Vista modulators for diagnosis and treatment of cancer

Abstract

The present disclosure relates to compositions and therapeutic methods for activating an immune response in a patient in need thereof. In a preferred embodiment, the subject methods and compositions are able to antagonize the activity of VISTA, a naturally occurring “checkpoint” protein which contributes to immune tolerance, optionally in combination with an antagonist of a second checkpoint pathway such as PD-1. For example, such methods and compositions may be suitable for preventing and treating colon cancer or another cancer. An exemplary VISTA antagonist, specifically, an anti-VISTA antibody, is demonstrated herein to activate an immune response against cancer cells in vitro and in vivo, thereby conferring protective anti-tumor immunity which decreased tumor burden. Additionally, an additive benefit was observed when a VISTA antagonist was used in combination with a second checkpoint protein antagonist, specifically, an antibody against PD-1 ligand (PD-L1).

1 - 130 . (canceled) 
     
     
         131 . A method for treating a subject having a condition that would benefit from upregulation of an immune response comprising: administering (i) administering a VISTA antagonist, thereby inhibiting the VISTA-mediated suppression of immune responses, such that a condition that would benefit from upregulation of an immune response is treated and/or removing immune cells from the subject, contacting said immune cells in vitro with a VISTA antagonist, thereby in vitro-stimulating said immune cells, and reintroducing said in vitro-stimulated immune cells into said subject and/or (iii) removing immune cells from the subject, transfecting said immune cells with a nucleic acid molecule encoding a form of VISTA that cannot bind its natural binding partner(s), such that the cells express all or a portion of the VISTA molecule, and reintroducing said transfected cells into the subject, whereby said transfected cells prevent a VISTA-mediated an inhibitory signal to immune cells, and thereby upregulating an immune response. And/or transfecting cancer cells from said subject with a nucleic acid molecule that inhibits VISTA activity, whereby said transfected cells prevent a VISTA-mediated an inhibitory signals to immune cells, removing immune cells from the subject, contacting said transfected cells with said immune cells, thereby upregulating an immune response against said cancer, and reintroducing said in vitro-stimulated immune cells into said subject. 
     
     
         132 . The method of  claim 131  wherein the condition is cancer or an infectious disease. 
     
     
         133 . The method of  claim 131 , wherein said immune cells in (ii) or (iii) comprise CD4+ T cells and/or CD8+ T cells, and the process optionally includes expanding said population of immune cells in vitro. 
     
     
         134 . A method for treating cancer or an infectious disorder in a subject comprising: transfecting cancer cells from said subject with a nucleic acid molecule that inhibits VISTA (PD-L3) activity, whereby said transfected cells prevent a VISTA-mediated an inhibitory signal to immune cells, and thereby upregulating an immune response against said cancer or infectious disorder, and wherein such which method optionally includes further transfecting said cancer cells with one or more additional polypeptides which effect immune system costimulation. 
     
     
         135 . The method of  claim 134 , wherein such additional polypeptides are selected from B7-1, B7-2, an MHC class I a chain polypeptide, a beta2 microglobulin polypeptide, an MHC class II .alpha. chain polypeptide, and/or an MHC class II .beta. chain polypeptide, thereby causing said cancer cells to express MHC class I or MHC class II polypeptides on the cell surface. 
     
     
         136 . The method of  claim 135  which further includes introducing in vivo or ex vivo siRNA or siRNA-encoding gene which inhibits expression of an MHC class II-associated polypeptide, optionally the invariant chain, thereby promoting presentation of tumor associated antigens. 
     
     
         137 . he method of  claim 131 , wherein said nucleic acid molecule that inhibits VISTA activity comprises one or more of: nucleic acid molecules which are antisense to VISTA, which encode non-activating anti-VISTA antibodies or the variable region thereof, or which encode a form of VISTA that cannot bind its natural binding partner(s). 
     
     
         138 . The method of  claim 131 , further comprising contacting said immune cells in vitro with one or more cancer cells of said subject. 
     
     
         139 . The method of  claim 131 , wherein said in vitro-stimulated immune cells are reintroduced into said subject at the site of said cancer or into a blood vessel that supplies blood to said cancer. 
     
     
         140 . The method of treating cancer or infection of  claim 134 , which further includes activating anti-cancer immunity or immunity against an infectious agent infected cells in a subject comprising: administering one or more cancer or infectious agent antigens and a VISTA antagonist to said subject. 
     
     
         141 . The method of  claim 131 , wherein said VISTA antagonist is an agent that inhibits the interaction between VISTA and its natural binding partner(s) on immune cells of the subject. 
     
     
         142 . The method of  claim 131 , wherein said VISTA antagonist is selected from an anti-VISTA antibody, an antibody against a VISTA natural binding partner, a small molecule inhibitor of VISTA signaling, a small molecule inhibitor of the interaction between VISTA and its natural binding partner(s) a VISTA fragment a form of VISTA that blocks the VISTA interaction with immune cells or a fragment thereof or a soluble form of VISTA that does not bind to Fc receptors on antigen presenting cells, a soluble form or fragment of a VISTA natural binding partner, an siRNA molecule that downregulates the expression of VISTA and/or which downregulates the expression of an mRNA transcribed from a VISTA DNA or an siRNA that downregulates the expression of a VISTA natural binding partner. 
     
     
         143 . The method of  claim 142 , wherein said siRNA molecule comprises a subsequence of the nucleic acid sequence of SEQ ID NO: 1 or 3, preferably a siRNA molecule that comprises the nucleic acid sequence of one or more of SEQ ID NOs: 38-67 or said siRNA molecule targets the ORF or UTR region of VISTA. 
     
     
         144 . The method of  claim 134 , wherein the cancer is colorectal cancer, sarcoma, melanoma, lymphoma, leukemia, neuroblastoma, or carcinoma. 
     
     
         145 . The method of  claim 131 , further comprising administering a PD-1 antagonist, optionally an anti-PD-1 antibody, an anti-PD-L1 antibody, an siRNA targeting expression of PD-1, an siRNA targeting the expression of PD-L1, or a peptide, fragment, dominant negative form, or soluble form of PD-1 or PD-L1 or a CTLA-4 antagonist, optionally an anti-CTLA-4 antibody, an siRNA targeting the expression of CTLA-4, or a peptide, fragment, dominant negative, or soluble form of CTLA-4 or a B7-H4 antagonist, optionally an anti-B7-H4 antibody, an siRNA targeting the expression of B7-H4, or a peptide, fragment, dominant negative, or soluble form of B7-H4 or a combination of an of the foregoing. 
     
     
         146 . The method of  claim 131 , further comprising determining the level of expression of VISTA in a sample from said subject. 
     
     
         147 . The method of  claim 146 , wherein said sample from said subject comprises one or more of the cells of said cancer, the tumor microenvironment, or peripheral blood and/or comprises one or more of Tregs, MDSCs, and/or tolerogenic DCs and/or comprises a tumor biopsy or sample comprising tumor cells. 
     
     
         148 . The method of  claim 146 , wherein an elevated level of VISTA expression is detected in said patient sample prior to the administration of said VISTA antagonist. 
     
     
         149 . The method of  claim 131 , further comprising administering one or more additional agents that upregulate immune responses. 
     
     
         150 . The method of  claim 149 , wherein said one or more additional agents comprise forms of B7 family members that transduce signals via costimulatory receptors thereby further augmenting the immune response or comprise one or more cytokines, adjuvants, stimulatory forms of costimulatory molecules or their ligands. 
     
     
         151 . The method of  claim 131 , which is effected in combination another cancer treatment, optionally radiotherapy, chemotherapy, and/or administration of an anti-cancer biologic, thereby increasing the efficacy of said other anti-cancer treatment. 
     
     
         152 . The method of any one of  claim 131 , wherein the disease is a cancer selected from Acanthoma, Acinic cell carcinoma, Acoustic neuroma, Acral lentiginous melanoma, Acrospiroma, Acute eosinophilic leukemia, Acute lymphoblastic leukemia, Acute megakaryoblastic leukemia, Acute monocytic leukemia, Acute myeloblastic leukemia with maturation, Acute myeloid dendritic cell leukemia, Acute myeloid leukemia, Acute promyelocytic leukemia, Adamantinoma, Adenocarcinoma, Adenoid cystic carcinoma, Adenoma, Adenomatoid odontogenic tumor, Adrenocortical carcinoma, Adult T-cell leukemia, Aggressive NK-cell leukemia, AIDS-Related Cancers, AIDS-related lymphoma, Alveolar soft part sarcoma, Ameloblastic fibroma, Anal cancer, Anaplastic large cell lymphoma, Anaplastic thyroid cancer, Angioimmunoblastic T-cell lymphoma, Angiomyolipoma, Angiosarcoma, Appendix cancer, Astrocytoma, Atypical teratoid rhabdoid tumor, Basal cell carcinoma, Basal-like carcinoma, B-cell leukemia, B-cell lymphoma, Bellini duct carcinoma, Biliary tract cancer, Bladder cancer, Blastoma, Bone Cancer, Bone tumor, Brain Stem Glioma, Brain Tumor, Breast Cancer, Brenner tumor, Bronchial Tumor, Bronchioloalveolar carcinoma, Brown tumor, Burkitt's lymphoma, Cancer of Unknown Primary Site, Carcinoid Tumor, Carcinoma, Carcinoma in situ, Carcinoma of the penis, Carcinoma of Unknown Primary Site, Carcinosarcoma, Castleman's Disease, Central Nervous System Embryonal Tumor, Cerebellar Astrocytoma, Cerebral Astrocytoma, Cervical Cancer, Cholangiocarcinoma, Chondroma, Chondrosarcoma, Chordoma, Choriocarcinoma, Choroid plexus papilloma, Chronic Lymphocytic Leukemia, Chronic monocytic leukemia, Chronic myelogenous leukemia, Chronic Myeloproliferative Disorder, Chronic neutrophilic leukemia, Clear-cell tumor, Colon Cancer, Colorectal cancer, Craniopharyngioma, Cutaneous T-cell lymphoma, Degos disease, Dermatofibrosarcoma protuberans, Dermoid cyst, Desmoplastic small round cell tumor, Diffuse large B cell lymphoma, Dysembryoplastic neuroepithelial tumor, Embryonal carcinoma, Endodermal sinus tumor, Endometrial cancer, Endometrial Uterine Cancer, Endometrioid tumor, Enteropathy-associated T-cell lymphoma, Ependymoblastoma, Ependymoma, Epithelioid sarcoma, Erythroleukemia, Esophageal cancer, Esthesioneuroblastoma, Ewing Family of Tumor, Ewing Family Sarcoma, Ewing's sarcoma, Extracranial Germ Cell Tumor, Extragonadal Germ Cell Tumor, Extrahepatic Bile Duct Cancer, Extramammary Paget's disease, Fallopian tube cancer, Fetus in fetu, Fibroma, Fibrosarcoma, Follicular lymphoma, Follicular thyroid cancer, Gallbladder Cancer, Gallbladder cancer, Ganglioglioma, Ganglioneuroma, Gastric Cancer, Gastric lymphoma, Gastrointestinal cancer, Gastrointestinal Carcinoid Tumor, Gastrointestinal Stromal Tumor, Gastrointestinal stromal tumor, Germ cell tumor, Germinoma, Gestational choriocarcinoma, Gestational Trophoblastic Tumor, Giant cell tumor of bone, Glioblastoma multiforme, Glioma, Gliomatosis cerebri, Glomus tumor, Glucagonoma, Gonadoblastoma, Granulosa cell tumor, Hairy Cell Leukemia, Hairy cell leukemia, Head and Neck Cancer, Head and neck cancer, Heart cancer, Hemangioblastoma, Hemangiopericytoma, Hemangiosarcoma, Hematological malignancy, Hepatocellular carcinoma, Hepatosplenic T-cell lymphoma, Hereditary breast-ovarian cancer syndrome, Hodgkin Lymphoma, Hodgkin's lymphoma, Hypopharyngeal Cancer, Hypothalamic Glioma, Inflammatory breast cancer, Intraocular Melanoma, Islet cell carcinoma, Islet Cell Tumor, Juvenile myelomonocytic leukemia, Kaposi Sarcoma, Kaposi's sarcoma, Kidney Cancer, Klatskin tumor, Krukenberg tumor, Laryngeal Cancer, Laryngeal cancer, Lentigo maligna melanoma, Leukemia, Leukemia, Lip and Oral Cavity Cancer, Liposarcoma, Lung cancer, Luteoma, Lymphangioma, Lymphangiosarcoma, Lymphoepithelioma, Lymphoid leukemia, Lymphoma, Macroglobulinemia, Malignant Fibrous Histiocytoma, Malignant fibrous histiocytoma, Malignant Fibrous Histiocytoma of Bone, Malignant Glioma, Malignant Mesothelioma, Malignant peripheral nerve sheath tumor, Malignant rhabdoid tumor, Malignant triton tumor, MALT lymphoma, Mantle cell lymphoma, Mast cell leukemia, Mediastinal germ cell tumor, Mediastinal tumor, Medullary thyroid cancer, Medulloblastoma, Medulloblastoma, Medulloepithelioma, Melanoma, Melanoma, Meningioma, Merkel Cell Carcinoma, Mesothelioma, Mesothelioma, Metastatic Squamous Neck Cancer with Occult Primary, Metastatic urothelial carcinoma, Mixed Mtillerian tumor, Monocytic leukemia, Mouth Cancer, Mucinous tumor, Multiple Endocrine Neoplasia Syndrome, Multiple Myeloma, Multiple myeloma, Mycosis Fungoides, Mycosis fungoides, Myelodysplastic Disease, Myelodysplastic Syndromes, Myeloid leukemia, Myeloid sarcoma, Myeloproliferative Disease, Myxoma, Nasal Cavity Cancer, Nasopharyngeal Cancer, Nasopharyngeal carcinoma, Neoplasm, Neurinoma, Neuroblastoma, Neuroblastoma, Neurofibroma, Neuroma, Nodular melanoma, Non-Hodgkin Lymphoma, Non-Hodgkin lymphoma, Nonmelanoma Skin Cancer, Non-Small Cell Lung Cancer, Ocular oncology, Oligoastrocytoma, Oligodendroglioma, Oncocytoma, Optic nerve sheath meningioma, Oral Cancer, Oral cancer, Oropharyngeal Cancer, Osteosarcoma, Osteosarcoma, Ovarian Cancer, Ovarian cancer, Ovarian Epithelial Cancer, Ovarian Germ Cell Tumor, Ovarian Low Malignant Potential Tumor, Paget's disease of the breast, Pancoast tumor, Pancreatic Cancer, Pancreatic cancer, Papillary thyroid cancer, Papillomatosis, Paraganglioma, Paranasal Sinus Cancer, Parathyroid Cancer, Penile Cancer, Perivascular epithelioid cell tumor, Pharyngeal Cancer, Pheochromocytoma, Pineal Parenchymal Tumor of Intermediate Differentiation, Pineoblastoma, Pituicytoma, Pituitary adenoma, Pituitary tumor, Plasma Cell Neoplasm, Pleuropulmonary blastoma, Polyembryoma, Precursor T-lymphoblastic lymphoma, Primary central nervous system lymphoma, Primary effusion lymphoma, Primary Hepatocellular Cancer, Primary Liver Cancer, Primary peritoneal cancer, Primitive neuroectodermal tumor, Prostate cancer, Pseudomyxoma peritonei, Rectal Cancer, Renal cell carcinoma, Respiratory Tract Carcinoma Involving the NUT Gene on Chromosome 15, Retinoblastoma, Rhabdomyoma, Rhabdomyosarcoma, Richter's transformation, Sacrococcygeal teratoma, Salivary Gland Cancer, Sarcoma, Schwannomatosis, Sebaceous gland carcinoma, Secondary neoplasm, Seminoma, Serous tumor, Sertoli-Leydig cell tumor, Sex cord-stromal tumor, Sézary Syndrome, Signet ring cell carcinoma, Skin Cancer, Small blue round cell tumor, Small cell carcinoma, Small Cell Lung Cancer, Small cell lymphoma, Small intestine cancer, Soft tissue sarcoma, Somatostatinoma, Soot wart, Spinal Cord Tumor, Spinal tumor, Splenic marginal zone lymphoma, Squamous cell carcinoma, Stomach cancer, Superficial spreading melanoma, Supratentorial Primitive Neuroectodermal Tumor, Surface epithelial-stromal tumor, Synovial sarcoma, T-cell acute lymphoblastic leukemia, T-cell large granular lymphocyte leukemia, T-cell leukemia, T-cell lymphoma, T-cell prolymphocytic leukemia, Teratoma, Terminal lymphatic cancer, Testicular cancer, Thecoma, Throat Cancer, Thymic Carcinoma, Thymoma, Thyroid cancer, Transitional Cell Cancer of Renal Pelvis and Ureter, Transitional cell carcinoma, Urachal cancer, Urethral cancer, Urogenital neoplasm, Uterine sarcoma, Uveal melanoma, Vaginal Cancer, Verner Morrison syndrome, Verrucous carcinoma, Visual Pathway Glioma, Vulvar Cancer, Waldenström's macroglobulinemia, Warthin's tumor, Wilms' tumor, or any combination thereof. 
     
     
         153 . A composition suitable for use in any of the methods of  claim 131 . 
     
     
         154 . A cancer or infectious disease vaccine for use in the method of  claim 131 , comprising an agent that inhibits VISTA activity or VISTA interaction with its natural binding partner(s) and a cancer or infectious agent antigen. 
     
     
         155 . A cancer vaccine for use in the method of  claim 131 , comprising a vector for anti-cancer vaccination, comprising genes which encode both a cancer antigen and nucleic acid molecule that inhibits VISTA activity. 
     
     
         156 . The method of  claim 131 , which includes a PD-1 ligand, e.g., an antibody against PD-L1. 
     
     
         157 . The method of  claim 131 , which is used to elicit immunity against an infectious agent. 
     
     
         158 . The method of  claim 157 , wherein the infectious agents include bacteria, yeast, fungi, protozoans,  mycoplasma , viruses, prions, and parasites.