WO2016161196A1 - Immunothérapie faisant intervenir le microarn-34 - Google Patents

Immunothérapie faisant intervenir le microarn-34 Download PDF

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Publication number
WO2016161196A1
WO2016161196A1 PCT/US2016/025410 US2016025410W WO2016161196A1 WO 2016161196 A1 WO2016161196 A1 WO 2016161196A1 US 2016025410 W US2016025410 W US 2016025410W WO 2016161196 A1 WO2016161196 A1 WO 2016161196A1
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mir
cancer
seq
oligonucleotide
synthetic
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PCT/US2016/025410
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Inventor
Andreas Bader
James Welsh
Maria Angelica CORTEZ
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Mirna Therapeutics, Inc.
Board Of Regents, The University Of Texas System
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Publication of WO2016161196A1 publication Critical patent/WO2016161196A1/fr

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/713—Double-stranded nucleic acids or oligonucleotides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • 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
    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/16011—Human Immunodeficiency Virus, HIV
    • C12N2740/16041—Use of virus, viral particle or viral elements as a vector
    • C12N2740/16043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/70596—Molecules with a "CD"-designation not provided for elsewhere in G01N2333/705
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • a PD-Ll expressing cancer in an individual in need thereof comprising: (a) identifying the cancer as a PD-Ll expressing cancer; and (b) providing a synthetic miR-34 oligonucleotide to the individual.
  • the methods further comprise providing a PD-1 or PD-Ll inhibitor to the individual.
  • the PD-1 or PD-Ll inhibitor is an antibody, small interfering RNA, or antisense RNA.
  • the synthetic miR-34 oligonucleotide and the PD-1 or PD- Ll inhibitor are synergistic.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-Ll inhibitor.
  • the methods further comprise providing radiotherapy to the individual.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-Ll inhibitor.
  • the cancer is a solid tumor.
  • the solid cancer is a melanoma, nasopharyngeal cancer,
  • the lung cancer is a non-small cell lung cancer (NSCLC).
  • the lung cancer is a small-cell lung cancer (SCLC).
  • the liver cancer is a hepatocellular carcinoma (HCC).
  • the cancer is a leukemia.
  • the cancer is a lymphoma.
  • the cancer as a PD-Ll expressing cancer comprises measuring the PD-Ll expression in a cancer cell from the individual and comparing to a control. In some embodiments, the PD-Ll expression is overexpressed compared to the control. In some embodiments, the methods further comprise selecting the individual having functional p53. In some embodiments, the synthetic miR-34 oligonucleotide is administered in a liposomal formulation. In some embodiments, T cell exhaustion is prevented or reduced.
  • the synthetic miR-34 oligonucleotide comprises: (a) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (b) a separate passenger strand that is at least 60% complementary to the active strand.
  • the passenger strand of the synthetic miR-34 oligonucleotide comprises a 5' terminal cap.
  • the 5' terminal cap is a lower alkylamine.
  • the 5' terminal cap is NH 2 -(CH 2 )6-0-.
  • the mature miRNA comprises: miR-34a (SEQ ID NO: 1), miR-34b (SEQ ID NO:2), miR-34c (SEQ ID NO:3), or a miR-34 consensus sequence (SEQ ID NO: 4).
  • the mature miRNA comprises: miR-449a (SEQ ID NO:5), miR-449b (SEQ ID NO:6), miR-449c (SEQ ID NO:7), or a miR-449 consensus sequence (SEQ ID NO: 8).
  • the mature miRNA comprises a miR-34/449 seed sequence (SEQ ID NO: 9).
  • the oligonucleotide to the individual; and (b) providing a PD-1 or PD-L1 inhibitor to the individual.
  • the PD-1 or PD-L1 inhibitor is an antibody, small interfering RNA, or antisense RNA.
  • the synthetic miR-34 oligonucleotide and the PD-1 or PD- Ll inhibitor are synergistic.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-L1 inhibitor.
  • the methods further comprise providing radiotherapy to the individual.
  • the cancer is a solid tumor.
  • the solid cancer is a melanoma, nasopharyngeal cancer,
  • the lung cancer is a non-small cell lung cancer (NSCLC).
  • the lung cancer is a small-cell lung cancer (SCLC).
  • the liver cancer is a hepatocellular carcinoma (HCC).
  • the cancer is a leukemia.
  • the cancer is a lymphoma.
  • identifying the cancer as a PD-L1 expressing cancer comprises measuring the PD-L1 expression in a cancer cell from the individual and comparing to a control. In some embodiments, the PD-L1 expression is overexpressed compared to the control. In some embodiments, the methods further comprise selecting the individual having functional p53. In some embodiments, the synthetic miR- 34 oligonucleotide is administered in a liposomal formulation. In some embodiments, T cell exhaustion is prevented or reduced.
  • the synthetic miR-34 oligonucleotide comprises: (a) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (b) a separate passenger strand that is at least 60% complementary to the active strand.
  • the passenger strand of the synthetic miR-34 oligonucleotide comprises a 5' terminal cap.
  • the 5' terminal cap is a lower alkylamine.
  • the 5' terminal cap is NH 2 -(CH 2 )6-0-.
  • the mature miRNA comprises: miR-34a (SEQ ID NO: 1), miR-34b (SEQ ID NO:2), miR-34c (SEQ ID NO:3), or a miR-34 consensus sequence (SEQ ID NO: 4).
  • the mature miRNA comprises: miR-449a (SEQ ID NO:5), miR-449b (SEQ ID NO:6), miR-449c (SEQ ID NO:7), or a miR-449 consensus sequence (SEQ ID NO: 8).
  • the mature miRNA comprises a miR-34/449 seed sequence (SEQ ID NO: 9).
  • a method of treating an individual suffering from a chronic infectious disease comprising: (a) providing a synthetic miR-34 oligonucleotide to the individual; and (b) providing a PD-1 or PD-L1 inhibitor to the individual.
  • the PD-1 or PD-L1 inhibitor is an antibody, small interfering RNA, or antisense RNA.
  • the synthetic miR-34 oligonucleotide and the PD-1 or PD-L1 inhibitor are synergistic.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-L1 inhibitor.
  • the infectious disease is a persistent viral infection.
  • the viral infection is human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), rhinovirus (common cold), herpes simplex virus (HSV), or respiratory syncytial virus (RSV).
  • the infectious disease is a persistent bacterial infection.
  • the bacterial infection is Helicobacter pylori, Mycobacterium tuberculosis, Mycobacterium leprae, or Chlamydia trachomatis.
  • the infectious disease is the result of infection by a parasite, protozoan, or metazoan.
  • the parasite, protozoan, or metazoan is Schistosoma mansoni, Taenia crassiceps, or Leishmania mexicana.
  • the methods further comprise selecting the individual having functional p53.
  • the synthetic miR-34 oligonucleotide is administered in a liposomal formulation.
  • the synthetic miR-34 oligonucleotide comprises: (a) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (b) a separate passenger strand that is at least 60% complementary to the active strand.
  • the passenger strand of the synthetic miR-34 oligonucleotide comprises a 5' terminal cap.
  • the 5' terminal cap is a lower alkylamine.
  • the 5' terminal cap is NH 2 -(CH 2 )6-0-.
  • the mature miRNA comprises: miR-34a (SEQ ID NO: 1), miR-34b (SEQ ID NO:2), miR-34c (SEQ ID NO:3), or a miR-34 consensus sequence (SEQ ID NO:4).
  • the mature miRNA comprises: miR-449a (SEQ ID NO:5), miR- 449b (SEQ ID NO:6), miR-449c (SEQ ID NO:7), or a miR-449 consensus sequence (SEQ ID NO: 8).
  • the mature miRNA comprises a miR-34/449 seed sequence (SEQ ID NO:9).
  • compositions comprising: (a) a synthetic miR-34 oligonucleotide, comprising: (i) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (ii) a separate passenger strand that is at least 60%
  • the passenger strand of the synthetic miR-34 oligonucleotide comprises a 5' terminal cap.
  • the 5' terminal cap is a lower alkylamine.
  • the 5' terminal cap is NH 2 -(CH 2 )6-0-.
  • the mature miRNA comprises: miR-34a (SEQ ID NO: 1), miR-34b (SEQ ID NO:2), miR-34c (SEQ ID NO:3), or a miR-34 consensus sequence (SEQ ID NO:4).
  • the mature miRNA comprises: miR-449a (SEQ ID NO:5), miR- 449b (SEQ ID NO:6), miR-449c (SEQ ID NO:7), or a miR-449 consensus sequence (SEQ ID NO: 8).
  • the mature miRNA comprises a miR-34/449 seed sequence (SEQ ID NO:9).
  • the PD-1 or PD-L1 inhibitor is an antibody, small interfering RNA, or antisense RNA.
  • the synthetic miR-34 oligonucleotide and the PD-1 or PD-L1 inhibitor are synergistic.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-L1 inhibitor.
  • FIGS. 1A-G illustrate p53 regulation of PD-L1 via miR-34.
  • FIG. IB illustrates downregulation of PD-L1 expression in HCT116 p53+/+ relative to p53-/- cells.
  • FIG. 1B illustrates downregulation of PD-L1 expression in HCT116 p53+/+ relative to p53-/- cells.
  • FIG. ID illustrates downregulation of PD-L1 in H1299 p53-inducible cells.
  • FIG. 1G illustrates immunohistochemical staining in samples from patients with NSCLC showing higher PD-Ll protein levels (top row) in tumors with p53 mutation than in tumors with wild-type (wt) p53 (3 patients per group)as well as chromogenic in situ hybridization staining (CISH; bottom row) indicating downregulation of miR- 34a in tumors with mutated p53 relative to tumors with wt p53.
  • CISH chromogenic in situ hybridization staining
  • FIGS. 2A-F illustrate p53 expression is inversely correlated with PD-Ll in patients with non-small cell lung cancer (NSCLC).
  • FIG. 2A illustrates correlation between p53 and PD-Ll (CD274) mRNA expression in samples from 181 patients with NSCLC from The Cancer Genome Atlas (TCGA) (P ⁇ 0.001).
  • FIGS. 3A-L illustrate regulation of PD-Ll by miR-34s.
  • FIG. 3A illustrates PD-Ll expression in A549, H460, and H1200 cells transfected with miR-34a, miR-34b, and miR-34c.
  • FIG. 3B illustrates the transfection efficiency of A549 cells 24 hours after treatment with 100 nM of miR-34a compared with a scrambled control.
  • FIG. 3C illustrates the transfection efficiency of H460 cells 24 hours after treatment with 100 nM of miR-34a compared with a scrambled control.
  • FIG. 3A illustrates PD-Ll expression in A549, H460, and H1200 cells transfected with miR-34a, miR-34b, and miR-34c.
  • FIG. 3B illustrates the transfection efficiency of A549 cells 24 hours after treatment with 100 nM of miR-34a compared with a scrambled control.
  • FIG. 3D illustrates the transfection efficiency of H1299 cells 24 hours after treatment with 100 nM of miR-34a compared with a scrambled control.
  • FIG. 3E exemplifies a western blot showing PD- Ll expression in A549 cells 96 hours after transfection with miR-34a compared.
  • FIG. 3F
  • FIG. 3H illustrates the transfection efficiency of A549 cells 24 hours after treatment with lOOnm of miR-34b compared with a scrambled control.
  • FIG. 31 illustrates the transfection efficiency of A549 cells 24 hours after treatment with lOOnm of miR-34c compared with a scrambled control.
  • FIG. 3J exemplifies a western blot showing PD-Ll expression in A549 cells 96 hours after transfection with miR-34b or miR-34c.
  • FIG. 3K illustrates luciferase activity in cells cotransfected with miR-34a, miR-34b, miR-34c, or a scrambled control and a luciferase reporter construct encoding the luciferase gene fused either to the wild-type PD-L1 3' UTR (PDL1 wt) or a mutated PD-L1 3' UTR (PDL1 mut).
  • FIG. 3L exemplifies predicted binding site of miR-34a in the 3' untranslated region (UTR) of PD-L1. Underlined residues indicate bases that have been changed by site-directed mutagenesis.
  • FIGS. 4A-H illustrate therapeutic delivery of miR-34a represses PD-L1 in vivo.
  • FIG. 4A illustrates miR-34a expression in 344SQ tumors treated with MRX34 by quantitative polymerase chain reaction (qPCR).
  • FIG. 4B illustrates PD-L1 expression in 344SQ tumors treated with MRX34 by flow cytometry.
  • FIG. 4C exemplifies a western blot showing PD-L1 expression in 344SQ tumors treated with MRX34.
  • FIG. 4D illustrates PD-L1 expression percentage, as determined from flow cytometry in 344SQ tumors treated with MRX34.
  • FIG. 4E illustrates immunohistochemical staining of 344SQ tumor tissue.
  • FIG. 4F illustrates PD-L1
  • FIG. 4G illustrates immunohistochemical staining of subcutaneous H1299 NSCLC xenografts.
  • FIG. 4H illustrates PD-L1 IHC scores of H1299 NSCLC xenografts treated with MRX34.
  • FIGS. 5A-W illustrate that therapeutic miR-34a delivery combined with radiation (RT) increases tumor-infiltrating CD8+ T cells and decreases PD-1+ T cells, macrophages, and T- regulatory cells one week after treatment completion.
  • FIG. 5B illustrates a contour plot of control CD8+ cell data after one week.
  • FIG. 5C illustrates a contour plot of CD8+ cell data one week after administration of MRX34.
  • FIG. 5D illustrates a contour plot of CD8+ cell data one week after administration of radiotherapy.
  • FIG. 5E illustrates a contour plot of CD8+ cell data one week after administration of MRX34 and radiotherapy.
  • FIG. 5G illustrates a contour plot of control PD-1+ T cell data after one week.
  • FIG. 5H illustrates a contour plot of PD-1+ T cell data one week after administration of MRX34.
  • FIG. 51 illustrates a contour plot of PD-1+ T cell one week after administration of radiotherapy.
  • FIG. 5J illustrates a contour plot of PD-1+ T cell one week after administration of MRX34 and radiotherapy.
  • FIG. 5L illustrates a contour plot of control macrophage data after one week.
  • FIG. 5M illustrates a contour plot of macrophage data one week after administration of MRX34.
  • FIG. 5N illustrates a contour plot of macrophage one week after administration of radiotherapy.
  • FIG. 50 illustrates a contour plot of macrophage one week after administration of MRX34 and radiotherapy.
  • FIG. 5P illustrates RT increased the numbers of T regulatory cells (Tregs) over the control condition, but none of the treatments showed significant effects on Tregs.
  • FIG. 5Q illustrates a contour plot of control T -regulatory (Treg) cell data after one week.
  • FIG. 5R illustrates a contour plot of Treg cell data one week after administration of MRX34.
  • FIG. 5S illustrates a contour plot of Treg cell one week after administration of radiotherapy.
  • FIG. 5T illustrates a contour plot of Treg cell one week after administration of MRX34 and radiotherapy.
  • FIG. 5U illustrates interferon gamma (IFNy) levels were increased by MRX34 only and MRX34 + RT versus control or RT alone.
  • FIG. 5V illustrates MRX34 + RT increased levels of tumor necrosis factor alpha (TNFa).
  • FIG. 5W illustrates MRX34 + RT delayed tumor growth compared with the control condition in a 344SQ mouse model.
  • IFNy interferon gamma
  • a PD-Ll expressing cancer in an individual in need thereof comprising: (a) identifying the cancer as a PD-Ll expressing cancer; and (b) providing a synthetic miR-34 oligonucleotide to the individual.
  • oligonucleotide to the individual; and (b) providing a PD-1 or PD-Ll inhibitor to the individual.
  • a method of treating an individual suffering from a chronic infectious disease comprising: (a) providing a synthetic miR-34 oligonucleotide to the individual; and (b) providing a PD-1 or PD-Ll inhibitor to the individual.
  • compositions comprising: (a) a synthetic miR-34 oligonucleotide, comprising: (i) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (ii) a separate passenger strand that is at least 60%
  • “about” can mean a range of up to 20%, up to 10%, up to 5%, or up to 1% of a given value.
  • the term can mean within an order of magnitude, preferably within 5-fold, and more preferably within 2-fold, of a value.
  • subject refers to a vertebrate, for example, a mammal.
  • Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets. Tissues, cells, and their progeny of a biological entity obtained in vivo or cultured in vitro are also encompassed. Designation as a "subject” does not necessarily entail supervision of a medical professional.
  • Treating" or "treatment” of a state, disorder or condition includes: ( 1) preventing or delaying the appearance of clinical or sub-clinical symptoms of the disorder developing in a human that is afflicted with or pre-disposed to the disorder but does not yet experience or display clinical or subclinical symptoms of the disorder; and/or (2) inhibiting the disorder, including arresting, reducing or delaying the clinical manifestation of the disorder or at least one clinical or sub-clinical symptom thereof; and/or (3) relieving the disorder, e.g., causing regression of the disorder or at least one of its clinical or sub-clinical symptoms; and/or (4) causing a decrease in the severity of one or more symptoms of the disorder.
  • the benefit to a subject to be treated is either statistically significant or at least perceptible to the patient or to the physician.
  • Inhibitory receptors are co-inhibitory molecules that negatively interfere with T cell activation and function.
  • T cell-related iRs is programmed cell death 1
  • PDCD 1, PD1, PD-1 which is induced by T cell receptor or B cell receptor signaling and remains high under persistent antigen stimulation.
  • PD-1 along with its ligands, PD-L1 and PD-L2 (and wherein PD-1 :PD-L refers to the pathway interaction between receptor and ligand), contributes to inducing and maintaining peripheral tolerance.
  • PD-1 : PD-L pathway Proper functioning of the PD-1 : PD-L pathway is therefore essential to thwart self-reactive T cells and protect against autoimmunity.
  • T cell exhaustion In some instances, persistent antigen stimulation and inflammation due to chronic infection leads to a loss of function in CD8 T cells, termed T cell exhaustion. Exhausted T cells lose robust effector functions, upregulate multiple inhibitory receptors (including PD-1), and are defined by an altered transcriptional activity. Thus, immunotherapeutic strategies focusing on blocking iRs in order to restore T cell function (“checkpoint blockade”) are promising.
  • T cell exhaustion occurs due to chronic viral, bacterial, or parasitic infections. In some embodiments, T cell exhaustion occurs due to cancer. In some embodiments, blocking or otherwise disrupting the PD-1 :PD-L pathway reverses, reduces, or suppresses T cell exhaustion.
  • the methods are applicable to the treatment of cancer, including cancer in an individual or in vitro treatment of isolated cancer cells.
  • the cancer is relapsed or refractory.
  • the cancer has metastasized.
  • the cancer is a solid tumor.
  • the solid tumor is a melanoma, neuroendocrine tumor, lung cancer, bladder cancer, glioblastoma, colon cancer, liver cancer, melanoma, multiple myeloma, ovarian cancer, kidney cancer, head and neck cancers, esophageal cancer, gastric carcinoma, pancreatic cancer, or breast cancer.
  • the solid tumor is a lung cancer.
  • the lung cancer is a non-small cell lung cancer (NSCLC) or small cell lung cancer (SCLC).
  • NSCLC non-small cell lung cancer
  • SCLC small cell lung cancer
  • the solid tumor is liver cancer.
  • the liver cancer is a hepatocellular carcinoma (HCC).
  • the cancer is a hematological malignancy.
  • the hematological malignancy is a leukemia or a lymphoma.
  • the leukemia is chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), myelodysplastic syndrome (MDS).
  • the lymphoma is a T- cell lymphoma, multiple myeloma, or B-cell lymphoma (BCL).
  • the B-cell lymphoma is a large diffuse B-cell lymphoma (DLBCL).
  • the cancer is a PD-L1 (e.g., PDL1, PD-L1, CD274, B7H, B7-H, B7H1, B7-H1) expressing cancer.
  • a method includes selecting the individual having PD-L1 overexpression.
  • any suitable diagnostic assays are used to detect biomarkers of PD-L1 overexpression.
  • an immunological assay immunohistochemistry, IHC; antibody based cell sorting
  • IHC immunohistochemistry
  • immune cells e.g., whether they are tumor infiltrating immune cells or circulating immune cells.
  • tissue is collected in a way that is applicable to histology (e.g., FFPE, fresh frozen or smears or cell suspension) and used in immunohistochemistry stainings (e.g., usually chromogenic, but also fluorescent) or antibody based cell sorting.
  • histology e.g., FFPE, fresh frozen or smears or cell suspension
  • immunohistochemistry stainings e.g., usually chromogenic, but also fluorescent
  • antibody based cell sorting e.g., usually chromogenic, but also fluorescent
  • chromogenic ISH are used for DNA mutations (e.g., such as gene recombinations, deletions, amplifications, mutations).
  • the cancer is a p53 expressing cancer.
  • the method includes selecting the individual having p53 overexpression.
  • the method includes selecting an individual having functional p53.
  • known diagnostic assays are used to detect biomarkers.
  • an immunological assay (IHC) on tissues using a D07 clone antibody is suitable to detect overexpressed nuclear staining of p53 which indicates mutated p53.
  • quantitative PCR methods, as well as FISH (fluorescent in situ hybridization), and CISH (chromogenic ISH) are applied.
  • the cancer is genotyped. In some embodiments, any suitable means of assaying genotype is contemplated for use with the method disclosed herein.
  • T cell exhaustion occurs during cancer. In some instances, blocking the
  • PD-1 :PD-L inhibitory receptor pathway reinvigorates CD8+ T cell responses.
  • the synthetic miR-34 oligonucleotide reverses, reduces, or suppresses T cell exhaustion.
  • these methods are applicable to the treatment of infectious disease.
  • the infectious disease is a chronic or persistent viral infection, bacterial infection, or parasitic, protozoan, or metazoan infection.
  • the viral infection is human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCB), rhinovirus (common cold), herpes simplex virus (HSV), or respiratory syncytial virus (RSV).
  • the bacterial infection is Helicobactor pylori, Mycobacterium tuberculosis,
  • Mycobacterium leprae or Chlamydia trachomatis .
  • the parasitic, protozoan, or metazoan infection is Schistosoma mansoni, Taenia crassiceps, or Lei shmania mexicana.
  • the infectious disease induces PD-1 overexpression in the individual.
  • the method includes selecting the individual having PD-1 overexpression.
  • any suitable diagnostic assays are used to detect biomarkers of PD- 1 overexpression.
  • an immunological assay immunohistochemistry, IHC; antibody based cell sorting
  • tissues for example tumor tissue and/or immune cells (e.g., whether they are tumor infiltrating immune cells or circulating immune cells).
  • tissue is collected in a way that is applicable to histology (e.g., FFPE, fresh frozen or smears or cell suspension) and used in immunohistochemistry stainings (e.g., usually chromogenic, but also fluorescent) or antibody based cell sorting.
  • histology e.g., FFPE, fresh frozen or smears or cell suspension
  • immunohistochemistry stainings e.g., usually chromogenic, but also fluorescent
  • antibody based cell sorting e.g., usually chromogenic, but also fluorescent
  • chromogenic ISH are used for DNA mutations (e.g., such as gene recombinations, deletions, amplifications, mutations).
  • the infectious disease is a p53 expressing infectious disease.
  • the method includes selecting the individual having p53 overexpression.
  • the method includes selecting an individual having functional p53.
  • known diagnostic assays are used to detect biomarkers.
  • an immunological assay (IHC) on tissues using a D07 clone antibody is suitable to detect
  • the parasite, protozoan, or metazoan causing the infectious disease is genotyped.
  • any suitable means of assaying genotype is contemplated for use with the method disclosed herein.
  • T cell exhaustion occurs during chronic viral, bacterial, and parasitic infections.
  • blocking the PD-1 :PD-L inhibitory receptor pathway reinvigorates CD8+ T cell responses.
  • the synthetic miR-34 oligonucleotide reverses, reduces, or suppresses T cell exhaustion.
  • MicroRNAs are small non-coding, naturally occurring RNA molecules that post- transcriptionally modulate gene expression and determine cell fate by regulating multiple gene products and cellular pathways. miRNAs interfere with gene expression by degrading the mRNA transcript by blocking the protein translation machinery. miRNAs target mRNAs with sequences that are fully or partially complementary which endows these regulatory RNAs with the ability to target a broad but nevertheless specific set of mRNAs. To date, there are -1,500 human annotated miRNA genes with roles in processes as diverse as cell proliferation, differentiation, apoptosis, stem cell development, and immune function. In some instances, the misregulation of miRNAs contributes to the development of human diseases, including cancer.
  • miRNAs deregulated in cancer function as bona fide tumor suppressors or oncogenes.
  • a single miRNA targets multiple oncogenes and oncogenic signaling pathways, and translating this ability into a future therapeutic may hold the promise of creating a remedy that is effective against tumor heterogeneity.
  • miRNAs have the potential of becoming powerful therapeutic agents for cancer that act in accordance with our current understanding of cancer as a "pathway disease" that is only successfully treated when intervening with multiple cancer pathways.
  • compositions comprising: (a) a synthetic miR-34 oligonucleotide, comprising: (i) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (ii) a separate passenger strand that is at least 60%
  • the passenger strand of the synthetic miR-34 oligonucleotide comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the 5 ' terminal cap is NH 2 -(CH 2 )6-0-.
  • the mature miRNA comprises: miR-34a (SEQ ID NO: 1), miR-34b (SEQ ID NO:2), miR-34c (SEQ ID NO:3), or a miR-34 consensus sequence (SEQ ID NO:4).
  • the mature miRNA comprises: miR-449a (SEQ ID NO:5), miR- 449b (SEQ ID NO:6), miR-449c (SEQ ID NO:7), or a miR-449 consensus sequence (SEQ ID NO: 8).
  • the mature miRNA comprises a miR-34/449 seed sequence (SEQ ID NO:9).
  • the PD-1 or PD-L1 inhibitor is an antibody, small interfering RNA, or antisense RNA.
  • the synthetic miR-34 oligonucleotide and the PD-1 or PD-L1 inhibitor are synergistic.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-L1 inhibitor.
  • the synthetic miR-34 oligonucleotide is a microRNA mimic. In some embodiments, the synthetic miR-34 oligonucleotide is administered by injection or transfusion. In some embodiments, the synthetic miR-34 oligonucleotide is provided in a vector (e .g., using a gene therapy methodology). Representative synthetic miR-34 oligonucleotide sequences are provided in Table 1 below.
  • the synthetic miR-34 oligonucleotide is 7-130 nucleotides long, double stranded RNA molecules. In some embodiments, a synthetic miR-34 oligonucleotide is 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 7-30, 7-25, 15-30, 15- 25, 17-30, or 17-25 nucleotides long.
  • the synthetic miR-34 oligonucleotide is two separate strands (i.e., an active strand and a separate passenger strand). In some embodiments, the synthetic miR-34
  • oligonucleotide is a hairpin structure.
  • the active strand comprises or consists of a sequence which is identical or substantially identical to a mature microRNA sequence. In some embodiments,
  • the mature microRNA sequence is miR-34a (SEQ ID NO: 1).
  • the mature microRNA sequence is miR-34b (SEQ ID NO: 2).
  • the mature microRNA sequence is miR-34c (SEQ ID NO: 3).
  • the mature microRNA sequence is miR-449a (SEQ ID NO: 5).
  • the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6). In some embodiments, the mature microRNA sequence is miR-449b (SEQ ID NO: 6).
  • the mature microRNA sequence is miR-449c (SEQ ID NO: 7).
  • the active strand comprises or consists of a sequence that is at least 80% identical to miR-34a (SEQ ID NO: 1). In some embodiments, the active strand comprises or consists of a sequence that is at least 80% identical to miR-34b (SEQ ID NO: 2). In some
  • the active strand comprises or consists of a sequence that is at least 80% identical to miR-34c (SEQ ID NO: 3). In some embodiments, the active strand comprises or consists of a sequence that is at least 80% identical to miR-449a (SEQ ID NO: 5). In some embodiments, the active strand comprises or consists of a sequence that is at least 80% identical to miR-449b (SEQ ID NO: 6). In some embodiments, the active strand comprises or consists of a sequence that is at least 80% identical to miR-449c (SEQ ID NO: 7). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34/449 seed sequence (SEQ ID NO: 9).
  • the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 4). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 8).
  • the active strand comprises or consists of a sequence that is at least 85% identical to miR-34a (SEQ ID NO: 1). In some embodiments, the active strand comprises or consists of a sequence that is at least 85% identical to miR-34b (SEQ ID NO: 2). In some embodiments, the active strand comprises or consists of a sequence that is at least 85% identical to miR-34c (SEQ ID NO: 3). In some embodiments, the active strand comprises or consists of a sequence that is at least 85% identical to miR-449a (SEQ ID NO: 5).
  • the active strand comprises or consists of a sequence that is at least 85% identical to miR-449b (SEQ ID NO: 6). In some embodiments, the active strand comprises or consists of a sequence that is at least 85% identical to miR-449c (SEQ ID NO: 7). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34/449 seed sequence (SEQ ID NO: 9). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 4). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 8).
  • the active strand comprises or consists of a sequence that is at least 90% identical to miR-34a (SEQ ID NO: 1). In some embodiments, the active strand comprises or consists of a sequence that is at least 90% identical to miR-34b (SEQ ID NO: 2). In some embodiments, the active strand comprises or consists of a sequence that is at least 90% identical to miR-34c (SEQ ID NO: 3). In some embodiments, the active strand comprises or consists of a sequence that is at least 90% identical to miR-449a (SEQ ID NO: 5). In some embodiments, the active strand comprises or consists of a sequence that is at least 90% identical to miR-449b (SEQ ID NO: 6).
  • the active strand comprises or consists of a sequence that is at least 90% identical to miR-449c (SEQ ID NO: 7). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34/449 seed sequence (SEQ ID NO: 9). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 4). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 8).
  • the active strand comprises or consists of a sequence that is at least 95% identical to miR-34a (SEQ ID NO: 1). In some embodiments, the active strand comprises or consists of a sequence that is at least 95% identical to miR-34b (SEQ ID NO: 2). In some embodiments, the active strand comprises or consists of a sequence that is at least 95% identical to miR-34c (SEQ ID NO: 3). In some embodiments, the active strand comprises or consists of a sequence that is at least 95% identical to miR-449a (SEQ ID NO: 5).
  • the active strand comprises or consists of a sequence that is at least 95% identical to miR-449b (SEQ ID NO: 6). In some embodiments, the active strand comprises or consists of a sequence that is at least 95% identical to miR-449c (SEQ ID NO: 7). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34/449 seed sequence (SEQ ID NO: 9). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 4). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 8).
  • the active strand comprises or consists of a sequence that is identical to miR-34a (SEQ ID NO: 1). In some embodiments, the active strand comprises or consists of a sequence that is identical to miR-34b (SEQ ID NO: 2). In some embodiments, the active strand comprises or consists of a sequence that is identical to miR-34c (SEQ ID NO: 3). In some embodiments, the active strand comprises or consists of a sequence that is identical to miR-449a (SEQ ID NO: 5). In some embodiments, the active strand comprises or consists of a sequence that is identical to miR-449b (SEQ ID NO: 6).
  • the active strand comprises or consists of a sequence that is identical to miR-449c (SEQ ID NO: 7). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34/449 seed sequence (SEQ ID NO: 9). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 4). In some embodiments, the active strand comprises or consists of a sequence which is identical or substantially identical to the miR-34 consensus sequence (SEQ ID NO: 8).
  • the passenger strand comprises a sequence that is at least 60% complementary to the active strand. In some embodiments, the passenger strand comprises a sequence that is at least 65% complementary to the active strand. In some embodiments, the passenger strand comprises a sequence that is at least 70% complementary to the active strand. In some embodiments, the passenger strand comprises a sequence that is at least 75% complementary to the active strand. In some embodiments, the passenger strand comprises a sequence that is at least 80% complementary to the active strand. In some embodiments, the passenger strand comprises a sequence that is at least 85% complementary to the active strand. In some embodiments,
  • the passenger strand comprises a sequence that is at least 90% complementary to the active strand. In some embodiments, the passenger strand comprises a sequence that is at least 95% complementary to the active strand. In some embodiments, the passenger strand comprises a sequence that is complementary to the active strand.
  • the synthetic miR-34 oligonucleotide is chemically modified or designed to comprise one or more specific sequence variations.
  • synthetic miR-34 oligonucleotide has a 5' terminal cap on the passenger strand. Any suitable cap may be used with the compositions disclosed herein.
  • the synthetic miR-34 oligonucleotide comprises a lower alkylamine cap on the 5' terminus of the passenger strand.
  • the synthetic miR-34 oligonucleotide comprises aNH 2 -(CH 2 )6-0- cap on the 5 ' terminus of the passenger strand.
  • the synthetic miR-34 oligonucleotide comprises a mismatch at the first and/or second nucleotide of the passenger strand.
  • at least one nucleotide of the passenger strand comprises a sugar modification.
  • at least one nucleotide of the active strand comprises a sugar modification.
  • at least one nucleotide of the passenger strand and at least one nucleotide if the active strand comprises a sugar modification.
  • chemical modifications include backbone modifications (e.g., phosphorothioate, morpholinos), ribose modifications (e.g., 2'-OMe, 2'-Me, 2'-F, 2 '-4 '-locked/bridged sugars (e.g., LNA, ENA, UNA), and nucleobase modifications.
  • backbone modifications e.g., phosphorothioate, morpholinos
  • ribose modifications e.g., 2'-OMe, 2'-Me, 2'-F, 2 '-4 '-locked/bridged sugars (e.g., LNA, ENA, UNA)
  • nucleobase modifications e.g., nucleobase modifications.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5' to 3' that is at least 80% identical to SEQ ID NO: 1, and (ii) a separate passenger strand comprising a sequence from 5' to 3' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5' terminal cap.
  • the 5' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5' to 3' that is at least 80% identical to SEQ ID NO: 2, and (ii) a separate passenger strand comprising or consisting of a sequence from 5 ' to 3 ' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5 ' to 3' that is at least 80% identical to SEQ ID NO: 3, and (ii) a separate passenger strand comprising or consisting of a sequence from 5 ' to 3 ' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5 ' to 3' that is at least 80% identical to SEQ ID NO: 4, and (ii) a separate passenger strand comprising or consisting of a sequence from 5 ' to 3 ' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5 ' to 3' that is at least 80% identical to SEQ ID NO: 5, and (ii) a separate passenger strand comprising or consisting of a sequence from 5 ' to 3 ' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5 ' to 3' that is at least 80% identical to SEQ ID NO: 6, and (ii) a separate passenger strand comprising or consisting of a sequence from 5 ' to 3 ' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5 ' to 3' that is at least 80% identical to SEQ ID NO: 7, and (ii) a separate passenger strand comprising or consisting of a sequence from 5 ' to 3 ' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5 ' to 3' that is at least 80% identical to SEQ ID NO: 8, and (ii) a separate passenger strand comprising or consisting of a sequence from 5 ' to 3 ' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) an active strand comprising or consisting of a sequence from 5 ' to 3' that is at least 80% identical to SEQ ID NO: 9, and (ii) a separate passenger strand comprising or consisting of a sequence from 5 ' to 3 ' that is at least 60% complementary to the active strand.
  • the passenger strand comprises a 5 ' terminal cap.
  • the 5 ' terminal cap is a lower alkylamine.
  • the synthetic miR-34 oligonucleotide comprises a sequence that is at least 80% identical to at least one of SEQ ID NO: 1-9. In some embodiments, the synthetic miR-34 oligonucleotide comprises a sequence that is at least 85% identical to at least one of SEQ ID NO: 1- 9. In some embodiments, the synthetic miR-34 oligonucleotide comprises a sequence that is at least 90% identical to at least one of SEQ ID NO: 1-9. In some embodiments, the synthetic miR-34 oligonucleotide comprises a sequence that is at least 95% identical to at least one of SEQ ID NO: 1- 9.
  • the synthetic miR-34 oligonucleotide comprises a sequence that is at least 100% identical to at least one of SEQ ID NO: 1-9. In some embodiments, the synthetic miR-34 oligonucleotide comprises a sequence that differs from at least one of SEQ ID NO: 1-9 by 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleobases.
  • the synthetic miR-34 oligonucleotide comprises a single
  • the synthetic miR-34 oligonucleotide comprises a hairpin polynucleotide.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises one or more of the following (i) a 5 ' terminal cap on the passenger strand; (ii) one or more sugar modifications in the first or last 1 to 6 residues of the passenger strand; or (iii) non-complementarity between one or more nucleotides in the last 1 to 5 residues at the 3 ' end of the passenger strand and the corresponding nucleotides of the active strand.
  • the synthetic miR-34 oligonucleotide is between 17 and 30 nucleotides in length and comprises (i) at least one modified nucleotide that blocks the 5 ' OH or phosphate at the 5 ' terminus of the passenger strand, wherein the at least one nucleotide modification is an NH 2 , biotin, an amine group, a lower alkylamine group, an acetyl group or 2 'oxygen-methyl (2'O-Me) modification; or (ii) at least one ribose modification to the active strand or the passenger strand selected from 2'F, 2' ⁇ ]3 ⁇ 4, 2'N3, 4'thio, or 2O-CH3.
  • the synthetic miR-34 oligonucleotide further comprises a complementary strand that is at least 60% complementary to the synthetic miR-34 oligonucleotide. In some embodiments, the complementary strand is not naturally occurring.
  • the complementary strand comprises (a) a chemical modification that improves uptake of the synthetic miR-34 oligonucleotide, (b) a chemical modification that enhances activity of the synthetic miR-34 oligonucleotide, (c) a chemical modification that enhances stability of the synthetic miR-34 oligonucleotide, (d) a chemical modification that inhibits uptake of the complementary strand, (e) a chemical modification that inhibits activity of the complementary strand.
  • the complementary strand comprises one or more nucleobases that are non-complementary with the synthetic miR-34 oligonucleotide.
  • PDCD1, PD1, PD-1) is a cell surface receptor that belongs to the immunoglobulin superfamily and is expressed on T cells and pro-B cells.
  • PD-1 is encoded by the PDCD1 gene.
  • PD-1 binds two ligands, PD-L1 and PD-L2.
  • PD-1 and its ligands play an important role in down regulating the immune system by preventing the activation of T-cells, which in turn can reduce autoimmunity and promote self-tolerance.
  • the inhibitory effect of PD-1 is accomplished through a dual mechanism of promoting apoptosis (programmed cell death) in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells (suppressor T cells).
  • PD-1 is a type I membrane protein of 268 amino acids.
  • PD-1 is a member of the extended CD28/CTLA-4 family of T cell regulators.
  • the protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail.
  • the intracellular tail contains two phosphorylation sites located in an immunoreceptor tyrosine-based inhibitory motif and an immunoreceptor tyrosine-based switch motif, which suggests that PD-1 negatively regulates TCR signals. This is consistent with binding of SHP-1 and SHP-2 phosphatases to the cytoplasmic tail of PD-1 upon ligand binding.
  • PD-1 is expressed on the surface of activated T cells, B cells, and macrophages, suggesting that compared to CTLA-4, PD-1 more broadly negatively regulates immune responses.
  • PDL1, PD-L1, and also known as CD274 - cluster of differentiation 274 or B7-H1 - B7 homolog 1 is encoded by the CD274 gene in humans.
  • PD-L1 is a 40 kDa type 1 transmembrane protein that has been speculated to play a major role in suppressing the immune system during particular events such as pregnancy, tissue allografts, autoimmune disease and other disease states such as hepatitis. Normally, the immune system reacts to foreign antigens where there is some accumulation in the lymph nodes or spleen which triggers a proliferation of antigen-specific CD8+ T cell.
  • PD-1 receptor / PD-Ll or B7.1 receptor /PD-Ll ligand complex transmits an inhibitory signal which reduces the proliferation of these CD8+ T cells at the lymph nodes and supplementary to that PD-1 is also able to control the accumulation of foreign antigen specific T cells in the lymph nodes through apoptosis which is further mediated by a lower regulation of the gene Bcl-2.
  • the methods use a PD-1 or PD-Ll inhibitor.
  • PD-1 or PD-Ll inhibitors include molecules that specifically interact with PD-1 or PD-Ll to inhibit immune system downregulation.
  • PD-1 or PD-Ll inhibitors are antibodies (e.g., commercially available antibodies, or other antibodies produced against PD-1 or PD-Ll - see Table 2 below for non-limiting examples), small molecule drugs, small interfering RNAs (siRNAs), short hairpin RNAs (shRNAs), antisense RNAs (such as locked nucleic acids, LNA), or interfering DNA molecules (DNAi).
  • Table 2 Selected PD-1 and PD-Ll inhibitors.
  • Radiotherapy e.g., radiation therapy, abbreviated RT, RTx, or XRT
  • RT radiation therapy
  • RTx RTx
  • XRT XRT
  • Radiotherapy is a therapy using ionizing radiation to control or kill malignant cells by damaging the DNA of cancerous tissue
  • radiotherapy is administered with the intent to cure, as an adjuvant, as a neoadjuvant, for therapeutic purposes, or for palliative purposes.
  • the purpose for which radiotherapy is administered is dependent on the tumor type, tumor location, tumor stage, and health of the individual.
  • radiation therapy is synergistic with another therapy (e.g., immunotherapy, chemotherapy, microRNA therapy), and is used before, during, and after the other therapy.
  • another therapy e.g., immunotherapy, chemotherapy, microRNA therapy
  • Ionizing radiation includes photon radiation (e.g. x-rays and gamma rays) or particle radiation (e.g. electrons, protons, neutrons, carbon ions, alpha particles, and beta particles).
  • photon radiation comes from a radioactive source such as cobalt, cesium, or a linear accelerator.
  • radiotherapy is delivered using external beam radiation therapy, brachytherapy, or systemic radioisotope therapy.
  • external beam radiation therapy is three-dimensional conformal radiation therapy (3D-CRT), intensity-modulated radiation therapy (IMRT), image-guided radiation therapy (IGRT), intensity modulated proton therapy (IMPT), stereotactic radiosurgery (SRS), stereotactic body radiation therapy (SBRT), intraoperative radiation therapy (IORT), or electromagnetic -guided radiation therapy.
  • brachytherapy radiation is interstitial radiation or intracavitary radiation.
  • brachytherapy is permanent or temporary.
  • temporary brachytherapy is high- dose rate (HDR) or low-dose rate (LDR)
  • An absorbed dose of radiation is measured in gray (Gy).
  • the typical dose for a solid epithelial tumor ranges from 40 to 80 Gy.
  • Preventive (adjuvant) doses are typically around 45-60 Gy in 1.8-2 Gy fractions (e.g., for breast, head, and neck cancers.)
  • radiation oncologists when selecting a dose, including whether the patient is receiving a combination therapy, patient comorbidities, whether radiation therapy is being administered before or after surgery or combination therapy, and the degree of success of the surgery or combination therapy.
  • Delivery parameters of a prescribed dose are determined during treatment planning (part of dosimetry).
  • treatment planning is performed on dedicated computers using specialized treatment planning software.
  • several angles or sources are used to sum to the total necessary dose.
  • a planner designs a treatment plan for an individual in need thereof.
  • the planner is a physician, radiation oncologist, or other health care professional.
  • the treatment plans calls for a uniform prescription dose of radiotherapy to the tumor.
  • a treatment plan is adapted from the approved clinical protocol.
  • a treatment plan is developed using established clinical trial protocols.
  • radiotherapy treatments are designed and implemented, for example, by radiation oncologists.
  • a PD-Ll expressing cancer in an individual in need thereof comprising: (a) identifying the cancer as a PD-Ll expressing cancer; and (b) providing a synthetic miR-34 oligonucleotide to the individual.
  • the methods further comprise providing a PD-1 or PD-Ll inhibitor to the individual.
  • the PD-1 or PD-Ll inhibitor is an antibody, small interfering RNA, or antisense RNA.
  • the synthetic miR-34 oligonucleotide and the PD-1 or PD- Ll inhibitor are synergistic.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-Ll inhibitor.
  • the methods further comprise providing radiotherapy to the individual.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-Ll inhibitor.
  • the cancer is a solid tumor.
  • the solid cancer is a melanoma, nasopharyngeal cancer,
  • the lung cancer is a non-small cell lung cancer (NSCLC).
  • the lung cancer is a small-cell lung cancer (SCLC).
  • the liver cancer is a hepatocellular carcinoma (HCC).
  • the cancer is a leukemia.
  • the cancer is a lymphoma.
  • the cancer as a PD-Ll expressing cancer comprises measuring the PD-Ll expression in a cancer cell from the individual and comparing to a control. In some embodiments, the PD-Ll expression is overexpressed compared to the control. In some embodiments, the methods further comprise selecting the individual having functional p53. In some embodiments, the synthetic miR-34 oligonucleotide is administered in a liposomal formulation. In some embodiments, T cell exhaustion is prevented or reduced.
  • the synthetic miR-34 oligonucleotide comprises: (a) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (b) a separate passenger strand that is at least 60% complementary to the active strand.
  • the passenger strand of the synthetic miR-34 oligonucleotide comprises a 5' terminal cap.
  • the 5' terminal cap is a lower alkylamine.
  • the 5' terminal cap is NH 2 -(CH 2 )6-0-.
  • the mature miRNA comprises: miR-34a (SEQ ID NO: 1), miR-34b (SEQ ID NO:2), miR-34c (SEQ ID NO:3), or a miR-34 consensus sequence (SEQ ID NO: 4).
  • the mature miRNA comprises: miR-449a (SEQ ID NO:5), miR-449b (SEQ ID NO:6), miR-449c (SEQ ID NO:7), or a miR-449 consensus sequence (SEQ ID NO: 8).
  • the mature miRNA comprises a miR-34/449 seed sequence (SEQ ID NO: 9).
  • a dosage amount is an amount of the synthetic miR-34
  • a dosing schedule is the schedule during which the synthetic miR-34 oligonucleotide is administered to an individual in need thereof.
  • the synthetic miR-34 oligonucleotide is continued until a clinical endpoint is met. In some embodiments, the synthetic miR-34 oligonucleotide is continued until disease progression or unacceptable toxicity occurs.
  • the synthetic miR-34 oligonucleotide is continued until achieving a pathological complete response (pCR) rate defined as the absence of the cancer being treated. In some embodiments, the synthetic miR-34 oligonucleotide is continued until partial or complete remission of the cancer. In some embodiments, the synthetic miR-34 oligonucleotide is continued until partial or complete remission of the liver cancer. In some embodiments, the synthetic miR-34 oligonucleotide reduces the size or number of the cancer tumor(s). In some embodiments, the synthetic miR-34 oligonucleotide prevents the cancer tumor(s) from increasing in size and/or number. In some embodiments, the synthetic miR-34 oligonucleotide prevents the cancer tumor(s) from metastasizing.
  • pCR pathological complete response
  • the synthetic miR-34 oligonucleotide is continued until the viral, bacterial, or parasitic/protozoan/metazoan infection is eliminated.
  • administration of the synthetic miR-34 oligonucleotide is not limited to any particular delivery system and includes, without limitation, parenteral (including subcutaneous, intravenous, intramedullary, intraarticular, intramuscular, or intraperitoneal injection), rectal, topical, transdermal, or oral (for example, in capsules, suspensions, or tablets) administration.
  • parenteral including subcutaneous, intravenous, intramedullary, intraarticular, intramuscular, or intraperitoneal injection
  • rectal topical
  • transdermal for example, in capsules, suspensions, or tablets
  • oral for example, in capsules, suspensions, or tablets
  • administration to an individual in need thereof occurs in a single dose or in repeat administrations, and in any of a variety of physiologically acceptable salt forms, or with an acceptable pharmaceutical carrier or additive as part of a pharmaceutical composition.
  • any suitable and physiological acceptable salt forms or standard pharmaceutical formulation techniques, dosages, and excipients are utilized.
  • effective dosages achieved in one animal are extrapolated for use in another animal, including humans, using conversion factors known in the art. See Table 3 for equivalent surface area dosage factors. Table 3: equivalent surface area dosage factors
  • the synthetic miR-34 oligonucleotide dosing amount or schedule follows clinically approved, or experimental, guidelines.
  • the dose of oligonucleotide is about 10, 20, 25, 30, 40, 50, 75, 100, 125, 150, 175, 200, 225, or 250 mg/m 2 per day.
  • the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5 daily doses over 5 days. In some embodiments, the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5, 6, or 7 daily doses over a single week (7 days). In some embodiments, the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 daily doses over 14 days. In some embodiments, the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 daily doses over 21 days. In some embodiments, the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5,
  • the synthetic miR-34 oligonucleotide is provided twice a week of a 21 or a 28 day cycle. In particular embodiments, the synthetic miR-34 oligonucleotide is provided on days 1, 4, 8, 11, 15 and 18 of a 21 day or 28 day cycle.
  • the synthetic miR-34 oligonucleotide is administered for: 2 weeks (total 14 days); 1 week with 1 week off (total 14 days); 3 consecutive weeks (total 21 days); 2 weeks with 1 week off (total 21 days); 1 week with 2 weeks off (total 21 days); 4 consecutive weeks (total 28 days); 3 consecutive weeks with 1 week off (total 28 days); 2 weeks with 2 weeks off (total 28 days); 1 week with 3 consecutive weeks off (total 28 days).
  • the synthetic miR-34 oligonucleotide is: administered on day 1 of a
  • the synthetic miR-34 oligonucleotide is administered once every 1, 2, 3, 4, 5, 6, 7, or 8 weeks. In some embodiments, the synthetic miR-34 oligonucleotide is administered for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 cycles.
  • the oligonucleotide to the individual; and (b) providing a PD-1 or PD-L1 inhibitor to the individual.
  • the PD-1 or PD-L1 inhibitor is an antibody, small interfering RNA, or antisense RNA.
  • the synthetic miR-34 oligonucleotide and the PD-1 or PD- Ll inhibitor are synergistic.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-L1 inhibitor.
  • the methods further comprise providing radiotherapy to the individual.
  • the cancer is a solid tumor.
  • the solid cancer is a melanoma, nasopharyngeal cancer,
  • the lung cancer is a non-small cell lung cancer (NSCLC).
  • the lung cancer is a small-cell lung cancer (SCLC).
  • the liver cancer is a hepatocellular carcinoma (HCC).
  • the cancer is a leukemia.
  • the cancer is a lymphoma.
  • identifying the cancer as a PD-L1 expressing cancer comprises measuring the PD-L1 expression in a cancer cell from the individual and comparing to a control. In some embodiments, the PD-L1 expression is overexpressed compared to the control. In some embodiments, the methods further comprise selecting the individual having functional p53. In some embodiments, the synthetic miR- 34 oligonucleotide is administered in a liposomal formulation. In some embodiments, T cell exhaustion is prevented or reduced.
  • the synthetic miR-34 oligonucleotide comprises: (a) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (b) a separate passenger strand that is at least 60% complementary to the active strand.
  • the passenger strand of the synthetic miR-34 oligonucleotide comprises a 5' terminal cap.
  • the 5' terminal cap is a lower alkylamine.
  • the 5' terminal cap is NH 2 -(CH 2 )6-0-.
  • the mature miRNA comprises: miR-34a (SEQ ID NO: 1), miR-34b (SEQ ID NO:2), miR-34c (SEQ ID NO:3), or a miR-34 consensus sequence (SEQ ID NO: 4).
  • the mature miRNA comprises: miR-449a (SEQ ID NO:5), miR-449b (SEQ ID NO:6), miR-449c (SEQ ID N0:7), or a miR-449 consensus sequence (SEQ ID NO: 8).
  • the mature miRNA comprises a miR-34/449 seed sequence (SEQ ID NO: 9).
  • a method of treating an individual suffering from a chronic infectious disease comprising: (a) providing a synthetic miR-34 oligonucleotide to the individual; and (b) providing a PD-1 or PD-L1 inhibitor to the individual.
  • the PD-1 or PD-L1 inhibitor is an antibody, small interfering RNA, or antisense RNA.
  • the synthetic miR-34 oligonucleotide and the PD-1 or PD-L1 inhibitor are synergistic.
  • the synthetic miR-34 oligonucleotide is provided before the PD-1 or PD-L1 inhibitor.
  • the infectious disease is a persistent viral infection.
  • the viral infection is human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), rhinovirus (common cold), herpes simplex virus (HSV), or respiratory syncytial virus (RSV).
  • the infectious disease is a persistent bacterial infection.
  • the bacterial infection is Helicobacter pylori, Mycobacterium tuberculosis, Mycobacterium leprae, or Chlamydia trachomatis.
  • the infectious disease is the result of infection by a parasite, protozoan, or metazoan.
  • the parasite, protozoan, or metazoan is Schistosoma mansoni, Taenia crassiceps, or Leishmania mexicana.
  • the methods further comprise selecting the individual having functional p53.
  • the synthetic miR-34 oligonucleotide is administered in a liposomal formulation.
  • the synthetic miR-34 oligonucleotide comprises: (a) an active strand comprising a sequence at least 80% identical to a mature miRNA; and (b) a separate passenger strand that is at least 60% complementary to the active strand.
  • the passenger strand of the synthetic miR-34 oligonucleotide comprises a 5' terminal cap.
  • the 5' terminal cap is a lower alkylamine.
  • the 5' terminal cap is NH 2 -(CH 2 )6-0-.
  • the mature miRNA comprises: miR-34a (SEQ ID NO: 1), miR-34b (SEQ ID NO:2), miR-34c (SEQ ID NO:3), or a miR-34 consensus sequence (SEQ ID NO:4).
  • the mature miRNA comprises: miR-449a (SEQ ID NO:5), miR- 449b (SEQ ID NO:6), miR-449c (SEQ ID NO:7), or a miR-449 consensus sequence (SEQ ID NO: 8).
  • the mature miRNA comprises a miR-34/449 seed sequence (SEQ ID NO:9).
  • the combination therapy is not limited to a particular course or regimen and are employed separately or in conjunction with other therapeutic modalities (e.g., chemotherapy or radiotherapy).
  • a combination therapy includes additional therapies (e.g., pharmaceutical, radiation, and the like) beyond a PD-1 or PD-Ll inhibitor and oligonucleotide.
  • additional therapies e.g., pharmaceutical, radiation, and the like
  • the compositions and combinations described herein are used as an adjuvant therapy (e.g., when combined with surgery).
  • the individual is also treated by surgical resection, percutaneous ethanol or acetic acid injection, transcatheter arterial chemoembolization, radiofrequency ablation, laser ablation, cryoablation, focused external beam radiation stereotactic radiotherapy, selective internal radiation therapy, intraarterial iodine- 131— lipiodol administration, and/or high intensity focused ultrasound.
  • the oligonucleotide is an additional therapeutic agent.
  • the additional therapeutic agent is a PD-1 or PD-Ll inhibitor, radiation, chemotherapy, an additional pharmaceutical agent, or a combination thereof.
  • a dosage amount is an amount of the synthetic miR-34
  • a dosing schedule is the schedule during which the synthetic miR-34 oligonucleotide or additional therapeutic agent is administered to an individual in need thereof.
  • the combination therapy is continued until a clinical endpoint is met. In some embodiments, the combination therapy is continued until disease progression or unacceptable toxicity occurs.
  • the combination therapy is continued until achieving a pathological complete response (pCR) rate defined as the absence of the cancer being treated. In some embodiments, the combination therapy is continued until partial or complete remission of the cancer. In some embodiments, the combination therapy is continued until partial or complete remission of the liver cancer. In some embodiments, the combination therapy reduces the size or number of the cancer tumor(s). In some embodiments, the combination therapy prevents the cancer tumor(s) from increasing in size or number. In some embodiments, the combination therapy prevents the cancer tumor(s) from metastasizing.
  • pCR pathological complete response
  • the combination therapy is continued until the viral, bacterial, or parasitic/protozoan/metazoan infection is eliminated.
  • administration of the combination therapy is not limited to any particular delivery system and includes, without limitation, parenteral (including subcutaneous, intravenous, intramedullary, intraarticular, intramuscular, or intraperitoneal injection), rectal, topical, transdermal, or oral (for example, in capsules, suspensions, or tablets) administration.
  • parenteral including subcutaneous, intravenous, intramedullary, intraarticular, intramuscular, or intraperitoneal injection
  • rectal topical, transdermal, or oral (for example, in capsules, suspensions, or tablets) administration.
  • administration to an individual in need thereof occurs in a single dose or in repeat administrations, and in any of a variety of physiologically acceptable salt forms, or with an acceptable pharmaceutical carrier or additive as part of a pharmaceutical composition.
  • any suitable and physiological acceptable salt forms or standard pharmaceutical formulation techniques, dosages, and excipients are utilized.
  • effective dosages achieved in one animal are extrapolated for use in another animal, including humans, using conversion factors known in the art. See Table 3 for equivalent surface area dosage factors.
  • the synthetic miR-34 oligonucleotide dosing amount or schedule follows clinically approved, or experimental, guidelines.
  • the dose of oligonucleotide is about 10, 20, 25, 30, 40, 50, 75, 100, 125, 150, 175, 200, 225, or 250 mg/m 2 per day.
  • the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5 daily doses over 5 days. In some embodiments, the oligonucleotide is administered to the individual in 1, 2, 3, 4, 5, 6, or 7 daily doses over a single week (7 days). In some embodiments, the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, or 14 daily doses over 14 days. In some embodiments, the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 daily doses over 21 days. In some embodiments, the synthetic miR-34 oligonucleotide is administered to the individual in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 daily doses over 28 days.
  • the synthetic miR-34 oligonucleotide is provided twice a week of a 21 or a 28 day cycle. In particular embodiments, the synthetic miR-34 oligonucleotide is provided on days 1, 4, 8, 1 1, 15 and 18 of a 21 day or 28 day cycle.
  • the synthetic miR-34 oligonucleotide is administered for: 2 weeks (total 14 days); 1 week with 1 week off (total 14 days); 3 consecutive weeks (total 21 days); 2 weeks with 1 week off (total 21 days); 1 week with 2 weeks off (total 21 days); 4 consecutive weeks (total 28 days); 3 consecutive weeks with 1 week off (total 28 days); 2 weeks with 2 weeks off (total 28 days); 1 week with 3 consecutive weeks off (total 28 days).
  • the synthetic miR-34 oligonucleotide is: administered on day 1 of a 7, 14, 21 or 28 day cycle; administered on days 1 and 15 of a 21 or 28 day cycle; administered on days 1, 8, and 15 of a 21 or 28 day cycle; or administered on days 1, 2, 8, and 15 of a 21 or 28 day cycle.
  • the synthetic miR-34 oligonucleotide is administered once every 1 , 2, 3, 4, 5, 6, 7, or 8 weeks.
  • the synthetic miR-34 oligonucleotide (and hence the combination therapy) is administered for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, or 12 cycles.
  • a dose of radiotherapy is 40 to 80 Gy.
  • the dose of radiotherapy is divided into fractions. In some embodiments the fraction is 1.8 to 2 Gy. In some embodiments, a fraction of radiotherapy is administered to the individual once a day. In some embodiments, a fraction of radiotherapy is administered to the individual multiple times a day. In some embodiments, radiotherapy is administered to the individual for five, six, seven, or eight weeks. In some embodiments, the dose of radiotherapy is 45 to 60 Gy in 1.8 to 2 Gy fractions. In some embodiments, the dose of radiotherapy is determined by a physician or radiation oncologist. In some embodiments, the radiotherapy is administered before, during, or after surgery. In some embodiments, the radiotherapy is administered before or after combination therapy.
  • a dosage amount of the additional therapeutic agent has a specific ratio of the components of the combination therapy (e.g., PD-1 or PD-Ll inhibitor: synthetic miR- 34 oligonucleotide).
  • the dose of the synthetic miR-34 oligonucleotide is set, within a therapeutically effective range, based upon a selected ratio and dose of the additional therapeutic agent (e.g. PD-1 or PD-Ll inhibitor).
  • the ratio of the components of the combination therapy are determined over different periods of time.
  • the ratio of PD-1 or PD-Ll inhibitor: synthetic miR-34 oligonucleotide is determined for a single day, a single week, 14 days, 21 days, or 28 days.
  • dosing or administration of a PD-1 or PD-Ll inhibitor will vary depending upon the specific PD-1 or PD-Ll inhibitor used. In some embodiments, for clinically approved PD-1 or PD-Ll inhibitors, dosing or administration is adapted from the approved clinical protocol or experimental guidelines. In some embodiments, for new PD-1 or PD-Ll inhibitors, dosing or administration is developed using established clinical trial protocols or experimental guidelines.
  • the PD-1 or PD-Ll inhibitor schedule follows clinically approved or experimental guidelines.
  • the synthetic miR-34 oligonucleotide is administered prior to the PD-1 or PD-Ll inhibitor, concurrently with the PD-1 or PD-Ll inhibitor, after the PD-1 or PD-Ll inhibitor, or a combination thereof.
  • the synthetic miR-34 oligonucleotide is administered intravenously.
  • the synthetic miR-34 oligonucleotide is administered systemically or regionally.
  • the combination of the synthetic miR-34 oligonucleotide and PD-1 or PD-Ll inhibitor is used as an adjuvant, neoadjuvant, concomitant, concurrent, or palliative therapy.
  • the combination of the synthetic miR-34 oligonucleotide and PD-1 or PD-L1 inhibitor is used as a first line therapy, second line therapy, or crossover therapy.
  • the therapeutically effective dose of PD-1 or PD-L1 inhibitor is reduced through combination with the synthetic miR-34 oligonucleotide.
  • the weekly or monthly dose of PD-1 or PD-L1 inhibitor is reduced by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more relative to the maximum recommended dose or the maximum tolerated dose.
  • the PD-1 or PD-L1 inhibitor is administered at an effective dose that at least 50%, 60%, 70%, 80%, 90% or more below the dose needed to be effective in the absence of the synthetic miR-34 oligonucleotide administration.
  • the IC50 of the PD-1 or PD-L1 inhibitor is reduced by at least 4-, 5-, 10-, 20-, 30-, 40-, 50-, or 100-fold relative to the IC50 in the absence of the synthetic miR-34 oligonucleotide.
  • combination index (CI) values are used to quantify the effects of various combination therapies (e.g., combinations of PD-1 or PD-L1 inhibitor and oligonucleotides).
  • the combination therapy exhibits synergy, for example, as quantified by a combination index (CI) ⁇ 1.
  • the combination index (CI) is less than about 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, or 0.20.
  • CI values are calculated based on linear regression trendlines using the CompuSyn software (ComboSyn Inc., Paramus, NJ), whereby the hyperbolic and sigmoidal dose-effect curves are transformed into a linear form.
  • the combination therapy (e.g., the ratio of PD-1 or PD-L1 inhibitoroligonucleotide) exhibits a CKl. In some embodiments, the combination therapy has a CI
  • CI is used in conjunction with other parameters, for example CI ⁇ 0.60, Dose
  • the CI ⁇ 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, or 0.50 (and optionally in combination with other parameters, for example DRI > 2, and Fa > 65%).
  • CI values cannot, practically speaking, be calculated in a human because that would require providing the therapy in serial dilution (e.g., generally be considered unethical). Therefore, in some embodiments, for human therapy, the CI value is considered to be the CI value of a reference system - a non-limiting example being a cell assay or an animal model.
  • Lung cancer cell lines A549, H460, H1299 were obtained from the American Type Culture Collection (ATCC; Manassas, VA, USA) and validated by MD Anderson's Characterized Cell Line Core facility by short-tandem-repeat (STR) DNA fingerprinting with an AmpFlSTR Identifiler PCR Amplification kit (Applied Biosystems #4322288) according to the manufacturer's recommendations. Cells were cultured in RPMI supplemented with 10% fetal bovine serum at 37°C in a humidified 5% CO 2 incubator.
  • ATCC American Type Culture Collection
  • STR short-tandem-repeat
  • HCT116 p53 v HCT116 p53 v
  • HCT116 p53 + + and H460 p53-knockdown cells were treated for 24 hours with 10 ⁇ nutlin 3 (Sigma) to stabilize p53 via MDM2 inhibition.
  • H1299-p53 cells were treated with 5 ⁇
  • the vectors pRS-shRNAp53 and an shRNA scramble control were transiently transfected with a pPACKHl HIV Lentivector Packaging Kit (System Biosciences) into 293TN cells using Lipofectamine 2000 and Plus reagents (both from Life Technologies, Carlsbad, CA, USA). Viral supernatant was collected 3 days after transfection and mixed with PEG-it Virus Precipitation Solution (System Biosciences) overnight at 4°C. H460 cells were infected and incubated with the viral particles supplemented with TransDux (System Biosciences) overnight at 37°C. Puromycin (1 ⁇ g/mL) was used to select and maintain p53-knockdown in H460 cells. Stable repression of p53 was verified by western blotting.
  • Binding sites for miR-34a in the PD-L1 3' UTR were identified by using the target prediction databases miRNA body map (https://www.mirnabodymap.org/; Ghent University, Belgium). These databases compare predicted targets from mirBase release 14, TargetScan 5.1, miRDB 3.0, MicroCosm v5, DIANA 3.0, TarBase v.5c, PITA catalog v6, RNA22 (March 2007), and miRecords v2. Transfection
  • Pre-miR-34a and negative controls were reverse- transfected into lung cancer cell lines with Lipofectamine 2000 (Life Technologies) at a final concentration of 100 nM.
  • H1299 cells were seeded into 96-well dishes at 4 x 10 4 cells/well.
  • Cells were transfected with miR-34a mimics or a scrambled control miRNA (100 nM) together with expression vectors encoding the luciferase gene fused to the PD-L1 3 ' UTR that is either wild type [wt] or contains a mutated miR-34 binding site (5-bp deletion; SwitchGear Genomics, Carlsbad, CA, USA).
  • a mutated miR-34 binding site (5-bp deletion; SwitchGear Genomics, Carlsbad, CA, USA).
  • Firefly luciferase activity was measured sequentially in luciferase assays (SwitchGear Genomics) using a Fluostar Optima plate reader (BMG Lab Technologies GmbH, Inc, Durham, NC, USA). Three independent experiments were performed, and values are shown as means ⁇ standard error of the mean (SEM).
  • FFPE paraffin-embedded NSCLC tissue samples, 4-5 um thick, from patients were mounted on Histogrip-treated microscope slides, dried at 37°C, and baked for 2-4 hours at 60°C. The slides were deparaffinized at 80°C for 30 minutes and then hydrated by dipping the slides into xylene, ethanol and phosphate buffered saline (PBS). A 15 ⁇ g/mL solution of pre- warmed (37°C) proteinase-K (miRCURY LNA microRNA ISH Buffer Set; Exiqon; cat# 90000) was applied and slides were incubated at 37°C for 20 minutes. Then, slides were dehydrated and dried.
  • pre- warmed (37°C) proteinase-K miRCURY LNA microRNA ISH Buffer Set; Exiqon; cat# 90000
  • Tissues were blocked for 15 minutes and incubated for 1 hour at room temperature with anti-DIG antibody alkaline phosphatase (AP) conjugate in a 1 : 1600 dilution (Roche Life Sciences, cat# 11093274910). After slides were rinsed in PBS-Tween20, freshly prepared AP substrate (NBT/BCIP; Roche Life Sciences) was applied. Slides were incubated for 2 hours at 30°C, protected from light. Tissue slides were rinsed in KTBT (50 mM Tris-HCl, 150 mM NaCl, 10 mM KC1) and nuclease-free water and counterstained with fast red counter stain (American Master Tech; cat# STNFR).
  • KTBT 50 mM Tris-HCl, 150 mM NaCl, 10 mM KC1
  • mice All mouse studies were approved by the Institutional Animal Care and Use Committee (IACUC) of The University of Texas MD Anderson Cancer Center before their initiation; animal care was provided according to IACUC standards, and all mice had been bred and were maintained in a pathogen-free mouse colony.
  • IACUC Institutional Animal Care and Use Committee
  • mice To create the tumors, syngeneic male 129/Sv mice three to four months of age were injected subcutaneously in the right flank with 10 6 344SQ murine lung adenocarcinoma cells (a lung cancer cell line derived from a spontaneous subcutaneous metastatic lesion in p53R172HAg/+K-rasLAl/+ mice) (12 mice per group).
  • mice were randomly assigned to one of the following groups such that each group has the same average tumor volume (12 mice per group): Control (no treatment); MRX34 (administered peritumorally three times a week at a dose level of 1 mg per kg mouse bodyweight; 8 total injections; Mirna Therapeutics, Austin, TX); radiotherapy (RT; 6 Gy once a day for 3 days, total 18 Gy); or MRX34 + RT (dose levels and regimens as described above). For the combination therapy group, MRX34 was given 1-2 hours before RT.
  • mice were immobilized in a jig, and tumors centered within a 3-cm-diameter circle were irradiated using a 137 Cesium device (dose rate 4 Gy/min). Tumor growth was assessed 2-3 times a week by
  • CD45 staining was used to distinguish immune cells from non-immune cells (tumor and other stromal cells) in tumor tissues, and cells quantified were CD8 + T cells, CD4 + T cells, macrophages (F4/80), myeloid-derived suppressor cells (MDSCs) (CD1 lb + Grl + ) and T- regulatory T cells (Tregs) (CD4 + CD25 + Foxp3 + ).
  • tumor cells were collected for PD- Ll analysis. Samples were analyzed with an LSRII Flow Cytometer (BD) and data analyzed with FlowJo Software (ThreeStar). Isotype control was used as negative control. The expression of each marker in an untreated control group was considered the basal expression level.
  • TCGA LUAD Adenocarcinoma
  • miR-34a levels were compared between p53 mutant tumors and p53 wt tumors with t tests, as miR-34a levels were normally distributed P>0.05 from the Shapiro Wilk normality test).
  • a box-and-whisker plot in which the box plot represents the first (lower bound) and the third (upper bound) quartiles, and the whiskers represent 1.5 times the interquartile range was used to visualize data for these comparisons (log2(x+l)).
  • their potential relationship with survival was analyzed as follows. Patients were first grouped into percentiles according to mRNA/miRNA expression.
  • miR-34 family members are well-characterized effector molecules that are transcriptionally induced by p53 and p53 regulates tumor cell recognition by NK cells via miR-34a.
  • miR-34a, miR-34b, and mi-R-34c were expressed at elevated levels in cells that express wild-type p53 (HCTl 16 p53 + + , p53-inducible H1299 treated with PoA, H460 transfected with scr shRNA) relative to their controls (HCTl 16 p53 " and p53-inducible H1299 in the absence of PoA), (FIGS. 1A, 1C).
  • NSCLC non-small cell lung cancer
  • the p53/miR-34a pair was contrasted against the two groups linked to a positive association: high p53/high miR-34a and low p53/low miR-34a.
  • miR-34a Directly Represses PD-Ll in NSCLC cell lines
  • PD-Ll expression in A549, H460, and H1299 cells transfected with miR-34a was analyzed by western blotting. As shown in FIGS. 3B-G, enforced overexpression of miR-34a suppressed the expression of PD-Ll protein compared with a scrambled control. In addition, enforced overexpression of miR-34b or miR-34c suppressed the expression of PD-Ll protein compared with a scrambled control (FIGS. 3H-J).
  • H1299 were co-transfected with miR-34a, miR-34b, or miR-34c mimics and a reporter vector encoding the luciferase gene that is fused to the 3' UTR of the PD-L1 gene (luc-PDLl).
  • luciferase activity was reduced in cells transfected with miR-34 and the luc-PD-Ll construct compared with scrambled controls.
  • MRX34 a liposomal nanoparticle loaded with miR-34a mimics
  • qRT-PCR quantitative real-time polymerase chain reaction
  • Subcutaneous tumors were created by inoculating 1 x 10 6 344SQ cells derived from a spontaneous subcutaneous lung metastasis from a p53R172HAg/+K-rasLAl/+ mouse into the right leg of each syngeneic 129Sv/Ev mouse.
  • mice were randomly assigned to one of four groups: control; MRX34 only; RT; and MRX34 plus RT.
  • the formulation was given as subcutaneous injections at a dose of 1 mg/kg (total of 8 injections), and local irradiation was given to a total dose of 18 Gy, in 6-Gy fractions given over 3 days starting when tumors were 8 mm in diameter.
  • MRX34 was given 1 hour before radiation.
  • MRX34 in combination with RT also counteracted the effects of RT on macrophages (FIGS. 5K, 5L, 50) and Tregs (FIGS. 5P, 5Q, 5T), both of which were lower in the combination relative to RT alone.
  • Example 2 Study to Evaluate the Effectiveness, Safety, and Tolerability of MRX34 and the Combination of MRX34 plus Atezolizumab in Subjects with Bladder Cancer
  • the first part of the study is a dose escalation phase designed to establish the safety of MRX34 at different dose levels for individuals with bladder cancer.
  • the second part of the study is the expansion phase designed to generate additional clinical data at specific doses and adds a second cohort to compare the efficacy of MRX34 plus atezolizumab in the treatment of bladder cancer.
  • 1200 mg of Atezolizumab is administered by intravenous infusion on day 1 of each 21 day cycle.
  • MRX34 is administered daily for the first five days of a 21 day cycle.
  • the dosage of MRX34 in the expansion phase is the dosage determined in the dose escalation phase.
  • Primary outcome measures include: 1) safety and tolerability of MRX34 as evaluated by incidence of adverse events, serious adverse events, adverse events leading to discontinuation, deaths, and clinical laboratory test abnormalities; 2) objective response rate during the expansion phase of MRX34; 3) safety and tolerability of MRX34 plus Atezolizumab is evaluated by incidence of adverse events, serious adverse events, adverse events leading to discontinuation, deaths, and clinical laboratory test abnormalities; and 4) objective response rate during MRX34 plus
  • Example 3 Clinical Trial of a MRX34 in combination with radiotherapy as a Treatment for Glioblastoma
  • the first part of the study is a dose escalation phase designed to establish the safety of MRX34 at different dose levels for individuals with glioblastoma.
  • the second part of the study is the expansion phase designed to generate additional clinical data at specific doses and adds a second cohort to compare the efficacy of MRX34 plus radiotherapy in the treatment of glioblastoma.
  • MRX34 is administered daily for the first five days of a 21 day cycle.
  • the dosage of MRX34 in the expansion phase is the dosage determined in the dose escalation phase.
  • Individuals undergo once-a-day (QD) radiation treatments 5 days a week for 6 weeks, the indivdual receiving 60 Gy of radiation.
  • QD once-a-day
  • the 21-day cycle of MRX34 repeats for up to 18 months in the absence of disease progression or unacceptable toxicity.
  • Primary outcome measures include: 1) safety and tolerability of MRX34 as evaluated by incidence of adverse events, serious adverse events, adverse events leading to discontinuation, deaths, and clinical laboratory test abnormalities; 2) objective response rate during the expansion phase of MRX34; 3) safety and tolerability of MRX34 plus Atezolizumab is evaluated by incidence of adverse events, serious adverse events, adverse events leading to discontinuation, deaths, and clinical laboratory test abnormalities; and 4) objective response rate during MRX34 plus

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Abstract

L'invention concerne une méthode de traitement d'un cancer exprimant PD-L1 chez un sujet en ayant besoin par administration d'un oligonucléotide miR-34 de synthèse ou d'une combinaison associant un oligonucléotide miR-34 de synthèse et un ligand PD-L1 ou un inhibiteur de PD-1. L'invention concerne également une méthode de traitement d'une maladie infectieuse chronique chez un sujet en ayant besoin par administration d'un oligonucléotide miR-34 de synthèse et d'un ligand PD-L1 ou d'un inhibiteur de PD-1.
PCT/US2016/025410 2015-04-03 2016-03-31 Immunothérapie faisant intervenir le microarn-34 WO2016161196A1 (fr)

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