15
  155	SLGEFLGSG	15
  173	LSKLTQEQK	15
  7	DLSVEVLAS	14
  31	GLSEIVLPI	14
  36	VLPIEWQQD	14
  85	PVVGVVTED	14
  129	PLWEFLLRL	14
  146	TLSLAFTSW	14
  148	SLAFTSWSL	14
  25	ANILRGGLS	13
  82	SQIPVVGVV	13
  126	GVGPLWEFL	13

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567789	score

  V8-HLA-A3-9mers-98P4B6

  4	FLEEGMGGT	14
  5	LEEGMGGTI	10
  3	QFLEEGMGG	9
  7	EGMGGTIPH	8
  6	EEGMGGTIP	6

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-A3-9mers-98P4B6

  4	SLSETFLPN	15
  9	FLPNGINGI	13
  1	SPKSLSETF	10
  8	TFLPNGING	8

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-A3-9mers-98P4B6

  1	NLPLRLFTF	21
  3	PLRLFTFWR	19
  5	RLFTFWRGP	14
  8	TFWRGPVVV	14
  9	FWRGPVVVA	13

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-A3-9mers-98P4B6

  2	KLTQEQKTK	27

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-A3-9mers-98P4B6

  2	LFLPCISQK	21
  1	ILFLPCISQ	15
  8	SQKLKRIKK	15
  7	ISQKLKRIK	12
  4	LPCISQKLK	11
  3	FLPCISQKL	10
  5	PCISQKLKR	10

• [1248]

  TABLE XXVI
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-A26-9mers-98P4B6

  352	EEVWRIEMY	29
  75	DVTHHEDAL	28
  441	IVILDLLQL	28
  177	QVIELARQL	26
  223	ATFFFLYSF	25
  231	FVRDVIHPY	25
  400	YVALLISTF	25
  200	EIENLPLRL	24
  261	IVAITLLSL	24
  217	VVAISLATF	23
  436	LVLPSIVIL	23
  96	EHYTSLWDL	22
  234	DVIHPYARN	22
  353	EVWRIEMYI	22
  390	EFSFIQSTL	22
  396	STLGYVALL	21
  90	FVAIHREHY	20
  148	VVSAWALQL	20
  253	EIVNKTLPI	20
  264	ITLLSLVYL	20
  15	ETCLPNGIN	19
  68	EFFPHVVDV	19
  115	DVSNNMRIN	19
  215	PVVVAISLA	19
  296	ETWLQCRKQ	19
  31	VTVGVIGSG	18
  187	FIPIDLGSL	18
  216	VVVAISLAT	18
  406	STFHVLIYG	18
  439	PSIVILDLL	18
  2	ESISMMGSP	17
  45	LTIRLIRCG	17
  46	TIRLIRCGY	17
  108	LVGKILIDV	17
  263	AITLLSLVY	17
  360	YISFGIMSL	17
  363	FGIMSLGLL	17
  30	KVTVGVIGS	16
  117	SNNMRINQY	16
  128	SNAEYLASL	16
  259	LPIVAITLL	16
  355	WRIEMYISF	16
  392	SFIQSTLGY	16
  405	ISTFHVLIY	16
  432	FVLALVLPS	16
  32	TVGVIGSGD	15
  34	GVIGSGDFA	15
  72	HVVDVTHHE	15
  147	NVVSAWALQ	15
  257	KTLPIVAIT	15
  268	SLVYLAGLL	15
  329	ERYLFLNMA	15
  340	QVHANIENS	15
  375	AVTSIPSVS	15
  378	SIPSVSNAL	15
  381	SVSNALNWR	15
  428	TPPNFVLAL	15
  55	HVVIGSRNP	14
  56	VVIGSRNPK	14
  57	VIGSRNPKF	14
  83	LTKTNIIFV	14
  131	EYLASLFPD	14
  138	PDSLIVKGF	14
  180	ELARQLNFI	14
  214	GPVVVAISL	14
  218	VAISLATFF	14
  254	IVNKTLPIV	14
  302	RKQLGLLSF	14
  303	KQLGLLSFF	14
  316	HVAYSLCLP	14
  365	IMSLGLLSL	14
  366	MSLGLLSLL	14
  430	PNFVLALVL	14
  444	LDLLQLCRY	14

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-A26-9mers-98P4B6

  17	FTPFSCLSL	18
  1	SGSPGLQAL	15
  15	SGFTPFSCL	14
  3	SPGLQALSL	11
  5	GLQALSLSL	11
  9	LSLSLSSGF	11
  18	TPFSCLSLP	11
  23	LSLPSSWDY	11
  12	SLSSGFTPF	10
  36	PCPADFFLY	10
  37	CPADFFLYF	10
  33	CPPPCPADF	9
  35	PPCPADFFL	9
  30	DYRCPPPCP	8
  34	PPPCPADFF	8

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-A26-9mers-98P4B6

  1	NLPLRLFTF	13
  7	FTFWRGPVV	13

  V5B-HLA-A26-9mers-98P4B6

  23	EFVFLLTLL	27
  24	FVFLLTLLL	24
  15	DTQTELELE	20
  19	ELELEFVFL	18
  22	LEFVFLLTL	18
  2	REFSFIQIF	17
  5	SFIQIFCSF	16
  16	TQTELELEF	14
  20	LELEFVFLL	14
  3	EFSFIQIFC	13

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-A26-9mers-98P4B6

  5	IVILGKIIL	23
  6	VILGKIILF	18
  41	GTIPHVSPE	18
  7	ILGKIILFL	15
  37	EGIGGTIPH	15
  30	EKSQFLEEG	14
  3	PSIVILGKI	12
  10	KIILFLPCI	12
  45	HVSPERVTV	12
  4	SIVILGKII	11
  14	FLPCISRKL	11
  27	KGWEKSQFL	11
  36	EEGIGGTIP	11

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-A26-9mers-98P4B6

  7	ETFLPNGIN	23
  1	SPKSLSETF	12

  V7B-HLA-A26-9mers-98P4B6

  9	STLGYVALL	21
  5	AYQQSTLGY	11
  3	NMAYQQSTL	10
  8	QSTLGYVAL	10

  V7C-HLA-A26-9mers-98P4B6

  169	ETIILSKLT	23
  34	EIVLPIEWQ	22
  11	EVLASPAAA	21
  151	FTSWSLGEF	21
  179	EQKSKHCMF	21
  126	GVGPLWEFL	20
  3	IVILDLSVE	19
  85	PVVGVVTED	18
  168	LETIILSKL	17
  125	NGVGPLWEF	16
  132	EFLLRLLKS	16
  95	EAQDSIDPP	15
  129	PLWEFLLRL	15
  7	DLSVEVLAS	14
  35	IVLPIEWQQ	14
  68	EAQESGIRN	14
  88	GVVTEDDEA	14
  89	VVTEDDEAQ	14
  98	DSIDPPESP	14
  122	PHTNGVGPL	14
  163	GTWMKLETI	14
  9	SVEVLASPA	13
  42	QQDRKIPPL	13
  92	EDDEAQDSI	13
  104	ESPDRALKA	13
  130	LWEFLLRLL	13
  2	SIVILDLSV	12
  5	ILDLSVEVL	12
  59	WTEEAGATA	12
  152	TSWSLGEFL	12
  176	LTQEQKSKH	12
  8	LSVEVLASP	11
  45	RKIPPLSTP	11
  51	STPPPPAMW	11
  62	EAGATAEAQ	11
  65	ATAEAQESG	11
  71	ESGIRNKSS	11
  82	SQIPVVGVV	11
  119	PVLPHTNGV	11
  141	QAASGTLSL	11
  143	ASGTLSLAF	11
  145	GTLSLAFTS	11
  158	EFLGSGTWM	11
  170	TIILSKLTQ	11
  171	IILSKLTQE	11
  185	CMFSLISGS	11

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-A26-9mers-98P4B6

  6	EEGMGGTIP	11
  7	EGMGGTIPH	11
  2	SQFLEEGMG	7

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-A26-9mers-98P4B6

  7	ETFLPNGIN	23
  1	SPKSLSETF	12

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-A26-9mers-98P4B6

  1	NLPLRLFTF	13
  7	FTFWRGPVV	13

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-A26-9mers-98P4B6

  6	EQKTKHCMF	20
  8	KTKHCMFSL	17
  3	LTQEQKTKH	11

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-A26-9mers-98P4B6

  3	FLPCISQKL	11
  6	CISQKLKRI	9
  2	LFLPCISQK	7
  5	PCISQKLKR	7
  1	ILFLPCISQ	6
  9	QKLKRIKKG	5

• [1249]

  TABLE XXVII
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-B0702-9mers-98P4B6

  428	TPPNFVLAL	24
  438	LPSIVILDL	24
  259	LPIVAITLL	21
  291	FPPWLETWL	21
  125	YPESNAEYL	20
  214	GPVVVAISL	20
  250	IPIEIVNKT	18
  62	NPKFASEFF	17
  211	LWRGPVVVA	17
  429	PPNFVLALV	17
  157	GPKDASRQV	16
  326	RRSERYLFL	16
  148	VVSAWALQL	15
  198	AREIENLPL	15
  365	IMSLGLLSL	15
  426	FYTPPNFVL	15
  93	IHREHYTSL	14
  220	ISLATFFFL	14
  261	IVAITLLSL	14
  287	KYRRFPPWL	14
  379	IPSVSNALN	14
  396	STLGYVALL	14
  5	SMMGSPKSL	13
  10	PKSLSETCL	13
  137	FPDSLIVKG	13
  173	QARQQVIEL	13
  200	EIENLPLRL	13
  264	ITLLSLVYL	13
  289	RRFPPWLET	13
  300	QCRKQLGLL	13
  315	VHVAYSLCL	13
  362	SFGIMSLGL	13
  390	EFSFIQSTL	13
  395	QSTLGYVAL	13
  430	PNFVLALVL	13
  436	LVLPSIVIL	13
  441	IVILDLLQL	13
  18	LPNGINGIK	12
  27	DARKVTVGV	12
  50	IRCGYHVVI	12
  70	FPHVVDVTH	12
  105	RHLLVGKIL	12
  128	SNAEYLASL	12
  133	LASLFPDSL	12
  188	IPIDLGSLS	12
  202	ENLPLRLFT	12
  204	LPLRLFTLW	12
  212	WRGPVVVAI	12
  219	AISLATFFF	12
  256	NKTLPIVAI	12
  299	LQCRKQLGL	12
  313	AMVHVAYSL	12
  324	PMRRSERYL	12
  360	YISFGIMSL	12
  366	MSLGLLSLL	12
  403	LLISTFHVL	12
  435	ALVLPSIVI	12
  25	IKDARKVTV	11
  37	GSGDFAKSL	11
  41	FAKSLTIRL	11
  68	EFFPHVVDV	11
  75	DVTHHEDAL	11
  85	KTNIIFVAI	11
  96	EHYTSLWDL	11
  100	SLWDLRHLL	11
  134	ASLFPDSLI	11
  146	FNVVSAWAL	11
  196	SSAREIENL	11
  237	HPYARNQQS	11
  253	EIVNKTLPI	11
  267	LSLVYLAGL	11
  271	YLAGLLAAA	11
  274	GLLAAAYQL	11
  292	PPWLETWLQ	11
  297	TWLQCRKQL	11
  323	LPMRRSERY	11
  328	SERYLFLNM	11
  378	SIPSVSNAL	11
  394	IQSTLGYVA	11
  425	RFYTPPNFV	11

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-B0702-9mers-98P4B6

  3	SPGLQALSL	23
  35	PPCPADFFL	22
  34	PPPCPADFF	20
  37	CPADFFLYF	20
  33	CPPPCPADF	18
  1	SGSPGLQAL	14
  15	SGFTPFSCL	14
  5	GLQALSLSL	13
  17	FTPFSCLSL	12
  25	LPSSWDYRC	12
  12	SLSSGFTPF	11
  31	YRCPPPCPA	11

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-B0702-9mers-98P4B6

  9	FWRGPVVVA	17
  2	LPLRLFTFW	13
  7	FTFWRGPVV	9
  8	TFWRGPVVV	9
  6	LFTFWRGPV	8

  V5B-HLA-B0702-9mers-98P4B6

  19	ELELEFVFL	15
  14	ADTQTELEL	14
  24	FVFLLTLLL	13
  12	SFADTQTEL	12
  22	LEFVFLLTL	12
  23	EFVFLLTLL	12
  20	LELEFVFLL	11
  21	ELEFVFLLT	10
  10	FCSFADTQT	9
  8	QIFCSFADT	8
  16	TQTELELEF	8
  1	WREFSFIQI	7
  2	REFSFIQIF	7
  5	SFIQIFCSF	7
  6	FIQIFCSFA	7
  17	QTELELEFV	7
  18	TELELEFVF	7

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-B0702-9mers-98P4B6

  43	IPHVSPERV	17
  7	ILGKIILFL	16
  2	LPSIVILGK	14
  27	KGWEKSQFL	12
  45	HVSPERVTV	12
  5	IVILGKIIL	11
  15	LPCISRKLK	11
  14	FLPCISRKL	10
  38	GIGGTIPHV	10
  44	PHVSPERVT	10
  35	LEEGIGGTI	9
  46	VSPERVTVM	9
  6	VILGKIILF	8
  10	KIILFLPCI	8
  17	CISRKLKRI	8
  26	KKGWEKSQF	8

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-B0702-9mers-98P4B6

  1	SPKSLSETF	16
  2	PKSLSETFL	14

  V7B-HLA-B0702-9mers-98P4B6

  9	STLGYVALL	14
  8	QSTLGYVAL	13
  3	NMAYQQSTL	11
  7	QQSTLGYVA	10
  2	LNMAYQQST	8
  6	YQQSTLGYV	6

  V7C-HLA-B0702-9mers-98P4B6

  102	PPESPDRAL	24
  15	SPAAAWKCL	22
  52	TPPPPAMWT	20
  55	PPAMWTEEA	18
  105	SPDRALKAA	18
  101	DPPESPDRA	16
  113	ANSWRNPVL	16
  5	ILDLSVEVL	14
  47	IPPLSTPPP	14
  84	IPVVGVVTE	14
  118	NPVLPHTNG	14
  141	QAASGTLSL	14
  160	LGSGTWMKL	14
  29	RGGLSEIVL	13
  42	QQDRKIPPL	13
  49	PLSTPPPPA	13
  121	LPHTNGVGP	13
  126	GVGPLWEFL	13
  128	GPLWEFLLR	13
  31	GLSEIVLPI	12
  48	PPLSTPPPP	12
  50	LSTPPPPAM	12
  54	PPPAMWTEE	12
  61	EEAGATAEA	12
  81	SSQIPVVGV	12
  122	PHTNGVGPL	12
  129	PLWEFLLRL	12
  139	KSQAASGTL	12
  142	AASGTLSLA	12
  143	ASGTLSLAF	12
  152	TSWSLGEFL	12
  17	AAAWKCLGA	11
  24	GANILRGGL	11
  27	ILRGGLSEI	11
  44	DRKIPPLST	11
  53	PPPPAMWTE	11
  125	NGVGPLWEF	11
  148	SLAFTSWSL	11
  158	EFLGSGTWM	11
  165	WMKLETIIL	11
  181	KSKHCMFSL	11

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-B0702-9mers-98P4B6

  8	GMGGTIPHV	10
  5	LEEGMGGTI	9
  1	KSQFLEEGM	7
  4	FLEEGMGGT	6
  7	EGMGGTIPH	6
  6	EEGMGGTIP	4

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-B0702-9mers-98P4B6

  1	SPKSLSETF	16
  2	PKSLSETFL	14

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-B0702-9mers-98P4B6

  9	FWRGPVVVA	17
  2	LPLRLFTFW	13
  7	FTFWRGPVV	9
  8	TFWRGPVVV	9
  6	LFTFWRGPV	8

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-B0702-9mers-98P4B6

  8	KTKHCMFSL	11
  5	QEQKTKHCM	7
  6	EQKTKHCMF	7
  9	TKHCMFSLI	7
  1	SKLTQEQKT	6

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-B0702-9mers-98P4B6

  3	FLPCISQKL	10
  4	LPCISQKLK	10
  6	CISQKLKRI	8
  1	ILFLPCISQ	4

• [1250]

  TABLE XXVIII
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-B08-9mers-98P4B6

  41	FAKSLTIRL	25
  203	NLPLRLFTL	25
  62	NPKFASEFF	22
  173	QARQQVIEL	22
  253	EIVNKTLPI	22
  57	VIGSRNPKF	20
  81	DALTKTNII	20
  285	GTKYRRFPP	20
  299	LQCRKQLGL	20
  326	RRSERYLFL	20
  385	ALNWREFSF	20
  93	IHREHYTSL	19
  140	SLIVKGFNV	19
  268	SLVYLAGLL	19
  9	SPKSLSETC	18
  28	ARKVTVGVI	18
  100	SLWDLRHLL	18
  171	NIQARQQVI	18
  214	GPVVVAISL	18
  259	LPIVAITLL	18
  428	TPPNFVLAL	18
  39	GDFAKSLTI	17
  107	LLVGLILID	17
  157	GPKDASRQV	17
  274	GLLAAAYQL	17
  291	FPPWLETWL	17
  378	SIPSVSNAL	17
  438	LPSIVILDL	17
  24	GIKDARKVT	16
  44	SLTIRLIRC	16
  125	YPESNAEYL	16
  155	QLGPKDASR	16
  184	QLNFIPIDL	16
  200	EIENLPLRL	16
  237	HPYARNQQS	16
  239	YARNQQSDF	16
  251	PIEIVNKTL	16
  258	TLPIVAITL	16
  283	YYGTKYRRF	16
  287	KYRRFPPWL	16
  300	QCRKQLGLL	16
  324	PMRRSERYL	16
  403	LLISTFHVL	16
  133	LASLFPDSL	15
  159	KDASRQVYI	15
  179	IELARQLNF	15
  187	FIPIDLGSL	15
  322	CLPMRRSER	15
  360	YISFGIMSL	15
  106	HLLVGKILI	14
  128	SNAEYLASL	14
  180	ELARQLNFI	14
  197	SAREIENLP	14
  245	SDFYKIPIE	14
  298	WLQCRKQLG	14
  323	LPMRRSERY	14
  433	VLALVLPSI	14
  5	SMMGSPKSL	13
  17	CLPNGINGI	13
  82	ALTKTNIIF	13
  91	VAIHREHYT	13
  103	DLRHLLVGK	13
  142	IVKGFNVVS	13
  146	FNVVSAWAL	13
  196	SSAREIENL	13
  205	PLRLFTLWR	13
  264	ITLLSLVYL	13
  304	QLGLLSFFF	13
  395	QSTLGYVAL	13
  396	STLGYVALL	13
  397	TLGYVALLI	13
  435	ALVLPSIVI	13
  37	GSGDFAKSL	12
  60	SRNPKFASE	12
  96	EHYTSLWDL	12
  105	RHLLVGKIL	12
  109	VGKILIDVS	12
  177	QVIELARQL	12
  247	FYKIPIEIV	12
  325	MRRSERYLF	12
  362	SFGIMSLGL	12
  365	IMSLGLLSL	12
  390	EFSFIQSTL	12
  414	GWKRAFEEE	12
  426	FYTPPNFVL	12
  436	LVLPSIVIL	12
  441	IVILDLLQL	12

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-B08-9mers-98P4B6

  3	SPGLQALSL	19
  5	GLQALSLSL	17
  35	PPCPADFFL	16
  12	SLSSGFTPF	14
  1	SGSPGLQAL	13
  15	SGFTPFSCL	12
  33	CPPPCPADF	12
  34	PPPCPADFF	12
  37	CPADFFLYF	12
  17	FTPFSCLSL	11
  28	SWDYRCPPP	11
  10	SLSLSSGFT	9

• [1251]

  TABLE XXIX
  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-B08-9mers-98P4B6

  1	NLPLRLFTF	21
  3	PLRLFTFWR	13

  V5B-HLA-B08-9mers-98P4B6

  19	ELELEFVFL	20
  12	SFADTQTEL	13
  20	LELEFVFLL	13
  23	EFVFLLTLL	12
  24	FVFLLTLLL	12
  14	ADTQTELEL	11
  22	LEFVFLLTL	11
  16	TQTELELEF	9

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-B08-9mers-98P4B6

  19	SRKLKRIKK	23
  6	VILGKIILF	22
  27	KGWEKSQFL	22
  17	CISRKLKRI	21
  7	ILGKIILFL	18
  14	FLPCISRKL	17
  21	KLKRIKKGW	17
  22	LKRIKKGWE	16
  24	RIKKGWEKS	14
  4	SIVILGKII	13
  5	IVILGKIIL	12
  25	IKKGWEKSQ	12
  46	VSPERVTVM	12
  10	KIILFLPCI	11
  23	KRIKKGWEK	11
  29	WEKSQFLEE	11

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-B08-9mers-98P4B6

  1	SPKSLSETF	24
  9	FLPNGINGI	14
  2	PKSLSETFL	11

  V7B-HLA-B08-9mers-98P4B6

  8	QSTLGYVAL	13
  9	STLGYVALL	13
  3	NMAYQQSTL	11
  1	FLNMAYQQS	7

  V7C-HLA-B08-9mers-98P4B6

  179	EQKSKHCMF	28
  42	QQDRKIPPL	21
  73	GIRNKSSSS	21
  165	WMKLETIIL	21
  27	ILRGGLSEI	20
  181	KSKHCMFSL	20
  5	ILDLSVEVL	19
  15	SPAAAWKCL	19
  113	ANSWRNPVL	19
  129	PLWEFLLRL	18
  148	SLAFTSWSL	18
  102	PPESPDRAL	17
  109	ALKAANSWR	17
  163	GTWMKLETI	17
  19	AWKCLGANI	16
  31	GLSEIVLPI	16
  137	LLKSQAASG	16
  24	GANILRGGL	15
  171	IILSKLTQE	15
  17	AAAWKCLGA	14
  141	QAASGTLSL	14
  134	LLRLLKSQA	13

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-B08-9mers-98P4B6

  4	FLEEGMGGT	9
  5	LEEGMGGTI	6

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-B08-9mers-98P4B6

  1	SPKSLSETF	24
  9	FLPNGINGI	14
  2	PKSLSETFL	11

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-B08-9mers-98P4B6

  1	NLPLRLFTF	21
  3	PLRLFTFWR	13

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-B08-9mers-98P4B6

  6	EQKTKHCMF	28
  8	KTKHCMFSL	20
  4	TQEQKTKHC	11

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-B08-9mers-98P4B6

  8	SQKLKRIKK	23
  6	CISQKLKRI	21
  3	FLPCISQKL	17

  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-B1510-9mers-98P4B6

  93	IHREHYTSL	23
  96	EHYTSLWDL	21
  105	RHLLVGKHL	20
  315	VHVAYSLCL	20
  200	EIENLPLRL	15
  426	FYTPPNFVL	15
  436	LVLPSIVIL	15
  54	YHVVIGSRN	14
  264	ITLLSLVYL	14
  360	YISFGIMSL	14
  365	IMSLGLLSL	14
  395	QSTLGYVAL	14
  77	THHEDALTK	13
  99	TSLWDLRHL	13
  125	YPESNAEYL	13
  173	QARQQVIEL	13
  177	QVIELARQL	13
  236	IHPYARNQQ	13
  261	IVAITLLSL	13
  297	TWLQCRKQL	13
  390	EFSFIQSTL	13
  428	TPPNFVLAL	13
  430	PNFVLALVL	13
  5	SMMGSPKSL	12
  37	GSGDFAKSL	12
  41	FAKSLTIRL	12
  71	PHVVDVTHH	12
  78	HHEDALTKT	12
  100	SLWDLRHLL	12
  128	SNAEYLASL	12
  133	LASLFPDSL	12
  146	FNVVSAWAL	12
  196	SSAREIENL	12
  214	GPVVVAISL	12
  220	ISLATFFFL	12
  251	PIEIVNKTL	12
  258	TLPIVAITL	12
  259	LPIVAITLL	12
  287	KYRRFPPWL	12
  324	PMRRSERYL	12
  326	RRSERYLFL	12
  396	STLGYVALL	12
  403	LLISTFHVL	12
  438	LPSIVILDL	12
  441	IVILDLLQL	12
  10	PKSLSETCL	11
  75	DVTHHEDAL	11
  148	VVSAWALQL	11
  184	QLNFIPIDL	11
  198	AREIENLPL	11
  201	IENLPLRLF	11
  203	NLPLRLFTL	11
  267	LSLVYLAGL	11
  274	GLLAAAYQL	11
  283	YYGTKYRRF	11
  300	QCRKQLGLL	11
  341	VHANIENSW	11
  351	EEEVWRIEM	11
  366	MSLGLLSLL	11
  378	SIPSVSNAL	11
  383	SNALNWREF	11
  411	LIYGWKRAF	11
  439	PSIVILDLL	11

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-B1510-9mers-98P4B6

  1	SGSPGLQAL	15
  35	PPCPADFFL	12
  5	GLQALSLSL	11
  15	SGFTPFSCL	11
  3	SPGLQALSL	10
  17	FTPFSCLSL	10
  33	CPPPCPADF	9
  12	SLSSGFTPF	8
  37	CPADFFLYF	8
  34	PPPCPADFF	7

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-B1510-9mers-98P4B6

  1	NLPLRLFTF	7
  8	TFWRGPVVV	7
  9	FWRGPVVVA	7
  7	FTFWRGPVV	3

  V5B-HLA-B1510-9mers-98P4B6

  19	ELELEFVFL	14
  12	SFADTQTEL	13
  14	ADTQTELEL	12
  20	LELEFVFLL	12
  22	LEFVFLLTL	12
  23	EFVFLLTLL	11
  18	TELELEFVF	10
  24	FVFLLTLLL	10
  16	TQTELELEF	9
  2	REFSFIQIF	7
  5	SFIQIFCSF	7

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-B1510-9mers-98P4B6

  44	PHVSPERVT	15
  5	IVILGKIIL	14
  7	ILGKIILFL	14
  14	FLPCISRKL	12
  27	KGWEKSQFL	11
  46	VSPERVTVM	10
  6	VILGKIILF	8
  26	KKGWEKSQF	7
  45	HVSPERVTV	7

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-B1510-9mers-98P4B6

  2	PKSLSEFTL	11
  1	SPKSLSETF	7

  V7B-HLA-B1510-9mers-98P4B6

  8	QSTLGYVAL	14
  3	NMAYQQSTL	12
  9	STLGYVALL	12

  V7C-HLA-B1510-9mers-98P4B6

  122	PHTNGVGPL	22
  5	ILDLSVEVL	15
  102	PPESPDRAL	15
  113	ANSWRNPVL	14
  126	GVGPLWEFL	13
  129	PLWEFLLRL	13
  130	LWEFLLRLL	13
  24	GANILRGGL	12
  29	RGGLSEIVL	12
  42	QQDRKIPPL	12
  50	LSTPPPPAM	12
  141	QAASGTLSL	12
  160	LGSGTWMKL	12
  15	SPAAAWKCL	11
  20	WKCLGANIL	11
  139	KSQAASGTL	11
  148	SLAFTSWSL	11
  152	TSWSLGEFL	11
  181	KSKHCMFSL	11
  127	VGPLWEFLL	10
  165	WMKLETIIL	10
  168	LETIILSKL	10
  183	KHCMFSLIS	10

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-B1510-9mers-98P4B6

  1	KSQFLEEGM	6
  4	FLEEGMGGT	4
  8	GMGGTIPHV	4
  5	LEEGMGGTI	3
  7	EGMGGTIPH	3
  9	MGGTIPHVS	3
  6	EEGMGGTIP	2

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-B1510-9mers-98P4B6

  2	PKSLSETFL	11
  1	SPKSLSETF	7

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-B1510-9mers-98P4B6

  1	NLPLRLFTF	7
  8	TFWRGPVVV	7
  9	FWRGPVVVA	7
  7	FTFWRGPVV	3

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-B1510-9mers-98P4B6

  8	KTKHCMFSL	11
  5	QEQKTKHCM	8
  6	EQKTKHCMF	7
  4	TQEQKTKHC

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-B1510-9mers-98P4B6

  3	FLPCISQKL	10
  7	ISQKLKRIK	6
  6	CISQKLKRI	4

• [1252]

  TABLE XXX
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-B2705-9mers-98P4B6

  326	RRSERYLFL	26
  424	YRFYTPPNF	26
  355	WRIEMYISF	26
  198	AREIENLPL	24
  240	ARNQQSDFY	22
  325	MRRSERYLF	22
  47	IRLIRCGYH	21
  50	IRCGYHVVI	21
  104	LRHLLVGKI	21
  289	RRFPPWLET	21
  416	KRAFEEEYY	21
  212	WRGPVVVAI	20
  302	RKQLGLLSF	20
  417	RAFEEEYYR	20
  28	ARKVTVGVI	19
  61	RNPKFASEF	19
  182	ARQLNFIPI	19
  199	REIENLPLR	19
  249	KIPIEIVNK	19
  303	KQLGLLSFF	19
  53	GYHVVIGSR	18
  105	RHLLVGKIL	18
  179	IELARQLNF	18
  214	GPVVVAISL	18
  241	RNQQSDFYK	18
  274	GLLAAAYQL	18
  282	LYYGTKYRR	18
  436	LVLPSIVIL	18
  21	GINGIKDAR	17
  174	ARQQVIELA	17
  223	ATFFFLYSF	17
  259	LPIVAITLL	17
  264	ITLLSLVYL	17
  330	RYLFLNMAY	17
  360	YISFGIMSL	17
  365	IMSLGLLSL	17
  366	MSLGLLSLL	17
  400	YVALLISTF	17
  430	PNFVLALVL	17
  441	IVILDLLQL	17
  22	INGIKDARK	16
  39	GDFAKSLTI	16
  40	DFAKSLTIR	16
  43	KSLTIRLIR	16
  56	VVIGSRNPK	16
  112	ILIDVSNNM	16
  175	RQQVIELAR	16
  177	QVIELARQL	16
  196	SSAREIENL	16
  206	LRLFTLWRG	16
  218	VAISLATFF	16
  225	FFFLYSFVR	16
  233	RDVIHPYAR	16
  313	AMVHVAYSL	16
  319	YSLCLPMRR	16
  396	STLGYVALL	16
  418	AFEEEYYRF	16
  443	ILDLLQLCR	16
  37	GSGDFAKSL	15
  82	ALTKTNIIF	15
  87	NIIFVAIHR	15
  93	IHREHYTSL	15
  96	EHYTSLWDL	15
  155	QLGPKDASR	15
  173	QARQQVIEL	15
  295	LETWLQCRK	15
  297	TWLQCRKQL	15
  329	ERYLFLNMA	15
  390	EFSFIQSTL	15
  401	VALLISTFH	15
  409	HVLIYGWKR	15
  411	LIYGWKRAF	15
  438	LPSIVILDL	15
  5	SMMGSPKSL	14
  10	PKSLSETCL	14
  18	LPNGINGIK	14
  33	VGVIGSGDF	14
  41	FAKSLTIRL	14
  57	VIGSRNPKF	14
  60	SRNPKFASE	14
  77	THHEDALTK	14
  120	MRINQYPES	14
  128	SNAEYLASL	14
  136	LFPDSLIVK	14
  146	FNVVSAWAL	14
  162	SRQVYICSN	14
  167	ICSNNIQAR	14
  193	GSLSSAREI	14
  200	EIENLPLRL	14
  201	IENLPLRLF	14
  217	VVAISLATF	14
  258	TLPIVAITL	14
  261	IVAITLLSL	14
  263	AITLLSLVY	14
  267	LSLVYLAGL	14
  280	YQLYYGTKY	14
  281	QLYYGTKYR	14
  299	LQCRKQLGL	14
  301	CRKQLGLLS	14
  308	LSFFFAMVH	14
  318	AYSLCLPMR	14
  363	FGIMSLGLL	14
  392	SFIQSTLGY	14
  395	QSTLGYVAL	14
  426	FYTPPNFVL	14
  439	PSIVILDLL	14
  444	LDLLQLCRY	14
  35	VIGSGDFAK	13
  98	YTSLWDLRH	13
  99	TSLWDLRHL	13
  103	DLRHLLVGK	13
  113	LIDVSNNMR	13
  117	SNNMRINQY	13
  124	QYPESNAEY	13
  129	NAEYLASLF	13
  138	PDSLIVKGF	13
  148	VVSAWALQL	13
  151	AWALQLGPK	13
  191	DLGSLSSAR	13
  203	NLPLRLFTL	13
  220	ISLATFFFL	13
  229	YSFVRDVIH	13
  239	YARNQQSDF	13
  246	DFYKIPIEI	13
  251	PIEIVNKTL	13
  268	SLVYLAGLL	13
  279	AYQLYYGTK	13
  283	YYGTKYRRF	13
  287	KYRRFPPWL	13
  291	FPPWLETWL	13
  300	QCRKQLGLL	13
  304	QLGLLSFFF	13
  306	GLLSFFFAM	13
  315	VHVAYSLCL	13
  337	AYQQVHANI	13
  348	SWNEEEVWR	13
  371	LSLLAVTSI	13
  378	SIPSVSNAL	13
  388	WREFSFIQS	13
  403	LLISTFHVL	13
  408	FHVLIYGWK	13
  435	ALVLPSIVI	13
  17	CLPNGINGI	12
  70	FPHVVDVTH	12
  71	PHVVDVTHH	12
  80	EDALTKTNI	12
  86	TNIIFVAIH	12
  89	IFVAIHREH	12
  106	HLLVGKILI	12
  114	IDVSNNMRI	12
  133	LASLFPDSL	12
  134	ASLFPDSLI	12
  164	QVYICSNNI	12
  184	QLNFIPIDL	12
  187	FIPIDLGSL	12
  205	PLRLFTLWR	12
  219	AISLATFFF	12
  231	FVRDVIHPY	12
  232	VRDVIHPYA	12
  256	NKTLPIVAI	12
  272	LAGLLAAAY	12
  288	YRRFPPWLE	12
  317	VAYSLCLPM	12
  322	CLPMRRSER	12
  328	SERYLFLNM	12
  349	WNEEEVWRI	12
  352	EEVWRIEMY	12
  362	SFGIMSLGL	12
  381	SVSNALNWR	12
  383	SNALNWREF	12
  385	ALNWREFSF	12
  428	TPPNFVLAL	12

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-B2705-9mers-98P4B6

  5	GLQALSLSL	17
  9	LSLSLSSGF	15
  15	SGFTPFSCL	15
  1	SGSPGLQAL	14
  3	SPGLQALSL	14
  12	SLSSGFTPF	14
  23	LSLPSSWDY	14
  17	FTPFSCLSL	13
  31	YRCPPPCPA	12
  33	CPPPCPADF	12
  34	PPPCPADFF	12
  35	PPCPADFFL	12
  24	SLPSSWDYR	11
  37	CPADFFLYF	11
  2	GSPGLQALS	9
  36	PCPADFFLY	8

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-B2705-9mers-98P4B6

  4	LRLFTFWRG	15
  1	NLPLRLFTF	13
  3	PLRLFTFWR	11
  5	RLFTFWRGP	7

  V5B-HLA-B2705-9mers-98P4B6

  2	REFSFIQIF	20
  1	WREFSFIQI	19
  5	SFIQIFCSF	16
  22	LEFVFLLTL	16
  24	FVFLLTLLL	16
  12	SFADTQTEL	15
  14	ADTQTELEL	15
  18	TELELEFVF	15
  23	EFVFLLTLL	15
  16	TQTELELEF	14
  20	LELEFVFLL	14
  19	ELELEFVFL	13

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-B2705-9mers-98P4B6

  23	KRIKKGWEK	29
  19	SRKLKRIKK	25
  6	VILGKIILF	19
  13	LFLPCISRK	19
  5	IVILGKIIL	18
  7	ILGKIILFL	18
  12	ILFLPCISR	18
  16	PCISRKLKR	16
  26	KKGWEKSQF	16
  2	LPSIVILGK	15
  18	ISRKLKRIK	15
  27	KGWEKSQFL	15
  37	EGIGGTIPH	15
  14	FLPCISRKL	14
  42	TIPHVSPER	14

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-B2705-9mers-98P4B6

  2	PKSLSETFL	14
  1	SPKSLSETF	13
  9	FLPNGINGI	12
  6	SETFLPNGI	8
  7	ETFLPNGIN	6
  8	TFLPNGING	6

  V7B-HLA-B2705-9mers-98P4B6

  9	STLGYVALL	16
  3	NMAYQQSTL	14
  8	QSTLGYVAL	14
  5	AYQQSTLGY	13
  4	MAYQQSTLG	7

  V7C-HLA-B2705-9mers-98P4B6

  21	KCLGANILR	18
  29	RGGLSEIVL	18
  69	AQESGIRNK	18
  167	KLETIILSK	18
  175	KLTQEQKSK	18
  74	IRNKSSSSS	17
  125	NGVGPLWEF	17
  128	GPLWEFLLR	17
  107	DRALKAANS	16
  131	WEFLLRLLK	16
  5	ILDLSVEVL	15
  20	WKCLGANIL	15
  37	LPIEWQQDR	15
  42	QQDRKIPPL	15
  67	AEAQESGIR	15
  100	IDPPESPDR	15
  126	GVGPLWEFL	15
  129	PLWEFLLRL	15
  135	LRLLKSQAA	15
  158	EFLGSGTWM	15
  160	LGSGTWMKL	15
  168	LETIILSKL	15
  24	GANILRGGL	14
  27	ILRGGLSEI	14
  28	LRGGLSEIV	14
  38	PIEWQQDRK	14
  113	ANSWRNPVL	14
  116	WRNPVLPHT	14
  139	KSQAASGTL	14
  141	QAASGTLSL	14
  143	ASGTLSLAF	14
  173	LSKLTQEQK	14
  13	LASPAAAWK	13
  31	GLSEIVLPI	13
  44	DRKIPPLST	13
  109	ALKAANSWR	13
  122	PHTNGVGPL	13
  148	SLAFTSWSL	13
  151	FTSWSLGEF	13
  159	FLGSGTWMK	13
  165	WMKLETIIL	13
  176	LTQEQKSKH	13
  181	KSKHCMFSL	13
  39	IEWQQDRKI	12
  102	PPESPDRAL	12
  103	PESPDRALK	12
  130	LWEFLLRLL	12
  136	RLLKSQAAS	12
  163	GTWMKLETI	12
  178	QEQKSKHCM	12
  19	AWKCLGANI	11
  45	RKIPPLSTP	11
  50	LSTPPPPAM	11
  108	RALKAANSW	11
  115	SWRNPVLPH	11
  127	VGPLWEFLL	11
  152	TSWSLGEFL	11
  157	GEFLGSGTW	11
  164	TWMKLETII	11
  179	EQKSKHCMF	11
  15	SPAAAWKCL	10
  30	GGLSEIVLP	10
  76	NKSSSSSQI	10
  92	EDDEAQDSI	10
  75	RNKSSSSSQ	8
  85	PVVGVVTED	8
  145	GTLSLAFTS	8
  171	IILSKLTQE	8
  185	CMFSLISGS	8

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-B2705-9mers-98P4B6

  7	EGMGGTIPH	13
  1	KSQFLEEGM	11
  5	LEEGMGGTI	9
  8	GMGGTIPHV	9

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-B2705-9mers-98P4B6

  2	PKSLSETFL	14
  1	SPKSLSETF	13
  9	FLPNGINGI	12
  6	SETFLPNGI	8
  7	ETFLPNGIN	6
  8	TFLPNGING	6

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-B2705-9mers-98P4B6

  4	LRLFTFWRG	15
  1	NLPLRLFTF	13
  3	PLRLFTFWR	11
  5	RLFTFWRGP	7

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-B2705-9mers-98P4B6

  2	KLTQEQKTK	18
  3	LTQEQKTKH	14
  8	KTKHCMFSL	13
  5	QEQKTKHCM	11
  6	EQKTKHCMF	11

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-B2705-9mers-98P4B6

  2	LFLPCISQK	18
  5	PCISQKLKR	16
  7	ISQKLKRIK	15
  8	SQKLKRIKK	15
  3	FLPCISQKL	14
  4	LPCISQKLK	13
  6	CISQKLKRI	12
  9	QKLKRIKKG	9
  1	ILFLPCISQ	8

• [1253]

  TABLE XXXI
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-B2709-9mers-98P4B6

  326	RRSERYLFL	25
  198	AREIENLPL	22
  424	YRFYTPPNF	22
  212	WRGPVVVAI	21
  28	ARKVTVGVI	20
  50	IRCGYHVVI	20
  325	MRRSERYLF	19
  104	LRHLLVGKI	19
  182	ARQLNFIPI	19
  355	WRIEMYISF	19
  274	GLLAAAYQL	18
  289	RRFPPWLET	18
  105	RHLLVGKIL	16
  193	GSLSSAREI	15
  214	GPVVVAISL	15
  441	IVILDLLQL	15
  37	GSGDFAKSL	14
  39	GDFAKSLTI	14
  48	RLIRCGYHV	14
  264	ITLLSLVYL	14
  306	GLLSFFFAM	14
  313	AMVHVAYSL	14
  425	RFYTPPNFV	14
  430	PNFVLALVL	14
  436	LVLPSIVIL	14
  47	IRLIRCGYH	13
  61	PNPKFASEF	13
  68	EFFPHVVDV	13
  99	TSLWDLRHL	13
  135	SLFPDSLIV	13
  148	VVSAWALQL	13
  177	QVIELARQL	13
  179	IELARQLNF	13
  206	LRLFTLWRG	13
  220	ISLATFFFL	13
  287	KYRRFPPWL	13
  297	TWLQCRKQL	13
  302	RKQLGLLSF	13
  396	STLGYVALL	13
  41	FAKSLTIRL	12
  85	KTNIIFVAI	12
  96	EHYTSLWDL	12
  114	IDVSNNMRI	12
  120	MRINQYPES	12
  125	YPESNAEYL	12
  146	FNVVSAWAL	12
  157	GPKDASRQV	12
  159	KDASRQVYI	12
  200	EIENLPLRL	12
  223	ATFFFLYSF	12
  227	FLYSFVRDV	12
  232	VRDVIHPYA	12
  261	IVAITLLSL	12
  267	LSLVYLAGL	12
  268	SLVYLAGLL	12
  303	KQLGLLSFF	12
  315	VHVAYSLCL	12
  317	VAYSLCLPM	12
  329	ERYLFLNMA	12
  365	IMSLGLLSL	12
  366	MSLGLLSLL	12
  395	QSTLGYVAL	12
  403	LLISTFHVL	12
  416	KRAFEEEYY	12
  426	FYTPPNFVL	12
  428	TPPNFVLAL	12
  439	PSIVILDLL	12

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-B2709-9mers-98P4B6

  5	GLQALSLSL	14
  3	SPGLQALSL	12
  15	SGFTPFSCL	12
  1	SGSPGLQAL	11
  9	LSLSLSSGF	11
  17	FTPFSCLSL	11
  31	YRCPPPCPA	11
  35	PPCPADFFL	11
  12	SLSSGFTPF	9
  33	CPPPCPADF	9
  34	PPPCPADFF	9
  37	CPADFFLYF	9
  32	RCPPPCPAD	6

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-B2709-9mers-98P4B6

  4	LRLFTFWRG	13
  7	FTFWRGPVV	11
  6	LFTFWRGPV	9
  8	TFWRGPVVV	9
  1	NLPLRLFTF	8
  5	RLFTFWRGP	6

  V5B-HLA-B2709-9mers-98P4B6

  1	WREFSFIQI	19
  2	REFSFIQIF	15
  14	ADTQTELEL	13
  20	LELEFVFLL	13
  22	LEFVFLLTL	13
  24	FVFLLTLLL	13
  19	ELELEFVFL	11
  23	EFVFLLTLL	11
  5	SFIQIFCSF	10
  12	SFADTQTEL	10
  16	TQTELELEF	10
  18	TELELEFVF	10

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-B2709-9mers-98P4B6

  7	ILGKIILFL	13
  23	KRIKKGWEK	13
  5	IVILGKIIL	12
  10	KIILFLPCI	12
  27	KGWEKSQFL	12
  38	GIGGTIPHV	12
  14	FLPCISRKL	11
  26	KKGWEKSQF	11
  3	PSIVILGKI	10
  6	VILGKIILF	10
  19	SRKLKRIKK	10
  31	KSQFLEEGI	10
  43	IPHVSPERV	10
  45	HVSPERVTV	10
  4	SIVILGKII	9
  17	CISRKLKRI	9
  35	LEEGIGGTI	9
  46	VSPERVTVM	9
  20	RKLKRIKKG	6
  41	GTIPHVSPE	6

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-B2709-9mers-98P4B6

  2	PKSLSETFL	10
  1	SPKSLSETF	9
  6	SETFLPNGI	9
  9	FLPNGINGI	8
  3	KSLSETFLP	5
  8	TFLPNGING

  V7B-HLA-B2709-9mers-98P4B6

  9	STLGYVALL	13
  8	QSTLGYVAL	12
  3	NMAYQQSTL	10
  6	YQQSTLGYV	9

  V7C-HLA-B2709-9mers-98P4B6

  28	LRGGLSEIV	18
  29	RGGLSEIVL	14
  31	GLSEIVLPI	14
  126	GVGPLWEFL	14
  24	GANILRGGL	13
  5	ILDLSVEVL	12
  107	DRALKAANS	12
  113	ANSWRNPVL	12
  116	WRNPVLPHT	12
  122	PHTNGVGPL	12
  129	PLWEFLLRL	12
  135	LRLLKSQAA	12
  139	KSQAASGTL	12
  141	QAASGTLSL	12
  168	LETIILSKL	12
  181	KSKHCMFSL	12
  4	VILDLSVEV	11
  20	WKCLGANIL	11
  42	QQDRKIPPL	11
  44	DRKIPPLST	11
  50	LSTPPPPAM	11
  74	IRNKSSSSS	11
  82	SQIPVVGVV	11
  102	PPESPDRAL	11
  119	PVLPHTNGV	11
  152	TSWSLGEFL	11
  163	GTWMKLETI	11
  2	SIVILDLSV	10
  15	SPAAAWKCL	10
  19	AWKCLGANI	10
  76	NKSSSSSQI	10
  79	SSSSQIPVV	10
  81	SSQIPVVGV	10
  112	AANSWRNPV	10
  127	VGPLWEFLL	10
  130	LWEFLLRLL	10
  143	ASGTLSLAF	10
  148	SLAFTSWSL	10
  158	EFLGSGTWM	10
  160	LGSGTWMKL	10
  165	WMKLETIIL	10
  27	ILRGGLSEI	9
  39	IEWQQDRKI	9
  78	SSSSSQIPV	9
  125	NGVGPLWEF	9
  179	EQKSKHCMF	9
  66	TAEAQESGI	8
  92	EDDEAQDSI	8
  151	FTSWSLGEF	8
  164	TWMKLETII	8
  178	QEQKSKHCM	8
  182	SKHCMFSLI	8

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-B2709-9mers-98P4B6

  8	GMGGTIPHV	12
  1	KSQFLEEGM	10
  5	LEEGMGGTI	8

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-B2709-9mers-98P4B6

  2	PKSLSETFL	10
  1	SPKSLSETF	9
  6	SETFLPNGI	9
  9	FLPNGINGI	8
  3	KSLSETFLP	5
  8	TFLPNGING	4

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-B2709-9mers-98P4B6

  4	LRLFTFWRG	13
  7	FTFWRGPVV	11
  6	LFTFWRGPV	9
  8	TFWRGPVVV	9
  1	NLPLRLFTF	8
  5	RLFTFWRGP	6

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-B2709-9mers-98P4B6

  8	KTKHCMFSL	12
  5	QEQKTKHCM	8
  6	EQKTKHCMF	8
  9	TKHCMFSLI	8

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-B2709-9mers-98P4B6

  3	FLPCISQKL	11
  6	CISQKLKRI	9
  2	LFLPCISQK	4

• [1254]

  TABLE XXXII
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-B4402-9mers-98P4B6

  352	EEVWRIEMY	26
  201	IENLPLRLF	24
  179	IELARQLNF	23
  14	SETCLPNGI	21
  419	FEEEYYRFY	21
  357	IEMYISFGI	20
  42	AKSLTIRLI	18
  436	LVLPSIVIL	18
  117	SNNMRINQY	17
  144	KGFNVVSAW	17
  259	LPIVAITLL	17
  441	IVILDLLQL	17
  5	SMMGSPKSL	16
  138	PDSLIVKGF	16
  177	QVIELARQL	16
  199	REIENLPLR	16
  203	NLPLRLFTL	16
  219	AISLATFFF	16
  223	ATFFFLYSF	16
  256	NKTLPIVAI	16
  263	AITLLSLVY	16
  290	RFPPWLETW	16
  392	SFIQSTLGY	16
  403	LLISTFHVL	16
  428	TPPNFVLAL	16
  439	PSIVILDLL	16
  67	SEFFPHVVD	15
  79	HEDALTKTN	15
  100	SLWDLRHLL	15
  130	AEYLASLFP	15
  182	ARQLNFIPI	15
  196	SSAREIENL	15
  200	EIENLPLRL	15
  212	WRGPVVVAI	15
  231	FVRDVIHPY	15
  252	IEIVNKTLP	15
  297	TWLQCRKQL	15
  363	FGIMSLGLL	15
  378	SIPSVSNAL	15
  389	REFSFIQST	15
  390	EFSFIQSTL	15
  396	STLGYVALL	15
  400	YVALLISTF	15
  421	EEYYRFYTP	15
  430	PNFVLALVL	15
  438	LPSIVILDL	15
  17	CLPNGINGI	14
  37	GSGDFAKSL	14
  82	ALTKTNIIF	14
  85	KTNIIFVAI	14
  96	EHYTSLWDL	14
  105	RHLLVGKIL	14
  148	VVSAWALQL	14
  198	AREIENLPL	14
  204	LPLRLFTLW	14
  218	VAISLATFF	14
  221	SLATFFFLY	14
  258	TLPIVAITL	14
  264	ITLLSLVYL	14
  272	LAGLLAAAY	14
  303	KQLGLLSFF	14
  313	AMVHVAYSL	14
  351	EEEVWRIEM	14
  355	WRIEMYISF	14
  360	YISFGIMSL	14
  365	IMSLGLLSL	14
  366	MSLGLLSLL	14
  383	SNALNWREF	14
  385	ALNWREFSF	14
  395	QSTLGYVAL	14
  411	LIYGWKRAF	14
  426	FYTPPNFVL	14
  435	ALVLPSIVI	14
  28	ARKVTVGVI	13
  46	TIRLIRCGY	13
  99	TSLWDLRHL	13
  126	PESNAEYLA	13
  129	NAEYLASLF	13
  133	LASLFPDSL	13
  134	ASLFPDSLI	13
  146	FNVVSAWAL	13
  158	PKDASRQVY	13
  180	ELARQLNFI	13
  184	QLNFIPIDL	13
  240	ARNQQSDFY	13
  251	PIEIVNKTL	13
  253	EIVNKTLPI	13
  268	SLVYLAGLL	13
  274	GLLAAAYQL	13
  286	TKYRRFPPW	13
  287	KYRRFPPWL	13
  302	RKQLGLLSF	13
  311	FFAMVHVAY	13
  323	LPMRRSERY	13
  326	RRSERYLFL	13
  328	SERYLFLNM	13
  330	RYLFLNMAY	13
  341	VHANIENSW	13
  347	NSWNEEEVW	13
  380	PSVSNALNW	13
  407	TFHVLIYGW	13
  418	AFEEEYYRF	13
  420	EEEYYRFYT	13
  424	YRFYTPPNF	13
  444	LDLLQLCRY	13
  10	PKSLSETCL	12
  39	GDFAKSLTI	12
  41	FAKSLTIRL	12
  57	VIGSRNPKF	12
  61	RNPKFASEF	12
  75	DVTHHEDAL	12
  81	DALTKTNII	12
  94	HREHYTSLW	12
  125	YPESNAEYL	12
  128	SNAEYLASL	12
  173	QARQQVIEL	12
  187	FIPIDLGSL	12
  214	GPVVVAISL	12
  217	VVAISLATF	12
  220	ISLATFFFL	12
  261	IVAITLLSL	12
  267	LSLVYLAGL	12
  280	YQLYYGTKY	12
  283	YYGTKYRRF	12
  299	LQCRKQLGL	12
  300	QCRKQLGLL	12
  324	PMRRSERYL	12
  325	MRRSERYLF	12
  350	NEEEVWRIE	12
  353	EVWRIEMYI	12
  362	SFGIMSLGL	12
  404	LISTFHVLI	12
  405	ISTFHVLIY	12

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-B4402-9mers-98P4B6

  1	SGSPGLQAL	18
  15	SGFTPFSCL	15
  33	CPPPCPADF	15
  3	SPGLQALSL	14
  23	LSLPSSWDY	14
  12	SLSSGFTPF	13
  21	SCLSLPSSW	13
  35	PPCPADFFL	13
  36	PCPADFFLY	13
  37	CPADFFLYF	13
  17	FTPFSCLSL	12
  34	PPPCPADFF	12
  5	GLQALSLSL	11
  9	LSLSLSSGF	11

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-B4402-9mers-98P4B6

  1	NLPLRLFTF	16
  2	LPLRLFTFW	13

  V5B-HLA-B4402-9mers-98P4B6

  2	REFSFIQIF	25
  22	LEFVFLLTL	25
  20	LELEFVFLL	23
  18	TELELEFVF	22
  5	SFIQIFCSF	16
  24	FVFLLTLLL	16
  19	ELELEFVFL	15
  14	ADTQTELEL	14
  23	EFVFLLTLL	14
  12	SFADTQTEL	12

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-B4402-9mers-98P4B6

  35	LEEGIGGTI	21
  6	VILGKIILF	17
  5	IVILGKIIL	15
  7	ILGKIILFL	15
  21	KLKRIKKGW	15
  3	PSIVILGKI	14
  10	KIILFLPCI	14
  14	FLPCISRKL	14
  17	CISRKLKRI	13
  26	KKGWEKSQF	12
  29	WEKSQFLEE	12
  36	EEGIGGTIP	12
  4	SIVILGKII	11
  27	KGWEKSQFL	11

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-B4402-9mers-98P4B6

  6	SETFLPNGI	21
  9	FLPNGINGI	14
  1	SPKSLSETF	12
  2	PKSLSETFL	12

  V7B-HLA-B4402-9mers-98P4B6

  5	AYQQSTLGY	15
  9	STLGYVALL	15
  8	QSTLGYVAL	14
  3	NMAYQQSTL	12

  V7C-HLA-B4402-9mers-98P4B6

  33	SEIVLPIEW	26
  157	GEFLGSGTW	24
  168	LETIILSKL	23
  39	IEWQQDRKI	20
  143	ASGTLSLAF	17
  51	STPPPPAMW	16
  70	QESGIRNKS	16
  103	PESPDRALK	16
  113	ANSWRNPVL	16
  131	WEFLLRLLK	16
  42	QQDRKIPPL	15
  5	ILDLSVEVL	14
  61	EEAGATAEA	14
  10	VEVLASPAA	13
  12	VLASPAAAW	13
  15	SPAAAWKCL	13
  20	WKCLGANIL	13
  29	RGGLSEIVL	13
  60	TEEAGATAE	13
  67	AEAQESGIR	13
  91	TEDDEAQDS	13
  102	PPESPDRAL	13
  108	RALKAANSW	13
  125	NGVGPLWEF	13
  126	GVGPLWEFL	13
  127	VGPLWEFLL	13
  130	LWEFLLRLL	13
  146	TLSLAFTSW	13
  160	LGSGTWMKL	13
  165	WMKLETIIL	13
  31	GLSEIVLPI	12
  122	PHTNGVGPL	12
  123	HTNGVGPLW	12
  129	PLWEFLLRL	12
  139	KSQAASGTL	12
  141	QAASGTLSL	12
  151	FTSWSLGEF	12
  179	EQKSKHCMF	12

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-B4402-9mers-98P4B6

  5	LEEGMGGTI	20
  6	EEGMGGTIP	12

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-B4402-9mers-98P4B6

  6	SETFLPNGI	21
  9	FLPNGINGI	14
  1	SPKSLSETF	12
  2	PKSLSETFL	12

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-B4402-9mers-98P4B6

  1	NLPLRLFTF	16
  2	LPLRLFTFW	13

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-B4402-9mers-98P4B6

  6	EQKTKHCMF	13
  5	QEQKTKHCM	11
  8	KTKHCMFSL	11
  9	TKHCMFSLI	10

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-B4402-9mers-98P4B6

  3	FLPCISQKL	13
  6	CISQKLKRI	12
  2	LFLPCISQK	8
  9	QKLKRIKKG	8

• [1255]

  TABLE XXXIIII
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V1-HLA-B5101-9mers-98P4B6

  81	DALTKTNII	29
  27	DARKVTVGV	26
  65	FASEFFPHV	23
  374	LAVTSIPSV	23
  434	LALVLPSIV	23
  438	LPSIVILDL	22
  246	DFYKIPIEI	21
  262	VAITLLSLV	21
  368	LGLLSLLAV	21
  428	TPPNFVLAL	21
  429	PPNFVLALV	21
  23	NGIKDARKV	20
  157	GPKDASRQV	20
  214	GPVVVAISL	20
  259	LPIVAITLL	20
  41	FAKSLTIRL	19
  125	YPESNAEYL	19
  133	LASLFPDSL	19
  173	QARQQVIEL	19
  250	IPIEIVNKT	19
  291	FPPWLETWL	19
  50	IRCGYHVVI	18
  228	LYSFVRDVI	17
  336	MAYQQVHAN	17
  371	LSLLAVTSI	17
  28	ARKVTVGVI	16
  39	GDFAKSLTI	16
  70	FPHVVDVTH	16
  104	LRHLLVGKI	16
  141	LIVKGFNVV	16
  160	DASRQVYIC	16
  204	LPLRLFTLW	16
  227	FLYSFVRDV	16
  237	HPYARNQQS	16
  317	VAYSLCLPM	16
  52	CGYHVVIGS	15
  137	FPDSLIVKG	15
  164	QVYICSNNI	15
  171	NIQARQQVI	15
  193	GSLSSAREI	15
  210	TLWRGPVVV	15
  212	WRGPVVVAI	15
  276	LAAAYQLYY	15
  349	WNEEEVWRI	15
  363	FGIMSLGLL	15
  397	TLGYVALLI	15
  425	RFYTPPNFV	15
  18	LPNGINGIK	14
  25	IKDARKVTV	14
  114	IDVSNNMRI	14
  152	WALQLGPKD	14
  209	FTLWRGPVV	14
  222	LATFFFLYS	14
  242	NQQSDFYKI	14
  258	TLPIVAITL	14
  278	AAYQLYYGT	14
  379	IPSVSNALN	14
  386	LNWREFSFI	14
  398	LGYVALLIS	14
  401	VALLISTFH	14
  404	LISTFHVLI	14
  433	VLALVLPSI	14
  435	ALVLPSIVI	14

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V2-HLA-B5101-9mers-98P4B6

  3	SPGLQALSL	18
  35	PPCPADFFL	16
  15	SGFTPFSCL	15
  1	SGSPGLQAL	13
  7	QALSLSLSS	13
  18	TPFSCLSLP	13
  25	LPSSWDYRC	13
  37	CPADFFLYF	13
  33	CPPPCPADF	12
  34	PPPCPADFF	12
  17	FTPFSCLSL	10
  4	PGLQALSLS	9
  5	GLQALSLSL	8

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V5A-HLA-B5101-9mers-98P4B6

  2	LPLRLFTFW	16
  8	TFWRGPVVV	15
  7	FTFWRGPVV	13
  6	LFTFWRGPV	10
  9	FWRGPVVVA	8
  4	LRLFTFWRG	7

  V5B-HLA-B5101-9mers-98P4B6

  20	LELEFVFLL	14
  1	WREFSFIQI	13
  22	LEFVFLLTL	13
  13	FADTQTELE	12
  12	SFADTQTEL	9
  17	QTELELEFV	9
  24	FVFLLTLLL	9
  14	ADTQTELEL	8
  18	TELELEFVF	8
  19	ELELEFVFL	8
  23	EFVFLLTLL	8
  15	DTQTELELE	6

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V6-HLA-B5101-9mers-98P4B6

  43	IPHVSPERV	23
  2	LPSIVILGK	16
  27	KGWEKSQFL	16
  35	LEEGIGGTI	15
  15	LPCISRKLK	14
  17	CISRKLKRI	14
  3	PSIVILGKI	13
  39	IGGTIPHVS	13
  38	GIGGTIPHV	12
  4	SIVILGKII	11
  7	ILGKIILFL	11
  10	KIILFLPCI	11
  14	FLPCISRKL	11
  45	HVSPERVTV	11

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V7A-HLA-B5101-9mers-98P4B6

  9	FLPNGINGI	14
  1	SPKSLSETF	12
  6	SETFLPNGI	12
  2	PKSLSETFL

  V7B-HLA-B5101-9mers-98P4B6

  4	MAYQQSTLG	16
  6	YQQSTLGYV	12
  9	STLGYVALL	12
  3	NMAYQQSTL	9
  8	QSTLGYVAL	7

  V7C-HLA-B5101-9mers-98P4B6

  66	TAEEAQSGI	22
  101	DPPESPDRA	20
  112	AANSWRNPV	19
  15	SPAAAWKCL	18
  160	LGSGTWMKL	18
  29	RGGLSEIVL	17
  84	IPVVGVVTE	17
  102	PPESPDRAL	17
  141	QAASGTLSL	17
  24	GANILRGGL	16
  39	IEWQQDRKI	16
  31	GLSEIVLPI	15
  68	EAQESGIRN	15
  82	SQIPVVGVV	15
  108	RALKAANSW	15
  149	LAFTSWSLG	15
  163	GTWMKLETI	15
  5	ILDLSVEVL	14
  27	ILRGGLSEI	14
  37	LPIEWQQDR	14
  47	IPPLSTPPP	14
  48	PPLSTPPPP	14
  54	PPPAMWTEE	14
  121	LPHTNGVGP	14
  127	VGPLWEFLL	14
  128	GPLWEFLLR	14
  4	VILDLSVEV	13
  13	LASPAAAWK	13
  18	AAWKCLGAN	13
  52	TPPPPAMWT	13
  53	PPPPAMWTE	13
  62	EAGATAEAQ	13
  95	EAQDSIDPP	13
  142	AASGTLSLA	13
  164	TWMKLETII	13
  17	AAAWKCLGA	12
  64	GATAEAQES	12
  76	NKSSSSSQI	12
  79	SSSSQIPVV	12
  92	EDDEAQDSI	12
  105	SPDRALKAA	12
  111	KAANSWRNP	12
  118	NPVLPHTNG	12
  129	PLWEFLLRL	12
  182	SKHCMFSLI	12
  16	PAAAWKCLG	11
  28	LRGGLSEIV	11
  56	PAMWTEEAG	11
  81	SSQIPVVGV	11
  119	PVLPHTNGV	11
  168	LETIILSKL	11
  19	AWKCLGANI	10
  23	LGANILRGG	10
  30	GGLSEIVLP	10
  55	PPAMWTEEA	10
  78	SSSSSQIPV	10
  113	ANSWRNPVL	10
  130	LWEFLLRLL	10

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V8-HLA-B5101-9mers-98P4B6

  5	LEEGMGGTI	16
  8	GMGGTIPHV	12
  9	MGGTIPHVS	12
  7	EGMGGTIPH	8

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V13-HLA-B5101-9mers-98P4B6

  9	FLPNGINGI	14
  1	SPKSLSETF	12
  6	SETFLPNGI	12
  2	PKSLSETFL	8

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V14-HLA-B5101-9mers-98P4B6

  2	LPLRLFTFW	16
  8	TFWRGPVVV	15
  7	FTFWRGPVV	13
  6	LFTFWRGPV	10
  9	FWRGPVVVA	8
  4	LRLFTFWRG	7

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V21-HLA-B5101-9mers-98P4B6

  9	TKHCMFSLI	13
  3	LTQEQKTKH	7
  8	KTKHCMFSL	6

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 9 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	123456789	score

  V25-HLA-B5101-9mers-98P4B6

  4	LPCISQKLK	14
  6	CISQKLKRI	14
  3	FLPCISQKL	10
  9	QKLKRIKKG	7

• [1256]

  TABLE XXXIV
  Each peptide is a portion of SEQ ID NO: 3;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V1-HLA-A1-10mers-98P4B6

  351	EEEVWRIEMY	26
  391	FSFIQSTLGY	26
  418	AFEEEYYRFY	26
  443	ILDLLQLCRY	26
  220	ISLATFFFLY	24
  262	VAITLISLVY	23
  327	RSERYLFLNM	23
  45	LTIRLIRCGY	22
  275	LLAAAYQLYY	22
  404	LISTFHVLIY	22
  116	VSNNMRINQY	20
  123	NQYPESNAEY	20
  271	TLAGLLAAAY	19
  279	AYQLYYGTKY	19
  427	YTPPNFVLAL	19
  38	SGDFAKSLTI	18
  274	GLLAAAYQLY	18
  101	LWDLRHLLVG	17
  157	GPKDASRQVY	17
  178	VIELARQLNF	17
  230	SFVRDVIHPY	17
  239	YARNQQSDFY	17
  396	STLGYVALLI	17
  66	ASEFFPHVVD	16
  89	IFVAIHREHY	16
  94	HREHYTSLWD	16
  129	NAEYLASLFP	16
  310	FFFAMVHVAY	16
  322	CLPMRRSERY	16
  329	ERYLFLNMAY	16
  350	NEEEVWRIEM	15
  414	GWKRAFEEEY	15
  415	WKRAFEEEYY	15
  13	LSETCLPNGI	14
  125	YPESNAEYLA	14
  244	QSDFYKIPIE	14
  257	KTLPIVAITL	14
  76	VTHHEDALTK	13
  198	AREIENLPLR	13
  366	MSLGLLSLLA	13
  420	EEEYYRFYTP	13
  25	IKDARKVTVG	12
  135	SLFPDSLIVK	12
  137	FPDSLIVKGF	12
  200	EIENLPLRLF	12
  221	SLATFFFLYS	12
  251	PIEIVNKTLP	12
  268	SLVYLAGLLA	12
  419	FEEEYYRFYT	12
  439	PSIVILDLLQ	12

  Each peptide is a portion of SEQ ID NO: 5;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V2-HLA-A1-10mers-98P4B6

  35	PPCPADFFLY	24
  22	CLSLPSSWDY	16
  28	SWDYRCPPPC	12
  2	GSPGLQALSL	11

  Each peptide is a portion of SEQ ID NO: 11;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V5A-HLA-A1-10mers-98P4B6

  8	FTFWRGPVVV	8
  1	ENLPLRLFTF	4
  2	NLPLRLFTFW	4
  4	PLRLFTFWRG	4
  10	FWRGPVVVAI	3

  V5B-HLA-A1-10mers-98P4B6

  14	FADTQTELEL	17
  18	QTELELEFVF	17
  22	ELEFVFLLTL	17
  20	ELELEFVFLL	14
  16	DTQTELELEF	12
  21	LELEFVFLLT	11
  2	WREFSFIQIF	10
  5	FSFIQIFCSF	8
  24	EFVFLLTLLL	8

  Each peptide is a portion of SEQ ID NO: 13;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V6-HLA-A1-10mers-98P4B6

  29	GWEKSQELEF	19
  35	FLEEGIGGTI	13
  36	LEEGIGGTIP	12
  1	LVLPSIVILG	11
  19	ISRKLKRIKK	11
  42	GTIPHVSPER	10
  9	LGKIILFLPC	9

  Each peptide is a portion of SEQ ID NO: 15;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V7A-HLA-A1-10mers-98P4B6

  6	LSETFLPNGI	14
  4	KSLSETFLPN	13
  8	ETFLPNGING	11

  V7B-HLA-A1-10mers-98P4B6

  5	MAYQQSTLGY	21
  10	STLGYVALLI	17

  V7C-HLA-A1-10mers-98P4B6

  131	LWEFLLRLLK	19
  33	LSEIVLPIEW	18
  91	VTEDDEAQDS	17
  60	WTEEAGATAE	16
  100	SIDPPESPDR	16
  70	AQESGIRNKS	14
  94	DDEAQDSIDP	14
  6	ILDLSVEVLA	13
  103	PPESPDRALK	13
  124	HTNGVGPLWE	13
  168	KLETIILSKL	13
  10	SVEVLASPAA	12
  39	PIEWQQDRKI	12
  43	QQDRKIPPLS	12
  52	STPPPPAMWT	12
  104	PESPDRALKA	12
  106	SPDRALKAAN	12
  128	VGPLWEFLLR	12
  170	ETIILSKLTQ	12
  97	AQDSIDPPES	11
  115	NSWRNPVLPH	11
  154	SWSLGEFLGS	11
  2	PSIVILDLSV	10
  61	TEEAGATAEA	10
  67	TAEAQESGIR	10
  92	TEDDEAQDSI	10
  93	EDDEAQDSID	10
  157	LGEFLGSGTW	10
  162	GSGTWMKLET	10
  178	TQEQKSKHCM	10
  51	LSTPPPPAMW	9
  146	GTLSLAFTSW	9
  182	KSKHCMFSLI	9

  Each peptide is a portion of SEQ ID NO: 17;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V8-HLA-A1-10mers-98P4B6

  5	FLEEGMGGTI	13
  6	LEEGMGGTIP	12

  Each peptide is a portion of SEQ ID NO: 27;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V13-HLA-A1-10mers-98P4B6

  6	LSETFLPNGI	14
  4	KSLSETFLPN	13
  8	ETFLPNGING	11

  Each peptide is a portion of SEQ ID NO: 29;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V14-HLA-A1-10mers-98P4B6

  8	FTFWRGPVVV	8
  1	ENLPLRLFTF	4
  2	NLPLRLFTFW	4
  4	PLRLFTFWRG	4
  10	FWRGPVVVAI	3

  Each peptide is a portion of SEQ ID NO: 43;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V21-HLA-A1-10mers-98P4B6

  9	KTKHCMFSLI	11
  5	TQEQKTKHCM	10
  1	LSKLTQEQKT	6
  4	LTQEQKTKHC	6
  10	TKHCMFSLIS	6

  Each peptide is a portion of SEQ ID NO: 51;
  each start position is specified, the length
  of peptide is 10 amino acids, and the end
  position for each peptide is the start
  position plus eight.

  Pos	1234567890	score

  V25-HLA-A1-10mers-98P4B6

  8	ISQKLKRIKK	11
  5	LPCISQKLKR	8
  3	LFLPCISQKL	6

• [1257]

  TABLE XXXV
  Pos	1234567890	score

  V1-HLA-A0201-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified,
  the length of peptides is 10 amino acids,
  and the end position for each peptide
  is the start position plus nine.

  373	LLAVTSIPSV	31
  266	LLSLVYLAGL	29
  107	LLVGKILIDV	28
  367	SLGLLSLLAV	28
  435	ALVLPSIVIL	28
  364	GIMSLGLLSL	27
  132	YLASLFPDSL	26
  370	LLSLLAVTSI	26
  437	VLPSIVILDL	26
  82	ALTKTNIIFV	25
  100	SLWDLRHLLV	25
  140	SLIVKGFNVV	25
  263	AITLLSLVYL	25
  306	GLLSFFFAMV	25
  402	ALLISTFHVL	25
  440	SIVILDLLQL	25
  258	TLPIVAITLL	24
  365	IMSLGLLSLL	24
  403	LLISTFHVLI	24
  427	YTPPNFVLAL	24
  24	GIKDARKVTV	23
  48	RLIRCGYHVV	23
  103	DLRHLLVGKI	23
  433	VLALVLPSIV	23
  92	AIHREHYTSL	22
  260	PIVAITLLSL	22
  261	IVAITLLSLV	22
  298	WLQCRKQLGL	22
  432	FVLALVLPSI	22
  207	RLFTLWRGPV	21
  210	TLWRGPVVVA	21
  257	KTLPIVAITL	21
  385	ALNWREFSFI	21
  49	LIRCGYHVVI	20
  98	YTSLWDLRHL	20
  172	IQARQQVIEL	20
  186	NFIPIDLGSL	20
  219	AISLATFFFL	20
  227	FLYSFVRDVI	20
  249	KTPIEIVNKT	20
  253	EIVNKTLPIV	20
  12	SLSETCLPNG	19
  135	SLFPDSLIVK	19
  142	IVKGFNVVSA	19
  197	SAREIENLPL	19
  209	FTLWRGPVVV	19
  211	LWRGPVVVAI	19
  271	YLAGLLAAAY	19
  312	FAMVHVAYSL	19
  396	STLGYVALLI	19
  16	TCLPNGINGI	18
  65	FASEFFPHVV	18
  67	SEFFPHVVDV	18
  113	LIDVSNNMRI	18
  359	MYISFGIMSL	18
  392	SFIQSTLGYV	18
  106	HLLVGKILID	17
  179	IELARQLNFI	17
  202	ENLPLRLFTL	17
  250	IPIEIVNKTL	17
  264	ITLLSLVYLA	17
  269	LVYLAGLLAA	17
  348	SWNEEEVWRI	17
  361	ISFGLMSLGL	17
  369	GLLSLLAVTS	17
  401	VALLISTFHV	17
  26	KDARKVTVGV	16
  41	FAKSLTIRLI	16
  111	KILIDVSNNM	16
  112	ILIDVSNNMR	16
  127	ESNAEYLASL	16
  195	LSSAREIENL	16
  223	ATFFFLYSFV	16
  226	FFLYSFVRDV	16
  268	SLVYLAGLLA	16
  299	LQCRKIQLGLL	16
  356	RIEMYISFGI	16
  362	SFGIMSLGLL	16
  377	TSWSVSNAL	16
  428	TPPNFVLALV	16
  434	LALVLPSIVI	16
  438	LPSIVILDLL	16
  443	ILDLLQLCRY	16
  27	DARKVTVGVI	15
  36	IGSGDFAKSL	15
  44	SLTIRLIRCG	15
  47	IRLIRCGYHV	15
  147	NVVSAWALQL	15
  166	YICSNNIQAR	15
  189	PLDLGSLSSA	15
  199	REIENLPLRL	15
  221	SLATFFFLYS	15
  255	VNKTLPIVAI	15
  273	AGLLAAAYQL	15
  275	LLAAAYQLYY	15
  314	MVHVAYSLCL	15
  335	NMAYQQVHAN	15
  336	MAYQQVHANI	15
  345	IENSWNEEEV	15
  394	IQSTLGYVAL	15
  395	QSTLGYVALL	15
  404	LISTFHVLIY	15
  411	LIYGWKRAFE	15

  V2-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 5; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  2	GSPGLQALSL	16
  5	GLQALSLSLS	15
  16	GFTPFSCLSL	15
  10	SLSLSSGFTP	14
  8	ALSLSLSSGF	13
  12	SLSSGFTPFS	13
  24	SLPSSWDYRC	13
  4	PGLQALSLSL	12
  7	QALSLSLSSG	12
  14	SSGFTPFSCL	11
  22	CLSLPSSWDY	10
  9	LSLSLSSGFT	8
  17	FTPFSCLSLP	8
  6	LQALSLSLSS	7
  34	PPPCPADFFL	7

  V5A-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  6	RLFTFWRGPV	21
  8	FTFWRGPVVV	18
  10	FWRGPVVVAI	18
  7	LFTFWRGPVV	11
  9	TFWRGPVVVA	11
  2	NLPLRLFTFW	10

  V5B-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  22	ELEFVFLLTL	22
  20	ELELEFVFLL	20
  14	FADTQTELEL	18
  23	LEFVFLLTLL	17
  19	TELELEFVFL	16
  17	TQTELELEFV	15
  12	CSFADTQTEL	13
  9	QIFCSFADTQ	11
  21	LELEFVFLLT	11
  1	NWREFSFIQI	10
  7	FIQIFCSFAD	10

  V6-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 13; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  7	VILGKIILFL	28
  35	FLEEGIGGTI	22
  5	SIVILGKIIL	20
  14	LFLPCISRKL	18
  43	TIPHVSPERV	18
  2	VLPSIVILGK	17
  13	ILFLPCLSRK	17
  3	LPSLVILGKI	16
  8	ILGKIILFLP	16
  10	GKIILFLPCI	16
  38	EGIGGIPWHV	16
  1	LVLPSIVILG	14
  46	HVSPERVTVM	14
  12	IILFLPCISR	13
  34	QFLEEGIGGT	13

  V7A-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  5	SLSETFLPNG	19
  9	TFLPNGINGI	18
  2	SPKSLSFTFL	11
  6	LSETFLPNGI	11
  10	FLPNGINGIK	11

  V7B-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  10	STLGYVALLI	19
  2	FLNMAYQQST	18
  6	AYQQSTLGYV	16
  3	LNMAYQQSTL	15
  9	QSTLGYVALL	15
  8	QQSTLGYVAL	13
  4	NMAYQQSTLG	9

  V7C-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  5	VILDLSVEVL	26
  168	KLETIILSKL	26
  27	NILRGGLSEI	24
  28	ILRGGLSEIV	24
  130	PLWEFLLRLL	24
  160	FLGSGTWMKL	23
  4	IVILDLSVEV	22
  66	ATAEAQESGI	19
  81	SSSQIPVVGV	19
  156	SLGEFLGSGT	19
  6	ILDLSVEVLA	18
  32	GLSFIVLPIE	18
  112	KAANSWRNPV	18
  113	AANSWRNPVL	18
  129	GPLWEFLLRL	18
  8	DLSVEVLASP	17
  19	AAWKCLGANI	17
  79	SSSSSQIPVV	17
  127	GVGPLWEFLL	17
  134	FLLRLLKSQA	17
  135	LLRLLKSQAA	17
  141	SQAASGTLSL	17
  31	GGLSEIVLPI	16
  42	WQQDRKIPPL	16
  58	AMWTEEAGAT	16
  82	SSQIPVVGVV	16
  84	QIPVVGVVTE	16
  122	LPHTNGVGPL	16
  137	RLLKSQAASG	16
  138	LLKSQAASGT	16
  148	LSLAFTSWSL	16
  3	VLASPAAAWK	15
  23	CLGANILRGG	15
  24	LGANILRGGL	15
  152	FTSWSLGEFL	15
  163	SGTWMKLETI	15
  3	SIVILDLSVE	14
  29	LRGGLSEIVL	14
  39	PIEWQQDRKI	14
  121	VLPHTNGVGP	14
  139	LKSQAASGTL	14
  142	QAASGTLSLA	14
  164	GTWMKLETII	14
  171	TIILSKLTQE	14
  172	IILSKLTQEQ	14
  18	AAAWKCLGAN	13
  50	PLSTPPPPAM	13
  100	SIDPPESPDR	13
  149	SLAFTSWSLG	13
  2	PSIVILDLSV	12
  20	AWKCLGANIL	12
  47	KIPPLSTPPP	12
  52	STPPPPAMWT	12
  83	SQIPVVGVVT	12
  102	DPPESPDRAL	12
  119	NPVLPHTNGV	12
  126	NGVGPLWEFL	12
  144	ASGTLSLAFT	12
  173	ILSKLTQEQK	12
  176	KLTQEQKSKII	12
  181	QKSKHCMIFSL	12

  V8-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 17; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  5	FLEEGMGGTI	22
  8	EGMGGTIPHV	15
  9	GMGGTIPHVS	12

  V13-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 27; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  5	SLSETFLPNG	19
  9	TFLPNGINGI	18
  2	SPKSLSETFL	11
  6	LSETFLPNGI	11
  10	FLPNGINGIK	11

  V14-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 29; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  6	RLFTFWRGPV	21
  8	FTFWRGPVVV	18
  10	FWRGPVVVAI	18
  7	LFTFWRGPVV	11
  9	TFWRGPVVVA	11
  2	NLPLRLFTFW	10

  V21-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 43; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  3	KITQEQKTKH	12
  9	KTKHCMFSLI	12
  8	QKTKHCMFSL	11
  1	LSKLTQEQKT	7
  4	LTQEQKTKHC	7
  2	SKLTQEQKTK	5

  V25-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  3	LFLPCISQKL	18
  2	ILFLPCLSQK	17
  1	IILFLPCISQ	13
  4	FLPCISQKIK	10
  6	PCISQKLKRI	10
  7	CISQKLKRIK	8

• [1258]

  XXXVI
  V1-HLA-A0203-10mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified,
  the length of peptides is 10 amino acids,
  and the end position for each peptide
  is the start position plus nine.

  270	VYLAGLLAAA	27
  269	LVYLAGLLAA	19
  144	KGFNVVSAWA	18
  271	YLAGLLAAAY	17

  V2-HLA-A0203-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 5; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  30	DYRCPPPCPA	10
  31	YRCPPPCPAD	9
  1	SGSPGLQALS	8
  32	RCPPPCPADF	8

  V5A-HLA-A0203-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  9	TFWRGPVVVA	10
  10	FWRGPVVVAI	9

  V5B-HLA-A0203-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  6	SFIQIFCSFA	10
  7	FIQIFCSFAD	9
  8	IQIFCSFADT	8

  V6-HLA-A0203-10mers-98P4B6

  NoResultsFound.

  V7A-HLA-A0203-10mers-98P4B6

  NoResultsFound.

  V7B-HLA-A0203-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  7	YQQSTLGYVA	10
  8	QQSTLGYVAL	9
  9	QSTLGYVALL	8

  V7C-HLA-A0201-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  11	VEVLASPAAA	27
  10	SVEVLASPAA	19
  105	ESPDRALKAA	19
  135	LLRLLKSQAA	19
  57	PAMWTEEAGA	18
  59	MWTEEAGATA	18
  61	TEEAGATAEA	18
  12	EVLASPAAAW	17
  106	SPDRALKAAN	17
  136	LRLLKSQAAS	17

  V8-HLA-A0203-10mers-98P4B6

  NoResultsFound.

  V13-HLA-A0203-10mers-98P4B6

  NoResultsFound.

  V14-HLA-A0203-10mers-98P4B6

  9	TFWRGPVVVA	10
  10	FWRGPVVVAI	9

  V21-HLA-A0203-10mers-98P4B6

  NoResultsFound.

  V25-HLA-A0203-10mers-98P4B6

  NoResultsFound.

• [1259]

  TABLE XXXVII
  Pos	1234567890	score

  V1-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 3; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  135	SLFPDSLIVK	28
  34	GVIGSGDFAK	26
  271	YLAGLLAAAY	26
  48	RLIRCGYIIVV	24
  21	GLNGIKDARK	23
  216	VVVAISLATF	23
  369	GLLSLLAVTS	23
  17	CLPNGINGIK	22
  17	HVVIGSRNPK	22
  275	LLAAAYQLYY	22
  278	AAYQLYYGTK	22
  307	LLSFFFAMVH	22
  112	ILIDVSNNMR	21
  142	IVKGFNVVSA	21
  155	QLGPKDASRQ	21
  210	TLWRGPVVVA	21
  76	VTHHEDALTK	20
  217	VVAISLATFF	20
  248	YKIPIEIVNK	20
  274	GLLAAAYQLY	20
  281	QLYYGTKYRR	20
  294	WLETWLQCRK	20
  402	ALLISTFHVL	20
  2	ESISMMGSPK	19
  7	LIRCGYHVVI	19
  7	VVIGSRNPKF	19
  102	WDLRHLLVGK	19
  147	NVVSAWALQL	19
  7	FLYSFVRDVI	19
  269	LVYLAGLLAA	19
  375	AVTSIPSVSN	19
  443	ILDLLQLCRY	19
  24	GIKDARKVTV	18
  140	SLIVKGFNVV	18
  333	FLNMAYQQVH	18
  410	VLIYGWKRAF	18
  411	LIYGWKRAFE	18
  435	ALVLPSIVIL	18
  442	VILDLLQLCR	18
  46	TLRLIRCGYH	17
  92	AIHREHYTSL	17
  164	QVYICSNNIQ	17
  177	QVIELARQLN	17
  254	IVNKTLPIVA	17
  261	IVAITLLSLV	17
  268	SLVYLAGLLA	17
  331	YLFLNMAYQQ	17
  400	YVALLISTFH	17
  403	LLISTFHVLI	17
  404	LISTFHVLIY	17
  30	KVTVGVIGSG	16
  123	NQYPESNAEY	16
  141	LIVKGFNVVS	16
  178	VIELARQLNF	16
  207	RLFTLWRGPV	16
  234	DVIHPYARNQ	16
  262	VAITLLSLVY	16
  263	AITLLSLVYL	16
  265	TLLSLVYLAG	16
  306	GLLSFFFAMV	16
  322	CLPMRRSERY	16
  340	QVHANIENSW	16
  367	SLGLLSLLAV	16
  385	ALNWREFSFI	16
  432	FVLALVLPSI	16
  433	VLALVLPSIV	16
  440	SIVILDLLQL	16
  441	IVILDLLQLC	16
  32	TVGVIGSGDF	15
  100	SLWDLRHLLV	15
  106	HLLVGKILID	15
  121	RINQYPESNA	15
  153	ALQLGPKDAS	15
  187	FIPIDLGSLS	15
  221	SLATFFFLYS	15
  235	VIHPYARNQQ	15
  257	KTLPIVAITL	15
  260	PIVAITLLSL	15
  320	SLCLPMRRSE	15
  372	SLLAVTSIPS	15
  393	FIQSTLGYVA	15
  436	LVLPSIVILD	15
  60	SRNPKFASEF	14
  88	IIFVAIHREH	14
  103	DLRHLLVGKI	14
  108	LVGKILIDVS	14
  111	KILIDVSNNM	14
  132	YLASLFPDSL	14
  150	SAWALQLGPK	14
  171	NIQARQQVIE	14
  180	ELARQLNFIP	14
  189	PIDLGSLSSA	14
  190	IDLGSLSSAR	14
  205	PLRLFTLWRG	14
  21	SPVVVAISLAT	14
  231	FVRDVIHPYA	14
  266	LLSLVYLAGL	14
  279	AYQLYYGTKY	14
  316	HVAYSLCLPM	14
  370	LLSLLAVTSI	14
  45	LTIRLIRCGY	13
  75	DVTHHEDALT	13
  82	ALTKTNIIFV	13
  128	SNAEYLASLF	13
  154	LQLGPKDASR	13
  157	GPKDASRQVY	13
  166	YICSNNIQAR	13
  191	DLGSLSSARE	13
  200	EIENLPLRLF	13
  204	LPLRLFTLWR	13
  240	ARNQQSDFYK	13
  298	WLQCRKQLGL	13
  304	QLGLLSFFFA	13
  310	FFFAMVHVAY	13
  314	MVHVAYSLCL	13
  321	LCLPMRRSER	13
  329	ERYLFLNMAY	13
  353	EVWRIEMYIS	13
  364	GIMSLGLLSL	13
  373	LLAVTSIPSV	13
  397	TLGYVALLIS	13
  399	GYVALLISTF	13
  409	HVLIYGWKRA	13
  437	VLPSIVILDL	13
  445	DLLQLCRYPD	13

  V2-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 5; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  8	ALSLSLSSGF	21
  10	SLSLSSGFTP	19
  22	CLSLPSSWDY	17
  5	GLQALSLSLS	15
  32	RCPPPCPADF	15
  12	SLSSGFTPFS	11
  24	SLPSSWDYRC	11
  2	GSPGLQALSL	10
  33	CPPPCPADFF	10

  V5A-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  6	RLFTFWRGPV	16
  4	PLRLFTFWRG	14
  1	ENLPLRLFTF	13
  2	NLPLRLFTFW	12
  9	TFWRGPVVVA	11
  3	LPLRLFTFWR	10
  10	FWRGPVVVAI	10
  8	FTFWRGPVVV	9
  7	LFTFWRGPVV	7

  V5B-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  9	QIFCSFADTQ	17
  22	ELEFVFLLTL	17
  18	QTELELEFVF	11
  20	ELELEFVFLL	11
  7	FIQIFCSFAD	10
  8	IQIFCSFADT	8

  V6-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 13; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  13	ILFLPCISRK	26
  2	VLPSLVILGK	23
  15	FLPCISRKLK	21
  18	CISRKLKRIK	21
  6	IVILGKIILF	20
  22	KLKRIKKGWE	19
  35	FLEEGIGGTI	19
  12	IILFLPCISR	18
  46	HVSPERVTVM	18
  23	LKRIKKGWEK	17
  11	KIILFLPCIS	16
  19	ISRKLKRIKK	16
  1	LVLPSIVILG	15
  7	VILGKIILFL	15
  25	RIKKGWEKSQ	15
  26	IKKGWEKSQF	15
  39	GIGGTTIHVS	15
  8	ILGKIILFLP	12

  V7A-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  10	FLPNGINGIK	22
  5	SLSETFLPNG	12

  V7B-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  5	MAYQQSTLGY	13
  2	FLNMAYQQST	12
  10	SILGYVALLI	11
  3	LNMAYQQSTL	9
  7	YQQSTLGYVA	7
  8	QQSTLGYVAL	7
  1	LFLNMAYQQS	6
  9	QSTLGYVALL	6

  V7C-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  13	VLASPAAAWK	28
  173	ILSKLTQEQK	25
  137	RLLKSQAASG	24
  72	EVLASPAAAW	21
  134	FLLRLLKSQA	21
  4	IVILDLSVEV	20
  36	IVLPIEWQQD	20
  120	PVLPHTNGVG	20
  176	KLTQEQKSKH	20
  83	SQIPVVGVVT	18
  84	QIPVVGVVTE	18
  156	SLGEFLGSGT	18
  167	MKLETIILSK	18
  3	SIVILDLSVE	17
  6	ILDLSVEVLA	17
  28	ILRGGLSEIV	17
  74	GIRNKSSSSS	17
  90	VVTEDDEAQD	17
  121	VLPHTNGVGP	17
  138	LLKSQAASGT	17
  27	NILRGGLSEI	16
  100	SIDPPESPDR	16
  110	ALKAANSWRN	16
  168	KLETIILSKL	16
  171	TIILSKLTQE	16
  5	VILDLSVEVL	15
  8	DLSVEVLASP	15
  26	ANILRGGLSE	15
  37	VLPIEWQQDR	15
  135	LLRLLKSQAA	15
  147	TLSLAFTSWS	15
  149	SLAFTSWSLG	15
  159	EFLGSGTWMK	15
  175	SKLTQEQKSK	15
  38	LPIEWQQDRK	14
  47	KIPPLSTPPP	14
  103	PPESPDRALK	14
  109	RALKAANSWR	14
  131	LWEFLLRLLK	14
  127	GVGPLWEFLL	13
  143	AASGTLSLAF	13

  V8-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 17; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  5	FLEEGMGGTI	19

  V13-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 27; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  10	FLPNGINGIK	22
  5	SLSETFLPNG	12

  V14-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 29; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  6	RLFTFWRGPV	16
  4	PLRLFTFWRG	14
  1	ENLPLRLFTF	13
  2	NLPLRLFTFW	12
  9	TFWRGPVVVA	11
  3	LPLRLFTFWR	10
  10	FWRGPVVVAI	10
  8	FTFWRGPVYV	9
  7	LFTFWRGPVV	7

  V21-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 43; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  3	KLTQEQKTKH	18
  2	SKLTQEQKTK	17

  V25-HLA-A3-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 51; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  2	ILFLPCISQK	29
  4	FLPCISQKLK	20
  7	CISQKLKRIK	18
  1	IILFLPCISQ	14

  V1-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 3; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  216	VVVALISLATF	27
  296	ETWLQCRKQL	27
  200	EIENLPLRLF	26
  147	NVVSAWALQL	25
  351	EEEVWRIEMY	25
  202	ENLPLRLFTL	24
  56	VVIGSRNPKF	23
  127	ESNAEYLASL	23
  427	YTPPNFVLAL	23
  440	SIVILDLLQL	23
  45	LTIRLIRCGY	22
  234	DVIHPYARNQ	22
  253	EIVNKTLPIV	22
  260	PLVALITLLSL	22
  329	ERYLFLNMAY	21
  15	ETCLPNGING	20
  32	TVGVIGSGDF	20
  98	YTSLWDLRHL	20
  353	EVWRIEMYIS	20
  68	EFFPHVYDVT	19
  75	DVTHIIEDALT	19
  115	DVSNNMRINQ	19
  186	NFIPIDLGSL	19
  230	SFVRDVIHPY	19
  257	KTLPIVAITL	19
  314	MVHVAYSLCL	19
  364	GIMSLGLLSL	19
  404	LISTFHVLIY	19
  217	VVAISLATFF	18
  359	MYTSFGIMSL	18
  399	GYVALLISTF	18
  441	IVILDLLQLC	18
  2	ESISMMGSPK	17
  30	KVTVGVIGSG	17
  40	DFAKSLTIRL	17
  81	DALTKTNJIF	17
  263	AITLLSLVYL	17
  406	STFHVLIYGW	17
  177	QVIELARQLN	16
  215	PVVVAISLAT	16
  269	LVYLAGLLAA	16
  435	ALVLPSIVIL	16
  436	LVLPSIVILD	16
  34	GVIGSGDFAK	15
  72	HVVDVTHHED	15
  116	VSNNMRJNQY	15
  142	IVKGFNVVSA	15
  199	REIENLPLRL	15
  250	IPIEIVNKTL	15
  261	IVATTLLSLV	15
  262	VAITLLSLVY	15
  310	FFFAMVIIVAY	15
  377	TSIPSVSNAL	15
  389	REFSFIQSTL	15
  391	FSFIQSTLGY	15
  432	FVLALVLPSI	15
  31	VTVGVIGSGD	14
  55	HVVIGSRNPK	14
  89	IFVAIHREHY	14
  103	DLRHLLVGKI	14
  108	LVGKILIDVS	14
  148	VVSAWALQLG	14
  222	LATFFFLYSF	14
  301	CRKQLGLLSF	14
  352	EEVWRIEMYI	14
  362	SFGIMSLGLL	14
  417	RAFEEEYYRF	14
  437	VLPSIVILDL	14
  443	ILDLLQLCRY	14
  27	DARKVTVGVI	13
  74	VDVTHHFDAL	13
  92	ALHREHYTSL	13
  137	FPDSLIVKGF	13
  172	IQARQQVIEL	13
  176	QQVIELARQL	13
  178	VIELARQLNF	13
  218	VAISLATFFF	13
  223	ATFFFLYSFV	13
  258	TLPIVAITLL	13
  299	LQCRKQLGLL	13
  302	RKQLGLLSFF	13
  358	EMYISFUIMS	13
  361	ISFGIMSLGL	13
  365	IMSLGLLSLL	13
  375	AVTSLPSVSN	13
  376	VTSIPSVSNA	13
  395	QSTLGYVALL	13
  410	VLIYGWKRAF	13

• [1260]

  TABLE XXXVIII
  Pos	1234567890	score

  V2-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 3; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  17	FTPFSCLSLP	13
  16	GFTPFSCLSL	12
  35	PPCPADFFLY	11
  2	GSPGLQALSL	10
  4	PGLQALSLSL	10
  14	SSGFTPFSCL	10
  22	CLSLPSSWDY	10
  8	ALSLSLSSGF	9
  11	LSLSSGFTPF	9
  32	RCPPPCPADF	9
  33	CPPPCPADFF	9
  36	PCPADFFLYF	9
  30	DYRCPPPCPA	8
  34	PPPCPADFFL	8
  7	QALSLSLSSG	7
  18	TPFSCLSLPS	7
  3	SPGLQALSLS	6

  V5A-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  1	ENLPLRLFTF	24
  8	FTFWRGPVVV	12

  V5B-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  16	DTQTELELEF	25
  22	ELEFVFLLTL	24
  24	EFVFLLTLLL	23
  20	ELELEFVFLL	22
  18	QTELELEFVF	16
  23	LEFVFLLTLL	16
  4	EFSFIQIFCS	14
  5	FSFIQIFCSF	13
  2	WREFSFIQIF	12
  12	CSFADTQTEL	12

  V6-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 13; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  6	IVILGKIILF	27
  5	SIVILGKIIL	18
  38	EGIGGTIPHV	18
  7	VILGKIILFL	17
  1	LVLPSIVILG	16
  46	HVSPERVTVM	15
  42	GTIPHVSPER	13

  V7A-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  8	ETFLPNGING	24

  V7B-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  9	QSTLGYVALL	13
  5	MAYQQSTLGY	11
  3	LNMAYQQSTL	10
  10	STLGYVALLI	10
  8	QQSTLGYVAL	9

  V7C-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  170	ETIILSKLTQ	24
  12	EVLASPAAAW	21
  35	EIVLPIEWQQ	19
  102	DPPESPDRAL	19
  127	GVGPLWEFLL	19
  5	VILDLSVEVL	17
  152	FTSWSLGEFL	17
  69	EAQESGIRNK	16
  105	ESPDRALKAA	16
  89	GVVTEDDEAQ	15
  133	EFLLRLLKSQ	15
  151	AFTSWSLGEF	15
  3	SLVILDLSVE	14
  4	IVILDLSVEV	14
  45	DRKIPPLSTP	14
  86	PVVGVVTEDD	14
  90	VVTEDDEAQD	14
  99	DSIDPPESPD	14
  130	PLWEFLLRLL	14
  168	KLETIILSKL	14
  171	TIILSKITQE	14
  8	DLSVEVLASP	13
  42	WQQDRKIPPL	13
  93	LiDDEAQDSID	13
  122	LPHTNGVGPL	13
  125	TNGVGPLWEF	13
  129	GPLWEFLLRL	13
  10	SVEVLASPAA	12
  36	IVLPIEWQQD	12
  72	ESGIRINKSSS	12
  95	DEAQDSIDPP	12
  120	PVLPHTNGVG	12
  126	NGVGPLWEFL	12
  41	EWQQDRKJPP	11
  60	WTEEAGATAE	11
  62	EFAGATAEAQ	11
  63	EAGATAEAQE	11
  66	ATAFAQESGI	11
  96	EAQDSIDPPE	11
  141	SQAASGTLSL	11
  159	EFLGSGTWMK	11
  180	EQKSKHCMFS	11

  V8-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 17; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  8	EGMGGTIPHV	14
  7	EEGMGGTIPH	11
  1	EKSQFLEEGM	10
  3	SQFLEEGMGG	6

  V13-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 27; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  8	ETFLPNGING	24

  V14-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 29; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  1	ENLPLRLFTF	24
  8	FTFWRGPVVV	12

  V21-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 43; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  4	LTQEQKTKHC	10
  7	EQKTKHCMFS	10
  8	QKTKHCMFSL	10
  6	QEQKTKHCMF	9
  9	KTKHCMFSLI	9

  V25-HLA-A26-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 51; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  2	ILFLPCISQK	10
  3	LFLPCISQKL	10
  6	PCISQKLKRI	9
  1	IILFLPCISQ	6
  9	SQKLKRIKKG	6
  7	CISQKLKRIK	4

• [1261]

  TBALE XXXIX
  Pos	1234567890	score

  V1-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 3; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  429	PPNFVLALVL	23
  438	LPSIVILDLL	22
  9	SPKSLSETCL	21
  250	IPIEIVNKTL	21
  323	LPMRRSERYL	21
  137	FPDSLIVKGF	18
  428	TPPNFVLALV	17
  125	YPESNAEYLA	16
  214	GPVVVAISLA	16
  219	AISLATFFFL	16
  394	IQSTLGYVAL	16
  36	IGSGDFAKSL	15
  197	SARE1ENLPL	15
  325	MRRSERYLFL	15
  361	ISFGIMSLGL	15
  379	IPSVSNALNW	15
  427	YTPPNEVLAL	15
  211	LWRGPVVVAI	14
  263	AITLLSLVYL	14
  402	ALLISTFHVL	14
  435	ALVLPSIVIL	14
  40	DFAKSLTIRL	13
  92	AIHREHYTSL	13
  127	ESNAEYLASL	i3
  172	IQARQQVIEL	13
  188	IP17DLGSLSS	13
  195	LSSAREIENL	13
  199	REIENLPLRL	13
  204	LPLRLFTLWR	13
  259	LPIVAITLLS	13
  260	PIVAITLLSL	13
  266	LLSLVYLAGL	13
  290	RFPPWLETWL	13
  364	GLMSLGLLSL	13
  365	TMSLGLLSLL	13
  4	ISMMGSPKSL	12
  18	LPNGINGIKD	12
  70	FPHVVDVTHH	12
  98	YTSLWDLRHL	12
  142	IVKGFNVVSA	12
  147	NVVSAWALQL	12
  157	GPKDASRQVY	12
  202	ENLPLRLFTL	12
  257	KTLPIVAITL	12
  6273	AGLLAAAYQL	12
  292	PPWLETWLQC	12
  296	ETWLQCRKQL	12
  298	WLQCRKQLGL	12
  314	MVHVAYSLCL	12
  377	TSIPSVSNAL	12
  395	QSTLGYVALL	12
  425	RFYTPPNFVL	12
  437	VLPSIVILDL	12
  440	SIVILDLLQL	12
  26	KDARKVTVGV	11
  27	DARKVTVGVI	11
  49	LIRCGYHVVI	11
  62	NPKFASEFFP	11
  74	VDVTHHEDAL	11
  95	REHYTSLWDL	11
  99	TSLWDLRIILL	11
  132	YLASLFPDSL	11
  145	GFNVVSAWAL	11
  183	RQLNFIPIDL	11
  186	NFIPIDLGSL	11
  201	IENLPLRIFT	11
  213	RGPVVVAISL	11
  237	HPYARNQQSD	11
  252	IEIVNKTLPI	11
  258	TLPIVAITLL	11
  286	TKYRRFPPWL	11
  291	FPPWLETWLQ	11
  312	FAMVHVAYSL	11
  362	SFGIMSLGLL	11
  389	REFSFIQSTL	11

  V2-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 5; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  34	PPPCPADFFL	21
  33	CPPPCPADFF	18
  2	GSPGLQALSL	14
  16	GFTPFSCLSL	13
  18	TPFSCLSLPS	13
  4	PGLQALSLSL	12
  14	SSGFTPFSCL	12
  25	LPSSWDYRCP	12
  35	PPCPADFFLY	12
  3	SPGLQALSLS	11
  8	ALSLSLSSGF	10
  36	PCPADFIFLYF	10

  V5A-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  10	FWRGPVVVAI	14
  3	LPLRIFTFWR	11
  9	TFWRGPVVVA	10
  6	RLFTFWRGPV	9
  8	FTFWRGPVVV	9
  1	ENLPLRLFTF	8
  7	LFTFWRGPVV	8

  V5B-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  19	TELELEFVFL	14
  24	EFVFLLTLLL	14
  14	FADIQIELEL	13
  22	ELEFVFLLTL	13
  12	CSFADTQTEL	12
  20	ELELEFVFLL	12
  23	LEFVFLLTLL	11
  1	NWREFSFIQI	9
  8	IQIFCSFADT	9
  21	LELEFVFLLT	9
  10	IFCSFADTQT	8
  16	DTQTELELEF	8
  5	FSFIQIFCSF	7
  6	SFIQIFCSFA	7
  17	TQTELELEFV	7
  18	QTELELEFVF	7
  2	WREFSFIQIF	6

  V6-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 13; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  3	LPSIVILGKI	18
  44	IPHVSPERVT	18
  7	VILGKIILFL	15
  27	KKGWEKSQFL	13
  16	LPCISRKLKR	12
  46	HVSPERVTVM	12
  14	LFLPCISRKL	11
  5	SIVILGKIIL	10
  38	EGIGGTIPHV	10
  26	IKKGWEKSQF	9
  31	EKSQFLEEGI	9
  45	PHVSPERVTV	9

  V7A-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  2	SPKSLSETFL	22
  8	QQSTLGYVAL	15
  3	LNMAYQQSTL	12
  9	QSTLGYVALL	12
  10	STLGYVALLI	10
  6	AYQQSTLGYV	8
  7	YQQSTLGYVA	7

  V7C-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  122	LPHTNGVGPL	22
  129	GPLWEFLLRL	22
  102	DPPESPDRAL	21
  49	PPLSTPPPPA	18
  55		PPPAMWTEEA	18
  119	NPVLPHTNGV	17
  141	SQAASGTLSL	15
  143	AASGTLSLAF	15
  29	LRGGLSEIVL	14
  113	AANSWRNPVL	14
  15	ASPAAAWKCL	13
  48	LPPLSTPPPP	13
  85	IPVVGVVTED	13
  106	SPDRALKAAN	13
  126	NGVGPLWEFL	13
  152	FTSWSLGEFL	13
  165	TWMKLETIIL	13
  181	QKSKHCMFSL	13
  1	LPSIVILDLS	12
  5	VILDLSVFVL	12
  16	SPAAAWKCLG	12
  20	AWKCLGANIL	12
  24	LGANTLRGGL	12
  42	WQQDRKIPPL	12
  54	PPPPAMWTEE	12
  56	PPAMWTEEAG	12
  103	PPESPDRALK	12
  127	GVGPLWEFLL	12
  139	LKSQAASGTL	12
  28	ILRGGLSEIV	11
  44	QDRKIPPLST	11
  53	TPPPPAMWTE	11
  81	SSSQIPVVGV	11
  104	PESPDRALKA	11
  144	ASGTLSLAFT	11
  148	LSLAFTSWSL	11
  160	FLUSGTWMKL	11
  168	KLETIILSKL	11
  6	ILDLSVEVLA	10
  17	PAAAWKCLGA	10
  19	AAWKCLGANI	10
  31	GGLSEIVLPI	10
  38	LPIEWQQDRK	10
  50	PLSTPPPPAM	10
  78	KSSSSSQIPV	10
  79	SSSSSQIPVV	10
  83	SQIPVVGVVT	10
  112	KAANSWRNPV	10
  130	PLWEFLLRLL	10

  V8-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 17; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  8	EGMGGTIPHV	11
  1	EKSQFLEEGM	9
  4	QFLEEGMGGT	6
  5	FLEEGMGGTI	6

  V13-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 27; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  2	SPKSLSETFL	22

  V14-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 29; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  10	FWRGPVVVAI	14
  3	LPLRLFTFWR	11
  9	TFWRGPVVVA	10
  6	RLFTFWRGPV	9
  8	FTFWRGPVVV	9
  1	ENLPLRLFTF	8
  7	LFTFWRGPVV	8

  V21-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 43; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  8	QKTKHCMFSL	11
  9	KTKHCMFSLI	8
  6	QEQKTKHCMF	7
  1	LSKITQEQKT	6
  5	TQEQKTKHCM	6

  V25-HLA-B0702-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 51; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  5	LPCISQKLKR	12
  3	LFLPCISQKL	11
  6	PCISQKLKRI	6

• [1262]

  TABLE XL
  Pos	1234567890	score

  V1-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V2-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V5A-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V5B-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V6-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V7A-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V7B-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V7C-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V8-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V13-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V14-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V21-HLA-B08-10mers-98P4B6

  NoResultsFound.

  V25-HLA-B08-10mers-98P4B6

  NoResultsFound.

• [1263]

  TABLE XLI
  Pos	1234567890	score

  V1-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V2-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V5A-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V5B-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V6-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V7A-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V7B-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V7C-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V8-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V13-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V14-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V21-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V25-HLA-B1510-10mers-98P4B6

  NoResultsFound.

  V1-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V2-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V5A-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V5B-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V6-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V7A-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V7B-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V7C-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V8-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V13-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V14-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V21-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V25-HLA-B2705-10mers-98P4B6

  NoResultsFound.

  V1-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V2-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V5A-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V5B-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V6-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V7A-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V7B-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V7C-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V8-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V13-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V14-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V21-HLA-B2709-10mers-98P4B6

  NoResultsFound.

  V25-HLA-B2709-10mers-98P4B6

  NoResultsFound.

• [1264]

  TABLE XLIV
  Pos	1234567890	score

  V1-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 3; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  199	REIENLPLRL	25
  351	EEEVWRIEMY	25
  252	IEIVNKTLPI	23
  389	REFSFIQSTL	23
  95	REHYTSLWDL	21
  179	IELARQLNFI	21
  352	EEVWRIEMYI	20
  79	HEDALTKTNI	19
  377	TSIPSVSNAL	19
  186	NFIPIDLGSL	18
  202	ENLPLRLFTL	18
  257	KTLPIVAITL	18
  427	YTPPNEVLAL	18
  435	ALVLPSIVIL	18
  273	AGLLAAAYQL	17
  289	RRFPPWLETW	17
  296	ETWLQCRKQL	17
  402	ALLISTFHVL	17
  16	TCLPNG1NGI	16
  116	VSNNMRINQY	16
  200	EIENLPLRLF	16
  219	AISLATFFFL	16
  230	SFVRDVIHPY	16
  250	IPIEIVNKTL	16
  262	VAITLLSLVY	16
  263	AITLLSLVYL	16
  359	MYISFGIMSL	16
  406	STFHVLIYGW	16
  410	VLIYGWKRAF	16
  36	IGSGDFAKSL	15
  45	LTIRLIRCGY	15
  56	VVIGSRNPKF	15
  60	SRNPKFASEF	15
  67	SEFFPHVVDV	15
  126	PESNAEYLAS	15
  130	AEYLASLFPD	15
  203	NLPLRLFTLW	15
  255	VNKTLPIVAI	15
  258	TLPIVAITLL	15
  279	AYQLYYGTKY	15
  310	FFFAMVHVAY	15
  329	ERYLFLNMAY	15
  394	IQSTLGYVAL	15
  437	VLPSIVILDL	15
  4	ISMMGSPKSL	14
  92	AIHREHYTSL	14
  98	YTSLWDLRHL	14
  99	TSLWDLRHLL	14
  123	NQYPESNAFY	14
  137	FPDSLLVKGF	14
  147	NVVSAWALQL	14
  183	RQLNFIPIDL	14
  195	LSSAREIENL	14
  218	VAISLATFFF	14
  271	YLAGLLAAAY	14
  290	RFPPWLETWL	14
  346	ENSWNEEEVW	14
  361	ISFGIMSLGL	14
  365	IMSLGLLSLL	14
  391	FSFI STLGY	14
  396	STLGYVALLI	14
  399	GYVALLISTF	14
  404	LISTFHVLIY	14
  418	AFEEEYYRFY	14
  420	EEEYYRFYTP	14
  440	SIVILDLLQL	14
  41	FAKSLTIRLI	13
  74	VDVTHHEDAL	13
  80	EDALTKTNII	13
  81	DALTKTNIIF	13
  84	TKTNIIFVAI	13
  104	LRHLLVGKIL	13
  127	ESNAEYLASL	13
  128	SNAEYLASLF	13
  143	VKGFNVVSAW	13
  145	GFNVVSAWAL	13
  157	GPKDASRQVY	13
  170	NNTQARQQVI	13
  172	IQARQQVLEL	13
  176	QQVIEILARQL	13
  201	IENLPLRLFT	13
  211	LWRGPVVVAI	13
  213	RGPVVVAISL	13
  220	ISLATFFFLY	13
  245	SDFYKIPIEI	13
  266	LLSLVYLAGL	13
  267	LSLVYLAGLL	13
  299	LQCRKQLGLL	13
  303	KQLGLLSFFF	13
  323	LPMRRSERYL	13
  324	PMRRSERYLF	13
  328	SERYLFLNMA	13
  350	NEEEVWRIEM	13
  362	SFGIMSLGLL	13
  364	GIMSLGLLSL	13
  379	IPSVSNALNW	13
  384	NALNWREFSF	13
  395	QSTLGYVALL	13
  403	LLISTFHVLI	13
  429	PPNEVLALVL	13
  438	LPSIVILDLL	13
  443	ILDLLQLCRY	13
  38	SGDFAKSLTI	12
  40	DFAKSLTIRL	12
  93	IHREHYTSLW	12
  105	RHLLVGKILI	12
  124	QYPESNAEYL	12
  178	VIELARQLNF	12
  192	LGSLSSAREI	12
  197	SAREIENLPL	12
  216	VVVAISLATF	12
  260	PIVAITLLSL	12
  274	GLLAAAYQLY	12
  282	LYYGTKYRRF	12
  286	TKYRRFPPWL	12
  295	LETWLQCRKQ	12
  301	CRKQLGLLSF	12
  302	RKQLGLLSFF	12
  312	FAMVHVAYSL	12
  357	IEMYISFGIM	12
  385	ALNWREFSFI	12
  417	RALFEEEYYRF	12
  421	EEYYRFYTPP	12
  425	RFYTPPNFVL	12

  V2-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 5; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  8	ALSLSLSSGF	15
  32	RCPPPCPADF	15
  33	CPPPCPADFF	15
  35	PPCPADFFLY	15
  2	GSPGLQALSL	14
  16	GFTPFSCLSL	14
  36	PCPADFFLYF	13
  4	PGLQALSLSL	12
  11	LSLSSGFTPF	12
  14	SSGFTPPFSCL	12
  20	FSCLSLPSSW	12
  22	CLSLPSSWDY	12
  34	PPPCPADFFL	11

  V5a-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  1	ENLPLRLFTF	18
  2	NLPLRLFTFW	14
  10	FWRGPVVVAI	13

  V5B-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 11; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  23	LEFVFLLTLL	24
  19	TELELEFVFL	23
  20	ELELEFVFLL	15
  22	ELEFVFLLTL	15
  24	EFVFLLTLLL	15
  21	LELEFVFLLT	14
  2	WREFSFIQIF	13
  3	REFSFIQIFC	13
  5	FSFIQIFCSF	13
  14	FADTQTELEL	13
  1	NWREFSFIQI	12
  12	CSFADTQTEL	12
  16	DTQTELELEF	12
  18	QTELELEFVF	12

  V6-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 13; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  6	IVLLGKIILF	19
  7	VILGKIILFL	16
  14	LFLPCISRKL	16
  17	PCISRKLKRI	14
  37	EEGIGGTLPH	14
  4	PSIVILGKIL	13
  21	RKLKRIKKGW	13
  5	SIVILGKLIL	12
  10	GKIILFLPCI	12
  26	IKKGWEKSQF	12
  3	LPSIVILGKI	11
  27	KKGWEKSQFL	11
  30	WEKSQFLEEG	11
  31	EKSQFLEEGI	11
  36	LEEGIGGTW	11
  35	FLEEGIGGTI	9
  38	EGIGGTWHV	9

  V7a-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  9	TFLPNGINGI	16
  1	GSPKSLSETF	12
  2	SPKSLSETFL	11
  6	LSETFLPNGI	11
  7	SETFLPNGIN	11

  V7B-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  8	QQSTLGYVAL	16
  10	SILGYVALLI	14
  9	QSTLGYVALL	13
  3	LNMAYQQSTL	12
  5	MAYQQSTLGY	12

  V7C-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 15; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  92	TEDDEAQDSI	20
  179	QEQKSKIICMF	20
  143	AASGTLSLAF	18
  34	SEIVLPIEWQ	17
  104	PESPDRALKA	17
  12	EVLASPAAAW	16
  15	ASPAAAWKCL	16
  62	EFAGATAEAQ	16
  132	WIBFLLRLLKS	16
  20	AWKCLGANIL	15
  5	VILDLSVEVL	14
  11	VEVLASPAAA	14
  42	WQQDRKJPPL	14
  51	LSTPPPPAMW	14
  68	AEAQESGIRN	14
  71	QESGIRNKSS	14
  102	DPPESPDRAL	14
  113	AANSWRNPVL	14
  127	GVGPLWEFLL	14
  151	AFTSWSLGEF	14
  168	KLETIILSKL	14
  29	LRGGLSEIVL	13
  40	IEWQQDRKTP	13
  95	DEAQDSIDPP	13
  108	DRALKAANSE	13
  129	GPLWEFLLRL	13
  130	PLWEFLLRLL	13
  141	SQAASGTLSL	13
  158	GEFLGSGTWM	13
  165	TWMKLETIIL	13
  169	LETIILSKLT	13
  24	LGANILRGGL	12
  27	NILRGGLSEI	12
  33	LSEIVLPIEW	12
  122	LPHTNGVGPL	12
  123	PHTNGVGPLW	12
  126	NGVGPLWEFL	12
  139	LKSQAASGTL	12
  146	GTLSLAFTSW	12
  19	AAWKCLGANI	11
  31	GGLSEIVLPI	11
  61	TEEAGATAEA	11
  66	ATAEAQESGI	11
  125	TNGVGPLWEF	11
  148	LSLAFTSWSL	11
  152	FTSWSLGEFL	11
  157	LGEFLGSGTW	11
  160	FLGSGTWMKL	11
  163	SGTWMKLETI	11
  181	QKSKHCMFSL	11
  182	KSKHCMIFSLI	11
  39	PIEWQQDRKI	10
  76	RNKSSSSSQI	9
  83	SQIPVVGVVT	9
  105	ESPDRALKAA	9

  V8-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 17; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  7	EEGMGGTIPH	14
  6	LEEGMGGTIP	11
  5	FLEEGMGGTI	9
  8	FGMGGTIPHV	7

  V13-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 27; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  9	TFLPNGINGI	16
  1	GSPKSLSETF	12
  2	SPKSLSETFL	11
  6	LSETFLPNGI	11
  7	SETFLPNGIN	11

  V14-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 29; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  1	ENLPLRLFTF	18
  2	NLPLRLFTFW	14
  10	FWRGPVVVAI	13

  V21-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 43; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  6	QEQKTKHCMF	20
  9	KTKHCMFSLI	11
  8	QKTKHCMFSL	10

  V25-HLA-B4402-10mers-98P4B6

  Each peptide is a portion of SEQ ID

  NO: 51; each start position is specified,

  the length of peptides is 10 amino acids,

  and the end position for each peptide

  is the start position plus nine.

  3	LFLPCISQKL	15
  6	PCISQKLKRI	14
  10	QKLKIUKKGW	13
  9	SQKLKRIKKG	8
  2	ILFLPCISQK	7

• [1265]

  TABLE XLV
  Pos	1234567890	score

  V1-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V2-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V2-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V5A-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V5B-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V6-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V7A-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V7B-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V7C-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V8-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V13-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V21-HLA-B5101-10mers-98P4B6
  NoResultsFound.
  V25-HLA-B5101-10mers-98P4B6
  NoResultsFound.

• [1266]

  TABLE XLVI
  Pos	123456789012345	score

  V1-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  143	VKGFNVVSAWALQLG
  266	LLSLVYLAGLLAAAY	33
  367	SLGLLSLLAVTSIPS	32
  1	MESISMMGSPKSLSE	31
  130	AEYLASLFPDSLIVK	30
  30	KVTVGVIGSGDFAKS	29
  431	NFVLALVLPSIVILD	29
  206	LRLFTLWRGPVVVAI	28
  215	PVVVAISLATFFFLY	28
  370	LLSLLAVTSIPSVSN	28
  438	LPSIVILDLLQLCRY	28
  101	LWDLRHLLVGKILID	27
  185	LNFIPIDLGSLSSAR	27
  356	RIEMYISFGIMSLGL	27
  360	YISFGIMSLGLLSLL	27
  397	TLGYVALLISTFHVL	27
  421	EEYYRFYTPPNFVLA	27
  38	SGDFAKSLTRLIRC	26
  102	WDLRHLLVGKILIDV	26
  122	INQYPESNAEYLASL	26
  149	VSAWALQLGPKDASR	26
  244	QSDFYKTPIEIVNKT	26
  249	KIPIEIYNKTLPIVA	26
  256	NKTLPIVAITLLSLV	26
  261	LVAITLLSLVYLAGL	26
  298	WLQCRKQLGLLSFFF	26
  368	LGLLSLLAVTSIPSV	26
  109	VGKILIDVSNNMRIN	25
  137	FPDSLIVKGFNVVSA	25
  145	GFNVVSAWALQLGPK	25
  198	AREIENLPLRLFTLW	25
  222	LATFFFLYSFVRDVI	25
  252	IEIVNKTLPIVAITL	25
  264	ITLLSLVYLAGLLAA	25
  302	RKQLGLLSFFFAMVH	25
  309	SFFFAMVHVAYSLCL	25
  354	VWRJEMYISFGIMSL	25
  362	SFGIMSLGLLSLLAV	25
  365	IMSLGLLSLLAVTSI	25
  51	RCGYHVVIGSRNPKLF	24
  98	YTSLWDLRHLLVGKJ	24
  106	HLLVGKILIDVSNNM	24
  150	SAWALQLGPKDASRQ	24
  184	QLNFIPIDLGSLSSA	24
  205	PLRLFTLWRGPVVVA	24
  229	YSFVRDVIHPYARNQ	24
  269	LVYLAGLLAAAYQLY	24
  330	RYLFLNMAYQQVHAN	24
  335	NMAYQQVHANTENSW	24
  388	WREFSFIQSTLGYVA	24
  391	FSFIQSTLGYVALLL	24
  398	LGYVALLISTFHVLI	24
  427	YTPPNFVLALVLPSI	24
  430	PNFVLALVLPSIVIL	24
  52	CGYHVVIGSRNPKFA	23
  55	HVVIGSRNPKLFASEF	23
  186	NFIPIDLGSLSSARE	23
  214	GPVVVAISLATFFFL	23
  258	TLPIVAITLLSLVYL	23
  351	EEEVWRIEMYISFGI	23
  352	EEVWPJEMYISFGIM	23
  127	ESNAEYLASLFPDSL	22
  178	VIELARQLNFIPIDL	22
  189	PIDLGSLSSARFIEN	22
  211	LWRGPVVVAISLATF	22
  216	VVVAISLATFFFLYS	22
  255	VNKTLPIVAITLLSL	22
  301	CRKQLGLLSFFFAMV	22
  312	FMAVHVAYSLCLPMR	22
  359	MYISFGIMSLGLLSL	22
  364	GIMSLGLLSLLAVTS	22
  395	QSTLGYVALLISTFH	22
  432	FVLALVLPSIVILDL	22
  435	ALVLPSIVILDLLQL	22
  20	NGINGIKDARKVTVG	21
  117	SNNMRTNQYPESNAE	21
  161	ASRQVYICSNNIQAR	21
  174	ARQQVIELARQLNEI	21
  277	AAAYQLYYGTKYRRF	21
  373	LLAVTSPSVSNALN	21
  399	GYVALLISTFHVLIY	21
  407	TFHVLIYGWKRAFEE	21
  31	VTVGVIGSGDFAKSL	20
  142	IVKGFNVVSAWALQL	20
  209	FTLWRGPVVVAISLA	20
  346	ENSWNEEEVWRIEMY	20
  385	ALNWREFSFIQSTLG	20
  429	PPNFVLALVLPSIVI	20
  45	LTIRLIRCGYHVVIG	19
  80	EDALTKTNIIFVAIH	19
  95	REHYTSLWDLRHLLV	19
  135	SLFPDSLIVKGFNVV	19
  139	DSLIVKGFNVVSAWA	19
  224	TFFFLYSFVRDVIHP	19
  259	LPIVAITLLSLVYLA	19
  280	YQLYYGTKYRRFPPW	19
  281	QLYYGTKYRRLFPPWL	19
  288	YRRFPPWLETWLQCR	19
  307	LLSFFFAMVHVAYSL	19
  322	CLPMRRSERYLFLNM	19
  328	SERYLFLNMAYQQVH	19
  357	IEMYISFGIMSLGLL	19
  400	YVALLISTFHVLIYG	19
  424	YRFYTPPNFVLALVL	19
  7	MGSPKSLSETCLPNG	18
  25	IKDARKVTVGVIGSG	18
  27	DARKVTVGVIGSGDF	18
  39	GDFAKSLTIRLIRCG	18
  47	IRLIRCGYHVVIGSR	18
  62	NPKFASEFFPHVVDV	18
  129	NAEYLASLFPDSLW	18
  163	RQVYICSNNIQARQQ	18
  167	ICSNNIQARQQVIEL	18
  179	IELARQLNFIPIDLG	18
  190	IDLGSLSSAREIENL	18
  236	IHPYARNQQSDFYKI	18
  267	LSLVYLAGLLAAAYQ	18
  268	SLVYLAGLLAAAYQL	18
  285	GTKYRRFPPWLETWL	18
  296	ETWLQCRKQLGLLSF	18
  299	LQCRKQLGLLSFFFA	18
  326	RRSERYLFLNMAYQQ	18
  380	PSVSNALNWREFSFI	18
  383	SNALNWREFSFIQST	18
  390	EFSFIQSTLGYVALL	18
  405	ISTFHVLLYGWKRAF	18
  410	VLIYGWKRAFEEFYY	18
  423	YYRFYTPPNFVLALV	18
  433	VLAIVLPSIVILDLL	18
  22	INGIKDARKVTVGVI	17
  29	RKVTVGVIGSGDFAK	17
  33	VGVIGSGDFAKSLTI	17
  34	GVIGSGDFAKSLTIR	17
  44	SLTIRLIRCGYHVVI	17
  46	TIRLIRCGYHVVIGS	17
  54	YHVVIGSRNPKFASE	17
  58	IGSRNPKFASEFFPH	17
  77	THHEDALTKTNTIFV	17
  87	NIIFVAIHREHYTSL	17
  90	FVAIHREHYTSLWDL	17
  105	RHLLVGKILIDVSNN	17
  119	NMRINQYPESNAEYL	17
  138	PDSLIVKGFNVVSAW	17
  140	SLIVKGFNVVSAWAL	17
  151	AWALQLGPKDASRQV	17
  154	LQLGPKDASRQVYIC	17
  176	QQVIELARQLNFIPI	17
  187	FIPIDLGSLSSAREI	17
  195	LSSAREIENLPLRLF	17
  217	VVAISLATFFFLYSF	17
  226	FFLYSFVRDVIHPYA	17
  232	VRDVIHPYARNQQSD	17
  251	PIEIVNKTLPIVAIT	17
  253	EIVNKTLPIVAUTLL	17
  270	VYLAGLLAAAYQLYY	17
  271	YLAGLLAAAYQLYYG	17
  305	LGLLSFFFAMVHVAY	17
  316	HVAYSLCLPMRRSER	17
  317	VAYSLCLPMRRSERY	17
  329	ERYLFLNMAYQQVHA	17
  361	ISFGIMSLGLLSLLA	17
  363	FGIMSLGLLSLLAVT	17
  389	REFSFIQSTLGYVAL	17
  392	SFIQSTLGYVALLIS	17
  406	STFHVLIYGWKRAFE	17
  408	FHVLIYGWKRAFEFE	17
  436	LVLPSIVLLDLLQLC	17
  2	ESISMMGSPKSLSET	16
  3	SISMMGSPKSLSETC	16
  8	GSPKSLSETCLPNGI	16
  11	KSLSETCLPNGINGI	16
  16	TCLPNGNGIKDARK	16
  24	GIKDARKVTVGVIGS	16
  59	GSRNPKFASEFFPHV	16
  67	SEFFPHVVDVTHHED	16
  71	PHVVDVTHHEDALTK	16
  103	DLRIILLVGKJLIDVS	16
  111	KILIDVSNNMRIINQY	16
  126	PESNAEYLASLFPDS	16
  153	ALQLGPKDASRQVYI	16
  166	YICSNNIQARQQVIE	16
  171	NTQARQQVIIELARQL	16
  175	RQQVIELARQLNFIP	16
  182	ARQLNFIPIDLGSLS	16
  200	FIENLPLRLFTLWRG	16
  208	LFTLWRGPVVVAISL	16
  219	AISLATFFFLYSFVR	16
  225	FFFLYSFVRDVIHPY	16
  263	AITLLSLVYLAGLLA	16
  265	TLLSLVYLAGLLAAA	16
  294	WLETWLQCRKQLGLL	16
  304	QLGLLSFFFAMVHVA	16
  308	LSFFFAMVHVAYSLC	16
  310	FFFAMVHVAYSLCLP	16
  314	MVHVAYSLCLPMRRS	16
  371	LSLLAVTSIPSVSNA	16
  394	IQSTLGYVALLISTF	16
  401	VALLISTFHVLIYGW	16
  420	EEEYYRFYTPPNFVL	16
  428	TPPNFVLALVLPSIV	16
  440	SLVILDLLQLCRYPD	16

  V2-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  17	FTPFSCLSLPSSWDY	26
  28	SWDYRCPPPCPADFF	26
  6	LQALSLSLSSGFTPF	25
  8	ALSLSLSSGFTPFSC	25
  3	SPGLQALSLSLSSGF	24
  10	SLSLSSGFTPFSCLS	22
  14	SSGFTPFSCLSLPSS	19
  26	PSSWDYRCPPPCPAD	16
  31	YRCPPPCPADFFLYF	16
  1	SGSPGLQALSLSLSS	15
  4	PGLQALSLSLSSGFT	15
  20	FSCLSLPSSWDYRCP	15
  2	GSPGLQALSLSLSSG	14
  7	QALSLSLSSGFTPFS	14
  13	LSSGFTPFSCLSLPS	14
  16	GFTPFSCLSLPSSWD	14
  19	PFSCLSLPSSWDYRC	14
  27	SSWDYRCPPPCPADF	14
  30	DYRCPPPCPADFFLY	14

  V5A-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  11	LRLFTFWRGPVVVAI	28
  3	AREIENLPLRLFTFW	25
  16	FWRGPVVVAISLATF	22
  14	FTFWRGPVVVAISLA	20
  13	LFTFWRGPVVVAISL	18
  5	EIENLPLRLFTFWRG	16
  10	PLRLFTFWRGPVVVA	16
  12	RLFTFWRGPVVVAIS	15
  2	SAREIENLPLRLFTF	14
  7	ENLPLRLFTFWRGPV	14
  15	TFWRGPVVVAISLAT	14

  V5B-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  7	WREFSFIQIFCSFAD	25
  9	EFSFIQIFCSFADTQ	24
  4	ALNWREFSFIQIFCS	20
  2	SNALNWREFSFIQLF	18
  20	ADTQTELELEFVFLL	18
  8	REFSFIQTFCSFADT	17
  10	FSFIQIFCSFADTQT	17
  22	TQTELELEFVFLLTL	17
  23	QTELELEFVFLLTLL	17
  12	FIQIFCSFADTQTEL	16
  16	FCSFADTQTELELEF	16
  17	CSFADTQTELELEFV	14

  V6-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  1	NFVLALVLPSIVILG	29
  8	LPSIVILGKIILFLP	29
  46	GGTIPHVSPERVTVM	28
  17	LILFLPCISRKLKRI	26
  11	IVILGKIILFLPCIS	24
  38	SQFLEEGIGGTIPHV	24
  39	QFLEEGIGGTIPHVS	24
  7	VLPSIVILGKIILFL	23
  14	LGKIILFLPCISRKL	23
  2	FVLALVLPSIVILGK	22
  42	EEGIGGTIPHVSPER	22
  13	ILGKIILFLPCISRK	19
  3	VLALVLPSIVILGKI	18
  6	LVLPSIVILGKIILF	18
  9	PS1YILGKIILFLPC	17
  15	GKIILFLPCISRKLK	17
  5	ALVLPSLVILGKIIL	16
  10	SIVILGKIILFLPCI	16
  18	ILFLPCISRKLKRIK	15
  25	SRKLKRIKKGWEKSQ	15
  30	RIKKGWEKSQFLEEG	14
  43	EGIGGTIPHVSPFRV	14

  V7A-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  12	SETFLPNGINGIKDA	21
  5	MGSPKSLSETFLPNG	18
  1	SISMMGSPKSLSETF	16
  4	MMGSPKSLSETFLPN	16
  6	GSPKSLSETFLPNGI	16
  9	KSLSETFLPNGINGI	16
  14	TFLPNGTNGIKDARK	16
  2	ISMMGSPKSLSETFL	14
  15	FLPNGINGIKDARKV	13
  10	SLSETFLPNGINGIK	10

  V7B-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  4	RYLFLNMAYQQSTLG	24
  14	QSTLGYVALLISTFH	22
  7	FLNMAYQQSTLGYVA	21
  2	SERYLFLNMAYQQST	19
  9	NMAYQQSTLGYVALL	18
  3	ERYLFLNMAYQQSTL	17
  11	AYQQSTLGYVALLIS	17
  10	MAYQQSTLGYVALLI	16
  13	QQSTLGYVALLISTF	16
  8	LNMAYQQSTLGYVAL	14

  V7C-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  23	AAAWKCLGANILRGG	36
  168	SGTWMKLETIILSKL	35
  138	EFLLRLLKSQAASGT	33
  13	DLSVEVLASPAAAWK	30
  50	DRKIPPLSTPPPPAM	30
  28	CLGAMLRGGLSEIV	28
  62	PAMWTEEAGATAEAQ	27
  110	ESPDRALKAANSWRN	26
  124	NPVLPHTNGVGPLWE	26
  141	LRLLKSQAASGTLSL	25
  8	SIVILDLSVEVLASP	24
  31	ANTLRGGLSELVLPI	24
  42	VLPIEWQQDRKIPPL	24
  77	ESGIRNKSSSSSQIP	24
  130	TNGVGPLWEFLLRLL	24
  137	WEFLLRLLKSQAASG	24
  7	PSIVILDLSVEVLAS	23
  12	LDLSVEVLASPAAAW	23
  150	SGTLSLAETSWSLGE	23
  171	WMKLETIILSKLTQE	23
  3	ALVLPSIVILDLSVE	22
  53	IPPLSTPPPPAMWTE	22
  157	FTSWSLGEFLGSGTW	22
  89	QIIPVVGVVTEDDEAQ	21
  6	LPSIVILDLSVEVLA	20
  58	TPPPPAMWTEEAGAT	20
  97	TEDDEAQDSIDPPES	20
  100	DEAQDSIDPPESPDR	20
  134	GPLWEFLLRLLKSQA	19
  154	SLAFTSWSLGEFLGS	19
  1	VLALVLPSIVILDLS	18
  22	PAAAWKCLGANTLRG	18
  44	PIE WQQDRKIPPLST	18
  122	WRNPVLPHTNGVGPL	18
  135	PLWEFLLRLLKSQAA	18
  140	LLRLLKSQAASGTLS	18
  148	AASGTLSLAFTSWSL	18
  159	SWSLGEFLGSGTWMK	18
  161	SLGEFLGSGTWMKLE	18
  169	GTWMKLETIILSKLT	18
  176	TIILSKLTQEQKSKH	18
  4	LVLPSIVILDLSVEV	17
  9	IVILDLSVEVLASPA	17
  30	GANILRGGLSEIVLP	17
  61	PPAMWTEEAGATAEA	17
  67	EEAGATAEAQESGIR	17
  94	GVVTEDDEAQDSIDP	17
  101	EAQDSIDPPESPDRA	17
  107	DPPESPDRALKAANS	17
  133	VGPLWEFLLRLLKSQ	17
  143	LLKSQAASGTLSLAE	17
  162	LGEFLGSGTWMKLET	17
  163	GEFLGSGTWMKLETI	17
  172	MKLETIILSKLTQEQ	17

  V8-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  8	SQFLEEGMGGTLPHV	24
  9	QFLEEGMGGTWHVS	24
  12	EEGMGGTWHVSPER	22
  13	EGMGGTIPHVSPERV	14
  7	KS FLEEGMGGTIPH	13
  2	KKGWEKSQFLEEGMG	12
  6	EKSQFLEEGMGGTIP	12

  V13-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  12	SETFLPNGINGIKDA	21
  5	MGSPKSLSETFLPNG	18
  1	SISMMGSPKSLSETF	16
  4	MMGSPKSLSETFLPN	16
  6	GSPKSLSETFLPNGI	16
  9	KSLSETFLPNGINGI	16
  14	TFLPNGINGIKDARK	16
  2	ISMMGSPKSLSETFL	14
  15	FLPNGINGIKDARKV	13
  10	SLSETFLPNGINGIK	10

  V14-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  10	LRLFTFWRGPVVVAI	28
  2	AREIENLPLRLFTFW	25
  15	FWRGPVVVALISLATF	22
  13	FTFWRGPVVVAISLA	20
  12	LFTFWRGPVVVAISL	18
  4	EIENLPLRLFTFWRG	16
  9	PLRLFTFWRGPVVVA	16
  11	RLFTFWRGPVVVAJS	15
  1	SAREIENLPLRLFTF	14
  6	ENLPLRLFTFWRGPV	14
  14	TFWRGPVVVAISLAT	14
  8	LPLRLFTFWRGPVVV	12

  V21-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  3	TIILSKLTQEQKTKH	18
  2	ETIILSKLTQEQKTK	14
  7	SKLTQEQKTKHCMFS	13
  6	LSKLTQEQKTKHCMF	11
  11	QEQKTKHCMFSLISG	11
  1	LETIILSKLTQEQKT	10
  9	LTQEQKTKHCMFSLI	10
  10	TQEQKTKHCMFSLIS	9
  12	EQKTKHCMFSLISGS	9
  5	ILSKLTQEQKTKHCM	8
  8	KLTQEQKTKHCMFSL	8

  V25-HLA-DRB1-0101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  6	IILFLPCISQKLKRI	25
  3	LGKIILFLPCISQKL	23
  2	ILGKIILFLPCISQK	19
  4	GKIILFLPCISQKLK	17
  7	ILFLPCISQKLKRIK	15
  9	FLPCISQKLKRIKKG	15
  14	SQKLKRIKKGWEKSQ	15
  15	QKLKRIKKGWEKSQF	13

• [1267]

  TABLE XLVII
  Pos	123456789012345	score

  V1-HLA-DRB1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  97	HYTSLWDLRJJLLVGK	28
  176	QQVIELARQLNFIPI	27
  228	LYSFVRDVIHPYARN	27
  322	CLPMRRSERYLFLNM	27
  54	YHVVIGSRINPKFASE	26
  296	ETWLQCRKQLGLLSF	26
  408	FHVLLYGWKRAFEEE	26
  273	AGLLAAAYQLYYGTK	25
  439	PSIVILDLLQLCRYP	25
  109	VGKILIDVSNNMRIN	24
  288	YRRFPPWLETWLQCR	24
  87	NIIFVAIHREHYTSL	23
  423	YYRFYTPPNFVLALV	23
  133	LASLFPDSLIVKGFN	22
  185	LNFIPIDLGSLSSAR	22
  261	IVAITLLSLVYLAGL	22
  272	LAGLLAAAYQLYYGT	22
  433	VLALVLPSIVILDLL	22
  145	GFNVVSAWALQLGPK	21
  214	GPVVVAISLATFFFL	21
  269	LVYLAGLLAAAYQLY	21
  362	SFGTMSLGLLSLLAV	21
  363	FGIMSLGLLSLLAVT	21
  175	RQQVIELARQLNFIP	20
  198	AREIENLPLRLFTLW	20
  258	TLPIVAITLLSLVYL	20
  264	ITLLSLVYLAGLLAA	20
  376	VTSIPSVSNALNWRE	20
  400	YVALLISTFHVLIYG	20
  435	ALVLPSIVILDLLQL	20
  438	LPSLVILDLLQLCRY	20
  440	SIVILDLLQLCRYPD	20
  30	KVTVGVIGSGDFAKS	19
  53	GYHVVIGSRNPKFAS	19
  110	GMUDVSNNMRIINQ	19
  130	AEYLASLFPDSLIVK	19
  151	AWALQLGPKDASRQV	19
  215	PVVVAISLATFFFLY	19
  217	VVAISLATFFFLYSF	19
  256	NKTLPIVAITLLSLV	19
  312	FAMVIIVAYSLCLPM	19
  320	SLCLPMRRSERYLFL	19
  402	ALLISTFHVLIYGWK	19
  3	SISMMGSPKSLSETC	18
  22	INGIKDARKVTVGVI	18
  34	GVIGSGDFAKSLTIR	18
  90	FVAIHREHYTSLWDL	18
  119	NMRINQYPESNAEYL	18
  139	DSLIVKGFNVVSAWA	18
  143	VKGFNVVSAWALQLG	18
  162	SRQVYICSNNTQARQ	18
  184	QLNFIPIDLGSLSSA	18
  195	LSSAREIENLPLRLF	18
  233	RDVIHPYARNQQSDF	18
  308	LSFFFAMVHVAYSLC	18
  331	YLFLNMAYQQVHANI	18
  360	YISFGIMSLGLLSLL	18
  409	HVLIYGWKRAFEEEY	18
  7	MGSPKSLSETCLPNG	17
  21	GINGIKDARKVTVGV	17
  38	SGDFAKSLTIRLIRC	17
  113	LIDVSNNMRINQYPE	17
  121	RINQYPESNAEYLAS	17
  155	QLGPKDASRQVYICS	17
  169	SNNIQARQQVIELAR	17
  178	VIELARQLNFIPIDL	17
  192	LGSLSSAREIENLPL	17
  225	FFFLYSFVRDVIHPY	17
  249	KIPIEIVNKTLPIVA	17
  292	PPWLETWLQCRKQLG	17
  318	AYSLCLPMRRSERYL	17
  327	RSERYLFLNMAYQQV	17
  338	YQQVHANIENSWNEE	17
  379	IPSVSNALNWREFSF	17
  416	KRAFEEEYYRFYTPP	17
  15	ETCLPNGINGLKDAR	16
  72	HVVDVTHHEDALTKT	16
  79	HEDALTKTNTIFVAI	16
  88	ILFVAIHREHYTSLW	16
  111	KILIDVSNNMRTNQY	16
  205	PLRLFTLWRGPVVVA	16
  248	YKIPIEIVNKTLPIV	16
  279	AYQLYYGTKYRRFPP	16
  342	HANIENSWNEEEVWR	16
  382	VSNALNWREFSFIQS	16
  413	YGWKRAFEEEYYRFY	16
  43	KSLTIRLIRCGYHVV	15
  263	AITLLSLVYLAGLLA	15
  294	WLETWLQCRKQLGLL	15
  321	LCLPMkRSERYLFLN	15
  367	SLGLLSLLAVTSIPS	15
  387	NWREFSFIQSTLGYV	15
  412	IYGWKRAFEEEYYRF	15
  73	VVDVTHHEDALTKTN	14
  104	LRHLLVGKILIDVSN	14
  236	IHPYARNQQSDFYKI	14
  267	LSLVYLAGLLAAAYQ	14
  304	QLGLLSFFFAMVHVA	14
  365	IMSLGLLSLLAVTSI	14
  373	LLAVTSWSVSNALN	14
  401	VALLISTFHVLIYGW	14
  434	LALVLPSIVILDLLQ	14
  1	MESISMMGSPKSLSE	13
  4	ISMMGSPKSLSFTCL	13
  32	TVGVIGSGDFAKSLT	13
  33	VGVIGSGDFAKSLTI	13
  101	LWDLRHLLVGKILID	13
  138	PDSL1YKGFNVVSAW	13
  164	QVYICSNNIQARQQV	13
  189	PIDLGSLSSAREIEN	13
  201	IENLPLRLFTLWRGP	13
  213	RGPVVVAISLATFFF	13
  266	LLSLVYLAGLLAAAY	13
  407	TFHVLIYGWKRAEEE	13

  V2-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  6	LQALSLSLSSGFTPF	20
  14	SSGFTPFSCLSLPSS	20
  20	FSCLSLPSSWDYRCP	20
  24	SLPSSWDYRCPPPCP	16
  2	GSPGLQALSLSLSSG	12
  3	SPGLQALSLSLSSGF	12
  8	ALSLSLSSGFTPFSC	12
  9	LSLSLSSGFTPFSCL	12
  10	SLSLSSGFTPFSCLS	11
  22	CLSLPSSWDYRCPPP	11
  30	DYRCPPPCPADFFLY	10
  31	YRCPPPCPADFFLYF	10
  12	SLSSGFTPFSCLSLP	9
  17	FTPFSCLSLPSSWDY	9

  V5A-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  3	AREIENLPLRLFTFW	20
  10	PLRLFTFWRGPVVVA	16
  2	SAREIENLPLRLFTF	12
  6	IENLPLRLFTFWRGP	12
  8	NLPLRLFTFWRGPVV	12
  5	EIENLPLRLFTFWRG	11
  13	LFTFWRGPVVVAISL	10
  4	REIENLPLRLFTFWR	9
  11	LRLFTFWRGPVVVAI	9

  V5B-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  15	IFCSFADTQTELELE	24
  23	QTELELEFVFLLTLL	20
  1	VSNALNWREFSFIQI	16
  19	FADTQTELELEFVFL	16
  21	DTQTELELEFVFLLT	16
  17	CSFADTQTELELEFV	15
  22	TQTELELEFVFLLTL	13
  2	SNALNWREFSFIQIF	11
  10	FSFIQWCSFADTQT	11

  V6-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  8	LPSIVILGKIILFLP	26
  3	VLALVLPSIVILGKI	22
  9	PSIVILGKIILFLPC	22
  10	SIVILGKIILFLPCI	21
  17	IILFLPCISRKLKRI	20
  18	ILFLPCISRKLKRIK	18
  25	SRKLKRLKKGWEKSQ	18
  21	LPCISRKLKRIKKGW	17
  28	LKRIKKGWEKSQFLE	17
  29	KRIKKGWEKSQFLEE	16
  4	LALVLPSIVILGKII	14
  14	LGKIILFLPCISRKL	13
  15	GKIILFLPCISRKLK	13
  1	NFVLALVLPSIVILG	12
  5	ALVLPSIVILGKIIL	12
  37	KSQFLEEGIGGTIPH	12

  V7A-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  1	SISMMGSPKSLSETF	18
  5	MGSPKSLSFTFLPNG	17
  13	ETFLPNGINGIKDAR	16
  2	ISMMGSPKSLSETFL	13
  12	SETFLPNGINGIKDA	13
  8	PKSLSETFLPNGING	12
  4	MMGSPKSLSETFLPN	9
  10	SLSETFLPNGINGIK	8

  V7B-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  5	YLFLNMAYQQSTLGY	18
  1	RSERYLFLNMAYQQS	17
  6	LFLNMAYQQSTLGYV	14
  12	YQQSTLGYVALLIST	12
  3	ERYLFLNMAYQQSTL	11
  4	RYLFLNMAYQQSTLG	11
  7	FLNMAYQQSTLGYVA	11
  11	AYQQSTLGYVALLIS	11
  14	QSTLGYVALLISTFH	11
  8	LNMAYQQSTLGYVAL	10

  V7C-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  93	VGVVTEDDEAQDSID	29
  130	TNGVGPLWEFLLRLL	26
  7	PSIVILDLSVEVLAS	24
  1	VLALVLPSIVILDLS	22
  8	SIVILDLSVEVLASP	21
  133	VGPLWEFLLRLLKSQ	21
  3	ALVLPSLVILDLSVE	20
  163	GEFLGSGTWMKLETI	20
  9	IVILDLSVEVLASPA	19
  123	RNPVLPHTNGVGPLW	19
  137	WEFLLRLLKSQAASG	19
  154	SLAFTSWSLGEFLGS	19
  171	WMKLETIILSKLTQE	19
  38	LSEIVLPIEWQQDRK	18
  179	LSKLTQEQKSKHCMF	18
  40	EIVLPIEWQQDRKIP	17
  44	PIEWQQDRKIPPLST	16
  90	WXTVGVVTEDDEAQD	16
  176	TIILSKLTQEQKSKH	16
  15	SVEVLASPAAAWKCL	15
  27	KCLGANILRGGLSEL	15
  32	NTLRGGLSE1VLPIE	15
  39	SEIVLPIEWQQDRKI	15
  116	LKAANSWRNPVLPHT	15
  138	EFLLRLLKSQAASGT	15
  175	ETIILSKLTQEQKSK	15
  2	LALVLPSIVILDLSV	14

  V8-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  7	KSQFLEEGMGGTIPH	12
  8	SQFLEEGMGGTIPHV	11
  12	EEGMGGTIPHVSPER	10
  1	IKKGWEKSQFLEEGM	9
  4	GWEKSQFLEEGMGGT	7
  5	WEKSQFLEEGMGGTI	7

  V13-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  1	SISMMGSPKSLSETF	18
  5	MGSPKSLSETFLPNG	17
  13	ETFLPNGINGIKDAR	16
  2	ISMMGSPKSLSETFL	13
  12	SETFLPNGINGIKDA	13
  8	PKSLSETFLPNGING	12
  4	MMGSPKSLSETFLPN	9
  10	SLSETFLPNGINGIK	8

  V14-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  2	AREIENLPLRLFTFW	20
  9	PLRLFTFWRGPVVVA	16
  1	SAREIENLPLRLFTF	12
  5	IENLPLRLFTFWRGP	12
  7	NLPLRLFTFWRGPVV	12
  4	EIENLPLRLFTFWRG	11
  12	LFTFWRGPVVVAISL	10
  3	REIENLPLRLFTFWR	9
  10	LRLFTFWRGPVVVAI	9

  V21-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  6	LSKLTQEQKTKHCMF	18
  3	TIILSKLTQEQKTKH	16
  2	ETIILSKLTQEQKTK	15
  1	LETIILSKLTQEQKT	13
  4	IILSKLTQEQKTKHC	10
  5	ILSKLTQEQKTKHCM	9
  9	LTQEQKTKHCMFSLI	9
  11	QEQKTKHCMFSLISG	9

  V25-HLA-DR1-0301-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  6	IILFLPCISQKLKRI	21
  7	ILFLPCISQKLKRIK	18
  14	SQKLKRIKKGWEKSQ	18
  10	LPCISQKLKRJKKGW	17
  3	LGKIILFLPCISQKL	13
  4	GKIILFLPCISQKLK	13
  5	KIILFLPCISQKLKR	11

• [1268]

  TABLE XLVIII
  Pos	123456789012345	score

  V1-HLA-DR1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  420	EEEYYRFYTPPNFVL	28
  98	YTSLWDLRIILLVGKI	26
  109	VGKILIDVSNNMRIN	26
  175	RQQVIELARQLNFIP	26
  205	PLRLFTLWRGPVVVA	26
  213	RGPVVVAISLATFFF	26
  225	FFFLYSFVRDVIHPY	26
  229	YSFVRDVIHPYARNQ	26
  312	FAMVHVAYSLCLPMR	26
  370	LLSLLAVTSIPSVSN	26
  373	LLAVTSIPSVSNALN	26
  376	VTSIPSVSNALNWRE	26
  38	SGDFAKSLTIRLIRC	22
  51	RCGYHVVIGSRNPKF	22
  62	NPKIFASEFFPHVVDV	22
  87	NTIFVALHREHYTSL	22
  143	VKGFNVVSAWALQLG	22
  163	RQVYICSNNIQARQQ	22
  184	QLNFIPIDLGSLSSA	22
  222	LATFFFLYSFVRDVI	22
  244	QSDFYKIPIEIVNKT	22
  307	LLSFFFAMVHVAYSL	22
  309	SFFFAMVHVAYSLCL	22
  328	SERYLFLNMAYQQVH	22
  346	ENSWNEEEVWRIEMY	22
  357	IEMYISFGIMSLGLL	22
  385	ALNWREFSFIQSTLG	22
  388	WREFSFIQSTLGYVA	22
  405	ISTFHVLIYGWKRAF	22
  423	YYRFYTPPNFVLALV	22
  429	PPNFVLALVLPSIVI	22
  1	MESISMMGSPKSLSE	20
  15	ETCLPNGINGIKDAR	20
  19	PNGINGIKDARKVTV	20
  22	INGLKDARKVTVGVI	20
  30	KVTVGVIGSGDFAKS	20
  47	IRLIRCGYHVVIGSR	20
  53	GYHVVIGSRNPKFAS	20
  70	FPHVVDVTHHEDALT	20
  71	PHVVDVTHHEDALTK	20
  86	TNIIFVAIHREHYTS	20
  90	FVAJHREHYTSLWDL	20
  101	LWDLRHLLVGKJLID	20
  106	HLLVGKILIDVSNNM	20
  110	GKILIDVSNNMRINQ	20
  111	KILIDVSNNMRINQY	20
  113	LIDVSNNMRINQYPE	20
  130	AEYLASLFPDSLIVK	20
  133	LASLFPDSLIVKGFN	20
  139	DSLLVKGFNVVSAWA	20
  140	SLIVKGFNVVSAWAL	20
  145	GFNVVSAWALQLGPK	20
  162	SRQVYICSNNIQARQ	20
  176	QQVIELARQLNELPI	20
  185	LNFLPIDLGSLSSAR	20
  189	PIDLGSLSSAREIEN	20
  192	LGSLSSAREIENLPL	20
  217	VVAISLATFFFLYSF	20
  219	AISLATFFFLYSFVR	20
  233	RDVIHPYARNQQSDF	20
  247	FYKLPIEIYNKTLPI	20
  256	NKTLPIVAITLLSLV	20
  258	TLPIVAITLLSLVYL	20
  261	IVAITLLSLVYLAGL	20
  264	ITLLSLVYLAGLLAA	20
  266	LLSLVYLAGLLAAAY	20
  267	LSLVYLAGLLAAAYQ	20
  273	AGLLAAAYQLYYGTK	20
  292	PPWLETWLQCRKQLG	20
  302	RKQLGLLSFFFAMVH	20
  304	QLGLLSFFFAMVHVA	20
  331	YLFLNMAYQQVHANI	20
  351	EEEVWRIEMYISFGI	20
  354	VWRIEMYISFGIMSL	20
  362	SFGIMSLGLLSLLAV	20
  365	IMSLGLLSLLAVTSI	20
  367	SLGLLSLLAVTSIPS	20
  368	LGLLSLLAVTSIPSV	20
  379	IPSVSNALNWREFSF	20
  395	QSTLGYVALLISTFH	20
  398	LGYVALLISTFHVLI	20
  401	VALLISTFHVLIYGW	20
  430	PNFVLALVLPSIVIL	20
  431	NFVLALVLPSIVILD	20
  435	ALVLPSIVLLDLLQL	20
  438	LPSIVILDLLQLCRY	20
  440	SIVILDLLQLCRYPD	20
  12	SLSETCLPNGINGIK	18
  21	GINGIKDAThVTVGV	18
  36	IGSGDFAKSLTIRLL	18
  76	VTHHEDALTKTNIIF	18
  97	HYTSLWDLRHLLVGK	18
  142	IVKGFNVVSAWALQL	18
  154	LQLGPKDASRQVYIC	18
  161	ASRQVYICSNNTQAR	18
  168	CSNNTQARQQVIELA	18
  186	NFIPIDLGSLSSARE	18
  195	LSSAREIENLPLRLF	18
  234	DVIHPYARNQQSDFY	18
  248	YKJPIELVNKTLPIV	18
  257	KTLPIVAITLLSLVY	18
  289	RRFPPWLETWLQCRK	18
  339	QQVHANTENSWNEEE	18
  348	SWNEEEVWRIEMYIS	18
  359	MYISFGIMSLGLLSL	18
  364	GIMSLGLLSLLAVTS	18
  384	NALNWREFSFIQSTL	18
  387	NWREFSFIQSTLGYV	18
  399	GYVALLISTFHVLIY	18
  432	FVLALVLPSIVILDL	18
  66	ASEFFPHVVDVTHHE	16
  67	SEFFPHVVDVTHHED	16
  95	REHYTSLWDLRIILLV	16
  122	INQYPESNAEYLASL	16
  129	NAEYLASLFPDSLIV	16
  206	LRLFTLWRGPVVVAI	16
  209	FTLWRGPVVVAISLA	16
  224	TFFFLYSFVRDVIHP	16
  226	FFLYSFVRDVIHPYA	16
  228	LYSFVRDVIHPYARN	16
  236	IHPYARNQQSDFYKJ	16
  245	SDFYKIPIEIVNKTL	16
  268	SLVYLAGLLAAAYQL	16
  285	GTKYRRFPPWLETWL	16
  288	YRRFPPWLETWLQCR	16
  308	LSFFFAMVHVAYSLC	16
  330	RYLFLNMAYQQVHAN	16
  335	NMAYQQVHANIENSW	16
  352	EEVWRIEMYISFGIM	16
  360	YISFGIMSLGLLSLL	16
  390	EFSFIQSTLGYVALL	16
  397	TLGYVALLISTFHVL	16
  412	IYGWKRAFEEEYYRF	16
  416	KRAFEEEYYRFYTPP	16
  424	YRFYTPPNFVLALVL	16
  296	ETWLQCRKQLGLLSF	15
  3	SISMMGSPKSLSETC	14
  4	ISMMGSPKSLSETCL	14
  32	TVGVIGSGDFAKSLT	14
  33	VGVIGSGDFAKSLTI	14
  44	SLTIRLIRCGYHVVI	14
  46	TIRLIRCGYHVVIGS	14
  54	YHVVIGSRNPKEASE	14
  73	VVDVTHHEDALTKTN	14
  80	EDALTKTNTIFVAIH	14
  85	KTNIIFVAIHREHYT	14
  88	IIFVAIHREHYTSLW	14
  117	SNNMRINQYPESNAE	14
  119	NMIUNQYPESNAEYL	14
  151	AWALQLGPKDASRQV	14
  178	VIELARQLNFIPIDL	14
  182	ARQLNFIPIDLGSLS	14
  187	FIPIDLGSLSSAREI	14
  198	AREIENLPLRLFTLW	14
  203	NLPLRLFTLWRGPVV	14
  208	LFTLWRGPVVVAISL	14
  214	GPVVVAISLATFFFL	14
  232	VRDVIHPYARNQQSD	14
  249	KIPIEIVNKTLPIVA	14
  252	IE1VNKTLPIVAITL	14
  259	LPIVAITLLSLVYLA	14
  263	AITLLSLVYLAGLLA	14
  269	LVYLAGLLAAAYQLY	14
  272	LAGLLAAAYQLYYGT	14
  305	LGLLSFFFAMVHVAY	14
  311	FFAMVHVAYSLCLPM	14
  314	MVHVAYSLCLPMRRS	14
  318	AYSLCLPMRRSERYL	14
  322	CLPMRRSERYLFLNM	14
  329	ERYLFLNMAYQQVHA	14
  333	FLNMAYQQVHANIEN	14
  342	HANIENSWNEEEVWR	14
  356	RIEMYISFGIMSLGL	14
  363	FGIMSLGLLSLLAVT	14
  371	LSLLAVTSIPSVSNA	14
  391	FSFIQSTLGYVALLI	14
  400	YVALLISTFHVLIYG	14
  402	ALLISTFHVLIYGWK	14
  407	TFHVLIYGWKRAFEE	14
  409	HVLIYGWKRAFEEEY	14
  433	VLALVLPSIVILDLL	14
  439	PSIVILDLLQLCRYP	14

  V5A-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  14	SSGFTPFSCLSLPSS	22
  17	FTPFSCLSLPSSWDY	22
  3	SPGLQALSLSLSSGF	20
  10	SLSLSSGFTPFSCLS	20
  2	GSPGLQALSLSLSSG	18
  7	QALSLSLSSGFTPFS	18
  28	SWDYRCPPPCPADFF	16
  6	LQALSLSLSSGFTPF	14
  20	FSCLSLPSSWDYRCP	14
  4	PGLQALSLSLSSGFT	12
  13	LSSGFTPFSCLSLPS	12
  16	GFTPFSCLSLPSSWD	12
  19	PFSCLSLPSSWDYRC	12
  24	SLPSSWDYRCPPPC	12

  V5B-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  4	ALNWREFSFIQIFCS	22
  7	WREFSFIQIFCSFAD	22
  9	EFSFIQIFCSFADTQ	22
  13	IQIFCSFADTQTELE	22
  10	FSFIQIFCSFADTQT	20
  23	QTELELEFVFLLTLL	20
  3	NALNWREFSFIQIFC	18
  15	IFCSFADTQTELELE	18
  16	FCSFADTQTELELEF	16
  12	FIQIFCSFADTQTEL	14
  6	NWREFSFIQIFCSFA	12
  14	QIFCSFADTQTELEL	12
  20	ADTQTELELEFVFLL	12
  22	TQTELELEFVFLLTL	12
  24	TELELEFVFLLTLLL	12

  V6-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  18	ILFLPCISRKLKRIK	26
  17	IILFLPCISRKLKRI	22
  37	KSQFLEEGIGGTIPH	22
  1	NFVLALVLPSIVILG	20
  5	ALVLPSIVILGKIIL	20
  8	LPSIVTLGKIILFLP	20
  14	LGKIILFLPCISRKL	20
  46	GGTIPHVSPERVTVM	20
  2	FVLALVLPSIVILGK	18
  22	PCISRKLKRIKKGWE	18
  30	RJKKGWEKSQFLEEG	18
  3	VLALVLPSIVILGKI	14
  11	IVILGKIILFLPCIS	14
  15	GKIILFLPCLSRKLK	14
  16	KIILFLPCISRKLKR	14
  25	SRKLKRIKKGWEKSQ	14
  28	LKRIKKGWEKSQFLE	14
  38	SQFLEEGIGGTIPHV	14
  42	EEGIGGTIPHVSPER	14
  6	LVLPSIVILGKIILF	12
  7	VLPSIVILGKIILFL	12
  13	ILGKIILFLPCISRK	12
  34	GWEKSQFLEEGIGGT	12
  43	EGIGGTIPHVSPERV	12

  V7A-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  13	ETFLPNGINGIKDAR	20
  10	SLSETFLPNGINGIK	18
  12	SETFLPNGINGIKDA	16
  1	SISMMGSPKSLSETF	14
  2	ISMMGSPKSLSETFL	14
  5	MGSPKSLSETFLPNG	12
  7	SPKSLSETFLPNGIN	12
  9	KSLSETFLPNG1NGI	12

  V7B-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  5	YLFLNMAYQQSTLGY	26
  2	SERYLFLNMAYQQST	22
  14	QSTLGYVALLISTFH	20
  4	RYLFLNMAYQQSTLG	16
  9	NMAYQQSTLGYVALL	16
  3	ERYLFLNMAYQQSTL	14
  7	FLNMAYQQSTLGYVA	14
  1	RSERYLFLNMAYQQS	12
  6	LFLNMAYQQSTLGYV	12
  11	AYQQSTLGYVALLIS	12
  15	STLGYVALLISTFHV	12

  V7C-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  134	GPLWEFLLRLLKSQA	28
  168	SGTWMKLETIWSKL	28
  7	PSIVILDLSVEVLAS	26
  13	DLSVEVLASPAAAWK	26
  113	DRALKAANSWRNPVL	26
  138	EFLLRLLKSQAASGT	26
  150	SGTLSLAFTSWSLGE	26
  176	TIILSKLTQEQKSKH	26
  23	AAAWKCLGANTLRGG	22
  62	PAMWTEEAGATAEAQ	22
  162	LGEFLGSGTWMKLET	22
  3	ALVLPSIVILDLSVE	10
  8	SIVILDLSVEVLASP	20
  31	ANTLRGGLSEIVLPI	20
  40	EIVLPIEWQQDRKIP	20
  50	DRKIPPLSTPPPPAM	20
  61	PPAMWTEEAGATAFA	20
  89	QIPVVGVVTEDDEAQ	20
  92	VVGVVTEDDEAQDSI	20
  130	TNGVGPLWEFLLRLL	20
  133	VGPLWEFLLRLLKSQ	20
  137	WEFLLRLLKSQAASG	20
  159	SWSLGEFLGSGTWMK	20
  169	GTWMKLETIILSKLT	20
  171	WMKLETIILSKLTQE	20
  27	KCLGANILRGGLSFI	18
  74	EAQESGIRNKSSSSS	18
  95	VVTEDDEAQDSIDPP	18
  142	RLLKSQAASGTLSLA	18
  151	GTLSLAFTSWSLGEF	18
  172	MKLETIILSKLTQEQ	18
  44	PIEWQQDRKIPPLST	16
  119	ANSWRNPVLPHTNGV	16
  157	FTSWSLGEFLGSGTW	16
  77	ESGIIRNKSSSSSQIP	15
  175	BTIILSKLTQEQKSK	15
  1	VLALVLPSIVILDLS	14
  6	LPSIVILDLSVEVLA	14
  9	IVILDLSVEVLASPA	14
  11	ILDLSVEVLASPAAA	14
  16	VEVLASPAAAWKCLG	14
  30	GANTLRGGLSEIVLP	14
  35	RGGLSEIVLPIEWQQ	14
  38	LSEIVLPIFWQQDRK	14
  39	SEIVLPIEWQQDRKI	14
  42	VLPIEWQQDRKIPPL	14
  53	IPPLSTPPPPAMWTE	14
  87	SSQIPVVGVVTEDDE	14
  90	IPVVGVVTEDDEAQD	14
  93	VGVVTEDDEAQDSID	14
  103	QDSIDPPESPDRALK	14
  123	RNPVLPHTNGVGPLW	14
  141	LRLLKSQAASGTLSL	14
  163	GEFLGSGTWMKLETI	14
  179	LSKLTQEQKSKHCMF	14

  V8-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  7	KSQFLEEGMGGTIPH	22
  8	SQFLEFGMGGTIPHV	14
  12	EEGMGGTIPIIVSPER	14
  4	GWEKSQFLEEGMGGT	12
  13	EGMGGTIPHVSPERV	12
  2	KKGWEKSQFLEEGMG	10

  V8-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  13	ETFLPNGINGIKDAR	20
  10	SLSETFLPNGINGIK	18
  12	SETFLPNGINGIKDA	16
  1	SISMMGSPKSLSETF	14
  2	ISMMGSPKSLSETFL	14
  5	SPKSLSETFLPNGIN	12
  7	KSLSETFLPNGINGI	12
  9	KSLSETFLPNGINGI	12

  V14-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  9	PLRLFTFWRGPVVVA	26
  10	LRLFTFWRGPVVVAJ	16
  12	LFTFWRGPVVVAISL	16
  13	FTFWRGPVVVAISLA	16
  2	AREIENLPLRLFTFW	14
  7	NLPLRLFTFWRGPVV	14
  3	REIENLPLRLFTFWR	12
  6	ENLPLRLFTFWRGPV	12
  14	TFWRGPVVVAISLAT	12
  15	FWRGPVVVAISLATF	12

  V21-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  3	TIILSKLTQEQKTKH	26
  2	ETIILSKLTQEQKTK	15
  6	LSKLTQEQKTKHCMF	14
  5	ILSKITQEQKTKHCM	12

  V25-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  7	ILFLPCISQKLKRIK	26
  6	IWFLPCISQKLKRI	22
  3	LGKIILFLPCISQKL	20
  4	GKIILFLPCISQKLK	20
  11	PCISQKLKRIKKGWE	18
  5	KIILFLPCLSQKIKR	14
  14	SQKLKRIKKGWEKSQ	14
  2	ILGKIILFLPCISQK	12

• [1269]

  TABLE XLIX
  Pos	123456789012345	score

  V1-HLA-DRB1-0401-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 3; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  249	KIPIEIVNKTLPIVA	27
  308	LSFFFAMVHVAYSLC	27
  229	YSFVRDVIHPYARNQ	26
  281	QLYYGTKYRRFPPWL	25
  295	LETWLQCRKQLGLLS	25
  87	NIIFVAIHREHYTSL	24
  388	WREFSFIQSTLGYVA	23
  309	SFFFAMVHVAYSLCL	22
  3	SISMMGSPKSLSETC	21
  71	PHVVDVTHHEDALTK	21
  98	YTSLWDLRIILLVGKI	21
  175	RQQVIELARQLNFIP	21
  205	PLRLFTLWRGPVVVA	21
  70	FPHVVDVTHHEDALT	20
  95	REHYTSLWDLRHLLV	20
  151	AWALQLGPKDASRQV	20
  263	AITLLSLVYLAGLLA	20
  1	MESISMMGSPKSLSE	19
  51	RCGYHVVIGSRNPKF	19
  106	HLLVGKILIDVSNNM	19
  182	ARQLNFIPHJLGSLS	19
  266	LLSLVYLAGLLAAAY	19
  351	EEEVWRIEMYISFGI	19
  395	QSTLGYVALLISTFH	19
  424	YRFYTPPNEVLALVL	19
  67	SEFFPHVVDVTHHED	18
  222	LATFFFLYSFVRDVI	18
  302	RKQLGLLSFFFAMVH	18
  307	LLSFFFAMVHVAYSL	18
  367	SLGLLSLLAVTSIPS	18
  370	LLSLLAVTSIPSVSN	18
  28	ARKVTVGVIGSGDFA	17
  86	TNIIFVAIHREHYTS	17
  99	TSLWDLRIILLVGKIL	17
  134	ASLFPDSLIVKGFNV	17
  143	VKGFNVVSAWALQLG	17
  225	FFFLYSFVRDVIHPY	17
  226	FFLYSFVRDVIHPYA	17
  244	QSDFYKIPIEIVNKT	17
  335	NMAYQQVHANIENSW	17
  360	YISFGIMSLGLLSLL	17
  405	ISTFHVLIYGWKRAF	17
  136	LFPDSLLVKGFNVVS	16
  163	RQVYICSNNLQARQQ	16
  184	QLNFIPIDLGSLSSA	16
  268	SLVYLAGLLAAAYQL	16
  279	AYQLYYGTKYRRFPP	16
  282	LYYGTKYRRFPPWLE	16
  328	SERYLFLNMAYQQVH	16
  330	RYLFLNMAYQQVHAN	16
  385	ALNWREFSFIQSTLG	16
  397	TLGYVALLLSTFHVL	16
  429	PPNFVLALVLPSIVI	16
  42	AKSLTIRLIRCGYHV	15
  47	IRLIRCGYHVVIGSR	15
  103	DLRHLLVGKILIDVS	15
  142	IVKGFNVVSAWALQL	15
  210	TLWRGPVVVAISLAT	15
  317	VAYSLCLPMRRSERY	15
  318	AYSLCLPMRRSERYL	15
  322	CLPMRRSERYLFLNM	15
  401	VALLISTFHVLIYGW	15
  408	FHVLIYGWKRAFEEE	15
  428	TPPNFVLALVLPSIV	15
  19	PNGINGLKDARKVTV	14
  22	INGIKDARKVTVGVI	14
  43	KSLTIRLIRCGYHVV	14
  52	CGYHVVIGSRNPKFA	14
  53	GYHVVIGSRNPKEAS	14
  56	VVIGSRNPKFASEFF	14
  66	ASEFFPHVVDVTHHE	14
  77	THHEDALTKTNIIFV	14
  85	KTNIIFVAIHREHYT	14
  89	IFVAIHREHYTSLWD	14
  113	LIDVSNNMRINQYPE	14
  189	PIDLGSLSSAREIEN	14
  198	AREIENLPLRLFTLW	14
  203	NLPLRLFTLWRGPVV	14
  212	WRGPVVVAISLATFF	14
  233	RDVIHPYARNQQSDF	14
  261	LVAITLLSLVYLAGL	14
  319	YSLCLPMRRSERYLF	14
  348	SWNEEEVWRIEMYIS	14
  373	LLAVTSIPSVSNALN	14
  381	SVSNALNWREFSFIQ	14
  407	TFHVLIYGWKRAFEE	14
  409	HVLIYGWKRAFEEEY	14
  430	PNFVLALVLPSIVIL	14
  435	ALVLPSIVILDLLQL	14
  30	KVTVGVIGSGDFAKS	13
  33	VGVIGSGDFAKSLTI	13
  101	LWDLRHLLVGKILID	13
  139	DSLIVKGFNVVSAWA	13
  146	FNVVSAWALQLGPKD	13
  178	VIELARQLNFIPIDL	13
  185	LNFIPIDLGSLSSAR	13
  206	LRLFTLWRGPVVVAI	13
  208	LFTLWRGPVYVAISL	13
  223	ATFFFLYSFVRDVIH	13
  252	IEIVNKTLPIVAITL	13
  256	NKTLPIVAITLLSLV	13
  280	YQLYYGTKYRRFPPW	13
  311	FFAMVHVAYSLCLPM	13
  358	EMYISFGIMSLGLLS	13
  364	GIMSLGLLSLLAVTS	13
  376	VTSIPSVSNALNWRE	13
  391	FSFIQSTLGYVALLI	13
  431	NFVLALVLPSIVILD	13

  V2-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 5; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  17	FTPFSCLSLPSSWDY	22
  3	SPGLQALSLSLSSGF	19
  28	SWDYRCPPPCPADFF	16
  24	SLPSSWDYRCPPPCP	14
  5	GLQALSLSLSSGFTP	12
  8	ALSLSLSSGFTPFSC	12
  10	SLSLSSGFTPFSCLS	12
  14	SSGFTPFSCLSLPSS	12
  26	PSSWDYRCPPPCPAD	10

  V5A-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  13	LFTFWRGPVVVAISL	17
  10	PLRLFTFWRGPVVVA	15
  15	TFWRGPVVVAISLAT	15
  3	AREIENLPLRLFTFW	14
  8	NLPLRLFTFWRGPVV	14
  11	LRLFTFWRGPVVVAI	13
  14	FTFWRGPVVVAISLA	12
  16	FWRGPVVVAISLATF	9
  4	RELENLPLRLFTFWR	8

  V5B-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 11; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  7	WREFSFIQIFCSFAD	22
  9	EFSFIQIFCSFADTQ	22
  16	FCSFADTQTELELEF	11
  4	ALNWREFSFIQIFCS	10
  13	IQIFCSFADTQTELE	10

  V6-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 13; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  8	LPSIVILGKIILFLP	21
  18	ILFLPCISRKLKRID	21
  25	SRKLKRIKKGWEKSQ	20
  43	EGIGGTIPHVSPERV	20
  11	IVILGKIILFLPCIS	19
  21	LPCISRKLKRIKKGW	16
  22	PCISRKLKRIKKGWE	15
  5	ALVILPSIVILGKIIL	14
  46	GGTIPHVSPERVTVM	14
  1	NFVLALVLPSIVILG	13
  4	LALVLPSIVILGKII	13
  14	LGKIILFLPCISRKI	13
  35	WEKSQFLEEGIGGTI	13
  39	QFLEEGIGGTIPHVS	13
  42	EEGIGGTWHVSPER	13
  15	GKIILFLPCISRKLK	12
  17	IILFLPCISRKILKRI	12
  32	KKGWEKSQFLEEGIG	10
  37	KSQFLEEGIGGTIPH	10

  V7A-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  1	SISMMGSPKSLFETF	21
  8	PKSLSETFLPNGING	12
  12	SETFLPNGINGIKDA	10

  V7B-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  4	RYLFLNMAYQQSTLG	22
  14	QSTLGYVALLISTFH	19
  2	SERYLFLNMAYQQST	16
  7	FLNMAYQQSTLGYVA	13
  9	NMAYQQSTLGYVALL	10

  V7C-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 15; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  137	WEFLLRLLKSQAASG	26
  134	GPLWEFLLRLLKSQA	25
  44	PIEWQQDRKIPPLST	24
  121	SWRNPVLPHTNGVGP	21
  13	DLSVEVLASPAAAWK	19
  50	DRKIPPLSTPPPPAM	18
  62	PAMWTEEAGATAEAQ	18
  138	EFLLRLLKSQAASGT	18
  23	AAAWKCLGANTLRGG	17
  168	SGTWMKLETIILSKL	17
  179	LSKLTQEQKSKHCMF	17
  157	FTSWSLGEFLGSGTW	16
  9	IVILDLSVEVLASPA	15
  11	ILDLSVEVLASPAAA	15
  19	LASPAAAWKCLGANI	15
  35	RGGLSEIVLPIEWQQ	15
  43	LPIEWQQDRKLPPLS	15
  73	AEAQESGIRNKSSSS	15
  3	ALVLPSIVILDLSVE	14
  27	KCLGANILRGGLSEI	14
  75	AQESGIRNKSSSSSQ	14
  89	QIPVVGVVTEDDFAQ	14
  135	PLWEFLLRILKSQAA	14
  173	KLETIILSKLTQEQK	14
  4	LVLPSIVILDLSVEV	13
  6	LPSIVILDLSVEVLA	13
  8	SIVILDLSVEVLASP	13
  26	WKCLGANILRGGLSE	13
  28	CLGANILRGGLSEIV	13
  87	SSQIPVVGVVTEDDE	13
  90	TPVVGVVTEDDEAQD	13
  123	RNPVLPHTNGVGPLW	13
  130	TNGVGPLWEFLLRLL	13
  152	TLSLAFTSWSLGEFL	13
  156	AFTSWSLGEFLGSGT	13
  169	GTWMKLETHLSKLT	13
  171	WIVIKLETIILSKLTQE	13
  10	VILDLSVEVLASPAA	12
  12	LDLSVEVLASPAAAW	12
  39	SEIVLPIEWQQDRKI	12
  58	TPPPPAMWTEEAGAT	12
  74	EAQESGIRNKSSSSS	12
  77	ESGIRNKSSSSSQIP	12
  100	DEAQDSIDPPESPDR	12
  110	ESPDRALKAANSWRN	12
  119	ANSWRNPVLPHTNGV	12
  124	NPVLPHTNGVGPLWE	12
  140	LLRLLKSQAASGTLS	12
  150	SGTLSLAFTSWSLGE	12
  154	SLAFTSWSLGEFLGS	12
  176	TIILSKLTQEQKSKH	12

  V8-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 17; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  13	EGMGGTIPHVSPERV	20
  9	QFLEEGMGGTIPHVS	13
  12	EEGMGGTIPHVSPER	13
  5	WEKSQFLEEGMGGTI	12
  2	KKGWEKSQFLEEGMG	10
  7	KSPFLEEGMGGTIPH	10

  V13-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 27; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  1	SISMMGSPKSLSETF	21
  8	PKSLSETFLPNGING	12
  12	SETFLPNGINGIKDA	10

  V14-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 29; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  12	LFTFWRGPVVVAISL	17
  9	PLRLFTFWRGPVVVA	15
  14	TFWRGPVVVAISLAT	15
  2	AREIENLPLRLFTFW	14
  7	NLPLRLFTFWRGPVV	14
  10	LRLFTFWRGPVVVAI	13
  13	FTFWRGPVVVAISLA	12
  15	FWRGPVVVAISLATF	9
  3	REIENLPLRLFTFWR	8

  V21-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 43; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  6	LSKLTQEQKTKHCMF	17
  3	TIILSKLTQEQKTKH	12
  8	KLTQEQKTKHCMFSL	8
  9	LTQEQKTKHCMFSLI	8

  V25-HLA-DRB1-1101-15mers-98P4B6
  Each peptide is a portion of SEQ ID
  NO: 51; each start position is specified,
  the length of peptides is 15 amino acids,
  and the end position for each peptide
  is the start position plus fourteen.

  14	SQKLKRIKKGWEKSQ	20
  10	LPCISQKLKRIKKGW	16
  11	PCISQKLKRIKKGWE	15
  3	LGKIILFLPCISQKL	13
  7	ILFLPCISQKLKRIK	13
  4	GKIILFLPCISQKLK	12
  6	IILFLPCISQKLKRI	11
  8	LFLPCISQKLKRIKK	9

• [1270]

  TABLE L
  Properties of 98P4B6

  	Bioinformatic
  	Program	URL	Outcome
  V.1
  ORF	ORF finder
  Protein length			454 aa
  Transmembrane region	TM Pred	https://www.ch.embnet.org/	6TM, aa 214-232, 261-286,
  			304-325, 359-379,
  			393-415, 426-447, N-
  			term inside
  	HMMTop	https://www.enzim.hu/hmmtop/	6TM, aa 215-232 261-279
  			306-325 360-379
  			396-415 428-447 N-
  			term out
  	Sosui	https://www.genome.ad.jp/SOSui/	6TM, aa 206-228, 255-277,
  			304-325, 359-381,
  			393-415, 428-450
  	TMHMM	https://www.cbs.dtu.dk/services/TMHMM	6TM, aa 210-232, 262-284,
  			304-323, 360-382,
  			392-414, 427-449
  Signal Peptide	Signal P	https://www.cbs.dtu.dk/services/SignalP/	none
  pI	pI/MW tool	https://www.expasy.ch/tools/	pI 8.74
  Molecular weight	pI/MW tool	https://www.expasy.ch/tools/	52.0 kD
  Localization	PSORT	https://psort.nibb.ac.jp/	Plasma membrane
  			60%, golgi 40%
  	PSORT II	https://psort.nibb.ac.jp/	Endoplasmic reticulum
  			39%, plasma membrane
  			34%
  Motifs	Pfam	https://www.sanger.ac.uk/Pfam/	no known motifs
  	Prints	https://www.biochem.ucl.ac.uk/	pyridine nucleotide
  			reductase
  	ProDom	https://prodes.toulouse.inra.f	Dudulin,
  			oxidoreductase
  	Blocks	https://www.blocks.fhcrc.org/	adenosyl-L-
  			homocysteine
  			hydrolase
  V.2
  ORF	ORF finder
  Protein length			45 aa
  Transmembrane region	TM Pred	https://www.ch.embnet.org/	1 TM, aa 5-23, N-term
  			inside
  	HMMTop	https://www.enzim.hu/hmmtop/	no TM
  	Sosui	https://www.genome.ad.jp/SOSui/	souble protein
  	TMHMM	https://www.cbs.dtu.dk/services/TMHMM	no TM
  Signal Peptide	Signal P	https://www.cbs.dtu.dk/services/SignalP/	none
  pI	pI/MW tool	https://www.expasy.ch/tools/	pI 4.2
  Molecular weight	pI/MW tool	https://www.expasy.ch/tools/	4.84 kD
  Localization	PSORT	https://psort.nibb.ac.jp/	Ouside 37%,
  			microbody 32%
  	PSORT II	https://psort.nibb.ac.jp/	Extracellular 33%,
  			nuclear 33%
  Motifs	Pfam	https://www.sanger.ac.uk/Pfam/	no known motifs
  	Prints	https://www.biochem.ucl.ac.uk/	no known motifs
  	Blocks	https://www.blocks.fhcrc.org/	no known motifs
  V.5
  ORF	ORF finder
  Protein length			419 aa
  Transmembrane region	TM Pred	https://www.ch.embnet.org/	4TM, aa 214-232, 261-286,
  			304-325, 359-379
  			N-term inside
  	HMMTop	https://www.enzim.hu/hmmtop/	4TM, aa 215-232, 259-278,
  			305-324, 360-379
  			N-term outside
  	Sosui	https://www.genome.ad.jp/SOSui/	4TM, aa 209-231, 255-277,
  			304-325, 356-379
  	TMHMM	https://www.cbs.dtu.dk/services/TMHMM	4TM, aa 210-232, 262-284,
  			304-323, 360-382
  Signal Peptide	Signal P	https://www.cbs.dtu.dk/services/SignalP/	none
  pI	pI/MW tool	https://www.expasy.ch/tools/	pI 8.1
  Molecular weight	pI/MW tool	https://www.expasy.ch/tools/	47.9 kD
  Localization	PSORT	https://psort.nibb.ac.jp/	Plasma membrane
  			60%, golgi 40%
  	PSORT II	https://psort.nibb.ac.jp/	Endoplasmic reticulum
  			44%, plasma membrane
  			22%
  Motifs	Pfam	https://www.sanger.ac.uk/Pfam/	no known motifs
  	Prints	https://www.biochem.ucl.ac.uk/	no known motifs
  	ProDom	https://prodes.toulouse.inra.f	Dudulin,
  			oxidoreductase
  	Blocks	https://www.blocks.fhcrc.org/	no known motifs
  V.6
  ORF	ORF finder
  Protein length			490 aa
  Transmembrane region	TM Pred	https://www.ch.embnet.org/	6TM, aa 214-232, 261-286,
  			304-325, 359-379,
  			393-415, 432-455
  	HMMTop	https://www.enzim.hu/hmmtop/	7TM, aa 140-158, 214-232,
  			259-280, 305-323,
  			361-383, 396-413, 432-455,
  			N-term out
  	Sosui	https://www.genome.ad.jp/SOSui/	6TM, aa 206-228, 255-277,
  			304-325, 359-381,
  			393-415, 428-450
  	TMHMM	https://www.cbs.dtu.dk/services/TMHMM	6TM, aa 210-232, 262-284,
  			304-323, 360-382,
  			392-414, 427-449
  Signal Peptide	Signal P	https://www.cbs.dtu.dk/services/SignalP/	none
  pI	pI/MW tool	https://www.expasy.ch/tools/	pI 9.2
  Molecular weight	pI/MW tool	https://www.expasy.ch/tools/	55.9 kD
  Localization	PSORT	https://psort.nibb.ac.jp/	Plasma membrane
  			60%, golgi 40%
  	PSORT II	https://psort.nibb.ac.jp/	Endoplasmic reticulum
  			39%, plasma membrane
  			34%
  Motifs	Pfam	https://www.sanger.ac.uk/Pfam/	no known motifs
  	Prints	https://www.biochem.ucl.ac.uk/	pyridine nucleotide
  			reductase
  	ProDom	https://prodes.toulouse.inra.f	Dudulin,
  			oxidoreductase
  	Blocks	https://www.blocks.fhcrc.org/	adenosyl-L-
  			homocysteine
  			hydrolase
  V.7
  ORF	ORF finder
  Protein length			576 aa
  Transmembrane region	TM Pred	https://www.ch.embnet.org/	6TM, aa 214-232, 262-280,
  			306-322, 331-360,
  			371-393, 525-544. N-
  			term out
  	HMMTop	https://www.enzim.hu/hmmtop/	5TM, aa 215-232, 261-279,
  			306-325, 342-359,
  			378-397 N -term out
  	Sosui	https://www.genome.ad.jp/SOSui/	5 TM, aa 206-228, 255-277,
  			304-325, 339-360,
  			380-402
  	TMHMM	https://www.cbs.dtu.dk/services/TMHMM	4TM, aa 210-232,
  			262-284, 304-323,
  			343-360
  Signal Peptide	Signal P	https://www.cbs.dtu.dk/services/SignalP/	none
  pI	pI/MW tool	https://www.expasy.ch/tools/	pI 8.5
  Molecular weight	pI/MW tool	https://www.expasy.ch/tools/	64.5 kD
  Localization	PSORT	https://psort.nibb.ac.jp/	Plasma membrane
  			60%, golgi 40%
  	PSORT II	https://psort.nibb.ac.jp/	Endoplasmic reticulum
  			44%, plasma membrane
  			22%
  Motifs	Pfam	https://www.sanger.ac.uk/Pfam/	no known motifs
  	Prints	https://www.biochem.ucl.ac.uk/	pyridine nucleotide
  			reductase
  	ProDom	https://prodes.toulouse.inra.f	Dudulin,
  			oxidoreductase
  	Blocks	https://www.blocks.fhcrc.org/	Ets domain, adenosyl-
  			L-homocysteine
  			hydrolase

• [1271]

  TABLE LI
  Exon boundaries of transcript 98P4B6 v.1

  	Exon Number	Start	End	Length

  	1	23	321	299
  	2	322	846	525
  	3	847	1374	528
  	4	1375	1539	165
  	5	1540	1687	148
  	6	1688	2453	766

• [1272]

  TABLE LII(a)
  Nucleotide sequence (partial, 5′ open) of
  transcript variant 98P4B6 v.2 (SEQ ID NO: 153)

  agtggatccc ccgggctgca ggctctctct ctctctctct cttccgggtt cacgccattc	60
  tcctgcctca gcctcccgag tagctgggac tacaggtgcc cgccaccatg cccggctgat	120
  ttctttttgt atttttagta cagacggagt ttcaccgtgt tagccaggat ggtctcgatc	180
  tcctgacctc gtgatccgcc cgccttggcc tccaaagtgc tgggattaca ggtgtgagct	240
  accgcgcccg gcctattatc ttgtactttc taactgagcc ctctattttc tttattttaa	300
  taatatttct ccccacttga gaatcacttg ttagttcttg gtaggaattc agttgggcaa	360
  tgataacttt tatgggcaaa aacattctat tatagtgaac aaatgaaaat aacagcgtat	420
  tttcaatatt ttcttattcc ttaaattcca ctcttttaac actatgctta accacttaat	480
  gtgatgaaat attcctaaaa gttaaatgac tattaaagca tatattgttg catgtatata	540
  ttaagtagcc gatactctaa ataaaaatac cactgttaca gataaatggg gcctttaaaa	600
  atatgaaaaa caaacttgtg aaaatgtata aaagatgcat ctgttgtttc aaatggcact	660
  atcttctttt cagtactaca aaaacagaat aattttgaag ttttagaata aatgtaatat	720
  atttactata attctaaatg tttaaatgct tttctaaaaa tgcaaaacta tgatgtttag	780
  ttgctttatt ttacctctat gtgattattt ttcttaattg ttatttttta taatcattat	840
  ttttctgaac cattcttctg gcctcagaag taggactgaa ttctactatt gctaggtgtg	900
  agaaagtggt ggtgagaacc ttagagcagt ggagatttgc tacctggtct gtgttttgag	960
  aagtgcccct tagaaagtta aaagaatgta gaaaagatac tcagtcttaa tcctatgcaa	1020
  aaaaaaaatc aagtaattgt tttcctatga ggaaaataac catgagctgt atcatgctac	1080
  ttagctttta tgtaaatatt tcttatgtct cctctattaa gagtatttaa aatcatattt	1140
  aaatatgaat ctattcatgc taacattatt tttcaaaaca tacatggaaa tttagcccag	1200
  attgtctaca tataaggttt ttatttgaat tgtaaaatat ttaaaagtat gaataaaata	1260
  tatttatagg tatttatcag agatgattat tttgtgctac atacaggttg gctaatgagc	1320
  tctagtgtta aactacctga ttaatttctt ataaagcagc ataaccttgg cttgattaag	1380
  gaattctact ttcaaaaatt aatctgataa tagtaacaag gtatattata ctttcattac	1440
  aatcaaatta tagaaattac ttgtgtaaaa gggcttcaag aatatatcca atttttaaat	1500
  attttaatat atctcctatc tgataactta attcttctaa attaccactt gccattaagc	1560
  tatttcataa taaattctgt acagtttccc ccaaaaaaag agatttattt atgaaatatt	1620
  taaagtttct aatgtggtat tttaaataaa gtatcataaa tgtaataagt aaatatttat	1680
  ttaggaatac tgtgaacact gaactaatta ttcctgtgtc agtctatgaa atccctgttt	1740
  tgaaataagt aaacagccta aaatgtgttg aaattatttt gtaaatccat gacttaaaac	1800
  aagatacata catagtataa cacacctcac agtgttaaga tttatattgt gaaatgagac	1860
  accctacctt caattgttca tcagtgggta aaacaaattc tgatgtacat tcaggacaaa	1920
  tgattagccc taaatgaaac tgtaataatt tcagtggaaa ctcaatctgt ttttaccttt	1980
  aaacagtgaa ttttacatga atgaatgggt tcttcacttt ttttttagta tgagaaaatt	2040
  atacagtgct taattttcag agattctttc catatgttac taaaaaatgt tttgttcagc	2100
  ctaacatact gagttttttt taactttcta aattattgaa tttccatcat gcattcatcc	2160
  aaaattaagg cagactgttt ggattcttcc agtggccaga tgagctaaat taaatcacaa	2220
  aagcagatgc ttttgtatga tctccaaatt gccaacttta aggaaatatt ctcttgaaat	2280
  tgtctttaaa gatcttttgc agctttgcag atacccagac tgagctggaa ctggaatttg	2340
  tcttcctatt gactctactt ctttaaaagc ggctgcccat tacattcctc agctgtcctt	2400
  gcagttaggt gtacatgtga ctgagtgttg gccagtgaga tgaagtctcc tcaaaggaag	2460
  gcagcatgtg tcctttttca tcccttcatc ttgctgctgg gattgtggat ataacaggag	2520
  ccctggcagc tgtctccaga ggatcaaagc cacacccaaa gagtaaggca gattagagac	2580
  cagaaagacc ttgactactt ccctacttcc actgcttttt cctgcattta agccattgta	2640
  aatctgggtg tgttacatga agtgaaaatt aattctttct gcccttcagt tctttatcct	2700
  gataccattt aacactgtct gaattaacta gactgcaata attctttctt ttgaaagctt	2760
  ttaaaggata atgtgcaatt cacattaaaa ttgattttcc attgtcaatt agttatactc	2820
  attttcctgc cttgatcttt cattagatat tttgtatctg cttggaatat attatcttct	2880
  ttttaactgt gtaattggta attactaaaa ctctgtaatc tccaaaatat tgctatcaaa	2940
  ttacacacca tgttttctat cattctcata gatctgcctt ataaacattt aaataaaaag	3000
  tactatttaa tgatttaaaa aaaaaaaaaa aaaaaaaaaa a	3041

• [1273]

  TABLE LIII(a)
  Nucleotide sequence alignment of 98P4B6 v.1
  (SEQ ID NO: 154) and 98P4B6 v.2 (SEQ ID NO: 155)
  Score = 1429 bits (743), Expect = 0.0Identities =
  750/751 (99%), Gaps = 1/751 (0%) Strand = Plus/Plus

  V.1:	1687	gatcttttgcagctttgcagatacccagactgagctggaactggaatttgtcttcctatt	1746
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2291	gatcttttgcagctttgcagatacccagactgagctggaactggaatttgtcttcctatt	2350
  V.1:	1747	gactctacttctttaaaagcggctgcccattacattcctcagctgtccttgcagttaggt	1806
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2351	gactctacttctttaaaagcggctgcccattacattcctcagctgtccttgcagttaggt	2410
  V.1:	1807	gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtg	1866
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2411	gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtg	2470
  V.1:	1867	tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctggcagc	1926
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2471	tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctggcagc	2530
  V.1:	1927	tgtctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaaagacc	1986
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2531	tgtctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaaagacc	2590
  V.1:	1987	ttgactacttccctacttccactgctttt-cctgcatttaagccattgtaaatctgggtg	2045
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2591	ttgactacttccctacttccactgctttttcctgcatttaagccattgtaaatctgggtg	2650
  V.1:	2046	tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgataccattt	2105
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2651	tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgataccattt	2710
  V.1:	2106	aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaaggata	2165
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2711	aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaaggata	2770
  V.1:	2166	atgtgcaattcacattaaaattgattttccattgtcaattagttatactcattttcctgc	2225
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2771	atgtgcaattcacattaaaattgattttccattgtcaattagttatactcattttcctgc	2830
  V.1:	2226	cttgatctttcattagatattttgtatctgcttggaatatattatcttctttttaactgt	2285
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2831	cttgatctttcattagatattttgtatctgcttggaatatattatcttctttttaactgt	2890
  V.1:	2286	gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattacacacca	2345
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2891	gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattacacacca	2950
  V.1:	2346	tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtactatttaa	2405
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.2:	2951	tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtactatttaa	3010

  V.1:	2406	tgatttaaaaaaaaaaaaaaaaaaaaaaaaa	2436
  		|||||||||||||||||||||||||||||||
  V.2:	3011	tgatttaaaaaaaaaaaaaaaaaaaaaaaaa	3041

• [1274]

  TABLE LIV(a)
  Peptide sequences (partial) of protein coded by
  98P4B6 v.2 (SEQ ID NO: 156)

  SGSPGLQALS LSLSSGFTPF SCLSLPSSWD YRCPPPCPAD	45
  FFLYF

• [1275]

  TABLE LV(a)
  Amino acid sequence alignment of 98P4B6 v.1
  and 98P4B6 v.2

  	NO SIGNIFICANT HOMOLOGY

• [1276]

  TABLE LII(b)
  Nucleotide sequence of transcript variant 98P486 v.3 (SEQ ID NO: 157)

  ttctgctata gagatggaac agtatatgga aagctcccaa gaaagtgaag agaggaaatt	60
  ggaaaattgt gagtggacct tctgatactg ctcctccttg cgtggaaaag gggaaagaac	120
  tgcatgcata ttattcagcg tcctatattc aaaggatatt cttggtgatc ttqgaagtgt	180
  ccgtatcatq gaatcaatct ctatgatggg aagccctaag agccttaqtg aaacttgttt	240
  acctaatggc ataaatggta tcaaagatgc aaggaaggtc actgtaggtg tgattggaag	300
  tggagatttt gccaaatcct tgaccattcg acttattaga tgcggctatc atgtggtcat	360
  aggaagtaga aatcctaagt ttgcttctga attttttcct catgtggtag atgtcactca	420
  tcatgaagat gctctcacaa aaacaaatat aatatttgtt gctatacaca gagaacatta	480
  tacctccctg tgggacctga gacatctgct tgtgggtaaa atcctgattg atgtgagcaa	540
  taacatgagg ataaaccagt acccagaatc caatgctgaa tatttggctt cattattccc	600
  agattctttg attgtcaaag gatttaatgt tgtctcagct tgggcacttc agttaggacc	660
  taaggatgcc agccggcagg tttatatatg cagcaacaat attcaagcgc gacaacaggt	720
  tattgaactt gcccgccagt tgaatttcat tcccattgac ttgggatcct tatcatcagc	780
  cagagagatt gaaaatttac ccctacgact ctttactctc tggagagggc cagtggtggt	840
  agctataagc ttggccacat tttttttcct ttattccttt gtcagagatg tqattcatcc	900
  atatgctaga aaccaacaga gtgactttta caaaattcct atagagattg tgaataaaac	960
  cttacctata gttgccatta ctttgctctc cctagtatac cttgcaggtc ttctggcagc	1020
  tgcttatcaa ctttattacg gcaccaagta taggagattt ccaccttggt tggaaacctg	1080
  gttacagtgt agaaaacagc ttggattact aagttttttc ttcgctatgg tccatgttgc	1140
  ctacagcctc tgcttaccga tgagaaggtc agagagatat ttgtttctca acatggctta	1200
  tcagcaggtt catgcaaata ttgaaaactc ttggaatgag gaagaagttt ggagaattga	1260
  aatgtatatc tcctttggca taatgagcct tggcttactt tccctcctgg cagtcacttc	1320
  tatcccttca gtgagcaatg ctttaaactg gagagaattc agttttattc agtctacact	1380
  tggatatgtc gctctgctca taagtacttt ccatgtttta atttatggat ggaaacgagc	1440
  ttttgaggaa gagtactaca gattttatac accaccaaac tttgttcttg ctcttgtttt	1500
  gccctcaatt gtaattctgg atcttttgca gctttgcaga tacocagact gagctggaac	1560
  tggaatttgt cttcctattg actctacttc tttaaaagcg gctgcccatt acattcctca	1620
  gctgtccttg cagttaggtg tacatgtgac tgagtgttgg ccagtgagat gaagtctcct	1680
  caaaggaagg cagcatgtgt cctttttcat cccttcatct tgctgctggg attgtggata	1740
  taacaggagc cctggcagct gtctccagag gatcaaagcc acacccaaag agtaaggcag	1800
  attagagaca agaaagacct tgactacttc cctacttcca ctgctttttc ctgcatttaa	1860
  gccattgtaa atctgggtgt gttacatgaa gtgaaaatta attctttctg cccttcagtt	1920
  ctttatcctg ataccattta acactgtctg aattaactag actgcaataa ttctttcttt	1980
  tgaaagcttt taaaggataa tgtgcaattc acattaaaat tgattttcca ttgtcaatta	2040
  gttatactca ttttcctgcc ttgatctttc attagatatt ttgtatctgc ttggaatata	2100
  ttatcttctt tttaactgtg taattggtaa ttactaaaac tctgtaatct ccaaaatatt	2160
  gctatcaaat tacacaccat gttttctatc attctcatag atctgcctta taaacattta	2220
  aataaaaaqt actatttaat gatttaactt ctgttttgaa aaaaaaaaaa aaaaaaaaaa	2280

• [1277]

  TABLE LIII(b)
  Nucleotide sequence alignment of 98P4B6 v.1
  (SEQ ID NO: 158) and 98P4B6 v.3 (SEQ ID NO: 159)
  Score = 4013 bits (2087), Expect = 0.0Identities =
  2116/2128 (99%), Gaps = 1/2128 (0%) Strand = Plus/Plus

  V.1:	320	aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa	379
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	153	aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa	212
  V.1:	380	gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa	439
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	213	gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa	272
  V.1:	440	ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac	499
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	273	ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac	332
  V.1:	500	ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat	559
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	333	ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat	392
  V.1:	560	tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa	619
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	393	tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa	452
  V.1:	620	tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg	679
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	453	tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg	512
  V.1:	680	tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca	739
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	513	tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca	572
  V.1:	740	atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg	799
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	573	atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg	632
  V.1:	800	tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca	859
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	633	tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca	692
  V.1:	860	gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc	919
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	693	gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc	752
  V.1:	920	ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct	979
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	753	ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct	812
  V.1:	980	ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt	1039
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	813	ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt	872
  V.1:	1040	attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca	1099
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	873	attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca	932
  V.1:	1100	aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc	1159
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	933	aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc	992
  V.1:	1160	tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata	1219
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	993	tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata	1052
  V.1:	1220	ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa	1279
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1053	ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa	1112
  V.1:	1280	gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag	1339
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1113	gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag	1172
  V.1:	1340	agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt	1399
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1173	agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt	1232
  V.1:	1400	ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttc	1459
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1233	ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg	1292
  V.1:	1460	gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga	1519
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1293	gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga	1352
  V.1:	1520	gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttcc	1579
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1353	gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttcc	1412
  V.1:	1580	atgttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacac	1639
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1413	atgttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacac	1472
  V.1:	1640	caccaaactttgttcttgctcttgttttgccctcaattgtaattctggatcttttgcagc	1699
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1473	caccaaactttgttcttgctcttgttttgccctcaattgtaattctggatcttttgcagc	1532
  V.1:	1700	tttgcagatacccagactgagctggaactggaatttgtcttcctattgactctacttctt	1759
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1533	tttgcagatacccagactgagctggaactggaatttgtcttcctattgactctacttctt	1592
  V.1:	1760	taaaagcggctgcccattacattcctcagctgtccttgcagttaggtgtacatgtgactg	1819
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1593	taaaagcggctgcccattacattcctcagctgtccttgcagttaggtgtacatgtgactg	1652
  V.1:	1820	agtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtgtcctttttcatcc	1879
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1653	agtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtgtcctttttcatcc	1712
  V.1:	1880	cttcatcttgctgctgggattgtggatataacaggagccctggcagctgtctccagagga	1939
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1713	cttcatcttgctgctgggattgtggatataacaggagccctggcagctgtctccagagga	1772
  V.1:	1940	tcaaagccacacccaaagagtaaggcagattagagaccagaaagaccttgactacttccc	1999
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1773	tcaaagccacacccaaagagtaaggcagattagagaccagaaagaccttgactacttccc	1832
  V.1:	2000	tacttccactgcttttacctgcatttaagccattgtaaatctgggtgtgttacatgaagt	2058
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1833	tacttccactgctttttcctgcatttaagccattgtaaatctgggtgtgttacatgaagt	1892
  V.1:	2059	gaaaattaattctttctgcccttcagttdtttatcctgataccatttaacactgtctgaa	2118
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1893	gaaaattaattctttctgcccttcagttctttatcctgataccatttaacactgtctgaa	1952
  V.1:	2119	ttaactagactgcaataattctttcttttgaaagcttttaaaggataatgtgcaattcac	2178
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	1953	ttaactagactgcaataattctttcttttgaaagcttttaaaggataatgtgcaattcac	2012
  V.1:	2179	attaaaattgattttccattgtcaattagttatactcattttcctgccttgatctttcat	2238
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	2013	attaaaattgattttccattgtcaattagttatactcattttcctgccttgatctttcat	2072
  V.1:	2239	tagatattttgtatctgcttggaatatattatcttctttttaactgtgtaattggtaatt	2298
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	2073	tagatattttgtatctgcttggaatatattatcttctttttaactgtgtaattggtaatt	2132
  V.1:	2299	actaaaactctgtaatctccaaaatattgctatcaaattacacaccatgttttctatcat	2358
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	2133	actaaaactctgtaatctccaaaatattgctatcaaattacacaccatgttttctatcat	2192
  V.1:	2359	tctcatagatctgccttataaacatttaaataaaaagtactatttaatgatttaaaaaaa	2418
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.3:	2193	tctcatagatctgccttataaacatttaaataaaaagtactatttaatgatttaacttct	2252

  V.1:	2419	aaaaaaaaaaaaaaaaaaaaaaaaaaaa	2446
  		||||||||||||||||||||||||||||
  V.3:	2253	gttttgaaaaaaaaaaaaaaaaaaaaaa	2280
  AN INSERTION OF A SINGLE BASE AT 1845 OF V.3

• [1278]

  TABLE LV(b)
  Peptide sequences of protein coded
  by 98P4B6 v.3 (SEQ ID NO: 160)

  MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD FAKSLTIRLI RCGYHVVIGS	60
  RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS LWDLRHLLVG KILIDVSNNM	120
  RINQYPESNA EYLASLFPDS LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE	180
  LARQLNFIPI DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA	240
  RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ	300
  CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN EEKVWRIEMY	360
  ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY VALLISTFHV LIYGWKRAFE	420
  EEYYRFYTPP NFVLALVLPS IVILDLLQLC RYPD	454

• [1279]

  TABLE LV(b)
  Amino acid sequence alignment of 98P4B6 v.1
  (SEQ ID NO: 161) and 98P4B6 v.3 (SEQ ID NO: 162)
  Score = 910 bits (2351), Expect = 0.0Identities =
  454/454 (100%), Positives = 454/454 (100%)

  V.1:	1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  		MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVICSGDFAKSLTIRLIRCGYHVVIGS
  V.3:	1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  V.1:	61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  		RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM
  V.3:	61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  V.1:	121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  		RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE
  V.3:	121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  V.1:	181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  		LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA
  V.3:	181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  V.1:	241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYCTKYRRFPPWLETWLQ	300
  		RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ
  V.3:	241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  V.1:	301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  		CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY
  V.3:	301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  V.1:	361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE	420
  		ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE
  V.3:	361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREESFIQSTLGYVALLISTEHVLIYGWKRAFE	420

  V.1:	421	EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD	454
  		EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD
  V.3:	421	EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD	454

• [1280]

  TABLE LII(c)
  Nucleotide sequence of transcript
  variant 98P4B6 v.4 (SEQ ID NO: 163)

  cccacgcgtc cgcggacgcg tgggcggacg cgtgggttcc tcgggccctc ggcgccacaa	60
  gctgtccggg cacgcagccc ctagcggcgc gtcgctgcca agccggcctc cgcgcgcctc	120
  cctccttcct tctcccctgg ctgttcgcga tccagcttgg gtaggcgggg aagcagctgg	180
  agtgcgaccg ccacggcagc caccctgcaa ccgccagtcg gagagctaag ggcaagtcct	240
  gaggttgggc ccaggagaaa gaaggcaagg agacattgtc ccaggatatt cttggtgatc	300
  ttggaagtgt ccgtatcatg gaatcaatct ctatgatggg aagccctaag agccttagtg	360
  aaacttgttt acctaatggc ataaatggta tcaaagatgc aaggaaggtc actgtaggtg	420
  tgattggaag tggagatttt gccaaatcct tgaccattcg acttattaga tgcggctatc	480
  atgtggtcat aggaagtaga aatcctaagt ttgcttctga attttttcct catgtggtag	540
  atgtcactca tcatgaagat gctctcacaa aaacaaatat aatatttgtt gctatacaca	600
  gagaacatta tacctccctg tgggacctga gacatctgct tgtgggtaaa atcctgattg	660
  atgtgagcaa taacatgagg ataaaccagt acccagaatc caatgctgaa tatttggctt	720
  cattattccc agattctttg attgtcaaag gatttaatgt tgtctcagct tgggcacttc	780
  agttaggacc taaggatgcc agccggcagg tttatatatg cagcaacaat attcaagcgc	840
  gacaacaggt tattgaactt gcccgccagt tgaatttcat tcccattgac ttgggatcct	900
  tatcatcagc cagagagatt gaaaatttac ccctacgact ctttactctc tggagagggc	960
  cagtggtggt agctataagc ttggccacat tttttttcct ttattccttt gtcagagatg	1020
  tgattcatcc atatgctaga aaccaacaga gtgactttta caaaattcct atagagattg	1080
  tgaataaaac cttacctata gttgccatta ctttgctctc cctagtatac cttgcaggtc	1140
  ttctggcagc tgcttatcaa ctttattacg gcaccaagta taggagattt ccaccttggt	1200
  tggaaacctg gttacagtgt agaaaacagc ttggattact aagttttttc ttcgctatgg	1260
  tccatgttgc ctacagcctc tgcttaccga tgagaaggtc agagagatat ttgtttctca	1320
  acatggctta tcagcaggtt catgcaaata ttgaaaactc ttggaatgag gaagaagttt	1380
  ggagaattga aatgtatatc tcctttggca taatgagcct tggcttactt tccctcctgg	1440
  cagtcacttc tatcccttca gtgagcaatg ctttaaactg gagagaattc agttttattc	1500
  agtctacact tggatatgtc gctctgctca taagtacttt ccatgtttta atttatggat	1560
  ggaaacgagc ttttgaggaa gagtactaca gattttatac accaccaaac tttgttcttg	1620
  ctcttgtttt gccctcaatt gtaattctgg atcttttgca gctttgcaga tacccagact	1680
  gagctggaac tggaatttgt cttcctattg actctacttc tttaaaagcg gctgcccatt	1740
  acattcctca gctgtccttg cagttaggtg tacatgtgac tgagtgttgg ccagtgagat	1800
  gaagtctcct caaaggaagg cagcatgtgt cctttttcat cccttcatct tgctgctggg	1860
  attgtggata taacaggagc cctggcagct gtctccagag gatcaaagcc acacccaaag	1920
  agtaaggcag attagagacc agaaagacct tgactacttc cctacttcca ctgcttttcc	1980
  tgcatttaag ccattgtaaa tctgggtgtg ttacatgaag tgaaaattaa ttctttctgc	2040
  ccttcagttc tttatcctga taccatttaa cactgtctga attaactaga ctgcaataat	2100
  tctttctttt gaaagctttt aaaggataat gtgcaattca cattaaaatt gattttccat	2160
  tgtcaattag ttatactcat tttcctgcct tgatctttca ttagatattt tgtatctgct	2220
  tggaatatat tatcttcttt ttaactgtgt aattggtaat tactaaaact ctgtaatctc	2280
  caaaatattg ctatcaaatt acacaccatg ttttctatca ttctcataga tctgccttat	2340
  aaacatttaa ataaaaagta ctatttaatg attt	2374

• [1281]

  TABLE LIII(c)
  Nucleotide sequence alignment of 98P4B6 v.1
  (SEQ ID NO: 164) and 98P4B6 v.4 (SEQ ID NO: 165)

  Score = 404 bits (210), Expect =
  e-109Identities = 210/210 (100%) Strand = Plus/Plus

  V.1: 1	ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagctgtccgggcac	60
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 14	ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagctgtccgggcac	73
  V.1: 61	gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttccttct	120
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 74	gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttccttct	133
  V.1: 121	cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgaccgcca	180
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 134	cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgaccgcca	193
  V.1: 181	cggcagccaccctgcaaccgccagtcggag	210
  	||||||||||||||||||||||||||||||
  V.4: 194	cggcagccaccctgcaaccgccagtcggag	223

  Score = 4022 bits (2092), Expect = 0.0Identities =

  2092/2092 (100%) Strand = Plus/Plus

  V.1: 320	aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa	379
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 283	aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa	342
  V.1: 380	gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa	439
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 343	gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa	402
  V.1: 440	ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac	499
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 403	ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac	462
  V.1: 500	ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat	559
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 463	ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat	522
  V.1: 560	tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa	619
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 523	tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa	582
  V.1: 620	tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg	679
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 583	tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg	642
  V.1: 680	tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca	739
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 643	tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca	702
  V.1: 740	atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg	799
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 703	atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg	762
  V.1: 800	tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca	859
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 763	tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca	822
  V.1: 860	gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc	919
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 823	gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc	882
  V.1: 920	ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct	979
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 883	ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct	942
  V.1: 980	ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt	1039
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 943	ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt	1002
  V.1: 1040	attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca	1099
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1003	attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca	1062
  V.1: 1100	aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc	1159
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1063	aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc	1122
  V.1: 1160	tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata	1219
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1123	tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata	1182
  V.1: 1220	ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa	1279
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1183	ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa	1242
  V.1: 1280	gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag	1339
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1243	gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag	1302
  V.1: 1340	agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt	1399
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1303	agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt	1362
  V.1: 1400	ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg	1459
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1363	ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg	1422
  V.1: 1460	gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga	1519
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1423	gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga	1482
  V.1: 1520	gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttcc	1579
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1483	gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttcc	1542
  V.1: 1580	atgttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacac	1639
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1543	atgttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacac	1602
  V.1: 1640	caccaaactttgttcttgctcttgttttgccctcaattgtaattctggatcttttgcagc	1699
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1603	caccaaactttgttcttgctcttgttttgccctcaattgtaattctggatcttttgcagc	1662
  V.1: 1700	tttgcagatacccagactgagctggaactggaatttgtcttcctattgactctacttctt	1759
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1663	tttgcagatacccagactgagctggaactggaatttgtcttcctattgactctacttctt	1722
  V.1: 1760	taaaagcggctgcccattacattcctcagctgtccttgcagttaggtgtacatgtgactg	1819
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1723	taaaagcggctgcccattacattcctcagctgtccttgcagttaggtgtacatgtgactg	1782
  V.1: 1820	agtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtgtcctttttcatcc	1879
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1783	agtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtgtcctttttcatcc	1842
  V.1: 1880	cttcatcttgctgctgggattgtggatataacaggagccctggcagctgtctccagagga	1939
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1843	cttcatcttgctgctgggattgtggatataacaggagccctggcagctgtctccagagga	1902
  V.1: 1940	tcaaagccacacccaaagagtaaggcagattagagaccagaaagaccttgactacttccc	1999
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1903	tcaaagccacacccaaagagtaaggcagattagagaccagaaagaccttgactacttccc	1962
  V.1: 2000	tacttccactgcttttcctgcatttaagccattgtaaatctgggtgtgttacatgaagtg	2059
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 1963	tacttccactgcttttcctgcatttaagccattgtaaatctgggtgtgttacatgaagtg	2022
  V.1: 2060	aaaattaattctttctgcccttcagttctttatcctgataccatttaacactgtctgaat	2119
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 2023	aaaattaattctttctgcccttcagttctttatcctgataccatttaacactgtctgaat	2082
  V.1: 2120	taactagactgcaataattctttcttttgaaagcttttaaaggataatgtgcaattcaca	2179
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 2083	taactagactgcaataattctttcttttgaaagcttttaaaggataatgtgcaattcaca	2142
  V.1: 2180	ttaaaattgattttccattgtcaattagttatactcattttcctgccttgatctttcatt	2239
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 2143	ttaaaattgattttccattgtcaattagttatactcattttcctgccttgatctttcatt	2202
  V.1: 2240	agatattttgtatctgcttggaatatattatcttctttttaactgtgtaattggtaatta	2299
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 2203	agatattttgtatctgcttggaatatattatcttctttttaactgtgtaattggtaatta	2262
  V.1: 2300	ctaaaactctgtaatctccaaaatattgctatcaaattacacaccatgttttctatcatt	2359
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 2263	ctaaaactctgtaatctccaaaatattgctatcaaattacacaccatgttttctatcatt	2322
  V.1: 2360	ctcatagatctgccttataaacatttaaataaaaagtactatttaatgattt	2411
  	||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.4: 2323	ctcatagatctgccttataaacatttaaataaaaagtactatttaatgattt	2374

• [1282]

  TABLE LIV(c)
  Peptide sequences of protein coded by 98P4B6 v.4 (SEQ ID NO: 166)

  MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD FAKSLTIRLI RCGYHVVIGS	60
  RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS LWDLRHLLVG KILIDVSNNM	120
  RINQYPESNA EYLASLFPDS LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE	180
  LARQLNFIPI DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA	240
  RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ	300
  CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN EEEVWRIEMY	360
  ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY VALLISTFHV LIYGWKRAFE	420
  EEYYRFYTPP NFVLALVLPS IVILDLLQLC RYPD	454

• [1283]

  TABLE LV(c)
  Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID NO: 167)
  and 98P4B6 v.4 (SEQ ID NO: 168) Score = 910 bits (2351),
  Expect = 0.0Identities = 454/454 (100%), Positives = 454/454 (100%)

  V.1: 1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
  V.4: 1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  V.1: 61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM
  V.4: 61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  V.1: 121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE
  V.4: 121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  V.1: 181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA
  V.4: 181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  V.1: 241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ
  V.4: 241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  V.1: 301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY
  V.4: 301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  V.1: 361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE	420
  	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE
  V.4: 361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE	420
  V.1: 421	EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD	454
  	EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD
  V.4: 421	EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD	454

• [1284]

  TABLE LII(d)
  Nucleotide sequence of transcript
  variant 98P4B6 v.5 (SEQ ID NO: 169)

  cccacgcgtc cgcggacgcg tgggcggacg cgtgggttcc tcgggccctc ggcgccacaa	60
  gctgtccggg cacgcagccc ctagcggcgc gtcgctgcca agccggcctc cgcgcgcctc	120
  cctccttcct tctcccctgg ctgttcgcga tccagcttgg gtaggcgggg aagcagctgg	180
  agtgcgaccg ctacggcagc caccctgcaa ccgccagtcg gagagctaag ggcaagtcct	240
  gaggttgggc ccaggagaaa gaaggcaagg agacattgtc ccaggatatt cttggtgatc	300
  ttggaagtgt ccgtatcatg gaatcaatct ctatgatggg aagccctaag agccttagtg	360
  aaacttgttt acctaatggc ataaatggta tcaaagatgc aaggaaggtc actgtaggtg	420
  tgattggaag tggagatttt gccaaatcct tgaccattcg acttattaga tgcggctatc	480
  atgtggtcat aggaagtaga aatcctaagt ttgcttctga attttttcct catgtggtag	540
  atgtcactca tcatgaagat gctctcacaa aaacaaatat aatatttgtt gctatacaca	600
  gagaacatta tacctccctg tgggacctga gacatctgct tgtgggtaaa atcctgattg	660
  atgtgagcaa taacatgagg ataaaccagt acccagaatc caatgctgaa tatttggctt	720
  cattattccc agattctttg attgtcaaag gatttaatgt tgtctcagct tgggcacttc	780
  agttaggacc taaggatgcc agccggcagg tttatatatg cagcaacaat attcaagcgc	840
  gacaacaggt tattgaactt gcccgccagt tgaatttcat tcccattgac ttgggatcct	900
  tatcatcagc cagagagatt gaaaatttac ccctacgact ctttactttc tggagagggc	960
  cagtggtggt agctataagc ttggccacat tttttttcct ttattccttt gtcagagatg	1020
  tgattcatcc atatgctaga aaccaacaga gtgactttta caaaattcct atagagattg	1080
  tgaataaaac cttacctata gttgccatta ctttgctctc cctagtatac cttgcaggtc	1140
  ttctggcagc tgcttatcaa ctttattacg gcaccaagta taggagattt ccaccttggt	1200
  tggaaacctg gttacagtgt agaaaacagc ttggattact aagttttttc ttcgctatgg	1260
  tccatgttgc ctacagcctc tgcttaccga tgagaaggtc agagagatat ttgtttctca	1320
  acatggctta tcagcaggtt catgcaaata ttgaaaactc ttggaatgag gaagaagttt	1380
  ggagaattga aatgtatatc tcctttggca taatgagcct tggcttactt tccctcctgg	1440
  cagtcacttc tatcccttcg gtgagcaatg ctttaaactg gagagaattc agttttattc	1500
  agatcttttg cagctttgca gatacccaga ctgagctgga actggaattt gtcttcctat	1560
  tgactctact tctttaaaag cggctgccca ttacattcct cagctgtcct tgcagttagg	1620
  tgtacatgtg actgagtgtt ggccagtgag atgaagtctc ctcaaaggaa ggcagcatgt	1680
  gtcctttttc atcccttcat cttgctgctg ggattgtgga tataacagga gccctggcag	1740
  ctgctccaga ggatcaaagc cacacccaaa gagtaaggca gattagagac cagaaagacc	1800
  ttgactactt ccctacttcc actgcttttt cctgcattta agccattgta aatctgggtg	1860
  tgttacatga agtgaaaatt aattctttct gcccttcagt tctttatcct gataccattt	1920
  aacactgtct gaattaacta gactgcaata attctttctt ttgaaagctt ttaaaggata	1980
  atgtgcaatt cacattaaaa ttgattttcc attgtcaatt agttatactc attttcctgc	2040
  cttgatcttt cattagatat tttgtatctg cttggaatat attatcttct ttttaactgt	2100
  gtaattggta attactaaaa ctctgtaatc tccaaaatat tgctatcaaa ttacacacca	2160
  tgttttctat cattctcata gatctgcctt ataaacattt aaataaaaag tactatttac	2220
  caaaaaaaaa aaaaaaaaaa aaaaaaaaa	2249

• [1285]

  TABLE LIII(d)
  Nucleotide sequence alignment of 98P4B6 v.1
  (SEQ ID NO: 170) and 98P4B6 v.5 (SEQ ID NO: 171)
  Score = 398 bits (207), Expect =
  e-107Identities = 209/210 (99%) Strand = Plus / Plus

  V.1: 1	ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagctgtccgggcac	60
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 14	ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagctgtccgggcac	73
  V.1: 61	gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttccttct	120
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 74	gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttccttct	133
  V.1: 121	cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgaccgcca	180
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 134	cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgaccgcta	193
  V.1: 181	cggcagccaccctgcaaccgccagtcggag	210
  	||||||||||||||||||||||||||||||
  V.5: 194	cggcagccaccctgcaaccgccagtcggag	223

  Score = 2334 bits (1214), Expect =

  0.0Identities = 1218/1220 (99%) Strand = Plus / Plus

  V.1: 320	aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa	379
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 283	aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa	342
  V.1: 380	gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa	439
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 343	gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa	402
  V.1: 440	ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac	499
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 403	ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac	462
  V.1: 500	ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat	559
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 463	ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat	522
  V.1: 560	tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa	619
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 523	tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa	582
  V.1: 620	tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg	679
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 583	tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg	642
  V.1: 680	tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca	739
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 643	tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca	702
  V.1: 740	atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg	799
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 703	atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg	762
  V.1: 800	tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca	859
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 763	tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca	822
  V.1: 860	gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc	919
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 823	gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc	882
  V.1: 920	ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct	979
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 883	ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct	942
  V.1: 980	ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt	1039
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 943	ttactttctggagagggccagtggtggtagctataagcttggccacattttttttccttt	1002
  V.1: 1040	attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca	1099
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1003	attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca	1062
  V.1: 1100	aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc	1159
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1063	aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc	1122
  V.1: 1160	tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata	1219
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1123	tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata	1182
  V.1: 1220	ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa	1279
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1183	ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa	1242
  V.1: 1280	gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag	1339
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1243	gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag	1302
  V.1: 1340	agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt	1399
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1303	agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt	1362
  V.1: 1400	ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg	1459
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1363	ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg	1422
  V.1: 1460	gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga	1519
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1423	gcttactttccctcctggcagtcacttctatcccttcggtgagcaatgctttaaactgga	1482
  V.1: 1520	gagaattcagttttattcag	1539
  	||||||||||||||||||||
  V.5: 1483	gagaattcagttttattcag	1502

  Score 1375 bits (715), Expect = 0.0Identities =

  741/749 (98%), Gaps = 2/749 (0%) Strand = Plus / Plus

  V.1: 1687	gatcttttgcagctttgcagatacccagactgagctggaactggaatttgtcttcctatt	1746
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1502	gatcttttgcagctttgcagatacccagactgagctggaactggaatttgtcttcctatt	1561
  V.1: 1747	gactctacttctttaaaagcggctgcccattacattcctcagctgtccttgcagttaggt	1806
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1562	gactctacttctttaaaagcggctgcccattacattcctcagctgtccttgcagttaggt	1621
  V.1: 1807	gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtg	1866
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1622	gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtg	1681
  V.1: 1867	tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctggcagc	1926
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1682	tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctggcagc	1741
  V.1: 1927	tgtctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaaagacc	1986
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1742	tg-ctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaaagacc	1800
  V.1: 1987	ttgactacttccctacttccactgctttt-cctgcatttaagccattgtaaatctgggtg	2045
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1801	ttgactacttccctacttccactgctttttcctgcatttaagccattgtaaatctgggtg	1860
  V.1: 2046	tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgataccattt	2105
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1861	tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgataccattt	1920
  V.1: 2106	aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaaggata	2165
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1921	aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaaggata	1980
  V.1: 2166	atgtgcaattcacattaaaattgattttccattgtcaattagttatactcattttcctgc	2225
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 1981	atgtgcaattcacattaaaattgattttccattgtcaattagttatactcattttcctgc	2040
  V.1: 2226	cttgatctttcattagatattttgtatctgcttggaatatattatcttctttttaactgt	2285
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 2041	cttgatctttcattagatattttgtatctgcttggaatatattatcttctttttaactgt	2100
  V.1: 2286	gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattacacacca	2345
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 2101	gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattacacacca	2160
  V.1: 2346	tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtactatttaa	2405
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.5: 2161	tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtactatttac	2220
  V.1: 2406	tgatttaaaaaaaaaaaaaaaaaaaaaaa	2434
  	|||||||||||||||||||||||||||||
  V.5: 2221	caaaaaaaaaaaaaaaaaaaaaaaaaaaa	2249

• [1286]

  TABLE LIV(d)
  Peptide sequences of protein
  coded by 98P4B6 v.5 (SEQ ID NO: 172)

  MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD FAKSLTIRLI RCGYHVVIGS	60
  RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS LWDLRHLLVG KILIDVSNNM	120
  RINQYPESNA EYLASLFPDS LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE	180
  LARQLNFIPI DLGSLSSARE IENLPLRLFT FWRGPVVVAI SLATFFFLYS FVRDVIHPYA	240
  RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ	300
  CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN EEEVWRIEMY	360
  ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQIFCSF ADTQTELELE FVFLLTLLL	419

• [1287]

  TABLE LV(d)
  Amino acid sequence alignment of 98P4B6 v.1
  (SEQ ID NO: 173) and 98P4B6 v.5 (SEQ ID NO: 174)
  Score = 788 bits (2036), Expect =
  0.0Identities = 394/395 (99%), Positives = 394/395 (99%)

  V.1: 1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
  V.5: 1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  V.1: 61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM
  V.5: 61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  V.1: 121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE
  V.5: 121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  V.1: 181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  	LARQLNFIPIDLGSLSSAREIENLPLRLFT WRGPVVVAISLATFFFLYSFVRDVIHPYA
  V.5: 181	LARQLNFIPIDLGSLSSAREIENLPLRLFTFWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  V.1: 241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ
  V.5: 241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  V.1: 301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY
  V.5: 301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  V.1: 361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQ	395
  	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQ
  V.5: 361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQ	395

• [1288]

  TABLE LII(e)
  Nucleotide sequence of transcript
  variant 98P4B6 v.6 (SEQ ID NO: 175)

  cccacgcgtc cgcggacgcg tgggcggacg cgtgggttcc tcgggccctc ggcgccacaa	60
  gctgtccggg cacgcagccc ctagcggcgc gtcgctgcca agccggcctc cgcgcgcctc	120
  cctccttcct tctcccctgg ctgttcgcga tccagcttgg gtaggcgggg aagcagctgg	180
  agtgcgaccg ccacggcagc caccctgcaa ccgccagtcg gagagctaag ggcaagtcct	240
  gaggttgggc ccaggagaaa gaaggcaagg agacattgtc ccaggatatt cttggtgatc	300
  ttggaagtgt ccgtatcatg gaatcaatct ctatgatggg aagccctaag agccttagtg	360
  aaacttgttt acctaatggc ataaatggta tcaaagatgc aaggaaggtc actgtaggtg	420
  tgattggaag tggagatttt gccaaatcct tgaccattcg acttattaga tgcggctatc	480
  atgtggtcat aggaagtaga aatcctaagt ttgcttctga attttttcct catgtggtag	540
  atgtcactca tcatgaagat gctctcacaa aaacaaatat aatatttgtt gctatacaca	600
  gagaacatta tacctccctg tgggacctga gacatctgct tgtgggtaaa atcctgattg	660
  atgtgagcaa taacatgagg ataaaccagt acccagaatc caatgctgaa tatttggctt	720
  cattattccc agattctttg attgtcaaag gatttaatgt tgtctcagct tgggcacttc	780
  agttaggacc taaggatgcc agccggcagg tttatatatg cagcaacaat attcaagcgc	840
  gacaacaggt tattgaactt gcccgccagt tgaatttcat tcccattgac ttgggatcct	900
  tatcatcagc cagagagatt gaaaatttac ccctacgact ctttactctc tggagagggc	960
  cagtggtggt agctataagc ttggccacat tttttttcct ttattccttt gtcagagatg	1020
  tgattcatcc atatgctaga aaccaacaga gtgactttta caaaattcct atagagattg	1080
  tgaataaaac cttacctata gttgccatta ctttgctctc cctagtatac cttgcaggtc	1140
  ttctggcagc tgcttatcaa ctttattacg gcaccaagta taggagattt ccaccttggt	1200
  tggaaacctg gttacagtgt agaaaacagc ttggattact aagttttttc ttcgctatgg	1260
  tccatgttgc ctacagcctc tgcttaccga tgagaaggtc agagagatat ttgtttctca	1320
  acatggctta tcagcaggtt catgcaaata ttgaaaactc ttggaatgag gaagaagttt	1380
  ggagaattga aatgtatatc tcctttggca taatgagcct tggcttactt tccctcctgg	1440
  cagtcacttc tatcccttca gtgagcaatg ctttaaactg gagagaattc agttttattc	1500
  agtctacact tggatatgtc gctctgctca taagtacttt ccatgtttta atttatggat	1560
  ggaaacgagc ttttgaggaa gagtactaca gattttatac accaccaaac tttgttcttg	1620
  ctcttgtttt gccctcaatt gtaattctgg gtaagattat tttattcctt ccatgtataa	1680
  gccgaaagct aaaacgaatt aaaaaaggct gggaaaagag ccaatttctg gaagaaggta	1740
  ttggaggaac aattcctcat gtctccccgg agagggtcac agtaatgtga tgataaatgg	1800
  tgttcacagc tgccatataa agttctactc atgccattat ttttatgact tctacgttca	1860
  gttacaagta tgctgtcaaa ttatcgtggg ttgaaacttg ttaaatgaga tttcaactga	1920
  cttagtgata gagttttctt caagttaatt ttcacaaatg tcatgtttgc caatatgaat	1980
  ttttctagtc aacatattat tgtaatttag gtatgttttg ttttgttttg cacaactgta	2040
  accctgttgt tactttatat ttcataatca gacaaaaata cttacagtta ataatataga	2100
  tataatgtta aaaacaattt gcaaaccagc agaattttaa gcttttaaaa taattcaatg	2160
  gatatacatt tttttctgaa gattaagatt ttaattattc aacttaaaaa gtagaaatgc	2220
  attattatac atttttttaa gaaaggacac gttatgttag catctaggta aggctgcatg	2280
  atagcattcc tatatttctc tcataaaata ggatttgaag gatgaaatta attgtatgaa	2340
  gcaatgtgat tatatgaaga gacacaaatt aaaaagacaa attaaacctg aaattatatt	2400
  taaaatatat ttgagacatg aaatacatac tgataataca tacctcatga aagattttat	2460
  tctttattgt gttacagagc agtttcattt tcatattaat atactgatca ggaagaggat	2520
  tcagtaacat ttggcttcca aaactgctat ctctaatacg gtaccaatcc taggaactgt	2580
  atactagttc ctacttagaa caaaagtatc aagtttgcac acaagtaatc tgccagctga	2640
  cctttgtcgc accttaacca gtcaccactt gctatggtat aggattatac tgatgttctt	2700
  tgagggattc tgatgtgcta ggcatggttc taagtacttt acttgtatta tcccatttaa	2760
  tacttagaac aaccccgtga gataagtagt tattatcctc attttacaca tgagggaccg	2820
  aaggatagaa aagttatttt tcaaaggtct tgcagttaat aaatggcaga gtgagcattc	2880
  aagtccaggt agtcatattc cagaggccac ggttttaacc actaggctct agagctcccg	2940
  ccgcgcccct atgcattatg ttcacaatgc caatctagat gcttcctctt ttgtataaag	3000
  tcactgacat tctttagagt gggttgggtg catccaaaaa tgtataaaaa tattattata	3060
  ataaacttat tactgcttgt agggtaattc acagttactt accctattct tgcttggaac	3120
  atgagcctgg agacccatgg cagtccatat gcctccctat gcagtgaagg gccctagcag	3180
  tgttaacaaa ttgctgagat cccacggagt ctttcaaaaa tctctgtaga gttagtcttc	3240
  tccttttctc ttcctgagaa gttctcctgc ctgcataacc attcattagg gagtacttta	3300
  caagcatgaa ggatattagg gtaagtggct aattataaat ctactctaga gacatataat	3360
  catacagatt attcataaaa tttttcagtg ctgtccttcc acatttaatt gcattttgct	3420
  caaactgtag aatgccctac attcccccca ccccaatttg ctatttcctt attaaaatag	3480
  aaaattatag gcaagataca attatatgcg ttcctcttcc tgaaattata acatttctaa	3540
  acttacccac gtagggacta ctgaatccaa ctgccaacaa taaaaagact tttatttagt	3600
  agaggctacc tttcccccca gtgactcttt ttctacaact gccttgtcag tttggtaatt	3660
  cacttatgat tttctaatgt tctcttggtg aattttatta tcttggaccc tctttttttt	3720
  tttttttaaa gacagagtct tgctctgtca ccca	3754

• [1289]

  TABLE LIII(e)
  Nucleotide sequence alignment of 98P4B6 v.1
  (SEQ ID NO: 176) and 98P4B6 v.6 (SEQ ID NO: 177)
  Score = 404 bits (210), Expect = e-109Identities =
  210/210 (100%) Strand = Plus / Plus

  V.1: 1	ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagctgtccgggcac	60
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 14	ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagctgtccgggcac	73
  V.1: 61	gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttccttct	120
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 74	gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttccttct	133
  V.1: 121	cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgaccgcca	180
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 134	cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgaccgcca	193
  V.1: 181	cggcagccaccctgcaaccgccagtcggag	210
  	||||||||||||||||||||||||||||||
  V.6: 194	cggcagccaccctgcaaccgccagtcggag	223

  Score = 2630 bits (1368), Expect =

  0.0Identities = 1368/1368 (100%) Strand = Plus / Plus

  V.1: 320	aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa	379
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 283	aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa	342
  V.1: 380	gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa	439
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 343	gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa	402
  V.1: 440	ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac	499
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 403	ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac	462
  V.1: 500	ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat	559
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 463	ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat	522
  V.1: 560	tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa	619
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 523	tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa	582
  V.1: 620	tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg	679
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 583	tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg	642
  V.1: 680	tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca	739
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 643	tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca	702
  V.1: 740	atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg	799
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 703	atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg	762
  V.1: 800	tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca	859
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 763	tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca	822
  V.1: 860	gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc	919
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 823	gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc	882
  V.1: 920	ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct	979
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 883	ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct	942
  V.1: 980	ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt	1039
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 943	ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt	1002
  V.1: 1040	attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca	1099
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1003	attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca	1062
  V.1: 1100	aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc	1159
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1063	aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc	1122
  V.1: 1160	tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata	1219
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1123	tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata	1182
  V.1: 1220	ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa	1279
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1183	ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa	1242
  V.1: 1280	gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag	1339
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1243	gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag	1302
  V.1: 1340	agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt	1399
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1303	agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt	1362
  V.1: 1400	ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg	1459
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1363	ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg	1422
  V.1: 1460	gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga	1519
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1423	gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga	1482
  V.1: 1520	gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttcc	1579
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1483	gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttcc	1542
  V.1: 1580	atgttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacac	1639
  	||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1543	atgttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacac	1602
  V.1: 1640	caccaaactttgttcttgctcttgttttgccctcaattgtaattctgg	1687
  	||||||||||||||||||||||||||||||||||||||||||||||||
  V.6: 1603	caccaaactttgttcttgctcttgttttgccctcaattgtaattctgg	1650

• [1290]

  TABLE LIV(e)
  Peptide sequences of protein coded by 98P4B6 v.6 (SEQ ID NO: 178)

  MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD FAKSLTIRLI RCGYHVVIGS	60
  RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS LWDLRHLLVG KILIDVSNNM	120
  RINQYPESNA EYLASLFPDS LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE	180
  LARQLNFIPI DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA	240
  RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ	300
  CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN EEEVWRIEMY	360
  ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY VALLISTFHV LIYGWKRAFE	420
  EEYYRFYTPP NFVLALVLPS IVILGKIILF LPCISRKLKR IKKGWEKSQF LEEGIGGTIP	480
  HVSPERVTVM	490

• [1291]

  TABLE LV(e)
  Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID NO: 179) and 98P4B6
  v.6 (SEQ ID NO: 180)
  Score = 888 bits (2294), Expect = 0.0Identities = 444/444 (100%),
  Positives = 444/444 (100%)

  V.1:	1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  		MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
  V.6:	1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  V.1:	61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  		RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM
  V.6:	61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  V.1:	121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  		RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE
  V.6:	121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  V.1:	181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  		LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA
  V.6:	181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  V.1:	241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  		RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ
  V.6:	241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  V.1:	301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  		CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY
  V.6:	301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  V.1:	361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE	420
  		ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE
  V.6:	361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE	420
  V.1:	421	EEYYRFYTPPNFVLALVLPSIVIL	444
  		EEYYRFYTPPNFVLALVLPSIVIL
  V.6:	421	EEYYRFYTPPNFVLALVLPSIVIL	444

• [1292]

  TABLE LII(f)
  Nucleotide sequence of transcript variant 98P4B6 v.7 (SEQ ID NO: 181)

  ggagaaaatt tacagaaacc cagagccaaa ggtgctctca ggggatcccc tgaaacattc	60
  aaagccattg cggccccaga agcttgggta ggcggggaag cagctggagt gcgaccgccg	120
  cggcagccac cctgcaaccg ccagtcggag gtgcagtccg taggccctgg cccccgggtg	180
  ggcccttggg gagtcggcgc cgctcccggg gagctgcaag gctcgcccct gcccggcgtg	240
  gagggcgcgg ggggcgcgga ggatattctt ggtgatcttg gaagtgtccg tatcatggaa	300
  tcaatctcta tgatgggaag ccctaagagc cttagtgaaa cttttttacc taatggcata	360
  aatggtatca aagatgcaag gaaggtcact gtaggtgtga ttggaagtgg agattttgcc	420
  aaatccttga ccattcgact tattagatgc ggctatcatg tggtcatagg aagtagaaat	480
  cctaagtttg cttctgaatt ttttcctcat gtggtagatg tcactcatca tgaagatgct	540
  ctcacaaaaa caaatataat atttgttgct atacacagag aacattatac ctccctgtgg	600
  gacctgagac atctgcttgt gggtaaaatc ctgattgatg tgagcaataa catgaggata	660
  aaccagtacc cagaatccaa tgctgaatat ttggcttcat tattcccaga ttctttgatt	720
  gtcaaaggat ttaatgttgt ctcagcttgg gcacttcagt taggacctaa ggatgccagc	780
  cggcaggttt atatatgcag caacaatatt caagcgcgac aacaggttat tgaacttgcc	840
  cgccagttga atttcattcc cattgacttg ggatccttat catcagccag agagattgaa	900
  aatttacccc tacgactctt tactctctgg agagggccag tggtggtagc tataagcttg	960
  gccacatttt ttttccttta ttcctttgtc agagatgtga ttcatccata tgctagaaac	1020
  caacagagtg acttttacaa aattcctata gagattgtga ataaaacctt acctatagtt	1080
  gccattactt tgctctccct agtatacctc gcaggtcttc tggcagctgc ttatcaactt	1140
  tattacggca ccaagtatag gagatttcca ccttggttgg aaacctggtt acagtgtaga	1200
  aaacagcttg gattactaag ttttttcttc gctatggtcc atgttgccta cagcctctgc	1260
  ttaccgatga gaaggtcaga gagatatttg tttctcaaca tggcttatca gcagtctaca	1320
  cttggatatg tcgctctgct cataagtact ttccatgttt taatttatgg atggaaacga	1380
  gcttttgagg aagagtacta cagattttat acaccaccaa actttgttct tgctcttgtt	1440
  ttgccctcaa ttgtaattct ggatctgtct gtggaggttc tggcttcccc agctgctgcc	1500
  tggaaatgct taggtgctaa tatcctgaga ggaggattgt cagagatagt actccccata	1560
  gagtggcagc aggacaggaa gatcccccca ctctccaccc cgccgccacc ggccatgtgg	1620
  acagaggaag ccggggcgac cgccgaggcc caggaatccg gcatcaggaa caagtctagc	1680
  agttccagtc aaatcccggt ggttggggtg gtgacggagg acgatgaggc gcaggattcc	1740
  attgatcccc cagagagccc tgatcgtgcc ttaaaagccg cgaattcctg gaggaaccct	1800
  gtcctgcctc acactaatgg tgtggggcca ctgtgggaat tcctgttgag gcttctcaaa	1860
  tctcaggctg cgtcaggaac cctgtctctt gcgttcacat cctggagcct tggagagttc	1920
  cttgggagtg ggacatggat gaagctggaa accataattc tcagcaaact aacacaggaa	1980
  cagaaatcca aacactgcat gttctcactg ataagtggga gttgaacaat gagaacacat	2040
  ggacacaggg aggggaacgt cacacaccag ggcctgtcgg gggtgggagg cctagcaatt	2100
  cattagaatt acctgtgaag cttttaaaat gtaaggtttg gatggaatgc tcagacccta	2160
  ccttagaccc aattaagccc acagctttga gg	2192

• [1293]

  TABLE LIII(f)
  Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID NO: 182) and 98P4B6 v.7
  (SEQ ID NO: 183)
  Score = 2350 bits (1222), Expect = 0.0Identities = 1230/1234 (99%)
  Strand = Plus/Plus

  V.1:	141	agcttgggtaggcggggaagcagctggagtgcgaccgccacggcagccaccctgcaaccg	200
  		||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
  V.7:	81	agcttgggtaggcggggaagcagctggagtgcgaccgccgcggcagccaccctgcaaccg	140
  V.1:	201	ccagtcggaggtgcagtccgtaggccctggcccccgggtgggcccttggggagtcggcgc	260
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	141	ccagtcggaggtgcagtccgtaggccctggcccccgggtgggcccttggggagtcggcgc	200
  V.1:	261	cgctcccgaggagctgcaaggctcgcccctgcccggcgtggagggcgcggggggcgcgga	320
  		|||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	201	cgctcccggggagctgcaaggctcgcccctgcccggcgtggagggcgcggggggcgcgga	260
  V.1:	321	ggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaag	380
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	261	ggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaag	320
  V.1:	381	ccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaag	440
  		||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
  V.7:	321	ccctaagagccttagtgaaacttttttacctaatggcataaatggtatcaaagatgcaag	380
  V.1:	441	gaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgact	500
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	381	gaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgact	440
  V.1:	501	tattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaatt	560
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	441	tattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaatt	500
  V.1:	561	ttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataat	620
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	501	ttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataat	560
  V.1:	621	atttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttgt	680
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	561	atttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttgt	620
  V.1:	681	gggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatccaa	740
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	621	gggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatccaa	680
  V.1:	741	tgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttgt	800
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	681	tgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttgt	740
  V.1:	801	ctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgcag	860
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	741	ctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgcag	800
  V.1:	861	caacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattcc	920
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	801	caacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattcc	860
  V.1:	921	cattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactctt	980
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	861	cattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactctt	920
  V.1:	981	tactctctggagagggccagtggtggtagctataagcttggccacattttttttccttta	1040
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	921	tactctctggagagggccagtggtggtagctataagcttggccacattttttttccttta	980
  V.1:	1041	ttcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttacaa	1100
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	981	ttcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttacaa	1040
  V.1:	1101	aattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccct	1160
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	1041	aattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccct	1100
  V.1:	1161	agtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtatag	1220
  		||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	1101	agtatacctcgcaggtcttctggcagctgcttatcaactttattacggcaccaagtatag	1160
  V.1:	1221	gagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaag	1280
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	1161	gagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaag	1220
  V.1:	1281	ttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcaga	1340
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	1221	ttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcaga	1280
  V.1:	1341	gagatatttgtttctcaacatggcttatcagcag	1374
  		||||||||||||||||||||||||||||||||||
  V.7:	1281	gagatatttgtttctcaacatggcttatcagcag	1314

  Score = 298 bits (155), Expect = 2e-77Identities = 155/155 (100%)
  Strand = Plus/Plus

  V.1:	1537	cagtctacacttggatatgtcgctctgctcataagtactttccatgttttaatttatgga	1596
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	1312	cagtctacacttggatatgtcgctctgctcataagtactttccatgttttaatttatgga	1371
  V.1:	1597	tggaaacgagcttttgaggaagagtactacagattttatacaccaccaaactttgttctt	1656
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.7:	1372	tggaaacgagcttttgaggaagagtactacagattttatacaccaccaaactttgttctt	1431
  V.1:	1657	gctcttgttttgccctcaattgtaattctggatct	1691
  		|||||||||||||||||||||||||||||||||||
  V.7:	1432	gctcttgttttgccctcaattgtaattctggatct	1466

• [1294]

  TABLE LIV(f)
  Peptide sequences of protein coded by 98P4B6 v.7 (SEQ ID NO: 184)

  MESISMMGSP KSLSETFLPN GINGIKDARK VTVGVIGSGD FAKSLTIRLI RCGYHVVIGS	60
  RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS LWDLRHLLVG KILIDVSNNM	120
  RINQYPESNA EYLASLFPDS LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE	180
  LARQLNFIPI DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA	240
  RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ	300
  CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ STLGYVALLI STFHVLIYGW	360
  KRAFEEEYYR FYTPPNFVLA LVLPSIVILD LSVEVLASPA AAWKCLGANI LRGGLSEIVL	420
  PIEWQQDRKI PPLSTPPPPA MWTEEAGATA EAQESGIRNK SSSSSQIPVV GVVTEDDEAQ	480
  DSIDPPESPD RALKAANSWR NPVLPHTNGV GPLWEFLLRL LKSQAASGTL SLAFTSWSLG	540
  EFLGSGTWMK LETIILSKLT QEQKSKHCMF SLISGS	576

• [1295]

  TABLE LV(f)
  Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID NO: 185) and 98P4B6
  v.7 (SEQ ID NO: 186)
  Score = 753 bits (1944), Expect = 0.0Identities = 390/446 (87%),
  Positives = 390/446 (87%), Gaps = 55/446 (12%)

  V.1:	1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  		MESISMMGSPKSLSET LPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
  V.7:	1	MESISMMGSPKSLSETFLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  V.1:	61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  		RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM
  V.7:	61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  V.1:	121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  		RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE
  V.7:	121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  V.1:	181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  		LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA
  V.7:	181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  V.1:	241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  		RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ
  V.7:	241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  V.1:	301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  		CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQ
  V.7:	301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQ--------------------	340
  V.1:	361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE	420
  		STLGYVALLISTFHVLIYGWKRAFE
  V.7:	341	-----------------------------------STLGYVALLISTFHVLIYGWKRAFE	365
  V.1:	421	EEYYRFYTPPNFVLALVLPSIVILDL	446
  		EEYYRFYTPPNFVLALVLPSIVILDL
  V.7:	366	EEYYRFYTPPNFVLALVLPSIVILDL	391

• [1296]

  TABLE LII(g)
  Nucleotide sequence of transcript variant 98P4B6 v.8 (SEQ ID NO: 187)

  gccccctccg agctccccga ctcctccccg cgctccacgg ctcttcccga ctccagtcag	60
  cgttcctcgg gccctcggcg ccacaagctg tccgggcacg cagcccctag cggcgcgtcg	120
  ctgccaagcc ggcctccgcg cgcctccctc cttccttctc ccctggctgt tcgcgatcca	180
  gcttgggtag gcggggaagc agctggagtg cgaccgccac ggcagccacc ctgcaaccgc	240
  cagtcggagg tgcagtccgt aggccctggc ccccgggtgg gcccttgggg agtcggcgcc	300
  gctcccgagg agctgcaagg ctcgcccctg cccggcgtgg agggcgcggg gggcgcggag	360
  gatattcttg gtgatcttgg aagtgtccgt atcatggaat caatctctat gatgggaagc	420
  cctaagagcc ttagtgaaac ttgtttacct aatggcataa atggtatcaa agatgcaagg	480
  aaggtcactg taggtgtgat tggaagtgga gattttgcca aatccttgac cattcgactt	540
  attagatgcg gctatcatgt ggtcatagga agtagaaatc ctaagtttgc ttctgaattt	600
  tttcctcatg tggtagatgt cactcatcat gaagatgctc tcacaaaaac aaatataata	660
  tttgttgcta tacacagaga acattatacc tccctgtggg acctgagaca tctgcttgtg	720
  ggtaaaatcc tgattgatgt gagcaataac atgaggataa accagtaccc agaatccaat	780
  gctgaatatt tggcttcatt attcccagat tctttgattg tcaaaggatt taatgttgtc	840
  tcagcttggg cacttcagtt aggacctaag gatgccagcc ggcaggttta tatatgcagc	900
  aacaatattc aagcgcgaca acaggttatt gaacttgccc gccagttgaa tttcattccc	960
  attgacttgg gatccttatc atcagccaga gagattgaaa atttacccct acgactcttt	1020
  actctctgga gagggccagt ggtggtagct ataagcttgg ccacattttt tttcctttat	1080
  tcctttgtca gagatgtgat tcatccatat gctagaaacc aacagagtga cttttacaaa	1140
  attcctatag agattgtgaa taaaacctta cctatagttg ccattacttt gctctcccta	1200
  gtataccttg caggtcttct ggcagctgct tatcaacttt attacggcac caagtatagg	1260
  agatttccac cttggttgga aacctggtta cagtgtagaa aacagcttgg attactaagt	1320
  tttttcttcg ctatggtcca tgttgcctac agcctctgct taccgatgag aaggtcagag	1380
  agatatttgt ttctcaacat ggcttatcag caggttcatg caaatattga aaactcttgg	1440
  aatgaggaag aagtttggag aattgaaatg tatatctcct ttggcataat gagccttggc	1500
  ttactttccc tcctggcagt cacttctatc ccttcagtga gcaatgcttt aaactggaga	1560
  gaattcagtt ttattcagtc tacacttgga tatgtcgctc tgctcataag tactttccat	1620
  gttttaattt atggatggaa acgagctttt gaggaagagt actacagatt ttatacacca	1680
  ccaaactttg ttcttgctct tgttttgccc tcaattgtaa ttctgggtaa gattatttta	1740
  ttccttccat gtataagccg aaagctaaaa cgaattaaaa aaggctggga aaagagccaa	1800
  tttctggaag aaggtatggg aggaacaatt cctcatgtct ccccggagag ggtcacagta	1860
  atgtgatgac aaatggtgtt cacagctgcc atataaagtt ctactcatgc cattattttt	1920
  atgacttcta cgttcagtta caagtatgct gtcaaattat cgtgggttga aacttgttaa	1980
  atgagatttc aactgactta gtgatagagt tttcttcaag ttaattttca caaatgtcat	2040
  gtttgccaat atgaattttt ctagtcaaca tattattgta atttaggtat gttttgtttt	2100
  gttttgcaca actgtaaccc tgttgttact ttatatttca taatcaggca aaaatactta	2160
  cagttaataa tatagatata atgttaaaaa caatttgcaa accagcagaa ttttaagctt	2220
  ttaaaataat tcaatggata tacatttttt tctgaagatt aagattttaa ttattcaact	2280
  taaaaagtag aaatgcatta ttatacattt ttttaagaaa ggacacgtta tgttagcatc	2340
  taggtaaggc tgcatgatag cattcctata tttctctcat aaaataggat ttgaaggatg	2400
  aaattaattg tatgaagcaa tgtgattata tgaagagaca caaattaaaa agacaaatta	2460
  aacctgaaat tatatttaaa atatatttga gacatgaaat acatactgat aatacatacc	2520
  tcatgaaaga ttttattctt tattgtgtta cagagcagtt tcattttcat attaatatac	2580
  tgatcaggaa gaggattcag taacatttgg cttccaaaac tgctatctct aatacggtac	2640
  caatcctagg aactgtatac tagttcctac ttagaacaaa agtatcaagt ttgcacacaa	2700
  gtaatctgcc agctgacctt tgtcgcacct taaccagtca ccacttgcta tggtatagga	2760
  ttatactgat gttctttgag ggattctgat gtgctaggca tggttctaag tactttactt	2820
  gtattatccc atttaatact tagaacaacc ccgtgagata agtagttatt atcctcattt	2880
  tacacatgag ggaccgaagg atagaaaagt tatttttcaa aggtcttgca gttaataaat	2940
  ggcagagtga gcattcaagt ccaggtagtc atattccaga ggccacggtt ttaaccacta	3000
  ggctctagag ctcccgccgc gcccctatgc attatgttca caatgccaat ctagatgctt	3060
  cctcttttgt ataaagtcac tgacattctt tagagtgggt tgggtgcatc caaaaatgta	3120
  taaaaatatt attataataa acttattact gcttgtaggg taattcacag ttacttaccc	3180
  tattcttgct tggaacatga gcctggagac ccatggcagt ccatatgcct ccctatgcag	3240
  tgaagggccc tagcagtgtt aacaaattgc tgagatccca cggagtcttt caaaaatctc	3300
  tgtagagtta gtcttctcct tttctcttcc tgagaagttc tcctgcctgc ataaccattc	3360
  attagggagt actttacaag catgaaggat attagggtaa gtggctaatt ataaatctac	3420
  tctagagaca tataatcata cagattattc ataaaatttt tcagtgctgt ccttccacat	3480
  ttaattgcat tttgctcaaa ctgtagaatg ccctacattc cccccacccc aatttgctat	3540
  ttccttatta aaatagaaaa ttataggcaa gatacaatta tatgcgttcc tcttcctgaa	3600
  attataacat ttctaaactt acccacgtag gtactactga atccaactgc caacaataaa	3660
  aagactttta tttagtagag gctacctttc ccaccagtga ctctttttct acaactgcct	3720
  tgtcagtttg gtaattcact tatgattttc taatgttctc ttggtgaatt ttattatctt	3780
  gtaccctctt tttttttttt ttttttttta aagacagagt cttgctctgt cacccaggct	3840
  ggagtgcagt ggcacgatct cggctcactg caagctctgc ctcccgggtt cacgccattc	3900
  tcctgcctca gcctcccgag tagctgggac tacaggtgcc cgccaccatg cccggctgat	3960
  ttctttttgt atttttagta gagacggagt ttcaccgtgt tagccaggat ggtctcgatc	4020
  tcctgacctc gtgatccgcc cgccttggcc tccaaagtgc tgggattaca ggtgtgagct	4080
  accgcgcccg gcctattatc ttgtactttc taactgagcc ctctattttc tttattttaa	4140
  taatatttct ccccacttga gaatcacttg ttagttcttg gtaggaattc agttgggcaa	4200
  tgataacttt tatgggcaaa aacattctat tatagtgaac taatgaaaat aacagcgtat	4260
  tttcaatatt ttcttattcc ttaaattcca ctcttttaac actatgctta accacttaat	4320
  gtgatgaaat attcctaaaa gttaaatgac tattaaagca tatattgttg catgtatata	4380
  ttaagtagcc gatactctaa ataaaaatac cactgttaca gataaatggg gcctttaaaa	4440
  atatgaaaaa caaacttgtg aaaatgtata aaagatgcat ctgttgtttc aaatggcact	4500
  atcttctttt cagtactaca aaaacagaat aattttgaag ttttagaata aatgtaatat	4560
  atttactata attctaaatg tttaaatgct tttctaaaaa tgcaaaacta tgatgtttag	4620
  ttgctttatt ttacctctat gtgattattt ttcttaattg ttatttttta taatcattat	4680
  ttttctgaac cattcttctg gcctcagaag taggactgaa ttctactatt gctaggtgtg	4740
  agaaagtggt ggtgagaacc ttagagcagt ggagatttgc tacctggtct gtgttttgag	4800
  aagtgcccct tagaaagtta aaagaatgta gaaaagatac tcagtcttaa tcctatgcaa	4860
  aaaaaaaaat caagtaattg ttttcctatg aggaaaataa ccatgagctg tatcatgcta	4920
  cttagctttt atgtaaatat ttcttatgtc tcctctatta agagtattta aaatcatatt	4980
  taaatatgaa tctattcatg ctaacattat ttttcaaaac atacatggaa atttagccca	5040
  gattgtctac atataaggtt tttatttgaa ttgtaaaata tttaaaagta tgaataaaat	5100
  atatttatag gtatttatca gagatgatta ttttgtgcta catacaggtt ggctaatgag	5160
  ctctagtgtt aaactacctg attaatttct tataaagcag cataaccttg gcttgattaa	5220
  ggaattctac tttcaaaaat taatctgata atagtaacaa ggtatattat actttcatta	5280
  caatcaaatt atagaaatta cttgtgtaaa agggcttcaa gaatatatcc aatttttaaa	5340
  tattttaata tatctcctat ctgataactt aattcttcta aattaccact tgccattaag	5400
  ctatttcata ataaattctg tacagtttcc ccccaaaaaa gagatttatt tatgaaatat	5460
  ttaaagtttc taatgtggta ttttaaataa agtatcataa atgtaataag taaatattta	5520
  tttaggaata ctgtgaacac tgaactaatt attcctgtgt cagtctatga aatccctgtt	5580
  ttgaaatacg taaacagcct aaaatgtgtt gaaattattt tgtaaatcca tgacttaaaa	5640
  caagatacat acatagtata acacacctca cagtgttaag atttatattg tgaaatgaga	5700
  caccctacct tcaattgttc atcagtgggt aaaacaaatt ctgatgtaca ttcaggacaa	5760
  atgattagcc ctaaatgaaa ctgtaataat ttcagtggaa actcaatctg tttttacctt	5820
  taaacagtga attttacatg aatgaatggg ttcttcactt tttttttagt atgagaaaat	5880
  tatacagtgc ttaattttca gagattcttt ccatatgtta ctaaaaaatg ttttgttcag	5940
  cctaacatac tgagtttttt ttaactttct aaattattga atttccatca tgcattcatc	6000
  caaaattaag gcagactgtt tggattcttc cagtggccag atgagctaaa ttaaatcaca	6060
  aaagcagatg cttttgtatg atctccaaat tgccaacttt aaggaaatat tctcttgaaa	6120
  ttgtctttaa agatcttttg cagctttgca gatacccaga ctgagctgga actggaattt	6180
  gtcttcctat tgactctact tctttaaaag cggctgccca ttacattcct cagctgtcct	6240
  tgcagttagg tgtacatgtg actgagtgtt ggccagtgag atgaagtctc ctcaaaggaa	6300
  ggcagcatgt gtcctttttc atcccttcat cttgctgctg ggattgtgga tataacagga	6360
  gccctggcag ctgtctccag aggatcaaag ccacacccaa agagtaaggc agattagaga	6420
  ccagaaagac cttgactact tccctacttc cactgctttt tcctgcattt aagccattgt	6480
  aaatctgggt gtgttacatg aagtgaaaat taattctttc tgcccttcag ttctttatcc	6540
  tgataccatt taacactgtc tgaattaact agactgcaat aattctttct tttgaaagct	6600
  tttaaaggat aatgtgcaat tcacattaaa attgattttc cattgtcaat tagttatact	6660
  cattttcctg ccttgatctt tcattagata ttttgtatct gcttggaata tattatcttc	6720
  tttttaactg tgtaattggt aattactaaa actctgtaat ctccaaaata ttgctatcaa	6780
  attacacacc atgttttcta tcattctcat agatctgcct tataaacatt taaataaaaa	6840
  gtactattta atgattt	6857

• [1297]

  TABLE LIII(g)
  Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID NO: 188) and 98P4B6 v.8
  (SEQ ID NO: 189)
  Score = 3201 bits (1665), Expect = 0.0Identities = 1665/1665 (100%)
  Strand = Plus/Plus

  V.1:	23	gttcctcgggccctcggcgccacaagctgtccgggcacgcagcccctagcggcgcgtcgc	82
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	62	gttcctcgggccctcggcgccacaagctgtccgggcacgcagcccctagcggcgcgtcgc	121
  V.1:	83	tgccaagccggcctccgcgcgcctccctccttccttctcccctggctgttcgcgatccag	142
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	122	tgccaagccggcctccgcgcgcctccctccttccttctcccctggctgttcgcgatccag	181
  V.1:	143	cttgggtaggcggggaagcagctggagtgcgaccgccacggcagccaccctgcaaccgcc	202
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	182	cttgggtaggcggggaagcagctggagtgcgaccgccacggcagccaccctgcaaccgcc	241
  V.1:	203	agtcggaggtgcagtccgtaggccctggcccccgggtgggcccttggggagtcggcgccg	262
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	242	agtcggaggtgcagtccgtaggccctggcccccgggtgggcccttggggagtcggcgccg	301
  V.1:	263	ctcccgaggagctgcaaggctcgcccctgcccggcgtggagggcgcggggggcgcggagg	322
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	302	ctcccgaggagctgcaaggctcgcccctgcccggcgtggagggcgcggggggcgcggagg	361
  V.1:	323	atattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaagcc	382
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	362	atattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaagcc	421
  V.1:	383	ctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaagga	442
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	422	ctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaagga	481
  V.1:	443	aggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgactta	502
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	482	aggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgactta	541
  V.1:	503	ttagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaatttt	562
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	542	ttagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaatttt	601
  V.1:	563	ttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataatat	622
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	602	ttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataatat	661
  V.1:	623	ttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttgtgg	682
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	662	ttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttgtgg	721
  V.1:	683	gtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatccaatg	742
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	722	gtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatccaatg	781
  V.1:	743	ctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttgtct	802
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	782	ctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttgtct	841
  V.1:	803	cagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgcagca	862
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	842	cagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgcagca	901
  V.1:	863	acaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattccca	922
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	902	acaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattccca	961
  V.1:	923	ttgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactcttta	982
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	962	ttgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactcttta	1021
  V.1:	983	ctctctggagagggccagtggtggtagctataagcttggccacattttttttcctttatt	1042
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1022	ctctctggagagggccagtggtggtagctataagcttggccacattttttttcctttatt	1081
  V.1:	1043	cctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttacaaaa	1102
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1082	cctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttacaaaa	1141
  V.1:	1103	ttcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccctag	1162
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1142	ttcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccctag	1201
  V.1:	1163	tataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtatagga	1222
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1202	tataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtatagga	1261
  V.1:	1223	gatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaagtt	1282
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1262	gatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaagtt	1321
  V.1:	1283	ttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcagaga	1342
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1322	ttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcagaga	1381
  V.1:	1343	gatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactcttgga	1402
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1382	gatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactcttgga	1441
  V.1:	1403	atgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttggct	1462
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1442	atgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttggct	1501
  V.1:	1463	tactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactggagag	1522
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1502	tactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactggagag	1561
  V.1:	1523	aattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttccatg	1582
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1562	aattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttccatg	1621
  V.1:	1583	ttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacaccac	1642
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1622	ttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacaccac	1681
  V.1:	1643	caaactttgttcttgctcttgttttgccctcaattgtaattctgg	1687
  		|||||||||||||||||||||||||||||||||||||||||||||
  V.8:	1682	caaactttgttcttgctcttgttttgccctcaattgtaattctgg	1726

  Score = 1381 bits (718), Expect = 0.0Identities = 725/726 (99%), Gaps =
  1/726 (0%) Strand = Plus/Plus

  V.1:	1687	gatcttttgcagctttgcagatacccagactgagctggaactggaatttgtcttcctatt	1746
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6132	gatcttttgcagctttgcagatacccagactgagctggaactggaatttgtcttcctatt	6191
  V.1:	1747	gactctacttctttaaaagcggctgcccattacattcctcagctgtccttgcagttaggt	1806
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6192	gactctacttctttaaaagcggctgcccattacattcctcagctgtccttgcagttaggt	6251
  V.1:	1807	gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtg	1866
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6252	gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtg	6311
  V.1:	1867	tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctggcagc	1926
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6312	tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctggcagc	6371
  V.1:	1927	tgtctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaaagacc	1986
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6372	tgtctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaaagacc	6431
  V.1:	1987	ttgactacttccctacttccactgctttt-cctgcatttaagccattgtaaatctgggtg	2045
  		||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
  V.8:	6432	ttgactacttccctacttccactgctttttcctgcatttaagccattgtaaatctgggtg	6491
  V.1:	2046	tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgataccattt	2105
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6492	tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgataccattt	6551
  V.1:	2106	aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaaggata	2165
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6552	aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaaggata	6611
  V.1:	2166	atgtgcaattcacattaaaattgattttccattgtcaattagttatactcattttcctgc	2225
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6612	atgtgcaattcacattaaaattgattttccattgtcaattagttatactcattttcctgc	6671
  V.1:	2226	cttgatctttcattagatattttgtatctgcttggaatatattatcttctttttaactgt	2285
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6672	cttgatctttcattagatattttgtatctgcttggaatatattatcttctttttaactgt	6731
  V.1:	2286	gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattacacacca	2345
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6732	gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattacacacca	6791
  V.1:	2346	tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtactatttaa	2405
  		||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
  V.8:	6792	tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtactatttaa	6851
  V.1:	2406	tgattt	2411
  		||||||
  V.8:	6852	tgattt	6857

• [1298]

  TABLE LIV(g)
  Peptide sequences of protein coded by 98P4B6 v.8 (SEQ ID NO: 190)

  MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD FAKSLTIRLI RCGYHVVIGS	60
  RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS LWDLRHLLVG KILIDVSNNM	120
  RINQYPESNA EYLASLFPDS LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE	180
  LARQLNFIPI DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA	240
  RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ	300
  CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN EEEVWRIEMY	360
  ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY VALLISTFHV LIYGWKRAFE	420
  EEYYRFYTPP NFVLALVLPS IVILGKIILF LPCISRKLKR IKKGWEKSQF LEEGMGGTIP	480
  HVSPERVTVM	490

• [1299]

  TABLE LV(g)
  Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID NO: 191) and 98P4B6
  v.8 (SEQ ID NO: 192)
  Score = 888 bits (2294), Expect = 0.0Identities = 444/444 (100%),
  Positives = 444/444 (100%)

  V.1:	1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  		MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
  V.8:	1	MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS	60
  V.1:	61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  		RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM
  V.8:	61	RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM	120
  V.1:	121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  		RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE
  V.8:	121	RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE	180
  V.1:	181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  		LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA
  V.8:	181	LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA	240
  V.1:	241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  		RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ
  V.8:	241	RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ	300
  V.1:	301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  		CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY
  V.8:	301	CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY	360
  V.1:	361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE	420
  		ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE
  V.8:	361	ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE	420
  V.1:	421	EEYYRFYTPPNFVLALVLPSIVIL	444
  		EEYYRFYTPPNFVLALVLPSIVIL
  V.8:	421	EEYYRFYTPPNFVLALVLPSIVIL	444

Claims (46)

1. A composition that comprises, consists essentially of, or consists of:

a) a peptide of eight, nine, ten, or eleven contiguous amino acids of a protein of FIG. 2;

b) a peptide of Tables VIII-XXI;

c) a peptide of Tables XXII to XLV; or,

d) a peptide of Tables XLVI to XLIX.

2. A composition of claim 1 that comprises a protein related to a protein of FIG. 2.

3. A protein of claim 2 that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% homologous to an entire amino acid sequence shown in FIG. 2.

4. A composition of claim 1 wherein the substance comprises a CTL polypeptide or an analog thereof, from the amino acid sequence of a protein of FIG. 2.

5. A composition of claim 4 further limited by a proviso that the epitope is not an entire amino acid sequence of FIG. 2.

6. A composition of claim 1 further limited by a proviso that the polypeptide is not an entire amino acid sequence of a protein of FIG. 2.

7. A composition of claim 1 that comprises an antibody polypeptide epitope from an amino acid sequence of FIG. 2.

8. A composition of claim 7 further limited by a proviso that the epitope is not an entire amino acid sequence of FIG. 2.

9. A composition of claim 7 wherein the antibody epitope comprises a peptide region of at least 5 amino acids of FIG. 2 in any whole number increment up to the end of said peptide, wherein the epitope comprises an amino acid position selected from:

a) an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of FIG. 5,

b) an amino acid position having a value less than 0.5 in the Hydropathicity profile of FIG. 6;

c) an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of FIG. 7;

d) an amino acid position having a value greater than 0.5 in the Average Flexibility profile of FIG. 8;

e) an amino acid position having a value greater than 0.5 in the Beta-turn profile of FIG. 9;

f) a combination of at least two of a) through e);

g) a combination of at least three of a) through e);

h) a combination of at least four of a) through e); or

i) a combination of five of a) through e).

10. A polynucleotide that encodes a protein of claim 1.

11. A polynucleotide of claim 10 that comprises a nucleic acid molecule set forth in FIG. 2.

12. A polynucleotide of claim 10 further limited by a proviso that the encoded protein is not an entire amino acid sequence of FIG. 2.

13. A composition of claim 11 wherein the substance comprises a polynucleotide that comprises a coding sequence of a nucleic acid sequence of FIG. 2.

14. A polynucleotide of claim 22 that further comprises an additional nucleotide sequence that encodes an additional peptide of claim 1.

15. A composition comprising a polynucleotide that is fully complementary to a polynucleotide of claim 10.

16. A method of generating a mammalian immune response directed to a protein of FIG. 2, the method comprising:

exposing cells of the mammal's immune system to a portion of

a) a 98B4B6-related protein and/or

b) a nucleotide sequence that encodes said protein,

whereby an immune response is generated to said protein.

17. A method of generating an immune response of claim 16, said method comprising:

providing a 98B4B6-related protein that comprises at least one T cell or at least one B cell epitope; and,

contacting the epitope with a mammalian immune system T cell or B cell respectively, whereby the T cell or B cell is activated.

18. A method of claim 17 wherein the immune system cell is a B cell, whereby the induced B cell generates antibodies that specifically bind to the 98B4B6-related protein.

19. A method of claim 17 wherein the immune system cell is a T cell that is a cytotoxic T cell (CTL), whereby the activated CTL kills an autologous cell that expresses the 98B4B6-related protein.

20. A method of claim 17 wherein the immune system cell is a T cell that is a helper T cell (HTL), whereby the activated HTL secretes cytokines that facilitate the cytotoxic activity of a cytotoxic T cell (CTL) or the antibody-producing activity of a B cell.

21. A method for detecting, in a sample, the presence of a 98B4B6-related protein or a 98B4B6-related polynucleotide, comprising steps of:

contacting the sample with a substance that specifically binds to the 98B4B6-related protein or to the 98B4B6-related polynucleofide, respectively; and,

determining that there is a complex of the substance with the 98B4B6-related protein or the substance with the 98B4B6-related polynucleofide, respectively.

22. A method of claim 21 for detecting the presence of a 98B4B6-related protein in a sample comprising steps of:

contacting the sample with an antibody or fragment thereof either of which specifically bind to the 98B4B6-related protein; and,

determining that there is a complex of the antibody or fragment thereof and the 98B4B6-related protein.

23. A method of claim 21 further comprising a step of:

taking the sample from a patient who has or who is suspected of having cancer.

24. A method of claim 21 for detecting the presence of a protein of FIG. 2 mRNA in a sample comprising:

producing cDNA from the sample by reverse transcription using at least one primer;

amplifying the cDNA so produced using 98B4B6 polynucleotides as sense and antisense primers, wherein the 98B4B6 polynucleotides used as the sense and antisense primers serve to amplify a 98B4B6 cDNA; and,

detecting the presence of the amplified 98B4B6 cDNA.

25. A method of claim 21 for monitoring one or more 98B4B6 gene products in a biological sample from a patient who has or who is suspected of having cancer, the method comprising:

determining the status of one or more 98B4B6 gene products expressed by cells in a tissue sample from an individual;

comparing the status so determined to the status of one or more 98B4B6 gene products in a corresponding normal sample; and,

identifying the presence of one or more aberrant gene products of 98B4B6 in the sample relative to the normal sample.

26. The method of claim 25 further comprising a step of determining if there are one or more elevated gene products of a 98B4B6 mRNA or a 98B4B6 protein, whereby the presence of one or more elevated gene products in the test sample relative to the normal tissue sample indicates the presence or status of a cancer.

27. A method of claim 26 wherein the cancer occurs in a tissue set forth in Table 1.

28. A composition comprising:

a substance that a) modulates the status of a protein of FIG. 2, or b) a molecule that is modulated by a protein of FIG. 2, whereby the status of a cell that expresses a protein of FIG. 2 is modulated.

29. A composition of claim 28, further comprising a physiologically acceptable carrier.

30. A pharmaceutical composition that comprises the composition of claim 28 in a human unit dose form.

31. A composition of claim 28 wherein the substance comprises an antibody or fragment thereof that specifically binds to a protein of FIG. 2.

32. An antibody or fragment thereof of claim 31, which is monoclonal.

33. An antibody of claim 31, which is a human antibody, a humanized antibody or a chimeric antibody.

34. A non-human transgenic animal that produces an antibody of claim 31.

35. A hybridoma that produces an antibody of claim 32.

36. A method of delivering a cytotoxic agent or a diagnostic agent to a cell that expresses a protein of FIG. 2, said method comprising:

providing the cytotoxic agent or the diagnostic agent conjugated to an antibody or fragment thereof of claim 4; and,

exposing the cell to the antibody-agent or fragment-agent conjugate.

37. A composition of claim 28 wherein the substance comprises a polynucleotide that encodes an antibody or fragment thereof, either of which immunospecifically bind to a protein of FIG. 2.

38. A composition of claim 28 wherein the substance comprises a) a ribozyme that cleaves a polynucleotide having a 98B4B6 coding sequence, or b) a nucleic acid molecule that encodes the ribozyme; and, a physiologically acceptable carrier.

39. A composition of claim 28 wherein the substance comprises human T cells, wherein said T cells specifically recognize a 98B4B6 peptide subsequence in the context of a particular HLA molecule.

40. A method of inhibiting growth of cancer cells that express a protein of FIG. 2, the method comprising:

administering to the cells the composition of claim 28.

41. A method of claim 40 of inhibiting growth of cancer cells that express a protein of FIG. 2, the method comprising steps of:

administering to said cells an antibody or fragment thereof, either of which specifically bind to a 98B4B6-related protein.

42. A method of claim 40 of inhibiting growth of cancer cells that express a protein of FIG. 2, the method comprising steps of:

administering to said cells a 98B4B6-related protein.

43. A method of claim 40 of inhibiting growth of cancer cells that express a protein of FIG. 2, the method comprising steps of:

administering to said cells a polynucleotide comprising a coding sequence for a 98B4B6-related protein or comprising a polynucleotide complementary to a coding sequence for a 98B4B6-related protein.

44. A method of claim 40 of inhibiting growth of cancer cells that express a protein of FIG. 2, the method comprising steps of:

administering to said cells a ribozyme that cleaves a polynucleotide that encodes a protein of FIG. 2.

45. A method of claim 40 of inhibiting growth of cancer cells that express a protein of FIG. 2 and a particular HLA molecule, the method comprising steps of:

administering human T cells to said cancer cells, wherein said T cells specifically recognize a peptide subsequence of a protein of FIG. 2 while the subsequence is in the context of the particular HLA molecule.

46. A method of claim 40, the method comprising steps of:

administering a vector that delivers a nucleotide that encodes a single chain monoclonal antibody, whereby the encoded single chain antibody is expressed intracellularly within cancer cells that express a protein of FIG. 2.

Images