EP1220905A2 - Zusammensetzung und verfahren zur behandlung von immunverwandten krankheiten - Google Patents

Zusammensetzung und verfahren zur behandlung von immunverwandten krankheiten

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Publication number
EP1220905A2
EP1220905A2 EP00913764A EP00913764A EP1220905A2 EP 1220905 A2 EP1220905 A2 EP 1220905A2 EP 00913764 A EP00913764 A EP 00913764A EP 00913764 A EP00913764 A EP 00913764A EP 1220905 A2 EP1220905 A2 EP 1220905A2
Authority
EP
European Patent Office
Prior art keywords
seq
antι
prol
pro
polypeptide
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP00913764A
Other languages
English (en)
French (fr)
Inventor
Avi J. Ashkenazi
Kevin P. Baker
Audrey Goddard
Austin L. Gurney
Caroline Hebert
William Henzel
Rhona C. Kabakoff
Yanmei Lu
James Pan
Diane Pennica
David L. Shelton
Victoria Smith
Timothy A. Stewart
Daniel Tumas
Colin K. Watanabe
William I. Wood
Minhong Yan
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Genentech Inc
Original Assignee
Genentech Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from PCT/US1999/005028 external-priority patent/WO1999046281A2/en
Priority claimed from PCT/US1999/008615 external-priority patent/WO1999055868A2/en
Priority claimed from PCT/US1999/012252 external-priority patent/WO1999063088A2/en
Priority claimed from PCT/US1999/020111 external-priority patent/WO2000012708A2/en
Priority claimed from PCT/US1999/020594 external-priority patent/WO2000015666A2/en
Priority claimed from PCT/US1999/020944 external-priority patent/WO2000015792A2/en
Priority claimed from PCT/US1999/021547 external-priority patent/WO2000015797A2/en
Priority claimed from PCT/US1999/021090 external-priority patent/WO2000015796A2/en
Priority claimed from PCT/US1999/023089 external-priority patent/WO2000021996A2/en
Priority claimed from PCT/US1999/028214 external-priority patent/WO2001019987A1/en
Priority claimed from PCT/US1999/028409 external-priority patent/WO2000032778A2/en
Priority claimed from PCT/US1999/028313 external-priority patent/WO2000032221A2/en
Priority claimed from PCT/US1999/028634 external-priority patent/WO2000036102A2/en
Priority claimed from PCT/US1999/028301 external-priority patent/WO2000032776A2/en
Priority claimed from PCT/US1999/028551 external-priority patent/WO2000053750A1/en
Priority claimed from PCT/US1999/028564 external-priority patent/WO2000055319A1/en
Priority claimed from PCT/US1999/028565 external-priority patent/WO2000037638A2/en
Priority claimed from PCT/US1999/030095 external-priority patent/WO2000037640A2/en
Priority claimed from PCT/US1999/030999 external-priority patent/WO2001005836A1/en
Priority claimed from PCT/US1999/031274 external-priority patent/WO2000053752A2/en
Priority claimed from PCT/US2000/000219 external-priority patent/WO2000053753A2/en
Priority claimed from PCT/US2000/000277 external-priority patent/WO2000053754A1/en
Priority claimed from PCT/US2000/000376 external-priority patent/WO2000053755A2/en
Priority claimed from PCT/US2000/003565 external-priority patent/WO2001053486A1/en
Priority claimed from PCT/US2000/004342 external-priority patent/WO2000078961A1/en
Priority claimed from PCT/US2000/004341 external-priority patent/WO2000053756A2/en
Priority claimed from PCT/US2000/004414 external-priority patent/WO2001004311A1/en
Application filed by Genentech Inc filed Critical Genentech Inc
Publication of EP1220905A2 publication Critical patent/EP1220905A2/de
Withdrawn legal-status Critical Current

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    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A61P11/02—Nasal agents, e.g. decongestants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61P17/00—Drugs for dermatological disorders
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/02—Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
    • A61P29/02—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID] without antiinflammatory effect
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P3/00—Drugs for disorders of the metabolism
    • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
    • A61P3/10—Drugs for disorders of the metabolism for glucose homeostasis for hyperglycaemia, e.g. antidiabetics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P5/00—Drugs for disorders of the endocrine system
    • A61P5/14—Drugs for disorders of the endocrine system of the thyroid hormones, e.g. T3, T4
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity
    • C07K14/4703—Inhibitors; Suppressors
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2799/00—Uses of viruses
    • C12N2799/02—Uses of viruses as vector
    • C12N2799/021—Uses of viruses as vector for the expression of a heterologous nucleic acid
    • C12N2799/026—Uses of viruses as vector for the expression of a heterologous nucleic acid where the vector is derived from a baculovirus

Definitions

  • the present invention relates to compositions and methods for the diagnosis and treatment of immune related diseases.
  • Immune reiated and inflammatory diseases are the manifestation or consequence of fairiy complex, often multiple interconnected biological pathways which in normal physiology are c ⁇ tical to respond to insult or in j ury, initiate repair from insult or injury, and mount innate and acquired defense against foreign organisms.
  • Disease or pathology occurs when these normal physiological pathways cause additional insult or injury either as directly related to the intensity of the response, as a consequence of abnormal regulation or excessive stimulation, as a reaction to self, or as a combination of these.
  • the genesis of these diseases often involves multistep pathways and often multiple different biological svstems/pathways. intervention at c ⁇ tical points in one or more of these pathways can have an ameliorative or therapeutic effect.
  • Therapeutic intervention can occur by either antagonism of a det ⁇ mental process/pathway or stimulation of a beneficial process/pathway.
  • immune reiated diseases are known and have been extensively studied. Such diseases include immune-mediated inflammatory diseases, non-immune-mediated inflammatory diseases, infectious diseases, immunodeficiency diseases, neoplasia, etc.
  • T lymphocytes are an important component of a mammalian immune response. T cells recognize antigens which are associated with a self-molecule encoded by genes within the major histocompatibility complex (MHC). The antigen may be displayed together with MHC molecules on the surface of antigen presenting cells, virus infected cells, cancer ceils, grafts, etc. The T cell system elimmates these altered cells which pose a health threat to the host mammal. T cells include helper T cells and cytotoxic T cells. Helper T cells proliferate extensively following recognition of an antigen -MHC complex on an antigen presenting cell. Helper T cells also secrete a variety of cytokines. i.e., lymphokines, which play a central role in the activation of B cells, cytotoxic T cells and a variety of other cells which participate in the immune response.
  • MHC major histocompatibility complex
  • helper T cell activation is initiated by the interaction of the T cell receptor (TCR) - CD3 complex with an antigen-MHC on the surface of an antigen presenting cell. This interaction mediates a cascade of biochemical events that induce the resting helper T cell to enter a cell cycle (the GO to Gl transition) and results in the expression of a high affinity receptor for IL-2 and sometimes IL-4.
  • TCR T cell receptor
  • the activated T cell progresses through the cycie proliferating and differentiating into memory cells or effector cells.
  • T cells In addition to the signals mediated through the TCR, activation of T cells involves additional cos ⁇ mulation induced by cytokines released by the antigen presenting cell or through interactions with membrane bound molecules on the antigen presenting cell and the T cell.
  • the cytokines IL-1 and IL-6 have been shown to provide a costimuiatory signal.
  • T-cell proliferation in a mixed Kmphocvte culture or mixed lymphocyte reaction is an established indication of the ability of a compound to stimulate the immune system In many immune responses inflammatory cells infiltrate the site ot mjurv or infection
  • the migrating cells mav be neutrophihc, eosinophihc monocytic or lymphocvtic as can be determined bv histologic examination of the affected tissues
  • Immune related diseases can be treated bv suppressing the immune response Using neutralizing antibodies that inhibit molecules having immune stimulatory activity would be beneficial in the treatment of immune-mediated and inflammatory diseases Molecules which inhibit the immune response can be utilized
  • the present inv ention concerns compositions and methods tor the diagnosis and treatment ot immune related disease in mammals including humans
  • the present invention is based on the identification of proteins (includinc agonist and antagonist antibodies) which either stimulate or inhibit the immune response in mammals
  • Immune related diseases can be treated by suppressing or enhancing the immune response Molecules that enhance the immune response stimulate or potentiate the immune response to an antigen Molecules w hich stimulate the immune response can be used therapeutically where enhancement of the immune response would be beneficial
  • Such stimulatory molecules can also be inhibited where suppression of the immune response would be of value
  • Neutralizing antibodies are examples of molecules that inhibit molecules having immune stimulatory activity and which would be beneficial in the treatment ot immune related and inflammator y diseases Molecules which inhibit the immune response can also be utilized (proteins directly or via the use ot antibody agonists I to inhibit the immune response and thus ameliorate immune related disease
  • the PRO polypeptides and anti-PRO antibodies and fragments thereof are useful foi the diagnosis and/or treatment (including prevention) of immune related diseases
  • Antibodies which bind to stimulatory proteins are useful to suppress the immune system and the immune response
  • Antibodies which bind to inhibitory proteins are useful to stimulate the immune system and the immune response
  • the PRO polypeptides and anti-PRO antibodies also useful to prepare medicines and medicaments for the treatment of immune related and inflammatory diseases
  • the mvention provides for isolated nucleic acid molecules comp ⁇ sing nucleotide sequences that encodes a PRO polypeptide
  • the isolated nucleic acid molecule comp ⁇ ses a nucleotide sequence having at least about 80% nucleic acid sequence identity, alternatively at least about 81% nucleic acid identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91% nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid
  • the isolated nucleic acid molecule comp ⁇ ses a nucleotide sequence having at least about 80% nucleic acid sequence identity, alternatively at least about 81% nucleic acid sequence identity. alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91% nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic
  • the invention concerns an isolated nucleic acid molecule comp ⁇ smg a nucleotide sequence having at least about 80% nucleic acid sequence identity, alternatively at least about 81% nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91% nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about
  • the invention provides for isolated nucleic acid molecule comp ⁇ smg a nucleotide sequence encodmg a PRO polypeptide with is either transmembrane domain-deleted or transmembrane domam-inactivated. or is complementary to such encoding nucleotide sequence, wherem the transmembrane doma ⁇ n(s) of such polypeptides are disclosed herein. Therefore, soluble extracellular domains of the herein desc ⁇ bed PRO polypeptides are contemplated.
  • nucleic acid fragments are usually at least about 20 nucleotides in length, alternatively at least about 30 nucleotides in length, alternatively at least about 40 nucleotides m length, alternatively at least about 50 nucleotides in length, alternatively at least about 60 nucleotides in length, alternatively at least about 70 nucleotides in length, alternatively at least about 80 nucleotides in length, alternatively at least about 90 nucleotides in length, alternatively at least about 100 nucleotides in length, alternatively at least about 1 10 nucleotides in length, alternatively at least about 120 nucleo
  • novel fragments of a nucieotide sequence encoding the respective PRO polypeptide may be determmed in a routine manner by alignmg the respective nucleotide encoding a PRO polypeptide with other known nucieotide sequences using any of a number of well known sequence alignment programs and determining which nucleotide sequence fragment(s) are novel. All such nucleotide sequences encoding the respective PRO polypeptides are contemplated herem. Also contemplated are the nucleotide molecules which encode fragments of the PRO polypeptides. preferably those polypeptide fragments that comp ⁇ se a binding site for an anti-PRO polypeptide antibody. In ano t her embodiment, the invention provides isolated PRO polypeptides encoded by any of the isolated nucleic acid sequences heremabove identified.
  • the invention concerns an isolated PRO polypeptide. comp ⁇ sing an am i no ac i d sequence having a t least about 80% ammo acid sequence identity, alternatively at least about 81% ammo ac i d sequence identity, alternatively at least about 82% ammo acid sequence identity, alternatively at least about 83% ammo acid sequence identity, alternatively at least about 84% amino acid sequence identity, alterna ti vely at least about 85% amino acid sequence identity, alternatively at least about 86% ammo acid sequence i dent i ty, al t erna t ively a t leas t about 87% ammo acid sequence identity, alternatively at least about 88% am i no ac i d sequence identity, al t erna t ively at least about 89% ammo acid sequence identity, alternatively at leas t about 90% ammo acid sequence identity, alternatively at least about 91% ammo acid sequence identity, alternatively at leas
  • t he invention concerns an isolated PRO polypeptide comp ⁇ sing an am i no ac i d sequence having a t least about 80% amino acid sequence identity, alternatively at least about 81% ammo ac i d sequence iden t i t y, alterna t ively at least about 82% ammo acid sequence identity, alternatively at leas t about
  • the invention concerns an isolated PRO polypeptide comp ⁇ sing an ammo ac i d sequence sco ⁇ ng at least about 80% positives, alternatively at least about 81% positives, alternatively at least about 82% posi t ives, alternatively at least about 83% positives, alternatively at least about 84% pos i tives, alternatively at least about 85% positives, alternatively at least about 86% positives, alternatively at least about 87% positives, alternatively at least about 88% positives, alternatively at least about 89% pos i t i ves, alterna t ively at least about 90% positives, alternatively at least about 91% positives, alternatively at least about 92% posi t ives, alternatively at least about 93% positives, alternatively at least about 94% positives, alternatively at least about 95% positives, alternatively at least about 96% positives, alternatively at least about 97% positives, alternatively at least about 98% positives, alternatively
  • the invention provides an isolated PRO polypeptide without the N-termmal signal sequence and'or the initiating methionine and is encoded by a nucleotide sequence that encodes such an ammo acid sequence as hereinbefore described Processes tor producing the same are also herein desc ⁇ bed. wherem those processes comp ⁇ se cultunng a host cell comp ⁇ sing a v ector which comp ⁇ ses the approp ⁇ ate encodmg nucleic acid molecule under conditions suitable for expression of the PRO polypeptide and recovermg the same from the cell culture.
  • the invention provides an isolated PRO polypeptide which is either transmembrane- deleted or transmembrane domam-inactivated Processes for producing the same are also herein desc ⁇ bed. wherein those processes comp ⁇ se cultunng a host cell comp ⁇ sing a vector which comp ⁇ ses the approp ⁇ ate encodine nucleic acid molecule under conditions suitable lor expression of the PRO polvpeptide and recovering the PRO polypeptide trom the cell culture
  • the invention provides vectors comp ⁇ sing DNA encoding anv of the PRO polypeptides
  • Host cells comprising any such vector are also provided
  • the host cells may be CHO cells.
  • E coli or yeast A process tor producing any of the herein described polypeptides is further provided and comp ⁇ ses culm ⁇ ng host cells under conditions suitable for expression of the desired polypeptides and recove ⁇ ng the desired polypeptide from the cell culture.
  • the invention provides chimenc molecules comprising any of the herem described polypeptides fused to a heterologous polypeptide or amino acid sequence
  • chimenc molecules comp ⁇ se anv of the herein desc ⁇ bed polypeptides fused to an epitope tag sequence or a Fc region ot an immunoglobulin
  • the invention provides oligonucleotide probes useful for isolating genomic and cDNA nucieotide sequences or as antisense probes, wherem those probes may be de ⁇ ved trom anv of the above or below described nucleotide sequences
  • the invention concerns agonists and antagonists of the PRO polypeptides. that mimic or inhibit one or more functions or activities of the PRO polypeptides
  • the agonist or antagonist is an antibody that bmds to the PRO polypeptides or a small molecule.
  • the invention provides an antibody which specifically binds to any of the above or below desc ⁇ bed polypeptides
  • the antibody is a monoclonal antibody, humanized antibody, antibody fragment or single-chain antibody
  • the present invention concerns an isolated antibody which bmds a PRO polypeptide
  • the antibody mimics the activity of a PRO polypeptide (an agonist antibody) or conversely the antibody inhibits or neutralizes the activity of a PRO polypeptide (an antagonist antibody)
  • the antibody is a monoclonal antibody, which preferably has nonhuman compiementanty determining region (CDR) residues and human framework region (FR) residues.
  • CDR nonhuman compiementanty determining region
  • FR human framework region
  • the antibody may be labeled and may be immobilized on a solid support.
  • the antibody is an antibody fragment, a monoclonal antibody, a smgle-cham antibody, or an anti-idiotypic antibody.
  • the invention concerns a method of identifying agonists or antagonists to a PRO polypeptide which comp ⁇ ses contacting the PRO polypeptide with a candidate molecule and monitoring a biological activity mediated by said PRO polypeptide
  • the PRO polypeptide is a native sequence PRO polypeptide.
  • the invention concerns a composition ot matter containing PRO polypeptide or an agonist or antagonist antibody which binds the polypeptide in admixture with a earner or excipient.
  • the composition contains a therapeutically effective amount of the peptide or antibody.
  • the composition when the composition contains an immune stimulating molecule, the composition is useful for: (a) increasing infiltration of inflammatory cells into a tissue of a mammal in need thereof, (b) stimulating or enhancing an immune response in a mammal in need thereof, or (c) increasing the proliferation of T- lymphocytes in a mammal in need thereof in response to an antigen.
  • the composition when the composition contains an immune inhibiting molecule, the composition is useful for: (a) decreasing infiltration of inflammatory cells into a tissue of a mammal in need thereof, (b) inhibiting or reducing an immune response in a mammal m need thereof or ( c) decreasing the proliferation of T-lymphocvtes in a mammal in need thereof in response to an antigen
  • the composition contains a tu ⁇ her active ingredient, which may. for example, be a fu ⁇ her antioody or a cytotoxic or chemotherapeutic agent
  • the composition is ste ⁇ ie.
  • the invention concerns the use of the polypeptides and antibodies of the invention to prepare a composition or medicament which has the uses descnbed above.
  • the invention concerns nucleic acid encoding an ant ⁇ -PRO200, ant ⁇ -PRO204, ant ⁇ -PR0212. ant ⁇ -PR0216. ant ⁇ -PR0226, ant ⁇ -PRO240, ant ⁇ -PR0235. ant ⁇ -PR0245. ant ⁇ -PR0172. anti- PR0273. ant ⁇ -PR0272, ant ⁇ -PR0332, ant ⁇ -PR0526, ant ⁇ -PRO701. ant ⁇ -PR0361. ant ⁇ -PR0362. ant ⁇ -PR0363, ant ⁇ -PR0364. ant ⁇ -PR0356. ant ⁇ -PR053 1. ant ⁇ -PR0533. ant ⁇ -PRO 1083.
  • the invention concerns a method for producing such an antibody by culm ⁇ ng a host cell transformed with nucleic acid encodmg the antibody under conditions such that the antibody is expressed, and recove ⁇ ng the antibody from the cell culture.
  • the invention concerns an isolated nucleic acid molecule that hybndizes to the a nucleic acid molecule encodmg a PRO polypeptide. or the complement thereof.
  • the nucleic acid preferably is DNA. and hyb ⁇ dization preferably occurs under st ⁇ ngent conditions.
  • Such nucleic acid molecules can act as antisense molecules of the amplified genes identified herem, which, in turn, can find use in the modulation of the respective amplified genes, or as antisense p ⁇ mers in amplification reactions.
  • sequences can be used as part of ⁇ bozyme and/or triple helix sequence which, in turn, may be used in regulation of the amplified genes.
  • the invention concerns a method for determining the presence of a PRO polypeptide comp ⁇ smg exposmg a cell suspected of contammg and or expressing the polypeptide to an anti- PRO200, ant ⁇ -PRO204, ant ⁇ -PR0212. ant ⁇ -PR0216. ant ⁇ -PR0226. ant ⁇ -PRO240. ant ⁇ -PR0235, ant ⁇ -PR0245. ant ⁇ -PR0172, ant ⁇ -PR0273. ant ⁇ -PR0272. ant ⁇ -PR0332. ant ⁇ -PR0526. ant ⁇ -PRO701. ant ⁇ -PR0361, anti- PR0362, ant ⁇ -PR0363, ant ⁇ -PR0364.
  • ant ⁇ -PR0356 ant ⁇ -PR0531 , ant ⁇ -PR0533, ant ⁇ -PRO1083.
  • ant ⁇ -PRO1007 anti-PROl 184.
  • the present invention concerns a method of diagnosmg an immune related disease in a mammal, comp ⁇ sing detecting the level of expression of a gene encodin ⁇ a PRO polypeptide (a) in a test sample ot tissue cells obtained trom the mammal, and (b) in a control sample ot known normal tissue cells of the same cell type, wherein a higher or lower expression level in the test sample as compared to the control sample indicates the presence ot immune related disease in the mammal trom which the test tissue cells were obtained
  • the present invention concerns a method of diagnosing an immune disease in a mammal, comp ⁇ sing (a) contacting an anti-PRO polypeptide antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between the antibody and the respective PRO polypeptide.
  • the detection may be qualitative or quantitative, and may be performed in compa ⁇ son with monitoring the complex formation in a control sample of known normal tissue ceils of the same cell type
  • a larger quantity of complexes formed in the test sample indicates the presence or absence ot an immune disease in the mammal from which the test tissue cells were obtained
  • the antibod y prcterablv cames a detectable label Complex formation can be monitored, for example, by light microscopy, flow cytometrv, fluo ⁇ metry. or other techniques known in the art
  • the test sample is usually obtained from an individual suspected of having a deficiency or abnormality of the immune system
  • the present invention concerns a diagnostic kit.
  • ant ⁇ -PRO200 containing an ant ⁇ -PRO200.
  • ant ⁇ -PRO204 ant ⁇ -PR0212.
  • ant ⁇ -PR0216 ant ⁇ -PR0226.
  • ant ⁇ -PRO240 ant ⁇ -PR0235, ant ⁇ -PR0245, anti- PR0172, ant ⁇ -PR0273, ant ⁇ -PR0272.
  • ant ⁇ -PR0332 ant ⁇ -PR0526, ant ⁇ -PRO701. ant ⁇ -PR0361.
  • ant ⁇ -PR0531 ant ⁇ -PRO200.
  • ant ⁇ -PRO204 containing an ant ⁇ -PRO200.
  • ant ⁇ -PR0216 containing an ant ⁇ -PR0212.
  • ant ⁇ -PR0226 containing an ant ⁇ -PR0212.
  • ant ⁇ -PR0226 containing an ant ⁇
  • ant ⁇ -PR01868 anti- PRO205, ant ⁇ -PR021, ant ⁇ -PR0269, ant ⁇ -PR0344, ant ⁇ -PR0333, ant ⁇ -PR0381, ant ⁇ -PRO720, ant ⁇ -PR0866, anti-PRO840.
  • the kit preferably contams instructions for usmg the antibody to detect the PRO polypeptide.
  • the invention concerns an article of manufacture, comp ⁇ sing: a container; an instruction on the container: and a composition comp ⁇ sing an active agent contained withm the container, wherein the composition is effective for stimulating or inhibiting an immune response in a mammal, the instruction on the container indicates that the composition can be used to treat an immune related disease, and the active agent in the composition is an agent stimulating or inhibiting the expression and/or activity of the PRO polypeptide.
  • the active agent is a PRO200. PRO204. PR0212. PR0216. PR0226. PRO240. PR0235. PR0245. PR0172. PR0273, PR0272, PR0332. PR0526. PRO701 , PR0361. PR0362.
  • ant ⁇ -PR0344 ant ⁇ -PR0333.
  • ant ⁇ -PR0866 anti- PRO840.
  • ant ⁇ -PR0836 anti-PROl 159, ant ⁇ -PR01358.
  • a further embodiment is a method for identifying a compound capable of inhibiting the expression and or activity ot a PRO polypeptide bv contacting a candidate compound with a PRO polypeptide under conditions and for a time sufficient to allow these two components to interact
  • either the candidate compound or the PRO polypeptide is immobilized on a solid support
  • the non- lmmobihzed component car ⁇ es a detectable label
  • Another embodiment of the present invention is directed to the use of a PRO polypeptide. or an agonist or antagonist thereof as hereinbefore desc ⁇ bed, or an anti-PRO antibody, for the preparation of a medicament useful m the treatment of a condition which is responsive to the PRO polypeptide. an agonist or antagonist thereof or an anti-PRO antibody.
  • Figure 1 shows DNA29101-1276 (SEQ ID NO: l).
  • Figure 2 shows the native sequence PRO200 polypeptide UNQ174 (SEQ ID NO:2).
  • FIG. 3 shows DNA30871-1157 (SEQ ID NO:l 1)
  • Figure 4 shows the native sequence partial length PRO204 polypeptide UNQ178 (SEQ ID NO: 12) .
  • Figure 5 shows DNA30942-1134 (SEQ ID NO: 13).
  • Figure 6 shows the native sequence PR0212 polypeptide UNQ 186 (SEQ ID NO 14)
  • Figure 7 shows DNA33087-1 158 (SEQ ID NO 18)
  • Figure 8 shows the native sequence PR0216 polypeptide UNQ190 (SEQ ID NO 19)
  • Figure 9 shows DNA33460-1 166 (SEQ ID NO 20)
  • Figure 10 shows the native sequence PR0226 polypeptide UNQ200 (SEQ ID NO 21)
  • Figure 1 1 shows DNA34387- 1 138 (SEQ ID NO 25)
  • Figure 12 shows the native sequence PRO240 polypeptide UNQ214 (SEQ ID NO 26)
  • Figure 13 shows DNA35558-1 167 (SEQ ID NO 30)
  • Figure 14 shows the native sequence PR0235 polypeptide UNQ209 (SEQ ID NO 31)
  • Figure 15 shows DNA35638- 1 141 (SEQ ID NO 35)
  • Figure 16 shows the native sequence PR0245 polypeptide UNQ219 (SEQ ID NO 36)
  • Figure 17 shows DNA35916- 1 161 (SEQ ID NO 40)
  • Figure 18 shows the native sequence PRO 172 polypeptide UNQ146 (SEQ ID NO 41 )
  • Figure 19 shows DNA39523- 1 192 (SEQ ID NO 45)
  • Figure 20 shows the native sequence PR0273 polypeptide UNQ240 (SEQ ID NO 46)
  • Figure 21 shows DNA40620-1 183 (SEQ ID NO 50)
  • Figure 22 shows the native sequence PR0272 polypeptide UNQ239 (SEQ ID NO 51 )
  • Figure 23 shows DNA40982- 1235 (SEQ ID NO 56)
  • Figure 24 shows the native sequence PR0332 polypeptide UNQ293 (SEQ ID NO 57)
  • Figure 25 shows DNA44184- 1319 (SEQ ID NO 61)
  • Figure 26 shows the native sequence PR0526 polypeptide UNQ330 (SEQ ID NO 62)
  • Figure 27 shows DNA44205- I285 (SEQ ID NO 66)
  • Figure 28 shows the native sequence PRO701 polypeptide UNQ365 (SEQ ID NO 67)
  • Figure 29 shows DNA45410- 1250 (SEQ ID NO 71)
  • Figure 30 shows the native sequence PR0361 polypeptide UNQ316 (SEQ ID NO 72)
  • Figure 3 1 shows DN A45416- 1251 (SEQ ID NO 79)
  • Figure 32 shows the native sequence PR0362 polypeptide UNQ317 (SEQ ID NO 80)
  • Figure 33 shows DNA45419- 1252 (SEQ ID NO 86)
  • Figure 34 shows the native sequence PR0363 polypeptide UNQ318 (SEQ ID NO 87)
  • Figure 35 shows DNA47365- 1206 (SEQ ID NO 91)
  • Figure 36 shows the native sequence PR0364 polypeptide UNQ319 (SEQ ID NO 92).
  • Figure 37 shows DNA47470-1 130 (SEQ ID NO 101 )
  • Figure 38 shows the native sequence PR0356 polypeptide UNQ313 (SEQ ID NO 102)
  • Figure 39 shows DNA48314-1320 (SEQ ID NO 106)
  • Figure 40 shows the native sequence PR0531 polypeptide UNQ332 (SEQ ID NO 107)
  • Figure 41 shows DNA49435-1219 (SEQ ID NO 111)
  • Figure 42 shows the native sequence PR0533 polypeptide UNQ334 (SEQ ID NO.112)
  • Figure 43 shows DNA50921-1458 (SEQ ID NO.l 16)
  • Figure 44 shows the native sequence PRO1083 polypeptide UNQ540 (SEQ ID NO 117).
  • Figure 45 shows DNA53974-1401 (SEQ ID NO. I23)
  • Figure 46 shows the native sequence PR0865 polypeptide UNQ434 (SEQ ID NO 124)
  • Figure 47 shows DNA54228- 1366 (SEQ ID NO 133)
  • Figure 48 shows the native sequence PRO770 polypeptide UNQ408 (SEQ ID NO 134)
  • Figure 49 shows DNA54231- 1366 (SEQ ID NO 139)
  • Figure 50 shows the native sequence PR0769 polypeptide UNQ407 (SEQ ID NO 140)
  • Figure 51 shows DNA56405- 1357 (SEQ ID NO 141 )
  • Figure 52 shows the native sequence PR0788 polypeptide UNQ430 (SEQ ID NO 142)
  • Figure 53 shows DNA57033- 1403 (SEQ ID NO 143)
  • Figure 54 shows the native sequence PRO l 1 14 polypeptide UNQ557 (SEQ ID NO 144)
  • Figure 55 shows DNA57690- 1374 (SEQ ID NO 145)
  • Figure 56 shows the native sequence PRO 1007 polypeptide UNQ491 (SEQ ID NO 146)
  • Figure 57 shows DNA59220- 1514 (SEQ ID NO 147)
  • Figure 58 shows the native sequence PRO l 184 polypeptide UNQ598 (SEQ ID NO 148)
  • FIG 59 shows DNA59294- 1381 (SEQ ID NO 149)
  • Tigure 60 shows the native sequence PRO 1031 polypeptide UNQ516 (SEQ ID NO 150 )
  • Figure 61 shows DNA59776- 1600 (SEQ ID NO 151 )
  • Figure 62 shows the native sequence PRO 1346 polypeptide UNQ70I (SEQ ID NO 152)
  • Figure 63 shows DNA59849- 1504 (SEQ ID NO 156)
  • Figure 64 shows the native sequence PROl 155 polypeptide UNQ585 (SEQ ID NO 157)
  • Figure 65 shows DNA60775- 1532 (SEQ ID NO 158)
  • Figure 66 shows the native sequence PRO 1250 polypeptide UNQ633 (SEQ ID NO 159)
  • Figure 67 shows DNA61873- 1574 (SEQ ID NO 160)
  • Figure 68 shows the native sequence PR01312 polypeptide UNQ678 (SEQ ID NO 161 )
  • Figure 69 shows DNA62814- 1521 (SEQ ID NO 162)
  • Figure 70 shows the nativ e sequence PROl 192 polypeptide UNQ606 (SEQ ID NO 163)
  • Figure 71 shows DNA64885- 1529 (SEQ ID NO 167)
  • Figure 72 shows the nativ e sequence PRO 1246 polypeptide UNQ630 (SEQ ID NO 168)
  • Figure 73 shows DNA65404- 1551 (SEQ ID NO 169)
  • Figure 74 shows the native sequence PRO 1283 polypeptide UNQ653 (SEQ ID NO 170)
  • Figure 75 shows DNA65412- 1523 (SEQ ID NO 177)
  • Figure 76 shows the native sequence PRO l 195 polypeptide UNQ608 (SEQ ID NO 178)
  • Figure 77 shows DNA66675- 1587 (SEQ ID NO 179)
  • Figure 78 shows the native sequence PRO 1343 polypeptide UNQ698 (SEQ ID NO 180)
  • Figure 79 shows DNA68864- 1629 (SEQ ID NO 184)
  • Figure 80 shows the native sequence PR01418 polypeptide UNQ732 (SEQ ID NO 185)
  • Figure 81 shows DNA68872- 1620 (SEQ ID NO 186)
  • Figure 82 shows the native sequence PR01387 polypeptide UNQ722 (SEQ ID NO 187)
  • Figure 83 shows DNA68874-1622 (SEQ ID NO 188)
  • Figure 84 shows the native sequence PRO1410 polypeptide UNQ728 (SEQ ID NO 189)
  • Figure 85 shows DNA76400-2528 (SEQ ID NO 190)
  • Figure 86 shows the native sequence PR01917 polypeptide UNQ900 (SEQ ID NO 191)
  • Figure 87 shows DNA77624-2515 (SEQ ID NO 192)
  • Figure 88 shows the nati e sequence PR01868 polypeptide UNQ859 (SEQ ID NO 193)
  • Figure 89 shows DNA30868- 1 156 (SEQ ID NO 228)
  • Figure 90 shows the partial nati e sequence PRO205 polypeptide UNQ 179 (SEQ ID NO 229)
  • Figure 91 shows DNA36638- 1056 (SEQ ID NO 230)
  • Figure 92 shows the native sequence PR021 polypeptide UNQ21 (SEQ ID NO 231)
  • Figure 93 shows DNA38260- 1 180 (SEQ ID NO 232)
  • Figure 94 shows the nativ e sequence PR0269 polypeptide UNQ236 (SEQ ID NO 233)
  • Figure 95 shows DNA40592 1242 (SEQ ID NO 240)
  • Figure 96 shows the native sequence PR0344 polypeptide UNQ303 (SEQ ID NO 241 )
  • Figure 97 shows DNA41374- 1312 (SEQ ID NO 248)
  • Figure 98 shows the partial length native sequence PR0333 polypeptide UNQ294 (SEQ ID NO 249)
  • Figure 99 shows DNA44194- 1317 (SEQ ID NO 250)
  • Figure 00 shows the nativ e sequence PR0381 polypeptide UNQ322 (SEQ ID NO 25 1 )
  • Figure 01 shows DNA53517 1366 (SEQ ID NO 255)
  • Figure 02 shows the nativ e sequence PRO720 polypeptide UNQ388 (SEQ ID NO 256)
  • Figure 03 shows DNA53971 1359 (SEQ ID NO 257)
  • Figure 04 shows the native sequence PRO866 polypeptide UNQ435 (SEQ ID NO 258)
  • Figure 05 shows DNA53987-1438 (SEQ ID NO 266)
  • Figure 06 shows the native sequence PRO840 polypeptide UNQ433 (SEQ ID NO 267)
  • Figure 07 shows DNA57700- 1408 (SEQ ID NO 268)
  • Figure 08 shows the nativ e sequence PR0982 polypeptide UNQ483 (SEQ ID NO 269)
  • Figure 09 shows DNA59620- 1463 (SEQ ID NO 270)
  • Figure 0 shows the nativ e sequence PR0836 polypeptide UNQ545 (SEQ
  • Figure 127 shows DNA98853- I739 (SEQ ID NO:296).
  • Figure 128 shows the native sequence PR05727 polypeptide UNQ2448 (SEQ ID NO:297).
  • PRO polypept ⁇ de(s) and PRO as used herem and when immediately followed by a nume ⁇ cal designation refer to va ⁇ ous polypeptides. wherein the complete designation (i.e.. "PRO/number” or more particularly. PRO200. PRO204. PR0212. PR0216, PR0226. PRO240. PR0235. PR0245. PROl 72, PR0273, PR0272, PR0332. PR0526. PRO701. PR0361. PR0362. PR0363. PR0364, PR0356. PR0531, PR0533.
  • PR04333, PRO4302. PRO4430 or PR05727) refers to particular polypeptide sequences as described herein.
  • PRO/numoer polypeptide and "PRO/number” wherein the term “number” is provided as an actual nume ⁇ cai designation (e g . as desc ⁇ bed above) as used herein encompass native sequence polypeptides and polypeptide variants (which are further defined herein)
  • the PRO polypeptides desc ⁇ bed herein may be isolated from a va ⁇ ety of sources, such as from human tissue types or from another source, or prepared by recombinant or synthetic methods.
  • a "native sequence PRO polypept ⁇ de(s)” comp ⁇ ses a polypeptide having the same amino acid sequence as the corresponding PRO polypeptide derived from nature. Such native sequence PRO/number polypeptides can be isolated from nature or can be produced by recombinant or synthetic means.
  • the term "native sequence PRO polypept ⁇ de(s)” specifically encompasses naturally-occurring truncated or secreted forms ot the specific PRO/number polypeptide (e g., an extracellular domain sequence), namrally-occumng va ⁇ ant forms (e g , alternatively spliced forms) and natural ly-occumng allelic va ⁇ ants of the polypeptide.
  • the native sequence PRO polypeptides disclosed herein are mature or full-length native sequence polypeptides comp ⁇ sing the full-length am o acids sequences shown in the accompanying figures. Start and stop codons are shown in bold font and underlmed in the figures.
  • the PRO/number polypeptides disclosed in the accompanying figures are shown to beg with methionine residues designated herein as ammo acid position 1 m the figures, it is conceivable and possible that other methionine residues located either upstream or downstream from the ammo acid position 1 in the figures may be employed as the starting amino acid residue for the PRO polypeptides.
  • PRO polypept ⁇ de(s) extracellular domam refers to a form of the said polypeptide which is essentially free of the transmembrane and cytoplasmic domams.
  • ECD extracellular domam
  • a PRO polypeptide ECD will have less than 1% of such transmembrane and or cytoplasmic domams and preferably, will have less than 0.5% of such domains. It will be understood that any transmembrane domains identified for the PRO polypeptides of the present mvention are identified pursuant to criteria routinely employed in the art for identifying that type of hydrophobic domain.
  • transmembrane domain may vary but most likely by no more than about 5 ammo acids at either end of the domain as initially identified herem.
  • an extracellular domain of a PRO polypeptide mav contain from about 5 or fewer ammo acids on either side of the transmembrane domain/extracellular domain boundary as identified in the Examples or specification and such polypeptides with or without the associated signal peptide and nucleic acid encodmg them, are contemplated bv the present invention
  • the approximate location of the 'signal peptides" of the vanous PRO/number PRO polypeptides disclosed herein are shown in the present specification and/or the accompanying figures It is noted, however, that the C-terminal boundar y of a signal peptide mav vary but most likely bv no more than about 5 amino acids on either side of the signal peptide C terminal boundary as initially identified herein, wherein the C- termmal boundary of the signal peptide mav be identified pursuant to c ⁇ te ⁇
  • PRO/number variant or PRO va ⁇ ant means an active PRO polypeptide as defined herein (e g below) having at least about 80% amino acid sequence identitv ith a full- length nativ e sequence PRO polypeptide sequence as disclosed herein a PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide with or without the signal peptide as disclosed herem or anv other fragment of a full-length PRO polypeptide sequence as disclosed herein
  • Such PRO polypeptide va ⁇ ants include for instance, polypeptides wherein one or more amino acid residues are added or deleted, at the N- or C-terminus of the full-length native ammo acid sequence
  • Ordina ⁇ K a PRO polypeptide va ⁇ ant will have at least about 80% ammo acid sequence identity alternatively at least about 81 % ammo acid sequence identity alternatively at least about 82% ammo acid sequence identity, alternatively at least about 83% amino acid sequence identity alternativelv at least about 84% amino
  • Percent (%) ammo acid sequence identity with respect to the PRO polypeptide sequences identified herein is defined as the percentage of ammo acid residues in a candidate sequence that are identical with the ammo acid residues m the specific PRO/number polypeptide sequence, after aligning the sequences and introducing gaps, if necessarv. to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part ot the sequence identify Alignment tor purposes of determining percent amino acid sequence identify can be achieved in vanous ways that are within the skill in the art. tor instance, using pub clv available computer software sucn as BLAST, BLAST-2.
  • ALIGN or Megahgn (DNASTAR) software
  • Those skilled in the art can determine approp ⁇ ate parameters for measu ⁇ ng alignment, including any algo ⁇ thms needed to achieve maximal alignment over the full length of the sequences being compared.
  • % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2. wherein the complete source code for the ALIGN-2 program is provided in Table 1 below.
  • the ALIGN-2 sequence compa ⁇ son computer program was authored by Genentech. Inc and the source code shown in Tables 1 below has been filed with user documentation in the U.S. Copy ⁇ ght Office. Washington D C, 20559 where it is registered under U S.
  • the ALIGN-2 program is pubhclv available through Genentech. Inc . South San Francisco. California or mav be compiled from the source code provided in Table 1 below
  • the ALIGN-2 program should be compiled tor use on a UNIX operating system, preferably digital UNIX V4 0D. All sequence compa ⁇ son parameters are set by the ALIGN-2 program and do not vary
  • % amino acid sequence identity of a given ammo acid sequence A to, with, or against a given ammo acid sequence B (which can alternatively be phrased as a given ammo acid sequence A that has or comp ⁇ ses a certain % ammo acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows:
  • Tables 2 and 3 demonstrate how to calculate the % amino acid sequence identity ot the amino acid sequence designated "Compa ⁇ son Protein to the amino acid sequence designated "PRO”, wherein 'PRO” represents the ammo acid sequence of a hypothetical PRO/number polypeptide of interest, Compa ⁇ son Protein” represents the ammo acid sequence of a polypeptide against which the PRO" polypeptide of interest is being compared, and 'X, "Y" and “Z" each represent different hypothetical ammo acid residues
  • % amino acid sequence identify values used herein are obtained as desc ⁇ bed in the immediately preceding paragraph using the ALIGN-2 computer program. However, % amino acid sequence identify values may also be obtained as desc ⁇ bed below by using the WU- BLAST 2 computer program (Altschul et al Methods in 266 460-480 ( 1996)) Most ot the WU- BLAST 2 search parameters are set to the default values Those not set to default values.
  • a % ammo acid sequence identity value is determmed bv dividing (a) the number of matchmg identical ammo acid residues between the amino acid sequence ot the PRO polypeptide of interest having a sequence de ⁇ ved from the native sequence PRO polvpeptide and the compa ⁇ son ammo acid sequence ot interest (i e the sequence against which the PRO polypeptide is being compared hich mav oe a PRO polypeptide a ⁇ ant) as determined bv WU-BLAST-2 by (b) the total number ot amino acid residues ot the PRO polypeptide of interest For example, in the statement 'a polypeptide comp ⁇ sing an amino acid sequence A which has or having at least 80% ammo acid sequence identify to the ammo acid sequence
  • Percent ammo acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST2 (Altschul et al Nucleic Acids Res 25 3389-3402 ( 1997))
  • the % ammo acid sequence identity of a given amino acid sequence A to, with, or against a given am o acid sequence B (which can alternatively be phrased as a giv en amino acid sequence A that has or comp ⁇ ses a certain % ammo acid sequence identity to, with, or agamst a given amino acid sequence B) is calculated as follows
  • PRO va ⁇ ant polynucleotide or "PRO va ⁇ ant nucleic acid sequence means a nucleic acid molecule which encodes an active PRO polypeptide as defined below and which has at least about 80% nucieic acid sequence identity with a nucleotide sequence encoding- ( 1 ) a full-length native sequence PRO polypeptide as disclosed herein, (2) a full-length native sequence PRO polypeptide lacking the signal peptide as disclosed herem; (3) an extracellular domain of a PRO polypeptide, with or without the signal peptide.
  • a PRO polypeptide va ⁇ ant polynucleotide will have at least about 80% nucleic acid sequence identity, alternatively at least about 81% nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identif y , alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89%o nucieic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91 % nucleic acid sequence identity alternatively at least about 92% nucleic acid sequence identit y du ely at least about 93% nucleic acid sequence
  • PRO polypeptide variant polynucleotides are at least about 30 nucleotides in length, alternatively at least about 60 nucleotides in length, alternatively at least about 90 nucleotides in length, alternati el y at least about 120 nucleotides in length, alternati ely at least about 150 nucleotides in length,
  • el y at least about 180 nucleotides in length, alternatively at least about 210 nucleotides in length.
  • alternativel y at least about 240 nucleotides in length, alternatively at least about 270 nucleotides length, alternatively at least about 300 nucleotides in length, alternatively at least about 450 nucleotides in length, alternatively at least about 500 nucleotides in length, alternatively at least about 600 nucleotides in length, alternatively at least about 700 nucleotides in length, alternatively at least about 800 nucieotides in length, alternatively at least about 900 nucleotides in length, alternatively at least about 1000 nucleotides in length, alternatively at least about 1200 nucleotides in length, alternatively at least about 1400 nucleotides in length, alternatively at least about 1600 nucleotides in length, alternatively at least about 1800 nucleotides in length, alternatively at least about 2000 nucleotides in length, alternatively at least about 2500 nucleotides in length, alternatively at least about 3000 nucleotides m length, alternatively at least about 3
  • Percent (%) nucieic acid sequence identity with respect to PRO-encoding nucleic acid sequences identified herem is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the PRO nucieic acid sequence of interest, after alignmg the sequences and mtroducmg gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid sequence identity can be achieved in va ⁇ ous ways that are within the skill in the art. for instance, using publicly available computer software such as BLAST. BLAST-2.
  • ALIGN or Mega gn (DNASTAR) software
  • % nucleic acid sequence identity values are generated usmg the sequence compa ⁇ son computer program ALIGN-2, wherem the complete source code for the ALIGN-2 program is provided in Table 1 below
  • the ALIGN-2 sequence compa ⁇ son computer program was authored by Genentech. Inc. and the source code shown in Table 1 below has been filed with user documentation in the U.S. Copy ⁇ ght Office. Washington D.C, 20559. where it is registered under U.S. Copy ⁇ ght Registration No. TXU510087
  • the ALIGN-2 program is pubhclv available through Genentech. Inc.. South San Francisco, California or may be compiled from the source code provided in Table 1 below.
  • the ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D. All sequence compa ⁇ son parameters are set by the ALIGN-2 program and do not vary
  • the % nucleic acid sequence identify of a given nucleic acid sequence C to. with, or against a given nucleic acid sequence D is calculated as follows'
  • PRO-DNA represents a hypothetical PRO polypeptide - encoding nucleic acid sequence of interest
  • Comparison DNA represents the nucleotide sequence of a nucleic acid molecule against which the "PRO-DNA” nucleic acid molecule of interest is being compared
  • N", “L” and “V” each represent different hypothetical nucleotides.
  • all % nucleic acid sequence identity values used herein are obtained as desc ⁇ bed in the immediately preceding paragraph using the ALIGN-2 computer program. However. % nucleic acid sequence identity values may also be obtained as desc ⁇ bed below by using the WU- BLAST-2 computer program (Altschul et al .
  • a % nucleic acid sequence identity value is determmed by dividing (a) the number of matching identical nucleotides between the nucleic acid sequence of the PRO polypeptide - encoding nucleic acid molecule of interest having a sequence de ⁇ ved from the native sequence PRO polypeptide - encoding nucleic acid (i.e., the reference sequence) and the compa ⁇ son nucleic acid molecule of interest (i e., the sequence agamst which the PRO polypeptide - encodmg nucleic acid molecule of interest is being compared - which mav be a PRO va ⁇ ant polynucleotide) as determmed by WU- BLAST-2 bv (b) the total number of nucleotides of the PRO reference sequence
  • WU-BLAST-2 bv
  • Percent nucleic acid sequence identify may also be determined usmg the sequence compa ⁇ son program NCBI-BLAST2 (Altschul et al Nucleic Acids Res 25 3389-3402 (1997))
  • NCBI-BLAST2 sequence compa ⁇ son program mav be downloaded from http //www ncbi nlm nih gov ' or otherwise obtained from the National Institute of Heath Bethesda MD
  • % nucleic acid sequence identify of a given nucleic acid sequence C to with or acainst a given nucieic acid sequence D is calculated as follows
  • PRO va ⁇ ant polvnucleotides are nucleic acid molecules that encode an active PRO polypeptide and which arc capable of hybridizing, preferably under stringent hv b ⁇ dization and wash conditions, to nucleotide sequences encoding a full-length PRO polypeptides as disclosed herein
  • PRO variant polypeptides mav be those that are encoded by a PRO variant polynucleotide
  • positives in the context of sequence comparison performed as desc ⁇ bed above, mcludes residues in the sequences compared that are not identical but have similar properties (e g , as a result of conservative substitutions, see Table 6 below)
  • the % value of positives is determined by dividing (a) the number of ammo acid residues sco ⁇ ng a positive value between the PRO polypeptide sequence of mterest havmg a sequence de ⁇ ved from a native sequence PRO polypeptide and the compa ⁇ son amino acid sequence of interest (
  • % value of positives is calculated as desc ⁇ bed in the immediately preceding paragraph
  • m cludes ammo acid residues m the sequences compared that are not onlv identical, but also those that have similar properties.
  • Ammo acid residues that score a positive value to an amino acid residue of interest are diose that are either identical to the amino acid residue of interest or are a preferred substitution (as defined in Table 1 below) of the ammo acid residue of mterest. For ammo acid sequence compa ⁇ sons using ALIGN-2 or NCBI-BLAST2.
  • % value of positives of a given ammo acid sequence A to. with, or agamst a given amino acid sequence B (which can alternatively be phrased as a given ammo acid sequence A that has or comp ⁇ ses a certain % positives to. with, or agamst a given ammo acid sequence B) is calculated as follows
  • isolated when used to describe the va ⁇ ous polypeptides disclosed herem. means polypeptide that has been identified and separated and/or recovered from a component of its natural environment Contaminant components of its namral environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide. and may include enzymes, hormones, and other protemaceous or non- prote aceous solutes
  • the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal ammo acid sequence by use of a spinning cup sequenator. or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or.
  • silver stain Isolated polypeptide includes polypeptide m situ within recombinant cells, since at least one component of the PRO polypeptide in its namral environment will not be present Ordma ⁇ ly. however isolated polypeptide will be prepared bv at least one purification step
  • An "isolated" PRO polypeptide - encodmg nucleic acid or other polypeptide-encoding nucieic acid is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordma ⁇ ly associated in the narurai source of the polypeptide-encoding nucleic acid.
  • An isolated polypeptide-encoding nucleic acid molecule is other than in the context or setting m which it is found in nature Isolated polypeptide - encoding nucleic acids therefore are distinguished from the polypeptide - encodmg nucleic acid molecule existing m natural cells.
  • control sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism
  • the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ⁇ bosome binding site.
  • Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
  • Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence.
  • DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotem that participates in the secretion of the polypeptide: a promoter or enhancer is operably linked to a coding sequence if it affects the transc ⁇ ption of the sequence: or a ribosome binding sue is operably linked to a coding sequence if it is positioned so as to facilitate translation.
  • "operably linked” means that the DNA sequences being linked are contiguous, and. in the case of a secretory leader, contiguous and in readmg phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
  • Hyb ⁇ dization generally depends on the ability of denatured DNA to reanneal when complementary strands are present in an environment below their melting temperamre. The higher the degree of desired homology between the probe and hyb ⁇ dizable sequence, the higher the relative temperamre which can be used.
  • “St ⁇ ngent conditions” or “high stringency conditions. ' as defined herein, may be identified by those that: ( 1 ) employ low ionic strength and high temperamre for washing, for example 0 015 M sodium chloride/0.0015 M sodium c ⁇ trate/0.1% sodium dodecyl sulfate at 50°C; (2) employ du ⁇ ng hyb ⁇ dization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum album ⁇ n/0.1% Ficoll/0.1% polyv ⁇ nylpyrrol ⁇ done/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chlo ⁇ de, 75 mM sodium citrate at 42°C, or (3) employ 50% formamide, 5 x SSC (0.75 M NaCl, 0.075 M sodium citrate).
  • formamide for example, 50% (v/v) formamide with 0.1% bovine serum album ⁇ n/0.1% Ficoll/0.1% polyv ⁇
  • Modely st ⁇ ngent conditions may be identified as desc ⁇ bed by Sambrook et al.. Molecular Cloning. A Laboratory Manual. New York: Cold Spring Harbor Press. 1989. and include the use of washmg solution and hyb ⁇ dization conditions ( g., temperamre. ionic strength and %SDS) less st ⁇ ngent that those desc ⁇ bed above.
  • An example of moderately st ⁇ ngent conditions is overnight incubation at 37°C in a solution comp ⁇ sing: 20% formamide. 5 x SSC (150 mM NaCl, 15 mM t ⁇ sodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhardt's solution.
  • Antibodies are glycoprotems having the same general structural characte ⁇ stics. While antibodies exhibit binding specificity to a specific antigen, immunoglobulins include both antibodies and other antibody-like molecules which lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by yeiomas.
  • antibody is used in the broadest sense and specifically covers, without limitation, mtact monoclonal antibodies (including agonist, antagonist and neutralizing antibodies), polyclonal antibodies, multispecific antibodies (e g , bispecific antibodies) formed trom at least two intact antibodies, s gie cham antibodies binding the epitopes specific to the PRO polypeptide and antibody fragments so long as they exhibit the desired biological activity
  • mtact monoclonal antibodies including agonist, antagonist and neutralizing antibodies
  • polyclonal antibodies include polyclonal antibodies, multispecific antibodies (e g , bispecific antibodies) formed trom at least two intact antibodies, s gie cham antibodies binding the epitopes specific to the PRO polypeptide and antibody fragments so long as they exhibit the desired biological activity
  • ant ⁇ -PR04333, ant ⁇ -PRO4302, ant ⁇ -PRO4430 or ant ⁇ -PR05727 antibody is an antibody which immunologically binds to a PRO200. PRO204. PR0212.
  • PR0356 PR053 1. PR0533.
  • PROl 1 14. PRO 1007 PRO l 184 PRO103 1. PR01346. PRO l 155. PRO 1250. PR01312.
  • the antibody may bind to any domain of the PRO polypeptide which may be contacted by the antibody
  • the antibody may bind to any extracellular domain of the polypeptide and when the entire polypeptide is secreted, to any domain on the polypeptide which is available to the antibody for binding.
  • “Native antibodies” and “native immunoglobulins” are usually heterotetrame ⁇ c glycoproteins of about 150,000 daltons. composed of two identical light (L) chains and two identical heavy (H) chains. Each light chain is linked to a heavy chain by one covalent disulfide bond, while the number ot disulfide linkages varies among the heaw chains ot different immunoglobulin isotvpes Each heaw and light cham also has regularl y spaced lntrachain disulfide b ⁇ dges. Each heavy chain has at one end a va ⁇ able domain ( V H ) followed by a number of constant domams.
  • V H va ⁇ able domain
  • Each light cham has a variable domain at one end ( V L ) and a constant domam at its other end: the constant domam of the light chain is aligned with the first constant domain of the heavy chain, and the light-chain va ⁇ able domain is aligned with the va ⁇ able domain of the heavy chain.
  • Particular ammo acid residues are believed to form an mterface between the light- and heavy-chain va ⁇ able domams.
  • va ⁇ abie refers to the fact that certain portions of the va ⁇ able domams differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly dist ⁇ ubbed throughout the va ⁇ able domams of antibodies. It is concentrated in three or four segments called “compleme ⁇ ta ⁇ ty-determining regions” (CDRs) or “hypervanable regions” in both in the light-chain and the heavy-chain va ⁇ able domams. The more highly conserved portions of va ⁇ able domams are called the framework (FR).
  • CDRs compact ⁇ ta ⁇ ty-determining regions
  • FR framework
  • va ⁇ able domams of native heavy and light chams each comp ⁇ se four or five FR regions, largely adoptmg a ⁇ -sheet configuration, connected by the CDRs, which form loops connecting, and in some cases forming part of, the ⁇ -sheet structure.
  • the CDRs m each cham are held together in close proximity by the FR regions and. with the CDRs from the other cham. conmbute to the formation of the antigen-binding site ot antibodies (see Kabat et al . NIH Publ. No.91-3242, Vol.
  • CDR's can also be defined using a hyb ⁇ d approach incorporating the residues identified by both of the previous techniques
  • the constant domams are not mvoived directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity
  • Antibody fragments comp ⁇ se a portion of an intact antibody, preferably the antigen binding or va ⁇ able region of the intact antibody
  • Examples of antibody fragments include Fab. Fab'. F(ab') 2 , and Fv fragments, diabodies. linear antibodies (Zapata et al . Protein Eng 8 ( 10) 1057- 1062 [1995]), singie-cham antibody molecules, and multispecific antibodies formed from antibody fragments.
  • Papain digestion of antibodies produces two identical antigen- binding fragments, called "Fab” tragments. each with a single antigen-binding site, and a residual c" fragment, whose name reflects its ability to crystallize readilv Pepsin treatment yields an 1 (ab'b fragment that has two antigen-combining sites and is still capable of cross-linking antigen
  • Fv is the minimum antibody fragment w hich contains a complete antigen-recognition and binding site. This region consists of a dimer of one heavy- and one light-chain variable domam m tight, non-covalent association it is in this configuration that the three CDRs of each va ⁇ able domain interact to define an antigen-binding site on the surface ot the V ⁇ -VJL dimer
  • the six CDRs confer antigen-binding specificity to the antibody
  • a single va ⁇ able domain or half of an Fv comp ⁇ sing only three CDRs specific for an antigen
  • the Fab fragment also contains the constant domain of the light chain and the first constant domain
  • (CH I ) of the heaw chain Fab' fragments differ from Fab fragments bv the addition ot a few residues at the carboxv terminus of the heaw chain CH I domain including one or more cysteines trom the antibody hinge region Fab'-SH is the designation herein for Fab' in which the cysteine res ⁇ due(s) of the constant domains bear a free thiol group.
  • F(ab')2 antibody fragments onginally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • the "light chains" of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa (K) and lambda ( ⁇ ). based on the ammo acid sequences of their constant domams.
  • immunoglobulins can be assigned to different classes. There are five ma j or classes of immunoglobulms: IgA, IgD, IgE. IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgGl, IgG2, IgG3, IgG4, IgA, and IgA2.
  • the heavy-chain constant domains that correspond to the different classes of immunoglobulms are called ⁇ , ⁇ , ⁇ , ⁇ , and ⁇ , respectively.
  • the subunit structures and three-dimensional configurations of different classes of immunoglobulms are well known.
  • monoclonal antibody refers to an antibody obtamed from a population of substantially homogeneous antibodies, i.e., the individual antibodies comp ⁇ sing the population are identical except for possible naturally occur ⁇ ng mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed agamst a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations which typically include different antibodies directed against different determinants (epitopes). each monoclonal antibody is directed agamst a single determinant on the antigen.
  • the monoclonal antibodies are advantageous in that they are synthesized by the hyb ⁇ doma culture, uncontaminated by other immunoglobulins.
  • the modifier "monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requi ⁇ ng production of the antibody by any particular method.
  • the monoclonal antibodies to be used in accordance with the present invention may be made by the hyb ⁇ doma method first desc ⁇ bed by Kohler et al , Nature, 256: 495 [1975], or may be made by recombinant DNA methods (see, e.g., U.S. Patent No 4,816,567).
  • the "monoclonal antibodies” may also be isolated from phage antibody bra ⁇ es using the techniques desc ⁇ bed in Clackson ct al.. Nature. 352:624-628 [1991 ] and Marks et al , J. Mol Biol.. 222.581 -597 ( 1991 ). tor example. See also U.S Patent Nos 5.750,373. 5,571.698, 5.403.484 and 5.223.409 which desc ⁇ be the preparation of antibodies using phagemid and phage vectors.
  • the monoclonal antibodies herein specifically include "chimenc" antibodies (immunoglobulins) in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies de ⁇ ved from a particular species or belonging to a particular antibody class or subclass, while the remainder of the cha ⁇ n(s) is identical with or homologous to corresponding sequences in antibodies de ⁇ ved from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Patent No. 4,816,567: Momson et al., Proc. Natl. Acad. Set. USA. 8 6851 -6855 [ 1984])
  • Humanized forms of non-human (e g , mu ⁇ ne) antibodies are chimenc immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab'. F(ab') 7 or other antigen-binding subsequences of antibodies) which contain minimal sequence de ⁇ ved from non-human immunoglobulin.
  • humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a compiementa ⁇ ty-determining region (CDR) of the recipient are replaced by residues from a CDR of a non- human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity, and capacity. In some instances.
  • humanized antibodies may comp ⁇ se residues which are found neither m the recipient antibody nor m the imported CDR or framework sequences. These modifications are made to further refine and maximize antibody performance.
  • the humanized antibody will comp ⁇ se substantially all of at least one. and typically two, va ⁇ able domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and ail or substantially all of the FR regions are those of a human immunoglobulin sequence.
  • the humanized antibody optimally also will comp ⁇ se at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • Fc immunoglobulin constant region
  • the humanized antibody includes a "primat ⁇ zed"ant ⁇ body where the antigen-bmding region of the antibody is derived from an antibody produced by immunizing macaque monkeys with the antigen ot mterest. Antibodies containmg residues from Old World monkeys are also possible within the invention. See, for example. U.S. Patent Nos. 5,658,570; 5,693,780; 5,681.722, 5,750,105; and 5.756,096.
  • Antibodies and fragments thereof this invention also include "affinity matured" antibodies in which an antibody is altered to change the amino acid sequence of one or more of the CDR regions and/or the framework regions to alter the affinity of the antibody or fragment thereof for the antigen to which it bmds.
  • Affinity maturation may result in an increase or in a decrease m the affinity of the matured antibody for the antigen relative to the starting antibody
  • the starting antibody will be a humanized, human, chimenc or murine antibody and the affinity matured antibody will have a higher affinity than the starting antibody.
  • the ammo acid residues in the CDRs or in the framework regions are changed to a different residue using any standard method.
  • Suitable methods include point mutations using well known cassette mutagenesis methods (Wells et al , 1985. Gene 34.315) or oligonucleotide mediated mutagenesis methods (Zoller et al , 1987, Nucleic Acids Res. J0.6487-6504).
  • Affinity maturation may also be performed using known selection methods in which many mutations are produced and mutants having the desired affinity are selected from a pool or library ot mutants based on improved affinity tor the antigen or ligand.
  • Known phage display techniques can be conveniently used in this approach See. for example, U S 5,750,373, U.S. 5,223,409, etc.
  • Human antibodies are also with in the scope of the antibodies of the invention. Human antibodies can be produced using various techniques known in the art, including phage display hbra ⁇ es [Hoogenboom and Winter. ./ Mol. Biol . 227.381 ( 1991 ), Marks et at , J. Mol. Biol . 222.581 ( 1991)]. The techniques of Cole et al. and Boemer et al. are also available for the preparation of human monoclonal antibodies (Cole et al.. Monoclonal Antibodies and Cancer Therapy, Alan R. Liss. p. 77 ( 1985); Boerner et al.. J Immunol., 147 (L:86-95 (1991 ); U. S.
  • human antibodies can be made by introducing of human immunoglobulin loci into transgenic animals, e g , mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in ail respects, including gene rearrangement, assembly, and antibody repertoire.
  • transgenic animals e g
  • mice in which the endogenous immunoglobulin genes have been partially or completely inactivated.
  • human antibody production is observed, which closely resembles that seen in humans in ail respects, including gene rearrangement, assembly, and antibody repertoire
  • This approach is described, for example, in U.S. Patent Nos 5,545,807, 5.545.806, 5.569,825. 5,625,126. 5,633,425; 5,661,016. and m the following scientific publications: Marks et al., Bio/Technology JO. 779-783 ( 1992); Lonberg et at .
  • Single-chain Fv or “sFv” antibody fragments comp ⁇ se the V H and V L domams of antibody, wherem these domains are present in a single polypeptide chain.
  • the Fv polypeptide further compnses a polypeptide linker between the V ⁇ and V ⁇ domams which enables the sFv to form the desired structure for antigen binding.
  • diabodies refers to small antibody fragments with two antigen-binding sites, which fragments comp ⁇ se a heavy-chain va ⁇ able domam (VJJ) connected to a light-chain va ⁇ able domain (VTJ in the same polypeptide chain (VJJ - VT .
  • VJJ heavy-chain va ⁇ able domam
  • VTJ light-chain va ⁇ able domain
  • VTJ light-chain va ⁇ able domain
  • Diabodies are desc ⁇ bed more tully in. for example, EP 404.097. WO 93/11161. and Holhnger et al . Proc. Natl. Acad. Sci USA. 90 6444-6448 ( 1993).
  • label when used herein refers to a detectable compound or composition which is conjugated directly or indirectly to the compound, e g , antibody or polypeptide. so as to generate a "labelled” compound.
  • the label may be detectable by itself (e g , radioisotope labels or fluorescent labels) or. m the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition which is detectable
  • solid phase is meant a non-aqueous mat ⁇ x to which the compound of the present invention can adhere
  • solid phases encompassed herem include those formed partially or entirely of glass (e g , controlled pore glass), polysacchandes (e g , agarose). polyacrylamides, polystyrene, polyvinyl alcohoi and si cones.
  • the solid phase can comp ⁇ se the well of an assay plate; in others it is a pu ⁇ fication column (e g , an affinity chromatography column) This term also includes a discontinuous solid phase of discrete particles, such as those described in U.S Patent No 4.275.149
  • immune reiated disease means a disease in which a component of the immune system of a mammal causes, mediates or otherwise contributes to a morbidity in the mammal
  • diseases in which stimulation or intervention of the immune response has an ameliorative effect on progression of the disease Included within this term are immune-mediated inflammatory diseases, non-immune-mediated inflammatory diseases, infectious diseases, immunodeficiency diseases, neoplasia. etc
  • T cell mediated disease means a disease in which T cells directly or indirectly mediate or otherwise cont ⁇ bute to a morbidity in a mammal.
  • the T cell mediated disease may be associated with cell mediated effects, lymphokine mediated effects, etc , and even effects associated with B cells if the B cells are stimulated, for example, by the lymphokines secreted by T cells.
  • immune-related and inflammatory diseases examples include systemic lupus ervthematosis. rheumatoid arth ⁇ tis. juvenile chronic arthritis, spondyloarthropathies. systemic sclerosis (scleroderma). idiopathic inflammatory myopathies (dermatomvositis polymyositis). Sjogren's syndrome, systemic v ascu tis, sarcoidosis. autoimmune hemolvtic anemia ( immune pancytopenia. paroxysmal nocturnal hemoglobinu ⁇ a), autoimmune thrombocytopenia (idiopathic thrombocytopenic purpura.
  • systemic lupus ervthematosis examples include systemic lupus ervthematosis. rheumatoid arth ⁇ tis. juvenile chronic arthritis, spondyloarthropathies. systemic sclerosis (scleroderma). idiopathic inflammatory myopathies (derm
  • immune-mediated thrombocytopenia immune-mediated thrombocytopenia
  • thyroiditis GRAve's disease, Hashimoto's thyroiditis, juvenile lymphocytic thyroiditis, atrophic thyroiditis
  • diabetes mel tus immune-mediated renal disease (glomeruloneph ⁇ tis.
  • tubulointerstitial neph ⁇ tis demye nating diseases of the central and pe ⁇ pheral nervous systems such as multiple sclerosis, idiopathic demyelinating polyneuropathy or Guillam-Barre syndrome, and chronic inflammatory demyehnating poiyneuropathy, hepatobi ary diseases such as infectious hepatitis (hepatitis A, B, C, D, E and other non- hepatotropic viruses), autoimmune chronic active hepatitis, p ⁇ mary biliary cirrhosis, granulomatous hepatitis.
  • infectious hepatitis hepatitis A, B, C, D, E and other non- hepatotropic viruses
  • autoimmune chronic active hepatitis p ⁇ mary biliary cirrhosis
  • granulomatous hepatitis granulomatous hepatitis.
  • sclerosmg cholangitis inflammatory bowel disease (ulceranve colitis: Crohn's disease), gluten-sensitive enteropathy, and Whipple's disease, autoimmune or immune-mediated skin diseases mcludmg bullous skin diseases, erythema multiforme and contact dermatitis, pso ⁇ asis, allergic diseases such as asthma, allergic rhinitis, atopic dermatitis, food hypersensitivity and urtica ⁇ a.
  • lmmunoiogic diseases of the lung such as eosuiophilic pneumonias, idiopathic pulmonary fibrosis and hypersensitivity pneumonitis, transplantation associated diseases including graft rejection and graft -versus-host-disease.
  • Infectious diseases mcludmg viral diseases such as AIDS (HIV infection), hepatitis A. B, C, D. and E. herpes, etc . bacte ⁇ al infections, fungal infections, protozoal infections and parasitic infections.
  • HIV infection HIV infection
  • bacte ⁇ al infections fungal infections, protozoal infections and parasitic infections.
  • Treatment is an intervention performed with the intention of preventing the development or alte ⁇ ng the pathology of a disorder
  • treatment refers to both therapeutic treatment and prophylactic or preventative measures.
  • Those in need of treatment include those already with the disorder as well as those in which the disorder is to be prevented.
  • a therapeutic agent may directly decrease or increase the magnitude of response of a component of the immune response, or render the disease more susceptible to treatment by other therapeutic agents, e g , antibiotics, antifu ⁇ gals, anti- lnflammatory agents, chemotherapeutics.
  • an effective amount is at least the minimum concentration or amount of a PRO polypeptide and or agonist antagonist which causes, induces or results in either a detectable improvement m a component of the immune response in mammals as measured in an in vitro assay. For example, an increase or decrease m the proliferation of T-cells and/or vascular permeability as measured in Examples provided herein.
  • a “therapeutically effective amount” is the minimum concentration or amount of a PRO polypeptide and/or agonist/antagonist which would be effective in at least attenuating a pathology (increasing or decreasing as the case may be) a component ot the immune response in mammals, the results of which effects a treatment as defined in the previous paragraph.
  • Chronic administration refers to administration of the agent(s) in a continuous mode as opposed to an acute mode, so as to mamtain the initial therapeutic effect (activity) for an extended period of time.
  • Intermittent administration is treatment that is not consecutively done without interruption, but rather is cyclic in nature.
  • the "pathology" of an immune related disease includes all phenomena that compromise the well- being of the patient This includes, without limitation, abnormal or uncontrollable cell growth, antibody production, auto-antibody production, complement production and activation, interference with the normal functioning of neighboring cells, release ot cytokines or other secretory products at abnormal levels, suppression or aggravation oi any inflammatory or immunoiogical response, infiltration of inflammatory cells (neutrophihc. eosinophihc. monocytic, lymphocytic) into tissue spaces, etc
  • “Mammal” for purposes of treatment refers to any animal classified as a mammal, mcludmg humans, domestic and farm animals, and zoo. sports, or pet animals, such as dogs, horses, cattle, pigs, apes, hamsters, ferrets, cats, etc Preferably, the mammal is human.
  • Administration "in combination with” one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.
  • Car ⁇ ers as used herem include pharmaceutically acceptable earners, excipients. or stabilizers which are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable earner is an aqueous pH buffered solution.
  • physiologically acceptable car ⁇ ers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid: low molecular weight (less than about 10 residues) polypeptide; protems, such as serum albumin, gelatm, or immunoglobulins; hydrophilic polymers such as polyvmylpyrrolidone; ammo acids such as glycme, glutamine, asparagine, arginine or lysme; monosaccha ⁇ des, disaccharides, and other carbohydrates including glucose, mannose.
  • buffers such as phosphate, citrate, and other organic acids
  • antioxidants including ascorbic acid: low molecular weight (less than about 10 residues) polypeptide
  • protems such as serum albumin, gelatm, or immunoglobulins
  • hydrophilic polymers such as polyvmylpyrrolidone
  • ammo acids such as glycme, glutamine, asparagine, arginine or lysme
  • chelating agents such as EDTA
  • sugar aicohols such as mannitol or sorbi t ol: salt-forming counte ⁇ ons such as sodium
  • noniomc surfactants such as TWEENTM, polyethylene glycol (PEG), and PLURONICSTM
  • cytotoxic agent refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells.
  • the term is intended to include radioactive isotopes (e.g , I 111 . 1 125 , Y 90 and Re ), chemotherapeutic agents, and toxins such as enzymatically active toxins of bacte ⁇ al. fungal, plant or animal o ⁇ gm, or fragments thereof.
  • a “chemotherapeutic agent” is a chemical compound useful in the treatment of cancer.
  • chemotherapeutic agents include adnamycm. doxorubicin. epirubicin. 5-fluorourac ⁇ l, cytosine arabinoside ("Ara-C " ) , cyclophosphamide. thiotepa, busulfan.
  • cytoxin. taxoids e.g . pac taxel (Taxol. Bristol-Myers Squibb Oncology, P ⁇ nceton. NJ), and doxetaxel (Taxotere, Rh ⁇ ne-Poulenc Rorer, Antony. France), toxotere. metho t rexate.
  • a “growth inhibitory agent” when used herein refers to a compound or composition which inhibits grow t h of a cell , especiall y cancer cell overexpressing any of the genes identified herein, either in vitro or in vivo
  • the growth inhibitory agent is one which significantly reduces the percentage of cells overexpressing such genes in S phase.
  • growth inhibitory agen t s include agents that block cell cycle progression (at a place other than S phase), such as agents that prise G l arrest and M-phase arrest.
  • Classical M-phase blockers include the vmcas (vinc ⁇ stine and vmblastine), t axol, and topo II inhibitors such as doxorubicin. epirubicin. daunorubicin.
  • cytokme is a generic term for proteins released by one cell population which act on another cell as intercellular mediators.
  • cytokines are lymphok es. monokines. and traditional polypeptide hormones. Included among the cytokines are grow t h hormone such as human growth hormone , N-methionyl human growth hormone, and bovine growth hormone: para t hyroid hormone; thyroxine; insulm; proinsuiin: reiaxm; prorelaxm: glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimuiatmg hormone (TSH), and luteimzing hormone (LH); hepatic growth factor: fibroblast growth factor: prolactin; placental lactogen tumor necrosis factor- ⁇ and - ⁇ ; mullenan-inhibiting substance: mouse gonadotropm-associated peptide: inhibm: activin; vascular endothelial grow t h factor
  • IL-CSF granulocyte-macrophage-CSF
  • G-CSF granulocyte-CSF
  • interieukins ILs
  • cytokme includes proteins from namral sources or from recombinant cell culture and biologically active equivalents of the native sequence cytokmes
  • the term 'epitope tagged ' when used herein refers to a chimenc polypeptide comp ⁇ sing a PRO polypeptide fused to a 'tag polypeptide '
  • the tag polypeptide has enough residues to provide an epitope agamst which an antibody can be made vet is short enough such that it does not interfere with activity of the polypeptide to which it is fused
  • the tag polypeptide preferably also is fairlv unique so that the antibody does not substantially cross-react with other epitopes
  • Suitable tag polypeptides generally have at least six ammo acid residues and usually between about 8 and 50 ammo acid residues (preferably, between about 10 and 20 ammo acid residues) "Active' or 'activity ' in the context of va ⁇ ants ot the PRO polypeptide refers to form(s) of proteins of the invention which retain the biologic and or the ability to mduce the production of an antibody agamst an antigenic epitope possessed by the PRO polypeptid
  • a "smail molecule ' is defined herein to have a molecular weight below about 600 daltons. and is generally an organic compound
  • a “liposome” is a smail vesicle composed of va ⁇ ous types of lipids, phospho pids and/or surfactant which is useful for delivery of a drug (optionally mcludmg a chemotherapeutic agent) to a mammal
  • the components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes
  • the term 'lmmunoadhesin ' designates antibody-like molecules which combme the binding specificity of a heterologous protein (an “adhesin 1 ) with the effector functions of immunoglobulin constant domams Structurally, the immunoadhesins comp ⁇ se a fusion of an ammo acid sequence with the desired binding specificitv which is other than the antigen recognition and binding site of an antibody (t e , is "heterologous '), and an immunoglobulin constant domam sequence
  • the immunoglobulin constant domain sequence in the lmmunoadhesin may be obtained from any immunoglobulin. such as IgG-1, IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-1 and IgA-2). IgE, IgD or IgM.
  • I*Q *l [0, 1.-5.2.2,-5.-1.3,-2.0, 1.-2. 1. l._M.0, 4. l.-l.-l.0.-2.-5.0,-4, 3 ⁇ , l*R*l -2.0.-4.-1.-1.-4,-3,2.-2,0.3.-3.0.0,_M.0.1.6.0.-1.0.-2.2.0.-4.0 ⁇ . l*S*l 1,0.0.0.0.-3.1.-1.-1,0.0.-3.- 2. l._M. l.-l.0.2.1.0.-1.-2.0,-3.0 ⁇ .
  • nvvi */ int dmaxO: /* final diag » ' int dna; /* set if dna: mainO */ int endgaps: /* set if penalizing end gaps */ int gapx, gapy; /* total gaps in seqs */ int lenO.
  • lenl /* seq lens */ int ngapx, ngapy; /* total size ot gaps */ int smax: /* max score: nw() */ int *xbm: /* bitmap tor matching */ long offset; /* current offset in mp file */ struct diag *dx: /* holds diagonals */ struct path PP[2]; /* holds path tor seqs */ char *calloc().
  • the program mav create a tmp file in /tmp to hold info about traceback Original version developed under BSD 43 ⁇ n a va ⁇ 8650
  • 0], &len0). seqx(l] getseq(namex
  • static nm /* matches in core - for checking */ static Imax: /* lengths ot stripped file names */ static ij[2]; /* jmp index for a path */ static nc(2]. /* number at start ot current iine */ static n ⁇ [2]; /* current elem number — for gapping */ static s ⁇ z[2]. static char *ps[2]. /* ptr to current element */ static char *po[2]. /* ptr to next output char slot */ static char oouutt((22]][[IP_LINE], /* output line */ static char starfP 1 il. * set by stars! ) *//
  • *py + + *px. else if (islower( *px))
  • *py++ loupper(*px) if( ⁇ ndex( ATGCU *(py-l))) natgc + + ⁇ ⁇
  • the present invention provides newly identified and isolated nucleotide sequences encoding the polypeptides in the present application as PRO polypeptides
  • cDNAs encoding vanous PRO polypeptides have been identified and isolated, as disclosed in further detail in the Examples below. It is noted that proteins produced in separete expression rounds may be given different PRO numbers but the UNQ number is unique for any given DNA and the encoded protein, and will not be changed.
  • the protein encoded by the full length native nucleic acid molecules disclosed herein as well as all further native homologues and va ⁇ ants included m the foregoing definition of PRO. will be referred to as "PRO/number" or even "PRO", regardless of their o ⁇ gm or mode of preparation.
  • DNA29101 -1276 DNA30871-1 157. DNA30942- 1 134. DNA33087- 1 158. DNA33460- 1 166. DNA34387- 1 138, DNA35558- 1 167, DNA35638-1141, DNA35916-1 161 , DNA39523-1192, DNA40620-1183, DNA40982-1235, DNA44184-1319, DNA44205-1285. DNA45410-1250, DNA45416-1251, DNA45419-1252. DNA47365- 1206. DNA47470-1130. DNA48314-1320. DNA49435-1219, DNA50921-1458, DNA53974-1401.
  • DNA64885- 1529. DNA65404-1551, DNA65412-1523, DNA66675- 1587, DNA68864- 1629, DNA68872-1620, DNA68874-1622, DNA76400-2528, DNA77624-2515, DNA30868-1156, DNA36638-1056, DNA38260- 1 180, DNA40592-1242.
  • PRO1007. PROl 184. PRO1031. PR01346. PROl 155. PRO1250. PR01312. PR01192, PR01246. PR01283, PROl 195. PR01343, PR01418. PROI387. PRO1410. PR01917, PR01868. PRO205, PR021, PR0269, PR0344. PR0333. PR0381. PRO720, PR0866, PRO840, PR0982, PR0836, PR01159, PR01358, PR01325, PR01338. PR01434, PR04333. PRO4302. PRO4430 and PR05727 polypeptides, respectively
  • PRO va ⁇ ants can be prepared PRO va ⁇ ants can be prepared bv introducing approp ⁇ ate nucleotide changes into the PRO DNA. and'or by synthesis ot the desired PRO polypeptide Those skilled the art will appreciate that amino acid changes mav alter post-translational processes ot the PRO. such as changing the number or position ot glycosviation sites or alte ⁇ ng the membrane anchoring characte ⁇ stics.
  • Va ⁇ ations in the native full-length PRO sequence or in various domains of the PRO described herein. can be made, for example, using any of the techniques and guidelines tor conservative and non-conservative mutations set forth, for instance.
  • U S Patent No 5,364,934 Va ⁇ ations may be a substitution, deletion or insertion of one or more codons encoding the PRO that results in a change m the ammo acid sequence of the PRO as compared with the native sequence PRO
  • the variation is by substitution of at least one ammo acid with any other amino acid in one or more of the domains of the PRO
  • Guidance determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the desired activity mav be found bv comparing the sequence ot the PRO with that of homologous known protein molecules and minimizing the number ot amino acid sequence changes made in regions ot high homology
  • Amino acid substitutions can be the result of replacing one ammo acid with another ammo acid having similar structural and or chemical properties, such
  • Insertions or deletions may optionally be in the range of about 1 to 5 am o acids.
  • the va ⁇ ation allowed may be determmed by systematically making insertions, deletions or substitutions of ammo acids in the sequence and testing the resulting va ⁇ ants for activity exhibited by the full-length or mature native sequence.
  • PRO polypeptide fragments are provided herein. Such fragments may be truncated at the N-terminus or C-termmus, or may lack internal residues, for example, when compared with a full length native protem. Certain fragments lack ammo acid residues that are not essential for a desired biological activity of the PRO polypeptide.
  • PRO fragments may be prepared by any of a number of conventional techniques. Desired peptide fragments may be chemically synthesized. An alternative approach involves generating PRO fragments by enzymatic digestion, e g., by treating the protein with an enzyme known to cleave protems at sites defined by particular ammo acid residues, or by digesting the DNA with suitable rest ⁇ ction enzymes and isolating the desired fragment. Yet another suitable technique mvolves isolating and amplifying a DNA fragment encoding a desired polypeptide fragment, by polymerase chain reaction (PCR). Oligonucleotides that define the desired termmi of the DNA fragment are employed at the 5' and 3' pnmers in the PCR. Preferably, PRO polypeptide fragments share at least one biological and ' or immunological activity with the native PRO polypeptide disclosed herein.
  • PCR polymerase chain reaction
  • conservative substimtions of mterest are shown in Table 6 under the headmg of preferred substitutions. If such substimtions result in a change in biological activity, then more substantial changes, denominated exemplary substimtions in Table 6. or as further desc ⁇ bed below in reference to ammo acid classes, are introduced and the products screened.
  • Substantial modifications in function or immunological identity of the invention polypeptide are accomplished by selecting substimtions that differ significantly in their effect on maintaining (a) the structore of the polypeptide backbone in the area of the substitution, tor example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side cham.
  • Naturally occumng residues are divided into groups based on common side-cham properties: ( 1 ) hydrophobic: norieucme. met, ala. val. leu, ile, 5 (2) neutral hydrophilic: cys, ser. thr;
  • Non-conservative substimtions will entail exchangmg a member of one of these classes for another class. Such substituted residues also may be introduced into the conservative substitution sites or. more preferably, into the remammg (non-conserved) sites.
  • va ⁇ ations can be made using methods known in the art such as ohgonucleotide-mediated (site- directed) mutagenesis. alanine scanning, and PCR mutagenesis Site-directed mutagenesis fCarter et al . Nucl.
  • Scanning amino acid analysis can also be employed to identify one or more ammo acids along a 0 contiguous sequence.
  • preferred scanning amino acids are relatively small, neutral amino acids.
  • ammo acids include alanine, glycme. se ⁇ ne, and cysteine.
  • Alanme is typically a preferred scanning ammo 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 vanant [Cunningham and Wells. Science. 244. 1081 -1085 ( 1989)].
  • Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found m 5 both buried and exposed positions [Creighton. The Proteins. (W H. Freeman & Co., N.Y.): Chothia. J. Mol. Biol . 150.1 ( 1976)] If alanine substitution does not yield adequate amounts of vanant. an lsote ⁇ c amino acid can be used.
  • Covalent modifications of PRO polypeptides are included within the scope of this invention.
  • One 0 type of covalent modification includes reacting targeted ammo acid residues of a PRO polypeptide with an organic de ⁇ vatizing agent that is capable of reacting with selected side chains or the N- or C- terminal residues of the PRO.
  • De ⁇ vatization with bifunctional agents is useful, for instance, for crosshnking PRO to a water- msoluble support mat ⁇ x or surface for use in the method for pu ⁇ fymg anti-PRO antibodies, and vice-versa.
  • Commonly used crosslinking agents include, e.g., l,l-bis(d ⁇ azoacetyl)-2-phenylethane, glutaraldehyde, N-
  • 35 hydroxysuccmimide esters for example, esters with 4-azidosalicylic acid, homobifimctional imidoesters, including disuccinimidyl esters such as 3,3'-dithiobis(succ ⁇ n ⁇ midylprop ⁇ onate), bifunctional maleimides such as bis-N-maieimido-l,8-octane and agents such as methyl-3-[(p-azidophenyl)dithio]prop ⁇ o ⁇ midate.
  • esters with 4-azidosalicylic acid homobifimctional imidoesters, including disuccinimidyl esters such as 3,3'-dithiobis(succ ⁇ n ⁇ midylprop ⁇ onate), bifunctional maleimides such as bis-N-maieimido-l,8-octane and agents such as methyl-3-[(p-azidophenyl)dithio]prop ⁇ o ⁇ midate.
  • Another type of covalent modification of the PRO polypeptide included withm the scope of this invention comp ⁇ ses alte ⁇ ng the native glycosylation pattern of the polypeptide.
  • "Altenng the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence PRO polypeptide (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 PRO.
  • the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the va ⁇ ous carbohydrate moieties present.
  • Addition of glycosylation sites to the PRO polypeptide may be accomplished by alte ⁇ ng the amino acid sequence.
  • the alteration may be made, for example, by the addition of. or substitution by, one or more serine or threonine residues to the native sequence PRO (for O-lmked glycosylation sites).
  • the PRO ammo acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding tne PRO polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids
  • Another means of increasing the number of carbohydrate moieties on the PRO polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g.. in WO 87 , 05330 published 1 1 September 1987. and in Aplin and Wr.ston. CRC Crit. Rev. Biochem . pp. 259- 306 ( 1981 )
  • Removal of carbohydrate moieties present on the PRO polypeptide may be accomplished chemically or enzymatically or by mutat.onal substitution of codons encoding for ammo acid residues that serve as targets for glycosylation.
  • Chemical deglycosyiation techniques are known in the art and described, for instance, by Hakimuddin. et al , Arch Biochem Biophvs . 259-52 ( 1987) and by Edge a al . Anal. Biochem .
  • Enzymatic cleavage ot carbohydrate moieties on polypeptides can be achieved by the use of a va ⁇ ery of endo- and exo-glycosidases as described by Thotakura et al., Met . Enzvmoi. _38.350 ( 1987)
  • Another type of covalent modification ot PRO compnses linking the PRO polypeptide to one ot a vanety of nonprotemaceous polymers .g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes. in the manner set forth in U.S. Patent Nos. 4,640.835; 4,496,689; 4,301 ,144: 4,670,417; 4,791.192 or 4,179,337.
  • PRO polypeptides may also be modified in a way to form a chimenc molecule comp ⁇ sing the invention polypeptide fused to another, heterologous polypeptide or ammo acid sequence.
  • such a chimenc molecule compnses a fusion of the PRO with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind.
  • the epitope tag is generally placed at the ammo- or carboxyl- terminus of the PRO. The presence of such epitope-tagged forms of the PRO polypeptide can be detected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the PRO to be readily pu ⁇ fied by affinity pu ⁇ fication using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag.
  • tag polypeptides and their respective antibodies are well known m the art.
  • poly-histidine poly-his
  • poly-histidine-glycine poly-his-glycine tags
  • flu HA tag polypeptide and its antibody 12CA5 [Field et al.. Mol. Cell. Biol., 8:2159-2165 (1988)]
  • c-myc tag and the 8F9. 3C7. 6E 10, G4.
  • B7 and 9E 10 antibodies thereto [ Ev an et al Molecular and Cellular Biology, 5:3610-3616 ( 1985)], and the Herpes Simplex virus glycoprotem D (gD) tag and its antibody [Paborsky et al..
  • tag polypeptides include the Flag-peptide [Hopp et al.. BioTechnology, 6. 1204-1210 ( 1988)]. the KT3 epitope peptide [Martin et al Science, 255.192-194 (1992)]; an ⁇ -tubuhn epitope peptide [Skinner et al , J Biol Chem , 266 15163-15166 ( 1991)]; and the T7 gene 10 protein peptide tag [Lutz-Freyermuth et al , Proc Natl Acad Set USA. 87 6393-6397 (1990)].
  • the chimenc molecule may comp ⁇ se a fusion of the PRO polypeptide with an immunoglobulin or a particular region of an immunoglobulin.
  • an immunoglobulin also referred to as an "lmmunoadhesin ).
  • 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 ot an mve ⁇ tion polypeptide in place of at least one va ⁇ able region withm an Ig molecule.
  • the immunoglobulin fusion includes the hmge. CH2 and CH3, or the hinge, CHI . CH2 and CH3 regions of an IgG I molecule
  • the desc ⁇ ption below relates to primarily lo production of PRO by culm ⁇ ng cells transformed or transfected with a vector containing PRO nucleic acid It is. ot course, contemplated that alternative methods, which are well known in the art. mav be employed to prepare PRO.
  • the PRO sequence, or portions thereof may be produced by direct peptide synthesis using solid-phase techniques [see, e g.. Stewart et al., Solid-Phase Peptide Svnthesis. W H Freeman Co , San Francisco, CA ( 1969).
  • In vitro protein synthesis may be performed using manual techniques or by automation Automated synthesis may be accomplished, for instance, using an Applied Biosystems Peptide Synthesizer (Foster City. CA) using the manufacmrer's instructions Va ⁇ ous portions of the PRO may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the full- length PRO
  • DNA encoding the PRO mav be obtained from a cDNA library prepared from tissue believed to possess the polypeptide mRNA and to express it at a detectable level. Accordingly, human PRO DNA can be conveniently obtained from a cDNA library prepared from human tissue, such as desc ⁇ bed in the Examples.
  • the PRO-encodmg gene may also be obtained from a genomic library, oligonucleotide synthesis, or other known synthetic procedures (e g , automated nucleic acid synthesis).
  • Libranes can be screened with probes (such as antibodies to the PRO polypeptide or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the prote encoded by it. Screenmg the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as desc ⁇ bed in Sambrook et al , Molecular Cloning A Laboratorv Manual (New York: Cold Sp ⁇ ng Harbor Laboratory Press, 1989). An alternative means to isolate the gene encoding the PRO polypeptide is to use PCR methodology [Sambrook et al., supra; Dieffenbach et al., PCR Primer: A Laboratory Manual (Cold Sp ⁇ ng Harbor Laboratory Press, 1995)].
  • the oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized.
  • the oligonucleotide is preferably labeled such that it can be detected upon hybndization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like : P-labeled ATP, biot ylation or enzyme labeling. Hybndization conditions, including moderate stringency and high stringency, are provided m Sambrook et al . supra.
  • Sequences identified in such library screening methods can be compared and aligned to other known sequences deposited and available m public databases such as GenBank or other private sequence databases. Sequence identity (at either the amino acid or nucleotide level) withm defined regions of the molecule or across the full-length sequence can be determined using methods known the art and as desc ⁇ bed herem.
  • Nucleic acid having protein coding sequence may be obtained by screening selected cDNA or genomic libranes using the deduced amino acid sequence disclosed herein for the first time. and. if necessary, using conventional p ⁇ er extension procedures as descnbed in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transc ⁇ bed into cDNA. 2. Selection and Transformation of Host Cells
  • Host cells are transfected or transformed with expression or cloning vectors desc ⁇ bed herein for production ot the PRO polypeptides and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transtormants. or amplifying the genes encoding the desired sequences
  • the culture conditions such as media, temperamre. pH and the like, can be selected by the skilled artisan without undue e.xpe ⁇ mentation
  • principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biotechnology A Practical Approach. M. Butler, cd (IRL Press. 1991 ) and Sambrook et al . supra.
  • Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or higher eukaryote cells.
  • Suitable prokaryotes include but are not limited to eubacteria. such as Gram- negative or Gram-positive organisms, for example, Enterobacteriaceae such as E. coli.
  • E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31,446); E.
  • coli X1776 ATCC 31,537); E. coli strain W3110 (ATCC 27,325) and K5 772 (ATCC 53,635).
  • Other suitable prokaryotic host cells include Enterobacte ⁇ aceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella. Proteus, Salmonella, e.g., Salmonella tvphimurium. Serraua. e g , Serrana marcescans. and Shigella. as well as Bacilli such as B. subttlis and B. lichemformts (e g., B.
  • Strain W31 10 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations. Preferably, the host cell secretes minimal amounts of proteolytic enzymes.
  • strain W31 10 may be modified to effect a genetic mutation in the genes encoding proteins endogenous to the host, with examples of such hosts including E. coli W31 10 strain 1A2. which has the complete genotype ton.4 : E. coli W3 1 10 strain 9E4.
  • E. coli W31 10 strain 27C7 ATCC 55,244. which has the complete genotype tonA ptri phoA E15 (argF-lac)l69 degP ompT kan .
  • in vitro methods of cloning e.g., PCR or other nucieic acid polymerase reactions, are suitable.
  • eukaryotic microbes such as filamentous fungi or veast are suitable cloning or expression hosts tor PRO-encodmg vectors Saccharomvces ccrevisiae is a commonly used lower eukaryotic host microorganism.
  • Others include Schizosaccharomvccs pombe (Beach and Nurse. Nature. 290: 140 [ 1981 ], EP 139.383 published 2 May 1985). Kluweromvces hosts (U S. Patent No.
  • yarrowia Pichia pastons (EP 183.070, Sreek ⁇ shna et at., J Basic Microbiol.. 28.265-278 [1988]); Candida. Tnchoderma reesia (EP 244,234). Neurospora crassa (Case et al , Proc. Natl Acad. Sci. USA, 76:5259-5263 [ 1979]). Schwanmomvc j uch as Schwannio mre.? occidentalis (EP 394.538 published 31 October 1990); and filamentous fungi such as. e g . Neuro pora. Penicillium.
  • Methylotropic yeasts are suitable herein and include, but are not limited to, yeast capable of growth on methanol selected from the genera consisting of Hansenula,
  • Candida Kloeckera. Pichia. Saccharomvces, Torulopsis, and Rhodotorula.
  • a list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The Biochemistry ofMethylotrophs, 269 ( 1982).
  • Suitable host ceils for the expression of glycosyiated PRO polypeptides are de ⁇ ved from multicellular organisms.
  • invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells.
  • useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al. J. Gen Virol. 36:59 ( 1977)); Chinese hamster ovary cellsADHFR (CHO, Urlaub and Chasm, Proc. Natl. Acad. Sci.
  • mice sertoli cells TM4, Mather, Biol. Reprod. 23:243-251 (1980)
  • human lung cells WI38, ATCC CCL 75
  • human liver cells Hep G2, HB 8065
  • mouse mammary tumor MMT 060562. ATCC CCL51
  • the selection of the approp ⁇ ate host cell is deemed to be withm the skill in the art.
  • the nucleic acid (e g., cDNA or genomic DNA) encodmg the PRO polypeptides may be inserted into a rephcable vector for clonmg (amplification of the DNA) or for expression.
  • a rephcable vector for clonmg (amplification of the DNA) or for expression.
  • the vector may. for example, be in the form of a plasmid. cosmid. viral particie. phagemid or phage.
  • the approp ⁇ ate nucleic acid sequence may be inserted into the vector by a va ⁇ efy of procedures. In generaL DNA is inserted into an approp ⁇ ate resr ⁇ ction endonuclease s ⁇ te(s) using techniques known in the art.
  • Vector components generally include, but are not limited to.
  • a signal sequence one or more of a signal sequence, an o ⁇ gin of replication.
  • one or more marker genes one or more marker genes, an enhancer element, a promoter, and a transcnption termination sequence. Construction of suitable vectors containmg one or more of these components employs standard ligation techniques which are known to the skilled artisan.
  • the PRO may be produced recombmantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide.
  • a heterologous polypeptide which may be a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide.
  • the signal sequence mav be a component of the vector, or it may be a part of the PRO-encoding DNA that is inserted into the vector.
  • the signal sequence may be a prokarvotic signal sequence selected, for example, from the group of the alkaline phosphatase. penicilhnase. Ipp, or heat-stable enterotoxin II leaders.
  • the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomvces and Kluvveromyces ⁇ -factor leaders, the latter desc ⁇ bed in U.S. Patent No. 5,010,182). or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362.179 published 4 Ap ⁇ l 1990), or the signal desc ⁇ bed in WO 90/13646 published 15 November 1990.
  • mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders
  • Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells Such sequences are well known for a va ⁇ ety of bactena. yeast, and viruses.
  • the o ⁇ gin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria
  • the 2 ⁇ plasmid o ⁇ gm is suitable for yeast
  • various viral origins SV40, polyoma. adenovirus.
  • VSV or BPV are useful for clonmg vectors in mammalian cells.
  • Expression and cloning vectors will typically contain a selection gene, also termed a selectable marker.
  • Typical selection genes encode protems that (a) confer resistance to antibiotics or other toxms, e.g., ampicillin. neomycin, methotrexate, or tetracycime, (b) complement auxotrophic deficiencies, or (c) supply c ⁇ tical nur ⁇ ents not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.
  • suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the PRO-encoding nucleic acid, such as DHFR or thymidine kinase.
  • An approp ⁇ ate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216 (1980).
  • a suitable selection gene for use in yeast is the trp ⁇ gene present m the yeast plasmid YRp7 [Stinchcomb et al. Nature, 282:39 (1979); Kingsman et al, Gene, 7:141 (1979); Tschemper et al.
  • the trpl gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4- 1 [Jones. Genetics. 85 12 (1977)]
  • Expression and cloning vectors usually contain a promoter operably linked to the PRO-encodmg nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a vanety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the ⁇ -lactamase and lactose promoter systems [Chang et al. Nature. 275:615 (1978); Goeddel et al . Nature, 28__:544 ( 1979)], alkaline phosphatase. a tryptophan (tip) promoter system [Goeddel.
  • Promoters for use in bacte ⁇ ai systems also will contain a Shine-Dalgarno (S.D.) sequence operably linked to the DNA encoding PRO.
  • suitable promoting sequences for use with yeast hosts include the promoters for 3- phosphogiycerate kinase [Hitzeman et al . J. Biol Chem . 255:2073 (1980)] or other glycolytic enzymes [Hess et al, J.
  • yeast promoters which are inducible promoters having the additional advantage of transc ⁇ ption controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2. isocytochrome C. acid phosphatase. degradative enzymes associated with nitrogen metabolism, metallothionein. glyceraldehyde-3- phosphate dehydrogenase. and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further desc ⁇ bed in EP 73,657.
  • PRO transc ⁇ ption from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2.21 1,504 published 5 July 1989).
  • adenovirus such as Adenovirus 2.
  • hepatitis-B virus and Simian Virus 40 (SV40). from heterologous mammalian promoters, e.g . the actm promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems.
  • Transc ⁇ ption ot a DNA encoding the PRO polypeptide by higher eukaryotes may be increased by inserting an enhancer sequence into the vector.
  • Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transc ⁇ ption.
  • Many enhancer sequences are now known from mammalian genes (globin. elastase, albumin, ⁇ -fetoprotem. and msuhn). Typically, however, one will use an enhancer from a eukaryotic cell virus.
  • Examples include the SV40 enhancer on the late side of the replication o ⁇ gm (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication o ⁇ gm, and adenovirus enhancers.
  • the enhancer may be spliced into the vector at a position 5' or 3' to the coding sequence of the PRO polypeptide. but is preferably located at a site 5' from the promoter.
  • Expression vectors used in eukaryotic host cells will also contain sequences necessary for the termination of transc ⁇ ption and for stabilizing the mRNA. Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transc ⁇ bed as polyadenylated fragments in the untranslated portion of the mRNA encodmg PRO.
  • antibodies may be employed that can recognize specific duplexes, including DNA duplexes.
  • RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes The antibodies m mm may be labeled and the assay may be 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.
  • Gene expression may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assav of cell culture or body fluids, to quantitate directly, the expression ot gene product.
  • Antibodies useful for immunohistochemical staining and or assay of sample fluids mav be either monoclonal or polyclonal. and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence PRO polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to DNA encoding the PRO polypeptide and encoding a specific antibody epitope. 5.
  • Forms of the PRO may be recovered from culture medium or from host cell lysates. If membrane- bound, it can be released from the membrane using a suitable detergent solution (e.g., Triton * -X 100) or by enzymatic cleavage.
  • a suitable detergent solution e.g., Triton * -X 100
  • Cells employed in expression of the PRO polypeptide can be disrupted by va ⁇ ous physical or chemical means, such as freeze-thaw cycling, sonication. mechanical disruption, or cell lysing agents
  • the following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column: ethanol precipitation: reverse phase HPLC, chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusmg; SDS-PAGE. ammonium sulfate precipitation; gel filtration using, for example. Sephadex G-75; protein A Sepharose columns to remove contammants such as IgG: and metal chelating columns to bind epitope-tagged forms of the PRO polypeptide.
  • protem pu ⁇ fication may be employed and such methods are known in the art and desc ⁇ bed for example m Deutscher. Methods in Enzvmology, ]__2 (1990); Scopes, Protein Purification: Principles and Practice, Springer- Verlag, New York (1982).
  • the pu ⁇ fication step(s) selected will depend, for example, on the nature of the production process used and the particular PRO polypeptide produced.
  • tissue expression in vanous human tissues can be identified by determining mRNA expression in vanous human tissues.
  • the location of such genes provides information about which tissues are most likely to be affected by the stimulating and inhibiting activities of the PRO polypeptides.
  • the location of a gene in a specific tissue also provides sample tissue for the activity blocking assays discussed below.
  • gene expression in vanous tissues mav be measured by conventional Southern blotting, Northern blotting to quantitate the transc ⁇ ption of mRNA (Thomas. Proc. Natl. Acad. Sci. USA. 77.5201 -5205 [ 1980]). dot blotting (DNA analysis), or in situ hybridization, usmg an approp ⁇ ately labeled probe , based on the sequences provided herein.
  • antibodies may be employed that can recognize specific duplexes, mcludmg DNA duplexes. RNA duplexes, and DNA-RNA hyb ⁇ d duplexes or DNA-protein duplexes.
  • Gene expression m va ⁇ ous tissues may be measured by immunological methods, such as immunohistochemical staining of tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product.
  • Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence of a PRO polypeptide or agamst a synthetic peptide based on the DNA sequences encoding the PRO polypeptide or agamst an exogenous sequence fused to a DNA encoding a PRO polypeptide and encoding a specific antibody epitope.
  • General techniques for generating antibodies , and special protocols for Northern blotting and in situ hyb ⁇ dization are provided below F Antibody Binding Studies
  • the activity of the PRO polypeptides can be further verified by antibody binding studies, in which the ability ot ant ⁇ -PRO200. ant ⁇ -PRO204. ant ⁇ -PR0212. ant ⁇ -PR0216. ant ⁇ -PR0226, ant ⁇ -PRO240. ant ⁇ -PR0235. ant ⁇ -PR0245. ant ⁇ -PR0172, ant ⁇ -PR0273. ant ⁇ -PR0272, ant ⁇ -PR0332, ant ⁇ -PR0526. ant ⁇ -PRO701 , anti- PR0361. ant ⁇ -PR0362. ant ⁇ -PR0363. ant ⁇ -PR0364. ant ⁇ -PR0356. ant ⁇ -PR0531 , ant ⁇ -PR0533.
  • Exemplary antibodies include polycional. monoclonal, humanized, bispecific. and heterocon j ugate antibodies, the preparation of which will be desc ⁇ bed hereinbelow.
  • Antibody binding studies may be earned out in any known assay method, such as competitive binding assays, direct and indirect sandwich assays, and immunoprecipitation assays. Zola, Monoclonal Antibodies: A Manual of Techniques, pp.147- 158 (CRC Press, Inc., 1987).
  • ком ⁇ онентs rely on the ability of a labeled standard to compete with the test sample analyte for binding with a limited amount of antibody.
  • the amount of target protein in the test sample is inversely proportional to the amount of standard that becomes bound to the antibodies.
  • the antibodies preferably are insolubilized before or after the competition, so that the standard and analyte that are bound to the antibodies may conveniently be separated from the standard and analyte which remain unbound.
  • Sandwich assays involve the use of two antibodies, each capable of binding to a different immunogenic portion, or epitope, of the protein to be detected.
  • the test sample analyte is bound by a first antibody which is immobilized on a solid support, and thereafter a second antibody binds to the analyte, thus forming an insoluble three-part complex.
  • a first antibody which is immobilized on a solid support
  • a second antibody binds to the analyte, thus forming an insoluble three-part complex.
  • the second antibody may itself be labeled with a detectable moiety (direct sandwich assays) or may be measured using an anti-immunoglobu n antibody that is labeled with a detectable moiety (indirect sandwich assay)
  • sandwich assay is an ELISA assay, in which case the detectable moiety is an enzyme.
  • the tissue sample may be fresh or frozen or may be embedded in paraffin and fixed with a preservative such as formalin, for example.
  • a preservative such as formalin, for example.
  • cells of a cell type known to be involved in a particular immune related disease are transfected with the cDNAs descnbed herein, and the ability of these cDNAs to stimulate or inhibit immune function is analyzed. Suitable cells can be transfected with the desired gene, and monitored for immune function activity. Such transfected cell lines can then be used to test the ability of poly- or monoclonal antibodies or antibody compositions to inhibit or stimulate immune function, for example to modulate T-cell proliferation or inflammatory cell infiltration. Cells transfected with the codmg sequences of the genes identified herein can further be used to identify drug candidates for the treatment of immune related diseases.
  • p ⁇ mary cultures derived from transgenic animals can be used in the cell-based assays herein, although stable cell lines are preferred. Techniques to de ⁇ ve continuous cell lines from transgenic animals are well known in the art (see, e.g.. Small et al. Mol Cell. Biol. 5: 642-648 [ 1985]).
  • MLR mixed lymphocyte reaction
  • a proliferative T cell response in an MLR assay may be due to direct mitogenic properties of an assayed molecule or to external antigen induced activation. Additional verification of the T cell stimulatory activity of the PRO polypeptides can be obtained by a costimulation assay.
  • T cell activation requires an antigen specific signal mediated through the T-cell receptor (TCR) and a costimuiatory signal mediated through a second ligand binding interaction, tor example, the B7 (CD80. CD86)/CD28 binding mteraction.
  • T cell activation has both negative and posi t ive controls through the bmdmg of ligands which have a negative or positive effect.
  • CD28 ana CTLA-4 are related glycoproteins in the Ig superfamily which bind to B7 CD28 bmding to B7 has a positive costimulation effect of T cell activation, conversely, CTLA-4 bmdmg t o B7 has a negative T cell deactivatmg effect Chambers.
  • PRO polypeptides. as well as other compounds of the invention, which are stimulators (costimulators) of T cell proliferation and agonists, e g , agonist antibodies, thereto as determined by MLR and costimulation assays , for example, are useful in treating immune related diseases characte ⁇ zed by poor, suboptimal or i nadequa t e immune function These diseases are treated by stimulating the proliferation and activation of T cells ( and T cell mediated immunit y ) and enhancing the immune response in a mammal through adminis t ration of a s t imulator y compound, such as the stimulating PRO polypeptides
  • the stimulating polypeptide mav. for example be a PRO200. PRO204.
  • an agonist stimulating compound has also been validated expe ⁇ mentallv Activation of 4- 1BB by treatment with an agonist ant ⁇ -4-l BB antibody enhances eradication of tumors Hellstrom. I. and Hellstrom. K. E. , Crit Rev Immunol ( 1998) ]8 1 Immunoadjuvant therapy for treatment of tumors, desc ⁇ bed in more detail below, is another example of the use of the stimulating compounds of the invention.
  • An immune stimulating or enhancing effect can also be achieved by antagonizing or blocking the activity of a PRO which has been found to be inhibiting in the MLR assay. Negatmg the inhibitory activity of the compound produces a net stimulatory effect.
  • Suitable antagonists/blocking compounds are antibodies or fragments thereof which recognize and bind to the inhibitory protein, thereby blocking the effective mteraction of the protein with its receptor and inhibiting signalmg through the receptor. This effect has been validated m expenments usmg ant ⁇ -CTLA-4 antibodies which enhance T cell proliferation, presumably by removal of the inhibitory signal caused by CTLA-4 bmdmg. Walunas, T. L. et al, Immunity (1994) VA05.
  • an immune stimulating or enhancing effect can also be achieved by administration of a PRO which has vascular permeability enhancing properties.
  • Enhanced vacuolar permeability would be beneficial to disorders which can be attenuated bv local infiltration of immune cells (e g , monocytes. eosmophils. PMNs) and inflammation
  • PRO polypeptides as well as other compounds of the mvention which are direct inhibitors of T cell proliferation/activation, lymphokine secretion, and/or vascular permeability can be directiy used to suppress the immune response
  • These compounds are useful to reduce the degree of the immune response and to treat immune related diseases characte ⁇ zed by a hyperactive superoptimal. or autoimmune response
  • This use of the compounds of the invention has been validated by the expenments desc ⁇ bed above in which CTLA-4 b dmg to receptor B7 deactivates T cells
  • the direct inhibitory compounds of the invention function in an analogous manner
  • the use of compound which suppress vascular permeability would be expected to reduce inflammation Such uses would be beneficial in treating conditions associated with excessive inflammation
  • results of the ceil based in itro assavs can be further v erified using in ⁇ ⁇ vo animal models and assays for T-cell function
  • a va ⁇ ety ot well known animal models can be used to further understand the role of the genes identified herein m the development and pathogenesis of immune related disease, and to test the efficacy of candidate therapeutic agents, including antibodies, and other antagonists of the native polypeptides.
  • Animal models of immune related diseases include both non-recombmant and recombinant (transgenic) animals
  • Non-recombmant animal models include, for example, rodent, e g , mu ⁇ ne models
  • Such models can be generated bv introducing cells into syngeneic mice using standard techniques, e subcutaneous injection, tail vein injection spleen implantation intrape ⁇ toneal implantation, implantation under the renal capsule, etc
  • Graft-versus-host disease occurs when lmmunocompetent cells are transplanted into immunosuppressed or tolerant patients The donor cells recogmze and respond to host antigens The response can varv from life threatening severe inflammation to mild cases of diarrhea and weight loss.
  • Graft-versus-host disease models provide a means of assessing T cell reactivity against MHC antigens and mmor transplant antigens A suitable procedure is desc ⁇ bed m detail in Current Protocols in Immunology, above, unit 4 3
  • An animal model for skin allograft rejection is a means of test g the ability of T cells to mediate in vivo tissue destruction and a measure of their role in transplant rejection
  • the most common and accepted models use mu ⁇ ne tail-skin grafts
  • skm allograft rejection is mediated by T cells, helper T cells and killer-effector T cells, and not antibodies.
  • transplant rejection models which can be used to test the compounds of the invention are the allogeneic heart transplant models descnbed by Tanabe. M. et al Transplantation ( 1 94) 58 23 and Tinubu. S. A. et al J Immunol (1994) 4330-4338.
  • Delayed type hypersensitivity reactions are a T cell mediated in vivo immune response charactenzed by inflammation which does not reach a peak until after a pe ⁇ od of time has elapsed after challenge with an antigen. These reactions also occur in tissue specific autoimmune diseases such as multiple sclerosis (MS) and expe ⁇ mental autoimmune encephalomyehtis (EAE. a model for MS) A suitable procedure is described in detail in Current Protocols in Immunology, above, unit 4.5
  • EAE is a T cell mediated autoimmune disease charactenzed by T cell and mononuclear cell inflammation and subsequent demyehnation of axons in the central nervous system.
  • EAE is generally considered to be a relevant animal model for MS in humans Bolton. C. Multiple Sclerosis ( 1995) ]_ 143. Both acute and relapsmg-remitting models have been developed.
  • the compounds of the mvention can be tested for T cell stimulatory or inhibitory activity agamst immune mediated demyehnating disease using the protocol described in Current Protocols in Immunologv, above, units 15 1 and 15 2. See also the models for myeiin disease in which o godendrocvtes or Schwann cells are grafted into the central nervous system as desc ⁇ bed in Duncan. I D et al Molec Med ( 1997) 554-561
  • Contact hypersensitivity is a simple delayed type hypersensitivity in v vo assay of cell mediated immune function
  • cutaneous exposure to exogenous haptens which gives rise to a delayed type hypersensitivity reaction which is measured and quantitated.
  • Contact sensitivity involves an initial sensitizing phase followed by an elicitation phase.
  • the elicitation phase occurs when the T lymphocytes encounter an antigen to which they have had previous contact. Swelling and inflammation occur, making this an excellent model of human allergic contact dermatitis.
  • a suitable procedure is desc ⁇ bed in detail m Current Protocols in Immunology, Eds. J. E. Cologan, A M Kruisbeek, D. H. Marguhes, E. M. Shevach and W Strober. John Wiley & Sons, Inc.. 1994. unit 4 2 See also Grabbe. S. and Schwarz. T, Immun Todav ]9 (1): 37-44 ( 1998)
  • An animal model for arthritis is collagen-induced arthntis
  • This model shares clinical, histological and immunological characte ⁇ stics of human autoimmune rheumatoid arthntis and is an acceptable model for human autoimmune arthntis.
  • Mouse and rat models are charactenzed by synovitis. erosion of cartilage and subchondral bone.
  • the compounds of the invention can be tested for activity agamst autoimmune arthntis using the protocols desc ⁇ bed in Current Protocols in Immunology, above, units 15 5. See also the model usmg a monoclonal antibody to CD 18 and VLA-4 integrals descnbed m Issekutz, A.C. et al, Immunology (1996) 88:569.
  • a model of asthma has been desc ⁇ bed in which antigen-induced airway hyper-reactivity, pulmonary eosinophiha and inflammation are induced by sensitizing an animal with ovalbumm and then challenging the animai with the same protem delivered by aerosol.
  • Several animal models (gumea pig, rat, non-human p ⁇ mate) show symptoms similar to atopic asthma in humans upon challenge with aerosol antigens.
  • Murine models have many of the features of human asthma. Suitable procedures to test the compounds of the mvention for activity and effectiveness m the treatment of asthma are desc ⁇ bed by Wolyniec. W. W. et al, Am. J. Resptr. Cell Mol. Biol. (1998) ]8:777 and the references cited therein.
  • the compounds of the invention can be tested on animal models for psonasis like diseases. Evidence suggests a T cell pathogenesis for pso ⁇ asis.
  • the compounds of the invention can be tested in the scid scid mouse model descnbed by Schon. M. P. et al, Nat. Med. (1997) 3: 183, in which the mice demonstrate histopathologic skin lesions resemblmg pso ⁇ asis.
  • Another suitable model is the human skin/scid mouse chimera prepared as desc ⁇ bed by Nickoloff. B. J. et al. Am. J. Path. (1995) 146:580.
  • Recombinant (transgenic) animal models can be engmeered by mtroducmg the coding portion of the genes identified herein into the genome of animals of mterest, using standard techniques for producing transgenic animals.
  • Animals that can serve as a target for transgenic manipulation mclude. without limitation. mice. rats, rabbits, guinea pigs, sheep, goats, pigs, and non-human primates, e.g., baboons, chimpanzees and monkeys.
  • Techniques known in the art to introduce a transgene into such animals include pronucleic microinjection (Hoppe and Wanger, U.S. Patent No.
  • transgenic animals include those that carry the transgene only in pan ot their cells ("mosaic animals")
  • the transgene can be integrated either as a single transgene. or m concatamers. e ., head-to-head or head-to-tail tandems.
  • Selective introduction of a transgene into a particular cell type is also possible by following, for example, the technique of Lasko et al, Proc. Natl. Acad. Sci. USA 89. 6232-636 ( 1992).
  • the expression of the transgene in transgenic animals can be monitored by standard techniques. For example. Southern blot analysis or PCR amplification can be used to venfy the integration of the transgene. The level of mR A expression can then be analyzed using techniques such as in situ hyb ⁇ dization. Northern blot analysis. PCR, or immunocytochemistry The animals may be further examined for signs of immune disease pathology, for example by histological examination to determine infiltration ot immune cells into specific tissues. Blocking experiments can also be pe ⁇ ormed m which the transgenic animals are treated with the compounds of the invention to determine the extent of the T cell proliferation stimulation or inhibition of the compounds. In these expenments. blocking antibodies which bind to the PRO polypeptide. prepared as descnbed above, are admmistered to the animal and the effect on immune function is determined.
  • "knock out" animals can be constructed which have a defective or altered gene encoding a polypeptide identified herein, as a result of homologous recombmation between the endogenous gene encoding the polypeptide and altered genomic DNA encoding the same polypeptide introduced into an embryonic cell of the animal.
  • cDNA encodmg a particular polypeptide can be used to clone genomic DNA encoding that polypeptide accordance with established techniques.
  • a portion of the genomic DNA encoding a particular polypeptide can be deleted or replaced with another gene, such as a gene encoding a selectable marker which can be used to monitor integration.
  • flanking DNA 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, Cell, 5__:503 (1987) for a desc ⁇ ption of homologous recombination vectors].
  • the vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells m which the introduced DNA has homologously recombined with the endogenous DNA are selected [see e g., Li et al. 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 Embrvomc Stem Cells. A Practical Approach. E. J. Robertson, ed. (IRL. Oxford. 1987), pp. 1 13-152].
  • a chimenc 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 harbo ⁇ ng 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. Knockout animals can be charactenzed for instance, for their ability to defend against certain pathological conditions and for their development of pathological conditions due to absence of the polypeptide.
  • the immunostimulating compounds of the invention can be used in immunoadjuvant therapy for the treatment of tumors (cancer).
  • tumors cancer
  • T cells recognize human tumor specific antigens.
  • DeSmet. C. et al . ( 1996) Proc. atl Acad. Sci USA. 93 7149 It has been shown that costimulation of T cells induces tumor regression and an antitumor response both in vitro and in vivo Melero, I. et al.
  • the stimulatory compounds of the invention can be administered as adjuvants, alone or together with a growth regulating agent, cytotoxic agent or chemotherapeutic agent, to stimulate T cell proliferation activation and an antitumor response to tumor antigens.
  • the growth regulating, cytotoxic. or chemotherapeutic agent may be administered in conventional amounts using known administration regimes. Immunostimulating activity by the compounds of the invention allows reduced amounts of the growth regulating, cytotoxic. or chemotherapeutic agents thereby potentially lowenng the toxicity to the patient.
  • Screening assays tor drug candidates are designed to identify compounds that bind to or complex with the polypeptides encoded by the genes identified herein or a biologically active fragment thereof, or otherwise interfere with the interaction of the encoded polypeptides with other cellular proteins.
  • Such screenmg assays will include assays amenable to high-throughput screenmg of chemical libranes, making them particularly suitable for identifying small molecule drug candidates.
  • Small molecules contemplated include synthetic organic or inorganic compounds, including peptides, preferably soluble peptides, (poly)pepttde- lmmunoglobulin fusions, and.
  • antibodies including, without limitation, poly- and monoclonal antibodies and antibody fragments, single-chain antibodies, anti-idiotypic antibodies, and chimenc or humanized versions of such antibodies or fragments, as well as human antibodies and antibody fragments.
  • the assays can be performed in a va ⁇ ety of formats, including protein-protein binding assays, biochemical screenmg assays, immunoassays and cell based assays, which are well charactenzed in the art.
  • the polypeptide encoded by the gene identified herem or the drug candidate is immobilized on a solid phase g on a microtiter plate, bv covalent or non-covalent attachments
  • Non-covalent attachment generally is accomplished by coatmg the solid surface with a solution of the polypeptide and drying Alternatively an immobilized antibody, e g a monoclonal antibody, specific for the polypeptide to be immobilized can be used to anchor it to a solid surface
  • the assav is performed by adding the non-immobilized component, which mav be labeled bv a detectable label, to the immobilized component, e g the coated surface containmg the anchored component
  • a gene identified herein its interaction with that protein can be assaved bv methods well known tor detecting protein- protein interactions
  • Such assays include traditional approaches such as. cross-linking, o- lmmunoprecipitation and co-pu ⁇ fication through gradients or hromatographic columns
  • protein- protein interactions can be monitored bv using a veast-based genetic system described bv Fields and co- workers [Fields and Song, Nature (London) 340 245-246 ( 1989), Chien et al . Pioc Natl Acad Sci USA 88, 9578-9582 ( 1991 )] as disclosed by Chevray and Nathans.
  • transc ⁇ ptional activators such as yeast GAL4, consist of two physically discrete modular domains, one acting as the DNA-binding domain, while the other one functioning as the transc ⁇ ption activation domain
  • the yeast expression system desc ⁇ bed in the foregoing publications (generally referred to as the "rvvo-hyb ⁇ d system ') takes advantage of this property and employs two hvb ⁇ d proteins one in which the target protem is fused to the DNA-bindmg domain of GAL4 and another, in which candidate activating proteins are fused to ihe activation domain
  • the expression ot a G ⁇ Ll-/ ⁇ ⁇ :Z reporter gene under control of a GAL4-act ⁇ vated promoter depends on reconstitution ot GAL4 activity via protein-protein interaction Colonies containing interacting polypeptides are detected with a chromogenic substrate for ⁇ -galactosidase
  • MATCH chromogenic substrate for ⁇ -galactosidase
  • a reaction mixmre is usually prepared containmg the product of the gene and the mtra- or extracellular component under conditions and for a time allowing for the mteraction and bmdmg of the rwo products
  • the reaction is run m the absence and in the presence of the test compound
  • a placebo may be added to a third reaction mixmre. to serve as positive control
  • the bindmg (complex formation) between the test compound and the mtra- or extracellular component present in the mixture is monitored as desc ⁇ bed above. The formation of a complex in the control react ⁇ on(s) but not m the reaction mixmre containmg the test compound indicates that the test compound interferes with the interaction of the test compound and its reaction partner.
  • compositions useful in the treatment of immune related diseases include, without limitation. proteins, antibodies, small organic molecules, peptides. phosphopeptides, antisense and ⁇ bozyme molecules. triple helix molecules, etc. that inhibit or stimulate immune function, for example. T cell proliferation activation, lymphokine release, or immune cell infiltration.
  • antisense RNA and RNA molecules act to directly block the translation of mRNA by hyb ⁇ dizing to targeted mRNA and preventing protein translation.
  • antisense DNA is used.
  • ohgodeoxy ⁇ bonucleotides de ⁇ ved from the translation initiation site e.g . between about -10 and +10 positions of the target gene nucleotide sequence, are preferred.
  • Ribozymes are enzymatic RNA molecules capable of catalyzmg the specific cleavage of RNA. Ribozymes act by sequence-specific hyb ⁇ dization to the complementary target RNA. followed by endonucleolytic cleavage. Specific ⁇ bozyme cleavage sites withm a potential RNA target can be identified by known techniques for further details see. e g . Rossi. Current B ⁇ olog ⁇ 4. 469-471 ( 1994). and PCT publication No WO 97/33551 (published September 18. 1997)
  • Nucleic acid molecules in triple helix formation used to inhibit transc ⁇ ption should be single-stranded and composed of deoxynucleotides.
  • the base composition of these oligonucleotides is designed such that it promotes triple helix formation via Hoogsteen base pai ⁇ ng rules, which generally require sizeable stretches of pu ⁇ nes or pynmidines on one strand of a duplex.
  • Antibodies The present invention further provides anti-PRO antibodies and fragments thereof which may inhibit
  • anti-PRO antibodies or fragments thereof include polyclonal. monoclonal, humanized, bispecific and heteroconjugate antibodies.
  • the anti-PRO antibodies may comp ⁇ se polyclonal antibodies. Methods of prepa ⁇ ng polyclonal antibodies are known to the skilled artisan. Polycionai 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 lntrape ⁇ toneai injections. The immunizing agent may mclude the PRO polypeptide or a fusion protein thereof. It may be useful to conjugate the unmumzing agent to a protein known to be immunogenic m the mammal being immunized.
  • immunogenic proteins include but are not limited to keyhole limpet hemocyanm. serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor.
  • adjuvants which may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation.
  • the anti-PRO antibodies may, alternatively, be monoclonal antibodies. Monoclonal antibodies may be prepared usmg hyb ⁇ doma methods, such as those desc ⁇ bed by Kohler and Milstem. Nature, 256:495
  • lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent.
  • the lymphocytes may be immunized in vitro.
  • the immunizing agent will typically include the PRO polypeptide or a fusion protein thereof.
  • PBLs pe ⁇ pheral blood lymphocytes
  • spleen cells or lymph node cells are used if non-human mammalian sources are desired.
  • the lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hyb ⁇ doma cell [Goding. Monoclonal Antibodies Principles and Practice, Academic Press. (1986) pp. 59- 103].
  • Immortalized cell Imes are usually transformed mammalian ceils, particularly myeioma cells of rodent, bovine and human ongm.
  • rat or mouse myeloma cell lines are employed.
  • the hyb ⁇ doma cells may be cultured in a suitable culture medium that preferably contams one or more substances that inhibit the growth or survival of the untused. immortalized cells
  • the culture medium for the hyb ⁇ domas typically will include hvpoxanthine. ammopte ⁇ n. and thymidine ("HAT medium"), which substances prevent the growth of HGPRT deficient cells
  • Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are mu ⁇ ne myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, California and the Ame ⁇ can Type Culture Collection. Manassas, Virginia Human myeloma and mouse-human heteromyeloma cell lines also have been desc ⁇ bed for the production of human monoclonal antibodies [Kozbor. J Immunol , 133.3001 (1984), Brodeur et al, Monoclonal Ant ⁇ odi Pioduction Techniques and Applications. Marcel Dekker, Inc.. New York, ( 1987) pp 51 -63]
  • the culture medium in which the hvb ⁇ doma cells are cultured can then be assayed for the presence of monoclonal antibodies directed agamst PRO
  • the binding specificity of monoclonal antibodies produced by the hyb ⁇ doma cells is determined by lmmunoprecipitation or by an in vitro bindmg assay, such as radioimmunoassay (PJA) or enzyme-linked lmmunoabsorbent assay (ELISA).
  • PJA radioimmunoassay
  • ELISA enzyme-linked lmmunoabsorbent assay
  • the bmdmg affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem., J07.220 (1980).
  • the alterations may be subcloned by limiting dilution procedures and grown by standard methods [Goding, supra). Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI- 1640 medium. Alternatively, the hyb ⁇ doma cells may be grown in vivo as ascites in a mammal.
  • the monoclonal antibodies secreted by the subclones may be isolated or pu ⁇ fied from the culture medium or ascites fluid by conventional immunoglobulin pu ⁇ fication procedures such as, for example, protem A-Sepharose, hydroxyapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
  • the monoclonal antibodies may also be made by recombinant DNA methods, such as those desc ⁇ bed in U.S. Patent No. 4,816,567.
  • DNA encodmg the monoclonal antibodies of the mvention can be readily isolated and sequenced using conventional procedures (e g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of mu ⁇ ne antibodies).
  • the hyb ⁇ doma ceils of the invention serve as a preferred source of such DNA.
  • the DNA may be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.
  • the DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domams m place of the homologous mu ⁇ ne sequences [U.S. Patent No. 4,816,567, Momson et al, supra] or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobuiin polypeptide.
  • non-immunoglobuiin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimenc bivalent antibody
  • the antibodies are preferably monovailing antibodies.
  • Methods for prepa ⁇ ng monovalent antibodies are well known in the art For example, one method involves recombinant expression of immunoglobulin light chain and modified heaw chain.
  • the heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain crosshnking.
  • the relevant cysteine residues are substituted with another ammo acid residue or are deleted so as to prevent crosshnking.
  • the anti-PRO antibodies of the invention may further comp ⁇ se humanized antibodies or human antibodies.
  • Humanized forms of non-human (e g., mu ⁇ ne) antibodies are chimenc immunoglobulins. immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab'. F(ab')2 or other antigen-binding subsequences of antibodies) which contain minimal sequence de ⁇ ved from non-human immunoglobulin.
  • Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non- human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity
  • CDR complementary determining region
  • donor antibody such as mouse, rat or rabbit having the desired specificity, affinity and capacity
  • Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • Humanized antibodies may also comp ⁇ se residues which are found neither m the recipient antibody nor in the imported CDR or framework sequences.
  • the humanized antibody will compnse substantially all of at least one, and typically two, va ⁇ able domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence.
  • the humanized antibody optimally also will comp ⁇ se at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al, Nature. 321:522-525 (1986); Riechmann et al, Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol.2:593-596 (1992)].
  • Fc immunoglobulin constant region
  • a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as "import" residues, which are typically taken from an "import 1 variable domain Humanization can be essentially performed following the method of Winter and coworkers [Jones et al , Nature, 32_ 522-525 ( 1986), Riechmann et al , Nature. 332.323-327 (1988); Verhoeven et al , Science.
  • humanized antibodies are chimenc antibodies (U S Patent No 4,816,567), wherein substantially less than an mtact human va ⁇ able domam has been substituted bv the corresponding sequence from a non-human species
  • humanized antibodies are rypicallv human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies
  • Human antibodies can also be produced using va ⁇ ous techniques known in the art. including phage display libranes [Hoogenboom and Winter. J Mol Biol . 227 381 ( 1991 ). Marks et al . J Mol Biol . 222.581 ( 1991 )] The techniques of Cole et al and Boerner et al are also available for the preparation of human monoclonal antibodies (Cole et al Monoclonal Antibodies and Cancer Tl erapv, Alan R Liss, p 77 ( 1985), Boerner et al J Immunol .
  • human antibodies can be made by introducing of human immunoglobulin loci into transgenic animals, e g mice in which the endogenous immunoglobulin genes have been partially or completely inactivated Upon challenge, human antibodv production is observed which closelv resembles that seen in humans in all respects, including gene rearrangement assembly , and antibodv repertoire Tins approach is descnbed. for example, in U S Patent Nos 5 545.807 5 545,806. 5.569,825. 5,625, 126. 5,633,425. 5,661.016.
  • the antibodies mav also be affinity matured using known selection and or mutagenesis methods as desc ⁇ bed abov e
  • Preferred affinity matured antibodies have an affinity which is five times, more preferably 10 tunes, ev en more preferably 20 or 30 times greater than the starting antibody (generally munne. humanized or human ) trom which the matured antibodv is prepared 4 Bispecific Antibodies
  • Bispecific antibodies arc monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens
  • one of the binding specificities may be for the PRO.
  • the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit
  • bispecific antibodies are known in the art Traditionally, the recombinant production of bispecific antibodies is based on the coexpression of two immunoglobulin heavy-chain/hght- cha pairs, where the two heavy chains have different specificities (Milstein and Cuello. Nature. 305 537-539 [1983]) Because of the random assortment of immunoglobulin heavy and light chams, these hyb ⁇ domas (quadromas) produce a potential mixmre of ten different antibody molecules, of which only one has the correct bispecific structure. The pu ⁇ fication of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed m WO 93/08829, published 13 May 1993. and m Traunecker et al, EMBO J , KU655-3659 ( 1991)
  • Antibody va ⁇ able domams with the desired bmdmg specificities can be fused to immunoglobulin constant domain sequences.
  • the fusion preferably is with an immunoglobulm heavy-chain constant domain, compnsing at least part ot the hmge. CH2 and CH3 regions It is preferred to have the first heavy-chain constant region (CHI ) containing the site necessary tor light-chain bmdmg present in at least one of the fusions DNAs encoding the immunoglobulin heavy-chain fusions and.
  • CHI first heavy-chain constant region
  • the immunoglobulm light cham are inserted into separate expression vectors, and are cotransfected into a suitable host organism.
  • the immunoglobulm light cham are inserted into separate expression vectors, and are cotransfected into a suitable host organism.
  • the interface between a pan of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture
  • the preferred interface compnses at least a part of the CH3 region of an antibodv constant domain
  • one or more small amino acid side chams from the interface of the first antibodv molecule are replaced with larger side chains (e g tyrosine or tryptophan)
  • Compensatory "cavities ' of identical or similar size to the large side cha ⁇ n(s) are created on the interface of the second antibodv molecule by replacing large ammo acid side chains with smaller ones (e g alanine or threonine)
  • Bispecific antibodies can be prepared as full length antibodies or antibodv fragments (e F(ab') 2 bispecific antibodies) Techniques for generating bispecific antibodies from antibodv fragments have been described in the literature For example bispecific antibodies can be prepared can be prepared using chemical linkage Brennan et al Science 229 81 ( 1985) desc ⁇ be a procedure wherein mtact antibodies are proteolvtically cleaved to generate F(ab') 2 fragments These fragments are reduced in the presence of the dithiol compiexing agent sodium arsemte to stabilize vicinal dithiols and prevent l ⁇ termolecular disulfide formation The Fab fragments generated are then converted to thionitrobenzoate (TNB) de ⁇ vatives One of the Fab TNB de ⁇ vatives is then reconverted to the Fab -thiol by reduction with mercaptoethvlamine and is mixed with an equimolar amount of the other Fab'-TNB de ⁇ vative to form
  • Fab' fragments mav be directlv recovered from E coli and chemicallv coupled to form bispecific antibodies Shalabv et al J Exp M d _____ 217-225 ( 1992) desc ⁇ be the production of a fully humanized bispecific antibody F(ab ) 2 molecule
  • Each Fab fragment was separately secreted from E colt and subjected to directed chemical coupling in vitro to form the bispecific antibody
  • the bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as t ⁇ gger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets
  • bispecific antibodies have been produced using leuci ⁇ e zippers Kostelny et al . J Immunol _48 (5) 1547-1553 (1992)
  • the leucme zipper peptides from the Fos and Jun proteins were linked to the Fab portions of rwo different antibodies by gene fusion
  • the antibody homodimers were reduced at the hmge region to form monomers and then re-oxidized to form the antibodv heterodimers This method can also be utilized for the production of antibody homodimers.
  • the fragments comp ⁇ se a heavy-chain vanable domam (V H ) connected to a light-cham va ⁇ able domam (V L ) by a lmker which is too short to allow pairing between the rwo domains on the same cham. Accordingly, the V H and V t domams of one fragment are forced to pan- with the complementary V L and V H domams of another fragment, thereby forming two antigen-binding sites.
  • bispecific antibodies may bind to two different epitopes on a given PRO polypepide herein.
  • an anti-PRO arm may be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g., CD2. CD3. CD28, or B7), or Fc receptors for IgG (Fc ⁇ R), such as Fc ⁇ RI (CD64), Fc ⁇ RII (CD32) and Fc ⁇ RIII (CD 16) so as to focus cellular defense mechanisms to the cell expressing the particular PRO polypeptide.
  • Bispecific antibodies may also be used to localize cytotoxic agents to cells which express a particular PRO polypeptide.
  • antibodies possess a PRO polypeptide - binding arm and an arm which binds a cytotoxic agent or a radionuclide chelator.
  • a cytotoxic agent or a radionuclide chelator such as EOTUBE, DPTA. DOTA. or TETA
  • Another bispecific antibody of interest binds the PRO polypeptide and further binds tissue factor ( TD).
  • Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells [U.S. Patent No. 4.676,980], and for treatment of HIV infection [WO 91/00360; WO 92/200373. EP 03089]. It is contemplated that the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosshnking agents. For example, immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyi-4-mercaptobuty ⁇ m ⁇ date and those disclosed, for example, in U.S. Patent No. 4.676,980.
  • effector function enginee ⁇ ng It may be desirable to modify the antibody of the invention with respect to effector function, so as to enhance the effectiveness of the antibody in treating an immune reiated disease, for example.
  • cysteine residue! s may be introduced in the Fc region, thereby allowing mtercham disulfide bond formation in this region.
  • the homodime ⁇ c antibody thus generated may have improved mtemalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicify (ADCC). See Caron el al. J. Exp Med. J_76:l 191-1 195 (1992) and Shopes, B. J. Immunol. 148:2918-2922 (1992).
  • Homodimeric antibodies with enhanced anti-tumor activity may also be prepared using heterobifunctional cross-linkers as desc ⁇ bed in Wolff « al. Cancer Research 53:2560-2565 (1993).
  • an antibody can be engineered which has dual Fc regions and may thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al. Anti-Cancer Drug Desig _3:219-230 (1989). 7. Immunoconiugates
  • the invention also pertains to immunoconjugates comp ⁇ sing an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacte ⁇ al, fungal, plant or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioco ⁇ jugate).
  • a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacte ⁇ al, fungal, plant or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioco ⁇ jugate).
  • Enzymatically active tox s and fragments thereof which can be used include diphtheria A chain, nonbmdtng active fragments of diphthe ⁇ a toxm. exotoxin A chain (from Pseudomonas aerugtnosa). ncin A chain, ab ⁇ n A chain, modeccm A cham. alpha-sarcin. Aleurites fordu proteins, dianthin proteins, Phvtolaca amertcana proteins (PAPI, PAPII. and PAP-S), momordica charantia inhibitor, curcm, crot .
  • Conjugates of the antibody and cytotoxic agent are made using a va ⁇ ety of bifunctional protein couplmg agents such as N-succ ⁇ n ⁇ m ⁇ dvl-3-(2-pyndyld ⁇ th ⁇ ol) propionate (SPDP).
  • SPDP N-succ ⁇ n ⁇ m ⁇ dvl-3-(2-pyndyld ⁇ th ⁇ ol) propionate
  • ncin immunotoxin can be prepared as desc ⁇ bed m Vitetta et al Science 238 1098 ( 1987) Carbon- 14- labeled l - ⁇ soth ⁇ ocvanatobenzyI
  • the antibody may be conjugated to a 'receptor" (such streptavidin) for utilization in tissue pretargeting wherein the antibodv-receptor con j ugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand” (e g , avidm) which is conjugated to a cytotoxic agent (e g , a radionucleotide) 8 Immunohposomes
  • Liposomes containing the antibodv are prepared bv methods known m the art. such as described in Epstein et al , Proc Natl Acad Sci USA. _82 3688 ( 1985) Hwang et al Proc Natl Acad Sci USA, 77 4030 ( 1980), and U S Pat Nos 4,485,045 and 4 544 545 Liposomes with enhanced circulation time are disclosed in U S Patent No 5.013.556
  • Particularly useful liposomes can be generated bv the reverse phase evaporation method with a lipid composition comp ⁇ sing phosphatidvlcholme.
  • cholesterol and PEG-de ⁇ vatized phosphatidviethanolamme (PEG-PE) Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter Fab' fragments of the antibodv of the present mvention can be conjugated to the liposomes as desc ⁇ bed in Martin et al ,_J Biol Chem 257 286-288 (1982) via a disulfide interchange reaction.
  • a chemotherapeutic agent such as doxorubicin
  • doxorubicin may be optionally contained withm the liposome
  • the active PRO molecules of the invention e g , PRO polypeptides, anti-PRO antibodies, and/or va ⁇ ants of each
  • odier molecules identified by the screenmg assays disclosed above can be administered for the treatment of immune related diseases, m the form of pharmaceutical compositions.
  • Therapeutic formulations of the active PRO molecule are prepared for storage by mixmg the active molecule havmg the desired degree of pu ⁇ ty with optional pharmaceuticallv acceptable earners, excipients or stabilizers (Remington's Pharmaceutical Sciences 16th edition. Osol. A. Ed. [1980]). in the form ot lyophilized formulations or aqueous solutions. Acceptable car ⁇ ers, excipients.
  • buffers such as phosphate, citrate, and other organic acids, antioxidants mcludmg ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyi ammonium chlo ⁇ de, hexamethonium chlo ⁇ de; benzalkomum chlo ⁇ de, benzethonium chlo ⁇ de, phenol, butyl or benzyl alcohol, alkyl parabens such as methyl or propyl paraben: catechol, resorcmol, cyclohexanol. 3-pentanoi. and m-cresol).
  • buffers such as phosphate, citrate, and other organic acids, antioxidants mcludmg ascorbic acid and methionine
  • preservatives such as octadecyldimethylbenzyi ammonium chlo ⁇ de, hexamethonium chlo ⁇ de;
  • polypeptides such as serum albumin, gelatin, or immunoglobulins: hydrophihc polymers such as polyvinylpyrrohdone, ammo acids such as glycine, glutamine. asparagine, histidine. arginine. or lysine; monosaccha ⁇ des disacchandes. and other carbohydrates mcludmg glucose. mannose. or dext ⁇ ns, chelating agents such as EDTA, sugars such as sucrose, mannitol.
  • hydrophihc polymers such as polyvinylpyrrohdone, ammo acids such as glycine, glutamine. asparagine, histidine. arginine. or lysine
  • monosaccha ⁇ des disacchandes. and other carbohydrates mcludmg glucose. mannose. or dext ⁇ ns
  • chelating agents such as EDTA
  • sugars such as sucrose, mannitol.
  • trehalose or sorbitol trehalose or sorbitol
  • salt-forming counter-ions such as sodium: metal complexes (e g , Zn-protein complexes), and/or non-ionic surfactants such as TWEENTM, PLURONICSTM or polyethylene glycol (PEG)
  • Lipofections or liposomes can also be used to deliver the PRO molecule into cells Where antibody fragments are used, the smallest inhibitor/ fragment which specifically binds to the binding domain of the target protein is preferred
  • peptide molecules can be designed which retain the ability to bmd the target protein sequence
  • Such peptides can be synthesized chemically and/or produced by recombinant DNA technology (see, e g . Marasco et al . Proc. Natl. Acad. Sci USA 90, 7889-7893 [1993])
  • the formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other Alternatively, or in addition, the composition may comp ⁇ se a cytotoxic agent, cvtokme or growth inhibitory agent Such molecules are suitably present in combination in amounts that are effective for the purpose intended
  • the active PRO molecules mav also be entrapped in microcapsules prepared, for example, by coacervation techniques or bv intertacial polyme ⁇ zation. for example, hydroxymethvlcellulose or gelatm- microcapsules and poly-(methvlmethacylate) microcapsules. respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres. microemulsions. nano-particles and nanocapsules) or macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres. microemulsions. nano-particles and nanocapsules
  • Such techniques are disclosed in Remington's Pharmaceutical Sciences 16th edition. Osol, A. Ed. (1980).
  • the formulations to be used for in vivo administration must be ste ⁇ le. This is readily accomplished by filtration through ste ⁇ le filtration membranes.
  • Sustamed-release preparations or the PRO molecules may be prepared.
  • Suitable examples of sustamed-release preparations include semipermeable matrices of solid hydrophobic polymers containmg the antibody, which matnces are m the form of shaped articles, e g , films, or microcapsules.
  • sustained-release matrices include polyesters, hydrogels (for example, p ⁇ ly(2-hydroxyethyl-methacrylate), or poly(v ⁇ nylalcohol)), polylactides (U.S. Pat. No.
  • copolymers of L-glutamic acid and ⁇ -ethyl-L- glutamate non-degradable ethylene-vmyl acetate
  • degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOTTM (in ectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate)
  • poly-D-(-)-3-hvdroxyburv ⁇ c acid While polymers such as ethylene-vmvl acetate and lactic acid- glycohc acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter tune pe ⁇ ods
  • encapsulated antibodies remain m the bodv for a long time, they mav denature or aggregate as a result of exposure to moisture at 37°C, resulting in a loss of biological activity and possible changes in immunogenicity Rational strategies can be devised for stabilization depending on the mechanism involved.
  • stabilization may be achieved bv modifying sulfhydryl residues, lyophi zing from acidic solutions, controlling moisture content, using approp ⁇ ate additives, and developmg specific polymer matnx compositions N Methods of Treatment
  • polypeptides, antibodies and other active compounds of the present invention mav be used to treat va ⁇ ous immune related diseases and conditions, such as T cell mediated diseases including those charactenzed by infiltration of inflammatory cells into a tissue, stimulation of T-ceil proliferation inhibition of T-cell proliferation increased or decreased vascular permeability or the inhibition thereof
  • antibodies and other compounds of the invention include, but are not limited to svstemic lupus erythematosis rheumatoid arthntis, juvenile chronic arthntis osteoarth ⁇ tis spondvloarthropathies systemic sclerosis (scleroderma), idiopathic inflammatory myopathies (dermatomyositts, polymyositis), S j ogren s syndrome, systemic vascu tis. sarcoidosis, autoimmune hemolytic anemia (immune pancytopema. paroxysmal nocmmal hemoglobinuna).
  • autoimmune thrombocytopenia idiopathic thrombocytopenic purpura, immune-mediated thrombocytopenia.
  • thyroiditis Grave's disease, Hashimoto's thyroiditis. juvenile lymphocytic thyroiditis. atrophic thvroiditis
  • diabetes mellitus idiopathic thrombocytopenic purpura, immune-mediated thrombocytopenia.
  • immune-mediated renal disease glomeruio ⁇ eph ⁇ tis, tubulointerstitial nephritis
  • demyehnating diseases of the central and pe ⁇ pheral nervous systems such as multiple sclerosis, idiopathic demyehnating polyneuropathv or Guilla -Barre syndrome, and chronic inflammatory demvehnating polyneuropathv hepatobi arv diseases such as infectious hepatitis (hepatitis A. B, C, D E and other non- hepatotropic v iruses), autoimmune chronic active hepatitis, p ⁇ marv biharv cirrhosis, granulomatous hepatitis.
  • infectious hepatitis hepatitis A. B, C, D E and other non- hepatotropic v iruses
  • autoimmune chronic active hepatitis p ⁇ marv biharv cirrhosis
  • granulomatous hepatitis granul
  • autoimmune or immune-mediated skin diseases including bullous skin diseases, erythema multiforme and contact dermatitis, pso ⁇ asis.
  • allergic diseases such as asthma, allergic rhinitis, atopic dermatitis, food hypersensitivity and urtica ⁇ a.
  • l mmunologic diseases of the lung such as eosinophi c pneumonias, idiopathic pulmonary fibrosis and hypersensitivity pneumonitis, transplantation associated diseases mcludmg graft rejection and graft -versus-host-disease
  • T lymphocytes In systemic lupus erythematosus. the central mediator of disease is the production of auto-reactive antibodies to self protems/tissues and the subsequent generation of immune-mediated inflammation antibodies either directly or mdirectlv mediate tissue injury Though T lymphocytes have not been shown to be directly involved m tissue damage, T lymphocytes are required for the development of auto-reactive antibodies.
  • Rheumatoid arthntis is a chronic systemic autoimmune inflammatory disease that mamly involves the synovial membrane of multiple joints with resultant injury to the articular cartilage.
  • the pathogenesis is T lymphocyte dependent and is associated with the production of rheumatoid factors, auto- antibodies directed against self IgG. with the resultant formation of immune complexes that attain high levels in joint fluid and blood.
  • the second form of extra-articular disease is the so cailed Felty's syndrome which occurs late in the RA disease course, sometimes after joint disease has become quiescent, and involves the presence of neutropenia. thrombocytopenia and splenomegaly. This can be accompanied by vascuhtis in multiple organs with formations of mfarcts. skin ulcers and gangrene. Patients often also develop rheumatoid nodules in the subcutis tissue overlying affected jomts; the nodules late stage have necrotic centers surrounded bv a mixed inflammatory ceil infiltrate.
  • Other manifestations which can occur in RA include: pe ⁇ carditis. pleu ⁇ tis. coronary a ⁇ e ⁇ tis. intestinal pneumonitis with pulmonary fibrosis. keratoconjunctivitis sicca. and rhematoid nodules.
  • Juvenile chronic arthritis is a chronic idiopathic inflammatory disease which begms often at less than 16 years of age. Its phenotype has ome similanties to RA; some patients which are rhematoid factor positive are classified as juvenile rheumatoid arthritis. The disease is sub-classified into three major categories: pauciarticular. polyarticular. and systemic. The arthritis can be severe and is typically destructive and leads to joint ankylosis and retarded growth Other manifestations can include chronic ante ⁇ or uveitis and systemic amyloidosis.
  • Spondyloanhropathies are a group of disorders with some common clinical features and the common association with the expression of HLA-B27 gene product.
  • the disorders include: ankvlosing sponyhtis.
  • Reiter's syndrome reactive arthntis.
  • arthntis associated with inflammatory bowel disease, spondylitis associated w ith psoriasis, luv cnile onset spondyloarthropathy and undifferentiated spondyloartliropathy.
  • Distinguishing features include sacroileitis with or without spondylitis; inflammatory asymmet ⁇ c arthritis; association with HLA-B27 (a serologically defined allele of the HLA-B locus of class I MHC); ocular inflammation, and absence ot autoantibodies associated with other rheumatoid disease.
  • the cell most implicated as key to mduction of the disease is the CD8+ T lymphocyte, a cell which targets antigen presented by class I MHC molecules.
  • CD8+ T cells may react agamst the class I MHC allele HLA-B27 as if it were a foreign peptide expressed by MHC class 1 molecules.
  • Systemic sclerosis (scleroderma) has an unknown etiology. A hallmark of the disease is induration of the skm: likely this is induced by an active inflammatory process. Scleroderma can be localized or systemic; vascular lesions are common and endothelial cell injury in the microvasculature is an early and important event in the development of systemic sclerosis: the vascular injury may be immune mediated.
  • ICAM- 1 is often upregulated on the cell surface of fibroblasts in skin lesions suggestmg that T cell interaction with these cells may have a role in the pathogenesis of the disease.
  • Other organs involved include, the gastrointestinal tract: smooth muscle atrophy and fibrosis resultmg m abnormal pe ⁇ stalsis/moti ty, kidney concenmc subendothe al intimal proliferation affecting small arcuate and lnteriobular arte ⁇ es with resultant reduced renal cortical blood flow, results in protemuna. azotemia and hypertension, skeletal muscle, atrophy, interstitial fibrosis. inflammation; lung, interstitial pneumomtis and interstitial fibrosis. and heart contraction band necrosis, scamng/ fibrosis
  • Idiopathic inflammatory myopathies mcludmg dermatomvositis, polymyositis and others are disorders of chronic muscle inflammation of unknown etiology resulting m muscle weakness. Muscle injury/ inflammation is often symmetric and progressive Autoantibodies are associated with most forms These myositis-specific autoantibodies are directed agamst and inhibit the function of components, proteins and RNA's. involved m protein synthesis
  • Sjogren's syndrome is due to immune-mediated inflammation and subsequent functional destruction of the tear glands and salivary glands
  • the disease can be associated with or accompanied bv inflammatory connective tissue diseases
  • the disease is associated with autoantibody production agamst Ro and La antigens. both ot w hich are small RNA-protein complexes Lesions result in kcratoconiunctivitis sicca. xerostomia, with other manifestations or associations including bilary cirrhosis, peripheral or sensory neuropathy, and palpable purpura
  • Systemic vascuhtis are diseases in which the p ⁇ marv lesion is inflammation and subsequent damage to blood vessels which results in ischemia/necrosis/degeneration to tissues supplied by the affected vessels and evenmal end-organ dysfunction in some cases
  • Vasculitides can also occur as a secondary lesion or sequelae to other immune- inflammatory mediated diseases such as rheumatoid arthntis, systemic sclerosis, etc .
  • diseases also associated with the formation of immune complexes Diseases in the p ⁇ marv systemic vascuhtis group include systemic necrotizing vascuhtis polyarte ⁇ tis nodosa. allergic angntis and granulomatosis. poiyangutis.
  • v asculitides include mucocutancous Ivmph node syndrome (MLNS or Kawasaki's disease), isolated CNS vascuhtis. Behet's disease, thromboangiitis obhterans (Buergers disease) and cutaneous necrotizing venuhtis The pathogenic mechanism of most ot the types of v ascuhtis listed is believed to be pnma ⁇ lv due to the deposition of immunoglobulin complexes in the vessel wall and subsequent induction of an inflammatory response either via ADCC.
  • Sarcoidosis is a condition of unknown etiology which is charactenzed by the presence of eptthehoid granulomas in nearly any tissue in the body, involvement of the lung is most common.
  • the pathogenesis involves the persistence of activated macrophages and lymphoid cells at sites of the disease with subsequent chronic sequelae resultant trom the release of locally and systemically active products released by these cell types Autoimmune hemolytic anemia including autoimmune hemolytic anemia, immune pancytopema.
  • paroxysmal noctural hemoglobmu ⁇ a is a result of production of antibodies that react with antigens expressed on the surface of red blood cells (and m some cases other blood cells mcludmg platelets as well) and is a reflection of the removal of those antibody coated cells via complement mediated lysis and or ADCC Fc- receptor-mediated mechanisms.
  • complement mediated lysis and or ADCC Fc- receptor-mediated mechanisms In autoimmune thrombocytopenia including thrombocytopenic purpura. and immune-mediated thrombocytopenia m other clinical settings, platelet destruction/removal occurs as a result of either antibody or complement attaching to platelets and subsequent removal by complement lysis, ADCC or FC-receptor mediated mechanisms.
  • Thyroiditis mcludmg Grave's disease. Hashimoto's thyroiditis.
  • juvenile lymphocytic thyroiditis and atrophic thyroiditis, are the result of an autoimmune response against thyroid antigens with production of antibodies that react with proteins present in and often specific for the thyroid gland.
  • Type I diabetes melhtus or insulin-dependent diabetes is the autoimmune destruction of pancreatic islet ⁇ cells, this destruction is mediated by auto-antibodies and auto-reactive T cells. Antibodies to insulin or the insulin receptor can also produce the phenotype of insulin-non-responsiveness.
  • Immune mediated renal diseases including glomeruloneph ⁇ tis and tubulointerstitial neph ⁇ tis. are the result of antibody or T lymphocyte mediated injury to renal tissue either directly as a result of the production of autoreac e antibodies or T cells against renal antigens or indirectly as a result of the deposition of antibodies and/or immune complexes in the kidney that are reactive against other, non-renal antigens.
  • immune-mediated diseases that result in the formation of immune-complexes can also mduce immune mediated renal disease as an indirect sequelae
  • Both direct and indirect immune mechanisms result in inflammatory response that produces/induces lesion development in renal tissues with resultant organ function impairment and in some cases progression to renal failure. Both humoral and cellular immune mechanisms can be involved in the pathogenesis of lesions.
  • Demyehnating diseases of the central and pe ⁇ pheral nervous systems mcluding Multiple Sclerosis; idiopathic demyehnating polyneuropathy or Guillain-Barre syndrome: and Chronic Inflammatory Demyehnating Polyneuropathy, are believed to have an autoimmune basis and result m nerve demyehnation as a result of damage caused to oligodendrocytes or to myehn directly In MS there is evidence to suggest that disease induction and progression is dependent on T lymphocvtes.
  • Multiple Sclerosis is a demyehnating disease that is T lymphocyte-dependent and has either a relapsing-remitting course or a chronic progressive course
  • the etiology is unknown: however, viral infections, genetic predisposition, environment, and autoimmuniry all cont ⁇ bute.
  • Lesions contain infiltrates of predominantly T lymphocyte mediated, microg al cells and mfiltratmg macrophages; CD4+T lymphocytes are the predominant cell type at lesions.
  • the mechanism of o godendrocyte cell death and subsequent demyehnation is not known but is likely T lymphocyte driven.
  • Inflammatory and Fibrotic Lung Disease including Eosinophi c Pneumonias; Idiopathic Pulmonary Fibrosis, and Hypersensitivity Pneumomtis may mvolve a deregulated immune-inflammatory response. Inhibition of that response would be of therapeutic benefit.
  • Pso ⁇ asis is a T lymphocyte-mediated inflammatory disease. Lesions contain infiltrates of T lymphocytes, macrophages and antigen processing cells, and some neutrophils. Allergic diseases, including asthma: allergic rhinitis: atopic dermatitis: food hypersensitivity; and urtica ⁇ a are T lymphocyte dependent. These diseases are predominantly mediated by T lymphocyte induced inflammation. IgE mediated-inflammation or a combmation of both.
  • Transplantation associated diseases mcludmg Graft rejection and Graft-Versus-Host-Disease (GVHD) are T lymphocyte-dependent; inhibition of T lymphocyte function is ameliorative.
  • infectious disease including but not limited to viral infection (mcludmg but not limited to AIDS, hepatitis A, B. C, D, E and he ⁇ es) bacte ⁇ al infection, fungal infections, and protozoal and parasitic fections (molecules (or de ⁇ vatives/agomsts) which stimulate the MLR can be utilized therapeutically to enhance the immune response to infectious agents), diseases of immunodeficiency (molecules/de ⁇ vatives/agomsts) which stimulate the MLR can be utilized therapeutically to enhance the immune response for conditions of inhented. acquired, infectious induced (as in HIV infection), or latrogenic (i e , as from chemotherapy) immunodeficiency), and neoplasm.
  • viral infection mcludmg but not limited to HIV, hepatitis A, B. C, D, E and he ⁇ es
  • bacte ⁇ al infection bacte ⁇ al infection
  • fungal infections and protozoal and parasitic
  • Molecules that inhibit the lymphocyte response in the MLR also function in vivo du ⁇ ng neoplasm to suppress the immune response to a neoplasm; such molecules can either be expressed by the neoplastic cells themselves or their expression can be induced by the neoplasm in other cells. Antagonism of such inhibitory molecules (either with antibody, small molecule antagonists or other means) enhances immune-mediated tumor rejection.
  • inhibition of molecules with proinflammatory properties may have therapeutic benefit in reperfusion injury: stroke; mvocardiai infarction, atherosclerosis, acute lung injury, hemorrhagic shock, bum: sepsis/septic shock, acute tubular necrosis: endomet ⁇ osis. degenerative joint disease and pancreatis
  • the compounds of the present invention are admmistered to a mammal, preferably a human, in accord with known methods, such as intravenous administration as a bolus or by cont uous infusion over a penod of time, by mtramuscular, intrape ⁇ toneal. lntracerobrospinal, subcutaneous, intra-articular. mtrasynovial. intrathecal. oral, topical, or mhalation (intranasal. intrapulmonary) routes. Intravenous or inhaled administration of polypeptides and antibodies is preferred.
  • immunoadjuvant therapy other therapeutic regimens, such administration of an anti-cancer agent, may be combmed with the administration of the proteins, antibodies or compounds of the instant invention.
  • the patient to be treated with a the immunoadjuvant of the mvention may also receive an anti- cancer agent (chemotherapeutic agent) or radiation therapy.
  • chemotherapeutic agent chemotherapeutic agent
  • Preparation and dosmg schedules for such chemotherapeutic agents may be used according to manufacturers' instructions or as determmed empincally by the skilled practitioner. Preparation and dosmg schedules for such chemotherapy are also desc ⁇ bed in Chemotherapy Service Ed., M.C. Perry, Williams & Wilkins, Baltimore, MD (1992).
  • the chemotherapeutic agent may precede, or follow administration of the immunoadjuvant or may be given simultaneously therewith. Additionally, an anti-oestrogen compound such as tamoxifen or an anti-progesterone such as onap ⁇ stone (see, EP 616812) may be given dosages known tor such molecules
  • admmister antibodies agamst other immune disease associated or tumor associated antigens, such as antibodies which bind to CD20, CD1 la. CD 18. ErbB2. EGFR, ErbB3. ErbB4, or vascular endothelial factor (VEGF)
  • VEGF vascular endothelial factor
  • t wo or more antibodies binding the same or two or more different antigens disclosed herein may be coadmmistered to the patient
  • the PRO polypeptides are coadmmistered with a growth inhibitory agent
  • t he growth inhibitory agent may be administered first , followed by a PRO polypeptide
  • simultaneous administration or administration first is also contemplated Suitable dosages for the growth inhibitory agent are those presently used and may be lowered due to the combined action (synergy) of the growth inhibitory agent and the PRO polypeptide
  • the approp ⁇ ate dosage of an a compound of the mvention will depend on the type of disease to be treated, as defined above, the seventy and course of t he disease , whether the agent is administered for preventive or therapeutic purposes, previous therapy the patient's clinical history and response to the compound, and the discretion of the at t ending physician
  • the compound is suitabl y admmistered to the patient at one time or over a series of treatments
  • polypeptide or antibodv is an initial candidate dosage tor administration to the patient whether, for example , bv one or more separate administrations or by continuous infusion
  • a typical dailv dosage might range from about 1 ⁇ g/kg to 100 mg/kg or more, depending on the factors mentioned above
  • the treatment is sustained until a desired suppression of disease s y mptoms occurs
  • other dosage regimens mav be useful
  • the progress of this therapv is easil y monitored bv conventional techniques and assays O Articles of Manufacture
  • the article of manufacture comp ⁇ ses a container and an instruction Suitable containers include, for example. bottles vials sv ⁇ nges and test tubes
  • the containers mav be formed from a va ⁇ e t y of ma t enals such as glass or plastic
  • the container holds a composition which is effective for diagnosmg or treating the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceabie by a hypodermic injection needle)
  • the active agen t m the composition is usually a polypeptide or an antibody of the invention An instruction or label on.
  • the container indicates that the composition is used for diagnosing or treating the condition of choice
  • the article of manufacture may further compnse a second container comp ⁇ sing a pharmaceutically-acceptable buffer, such as phosphate-buffered saline. Ringer's solution and dextrose solution It may further mclude other matenals desirable from a commercial and user standpoint including other buffers, diluents, filters, needles, synnges, and package inserts with instructions for use p - Diagnosis and Prognosis of Immune Related Disease
  • Cell surface protems such as proteins which are overexpressed m certain immune related diseases, are excellent targets for drug candidates or disease treatment
  • the same protems along with secreted protems encoded bv the genes amplified in immune related disease states find additional use m the diagnosis and prognosis of these diseases.
  • antibodies directed agamst the protem products of genes amplified in multiple sclerosis, rheumatoid arthntis, or another immune related disease can be used as diagnostics or prognostics.
  • antibodies can be used to qualitatively or quantitatively detect the expression of proteins encoded by amplified or overexpressed genes ("marker gene products").
  • the antibody preferably is equipped with a detectable, e.g., fluorescent label, and binding can be monitored by light microscopy, flow cytometry, fluo ⁇ metry, or other techniques known in the art. These techniques are particularly suitable, if the overexpressed gene encodes a cell surface protem Such binding assays are performed essentially as described above. In situ detection of antibody binding to the marker gene products can be performed, for example, by immunofluorescence or lmmunoelectron microscopy.
  • a histological specimen is removed from the patient, and a labeled antibody is applied to it. preferably by overlaying the antibody on a biological sample.
  • This procedure also allows for determining the dist ⁇ bution of the marker gene product in the tissue examined. It will be apparent for those skilled in the art that a wide va ⁇ ety of histological methods are readily available for m situ detection.
  • EXAMPLE 1 Isolation of cDNA clones Encoding Human PRO200, PRO204, PR0212, PR0216. PR0226, PRO240, PR0235. PR0245, PR0172, PR0273, PR0272, PR0332, PR0526, PRO701 , PR0361. PR0362, PR0363, PR0364. PR0356, PR0531, PR0533, PRO1083, PR0865, PRO770, PR0769, PR0788, PROl 114, PRO1007, PROl 184. PRO1031, PR01346, PROl 155, PRO1250, PR01312, PROl 192, PR01246. PR01283, PROl 195, PR01343.
  • PR0381. PRO720, PRO866, PRO840, PR0982, PR0836, PROl 159, PR01358, PR01325, PR01338. PR01434.
  • PR04333. PRO4302. PRO4430 and PR05727 polypeptide.
  • the extracellular domain (ECD) sequences (including the secretion signal sequence, if any) from about 950 known secreted proteins from the Swiss-Prot public database were used to search EST databases.
  • the EST databases included public EST databases (e.g , GenBank), a pnvate EST database (LIFESEQ Incyte Pharmaceuticals. Palo Alto, CA), and proprietary ESTs from Genentech.
  • the search was performed using the computer program BLAST or BL ⁇ ST2 [Altschul et al . Methods m 266- 460-480 ( 1996)] as a companson of the ECD protein sequences to a 6 frame translation of the EST sequences.
  • RNA for construction of the cDNA libranes was isolated from va ⁇ ous human tissue libranes. including, e.g.. fetal lung, fetal liver, fetal brain, small intestine, smooth muscle cells, etc.
  • the cDNA libranes used to isolated the cDNA clones were constructed by standard methods using commercially available reagents such as those from Invitrogen, San Diego, CA.
  • the cDNA was primed with oligo dT containing a Notl site, linked with blunt to Sail hemikinased adaptors, cleaved with Notl, sized approp ⁇ ately by gel electrophoresis, and cloned in a defined o ⁇ entation into a suitable cloning vector (such as pRKB; pR 5B is a precursor of pRK5D that does not contain the Sfil site; see. Holmes et al. Science. 253: 1278-1280 (1991)) in the unique Xhol and Notl sites.
  • a suitable cloning vector such as pRKB; pR 5B is a precursor of pRK5D that does not contain the Sfil site; see. Holmes et al. Science. 253: 1278-1280 (1991)
  • the clones were sequenced using known and readily available methodology.
  • Amylase yeast screen is a Amylase yeast screen:
  • oligo dT primed cDNA library mRNA was isolated from vanous tissues (e.g., such as those indicated above under the ECD homology procedure) using reagents and protocols from Invitrogen, San Diego, CA (Fast Track 2). This RNA was used to generate an oligo dT primed cDNA library in the vector pRK5D using reagents and protocols from Life Technologies, Gaithersburg, MD (Super Sc ⁇ pt Plasmid System). In this procedure, the double stranded cDNA was sized to greater than 1000 bp and the Sall/Notl hnkered cDNA was cloned into Xhol/Notl cleaved vector.
  • pRK5D is a cloning vector that has an sp6 transcnption initiation site followed by an Sfil rest ⁇ ction enzyme site preceding the Xhol Notl cDNA clonmg sites.
  • pSST-AMY.O is a cloning vector that has a yeast alcohol dehydrogenase promoter preceding the cDNA clonmg sites and the mouse amylase sequence (the mature sequence without the secretion signal ) followed by the yeast alcohol dehydrogenase terminator, after the cloning sites.
  • cDNAs cloned into this vector that are fused in frame with amylase sequence will lead to the secretion of amylase from appropriately transfected yeast colonies.
  • Transformation and Detection DNA from the library desc ⁇ bed in paragraph 2 above was chilled on ice to which was added electrocompetent DH10B bacte ⁇ a (Life Technologies, 20 ml). The bactena and vector mixmre was then electroporated as recommended by the manufacturer. Subsequently, SOC media (Life Technologies. 1 ml) was added and the mixmre was incubated at 37°C for 30 minutes. The transformants were then plated onto 20 standard 150 mm LB plates containing ampicillin and mcubated for 16 hours (37°C). Positive colonies were scraped off the plates and the DNA was isolated from the bacte ⁇ al pellet using standard protocols, e g , Cisco- gradient. The purified DNA was then earned on to the yeas t pro t ocols below.
  • the yeast methods were divided into three catego ⁇ es: ( 1 ) Transformation of yeast with the plasmid cDNA combined vector; (2) Detection and isolation of yeast clones secretmg amylase; and (3) PCR amplification of the insert directiy from the yeast colony and punfication of the DNA for sequencing and further analysis.
  • yeast strain used was HD56-5A (ATCC-90785). This strain has the following genotype: MAT alpha, ura3-52, leu2-3, leu2-1 12, his3-l l, his3-15, MAL ⁇ SUC". GAl ⁇
  • yeast mutants can be employed that have deficient post-translational pathways. Such mutants may have translocation deficient alleles in seel I, secll. sec62. with truncated ⁇ ?C71 being most preferred.
  • antagonists including antisense nucleotides and or ligands which interfere with the normal operation of these genes, other proteins implicated m this post translation pathway (e.g., SEC ⁇ lp, SEC72p, SEC62p, SEC63p, TDJlp or SSAlp-4p) or the complex formation of these proteins may also be preferably employed in combination with the amylase- expressing yeast.
  • Transformation took place by mixing the prepared cells (100 ⁇ l) with freshly denatured single stranded salmon testes DNA (Lofstrand Labs. Gaithersburg, MD) and transforming DNA (I ⁇ g, vol. ⁇ 10 ⁇ l) in microfiige tubes The mixmre was mixed b ⁇ efly by vortexing, then 40% PEG/TE (600 ⁇ l, 40% polyethylene glycol-4000, 10 M T ⁇ s-HCI, 1 mM EDTA, 100 mM L ⁇ 2Ac, pH 7.5) was added.
  • PEG/TE 600 ⁇ l, 40% polyethylene glycol-4000, 10 M T ⁇ s-HCI, 1 mM EDTA, 100 mM L ⁇ 2Ac, pH 7.5
  • the transformation was performed using a single, large scale reaction, wherein reagent amounts were scaled up accordingly.
  • the selective media used was a synthetic complete dextrose agar lackmg uracii (SCD-Ura) prepared as desc ⁇ bed in Kaiser et al , Methods in Yeast Genetics, Cold Sp ⁇ ng Harbor Press. Cold Sp ⁇ ng Harbor, NY, p. 208-210 ( 1994) Transformants were grown at 30°C for 2-3 days.
  • SCD-Ura synthetic complete dextrose agar lackmg uracii
  • the detection of colonies secreting amylase was performed by mcludmg red starch in the selective growth media.
  • Starch was coupled to the red dye (Reactive Red- 120, Sigma) as per the procedure descnbed by Biely et al. Anal Biochem . _72 176- 179 ( 1988)
  • the coupled starch was inco ⁇ orated into the SCD-Ura agar plates at a final concentration of 0 15% (w/v). and was buffered with potassium phosphate to a pH of 7 0 (50- 100 mM final concentration)
  • the positive colonies were picked and streaked across fresh selective media (onto 150 mm plates) in order to obtain well isolated and identifiable single colonies.
  • Well isolated single colonies positive for amylase secretion were detected by direct inco ⁇ oration of red starch into buffered SCD-Ura agar. Positive colonies were determmed by their ability to break down starch resulting m a clear halo around the positive colony visualized directly.
  • the yeast EST fragment identified above was used to search va ⁇ ous expressed sequence tag (EST ) databases.
  • the EST databases included public EST databases (e g., GenBank, Merck/Wash U) and a prop ⁇ etary EST DNA database (LIFESEQ W , Incyte Pharmaceuticals, Palo Alto, CA).
  • the search was performed usmg the computer program BLAST or BLAST2 (Altshul et al. Methods in Enzvmology 266:460-480 (1996)) as a compa ⁇ son of the ECD protem sequences to a 6 frame translation of the EST sequence.
  • a consensus DNA sequence was assembled relative to other EST sequences using phrap.
  • the consensus DNA sequence was extended using repeated cycles of BLAST and phrap to extend the consensus sequence as far as possible using the sources of EST sequences discussed above as well as EST sequences propnetary to Genentech. Based on this consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone encoding the particular PRO polypeptide.
  • DNA from the libranes was screened by PCR amplification, as per Ausubel et al, Current Protocols in Molecular Biology, with the PCR p ⁇ mer pair. A positive library was then used to isolate clones encoding the gene of interest using the probe oligonucleotide and one of the primer pairs
  • RNA for construction of the cDNA libranes was isolated from vanous human tissues.
  • the cDNA libranes used to isolate the cDNA clones were constructed by standard methods using commercially available reagents such as those from Invitrogen. San Diego, CA
  • the cDNA was primed with oligo dT containing a Notl site, linked with blunt to Sail hemikinased adaptors, cleaved with Notl. sized appropriately by gel electrophoresis. and cloned in a defined onentation into a suitable cloning vector (such as pRKB or pRKD.
  • pRK5B is a precursor of pRK5D that does not contain the Sfil site; Holmes et al.. Science, 253: 1278-1280 (1991)) in the unique Xhol and Notl sites.
  • ESTs Expressed Sequence Tags
  • the signal sequence algo ⁇ thm computes a secretion signal score based on the character of the DNA nucleotides surrounding the first and optionally the second methionine codon(s) (ATG) at the 5'-end of the sequence or sequence fragment under consideration.
  • the nucleotides following the first ATG must code for at least 35 unambiguous amino acids without any stop codons. If the first ATG has the required ammo acids, the second is not examined. If neither meets the requirement, the candidate sequence is not scored.
  • the DNA and corresponding ammo acid sequences surrounding the ATG codon are scored using a set of seven sensors (evaluation parameters) known to be associated with secretion signals.
  • EST sequences which were compared to a va ⁇ ety of expressed sequence tag (EST) databases which mcluded public EST databases (e.g., GenBank) and a prop ⁇ etary EST DNA database (LIFESEQ R , Incyte Pharmaceuticals, Palo Alto, CA).
  • EST expressed sequence tag
  • LIFSEQ R prop ⁇ etary EST DNA database
  • the homology search was performed using the computer program BLAST or BLAST2 (Altshul et al, Methods in Enzymology 266:460-480 (1996)).
  • Probes based on an expressed sequence tag (EST) identified from the Incyte Pharmaceuticals database due to homology with VEGF were used to screen a cDNA library de ⁇ ved from the human glioma cell line G61. Screening may be conducted in a manner similar to the procedure disclosed elsewhere in this application. In particular, Incyte Clone "INC 1302516" was used to generate the following four probes-
  • ORF open reading frame
  • CMV-based expression vector An epitope-tag (FLAG, Kodak) and Histidine-tag (His8) were inserted between the ORF and stop codon.
  • UNQ174-H ⁇ s8 and UNQ174-FLAG were transfected into human embryonic kidney 293 cells by SuperFect (Qiagen) and pulse-labeled for 3 hours with [ 35 S]meth ⁇ on ⁇ ne and [ 35 C]cyste ⁇ ne.
  • the UNQ174-IgG plasmid was co-transtected with Baculogold Baculovirus DNA (Pharmmgen) using Lipofectin (GibcoBRL) into 10 5 Sf9 cells grown in Hmk's TNM-FH medium (JRH Biosciences) supplemented with 10% fetal bovine serum Cells were incubated for 5 days at 28°C.
  • the supernatant was harvested and subsequently used for the first viral amplification by infecting Sf9 cells at an approximate multiplicity of mfection (MOI) of 10 Cells were incubated for 3 days, then supernatant harvested, and expression of the recombinant plasmid determmed by binding of 1 ml of supernatant to 30 ⁇ l of Protem-A Sepharose CL-4B beads (Pharmacia) followed by subsequent SDS-PAGE analysis
  • the first amplification supernatant was used to mfect a 500 ml spinner culmre of Sf9 cells grown in ESF-921 medium (Expression Systems LLC) at an approximate MOI ot 0 1 Cells were treated as above, except harvested supernatant was sterile filtered Specific protein was pu ⁇ fied bv binding to Protein-A Sepharose 4 Tast Flow (Pharmacia) column
  • Figure 4 A cDNA containing DNA encoding UNQ 178 (SEQ ID NO 12) has been deposited with the ATTC on October 16 1997 and has been assigned deposit number 209380
  • PCR pnmers forward and reverse
  • probes used in the procedure were the following forward p ⁇ mer 3 CACGCTGGTTTCTGCTTGGAG-3' (SEQ ID NO 15) reverse pnmer 5 AGCTGGTGC ⁇ CAGGGTGTCATG-3' (SEQ ID NO 16) hybridization probe (SEQ ID NO 17)
  • DNA33087 contams a single open reading frame with an apparent translation initiation site nucleotide residues 268-270 and ending at the stop codon (TAG) are residues 1531-1533 (Fig. 7, SEQ ID NO: 18), as indicated by bolded underline.
  • the predicted PR0215 polypeptide precursor i.e , UNQ 190, SEQ ID NO: 19
  • UNQ 190 SEQ ID NO: 19
  • a cDNA clone containing DNA33087 (identified as DNA33087-1 158) has been deposited with the ⁇ mencan Type Culture Collection (ATCC) on September 16, 1997 and has been assigned ATCC Dep. No 209381
  • DNA33460 contains a single open reading frame with an apparent translation initiation site at nucleotide residues 62-64 and ending at the stop codon (TGA) at residues 1391-1393 (Fig. 9. SEQ ID NO 20), as indicated by bolded underline.
  • the predicted PR0226 polypeptide precursor i e , UNQ200.
  • SEQ ID NO 21 is 443 ammo acids long, has a calculated molecular weight of 49.391 daltons, a pi of 4 82 and is shown m Figure 10 as UNQ200 (SEQ ID NO.21)
  • a cDNA clones containing DNA33460 (SEQ ID NO:20), designated as DNA33460-1166. has been deposited with the ATCC on October 16, 1997 and has been assigned ATCC deposit number 209376
  • oligonucleotide sequences used m the above procedure were the following: 28722-p (OLI488) (SEQ ID NO: 22)
  • DNA34387 contains a single open reading frame with an apparent translation initiation site at nucleotide positions 12-14 and ending at the stop codon (TGA) at nucleotide positions 699-701 (Fig 11, SEQ ID NO 25), as indicated by bolded underline
  • the predicted PRO240 polypeptide precursor i e , UNQ214. SEQ ID NO 26
  • SEQ ID NO 26 is 229 ammo acids long, has a calculated molecular weight of 24 689 daltons. a pi of 7 83 and is shown in Figure 12
  • a cDNA clone containing DNA34387 (SEQ ID NO 25) has been deposited with ATCC on September 16, 1997 and is assigned ATCC deposit no 209260
  • PCR pnmers forward and reverse
  • hybndization probe synthesized for use in the above- desc ⁇ bed procedure were the following forward PCR p ⁇ mer 5'-TCAGCTCCAGACTCTGATACTGCC-3' (SEQ ID NO 27) reverse PCR primer 5'-TGCCTTTCTAGGAGGC ⁇ GAGCTCC-3* (SEQ ID NO 28) hybndization probe (SEQ ID NO 29)
  • DNA35558 clone shown in Figure 13 contains a single open reading frame with an apparent translation initiation site at nucleotide positions 667-669 and ending at the stop codon (TGA) at nucieotide positions 2323-
  • a cDNA clone containing DNA35558 has been deposited with ATCC on October 16, 1997 and is assigned ATCC deposit no 209374
  • the PCR pnmers (forward and reverse) and hybndization probe synthesized for use in the above procedure were forward PCR primer 5'-TGGAATACCGCCTCCTGCAG-3' (SEQ ID NO 32) reverse PCR p ⁇ mer 5'-CTTCTGCCCTTTGGAGAAGATGGC-3' (SEQ ID NO 33) hybndization probe 5'-GGACTCACTGGCCCAGGCCTTCAATATCACCAGCCAGGACGAT-3' (SEQ ID NO 34) H.
  • PCR pnmers forward and reverse
  • hybndization probes synthesized for use with the above- desc ⁇ bed method were the following: forward PCR p ⁇ mer 5'-ATCGTTGTGAAGTTAGTGCCCC-3' (SEQ ID NO:37) reverse PCR pnmer 5 , -ACCTGCGATATCCAACAGAATTG-3' (SEQ ID NO:38) hybndization probe (SEQ ID NO:39) 5'-GGAAGAGGATACAGTCACTCTGGAAGTATTAGTGGCTCCAGCAGTTCC-3'
  • DNA35638- 1 141 The entire nucleotide sequence of DNA35638 (SEQ ID N0 35) is shown in Figure 15.
  • Clone DNA35638 contains a single open reading frame with an apparent translation mitiation site at nucleotide positions 89-91 and endmg at the stop codon (TAG) at nucleotide positions 1025-1027 (Fig. 15; SEQ ID NO-35)
  • the predicted PR0245 polypeptide precursor i e , UNQ219, SEQ ID NO.36
  • a clone containing DNA35638 (SEQ ID NO 35). designated as DNA35638- 1 141 has been deposited with ATCC on September 16. 1997 and is assigned ATCC deposit no 209265.
  • UNQ 146. SEQ ID NO 41 is 723 amino acids long, has a calculated molecular weight of 78.055 daltons and a pi of 6 17 (Fig. 18).
  • a cDNA clone containing DNA35916 (SEQ ID NO 40) has been deposited with ATCC on October 28, 1997 (designated as DNA35916-1 161) and has been assigned ATCC deposit no. 209419.
  • the oligonucleotide sequences used in the above procedure were the following: 28765.p (OLI633)
  • PR0272 encoding DNA sequences were the following forward PCR p ⁇ mer ( fl) 5'-CGCAGGCCCTCATGGCCAGG-3' (SEQ ID NO 52) forward PCR p ⁇ mer ( f2) 5'-GAAATCCTGGGTAATTGG-3' (SEQ ID NO 53) reverse PCR p ⁇ mer 5'-GTGCGCGGTGCTCACAGCTCATC-3' (SEQ ID NO 54) hyb ⁇ dization probe
  • Clone DNA40620 (SEQ ID NO 50) contams a single open readmg frame with an apparent translation initiation site at nucleotide positions 35-37 and endmg at the stop codon (TGA) at nucleotide positions 1020-
  • the ent i re nucleotide sequence of DNA40982 (SEQ ID NO:56) is shown in Figure 23.
  • Clone DNA40982 (SEQ ID NO:56) contains a single open reading frame with an apparent translation initiation site at nucleotide pos i t i ons 342-344 and ending at the stop codon (TAG) at nucleotide posi t ions 2268-2270, as ind i cated i n Figure 23 by bolded underline.
  • the predicted PR0332 polypeptide precursor i.e. , UNQ293 , SEQ ID NO:57, Fig.
  • a cDNA clone con t a i nmg DNA40982 (SEQ ID NO:56) (designated as DNA40982-1235) has been deposited w i th ATCC on November 7, 1997 and is assigned ATCC deposit no. 209433.
  • PCR pnmers forward and reverse
  • hybridization probes synthesized were t he following: forward PCR p ⁇ mer: 5'-TGGCTGCCCTGCAGTACCTCTACC-3' (SEQ ID NO:63) reverse PCR p ⁇ mer: 5'-CCCTGCAGGTCATTGGCAGCTAGG-3' (SEQ ID NO:64) hybridization probe: (SEQ - D NQ . 65)
  • Clone DNA44184 (SEQ ID NO:61 ) contains a single open reading frame wi t h an apparen t t ransla t ion init i at i on sue at nucleo t .de positions 514-516 and ending at the stop codon (TGA) a t nucleotide positions 1933- 1935 (F i gure 61 ), as i ndicated by bolded underline.
  • the predicted PR0526 polypep t ide precursor i.e . UNQ330, SEQ ID N0.62
  • i s 473 ammo acids long ( Figure 62).
  • the UNQ330 (SEQ ID NO.62) pro t ein shown i n F i gure 62 has an es ti mated molecular weight of about 50708 daltons and a pi of about 9.28.
  • a cDNA clone conta i nmg DNA44184 has been deposited with the ATCC on 26 March 1998 (under the designa t ion DNA44184- 1319) and is assigned deposit number 209704.
  • Analys i s of UNQ330 (SEQ ID NO:62) reveals that the signal pep t ide sequence is at about ammo acids 1-26.
  • a leucine z i pper pa t tern is at about ammo acids 135-156.
  • a glycosammoglycan attachment is at about amino ac i ds 436-439.
  • N- lycosylation sites are at about ammo acids 82-85, 179-182, 237-240 and 423-426.
  • a von Willebrand factor (VWF) type C domain(s) is found at about ammo acids 411-425. The skilled artisan can understand which nucleotides correspond to these ammo acids based on the sequences provided herein.
  • Clone DNA44205 (SEQ ID NO:66) contains a single open reading frame (with an apparent translation initiation site at nucleotide positions 50-52 and ending at the stop codon (TAG) at nucleotide positions 2498- 3000, as indicated by bolded underline in Figure 27
  • the predicted PRO701 polypeptide precursor i.e , Fig. 28, UNQ365, SEQ ID N0 67
  • a cDNA clone contaming DNA44205 (SEQ ID NO-66) (designated as DNA44205-1285) has been deposited with ATCC on March 31 , 1998 and is assigned ATCC deposit no 209720.
  • UNQ365 (SEQ ID NO 67) contains a potential signal peptide cleavage site at about amino acid position 25 There are potential N-glycosylation sites at about ammo acid positions 83, 511, 716 and 803.
  • the carboxylesterases type-B signature 2 sequence is at about residues 125 to 135 Regions homologous with carboxylesterase type-B are also at about residues 54-74 197-212 and 221 -261
  • a potential transmembrane region corresponds approximately to amino acids 671 through about 700
  • the corresponding nucleic acids can be routinely determmed from the sequences provided herem.
  • regions mdicattve of the arginase family protems are present at about residues F3 to V14 and again at 139 to T57, while a transmembrane domam exists at about residues P380 to S409.
  • a cDNA clone contaming DNA45410 (SEQ ID NO 71) has been deposited with ATCC on February 5. 1998 and is assigned ATCC deposit no 209621
  • the PCR pnmers (forward and reverse) and hybndization probe synthesized for use m the above procedure were- forward PCR p ⁇ mer 1 - S'-TATCCCTCCAATTGAGCACCCTGG-S' (SEQ ID NO 81 ) forward PCR p ⁇ mer 2 S'-GTCGGAAGACATCCCAACAAG-S' (SEQ ID NO 82) reverse PCR p ⁇ mer I 5'-CTTCACAATGTCGCTGTGCTGCTC-3' (SEQ ID NO 83) reverse PCR p ⁇ mer 2 5'-AGCCAAATCCAGCAGCTGGCTTAC-3' (SEQ ID NO 84) hyb ⁇ dization probe
  • Clone DNA45416 (SEQ ID NO 79) contains a single open reading frame with an apparent translation initiation site at nucleotide positions 1 19- 121 and ending at the stop codon (TAA) at nucleotide positions 1082-
  • UNQ317, SEQ ID NO 80) is 321 amino acids long ( Figure 32)
  • the UNQ317 protem (SEQ ID NO 80) shown in Figure 32 has an estimated molecular weight of about 35,544 daltons and a pl of about 8 51 Analysis of the
  • UNQ317 polypeptide as shown in Figure 32 evidences the presence of a glycosaminoglycan attachment site at about amino acid 149 to about amino acid 152 and a transmembrane domam from about ammo acid 276 to about amino acid 306
  • a cDNA clone containing DNA45416 (SEQ ID NO 79) has been deposited with ATCC on February 5, 1998 and is assigned ATCC deposit no 209620
  • PCR pnmers forward and reverse
  • hybndization probe synthesized for use in the above procedure were: forward PCR p ⁇ mer-
  • the UNQ318 protem (SEQ ID NO:87) shown in Figure 34 has an estimated molecular weight of about 41,281 daltons and a pi of about 8.33. Analysis of the UNQ318 polypeptide as shown in Figure 34 evidences the presence of a transmembrane domain at about ammo acid residue 221 to about residue 254.
  • a cDNA clone contammg DNA45419 (SEQ ID NO:86) has been deposited with ATCC on February 5, 1998 and is assigned ATCC deposit no. 209616.
  • EST expressed sequence tag
  • PCR pnmers forward and reverse
  • hybndization probes synthesized for use in the above- desc ⁇ bed screening procedure were: forward PCR p ⁇ mer (44825.fl). 5'-CACAGCACGGGGCGATGGG-3' (SEQ ID NO:93) forward PCR p ⁇ mer (44825.Q): 5'-GCTCTGCGTTCTGCTCTG-3' (SEQ ID NO:94) forward PCR p ⁇ mer (44825.GITR.Q:
  • Clone DNA47365 (SEQ ID NO:91 ) contains a single open reading frame with an apparent translation initiation site at nucleotide positions 121-123 and ending at the stop codon (TGA) at nucleotide positions 844-
  • the predicted PR0364 polypeptide precursor i.e., UNQ319, SEQ ID NO:92
  • the UNQ319 (SEQ ID NO:92) protem shown in Figure 36 has an estimated molecular weight of about 26.000 daltons and a pi of about 6.34.
  • a potential N- glycosylation sites exists between amino acids 146 and 149 of the amino acid sequence shown in Figure 36.
  • a putative signal sequence is from amino acids 1 to 25 and a potential transmembrane domain exists between amino acids 162 to 180 of the sequence shown in Figure 36.
  • a cDNA clone containing DNA47365 (designated DNA47365-1206) has been deposited with ATCC on November 7, 1997 and is assigned ATCC Deposit No. ATCC 209436.
  • Oligo dT pruned cDNA libranes were prepared from uterus mRNA purchased from Clontech, Inc. (Palo Alto. CA, USA, catalog # 6537-1) in the vector pRK5D using reagents and protocols from Life Technologies, Gaithersburg, MD (Super Script Plasmid System)
  • pRK5D is a cloning vector that has an sp6 transcnption initiation site followed by an Sfil rest ⁇ ction enzyme site preceding the Xhol/Notl cDNA cloning sites
  • the cDNA was pnmed with oligo dT contammg a Notl site, linked with blunt to Sail hemikinased adaptors, cleaved with Notl, sized to greater than 1000 bp approp ⁇ ately by gel electrophoresis.
  • DNA sequencing of the clones isolated as desc ⁇ bed above gave a full-length DNA sequence encoding the native sequence PR0356 (NL4) (i e , DNA47470, SEQ ID NO 101 ) and the de ⁇ ved PR0356 protem sequence UNQ313 (SEQ ID NO 102)
  • PCR pnmers forward and reverse
  • hybridization probe synthesized were: forward PCR p ⁇ mer: 5'-CTGAGAACGCGCCTGAAACTGTG-3' (SEQ ID NO: 108) reverse PCR p ⁇ mer: 5VAGCGTTGTCATTGACATCGGCG-3' (SEQ ID NO.109) hyb ⁇ dization probe (SEQ ID NO 1 10)
  • Clone DNA48314 contains a smgle open readmg frame with an apparent translat i on i n i tiation site at nucleotide positions 171-173 and endmg at the stop codon (TGA) at nucleotide pos i t i ons 2565-2567 ( Figure 39), as mdicated by bolded underime
  • the predicted PR0531 polypeptide precursor i e , UNQ332, SEQ ID NO 107) is 789 ammo acids long
  • the UNQ332 protem shown i n F i gure 39 has an estimated molecular weight of about 87552 daltons and a pi of about 4 84
  • a clone contammg DNA48314 (SEQ ID NO 106) has been deposited with the ATCC on 26 March 1998, and has been assigned deposit number 209702
  • Analys i s of the UNQ332 ammo acid sequence of SEQ ID NO 107 reveals a cadhenn extracellular repeated domam signature at about amino acids 122-132, 231-241 , 336-346 439-449 and 549-559
  • An ATP/GTP-bmd i ng s i te motif A (P-loop) is found at about amino acids 285-292 of SEQ ID NO 107
  • N- glycosvlat i on s i tes are found at least at about amino acids 567-570, 786-790, 418-421 and 336-339
  • the signal pept i de i s at about amino acids 1 -26 and the transmembrane domain is at about ammo acids 685-712 of SEQ ID NO 107
  • the EST sequence accession number AF007268 The EST sequence accession number AF007268.
  • a mu ⁇ ne fibroblast growth factor (FGF- 15) was used to search va ⁇ ous public EST databases (e g , GenBank, Dayhoff, etc )
  • the search was performed using the computer program BLAST or BLAST2 [Altschul et al Methods in Enzvmology, 266 460-480 ( 1996)] as a compa ⁇ son of the ECD protem sequences to a 6 frame translation of the EST sequences
  • sequence oligonucleotides were synthesized 1 ) to identify by PCR a cDNA library that conta i ned the sequence of interest and 2) for use as probes to isolate a clone of the full-length coding sequence
  • a source ot a full-length clone DNA from the libranes was screened bv PCR amplification as per Ausubel et al Current Protocols m Molecular Biology , with the PCR pr i mer pa i r
  • a pos i t i ve library was then used to isolate clones encoding the PR0533 gene of mterest by an in v i vo clonmg procedure using the probe oligonucleotide and one of the PCR pnmers RNA for construction of the cDNA libranes was isolated from human fetal retina
  • Notl s i te l i nked w i th blunt to Sail hemikinased adaptors, cleaved with Notl, sized approp ⁇ ately by gel electrophores i s, and cloned m a defined o ⁇ entation mto a suitable clonmg vector (such as pRKB or pRKD, P RK5B i s a precursor of pRK5D that does not contain the Sfil site, Holmes et al , Science. 253 1278-1280
  • a cDNA clone was sequenced m its entirety The full length nucleotide sequence DNA49435 (SEQ ID NO 1 11) i s shown i n F i gure 41 Clone DNA49435 (SEQ ID NO 1 1 1) contams a smgle open reading frame w i th an apparent translat i on initiation site at nucleotide positions 464-466 and endmg at the stop codon (TAA) at nucleot i de pos i t i ons 649-651. as indicated by bolded underline m Fig 41
  • the predicted PR0533 polypeptide precursor i.e..
  • UNQ334, SEQ ID NO: 112) is 216 ammo acids long, has a calculated molecular weight of 24,003 daltons and a pl of 6.99.
  • Clone DNA49435-1219 has been deposited with ATCC (under the designation DNA49435-1219) on November 21, 1997 and is assigned ATCC deposit no. 209480.
  • oligonucleotide sequences used in the above procedure were the following: FGF15.f: 5'-ATCCGCCCAGATGGCTACAATGTGTA-3' (SEQ ID NO 113)
  • FGF15.p 5'-GCCTCCCGGTCTCCCTGAGCAGTGCCAAACAGCGGCAGTGTA-3' (SEQ ID NO 114)
  • FGF15.r 5'-CCAGTCCGGTGACAAGCCCAAA-3' (SEQ ID NO 115)
  • PCR pnmers forward and reverse
  • hybndization probes synthesized for use in the above procedure were the following: forward pnmer: (43422.fi ): 5'-GGC ATTGGAGC AGTGCTGGGTG-3' (SEQ ID NO: 1 18) forward p ⁇ mer: (43422.C): 5'-AGAGCAACTCAGACAGCG-3' (SEQ ID NO: 1 19) reverse p ⁇ mer: (43422.rl ): 5'-TGGAGGCCTAGATGCGGCTGGACG-3' (SEQ ID NO: 120) reverse p ⁇ mer: (43422.r2): 5'-CGAGGAGACCATCAGCAC-3' (SEQ ID NO: 121) hybridization probe: (43422.pl): (SEQ ID NO: 122)
  • DNA50921 (SEQ ID NO: 116) contams a single open reading frame with an apparent translation initiation sue at nucleotide positions 154-156 and ending at the stop codon (TAG) at nucleotide positions 2233-2235 ( Figure 43). as indicated by bolded underline.
  • the predicted PRO 1083 polypeptide precursor i.e., UNQ540, SEQ ID NO.117, Figure 44
  • the UNQ540 (SEQ ID NO: l 17) protein shown m Figure 44 has an estimated molecular weight of about 77738 and a pi of about 8.87.
  • a clone contammg DNA50921 has been deposited with the ATCC on May 12, 1998 and has been assigned deposit number 209859.
  • DNA sequence DNA53974 (Fig. 45, SEQ ID NO: 123) and the denved PR0865 native sequence protein UNQ434 (SEQ ID NO: 124).
  • DNA53974 (SEQ ID NO: 123) contains a single open reading frame with an apparent translation initiation site at nucleotide positions 173-175 and ending at the stop codon (TAA) at nucleotide positions 1577- 1579 ( Figure 45). as indicated by bolded underline.
  • the predicted PR0865 polypeptide precursor i.e.. UNQ865. SEQ ID NO: 124) is 468 amino acids long.
  • the UNQ434 (SEQ ID NO: 124) protein shown in Figure 46 has an estimated molecular weight of about 54,393 and a pi of about 5.63.
  • a clone containing DNA53974 (SEQ ID NO.123) has been deposited with the ATCC on April 14, 1998 and has been assigned deposit number 209774
  • EST expressed sequence tag
  • the full-length clone corresponding to the EST AA524300 was purchased from Incyte (Incyte Pharmaceuticals, Palo Alto, CA) and sequenced in entirety.
  • FIG. 47 This full-length clone, designated DNA54228 (SEQ ID NO: 133), contains a single open reading frame with an apparent translation initiation site at nucleotide positions 100-102 (Fig.47; SEQ ID NO: 133) and ending at the stop codon (TGA) at residues 433-435, as indicated by bolded underime.
  • the predicted PRO770 polypeptide precursor (including a putative signal sequence of 20 amino acids) (i.e., UNQ408, SEQ ID NO: 134) is 11 1 ammo acids long, has a calculated molecular weight of 1 1,730 daltons and a pl of 7 82.
  • mice Female Balb/C mice, 6 to 8 weeks of age, were separated into two expe ⁇ mental groups: controls and asthmatics.
  • the asthmatic group was immunized intrapentoneally with 10 ⁇ g ovalbumm -i- 1 mg alum, while the control group was not.
  • mice Two weeks later, mice were exposed daily to an aerosol of 10 mg/ml ovalbumm in PBS aerosolized with a UlrraNeb nebulizer (DeVilbiss) at the rate of 2 ml/mm for 30 mm each day.
  • UlrraNeb nebulizer UlrraNeb nebulizer
  • T ⁇ cine gel shows that a low molecular weight protein is expressed in the BAL samples from asthmatic mice but not in the BAL samples from control mice This low molecular weight protein was termed m-FIZZl and was seen to co-migrate with a 8300 Dalton marker protein.
  • Partial protein sequence The protein of interest was transferred upon a PVDF membrane and sequenced by Edman degradation Tins sequence served as a template for the preparation of various cloning ohgos as desc ⁇ bed below.
  • Partial cDNA sequence We designed two degenerate oligonucleotide PCR primers corresponding to the putative DNA sequence for the first 7 and the last 7 ammo acids of the partial protein sequence..
  • This oligo was used as an RT-PCR p ⁇ mer in combination with 5' and 3' amphmers from Clontech. Ohgo #4-
  • This oligo was used as an RT-PCR p ⁇ mer in combination with oligo d(T).
  • DNA 54231 contains a single open reading frame with an apparent translation initiation site at nucleotide positions 75-77 and ending at the stop codon (TGA) at residues 417-419 as indicated by bolded underline (Fig 49)
  • the predicted PR0769 polypeptide precursor (mcludmg a signal sequence ot 10 ammo ac ⁇ ds)(; e , UNQ407, SEQ ID NO 140) is 1 14 amino acids long, has a calculated molecular weight of 12,492 daltons and a pi of 8 19 Based on its homology to m-FIZZl (34%, using the ALIGN software) the protein was designated m-FIZZ3
  • a clone containing DNA54231 (designated DNA54231-1366) has been deposited with ATCC on Ap ⁇ l 23. 1998 and has been assigned ATCC
  • Clone DNA56405 (SEQ ID NO 141 ) contains a single open reading frame with an apparent translation initiation site at nucleotide positions 84-86 and ending at the stop codon (TAG) at nucleotide positions 459-461 ( Figure 51 ) as indicated by bolded underline
  • the predicted native sequence PR0788 polypeptide precursor (; c UNQ430 SEQ ID NO 142) is 125 ammo acids long ( Figure 52).
  • PCR pnmers used in the isolation screen descnbed m the previous paragraph were: forward pnmer: (48466.fl): 5'-AGGCTTCGCTGCGACTAGACCTC-3' (SEQ ID NO: 145) reverse p ⁇ mer: (48466.rl): 5'-CCAGGTCGGGTAAGGATGGTTGAG-T (SEQ ID NO: 146) hybndization probe- 48466 pl )

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PCT/US1999/005028 WO1999046281A2 (en) 1998-03-10 1999-03-08 Novel polypeptides and nucleic acids encoding the same
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PCT/US1999/008615 WO1999055868A2 (en) 1998-04-24 1999-04-20 Fizz proteins
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PCT/US1999/012252 WO1999063088A2 (en) 1998-06-02 1999-06-02 Membrane-bound proteins and nucleic acids encoding the same
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US14622299P 1999-07-28 1999-07-28
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PCT/US1999/020111 WO2000012708A2 (en) 1998-09-01 1999-09-01 Further pro polypeptides and sequences thereof
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PCT/US1999/020594 WO2000015666A2 (en) 1998-09-10 1999-09-08 Compositions and methods for the treatment of tumors
WOPCT/US99/20594 1999-09-08
WOPCT/US99/20944 1999-09-13
PCT/US1999/020944 WO2000015792A2 (en) 1998-09-14 1999-09-13 Promotion or inhibition of angiogenesis and cardiovascularization
PCT/US1999/021547 WO2000015797A2 (en) 1998-09-17 1999-09-15 Compositions and methods for the treatment of immune related diseases
WOPCT/US99/21090 1999-09-15
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PCT/US1999/021090 WO2000015796A2 (en) 1998-09-16 1999-09-15 Secreted and transmembrane polypeptides and nucleic acids encoding the same
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US16250699P 1999-10-29 1999-10-29
US162506P 1999-10-29
WOPCT/US99/28214 1999-11-29
PCT/US1999/028214 WO2001019987A1 (en) 1999-09-13 1999-11-29 Promotion or inhibition of angiogenesis and cardiovascularization
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PCT/US1999/028409 WO2000032778A2 (en) 1998-12-01 1999-11-30 Methods and compositions for inhibiting neoplastic cell growth
WOPCT/US99/28409 1999-11-30
PCT/US1999/028313 WO2000032221A2 (en) 1998-12-01 1999-11-30 Promotion or inhibition of angiogenesis and cardiovascularization
WOPCT/US99/28301 1999-12-01
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PCT/US1999/028634 WO2000036102A2 (en) 1998-12-16 1999-12-01 Secreted and transmembrane polypeptides and nucleic acids encoding the same
PCT/US1999/028301 WO2000032776A2 (en) 1998-12-01 1999-12-01 Secreted amd transmembrane polypeptides and nucleic acids encoding the same
WOPCT/US99/28551 1999-12-02
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PCT/US1999/028551 WO2000053750A1 (en) 1999-03-08 1999-12-02 Compositions and methods for the treatment of tumors
WOPCT/US99/28564 1999-12-02
PCT/US1999/028564 WO2000055319A1 (en) 1999-03-12 1999-12-02 Methods and compositions for inhibiting neoplastic cell growth
PCT/US1999/028565 WO2000037638A2 (en) 1998-12-22 1999-12-02 Methods and compositions for inhibiting neoplastic cell growth
WOPCT/US99/30095 1999-12-16
PCT/US1999/030095 WO2000037640A2 (en) 1998-12-22 1999-12-16 Compositions and methods for the treatment of tumor
WOPCT/US99/30999 1999-12-20
PCT/US1999/030999 WO2001005836A1 (en) 1999-07-20 1999-12-20 Polypeptidic compositions and methods for the treatment of tumors
PCT/US1999/031274 WO2000053752A2 (en) 1999-03-08 1999-12-30 Promotion or inhibition of angiogenesis and cardiovascularization
WOPCT/US99/31274 1999-12-30
WOPCT/US00/00219 2000-01-05
PCT/US2000/000219 WO2000053753A2 (en) 1999-03-08 2000-01-05 Promotion or inhibition of angiogenesis and cardiovascularization
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WOPCT/US00/00376 2000-01-06
PCT/US2000/000277 WO2000053754A1 (en) 1999-03-08 2000-01-06 Compositions and methods for the treatment of tumor
PCT/US2000/000376 WO2000053755A2 (en) 1999-03-08 2000-01-06 Compositions and methods for the treatment of tumor
WOPCT/US00/03565 2000-02-11
PCT/US2000/003565 WO2001053486A1 (en) 1999-03-08 2000-02-11 Compositions and methods for the treatment of tumor
WOPCT/US00/04341 2000-02-18
PCT/US2000/004342 WO2000078961A1 (en) 1999-06-23 2000-02-18 Secreted and transmembrane polypeptides and nucleic acids encoding the same
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PCT/US2000/004414 WO2001004311A1 (en) 1999-07-07 2000-02-22 Secreted and transmembrane polypeptides and nucleic acids encoding the same
WOPCT/US00/04414 2000-02-22
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