BACKGROUND

Despite advances, targeted cancer therapy has largely failed to produce durable complete responses and cures in large numbers of patients with cancer. Additionally, systemic treatments such as chemotherapies are often toxic and cause undesirable side effects for patients. The lack of specific patient-selection biomarkers has also complicated development and application of targeted cancer treatments.

One approach for treating cancer cells includes identifying target genes and biomarkers which identify which cancer cells may be sensitive to alteration in the activity of those target genes. Recent advances in functional genomic screening have enabled identification of such target genes and biomarkers. However, for many human cancers, there remain limited suitable biomarkers that indicate that a cancer will respond to a targeted cancer therapy.

SUMMARY

In some aspects, the present disclosure provides a method for treating a subject having or suspected of having a cancer, comprising administering to the subject a therapeutically effective amount of a bromodomain and extra terminal containing (BET) polypeptide-targeting therapeutic agent that alters the expression and/or activity of one or BET polypeptides in the subject, wherein the cancer is associated with cancerous tissue comprising a cell or a plurality of cells comprising (i) a difference in expression or activity level of one or more genes compared to a healthy control, and/or (ii) a mutation or deletion in one or more genes as compared to a healthy control, wherein the one or more genes is in a list selected by computational inference of cancer cell susceptibility to decrease in activity of one or more BET polypeptides, thereby treating the cancer in the subject.

In any of the foregoing or related aspects, the cancerous tissue comprises a cell or a plurality of cells comprising a difference in expression or activity level of one or more genes compared to a healthy control. In some aspects, the cancerous tissue comprises a cell or a plurality of cells comprising a mutation and/or deletion in one or more genes as compared to a healthy control. In some aspect, the cancerous tissue comprises a cell or a plurality of cells comprising a difference in expression or activity level of one or more genes compared to a healthy control and a mutation and/or deletion in the one or more genes as compared to a healthy control. In some aspects, the difference in expression or activity level is a decrease in expression or activity level of the one or more genes compared to a healthy control. In some aspects, the mutation is a loss of function mutation. In some aspects, the presence or absence of the mutation and/or deletion is identified by an assay of cells derived from a cancerous tissue sample obtained from the subject. In some aspects, the assay is a next generation sequencing-based assay or oligomer hybridization.

In any of the foregoing or related aspects, the one or more genes are selected using a predictive algorithm, a machine learning algorithm, or both. In some aspects, the difference in expression or activity level of the one or more genes has a prevalence of about 5% or higher in at least one cancer. In some aspects, the mutation or deletion in the one or more genes has a prevalence of about 5% or higher in at least one cancer. In some aspects, the difference in expression or activity level of the one or more genes has a prevalence of about 3% or higher in at least two cancers. In some embodiments, the mutation or deletion in the one or more genes has a prevalence of about 3% or higher in at least two cancers. In some aspects, the difference in expression or activity level of the one or more genes has a prevalence of about 5% or higher in at least one cancer and a prevalence of about 3% or higher in at least two cancers. In some embodiments, the mutation and/or deletion in the one or more genes has a prevalence of about 5% or higher in at least one cancer and a prevalence of about 3% or higher in at least two cancers. In some aspects, the difference in expression or activity level of the one or more genes and/or the mutation or deletion in the one or more genes has a prevalence of about 5% or higher in at least one cancer and a prevalence of about 3% or higher in at least one additional cancer. In some aspects, the cancer is selected from a cancer type listed in The Cancer Genome Atlas (TCGA). In some aspects, the cancer is selected from a leukemia, lymphoma, and myeloma. In some aspects, the cancer is a solid tumor malignancy of the prostate, uterus, colon, rectum, liver, bladder, ovaries, lung, breast, skin, stomach, esophagus, cervix, pancreas, testes, eye, mucosal tissue, adrenal gland, brain, thyroid, or thymus. In some aspects, the cancer is selected from prostate adenocarcinoma (PRAD), uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), uterine carcinosarcoma (UCS), liver hepatocellular carcinoma (LIHC), bladder urothelial carcinoma (BLCA), ovarian serous cystadenocarcinoma (OV), lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LU AD), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), esophageal carcinoma (ESCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), sarcoma (SARC), testicular germ cell tumors (TGCT), kidney renal clear cell carcinoma (KIRC), uveal melanoma (UVM), adrenocortical carcinoma (ACC), acute myeloid leukemia (LAML), kidney renal papillary cell carcinoma (KIRP), glioblastoma multiforme (GBM), brain lower grade glioma (LGG), kidney chromophobe (KICH), mesothelioma (MESO), pheochromocytoma and paraganglioma (PCPG), thyroid carcinoma (THCA), and thymoma (THYM).

In any of the foregoing or related aspects, the one or more genes is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8. In some aspects, the one or more genes is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP. In some aspects, the one or more genes is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8. In some aspects, the one or more genes is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP. In some aspects, the one or more genes comprises a gene encoding Tankyrase (TNKS). In some aspects, the one or more biomarkers comprises a gene encoding phosphatidylinositol 3, 4, 5 -trisphosphate 3 -phosphatase and dualspecificity protein phosphatase (PTEN). In some aspects, the one or more biomarkers comprises a gene encoding retinoblastoma-associated protein (RBI). In some aspects, the one or more biomarkers comprises tyrosine-protein kinase JAK1 (JAK1).

In some aspects, the disclosure provides a method of identifying a subject having a disease or disorder for treatment with one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a diseased tissue sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8, wherein the diseased tissue sample comprises (a) a decreased expression level and/or decreased activity in the one or more biomarkers relative to a reference tissue sample; and/or (b) a loss-of-function mutation in the one or more biomarkers.

In some aspects, the disclosure provides a method of identifying a subject having a disease or disorder for treatment with one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a diseased tissue sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP, wherein the diseased tissue sample comprises (a) a decreased expression level and/or decreased activity in the one or more biomarkers relative to a reference tissue sample; and/or (b) a loss-of-function mutation in the one or more biomarkers.

In some aspects, the disclosure provides a method of identifying a subject having a disease or disorder for treatment with one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a diseased tissue sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8, wherein the diseased tissue sample comprises (a) a decreased expression level and/or decreased activity in the one or more biomarkers relative to a reference tissue sample; and/or (b) a loss-of-function mutation in the one or more biomarkers.

In some aspects, the disclosure provides a method of identifying a subject having a disease or disorder for treatment with one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a diseased tissue sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP, wherein the diseased tissue sample comprises (a) a decreased expression level and/or decreased activity in the one or more biomarkers relative to a reference tissue sample; and/or (b) a loss-of-function mutation in the one or more biomarkers.

In some aspects, the disclosure provides a method of determining responsiveness of a subject having a disease or disorder to one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a diseased tissue sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8, wherein the diseased tissue sample comprises (a) a decreased expression level and/or decreased activity in the one or more biomarkers relative to a reference tissue sample; and/or (b) a loss-of-function mutation in the one or more biomarkers. In some aspects, the disclosure provides a method of determining responsiveness of a subject having a disease or disorder to one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a diseased tissue sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP, wherein the diseased tissue sample comprises (a) a decreased expression level and/or decreased activity in the one or more biomarkers relative to a reference tissue sample; and/or (b) a loss-of-function mutation in the one or more biomarkers.

In some aspects, the disclosure provides a method of determining responsiveness of a subject having a disease or disorder to one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a diseased tissue sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8, wherein the diseased tissue sample comprises (a) a decreased expression level and/or decreased activity in the one or more biomarkers relative to a reference tissue sample; and/or (b) a loss-of-function mutation in the one or more biomarkers.

In some aspects, the disclosure provides a method of determining responsiveness of a subject having a disease or disorder to one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a diseased tissue sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP, wherein the diseased tissue sample comprises (a) a decreased expression level and/or decreased activity in the one or more biomarkers relative to a reference tissue sample; and/or (b) a loss-of-function mutation in the one or more biomarkers.

In any of the foregoing or related aspects, the subject has cancer and the diseased tissue sample comprises a tumor sample, a circulating tumor DNA sample, a tumor biopsy sample, or a fixed tumor sample. In some aspects, the diseased tissue sample comprises a plurality of tumor cells comprising the loss of function mutation in the one or more biomarkers. In some aspects, the one or more biomarkers comprises TNKS. In some aspects, the one or more biomarkers comprises PTEN. In some aspects, the one or more biomarkers comprises RBI. In some aspects, the one or more biomarkers comprises JAK1. In some aspects, the loss of function mutation is a deletion. In some aspects, the mutation is detected by an assay of genomic DNA in the diseased tissue sample, optionally via next generation sequencing or oligomer hybridization.

In some aspects, the disclosure provides a method of identifying a subject having cancer for treatment with one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of TNKS in a tumor sample obtained from the subject, wherein the tumor sample comprises (a) a decreased expression level and/or decreased activity of TNKS relative to a reference tissue sample; and/or (b) a loss-of-function mutation in TNKS relative to a reference tissue sample.

In some aspects, the disclosure provides a method of identifying a subject having cancer for treatment with one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of PTEN in a tumor sample obtained from the subject, wherein the tumor sample comprises (a) a decreased expression level and/or decreased activity of PTEN relative to a reference tissue sample; and/or (b) a loss-of-function mutation in PTEN relative to a reference tissue sample.

In some aspects, the disclosure provides a method of identifying a subject having cancer for treatment with one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of JAK1 in a tumor sample obtained from the subject, wherein the tumor sample comprises (a) a decreased expression level and/or decreased activity of JAK1 relative to a reference tissue sample; and/or (b) a loss-of-function mutation in JAK1 relative to a reference tissue sample.

In some aspects, the disclosure provides a method of identifying a subject having cancer for treatment with one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of RBI in a tumor sample obtained from the subject, wherein the tumor sample comprises (a) a decreased expression level and/or decreased activity of RBI relative to a reference tissue sample; and/or (b) a loss-of-function mutation in RBI relative to a reference tissue sample.

In some aspects, the disclosure provides a method of determining responsiveness of a subject having cancer to one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of TNKS in a tumor sample, wherein the tumor sample has (a) a decreased expression level and/or decreased activity of TNKS relative to a reference tissue sample; and/or (b) a loss-of- function mutation in TNKS.

In some aspects, the disclosure provides a method of determining responsiveness of a subject having cancer to one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of PTEN in a tumor sample, wherein the tumor sample has (a) a decreased expression level and/or decreased activity of PTEN relative to a reference tissue sample; and/or (b) a loss-of- function mutation in PTEN.

In some aspects, the disclosure provides a method of determining responsiveness of a subject having cancer to one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of JAK1 in a tumor sample, wherein the tumor sample has (a) a decreased expression level and/or decreased activity of JAK1 relative to a reference tissue sample; and/or (b) a loss-of- function mutation in JAKE

In some aspects, the disclosure provides a method of determining responsiveness of a subject having cancer to one or more BET polypeptide-targeting therapeutic agents, the method comprising determining the presence of a mutation in, the expression level of, and/or the activity of RBI in a tumor sample, wherein the tumor sample has (a) a decreased expression level and/or decreased activity of RBI relative to a reference tissue sample; and/or (b) a loss-of-function mutation in RB 1.

In any of the foregoing or related aspects, the method further comprises administering a BET polypeptide-targeting therapeutic agent to the subject. In some aspects, the administering results in a reduced expression level and/or activity of one or more BET polypeptides in a tumor of the subject. In some aspects, the one or more BET polypeptides is selected from BRD1, BRD2, BRD3, and BRD4. In some aspects, the one or more BET polypeptides is selected from BRD2, BRD3, and BRD4. In some aspects, the administering results in a reduced expression level and/or activity of BRD1 in a tumor of the subject. In some aspects, the administering results in a reduced expression level and/or activity of BRD2 in a tumor of the subject. In some aspects, the administering results in a reduced expression level and/or activity of BRD3 in a tumor of the subject. In some aspects, the administering results in a reduced expression level and/or activity of BRD4 in a tumor of the subject. In some aspects, the reduced expression level and/or activity of the one or more BET polypeptides induces synthetic lethality in the tumor. In some aspects, the synthetic lethality promotes tumor regression. In some aspects, the synthetic lethality delays or inhibits tumor progression.

In some aspects, the disclosure provides a method of treating a cancer or promoting tumor regression in a subject having a tumor comprising a mutation in, an altered expression level of, and/or an altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8, the method comprising: administering to the subject a therapeutically effective amount of a BET polypeptide-targeting therapeutic agent. In some aspects, the tumor comprises a loss of function mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers as measured in a tumor sample obtained from the subject relative to a reference tissue sample.

In some aspects, the disclosure provides a method of treating a cancer or promoting tumor regression in a subject having a tumor comprising a mutation in, an altered expression level of, and/or an altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP, the method comprising: administering to the subject a therapeutically effective amount of a BET polypeptide-targeting therapeutic agent. In some aspects, the tumor comprises a loss of function mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers as measured in a tumor sample obtained from the subject relative to a reference tissue sample.

In some aspects, the disclosure provides a method of treating a cancer or promoting tumor regression in a subject having a tumor comprising a mutation in, an altered expression level of, and/or an altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8, the method comprising: administering to the subject a therapeutically effective amount of a BET polypeptide-targeting therapeutic agent. In some aspects, the tumor comprises a loss of function mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers as measured in a tumor sample obtained from the subject relative to a reference tissue sample.

In some aspects, the disclosure provides a method of treating a cancer or promoting tumor regression in a subject having a tumor comprising a mutation in, an altered expression level of, and/or an altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP, the method comprising: administering to the subject a therapeutically effective amount of a BET polypeptide-targeting therapeutic agent. In some aspects, the tumor comprises a loss of function mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers as measured in a tumor sample obtained from the subject relative to a reference tissue sample.

In some aspects, the disclosure provides a method of treating a cancer or promoting tumor regression in a subject having a tumor comprising a mutation in, an altered expression level of, and/or an altered activity of TNKS, the method comprising: administering to the subject a therapeutically effective amount of a BET polypeptide-targeting therapeutic agent. In some aspects, the tumor comprises a loss of function mutation in, a reduced expression level of, and/or a reduced activity of TNKS as measured in a tumor sample obtained from the subject relative to a reference tissue sample.

In some aspects, the disclosure provides a method of treating a cancer or promoting tumor regression in a subject having a tumor comprising a mutation in, an altered expression level of, and/or an altered activity of PTEN, the method comprising: administering to the subject a therapeutically effective amount of a BET polypeptide-targeting therapeutic agent. In some aspects, the tumor comprises a loss of function mutation in, a reduced expression level of, and/or a reduced activity of PTEN as measured in a tumor sample obtained from the subject relative to a reference tissue sample.

In some aspects, the disclosure provides a method of treating a cancer or promoting tumor regression in a subject having a tumor comprising a mutation in, an altered expression level of, and/or an altered activity of JAK1, the method comprising: administering to the subject a therapeutically effective amount of a BET polypeptide-targeting therapeutic agent. In some aspects, the tumor comprises a loss of function mutation in, a reduced expression level of, and/or a reduced activity of JAK1 as measured in a tumor sample obtained from the subject relative to a reference tissue sample.

In some aspects, the disclosure provides a method of treating a cancer or promoting tumor regression in a subject having a tumor comprising a mutation in, an altered expression level of, and/or an altered activity of RBI, the method comprising: administering to the subject a therapeutically effective amount of a BET polypeptide-targeting therapeutic agent. In some aspects, the tumor comprises a loss of function mutation in, a reduced expression level of, and/or a reduced activity of RBI as measured in a tumor sample obtained from the subject relative to a reference tissue sample.

In some aspects, the disclosure provides a method of identifying a cancer subject to receive one or more BET polypeptide therapeutic agents, comprising (i) determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8; and (11) administering a BET polypeptide therapeutic agents to the subject based on presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers relative to a healthy control.

In some aspects, the disclosure provides a method of identifying a cancer subject to receive one or more BET polypeptide therapeutic agents, comprising (i) determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP; and (h) administering a BET polypeptide therapeutic agents to the subject based on presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers relative to a healthy control.

In some aspects, the disclosure provides a method of identifying a cancer subject to receive one or more BET polypeptide therapeutic agents, comprising (i) determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8; and (h) administering a BET polypeptide therapeutic agents to the subject based on presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers relative to a healthy control.

In some aspects, the disclosure provides a method of identifying a cancer subject to receive one or more BET polypeptide therapeutic agents, comprising (i) determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP; and (11) administering a BET polypeptide therapeutic agents to the subject based on presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers relative to a healthy control.

In some aspects, the disclosure provides a method of identifying a cancer subject to receive one or more BET polypeptide therapeutic agents, comprising (i) determining the presence of a mutation in, the expression level of, and/or the activity of TNKS in a tumor sample obtained from the subject; and (ii) administering a BET polypeptide therapeutic agents to the subject based on presence of a mutation in, a reduced expression level of, and/or a reduced activity of TNKS relative to a healthy control.

In some aspects, the disclosure provides a method of identifying a cancer subject to receive one or more BET polypeptide therapeutic agents, comprising (i) determining the presence of a mutation in, the expression level of, and/or the activity of PTEN in a tumor sample obtained from the subject; and (ii) administering a BET polypeptide therapeutic agents to the subject based on presence of a mutation in, a reduced expression level of, and/or a reduced activity of PTEN relative to a healthy control.

In some aspects, the disclosure provides a method of identifying a cancer subject to receive one or more BET polypeptide therapeutic agents, comprising (i) determining the presence of a mutation in, the expression level of, and/or the activity of JAK1 in a tumor sample obtained from the subject; and (ii) administering a BET polypeptide therapeutic agents to the subject based on presence of a mutation in, a reduced expression level of, and/or a reduced activity of JAK1 relative to a healthy control.

In some aspects, the disclosure provides a method of identifying a cancer subject to receive one or more BET polypeptide therapeutic agents, comprising (i) determining the presence of a mutation in, the expression level of, and/or the activity of RBI in a tumor sample obtained from the subject; and (ii) administering a BET polypeptide therapeutic agents to the subject based on presence of a mutation in, a reduced expression level of, and/or a reduced activity of RBI relative to a healthy control. In any of the foregoing or related aspects, the tumor sample is a circulating tumor DNA sample, a tumor biopsy sample, or a fixed tumor sample. In some aspects, the tumor sample comprises a mutation in the one or more biomarkers. In some aspects, the mutation is a loss of function mutation. In some aspects, the loss of function mutation is a deletion. In some aspects, the mutation is detected by an assay of genomic tumor DNA. In some aspects, the mutation is detected by next generation sequencing or oligomer hybridization. In some aspects, the tumor sample comprises a plurality of tumor cells comprising the mutation.

In any of the foregoing or related aspects, the administering results in a reduced expression level and/or activity of one or more BET polypeptides in a tumor of the subject. In some aspects, the one or more BET polypeptides is selected from BRD1, BRD2, BRD3, and BRD4. In some aspects, the one or more BET polypeptides is selected from BRD2, BRD3, and BRD4. In some aspects, the administering results in a reduced expression level and/or activity of BRD1 in a tumor of the subject. In some aspects, the administering results in a reduced expression level and/or activity of BRD2 in a tumor of the subject. In some aspects, the administering results in a reduced expression level and/or activity of BRD3 in a tumor of the subject. In some aspects, the administering results in a reduced expression level and/or activity of BRD4 in a tumor of the subject. In some aspects, the reduced expression level and/or activity of a BET- containing polypeptide induces synthetic lethality in the tumor. In some aspects, the synthetic lethality promotes tumor regression. In some aspects, the synthetic lethality delays or inhibits tumor progression.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of TNKS in a tumor sample obtained from the subject.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of PTEN in a tumor sample obtained from the subject.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of JAK1 in a tumor sample obtained from the subject.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of RBI in a tumor sample obtained from the subject.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of TNKS in a tumor sample obtained from the subject.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of PTEN in a tumor sample obtained from the subject.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of RBI in a tumor sample obtained from the subject.

In some aspects, the disclosure provides use of a BET polypeptide-targeting therapeutic agent in the manufacture of a medicament for treating a cancer or promoting tumor regression in a subject, wherein the subject has been identified based on the presence of a mutation in, an altered expression level and/or altered activity of JAK1 in a tumor sample obtained from the subject.

In any of the foregoing or related aspects, the BET polypeptide-targeting therapeutic agent is selected from a small molecule, a peptide, a protein, and a nucleic acid. In some aspects, the BET polypeptide-targeting therapeutic agent comprises an anti-BET polypeptide antibody or fragment thereof. In some aspects, the one or more BET polypeptide-targeting therapeutic agent comprises an anti-BET polypeptide intrabody or fragment thereof. In some aspects, the BET polypeptide-targeting therapeutic agent comprises an antisense oligonucleotide, an RNAi molecule, or an aptamer. In some aspects, the BET polypeptide-targeting therapeutic agent comprises a small molecule inhibitor. In some aspects, the BET polypeptide-targeting therapeutic agent comprises a proteolysis targeting chimera. In some aspects, the small molecule inhibitor is selected from GSK-2820151, GSK525762, GSK046, GSK778, RG-6146, birabresib dihydrate, BAY-1238097, BMS-986158, BMS-986378, CC-90010, CC-95775, Apabetalone, RVX-208, RVX-000222, INCB054329, INCB057643, AZ-5153, ABBV-744, ABBV-075, CPI- 203, BAY 1238079, and PLX51107. In some aspects, the small molecule inhibitor is selected from birabresib, CPI-203, BAY 1238079, and PLX51107. In some aspects, the BET polypeptide-targeting therapeutic agent comprises a gene editing technology for introducing a genetic knockout of a gene encoding a BET polypeptide. In some aspects, the gene editing technology comprises CRISPR/Cas9. In some aspects, the method or use further comprises administering one or more additional agents.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for administering the BET polypeptide-targeting therapeutic agent to a subject having a cancer comprising a mutation in, an altered expression level and/or altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for administering the BET polypeptide-targeting therapeutic agent to a subject having a cancer comprising a mutation in, an altered expression level and/or altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for administering the BET polypeptide-targeting therapeutic agent to a subject having a cancer comprising a mutation in, an altered expression level and/or altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for administering the BET polypeptide-targeting therapeutic agent to a subject having a cancer comprising a mutation in, an altered expression level and/or altered activity of one or more biomarkers, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for administering the BET polypeptide-targeting therapeutic agent to a subject having a cancer comprising a mutation in, an altered expression level and/or altered activity of TNKS.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for administering the BET polypeptide- targeting therapeutic agent to a subject having a cancer comprising a mutation in, an altered expression level and/or altered activity of PTEN.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for administering the BET polypeptide-targeting therapeutic agent to a subject having a cancer comprising a mutation in, an altered expression level and/or altered activity of JAK1.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for administering the BET polypeptide-targeting therapeutic agent to a subject having a cancer comprising a mutation in, an altered expression level and/or altered activity of RBI.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8; and (h) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP; and (ii) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8; and (ii) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP; and (ii) administering an effective amount of the BET polypeptide- targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of TNKS in a tumor sample obtained from the subject; and (ii) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of TNKS in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of PTEN in a tumor sample obtained from the subject; and (ii) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of PTEN in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of JAK1 in a tumor sample obtained from the subject; and (ii) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of JAK1 in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of RBI in a tumor sample obtained from the subject; and (ii) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of RBI in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of a panel of biomarkers in a tumor sample obtained from the subject, wherein panel comprises one or more biomarkers selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8; and (ii) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of a panel of biomarkers in a tumor sample obtained from the subject, wherein panel comprises one or more biomarkers selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP; and (11) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of a panel of biomarkers in a tumor sample obtained from the subject, wherein panel comprises one or more biomarkers selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8; and (h) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers in the tumor sample relative to a healthy control.

In some aspects, the disclosure provides a kit comprising a BET polypeptide-targeting therapeutic agent, and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, the expression level of, and/or the activity of a panel of biomarkers in a tumor sample obtained from the subject, wherein panel comprises one or more biomarkers selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP; and (ii) administering an effective amount of the BET polypeptide-targeting therapeutic agent to the subject based on the presence of a mutation in, a reduced expression level of, and/or a reduced activity of the one or more biomarkers in the tumor sample relative to a healthy control.

In any of the foregoing or related aspects, the cancer comprises a hematological malignancy or myeloproliferative disorder. In some aspects, the cancer comprises a solid tumor. In some aspects, the solid tumor is of the prostate, uterus, colon, rectum, liver, bladder, ovaries, lung, breast, skin, stomach, esophagus, cervix, pancreas, testes, eye, mucosal tissue, adrenal gland, brain, thyroid, or thymus, or combinations thereof. In some aspects, the cancer is breast cancer, ovarian cancer, prostate cancer, uterine cancer, bladder cancer, liver cancer, mesothelioma, pancreatic cancer, colorectal cancer, lung cancer, lymphoma, melanoma, or headneck cancer. In some aspects, the cancer is prostate cancer. In some aspects, the cancer is colorectal cancer. In some aspects, the cancer is ovarian cancer. In some aspects, the cancer is an advanced and/or metastatic cancer.

In any of the foregoing or related aspects, the cancer is selected from: prostate adenocarcinoma (PRAD), uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), uterine carcinosarcoma (UCS), liver hepatocellular carcinoma (LIHC), bladder urothelial carcinoma (BLCA), ovarian serous cystadenocarcinoma (OV), lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LU AD), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), esophageal carcinoma (ESCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), sarcoma (SARC), testicular germ cell tumors (TGCT), kidney renal clear cell carcinoma (KIRC), uveal melanoma (UVM), adrenocortical carcinoma (ACC), acute myeloid leukemia (LAML), kidney renal papillary cell carcinoma (KIRP), glioblastoma multiforme (GBM), brain lower grade glioma (LGG), kidney chromophobe (KICH), mesothelioma (MESO), pheochromocytoma and paraganglioma (PCPG), thyroid carcinoma (THCA), thymoma (THYM).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a plot of frequency of an inactivation or deficiency in the gene encoding tankyrase (TNKS) that is a missense mutation, a protein truncation variant, or a homozygous deletion in human cancers that include prostate adenocarcinoma (PRAD), uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), uterine carcinosarcoma (UCS), liver hepatocellular carcinoma (LIHC), bladder urothelial carcinoma (BLCA), ovarian serous cystadenocarcinoma (OV), lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LU AD), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), esophageal carcinoma (ESCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), sarcoma (SARC), testicular germ cell tumors (TGCT), kidney renal clear cell carcinoma (KIRC), uveal melanoma (UVM), adrenocortical carcinoma (ACC), acute myeloid leukemia (LAML), kidney renal papillary cell carcinoma (KIRP), glioblastoma multiforme (GBM), brain lower grade glioma (LGG), kidney chromophobe (KICH), mesothelioma (MESO), pheochromocytoma and paraganglioma (PCPG), thyroid carcinoma (THCA), and thymoma (THYM).

FIG. 2 provides an image of an immunoblot showing expression of tankyrase in HT29 cancer cells having a CRISPR/Cas-gene knockout of the TNKS gene (“KO”) or control HT29 cancer cells (“NTC”).

FIGs. 3A-3D provides graphs showing percentage of viable cells among TNKS-KO HT29 cells or control HT29 cancer cells treated in vitro with the BET inhibitor birabresib (FIG. 3 A), CPI-203 (FIG. 3B), BAY1238079 (FIG. 3C), or PLX51107 (FIG. 3D) at the indicated concentrations.

FIG. 4 provides a graph showing fold-change in IC50 value measured for TNKS-KO HT29 cells vs control HT29 cancer cells treated as described in FIGs. 3A-3D.

FIGs. 5A-5E provide graphs showing normalized cell density following treatment with BET2/3/4 inhibitor PLX51107 (at a concentration of 0.001 uM to 100 uM) in PTEN-knockout HT29 cancer cells (FIG. 5A), RBI -knockout HT29 cancer cells (FIG. 5B), JAK1 -knockout HT29 cancer cells (FIG. 5C), PTEN-knockout OVCAR3 cancer cells (FIG. 5D), RBI -knockout OVCAR3 cancer cells (FIG. 5E), and JAKl-knockout OVCAR3 cancer cells (FIG. 5F). Gene knockouts were generated by CRISPR/Cas and control cancer cells (NTC) were transfected with a non-specific single guide RNA (NTC sgRNA). Graphs show calculated IC50 values for gene depleted cancer cell lines and NTC cancer cell lines.

DETAILED DESCRIPTION

Overview The present disclosure is based, at least in part, on the identification of biomarkers present in one or more human cancers that form a synthetic lethal pair with a bromodomain and extra terminal containing (BET) polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), wherein an altered (e.g., increased or decreased) expression level and/or activity of the biomarker in a cancer renders it responsive to one or more therapeutic agents that targets a gene encoding a BET polypeptide or a transcriptional or translational product thereof. As described herein, computational methods were developed to identify biomarkers that are deficient and/or mutated in one or more human cancers, that alone may not substantially impact viability of tumor cells, but when combined with modulation (e.g., inhibition) of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), such as by gene knockout, antisense or RNAi technology, or pharmacological inhibition, result in synthetic lethality to the tumor cells. Moreover, the disclosure provides gene editing technologies, for example based on CRISPR/Cas9 gene editing, to evaluate the biomarkers for a synthetic lethal phenotype following knockout of the biomarker and inhibition of the BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), for example by pharmacological inhibition or gene knockout.

As described herein, the gene encoding human tankyrase (TNKS) was identified using computational methods of the disclosure as having a deletion and/or mutation in a substantial number of human cancers and as forming a synthetic lethal pair with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). Moreover, it was demonstrated that genetic knockout of TNKS renders cancer cells susceptible to a pharmacological therapeutic agent targeting a BET polypeptide (e.g., BRD2 and/or BRD4). Indeed, it was shown that treatment of cancer cells having a genetic knockout of TNKS with a BET polypeptide small molecule inhibitor (e.g., Birabresib, PLX51107, CPI-203, and BAY123897) resulted in an IC50 that was at least about 20-fold and up to about 150-fold lower than the IC50 observed for treated cancer cells expressing TNKS. Moreover, as described herein, a gene knockout of PTEN, JAK1, or RBI, genes, which were also identified using computational methods described herein as forming a synthetic lethal pair with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), was shown to sensitize cancer cells (e.g., colorectal cancer cells, e.g., ovarian cancer cells) to treatment with a BET polypeptide small molecule inhibitor. Without being bound by theory, a mutation in (e.g., a loss of function mutation or inactivating mutation), an altered (e.g., decreased) expression level of, and/or an altered (e.g., decreased) activity of one or more biomarkers of the disclosure (e.g., TNKS and/or a biomarker listed in Table 2) in a cancer in a subject provides a predictive indicator that the cancer will respond or will likely respond to one or more therapeutic agents that modulates (e.g., decreases) an expression level and/or activity of a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide).

Accordingly, the present disclosure provides methods for treating a cancer or cancerous cells thereof having a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered activity of, a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2), the method comprising administering one or more therapeutic agents targeting a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide), wherein the one or more therapeutic agents results in an altered (e.g., increased or decreased) expression level and/or activity of the BET polypeptide. In some aspects, the presence of a mutation in the biomarker results in a loss of function (e.g., decreased expression level and/or activity of the biomarker). In some aspects, a decrease in the expression level and/or activity of the biomarker and the BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) in a tumor cell results in lethality to the tumor cell. In some aspects, a decrease in the expression level and/or activity of both the biomarker and a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) in a tumor cell results in substantially reduced viability of the tumor cell.

In some aspects, the disclosure provides a method for identifying or selecting a subject having cancer to receive one or more therapeutic agents targeting a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide), wherein the method comprises determining the expression level and/or activity of a biomarker described herein (e.g., TNKS) in a tumor sample obtained from the subject, wherein an altered (e.g., increased or decreased) expression level and/or activity of the biomarker relative to a reference tissue sample (e.g., a healthy tissue sample) indicates the subject will respond or will likely to respond to treatment with one or more therapeutic agents which modulate (e.g., decrease) the expression level and/or activity of the BET polypeptide. In some aspects, the method comprises providing a report predicting the responsiveness of the subject to the treatment based upon detection of an altered (e.g., increased or decreased) expression level and/or activity of the biomarker in the tumor sample obtained from the subject relative to a reference tissue sample (e.g., a healthy tissue sample). In some aspects, the tumor sample is a tumor biopsy sample (e.g., fresh or fixed tumor biopsy sample). In some aspects, the tumor sample is a blood sample comprising circulating tumor DNA. In some aspects, a decreased expression level and/or activity of the biomarker indicates the subject will respond or will likely respond following administration of one or more therapeutic agents that decreases the expression level and/or activity of the BET polypeptide.

In some aspects, the disclosure provides a method for identifying or selecting a subject with cancer to receive one or more therapeutic agents targeting a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide), wherein the method comprises determining the presence of a mutation (e.g., a loss of function mutation or inactivating mutation) in a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) in a tumor sample obtained from the subject, wherein the presence of a mutation in the biomarker relative to a reference tissue sample (e.g., a healthy tissue sample) indicates the subject will respond or will likely to respond to treatment to one or more therapeutic agents that modulates (e.g., increases or decreases) the expression level and/or activity of the BET polypeptide. In some aspects, the method comprises providing a report predicting the responsiveness of the subject to the treatment based upon detection of a mutation in the biomarker in the tumor sample obtained from the subject. In some aspects, the tumor sample is a tumor biopsy sample (e.g., fresh or fixed tumor biopsy sample). In some aspects, the tumor sample is a blood sample comprising circulating tumor DNA. In some aspects, the presence of a mutation in the biomarker indicates the subject will respond or will likely respond following administration of one or more therapeutic agents that decreases the expression level and/or activity of the BET polypeptide.

In some aspects, the one or more therapeutic agents that modulates (e.g., decreases) the expression level and/or activity of the BET polypeptide comprises a therapeutic inhibitor of a gene encoding a BET polypeptide (e.g., a gene-editing technology). In some aspects, the one or more therapeutic agents comprises a therapeutic inhibitor of an RNA transcript encoding a BET polypeptide (e.g., an antisense oligonucleotide or an RNAi molecule targeting a pre-mRNA or mRNA encoding a BET polypeptide). In some aspects, the one or more therapeutic agents comprises a therapeutic agent targeting a BET polypeptide (e.g., a pharmacological inhibitor).

In some aspects, the mutation in the biomarker (e.g., TNKS and/or a biomarker listed in Table 2) is an inactivating mutation or loss of function mutation in a biomarker (such as any inactivating or loss of function mutations described herein or known in the art). In some aspects, the mutation in the biomarker results in a partial loss of function of the biomarker. In some aspects, the mutation in the biomarker results in a complete loss of function of the biomarker. In some aspects, the mutation in the biomarker results in a partial loss of expression and/or activity of the biomarker. In some aspects, the mutation in the biomarker results in a complete loss of expression and/or activity of the biomarker. In some aspects, the mutation is a null mutation (leading to the deletion of the gene encoding the biomarker).

In some aspects, the disclosure provides a method of identifying or selecting a patient to receive one or more therapeutic agents that modulates (e.g., decreases) the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), wherein the method comprises detecting a mutation in or determining the expression level and/or activity of a panel of biomarkers described herein (e.g., TNKS and/or a biomarker listed in Table 2) in a tumor sample obtained from the subject, wherein the presence of a mutation (e.g., an inactivating mutation or loss of function mutation) in and/or an altered (e.g., increased or decreased) expression level and/or activity of at least one biomarker of the panel relative to a reference tissue sample (e.g., a healthy tissue sample) indicates the subject will respond or will likely to respond to administration of one or more therapeutic agents that manipulates the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some aspects, the method comprises providing a report predicting the responsiveness of the subject to the treatment based upon detection of a mutation in at least one biomarker of the panel in the tumor sample obtained from the subject and/or based upon detection of an altered (e.g., increased or decreased) expression level and/or activity of at least one biomarker of the panel in the tissue sample obtained from the subject relative to a reference tissue sample (e.g., a healthy tissue sample). In some aspects, the tumor sample is a tumor biopsy sample (e.g., fresh or fixed tumor biopsy sample). In some aspects, the tumor sample is a blood sample comprising circulating tumor DNA. In some aspects, the presence of a mutation (e.g., an inactivating mutation or loss of function mutation) in at least one biomarker of the panel indicates the subject will respond or will likely respond following administration of one or more therapeutic agents that decreases the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some aspects, a decreased expression level and/or activity of at least one biomarker of the panel indicates the subject will respond or will likely respond following administration of one or more therapeutic agents that decreases the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some aspects, the response is reduced tumor progression. In some aspects, the response is reduced tumor burden. In some aspects, the response is reduced risk of metastasis.

Synthetic Lethality Biomarkers of the Disclosure

In some embodiments, the disclosure provides biomarkers having altered (e.g., increased or decreased) expression level and/or activity in one or more human cancers, wherein the biomarker forms a synthetic lethal pair with at least one or more target genes. As used herein, a “target gene” refers to a gene or a transcriptional or translational product thereof whose expression level and/or activity in a cell is selectively modulated by a therapeutic agent (e.g., a gene editing technology or a pharmacological inhibitor). In some embodiments, the target gene encodes a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4).

As used herein, a “synthetic lethal pair” refers to a pair of genes in a cell (e.g., a biomarker and a target gene), wherein an altered (e.g., increased or decreased) expression level and/or activity of both genes, or the transcriptional or translational products thereof, impairs viability of the cell (e.g., substantially reduced cell viability). In some embodiments, an altered (e.g., increased or decreased) expression level and/or activity of one gene of a synthetic lethal pair, but not both, has minimal effect on cell viability. In some embodiments, a cell comprising a decreased expression level and/or activity of both genes of the synthetic lethal pair, or transcriptional or translational products thereof, has substantially reduced viability. In some embodiments, the synthetic lethal pair comprises a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) and a target gene. In some embodiments, the synthetic lethal pair comprises a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) and a target gene encoding a BET polypeptide. In some embodiments, the synthetic lethal pair comprises a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) and a target gene encoding BRD1. In some embodiments, the synthetic lethal pair comprises a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) and a target gene encoding BRD2. In some embodiments, the synthetic lethal pair comprises a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) and a target gene encoding BRD3. In some embodiments, the synthetic lethal pair comprises a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) and a target gene encoding BRD4.

As used herein, a “biomarker” refers to a gene, or a transcriptional or translational product thereof, whose expression level and/or activity can be detected in a tissue sample obtained from a subject having a disease or disorder (e.g., cancer), wherein an altered (e.g., increased or decreased) expression level and/or activity of the biomarker, e.g., relative to a reference tissue sample, functions as an indicator (e.g., diagnostic, predictive, and/or prognostic indicator). In some embodiments, the biomarker is a predictive indicator, wherein an altered expression level and/or activity of the biomarker in a diseased (e.g., cancerous) tissue sample indicates responsiveness of the disease (e.g., cancer) to a particular therapeutic intervention (e.g., administration of one or more therapeutic agents for modulation of an expression level and/or an activity of a BET polypeptide). In some embodiments, the expression level and/or activity of the biomarker is detected in a tissue sample obtained from a subject having cancer. In some embodiments, an altered (e.g., increased or decreased) expression level and/or activity of the biomarker is a predictive indicator that the subject will respond or will likely respond to therapeutic manipulation of a target gene (e.g., a gene encoding a BET polypeptide) described herein or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide). In some embodiments, a decreased expression level and/or activity of the biomarker is a predictive indicator that the subject will respond or will likely respond to a therapeutic inhibition of a target gene (e.g., a gene encoding a BET polypeptide) described herein or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide).

In some embodiments, the presence of one or more mutations (e.g., a loss of function mutation) in, an altered (e.g., increased or decreased) expression level, and/or an altered (e.g., increased or decreased) activity of the biomarker in a diseased (e.g., cancerous) tissue sample, e.g., relative to a reference tissue sample, indicates responsiveness of the disease (e.g., cancer) to a particular therapeutic intervention (e.g., administration of one or more therapeutic agents for modulation of an expression level and/or an activity of a BET protein described herein, e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the presence of one or more mutations (e.g., a loss of function mutation) in, an altered (e.g., increased or decreased) expression level, and/or an altered (e.g., increased or decreased) activity of the biomarker is detected in a tissue sample obtained from a subject having cancer.

In some embodiments, the presence of one or more mutations (e.g., a loss of function mutation) in, an altered (e.g., increased or decreased) expression level, and/or an altered (e.g., increased or decreased) activity of the biomarker indicates the subject will respond or will likely respond to therapeutic manipulation of a target gene (e.g., a gene encoding a BET polypeptide described herein, e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional or translation product thereof (e.g., an RNA transcript encoding the BET polypeptide or the BET polypeptide). In some embodiments, a decreased expression level and/or activity of the biomarker indicates the subject will respond or will likely respond to a therapeutic inhibition of the target gene (e.g., a gene encoding a BET protein described herein, e.g., BRD1, BRD2, BRD3, and/or BRD4) described herein or a transcriptional or translation product thereof (e.g., an RNA transcript encoding the BET polypeptide or the BET polypeptide). In some embodiments, the presence of a loss of function mutation in the biomarker is a predictive indicator that the subject will respond or will likely respond to a therapeutic inhibition of the target gene (e.g., a gene encoding a BET polypeptide described herein, e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional or translation product thereof (e.g., an RNA transcript encoding the BET polypeptide or the BET polypeptide).

As used herein, a “tissue sample” refers to a collection of similar cells obtained from a tissue of the subject, e.g., cancer tissue. In some embodiments, the tissue sample is a fresh, frozen, and/or preserved organ, biopsy, and/or aspirate obtained from the subject. In some embodiments, the tissue sample is blood or any blood constituent (e.g., plasma) collected from the subject. In some embodiments, the tissue sample is blood or any blood constituent (e.g., plasma) collected from the subject containing circulating DNA of the diseased tissue (e.g., circulating tumor DNA). In some embodiments, the tissue sample is a bodily fluid (e.g., cerebral spinal fluid, amniotic fluid, peritoneal fluid, or interstitial fluid) obtained from the subject. In some embodiments, the tissue sample is obtained from the diseased tissue or organ (e.g., a cancerous tissue or organ). In some embodiments, the tissue sample comprises non-natural compounds, e.g., preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics.

As used herein, the term “responsiveness” refers to the degree to which a diseased tissue (e.g., a tumor) in a subject undergoes a desirable therapeutic change upon exposure to an inhibitor of a target gene described herein (e.g., a gene encoding a BET polypeptide) or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide). In some embodiments, the diseased tissue sample is a tumor and the desirable therapeutic outcome is reduced tumor burden, regression of tumor burden, and/or reduced growth of the tumor.

In some embodiments, an altered (e.g., increased or decreased) expression level of the biomarker in a tissue sample (e.g., cancer sample) obtained from a subject with cancer is a predictive indicator that the subject will respond or will likely respond to therapeutic manipulation of a target gene (e.g., a gene encoding a BET polypeptide) described herein or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide). As used herein, an “altered expression level” refers to an increased or decreased expression level of the biomarker in a diseased tissue sample (e.g., cancer sample) obtained from the subject relative to a reference sample. In some embodiments, a decreased expression level of the biomarker in a diseased tissue sample (e.g., cancer sample) obtained from a subject with cancer is a predictive indicator that the subject will respond or will likely respond to therapeutic inhibition of a target gene (e.g., a gene encoding a BET polypeptide) described herein or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide).

In some embodiments, an altered (e.g., increased or decreased) activity of the biomarker in a tissue sample (e.g., cancer sample) obtained from a subject with cancer is a predictive and/or prognostic indicator that the subject will respond or will likely respond to therapeutic manipulation of a target gene (e.g., a gene encoding a BET polypeptide) described herein or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide). As used herein, an “altered activity level” refers to an increased or decreased activity of the biomarker in a diseased tissue sample (e.g., cancer sample) obtained from the subject relative to a reference sample. In some embodiments, a decreased activity of the biomarker in a tissue sample (e.g., cancer sample) obtained from a subject with cancer is a predictive indicator that the subject will respond or will likely respond to therapeutic inhibition of a target gene (e.g., a gene encoding a BET polypeptide) described herein or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide).

As used herein, a “reference sample,” “reference cell,” “reference tissue,” “control sample,” “control cell,” or “control tissue” each refer to a sample, cell, tissue, standard, or level that is used for comparison to establish whether the expression level and/or activity of the biomarker in a subject having a disease (e.g., cancer) is altered (e.g., increased or decreased) relative to a subject not having the disease (e.g., a non-cancerous subject). For example, in some embodiments, a reference sample is obtained from a subject or subjects lacking the disease or disorder (e.g., a non-cancer subject or subjects). In some embodiments, the reference sample is a non-diseased tissue obtained from the subject having the disease (e.g., cancer).

In some embodiments, the disclosure provides a biomarker comprising one or more mutations (e.g., a loss of function mutation or inactivating mutation resulting in a decreased expression level and/or activity of the biomarker) in one or more human cancers, wherein the biomarker forms a synthetic lethal pair with a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide). In some embodiments, the presence of one or more mutations in the biomarker in a diseased (e.g., cancerous) tissue sample indicates responsiveness of the disease (e.g., cancer) to a particular therapeutic intervention directed to the target gene encoding a BET polypeptide, or a transcriptional or translation product thereof, (e.g., administration of one or more therapeutic agents for modulating (e.g., decreasing) an expression level and/or activity of a BET polypeptide. In some embodiments, the presence of one or more mutations in the biomarker is detected in a tissue sample obtained from a subject having cancer. In some embodiments, the presence of one or more mutations in the biomarker is a predictive indicator that the subject’s cancer will respond or will likely respond to therapeutic manipulation of the target gene encoding a BET polypeptide, or a transcriptional or translation product thereof. In some embodiments, the presence of one or more mutations in the biomarker that is a loss of function mutation (e.g., results in a decreased expression level and/or activity of the biomarker) is a predictive indicator that the subject’s cancer will respond or will likely respond one or more therapeutic agents for modulating the target gene encoding a BET polypeptide, or a transcriptional or translation product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide).

In some embodiments, the expression level and/or activity of the biomarker is altered (e.g., increased or decreased) due to one or more mutations. In some embodiments, the one or more mutations occur in the gene encoding the biomarker (e.g., homozygous mutation).

In some embodiments, the one or more mutations comprises a nonsynonymous mutation (which results in a change to the encoded protein sequence). In some embodiments, the nonsynonymous mutation occurs adjacent to or proximal to the 5' end of the open reading frame of the gene encoding the biomarker. Without being bound by theory, a nonsynonymous mutation occurring adjacent to or proximal to the 5' end of the open reading frame has increased likelihood of generating a loss of function or inactivation of the biomarker.

In some embodiments, the one or more mutations (e.g., the nonsynonymous mutation) comprises a missense mutation (point mutation that results in a codon that encodes a different amino acid residue compared to the wild-type or non-mutated amino acid sequence). In some embodiments, the missense mutation occurs adjacent to or proximal to the 5' end of the open reading frame of the gene encoding the biomarker.

In some embodiments, the one or more mutations (e.g., the nonsynonymous mutation) comprises a nonsense mutation (point mutation in the gene sequence that results in a premature stop codon or nonsense codon on the transcribed mRNA that produces a translation product that is a truncated or incomplete). In some embodiments, the nonsense mutation occurs adjacent to or proximal to the 5' end of the open reading frame of the gene encoding the biomarker.

In some embodiments, the one or more mutations (e.g., nonsynonymous mutation) comprises a nonstop mutation (point mutation occurring within translational stop codons that result in continued and inappropriate translation of mRNA transcript into the 3' untranslated region).

In some embodiments, the one or more mutations (e.g., nonsynonymous mutation) comprises an insertion of one or more nucleotides in the gene encoding the biomarker. In some embodiments, the insertion results in a frameshift mutation (change in the open reading frame of the gene encoding the biomarker).

In some embodiments, the one or more mutations (e.g., nonsynonymous mutation) comprises a deletion of one or more nucleotides in the gene encoding the biomarker. In some embodiments, the deletion results in a frameshift mutation. In some embodiments, the frameshift mutation results in a gene encoding an altered (e.g., inactivated) protein product.

In some embodiments, the one or more mutations comprises an inversion.

In some embodiments, the one or more mutations comprises a deletion-insertion.

In some embodiments, the one or more mutations comprises a missense mutation in the gene encoding the biomarker, wherein the mutated gene is predicted to encode a nonfunctional protein. For example, the mutated gene is predicted to encode a nonfunctional protein using a SIFT algorithm (see, e.g., Nature Protocols (2016) 11 : 1-9), wherein the SIFT value is equal to or approximately zero. SIFT is a sequence homology-based tool that sorts intolerant from tolerant amino acid substitutions and predicts whether an amino acid substitution in protein is likely to have a phenotypic effect. The tool is based on the premise that protein evolution correlates with protein function, wherein amino acid positions important for function are more likely to be conserved in an alignment of the protein family and less important amino acid positions will be more diverse in the alignment. A SIFT score ranges from 0 to 1 , wherein an amino acid substitution is predicted as intolerant (e.g., resulting in a nonfunctional protein) if the score is < 0.05 and tolerated if the score is > 0.05. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations

In some embodiments, the one or more mutations is a duplication, a deletion, or an insertion in the gene encoding the biomarker. In some embodiments, the duplication, deletion, or insertion results in a frameshift mutation.

In some embodiments, the one or more mutation alters (e.g., increases or decreases) the expression of the gene encoding the biomarker. In some embodiments, the one or more mutations comprises a splice site mutation. In some embodiments, the one or more mutations (e.g., splice site mutation) results in altered splicing of a transcriptional product of the gene encoding the biomarker. In some embodiments, the one or more mutations results in a transcriptional product having impaired nuclear translocation. In some embodiments, the one or more mutations results in a transcriptional product having impaired translation. In some embodiments, the one or more mutations results in a translational product having a non-natural substitution of one amino acid for another. In some embodiments, the one or more mutations results in a translational product having a deletion or an insertion of one or more amino acid residues. In some embodiments, the one or more mutations results in a truncated translational product. In some embodiments, the one or more mutations results in translational product that is a fusion with another protein. In some embodiments, the translational product is inactive or has low activity relative to a translational product expressed from a wild-type gene encoding the biomarker.

In some embodiments, the expression level and/or activity of the biomarker is altered (e.g., increased or decreased) due to one or more deficiency in the biomarker. In some embodiments, the one or more deficiencies are selected from multiple copies of the same gene, hypermethylation, deep deletion, mutation in the gene encoding the biomarker, or a combination thereof.

In some embodiments, the presence of a mutation and/or a deficiency in the biomarker is measured in a tissue sample (e.g., cancer sample) obtained from the subject using a method of mutational detection analysis (e.g., next generation sequencing). In some embodiments, the tissue sample is a tumor biopsy sample (e.g., fresh or fixed tumor biopsy sample). In some embodiments, the tissue sample is a blood sample comprising circulating tumor DNA.

In some embodiments, the one or more mutations and/or deficiencies in the biomarker are prevalent in one or more human cancers. As used herein, “prevalent” refers to the frequency in which a mutation in, an altered expression level of, and/or an altered activity of a biomarker relative to a reference sample occurs in a demographic of subjects affected by a particular type of cancer (e.g., colon adenocarcinoma). In some embodiments, the one or more deficiencies is prevalent (e.g., frequency greater than about 0.5%, about 1%, about 2%, about 3%, about 4%, about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, or about 50%) in one or more human cancers. In some embodiments, the one or more human cancers is selected from prostate adenocarcinoma (PRAD), uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), uterine carcinosarcoma (UCS), liver hepatocellular carcinoma (LIHC), bladder urothelial carcinoma (BLCA), ovarian serous cystadenocarcinoma (OV), lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LU AD), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), esophageal carcinoma (ESCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), sarcoma (SARC), testicular germ cell tumors (TGCT), kidney renal clear cell carcinoma (KIRC), uveal melanoma (UVM), adrenocortical carcinoma (ACC), acute myeloid leukemia (LAML), kidney renal papillary cell carcinoma (KIRP), glioblastoma multiforme (GBM), brain lower grade glioma (LGG), kidney chromophobe (KICH), mesothelioma (MESO), pheochromocytoma and paraganglioma (PCPG), thyroid carcinoma (THCA), thymoma (THYM).

In some embodiments, the presence of such genetic mutations is identified by assaying tissue-derived cells obtained from a subject. For example, suitable assays for use in the present disclosure include those involving genomic DNA, mRNA, or cDNA. For a nucleic acid-based detection method, genomic DNA is first obtained (using any standard technique) from cells (e.g., ovarian cells) of a subject to be tested. If appropriate, cDNA can be prepared or mRNA can be obtained. In some instances, nucleic acids can be amplified by any known nucleic acid amplification technique (e.g., polymerase chain reaction) to a sufficient quantity and purity, and further analyzed to detect mutations. For example, genomic DNA can be isolated from a sample, and all exonic sequences, and the intron/exon junction regions including the regions required for exon/intron splicing, can be amplified into one or more amplicons and further analyzed for the presence or absence of mutations. In some instances, the assay is a next generation sequencingbased assay, such as FoundationOne®CDx™ or Tempus xT™. In some embodiments, the presence of a mutation in a biomarker of the disclosure is detected using any method of mutational detection analysis that is known in the art. Non-limiting exemplary methods of mutational detection analysis include fluorescence in situ hybridization (FISH), PCR, RT-PCR, gel electrophoresis, DNA microarray, DNA sequencing (e.g., via next generation sequencing or Sanger sequencing), multiplex ligation-dependent probe amplification, fluorescent melting curve analysis, allele-specific oligonucleotide hybridization, and pyrosequencing.

Exemplary Synthetic Lethality Biomarkers

In some embodiments, the disclosure provides one or more biomarkers having an altered expression level and/or activity in one or more human cancers, wherein the one or more biomarkers each form a synthetic lethal pair with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4).

In humans, the family of bromodomain and extra terminal containing (BET)-containing proteins includes BRD1, BRD2, BRD3, and BRD4. The bromodomain motif mediates protein- protein interactions with acetylated lysine residues (Ali, et al (2018) Chem Rev 118:1216), allowing the BET proteins to bind to acetylated histones at transcription start sites and function in regulating gene transcription (Hajmirza, et al (2018) Biomedicines 6: 16). Therapeutic inhibition of BET proteins for treatment of cancer has been explored, but clinical progression has been hampered due to variable clinical responses, dose-limiting toxicities, and development of resistance (Marcotte et al (2016) Cell 164:293). Without being bound by theory, therapeutic inhibition of one or more BET proteins in a subject having a cancer comprising a mutation in (e.g., a loss of function mutation in), an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity of one or more biomarkers described herein (e.g., a biomarker listed in Table 2) results in an improved response to the therapeutic inhibition as compared to a subject without the mutation, altered expression level, and/or altered activity. In some embodiments, the improved response comprises decreased tumor progression. In some embodiments, the improved response comprises tumor shrinkage. In some embodiments, the improved response comprises reduced risk of metastasis. In some embodiments, the improved response comprises reduced risk of recurrence. In some embodiments, the improved response is achieving complete response, partial response or stable disease.

In some embodiments, the disclosure provides one or more biomarkers having a loss of function in one or more human cancers, wherein the one or more biomarkers each form a synthetic lethal pair with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the disclosure provides one or more biomarkers comprising a mutation in one or more human cancers, wherein the one or more biomarkers each form a synthetic lethal pair with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the disclosure provides one or more biomarkers that are mutated in one or more human cancers, wherein the one or more biomarkers each form a synthetic lethal pair with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM).

In some embodiments, an altered (e.g., increased or decreased) expression level of the biomarker in a cancer tissue obtained from a subject is a predictive indicator that the subject will or will likely respond to therapeutic manipulation of a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM) or a transcriptional product thereof or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide). In some embodiments, a decreased expression level of the biomarker in a cancer tissue obtained from a subject is a predictive indicator the subject will or will likely respond to therapeutic inhibition of a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional product thereof or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide). In some embodiments, a mutation in the biomarker (e.g., a loss of function mutation resulting in a decreased expression level and/or activity of the biomarker) in a cancer tissue obtained from a subject is a predictive indicator that the subject will or will likely respond to therapeutic manipulation of a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional product thereof or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide). In some embodiments, the response comprises decreased tumor progression. In some embodiments, the response comprises tumor shrinkage. In some embodiments, the response comprises reduced risk of metastasis.

In some embodiments, a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) and a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) form a synthetic lethal pair, such that a decreased expression level and/or activity of (i) the gene encoding the biomarker or a transcriptional or translation product thereof; and (ii) target gene encoding a BET polypeptide or a transcriptional product thereof or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide) is lethal to the cell (e.g., results in apoptosis, necrosis, inhibition of proliferation, or substantially reduced viability), whereas a decreased expression level and/or activity of either (i) or (ii) alone has minimal or no substantial effect on the viability of the cell (e.g., is not sufficient to kill the cell). In some embodiments, a cell or a population of cells having an altered (e.g., decreased or diminished) expression level and/or activity of (i) the gene encoding a biomarker described herein (e.g., TNKS) or a transcriptional or translation product thereof, or (ii) a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional product thereof or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide) has decreased viability, but a combination of (i) and (ii) results in a greater reduction in viability of the cell or the population of cells in comparison. In some embodiments, a population of cells (e.g., a population of cancer cells) comprising a decreased expression level and/or activity of (i) the gene encoding a biomarker described herein (e.g., TNKS and/or a biomarker listed in Table 2) or a transcriptional or translation product thereof; and (ii) a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or a transcriptional product thereof or translational product thereof (e.g., an RNA transcript encoding a BET polypeptide or a BET polypeptide) has a proportion of dead or dying cells that is greater (e.g., than the sum proportion of the dead or dying cells in a first cell population comprising (i) and a second cell population comprising (ii).

In some embodiments, the biomarker is a polypeptide that regulates the beta-catenin pathway. In some embodiments, the biomarker is a polypeptide that promotes the function or activity of beta-catenin. In some embodiments, the biomarker that regulates the beta-catenin pathway is TNKS. In some embodiments, the target gene encodes a polypeptide that regulates the beta-catenin pathway. In some embodiments, the target gene encodes a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a cancer cell or a population of cells having a decreased expression level and/or activity of (i) the gene encoding a biomarker that regulates the beta-catenin pathway (e.g., TNKS), or a transcriptional or translational product thereof, or (ii) a target gene encoding a polypeptide that regulates the beta-catenin pathway (e.g., a BET polypeptide), or a transcriptional product thereof or translational product thereof, undergoes proliferation mediated by the beta-catenin pathway; but a combination of (i) and (ii) results in reduced proliferation as a result of decreased activity and/or expression of beta-catenin.

In some embodiments, a biomarker of the disclosure is one identified as forming a synthetic lethal pair with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) using a method described herein. Table 2 provides biomarkers that are human genes identified as synthetic lethal pairs with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) using a computational method described herein. Table 2 further provides a gene identification number for each human gene that the skilled artisan may use to identify the gene in the National Library of Medicine National Center for Biotechnology Information (NCBI) Gene Database (accessible via the world wide web: ncbi.nlm.nih.gov/). The Gene Database is a searchable database of genes that provides nomenclature, chromosomal localization, gene products, attributes of the gene, associated markers, phenotypes, interactions, links to citations, sequence information, information regarding sequence variants, gene maps, expression reports, homologs, protein domain content, and access to external databases. As is understood by the skilled artisan, the nucleotide sequence corresponding to each gene in Table 2 is accessed by entering the corresponding Gene ID into the NCBI Gene Database and selecting the genomic sequence in the desired format computer-readable formats (e.g., FASTA).

In some embodiments, a biomarker of the disclosure is selected from Table 2. In some embodiments, the biomarker is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP. In some embodiments, the biomarker is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8. In some embodiments, the biomarker is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP.

In some embodiments, a biomarker of the disclosure is TP53. In some embodiments, a biomarker of the disclosure is SMAD4. In some embodiments, a biomarker of the disclosure is PTEN. In some embodiments, a biomarker of the disclosure is CREBBP. In some embodiments, a biomarker of the disclosure is SMARCA4. In some embodiments, a biomarker of the disclosure is PBRM1. In some embodiments, a biomarker of the disclosure is VHL. In some embodiments, a biomarker of the disclosure is APC. In some embodiments, a biomarker of the disclosure is JAKE In some embodiments, a biomarker of the disclosure is RBI. In some embodiments, a biomarker of the disclosure is MLH1. In some embodiments, a biomarker of the disclosure is STAG2. In some embodiments, a biomarker of the disclosure is LTK. In some embodiments, a biomarker of the disclosure is CTCF. In some embodiments, a biomarker of the disclosure is ADAMTS12. In some embodiments, a biomarker of the disclosure is B2M. In some embodiments, a biomarker of the disclosure is BRAF. In some embodiments, a biomarker of the disclosure is CDCA2. In some embodiments, a biomarker of the disclosure is CDH13. In some embodiments, a biomarker of the disclosure is CDK7. In some embodiments, a biomarker of the disclosure is CHD3. In some embodiments, a biomarker of the disclosure is TNKS. In some embodiments, a biomarker of the disclosure is TENM3. In some embodiments, a biomarker of the disclosure is THSD7B. In some embodiments, a biomarker of the disclosure is SETDB2. In some embodiments, a biomarker of the disclosure is TUSC3. In some embodiments, a biomarker of the disclosure is PCLO. In some embodiments, a biomarker of the disclosure is PLK2. In some embodiments, a biomarker of the disclosure is PSD3. In some embodiments, a biomarker of the disclosure is REV3L. In some embodiments, a biomarker of the disclosure is JAK2. In some embodiments, a biomarker of the disclosure is KRAS. In some embodiments, a biomarker of the disclosure is DNAH3. In some embodiments, a biomarker of the disclosure is ERBB2. In some embodiments, a biomarker of the disclosure is FGFR1. In some embodiments, a biomarker of the disclosure is GRM2. In some embodiments, a biomarker of the disclosure is IKBKB. In some embodiments, a biomarker of the disclosure is KAT6A. In some embodiments, a biomarker of the disclosure is KMT2C. In some embodiments, a biomarker of the disclosure is MAST4. In some embodiments, a biomarker of the disclosure is MBP. In some embodiments, a biomarker of the disclosure is CHD4. In some embodiments, a biomarker of the disclosure is CHD8.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TP53. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker SMAD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PTEN. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CREBBP. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker SMARCA4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PBRM1.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker VHL and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker APC and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK1 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker RBI and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MLH1 and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker STAG2 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker LTK and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CTCF and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ADAMTS12 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker B2M and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker BRAF and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDCA2 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDH13 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDK7 and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD3 and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TNKS and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TENM3 and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker THSD7B and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker SETDB2 and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TUSC3 and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PCLO and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PLK2 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PSD3 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker REV3L and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK2 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KRAS and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker DNAH3 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ERBB2 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker FGFR1 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker GRM2 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker IKBKB and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KAT6A and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KMT2C and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MAST4 and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MBP and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD4 and a target gene encoding a BET polypeptide (e.g., BRD1, BRIM, BRIM, and/or BRIM). In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD8 and a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4).

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) VHL; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) APC; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) JAK1; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) RBI; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) MLH1; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) STAG2; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) LTK; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) CTCF; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) ADAMTS12; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) B2M; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) BRAF; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) CDCA2; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRIM, and/or BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) CDH13; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRIM, and/or BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) CDK7; and (ii) one or more BET polypeptides selected from BRD1, BRIM, BRIM, and/or BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) CHD3; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) TNKS; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) TENM3; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) THSD7B; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) SETDB2; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) TUSC3; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) PCLO; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) PLK2; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) PSD3; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) REV3L; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) JAK2; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) KRAS; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) DNAH3; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) ERBB2; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) FGFR1; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) GRM2; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) IKBKB; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) KAT6A; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) KMT2C; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) MAST4; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) MBP; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) CHD4; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker (i) CHD8; and (ii) one or more BET polypeptides selected from BRD1, BRD2, BRD3, and/or BRD4.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker VHL and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker APC and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK1 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker RBI and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MLH1 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker STAG2 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker LTK and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CTCF and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ADAMTS12 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker B2M and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker BRAF and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDCA2 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDH13 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDK7 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD3 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TNKS and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TENM3 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker THSD7B and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker SETDB2 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TUSC3 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PCLO and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PLK2 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PSD3 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker REV3L and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK2 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KRAS and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker DNAH3 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ERBB2 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker FGFR1 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker GRM2 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker IKBKB and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KAT6A and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KMT2C and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MAST4 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MBP and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD4 and BRD1. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD8 and BRD1.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker VHL and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker APC and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK1 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker RBI and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MLH1 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker STAG2 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker LTK and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CTCF and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ADAMTS12 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker B2M and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker BRAF and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDCA2 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDH13 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDK7 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD3 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TNKS and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TENM3 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker THSD7B and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker SETDB2 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TUSC3 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PCLO and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PLK2 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PSD3 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker REV3L and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK2 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KRAS and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker DNAH3 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ERBB2 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker FGFR1 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker GRM2 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker IKBKB and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KAT6A and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KMT2C and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MAST4 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MBP and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD4 and BRD2. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD8 and BRD2.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker VHL and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker APC and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK1 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker RBI and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MLH1 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker STAG2 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker LTK and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CTCF and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ADAMTS12 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker B2M and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker BRAF and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDCA2 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDH13 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDK7 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD3 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TNKS and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TENM3 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker THSD7B and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker SETDB2 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TUSC3 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PCLO and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PLK2 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PSD3 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker REV3L and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK2 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KRAS and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker DNAH3 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ERBB2 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker FGFR1 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker GRM2 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker IKBKB and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KAT6A and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KMT2C and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MAST4 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MBP and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD4 and BRD3. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD8 and BRD3.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker VHL and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker APC and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK1 and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker RBI and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MLH1 and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker STAG2 and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker LIK and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CTCF and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ADAMTS12 and BRIM. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker B2M and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker BRAF and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDCA2 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDH13 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CDK7 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD3 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TNKS and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TENM3 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker THSD7B and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker SETDB2 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TUSC3 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PCLO and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PLK2 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PSD3 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker REV3L and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK2 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KRAS and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker DNAH3 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker ERBB2 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker FGFR1 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker GRM2 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker IKBKB and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KAT6A and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker KMT2C and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MAST4 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker MBP and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD4 and BRD4. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker CHD8 and BRD4.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker TNKS and a target gene encoding a BET polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker TNKS and a target gene encoding a BRD1 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker TNKS and a target gene encoding a BRD2 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker TNKS and a target gene encoding a BRD3 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker TNKS and a target gene encoding a BRD4 polypeptide. In some embodiments, the expression level and/or activity of TNKS is decreased in one or more human cancers due to at least one mutation. In some embodiments, the at least one mutation is selected from a duplication, a deletion, and an insertion in the TNKS gene. In some embodiments, the duplication, deletion, or insertion results in a frameshift mutation in the TNKS gene. In some embodiments, the at least one mutation is a deletion of the TNKS gene. In some embodiments, the at least one mutation is a homozygous deletion of the TNKS gene. In some embodiments, the at least one mutation is a missense mutation in the TNKS gene. In some embodiments, the missense mutation in the TNKS gene encodes a nonfunctional TNKS polypeptide. In some embodiments, the at least one mutation is a nonsense mutation in the TNKS gene. In some embodiments, the nonsense mutation results in a premature stop codon or nonsense codon in the TNKS RNA transcript, wherein translation of the RNA transcript produces a truncated or incomplete TNKS polypeptide. In some embodiments, the at least one mutation comprises a nonstop mutation in the TNKS gene. In some embodiments, the nonstop mutation in the TNKS gene produces a RNA transcript that continues into the 3'UTR. In some embodiments, the RNA transcript encodes a longer TNKS protein that is non- functional or inactivated. In some embodiments, the at least one mutation comprises an insertion of one or more nucleotides in the TNKS gene. In some embodiments, the insertion results in a frameshift mutation in the TNKS gene or a change in the open reading frame of the TNKS gene. In some embodiments, the at least one mutation comprises a deletion of one or more nucleotides in the TNKS gene. In some embodiments, the deletion results in a frameshift mutation. In some embodiments, the frameshift mutation results in a TNKS gene encoding an altered TNKS polypeptide that is inactivated. In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker PTEN and a target gene encoding a BET polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker PTEN and a target gene encoding a BRD1 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker PTEN and a target gene encoding a BRD2 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker PTEN and a target gene encoding a BRD3 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker PTEN and a target gene encoding a BRD4 polypeptide. In some embodiments, the expression level and/or activity of PTEN is decreased in one or more human cancers due to at least one mutation. In some embodiments, the at least one mutation is selected from a duplication, a deletion, and an insertion in the PTEN gene. In some embodiments, the duplication, deletion, or insertion results in a frameshift mutation in the PTEN gene. In some embodiments, the at least one mutation is a deletion of the PTEN gene. In some embodiments, the at least one mutation is a homozygous deletion of the PTEN gene. In some embodiments, the at least one mutation is a missense mutation in the PTEN gene. In some embodiments, the missense mutation in the PTEN gene encodes a nonfunctional PTEN polypeptide. In some embodiments, the at least one mutation is a nonsense mutation in the PTEN gene. In some embodiments, the nonsense mutation results in a premature stop codon or nonsense codon in the PTEN RNA transcript, wherein translation of the RNA transcript produces a truncated or incomplete PTEN polypeptide. In some embodiments, the at least one mutation comprises a nonstop mutation in the PTEN gene. In some embodiments, the nonstop mutation in the PTEN gene produces a RNA transcript that continues into the 3 TJTR. In some embodiments, the RNA transcript encodes a longer PTEN protein that is non-functional or inactivated. In some embodiments, the at least one mutation comprises an insertion of one or more nucleotides in the PTEN gene. In some embodiments, the insertion results in a frameshift mutation in the PTEN gene or a change in the open reading frame of the PTEN gene. In some embodiments, the at least one mutation comprises a deletion of one or more nucleotides in the PTEN gene. In some embodiments, the deletion results in a frameshift mutation. In some embodiments, the frameshift mutation results in a PTEN gene encoding an altered PTEN polypeptide that is inactivated.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker RBI and a target gene encoding a BET polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker RBI and a target gene encoding a BRD1 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker RBI and a target gene encoding a BRD2 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker RBI and a target gene encoding a BRD3 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker RBI and a target gene encoding a BRD4 polypeptide. In some embodiments, the expression level and/or activity of RBI is decreased in one or more human cancers due to at least one mutation. In some embodiments, the at least one mutation is selected from a duplication, a deletion, and an insertion in the RBI gene. In some embodiments, the duplication, deletion, or insertion results in a frameshift mutation in the RBI gene. In some embodiments, the at least one mutation is a deletion of the RBI gene. In some embodiments, the at least one mutation is a homozygous deletion of the RBI gene. In some embodiments, the at least one mutation is a missense mutation in the RBI gene. In some embodiments, the missense mutation in the RBI gene encodes a nonfunctional RBI polypeptide. In some embodiments, the at least one mutation is a nonsense mutation in the RBI gene. In some embodiments, the nonsense mutation results in a premature stop codon or nonsense codon in the RBI RNA transcript, wherein translation of the RNA transcript produces a truncated or incomplete RBI polypeptide. In some embodiments, the at least one mutation comprises a nonstop mutation in the RBI gene. In some embodiments, the nonstop mutation in the RBI gene produces a RNA transcript that continues into the 3 TJTR. In some embodiments, the RNA transcript encodes a longer RBI protein that is non-functional or inactivated. In some embodiments, the at least one mutation comprises an insertion of one or more nucleotides in the RBI gene. In some embodiments, the insertion results in a frameshift mutation in the RBI gene or a change in the open reading frame of the RBI gene. In some embodiments, the at least one mutation comprises a deletion of one or more nucleotides in the RBI gene. In some embodiments, the deletion results in a frameshift mutation. In some embodiments, the frameshift mutation results in a RBI gene encoding an altered RBI polypeptide that is inactivated.

In some embodiments, a synthetic lethal pair of the disclosure comprises the biomarker JAK1 and a target gene encoding a BET polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker JAK1 and a target gene encoding a BRD1 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker JAK1 and a target gene encoding a BRD2 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker JAK1 and a target gene encoding a BRD3 polypeptide. In some embodiments, the synthetic lethal pair comprises the biomarker JAK1 and a target gene encoding a BRD4 polypeptide. In some embodiments, the expression level and/or activity of JAK1 is decreased in one or more human cancers due to at least one mutation. In some embodiments, the at least one mutation is selected from a duplication, a deletion, and an insertion in the JAK1 gene. In some embodiments, the duplication, deletion, or insertion results in a frameshift mutation in the JAK1 gene. In some embodiments, the at least one mutation is a deletion of the JAK1 gene. In some embodiments, the at least one mutation is a homozygous deletion of the JAK1 gene. In some embodiments, the at least one mutation is a missense mutation in the JAK1 gene. In some embodiments, the missense mutation in the JAK1 gene encodes a nonfunctional JAK1 polypeptide. In some embodiments, the at least one mutation is a nonsense mutation in the JAK1 gene. In some embodiments, the nonsense mutation results in a premature stop codon or nonsense codon in the JAK1 RNA transcript, wherein translation of the RNA transcript produces a truncated or incomplete JAK1 polypeptide. In some embodiments, the at least one mutation comprises a nonstop mutation in the JAK1 gene. In some embodiments, the nonstop mutation in the JAK1 gene produces a RNA transcript that continues into the 3TJTR. In some embodiments, the RNA transcript encodes a longer JAK1 protein that is non-functional or inactivated. In some embodiments, the at least one mutation comprises an insertion of one or more nucleotides in the JAK1 gene. In some embodiments, the insertion results in a frameshift mutation in the JAK1 gene or a change in the open reading frame of the JAK1 gene. In some embodiments, the at least one mutation comprises a deletion of one or more nucleotides in the JAK1 gene. In some embodiments, the deletion results in a frameshift mutation. In some embodiments, the frameshift mutation results in a JAK1 gene encoding an altered JAK1 polypeptide that is inactivated.

In some embodiments, the at least one mutation comprises an inversion. In some embodiments, the at least one mutation comprises a deletion-insertion.

Methods of Identifying Synthetic Lethal Pairs

The present disclosure provides methods for identifying a biomarker that forms a synthetic lethal pair with a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the biomarker has altered (e.g., increased or decreased) expression level and/or activity in one or more human cancers, e.g., due to one or more mutations in the gene encoding the biomarker. In some embodiments, the presence of a mutated biomarker in a human cancer is an indicator (e.g., predictive indicator) that the cancer will respond or will likely respond to one or more therapeutic agents targeting the target gene (e.g., one or more therapeutic agents targeting a BET polypeptide), such as one or more therapeutic agents that inhibit the target gene or a transcriptional or translational product thereof.

Computational Approaches

In some embodiments, the disclosure provides one or more biomarkers identified using a computational approach described herein. In some embodiments, one or more biomarkers having altered expression level and/or activity in one or more human cancers that potentially form a synthetic lethal pair with a target gene (e.g., a gene encoding a BET polypeptide) are identified based on the literature and public data, and candidates identified by, for example, criteria including multi-omics analysis, evaluation of tumor type (e.g., primary tumor), experimental data in relevant cell lines, target tractability, biomarker prevalence, etc.

In some embodiments, a predictive algorithm is applied to a dataset compiled from functional gene interference screens to identify a biomarker of the disclosure. Functional genomic screens based on RNA interference technologies (e.g., short hairpin (shRNA)-based technology) and/or gene-editing technologies (e.g., CRISPR/Cas technology) enable geneknockout studies to be performed across many different genetic contexts (see, e.g., Huang, et al (2020) Nat. Rev. Drug Disc. 19:23). Several public databases provide catalogs of such data, including, for example, Project DRIVE (see, e.g., McDonald, et al (2017) Cell 170:577); Project Achilles (see, e.g., word wide web: depmap.org/portal/achilles); and Project Score (see, e.g., Behan, et al (2019) Nature 568:511). Predictive algorithms are applied to such large datasets to identify for correlations between target gene silencing, functional outcome (e.g., lethality), and genetic background to identify putative synthetic lethal interactions in human cancer cells. In some embodiments, a predictive algorithm of the disclosure comprises one or more prediction criteria to predict a biomarker that will form a synthetic lethal pair with a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4).

In some embodiments, a machine learning approach is used in conjunction with a database of known synthetic lethal gene interactions to identify a biomarker of the disclosure. In some embodiments, the database comprises comprehensive and rigorously curated information on synthetic lethal interactions collected from publications and/or experimental datasets. In some embodiments, the machine learning algorithm considers one or more different features of the interacting genes based on a genetic interaction database. In some embodiments, the one or more different features are intended to capture the genomics, network and functional relationships between the putative synthetic lethal gene pairs. In some embodiments, a machine learning approach comprises one or more prediction criteria to predict a biomarker that will form a synthetic lethal pair with a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4).

In some embodiments, a biomarker of the disclosure is identified according to a predictive algorithm and/or machine learning algorithm described herein and comprises an inactivating mutation in a gene in a cancer. In some embodiments, the cancer is any one or any combination of human cancers listed in the TCGA (Cancer Genome Atlas Program; see world wide web: cancer.gov/tcga). In some embodiments, the cancer is any one or any combination of prostate adenocarcinoma (PRAD), uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), uterine carcinosarcoma (UCS), liver hepatocellular carcinoma (LIHC), bladder urothelial carcinoma (BLCA), ovarian serous cystadenocarcinoma (OV), lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LU AD), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), esophageal carcinoma (ESCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), sarcoma (SARC), testicular germ cell tumors (TGCT), kidney renal clear cell carcinoma (KIRC), uveal melanoma (UVM), adrenocortical carcinoma (ACC), acute myeloid leukemia (LAML), kidney renal papillary cell carcinoma (KIRP), glioblastoma multiforme (GBM), brain lower grade glioma (LGG), kidney chromophobe (KICH), mesothelioma (MESO), pheochromocytoma and paraganglioma (PCPG), thyroid carcinoma (THCA), thymoma (THYM).

In some embodiments, the inactivating mutation is a homozygous deletion of a gene. In some embodiments, the inactivating mutation is a missense mutation in a gene predicted to encode a nonfunctional protein. In some embodiments, the inactivating mutation is a missense mutation in a gene predicted to encode a truncated protein. In some embodiments, the inactivating mutation occurs in at least about 1%, about 1.5%, about 2%, about 2.5%, about 3%, about 3.5%, about 4%, about 4.5%, or about 5% subjects having the cancer (e.g., any one or any combination of human cancers listed in the TCGA). In some embodiments, the inactivating mutation occurs in more than about 5% of subjects having the cancer (e.g., any one or any combination of human cancers listed in the TCGA).

In some embodiments, the inactivating mutation occurs in at least about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 12%, about 15%, or about 20% subjects having the cancer (e.g., any one or any combination of human cancers listed in the TCGAj.In some embodiments, the inactivating mutation occurs in at least about 1%, about 1.5%, about 2%, about 2.5%, about 3%, about 3.5%, about 4%, about 4.5%, or about 5% subjects of a first cancer (e.g., a first human cancer listed in the TCGA), and in at least about 1%, about 1.5%, about 2%, about 2.5%, about 3%, about 3.5%, about 4%, about 4.5%, or about 5% subjects of a second cancer (e.g., a second human cancer listed in the TCGA).

In some embodiments, the inactivating mutation occurs in (i) at least about 5% of subject having a cancer (e.g., any one or any combination of human cancers listed in the TCGA); and (ii) at least about 3% of subjects having a first cancer (e.g., a first human cancer listed in the TCGA) and at least about 3% of subjects having a second cancer (e.g., a second human cancer listed in the TCGA).

In some embodiments, the biomarker that form a synthetic lethal pair with a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) is TNKS.

In some embodiments, the inactivating mutation is a homozygous deletion of TNKS. In some embodiments, the homozygous deletion occurs in at least about 0.5%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, or about 15% of subjects having the cancer. In some embodiments, the cancer is selected from prostate adenocarcinoma (PRAD), uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), uterine carcinosarcoma (UCS), liver hepatocellular carcinoma (LIHC), bladder urothelial carcinoma (BLCA), ovarian serous cystadenocarcinoma (OV), lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LU AD), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), esophageal carcinoma (ESCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), cholangiocarcinoma (CHOL), pancreatic adenocarcinoma (PAAD), sarcoma (SARC), testicular germ cell tumors (TGCT), kidney renal clear cell carcinoma (KIRC), uveal melanoma (UVM), adrenocortical carcinoma (ACC), and kidney renal papillary cell carcinoma (KIRP).

In some embodiments, the inactivating mutation is a missense mutation encoding a nonfunctional TNKS polypeptide. In some embodiments, the missense mutation occurs in at least about 0.1%, about 0.5%, about 1%, about 1.5%, about 2%, about 2.5%, about 3%, about 3.5%, about 4%, about 4.5%, or about 5% subjects having the cancer. In some embodiments, the cancer is selected from, uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), bladder urothelial carcinoma (BLCA), lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LU AD), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), esophageal carcinoma (ESCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), pancreatic adenocarcinoma (PAAD), sarcoma (SARC), kidney renal clear cell carcinoma (KIRC), and glioblastoma multiforme (GBM).

In some embodiments, the inactivating mutation is a mutation in the TNKS gene that produces a truncated or incomplete TNKS polypeptide. In some embodiments, the inactivating mutation is a nonsense mutation in the TNKS gene that results in a premature stop codon or nonsense codon in the TNKS RNA transcript, wherein translation of the RNA transcript produces a truncated or incomplete TNKS polypeptide. In some embodiments, the mutation that produces a truncated TNKS polypeptide occurs in at least about 0.1%, about 0.5%, about 1%, about 1.5%, about 2%, about 2.5%, about 3%, about 3.5%, about 4%, about 4.5%, or about 5% subjects having the cancer. In some embodiments, the cancer is selected from uterine corpus endometrial carcinoma (UCEC), colon adenocarcinoma (COAD), rectum adenocarcinoma (READ), liver hepatocellular carcinoma (LIHC), ovarian serous cystadenocarcinoma (OV), lung adenocarcinoma (LU AD), breast invasive carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), testicular germ cell tumors (TGCT), acute myeloid leukemia (LAML), and glioblastoma multiforme (GBM). In some embodiments, the inactivating mutation is in TNKS in a cancer selected from prostate cancer (e.g., prostate adenocarcinoma (PRAD)) and colorectal cancer (e.g., colon adenocarcinoma (COAD)).

In some embodiments, the inactivating mutation is in JAK1. In some embodiments, the inactivating mutation is a missense mutation in JAK1. In some embodiments, the inactivating mutation is a heterozygous deletion of JAK1. In some embodiments, the inactivating mutation is a homozygous deletion of JAK1. In some embodiments, the inactivating mutation is a missense mutation encoding a nonfunctional JAK1 polypeptide. In some embodiments, the inactivating mutation is a mutation in the JAK1 gene that produces a truncated or incomplete JAK1 polypeptide. In some embodiments, the inactivating mutation is a nonsense mutation in the JAK1 gene that results in a premature stop codon or nonsense codon in the JAK1 RNA transcript, wherein translation of the RNA transcript produces a truncated or incomplete JAK1 polypeptide. In some embodiments, the inactivating mutation in JAK1 occurs in at least about 0.5%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, or about 15% of subjects having the cancer. In some embodiments, the inactivating mutation is in JAK1 in uterine cancer (e.g., uterine corpus endometrial carcinoma (UCEC) or uterine carcinosarcoma (UCS)).

In some embodiments, the inactivating mutation is in RBI. In some embodiments, the inactivating mutation is a missense mutation in RBI. In some embodiments, the inactivating mutation is a heterozygous deletion of RBI. In some embodiments, the inactivating mutation is a homozygous deletion of RBI. In some embodiments, the inactivating mutation is a missense mutation encoding a nonfunctional RBI polypeptide. In some embodiments, the inactivating mutation is a mutation in the RBI gene that produces a truncated or incomplete RBI polypeptide. In some embodiments, the inactivating mutation is a nonsense mutation in the RBI gene that results in a premature stop codon or nonsense codon in the RBI RNA transcript, wherein translation of the RNA transcript produces a truncated or incomplete RBI polypeptide. In some embodiments, the inactivating mutation in RBI occurs in at least about 0.5%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, or about 15% of subjects having the cancer. In some embodiments, the inactivating mutation is in RBI in a cancer selected from bladder cancer (e.g., bladder urothelial carcinoma (BLC)), liver cancer (e.g., liver hepatocellular carcinoma (LIHC)) and lung cancer (e.g., lung squamous cell carcinoma (LUSC), lung adenocarcinoma (LUAD)).

In some embodiments, the inactivating mutation is in PTEN. In some embodiments, the inactivating mutation is a missense mutation in PTEN. In some embodiments, the inactivating mutation is a heterozygous deletion of PTEN. In some embodiments, the inactivating mutation is a homozygous deletion of PTEN. In some embodiments, the inactivating mutation is a missense mutation encoding a nonfunctional PTEN polypeptide. In some embodiments, the inactivating mutation is a mutation in the PTEN gene that produces a truncated or incomplete PTEN polypeptide. In some embodiments, the inactivating mutation is a nonsense mutation in the PTEN gene that results in a premature stop codon or nonsense codon in the PTEN RNA transcript, wherein translation of the RNA transcript produces a truncated or incomplete PTEN polypeptide. In some embodiments, the inactivating mutation in PTEN occurs in at least about 0.5%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, or about 15% of subjects having the cancer. In some embodiments, the inactivating mutation is in PTEN in a cancer selected from breast cancer (e.g., breast invasive carcinoma (BRCA)), lung small cell cancer, and prostate cancer (e.g., prostate adenocarcinoma (PRAD)).

Methods of Validating Synthetic Lethal Pairs

In some embodiments, a biomarker that forms a synthetic lethal pair with a target gene (e.g., a target gene encoding a BET polypeptide) identified by one or more computational approaches described herein is further validated using one or more experimental approaches. In some embodiments, the experimental approach comprises a gene-editing approach to validate synthetic lethal pairs. In some embodiments, a first gene encoding the biomarker identified by the one or more computational approaches described herein and a second gene encoding the target gene (e.g., BET polypeptide) are knocked down, individually or in combination, in a population of cancer cells using CRISPR/Cas gene editing, and the effect on proliferation is determined.

In some embodiments, a population of cancer cells is contacted with a first gRNA directed to a gene encoding the biomarker, wherein the first gRNA comprises a spacer sequence having sequence homology to a target sequence in the gene encoding the biomarker, and optionally a second gRNA directed to the target gene (e.g., a gene encoding a BET polypeptide) wherein the second gRNA comprises a spacer sequence having sequence homology to a target sequence in the target gene. In some embodiments, the first gRNA, and optionally second gRNA, is introduced to the population of cancer cells in combination with a site-directed endonuclease (e.g., Cas9), or a nucleic acid encoding a site-directed endonuclease, wherein the first gRNA combines with the site-directed endonuclease to introduce a first genomic cleavage proximal to the target sequences in the gene encoding the biomarker, wherein the optional second gRNA combines with the site-directed endonuclease to introduce a second genomic cleavage proximal to the target sequence in the target gene (e.g., a gene encoding a BET polypeptide), and wherein repair of the first and second genomic cleavage by an endogenous DNA repair pathway introduces a mutation (e.g., insertion or deletion) at the sites of genomic cleavage, thereby disrupting expression of the gene encoding the biomarker and the target gene (e.g., a gene encoding a BET polypeptide). In some embodiments, the expression construct comprises replacement genes to replace TNKS in the genome (e.g., dysfunctional sequences, random DNA sequences).

In some embodiments, to determine if a predicted gene pair (e.g., a gene pair comprising a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) and a biomarker identified according to a computational method described herein) is synthetically lethal, the effect of disrupting the genes of the predicted synthetic lethal pair is determined individually and in combination by contacting a population of cells with a CRISPR/Cas system comprising a Cas nuclease, or nucleic acid or recombinant expression vector encoding the Cas nuclease, and one or more gRNAs or sgRNAs targeting a gene of the predicted gene pair, or a nucleic acid or recombinant expression vector encoding the one or more gRNAs or sgRNAs. In some embodiments, a population of cells is contacted with a control expression vector (e.g., lentiviral expression vector). For example, in some embodiments, to determine if a predicted gene pair is synthetically lethal, it is necessary to monitor the effect of disrupting either gene of the predicted synthetic lethal pair individually as well as the combination of the gene pair. Moreover, in some embodiments, it is necessary to monitor the effect of a negative control, in which a control expression vector comprises a nucleic acids sequence encoding an ineffective gRNA e.g., nonspecific gRNA, as a “non-cutting” control for one or both genes. In some embodiments, a control expression vector is a vehicle control. In some embodiments, a control expression vector is a positive control. For example, in some embodiments, an expression vector comprises a nucleic acids sequence encoding a gRNA directed to a polymerase (e.g., an RNA polymerase, e.g., P0LR2D), which can demonstrate that knockout (and the delivery mechanisms of doing so) of a gene that is essential for cell viability or proliferation results in lethality. In another example of a positive control, knockout of two genes known to be a synthetic lethal pair (e.g., methylthioadenosine phosphorylase (MTAP) and protein arginine methyltransferase 5 (PRMT5)) may be performed, e.g., using expression vectors comprising a nucleic acid sequence encoding a pair of gRNAs directed to each of the known synthetic lethal genes.

The term “contacting” as used herein means establishing a physical connection between two or more entities. Methods of contacting cells with external entities both in vivo, in vitro, and ex vivo are well known in the biological arts. In exemplary embodiments of the disclosure, the step of contacting a mammalian cell with a composition (e.g., a composition comprising a therapeutic agent described herein) is performed in vivo. For example, contacting a composition and a cell (for example, a mammalian cell) which may be disposed within an organism (e.g., a mammal) may be performed by any suitable administration route (e.g., parenteral administration to the organism, including intravenous, intramuscular, intradermal, and subcutaneous administration). For a cell present in vitro, a composition (e.g., a composition comprising a therapeutic agent described herein) and a cell may be contacted, for example, by adding the composition to the culture medium of the cell and may involve or result in transfection. Moreover, more than one cell may be contacted by the composition.

In some embodiments, to determine if a predicted gene pair (e.g., a gene pair comprising a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM) and a biomarker identified according to a computational method described herein) induces a synthetic lethal phenotype, the expression of genes of the predicted synthetic lethal pair are knocked down individually and in combination by contacting a population of cells with one or more RNAi molecules (e.g., siRNAs) targeting the genes or transcriptional products thereof. In some embodiments, comparison is made to a negative control, e.g., a cell population contacted with a control siRNA comprises a nucleic acid sequence of an ineffective siRNA, e.g., a non-specific siRNA, as a “non-targeting” control for one or both genes. In some embodiments, comparison is made to a positive control, e.g., a cell population contacted with an siRNA comprising a nucleic acid sequence which is directed to a polymerase (e.g., an RNA polymerase, e.g., P0LR2D) to demonstrate that knockdown (and the delivery mechanisms of doing so) of a gene that is essential for cell viability or proliferation results in lethality. In another example of a positive control, knockdown of two genes known to be a synthetic lethal pair (e.g., methylthioadenosine phosphorylase (MTAP) and protein arginine methyltransferase 5 (PRMT5); MTAP-PRMT5) may be performed, e.g., using siRNA sequences directed to each of the known synthetic lethal genes.

In some embodiments, the population of cancer cells comprise cells from a primary source (e.g., isolated from a tumor or cancer) or a cell line, such as any cancer cell line known in the art or described herein.

In some embodiments, the gRNAs, nucleic acids, and/or expression vectors are introduced to the population of cancer cells via transfection (e.g., using a liposome or other nanoparticle) or transduction (e.g., using a virus). In some embodiments, the site-directed endonuclease (e.g., Cas9), or a nucleic acid encoding the site-directed endonuclease (e.g., mRNA or plasmid encoding the site-directed endonuclease or Cas9), is introduced to the population of cancer cells via transfection (e.g., using a liposome or other nanoparticle) or transduction (e.g., using a virus). In some embodiments, the population of cancer cells is engineered to stably express the site-directed endonuclease. In some embodiments, the population of cancer cells is contacted with the expression vectors and/or site-directed endonuclease for a duration that is sufficient to allow for development of synthetic lethal phenotypes. In some embodiments, the population of cancer cells is contacted with the RNAi technology (e.g., siRNA) for a duration that is sufficient to allow for development of synthetic lethal phenotypes. In some embodiments, the contacting is performed for a duration of at least 5-30 days. In some embodiments, the contacting is performed for a duration that is about 7 days, about 14 days, about 21 days, about 28 days, or about 35 days. In some embodiments, proliferation or viability of the population of cancer cells is monitored over the duration. In some embodiments, the viability of the population of cancer cells is normalized or compared to a population of cancer cells contacted with a negative control expression vector or control population of cancer cells that was not treated. Methods of measuring cell viability are known in the art. In some embodiments, the method comprises a PrestoBlue viability assay. In some embodiments, the method comprises a CellTiter Gio viability assay. In some embodiments, a biomarker that forms a synthetic lethal pair with a target gene described herein (e.g., a target gene encoding a BET polypeptide) is one wherein a knockdown of the biomarker in a population of cancer cells renders the cancer cells more sensitive to treatment with an inhibitor of a target gene described herein (e.g., a gene encoding a BET polypeptide) or a transcriptional or translation product thereof. In some embodiments, the sensitivity is determined by measuring the ICso of the inhibitor in a population of cancer cells comprising a knockdown of the biomarker compared to the IC50 of the inhibitor in a control population of cancer cells (e.g., a population of cancer cells comprising normal, unmodified or wild-type expression of the biomarker). In some embodiments, the IC50 of the inhibitor in the population of cells comprising the knockdown of the biomarker is at least about 10 ¹ , about 10 ² , or about 10 ³ -fold lower than the IC50 of the inhibitor in a control population of cancer cells (e.g., a population of cancer cells comprising normal, unmodified or wild-type expression of the biomarker). In some embodiments, the knockdown of the biomarker is at least about 5-fold, about 10-fold, about 20-fold, about 30-fold, about 40-fold, about 50-fold, about 60-fold, about 70-fold, about 80-fold, about 90-fold, about 100-fold, about 110-fold, about 120-fold, about 130- fold, about 140-fold, about 150-fold, about 160-fold, about 170-fold, about 180-fold, about 190- fold, or about 200-fold lower than the IC50 of the inhibitor in a control population of cancer cells (e.g., a population of cancer cells comprising normal, unmodified or wild-type expression of the biomarker).

Methods of Use

The present disclosure provides methods for treating a subject having cancer comprising administering a therapeutic agent described herein that alters (e.g., increase or decrease) the expression and/or activity of a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the subject has a tumor characterized by the presence of a mutation in, an altered expression level of, and/or an altered activity of one or more biomarkers disclosed herein relative to a reference tissue.

The present disclosure provides methods for treating a subject having cancer comprising administering a therapeutic agent described herein (e.g., one or more therapeutic agents for decreasing the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)), wherein the subject has a tumor characterized by the presence of a mutation in (e.g., a loss of function mutation in), an altered (e.g., decreased) expression level of, and/or an altered (e.g., decreased) activity of one or more biomarkers disclosed herein (e.g., one or more biomarkers listed in Table 2) relative to a reference tissue.

The present disclosure provides methods for determining the responsiveness of a subject having cancer to treatment with a therapeutic agent described herein that alters (e.g., increase or decrease) the expression and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, the method comprising detecting the presence of a mutation in, an altered expression level of, and/or an altered activity of one or more biomarkers disclosed herein in a cancerous tissue sample obtained from the subject, wherein the presence of a mutation, an altered expression level, and or an altered activity in the cancerous tissue sample relative to a reference tissue indicates the subject will respond or will likely respond to the therapeutic agent.

Clinical Indication

As used herein, the terms "treat," "treating" and "treatment" refer to an action that occurs while the subject has a disease, disorder or condition described herein. "Treat," "treatment" and "treating" also refer to the reduction or amelioration of the progression, severity, and/or duration of a disease, disorder or condition described herein resulting from the administration of one or more therapeutic agents described herein.

As used herein, the terms "cancer" and "cancerous" refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. In some embodiments, the subject has a hematological cancer. Hematological cancer as used herein refers to blood-borne tumors (e.g., multiple myeloma, lymphoma and leukemia). In some embodiments, the subject has a solid tumor. "Tumor" and "solid tumor" as used herein, refer to all lesions and neoplastic cell growth and proliferation, whether malignant or benign, and all pre- cancerous and cancerous cells and tissues. "Neoplastic," as used herein, refers to any form of dysregulated or unregulated cell growth, whether malignant or benign, resulting in abnormal tissue growth. Thus, "neoplastic cells" include malignant and benign cells having dysregulated or unregulated cell growth.

In some embodiments, the solid tumor is a sarcoma (e.g., a solid tumor comprising closely packed cells embedded in a fibrillar or homogeneous substance). Exemplary sarcomas for treatment, prevention, and/or management using the compositions and methods described herein include chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abernethy's sarcoma, adipose sarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, immunob lastic sarcoma of B cells, lymphoma, immunoblastic sarcoma of T-cells, Jensen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma, serocystic sarcoma, synovial sarcoma, and telangiectaltic sarcoma.

In some embodiments, the solid tumor is a carcinoma (e.g., a malignant growth comprising epithelial cells that have infiltrated surrounding tissues). Exemplary carcinomas for treatment, prevention, and/or management using the compositions and methods described herein include, adenocarcimonas, colorectal carcinoma, colorectal adenocarcinoma, acinar carcinoma, lung carcinoma, alveolar cell carcinoma, basal cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogenic carcinoma, cerebriform carcinoma, chorionic carcinoma, colloid carcinoma, corpus carcinoma, cribriform carcinoma, cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma, gelatiniforni carcinoma, gelatinous carcinoma, giant cell carcinoma, carcinoma gigantocellulare, glandular carcinoma, hematoid carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma, Krompecher's carcinoma, Kulchitzky-cell carcinoma, large-cell carcinoma, lymphoepithelial carcinoma, nasopharyngeal carcinoma, papillary carcinoma, renal cell carcinoma of kidney, scirrhous carcinoma, small-cell carcinoma, spheroidal cell carcinoma, squamous carcinoma, squamous cell carcinoma, carcinoma telangiectaticum, and verrucous carcinoma.

In some embodiments, the solid tumor is oral, lung, gastrointestinal, genitourinary, liver, bone, nervous system, gynecological, skin, thyroid gland, or adrenal gland. In some embodiments, the solid tumor is oral (buccal cavity, lip, tongue, mouth, pharynx); cardiac (sarcoma (angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma), myxoma, rhabdomyoma, fibroma, lipoma and teratoma); lung (bronchogenic carcinoma (squamous cell or epidermoid, undifferentiated small cell, undifferentiated large cell, adenocarcinoma), alveolar

IQ (bronchiolar) carcinoma, bronchial adenoma, sarcoma, lymphoma, chondromatous hamartoma, mesothelioma); gastrointestinal (esophagus (squamous cell carcinoma, larynx, adenocarcinoma, leiomyosarcoma, lymphoma), stomach (carcinoma, lymphoma, leiomyosarcoma), pancreas (ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoid tumors, vipoma), small bowel or small intestines (adenocarcinoma, lymphoma, carcinoid tumors, Karposi's sarcoma, leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), large bowel or large intestines (adenocarcinoma, tubular adenoma, villous adenoma, hamartoma, leiomyoma), colon, colon-rectum, colorectal, rectum); genitourinary tract (kidney (adenocarcinoma, Wilm's tumor [nephroblastoma], lymphoma, leukemia), bladder and urethra (squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma), prostate (adenocarcinoma, sarcoma), testis (seminoma, teratoma, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, interstitial cell carcinoma, fibroma, fibroadenoma, adenomatoid tumors, lipoma); liver (hepatoma (hepatocellular carcinoma), cholangiocarcinoma, hepatoblastoma, angiosarcoma, hepatocellular adenoma, hemangioma, biliary passages); bone (osteogenic sarcoma (osteosarcoma), fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma (reticulum cell sarcoma), multiple myeloma, malignant giant cell tumor chordoma, osteochronfroma (osteocartilaginous exostoses), benign chondroma, chondroblastoma, chondromyxofibroma, osteoid osteoma and giant cell tumors); nervous system (skull (osteoma, hemangioma, granuloma, xanthoma, osteitis deformans), meninges (meningioma, meningiosarcoma, gliomatosis), brain (astrocytoma, medulloblastoma, glioma, ependymoma, germinoma [pinealoma], glioblastoma multiform, oligodendroglioma, schwannoma, retinoblastoma, congenital tumors), spinal cord neurofibroma, meningioma, glioma, sarcoma); gynecological (uterus (endometrial carcinoma), cervix (cervical carcinoma, pre-tumor cervical dysplasia), ovaries (ovarian carcinoma [serous cystadenocarcinoma, mucinous cystadenocarcinoma, unclassified carcinoma], granulosa-thecal cell tumors, Sertoli- Leydig cell tumors, dysgerminoma, malignant teratoma), vulva (squamous cell carcinoma, intraepithelial carcinoma, adenocarcinoma, fibrosarcoma, melanoma), vagina (clear cell carcinoma, squamous cell carcinoma, botryoid sarcoma (embryonal rhabdomyosarcoma), fallopian tubes (carcinoma), breast; hematologic (blood (myeloid leukemia [acute and chronic], acute lymphoblastic leukemia, chronic lymphocytic leukemia, myeloproliferative diseases, multiple myeloma, myelodysplastic syndrome), Hodgkin's disease, non-Hodgkin's lymphoma [malignant lymphoma] hairy cell, lymphoid disorders); skin (malignant melanoma, basal cell carcinoma, squamous cell carcinoma, Karposi's sarcoma, keratoacanthoma, moles dysplastic nevi, lipoma, angioma, dermatofibroma, keloids, psoriasis), thyroid gland (papillary thyroid carcinoma, follicular thyroid carcinoma, undifferentiated thyroid cancer, medullary thyroid carcinoma, multiple endocrine neoplasia type 2A, multiple endocrine neoplasia type 2B, familial medullary thyroid cancer, pheochromocytoma, paraganglioma); and adrenal glands (neuroblastoma).

In some embodiments, the disclosure provides methods for treating a subject having a myeloproliferative disorder. The term “myeloproliferative disorders” includes disorders such as polycythemia vera, thrombocythemia, myeloid metaplasia with myelofibrosis, hypereosinophilic syndrome, juvenile myelomonocytic leukemia, systemic mast cell disease, and hematopoietic disorders, in particular, acute-myelogenous leukemia (AML), chronic-myelogenous leukemia (CML), acute-promyelocytic leukemia (APL), and acute lymphocytic leukemia (ALL).

In some embodiments, the disclosure provides a method for treating a subject having cancer who has received one or more prior cancer treatments, comprising administering to the subject one or more therapeutic agents described herein (e.g., one or more therapeutic agents for decreasing the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)), wherein the cancer comprises a cancer cell or a plurality of cancer cells comprising a mutation in (e.g., a loss of function mutation in), an altered (e.g., decreased) expression level of, and/or an altered (e.g., decreased) activity of one or more biomarkers described herein (e.g., one or more biomarkers listed in Table 2). In some embodiments, the one or more prior cancer treatments comprising surgery, radiotherapy (e.g., gamma-radiation, neutron beam radiotherapy, electron beam radiotherapy, proton therapy, brachytherapy, and/or systemic radioactive isotopes), chemotherapy, immunotherapy, endocrine therapy, hyperthermia, cryotherapy, agents to attenuate adverse effects, or a combination thereof. In some embodiments, the subject has a cancer that failed to respond to the one or more prior cancer treatments, wherein the one or more therapeutic agents is administered to promote tumor regression in the subject. In some embodiments, the subject has a cancer that developed resistance to the one or more prior cancer treatments following a duration of time, wherein the one or more therapeutic agents is administered to promote tumor regression in the subject. In some embodiments, the subject has a cancer that recurs or returns after a duration of time following cessation of the one or more prior cancer treatments, wherein the one or more therapeutic agents is administered to treat the recurrent cancer. In some embodiments, the subject has a cancer that responds to the one or more prior cancer treatments, wherein the one or more therapeutic agents is administered to enhance the response.

In some embodiments, the disclosure provides a method for treating a subject having a cancer that is resistant or refractory to one or more cancer agents, comprising administering to the subject one or more therapeutic agents described herein (e.g., one or more therapeutic agents for decreasing the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)), wherein the cancer comprises a cancer cell or a plurality of cancer cells comprising a mutation in (e.g., a loss of function mutation in), an altered (e.g., decreased) expression level of, and/or an altered (e.g., decreased) activity of one or more biomarkers described herein (e.g., one or more biomarkers listed in Table 2). As used herein, the term "refractory” or “resistant” refers to a cancer that does not respond at all to treatment with a cancer agent or class of agents (e.g., a standard of care chemotherapeutic agent or class of chemotherapeutic agents) or initially responds but starts to grow again following a short period of time. In some embodiments, the subject received the one or more cancer agents prior to administration of the one or more therapeutic agents, wherein the subject’s cancer does not respond to the one or more cancer agents. In some embodiments, the subject received the one or more cancer agents prior to administration of the one or more therapeutic agents, wherein the subject’s cancer begins to grow following an initial response to the one or more cancer agents.

Therapeutic Methods

In some embodiments, the disclosure provides a method for inhibiting proliferation of a cancer cell or population of cancer cells in a subject. As used herein, the term “inhibit”, “inhibiting”, or “inhibit the growth” or “inhibiting the proliferation” of a cancer cell refers to slowing, interrupting, arresting or stopping the growth of the cancer cell. In some embodiments, cancer cell growth is completely eliminated. In some embodiments, cancer cell growth is slowed or reduced.

In some embodiments, the method comprises administering an effective amount of one or more therapeutic agents described herein (e.g., one or more therapeutic agents for decreasing the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)). As used herein, the term “effective amount” refers to an amount sufficient to effect beneficial or desired results. In some embodiments, the effective amount is administered in a single dose. In some embodiments, the effective amount is administered in more than one dose, each given to the subject at a different time point. In some embodiments, administering an effective amount of the one or more BET polypeptide-targeting therapeutic agents described herein results in a decrease in the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4) as compared to prior to the administering. In some embodiments, administering an effective amount of the one or more therapeutic agents results in death of cancer cells and/or reduced proliferation of cancer cells.

In some embodiments, the present disclosure provides methods for the treatment of cancer (e.g., a cancer having a loss of function mutation or an inactivating mutation in a biomarker that forms a synthetic lethal pair with a BET polypeptide, e.g., TNKS). In some embodiments, the cancer is characterized by an altered (e.g., increased or decreased) expression level and/or activity of a biomarker of the disclosure (e.g., a biomarker that forms a synthetic lethal pair with a BET polypeptide, e.g., TNKS and/or a biomarker listed in Table 2). In some embodiments, the cancer is characterized by the presence of a loss of function mutation or an inactivating mutation in a biomarker of the disclosure (e.g., TNKS and/or a biomarker listed in Table 2). In some embodiments, the method comprises administering one or more therapeutic agents for modulating the expression level and/or activity of a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof.

In some embodiments, the disclosure provides a method of treating cancer in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer, or a plurality of cancer cells thereof, comprises one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) expression level of activity a biomarker described herein, wherein the biomarker forms a synthetic lethal pair with the target gene encoding a BET polypeptide. In some embodiments, the biomarker is selected from Table 2. In some embodiments, the biomarker is TNKS. In some embodiments, the biomarker is PTEN. In some embodiments, the biomarker is JAKE In some embodiments the biomarker is RBI. In some embodiments, the disclosure provides a method of treating cancer in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer, or a plurality of cancer cells thereof, comprises one or more mutations resulting in a decreased expression level and/or activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method of treating cancer in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer, or a plurality of cancer cells thereof, comprises one or more mutations resulting in a decreased expression level and/or activity of TNKS. In some embodiments, the biomarker is PTEN. In some embodiments, the biomarker is JAKE In some embodiments the biomarker is RBI.

In some embodiments, the disclosure provides a method of treating cancer in a subject, comprising administering to the subject one or more therapeutic agents for decreasing an expression level and/or activity of a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer, or a plurality of cancer cells thereof, comprise a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method of treating cancer in a subject, comprising administering to the subject one or more therapeutic agents for decreasing an expression level and/or activity of a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer, or a plurality of cancer cells thereof, comprise a loss of function mutation or an inactivating mutation in TNKS. In some embodiments, the biomarker is PTEN. In some embodiments, the biomarker is JAKE In some embodiments the biomarker is RBI.

In some embodiments, the disclosure provides a method of treating cancer in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer, or a plurality of cancer cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method of treating cancer in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer, or a plurality of cancer cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of TNKS. In some embodiments, the biomarker is PTEN. In some embodiments, the biomarker is JAKE In some embodiments the biomarker is RBI.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) expression level of activity a biomarker described herein, wherein the biomarker forms a synthetic lethal pair with the target gene encoding a BET polypeptide. In some embodiments, the biomarker is selected from Table 2. In some embodiments, the biomarker is TNKS. In some embodiments, the biomarker is PTEN. In some embodiments, the biomarker is JAK1. In some embodiments the biomarker is RBI.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of TNKS.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of PTEN.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of JAK1.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of RBI. In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in TNKS. In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in PTEN.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in JAKE

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in RBI.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of TNKS. In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of PTEN.

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of JAKE

In some embodiments, the disclosure provides a method of promoting tumor regression in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of RBI.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) expression level of activity a biomarker described herein, wherein the biomarker forms a synthetic lethal pair with the target gene encoding a BET polypeptide. In some embodiments, the biomarker is selected from Table 2. In some embodiments, the biomarker is TNKS. In some embodiments, the biomarker is PTEN. In some embodiments, the biomarker is JAK1. In some embodiments the biomarker is RBI.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of a biomarker selected from Table 2. In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of TNKS.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of PTEN.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of JAK1.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises one or mutations resulting in a decreased expression level and/or activity of RBI.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2. In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in TNKS.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in PTEN.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in JAK1.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises a loss of function mutation or an inactivating mutation in RB 1.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of a biomarker selected from Table 2. In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of TNKS.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of PTEN.

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of JAKE

In some embodiments, the disclosure provides a method of promoting or inducing synthetic lethality in a tumor in a subject, comprising administering to the subject one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the tumor, or a plurality of tumor cells thereof, comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of RBI.

In some embodiments, the one or more mutations is detected in a tissue sample obtained from the subject. In some embodiments, the tissue sample is a tumor biopsy sample (e.g., a fresh or fixed biopsy sample). In some embodiments, the tissue sample is a blood sample or a blood component sample (e.g., plasma) comprising circulating tumor DNA.

In some embodiments, the one or more mutations results in an altered (e.g., increased or decreased) expression level of a biomarker selected from Table 2 in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in an altered (e.g., increased or decreased) expression level of TNKS in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in an altered (e.g., increased or decreased) expression level of PTEN in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in an altered (e.g., increased or decreased) expression level of JAK1 in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in an altered (e.g., increased or decreased) expression level of RBI in the tumor relative to a reference tissue sample (e.g., healthy control tissue).

In some embodiments, the one or more mutations results in a decreased expression level of a biomarker selected from Table 2 (e.g., partial or complete loss of expression of the biomarker) in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a decreased expression level of TNKS (e.g., partial or complete loss of expression of TNKS) in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a decreased expression level of PTEN (e.g., partial or complete loss of expression of PTEN) in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a decreased expression level of RBI (e.g., partial or complete loss of expression of RBI) in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a decreased expression level of JAK1 (e.g., partial or complete loss of expression of JAK1) in the tumor relative to a reference tissue sample (e.g., healthy control tissue).

In some embodiments, the one or more mutations results in a deficient activity (e.g., increased or decreased) of a biomarker selected from Table 2 in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a deficient activity (e.g., increased or decreased) of TNKS in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a deficient activity (e.g., increased or decreased) of PTEN in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a deficient activity (e.g., increased or decreased) of JAK1 in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a deficient activity (e.g., increased or decreased) of RBI in the tumor relative to a reference tissue sample (e.g., healthy control tissue).

In some embodiments, the one or more mutations results in a decreased activity of a biomarker selected from Table 2 (e.g., partial or complete loss of activity of the biomarker) in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a decreased activity of TNKS (e.g., partial or complete loss of activity of TNKS) in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a decreased activity of PTEN (e.g., partial or complete loss of activity of PTEN) in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a decreased activity of JAK1 (e.g., partial or complete loss of activity of JAK1) in the tumor relative to a reference tissue sample (e.g., healthy control tissue). In some embodiments, the one or more mutations results in a decreased activity of RBI (e.g., partial or complete loss of activity of RBI) in the tumor relative to a reference tissue sample (e.g., healthy control tissue).

In some embodiments, the cancer or a plurality of cancer cells comprise a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2, a deficient expression level of the biomarker (e.g., under-expressed, mutated, over-expressed), and/or a deficient activity of the biomarker. In some embodiments, the cancer comprises a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2, a decreased expression level of the biomarker, and/or a decreased activity of the biomarker. In some embodiments, a plurality of cancer cells comprises a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2, a decreased expression level of the biomarker, and/or a decreased activity of the biomarker. In some embodiments, the plurality of cancer cells is at least about 5% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is at least about 10% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100% of the total number of cancer cells in the subject. In some embodiments, the expression level of the biomarker selected from Table 2 is at least 1.1-fold, 1.5-fold, 2-fold, 3-fold, 5-fold, 10-fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue). In some embodiments, the activity of the biomarker selected from Table 2 is at least 1.1 -fold, 1.5-fold, 2- fold, 3-fold, 5-fold, 10-fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue).

In some embodiments, the cancer or a plurality of cancer cells comprise a loss of function mutation or an inactivating mutation in TNKS, a deficient expression level of TNKS (e.g., underexpressed, mutated, over-expressed), and/or a deficient activity of TNKS. In some embodiments, the cancer comprises a loss of function mutation or an inactivating mutation in TNKS, a decreased expression level of TNKS, and/or a decreased activity of TNKS. In some embodiments, a plurality of cancer cells comprises a loss of function mutation or an inactivating mutation in TNKS, a decreased expression level of TNKS, and/or a decreased activity of TNKS. In some embodiments, the plurality of cancer cells is at least about 5% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is at least about 10% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100% of the total number of cancer cells in the subject. In some embodiments, the expression level of TNKS is at least 1.1-fold, 1.5-fold, 2-fold, 3-fold, 5- fold, 10-fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue). In some embodiments, the activity of TNKS is at least 1.1 -fold, 1.5-fold, 2-fold, 3-fold, 5-fold, 10- fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue).

In some embodiments, the cancer or a plurality of cancer cells comprise a loss of function mutation or an inactivating mutation in PTEN, a deficient expression level of PTEN (e.g., underexpressed, mutated, over-expressed), and/or a deficient activity of PTEN. In some embodiments, the cancer comprises a loss of function mutation or an inactivating mutation in PTEN, a decreased expression level of PTEN, and/or a decreased activity of PTEN. In some embodiments, a plurality of cancer cells comprises a loss of function mutation or an inactivating mutation in PTEN, a decreased expression level of PTEN, and/or a decreased activity of PTEN. In some embodiments, the plurality of cancer cells is at least about 5% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is at least about 10% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100% of the total number of cancer cells in the subject. In some embodiments, the expression level of PTEN is at least 1.1 -fold, 1.5-fold, 2-fold, 3-fold, 5- fold, 10-fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue). In some embodiments, the activity of PTEN is at least 1.1 -fold, 1.5 -fold, 2-fold, 3 -fold, 5 -fold, 10- fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue).

In some embodiments, the cancer or a plurality of cancer cells comprise a loss of function mutation or an inactivating mutation in JAK1, a deficient expression level of JAK1 (e.g., underexpressed, mutated, over-expressed), and/or a deficient activity of JAK1. In some embodiments, the cancer comprises a loss of function mutation or an inactivating mutation in JAK1, a decreased expression level of JAK1, and/or a decreased activity of JAKE In some embodiments, a plurality of cancer cells comprises a loss of function mutation or an inactivating mutation in JAK1, a decreased expression level of JAK1, and/or a decreased activity of JAKl. In some embodiments, the plurality of cancer cells is at least about 5% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is at least about 10% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100% of the total number of cancer cells in the subject. In some embodiments, the expression level of JAKl is at least 1.1-fold, 1.5-fold, 2-fold, 3-fold, 5-fold, 10-fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue). In some embodiments, the activity of JAKl is at least 1.1-fold, 1.5-fold, 2-fold, 3-fold, 5-fold, 10-fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue).

In some embodiments, the cancer or a plurality of cancer cells comprise a loss of function mutation or an inactivating mutation in RBI, a deficient expression level of RBI (e.g., underexpressed, mutated, over-expressed), and/or a deficient activity of RBI. In some embodiments, the cancer comprises a loss of function mutation or an inactivating mutation in RBI, a decreased expression level of RBI, and/or a decreased activity of RBI. In some embodiments, a plurality of cancer cells comprises a loss of function mutation or an inactivating mutation in RBI, a decreased expression level of RBI, and/or a decreased activity of RBI. In some embodiments, the plurality of cancer cells is at least about 5% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is at least about 10% of the total number of cancer cells in the subject. In some embodiments, the plurality of cancer cells is about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or about 100% of the total number of cancer cells in the subject. In some embodiments, the expression level of RBI is at least 1.1-fold, 1.5-fold, 2-fold, 3-fold, 5-fold, 10-fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue). In some embodiments, the activity of RBI is at least 1.1-fold, 1.5-fold, 2-fold, 3-fold, 5-fold, 10-fold lower in the cancer compared to a reference tissue (e.g., healthy control tissue).

In some embodiments, the method comprises administering a therapeutically effective amount of the one or more therapeutic agents. In some embodiments, administering a therapeutically effective amount of the one or more therapeutic agents alters (e.g., increases or decreases) the expression level of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof. In some embodiments, administering a therapeutically effective amount of the one or more therapeutic agents decreases the activity of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof.

In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising an altered (e.g., increased or decreased) expression level and/or activity of a biomarker selected from Table 2. In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising a mutation or deletion in a biomarker selected from Table 2.

In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising an altered (e.g., increased or decreased) expression level and/or activity of TNKS. In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising a mutation or deletion in TNKS. In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising an altered (e.g., increased or decreased) expression level and/or activity of PTEN. In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising a mutation or deletion in PTEN. In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising an altered (e.g., increased or decreased) expression level and/or activity of JAKE In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising a mutation or deletion in JAKE In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising an altered (e.g., increased or decreased) expression level and/or activity of RBI. In some embodiments, the administration of the one or more therapeutic agents results in the inhibition or death of cancer cells comprising a mutation or deletion in RBI.

In some cases, the cancerous tissue is breast tissue, pancreatic tissue, uterine tissue, bladder tissue, colorectal tissue, prostate tissue, liver tissue, or ovarian tissue. In some embodiments, the cancerous tissue is liver tissue. In some embodiments, cancerous tissue is ovarian tissue.

In some embodiments, the inhibition of expression level and/or activity (e.g., via genetic manipulation resulting in a knock down or knock out, suppression of an RNA transcript, or via pharmacological inhibition) of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, in a cancer cell or a population thereof having a mutation (e.g., a loss of function mutation or an inactivating mutation) in a biomarker selected from Table 2 is lethal to the cancer cell or population thereof, but non-toxic or non-lethal to a control cell or population thereof (e.g., a healthy cell or healthy population of cells) expressing wild-type biomarker. In some embodiments, a method of treating a subject having a cancer described herein comprising administering a therapeutic agent that alters (e.g., increases or decreases) the expression level of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a mutation (e.g., a loss of function mutation or an inactivating mutation) in a biomarker selected from Table 2, results in reduced tumor progression or growth without inducing substantial toxicity to normal cells of the subject.

In some embodiments, the inhibition of expression level and/or activity (e.g., via genetic manipulation resulting in a knock down or knock out, suppression of an RNA transcript, or via pharmacological inhibition) of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, in a cancer cell or a population thereof having a mutation (e.g., a loss of function mutation or an inactivating mutation) in the TNKS gene is lethal to the cancer cell or population thereof, but non-toxic or non-lethal to a control cell or population thereof (e.g., a healthy cell or healthy population of cells) having a wild-type TNKS gene. In some embodiments, a method of treating a subject having a cancer described herein comprising administering a therapeutic agent that alters (e.g., increases or decreases) the expression level of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a mutation (e.g., a loss of function mutation or an inactivating mutation) in the TNKS gene, results in reduced tumor progression or growth without inducing substantial toxicity to normal cells of the subject.

In some embodiments, the inhibition of expression level and/or activity (e.g., via genetic manipulation resulting in a knock down or knock out, suppression of an RNA transcript, or via pharmacological inhibition) of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, in a cancer cell or a population thereof having a mutation (e.g., a loss of function mutation or an inactivating mutation) in the PTEN gene is lethal to the cancer cell or population thereof, but non-toxic or non-lethal to a control cell or population thereof (e.g., a healthy cell or healthy population of cells) having a wild-type PTEN gene. In some embodiments, a method of treating a subject having a cancer described herein comprising administering a therapeutic agent that alters (e.g., increases or decreases) the expression level of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a mutation (e.g., a loss of function mutation or an inactivating mutation) in the PTEN gene, results in reduced tumor progression or growth without inducing substantial toxicity to normal cells of the subject.

In some embodiments, the inhibition of expression level and/or activity (e.g., via genetic manipulation resulting in a knock down or knock out, suppression of an RNA transcript, or via pharmacological inhibition) of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, in a cancer cell or a population thereof having a mutation (e.g., a loss of function mutation or an inactivating mutation) in the JAK1 gene is lethal to the cancer cell or population thereof, but non-toxic or non-lethal to a control cell or population thereof (e.g., a healthy cell or healthy population of cells) having a wild-type JAK1 gene. In some embodiments, a method of treating a subject having a cancer described herein comprising administering a therapeutic agent that alters (e.g., increases or decreases) the expression level of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a mutation (e.g., a loss of function mutation or an inactivating mutation) in the JAK1 gene, results in reduced tumor progression or growth without inducing substantial toxicity to normal cells of the subject.

In some embodiments, the inhibition of expression level and/or activity (e.g., via genetic manipulation resulting in a knock down or knock out, suppression of an RNA transcript, or via pharmacological inhibition) of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, in a cancer cell or a population thereof having a mutation (e.g., a loss of function mutation or an inactivating mutation) in the RBI gene is lethal to the cancer cell or population thereof, but non-toxic or non- lethal to a control cell or population thereof (e.g., a healthy cell or healthy population of cells) having a wild-type RBI gene. In some embodiments, a method of treating a subject having a cancer described herein comprising administering a therapeutic agent that alters (e.g., increases or decreases) the expression level of the target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a mutation (e.g., a loss of function mutation or an inactivating mutation) in the RBI gene, results in reduced tumor progression or growth without inducing substantial toxicity to normal cells of the subject.

In any of the foregoing embodiments, the biomarker selected from Table 2 is TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, or MBP. In some embodiments, the biomarker selected from Table 2 is TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, or CHD4, CHD8. In some embodiments, the biomarker selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, or MBP.

Diagnostic Methods In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity of a biomarker that forms a synthetic lethal pair with a target gene encoding a BET polypeptide. In some embodiments, the biomarker is selected from Table 2. In some embodiments, the biomarker is TNKS. In some embodiments, the method comprises generating a report indicating a subject will respond or will likely respond to the one or more therapeutic agents based upon the presence of one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity of a biomarker that forms a synthetic lethal pair with a target gene encoding a BET polypeptide.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of TNKS.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of PTEN.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of JAKl.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of RBI.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in TNKS.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in PTEN.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in JAKl.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in RBI .

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of TNKS.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of PTEN.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of JAK1.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of RBI.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the comprises one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity of a biomarker that forms a synthetic lethal pair with a target gene encoding a BET polypeptide. In some embodiments, the biomarker is selected from Table 2. In some embodiments, the biomarker is TNKS. In some embodiments, the biomarker is PTEN. In some embodiments, the biomarker is JAKE In some embodiments, the biomarker is RBI.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of TNKS.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of PTEN.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of JAK1. In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of RBI.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in TNKS.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in PTEN.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in JAK1.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in RBI. In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of TNKS. In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity of a biomarker that forms a synthetic lethal pair with a target gene encoding a BET polypeptide. In some embodiments, the biomarker is selected from Table 2. In some embodiments, the biomarker is TNKS. In some embodiments, the biomarker is PTEN. In some embodiments, the biomarker is RBI. In some embodiments, the biomarker is JAKE

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of TNKS. In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of PTEN.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of JAKE

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises one or more mutations resulting in a decreased expression level and/or activity of RBI.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in TNKS.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in PTEN. In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in JAK1.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises a loss of function mutation or an inactivating mutation in RB 1.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of a biomarker selected from Table 2.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of TNKS.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of PTEN.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of JAKE In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, wherein the cancer comprises an altered (e.g., increased or decreased) expression level and/or altered (e.g., increased or decreased) activity of RBI.

In some embodiments, the method comprises obtaining a cancer sample from the subject and detecting a mutation in a biomarker, wherein the presence of a mutation indicates the subject will respond or will likely respond to the one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof.

In some embodiments, the method comprises determining the expression level and/or activity of the biomarker in a cancer sample obtained from the subject, wherein an altered (e.g., increased or decreased) expression level and/or activity relative to a reference tissue sample indicates the subject will respond or will likely respond to the one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof.

In any of the foregoing embodiments, the biomarker selected from Table 2 is TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, or MBP. In some embodiments, the biomarker selected from Table 2 is TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, or CHD4, CHD8. In some embodiments, the biomarker selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, or MBP. In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, comprising determining the expression level and/or activity of a panel of biomarkers in a cancer sample obtained from the subject, wherein the panel comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers described herein (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers selected from Table 2), wherein an altered (e.g., increased or decreased) expression level and/or activity relative to a reference tissue sample of at least one biomarker of the panel indicates the subject will respond or will likely respond to the one or more therapeutic agents.

In some embodiments, the disclosure provides a method for determining whether a subject with cancer will respond or will likely respond to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, comprising determining the presence of a mutation in a panel of biomarkers in a cancer sample obtained from the subject, wherein the panel comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers described herein (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers selected from Table 2), wherein the presence of a mutation in at least one biomarker of the panel indicates the subject will respond or will likely respond to the one or more therapeutic agents.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, comprising determining the expression level and/or activity of a panel of biomarkers in a cancer sample obtained from the subject, wherein the panel comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers described herein (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers selected from Table 2), wherein an altered (e.g., increased or decreased) expression level and/or activity relative to a reference tissue sample of at least one biomarker of the panel indicates the subject will respond or will likely respond to the one or more therapeutic agents.

In some embodiments, the disclosure provides a method for predicting responsiveness of a subject having cancer to one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, comprising determining the presence of a mutation in a panel of biomarkers in a cancer sample obtained from the subject, wherein the panel comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers described herein (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers selected from Table 2), wherein the presence of a mutation in at least one biomarker of the panel indicates the subject will respond or will likely respond to the one or more therapeutic agents.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, comprising determining the expression level and/or activity of a panel of biomarkers in a cancer sample obtained from the subject, wherein the panel comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers described herein (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers selected from Table 2), wherein an altered (e.g., increased or decreased) expression level and/or activity relative to a reference tissue sample of at least one biomarker of the panel indicates the subject will respond or will likely respond to the one or more therapeutic agents.

In some embodiments, the disclosure provides a method for selecting a subject having cancer to receive one or more therapeutic agents for modulating a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof, comprising determining the presence of a mutation in a panel of biomarkers in a cancer sample obtained from the subject, wherein the panel comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers described herein (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers selected from Table 2), wherein the presence of a mutation in at least one biomarker of the panel indicates the subject will respond or will likely respond to the one or more therapeutic agents.

In some embodiments, the panel of biomarkers comprises TP53 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises SMAD4 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises PTEN and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises CREBBP and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises SMARCA4 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises PBRM1 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises VHL and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises APC and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises JAK1 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises RBI and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises MLH1 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises STAG2 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises LTK and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises CTCF and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises ADAMTS12 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises B2M and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises BRAF and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises CDCA2 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises CDH13 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises CDK7 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises CHD3 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises TNKS and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises TENM3 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises THSD7B and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises SETDB2 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises TUSC3 and one or more (e.g.,

1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises PCLO and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises PLK2 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises PSD3 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises REV3L and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises JAK2 and one or more (e.g., 1,

2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises KRAS and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises DNAH3 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises ERBB2 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises FGFR1 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises GRM2 and one or more (e.g.,

1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises IKBKB and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises KAT6A and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises KMT2C and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises MAST4 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises MBP and one or more (e.g., 1,

2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises CHD4 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein. In some embodiments, the panel of biomarkers comprises CHD8 and one or more (e.g., 1, 2, 3, 4, 5, or more) additional biomarkers described herein.

In some embodiments, the additional biomarker is selected from Table 2.

Therapeutic Agents

In some embodiments, the disclosure provides a method of treating cancer in a subject, comprising administering to the subject a therapeutically effective amount of one or more therapeutic agents that alters (e.g., increase or decrease) the expression and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof.

As used herein, the term “BET polypeptide” or “BET protein” refers to a member of the bromodomain and extra-terminal (BET) containing protein family. In humans, genes encoding BET polypeptides include BRD1 (also known as BRPF2 and BRL), BRD2 (also known as FSRG1, RING3, RNF3, FSH, or D6S113E), BRD3 (also known as ORFX or RING3L), BRD4 (also known as MCAP or HUNK1) and BRDT (also known as BRD6, CT9, or SPGF21). Humans express a short and a long isoform of BRD4 (respectively referred to as BRIMS that is expressed from an splice variant lacking exons 12-20 and BRD4L that is expressed from the full- length gene transcript (see Wu, et al (2007) JBC 282:13141)). BET proteins are highly conserved in mammals and have homologs in other species such as Drosophila and yeast (see Wang, et al (2021) Sig. Trans. Targ. Ther. 6:23). Accession numbers providing information for gene transcripts encoding representative BET family members as provided in the GenBank database include NM_005104 (human BRD2); NM 007371.4 (human BRIM); NM_058243 (human BRD4L); NM_014299 (human BRIMS); NM_001242805 (human BRDT; and NC_000022.11 (BRD1); and NM 001394551.1 (human BRD1).

As used herein, the term “therapeutic agents” refers to one or more agents that reduce an expression level and/or activity level of a target, e.g., a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the one or more therapeutic agents reduces transcription of a gene encoding the target, e.g., a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the one or more therapeutic agents reduces maturation of an RNA transcript encoding the target, e.g., an RNA transcript encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the one or more therapeutic agents impair splicing of an RNA transcript encoding the target, e.g., an RNA transcript encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, one or more therapeutic agents impairs translation of mRNA encoding the target, e.g., mRNA encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the one or more therapeutic agents impairs cellular trafficking of the target, e.g., cellular trafficking of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), thereby reducing activity of the target. In some embodiments, the one or more therapeutic agents reduces enzymatic activity of the target, e.g., enzymatic activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the one or more therapeutic agents blocks an interaction of the target with a substrate (e.g., binding to DNA and/or a transactivating cofactor). In some embodiments, the one or more therapeutic agents functions to inhibit or abrogate the normal cellular function of the target, e.g., by competitive inhibition of the active site, allosteric modulation of the protein structure, disruption of protein-protein interactions, or by inhibiting the transcription, translation, or stability of the protein.

In some embodiments, the one or more therapeutic agent used to alter (e.g., decrease or increase) expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), or a transcriptional or translational product thereof comprises a small molecule (e.g., a molecule having a molecular weight of less than 900 Daltons), a protein, an intrabody, a peptide, a ribonucleic acid (RNA) molecule, a deoxyribonucleic acid (DNA) construct, or a combination thereof (e.g., a protein-nucleic acid complex).

(i) Gene-Editing

In some embodiments, the therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises a gene-editing technology. In some embodiments, the gene-editing technology targets a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) and when introduced to a cell, induces a DNA double-stranded (DSB) break in the gene, wherein repair of the DNA DSB by an endogenous DNA damage repair pathway results in a mutation in the gene that reduces an expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the gene-editing technology is selected from CRISPR/Cas, TALEN, or a zinc finger nuclease. (a) CRISPR/Cas

In some embodiments, the one or more therapeutic agents comprises a protein-nucleic acid complex, e.g., an endonuclease complex and a nucleic acid construct. In some cases, the endonuclease complex comprises a clustered regularly interspaced short palindromic repeat (CRISPR) associated (Cas) protein or variant thereof (e.g., an engineered variant) or a nucleic acid encoding the Cas protein or variant thereof. In some embodiments, the endonuclease complex comprises a clustered regularly interspaced short palindromic repeat (CRISPR) associated (Cas) protein or variant thereof (e.g., an engineered variant). In some embodiments, the nucleic construct is co-administered with the endonuclease complex. In some embodiments, the nucleic acid comprises an endonuclease gene. In some embodiments, the nucleic acid comprises a gene encoding a Cas protein or variant thereof (e.g., an engineered variant). In some embodiments, the nucleic acid is transcribed and translated by the cell using the cell’s own machinery (e.g., polymerases, ribosomes, etc.) once the nucleic acid is introduced or delivered to a cell (e.g., cancer cell).

In some embodiments, the endonuclease complex comprises an endonuclease, e.g., a Cas protein, or other nucleic acid-interacting enzyme (e.g., ligase, helicase, reverse transcriptase, transcriptase, polymerase, etc.). In some embodiments, the Cas protein comprises any Cas type (e.g., Cas I, Cas IA, Cas IB, Cas IC, Cas ID, Cas IE, Cas IF, Cas IU, Cas III, Cas IIIA, Cas IIIB, Cas IIIC, Cas IIID, Cas IV, Cas IVA, Cas IVB, Cas II, Cas IIA, Cas IIB, Cas IIC, Cas V, Cas VI). In some embodiments, the Cas protein comprises other proteins (e.g., a fusion protein). In some embodiments, the Cas protein comprises an additional enzyme that associates with a nucleic acid molecule (e.g., ligase, transcriptase, transposase, nuclease, endonuclease, reverse transcriptase, polymerase, helicase, etc.). In some embodiments, the endonuclease complex is delivered exogenously or is encoded in the nucleic acid construct for transcription and translation within the cell.

In some embodiments, the agent comprises a CRISPR/Cas system comprising a Cas nuclease described herein (e.g., a Cas9 nuclease) and a guide RNA (gRNA) comprising a spacer sequence substantially complementary to a target sequence in a target gene described herein. As used herein, the term “target sequence” refers to a contiguous nucleotide sequence present in a target gene described herein. “Contiguous nucleotides” is intended to mean nucleotides that are covalently linked and immediately adjacent to each other. Methods for selecting a gRNA directed to a target gene are known in the art. For example, in some embodiments, the spacer sequence is designed in silico by locating a target sequence (e.g., a 19-30 bp sequence) adjacent a PAM sequence in the target gene (e.g., a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)), wherein the PAM sequence is recognized by a Cas nuclease described herein. Non-limiting exemplary PAM sequences include NGG (SpCas9 WT, SpCas9 nickase, dimeric dCas9-Fokl, SpCas9-HFl, SpCas9 K855A, eSpCas9 (1.0), eSpCas9 (1.1)), NGAN or NGNG (SpCas9 VQR variant), NGAG (SpCas9 EQR variant), NGCG (SpCas9 VRER variant), NAAG (SpCas9 QQR1 variant), NNGRRT or NNGRRN (SaCas9), NNNRRT (KKH SaCas9), NNNNRYAC (CjCas9), NNAGAAW (StlCas9), NAAAAC (TdCas9), NGGNG (St3Cas9), NG (FnCas9), NAAAAN (TdCas9), NNAAAAW (StCas9), NNNNACA (CjCas9), GNNNCNNA (PmCas9), NNGG (SluCas9), and NNNNGATT (NmCas9) (see e.g., Cong et al., (2013) Science 339:819-823; Kleinstiver et al., (2015) Nat Biotechnol 33: 1293-1298; Kleinstiver et al., (2015) Nature 523:481-485; Kleinstiver et al., (2016) Nature 529:490- 495; Tsai et al., (2014) Nat Biotechnol 32:569-576; Slaymaker et al., (2016) Science 351:84-88; Anders et al., (2016) Mol Cell 61:895- 902; Kim et al., (2017) Nat Comm 8:14500; Fonfara et al., (2013) Nucleic Acids Res 42:2577- 2590; Garneau et al., (2010) Nature 468:67-71; Magadan et al., (2012) PLoS ONE 7:e40913; Esvelt et al., (2013) Nat Methods 10(11): 1116-1121 (wherein N is defined as any nucleotide, W is defined as either A or T, R is defined as a purine (A) or (G), and Y is defined as a pyrimidine (C) or (T)).

In some embodiments, a target sequence that perfectly hybridizes with the gRNA spacer sequence occurs only once in a given eukaryotic genomes. In some embodiments, the genome comprises additional sequences that imperfectly hybridize with the gRNA spacer sequence, for example, sequences having one or more mismatches (e.g., 1, 2, 3, 4, or 5 mismatches) and/or bulges, relative to the gRNA spacer sequence. In some embodiments, the genome comprises sequences that hybridize the gRNA spacer sequence that are adjacent a PAM sequence having at least one mismatch relative to the canonical PAM sequence. Such genomic sequences (e.g., target sequences that imperfectly hybridize the gRNA spacer sequence or target sequences comprising a non-canonical PAM sequences) are referred to herein as off- target sites.

In some embodiments, the method of in silico screening is used to predict cleavage efficiency of a gRNA spacer sequence at both on-target and off-target sites, thereby allowing selection of a gRNA with high cleavage efficiency at a target sequence in the genome comprising a target gene described herein, with low or minimal cutting efficiency at off-target sites in the genome (i.e., low or minimal frequency of DNA DSBs occurring at sites other than the selected target sequence).

As described herein, selection of gRNAs with a favorable off-target profile is critical for use in a therapeutic method of the disclosure, for example, to eliminate or reduce the risk of undesirable chromosomal rearrangements or off-target mutations. In some embodiments, a favorable off-target profile in one that minimizes or eliminates the number of off-target sites and/or the frequency of cutting at these sites. In some embodiments, a favorable off-target profile is one that minimizes or eliminates off-target sites in specific regions of the genome, for example within or proximal to an oncogene.

As is known in the art, the occurrence of off-target activity can be influenced by a number of factors including similarities and dissimilarities between the target site and various off-target sites, as well as the particular endonuclease used. For example, the ability of a given gRNA to promote cleavage at a target sequence in a genomic DNA molecule relates to, for example, the accessibility of the target sequence, which depends on one or more factors that include the chromatin structure of the genomic DNA molecule and/or proximity to transcription factor binding sites. For example, target sequences located within a region of the genomic DNA molecule having a high condensed chromatin structure are less accessible than target sequences located within a region of the genomic DNA molecule having an open chromatin structure. As a further example, target sequences proximal to a region of the genomic DNA molecule bound by a transcription factor or other regulatory protein may be less accessible than target sequences proximal a region of the genomic DNA molecule that is unbound by regulatory proteins. Moreover, the cell state and type of cell may influence the accessibility of target sequences, for example, by influencing the chromatin structure of genomic DNA.

In some embodiments, the nucleotide sequence of the spacer is designed or chosen using an algorithm or method known in the art. In some embodiments, the algorithm uses variables to screen for suitable gRNA spacer sequences and corresponding target sequences. Non-limiting examples of such variables include predicted melting temperature of the gRNA sequence, secondary structure formation of the gRNA sequence, predicted annealing temperature of the gRNA sequence, sequence identity, genomic context of the target sequence, chromatin accessibility of the target sequence, % GC, frequency of genomic occurrence of the target sequence (e.g., of sequences that are identical or are similar but vary in one or more spots as a result of mismatch, insertion or deletion), methylation status of the target sequence, and/or presence of SNPs within the target sequence.

In some embodiments, one or more bioinformatics tools known in the art are used to predict the off-target activity of a gRNA spacer sequence and/or identify the most likely sites of off-target activity. Non-limiting examples of bioinformatics tools for use in the present disclosure include CCTop, CRISPOR, and COSMID.

In some embodiments, identification of gRNA target sequences is best achieved through a combination of in silico selection and experimental evaluation. Experimental methods to evaluate, for example, gRNA on-target and off-target cleavage efficiency are known in the art and further described herein.

In some embodiments, cleavage efficiency is measured as frequency of INDELs proximal the target sequence targeted by the gRNA spacer sequence. Methods to measure frequency of INDELs at a particular target sequence in a genome are known in the art. An exemplary method to measure frequency of INDELs at a predicted cut site in a given target sequence comprises, (i) isolation of genomic DNA from the edited cell population and/or tissue, (ii) amplification of the DNA region comprising the target sequence (e.g., by PCR), (iii) sequencing of the amplified DNA region (e.g., by Sanger sequencing), and (iv) determining frequency of INDELs at the predicted cut site by Tracking of Indels decomposition (UDE) assay, for example, as described by Brinkman, et al (2014) NUCLEIC ACIDS RESEARCH 42:el68. A further exemplary method comprises sequencing of the amplified DNA region by next- generation sequencing (NGS) and analysis of INDEL frequency at the predicted cut site in the target sequence, for example, as described by Bell et al (2014) BMC Genomics 15:1002.

(b) TALENs

In some embodiments, the gene-editing system comprises a TALEN. By “TALEN” or “TALEN to target” or “TALEN to inhibit target” and the like is meant a transcription activatorlike effector nuclease, an artificial nuclease which can be used to edit a target gene, e.g., a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). TALENs are produced artificially by fusing a TAL effector DNA binding domain to a DNA cleavage domain. Transcription activator-like effects (TALEs) can be engineered to bind any desired DNA sequence, including a portion of the target gene (e.g., a gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). By combining an engineered TALE with a DNA cleavage domain, a restriction enzyme can be produced which is specific to any desired DNA sequence, including a target sequence in a gene or transcript encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). These can then be introduced into a cell, wherein they can be used for genome editing. Boch 2011 Nature Biotech. 29: 135-6; and Boch et al. 2009 Science 326: 1509-12; Moscou et al. 2009 Science 326: 3501.

TALEs are proteins secreted by Xanthomonas bacteria. The DNA binding domain contains a repeated, highly conserved 33-34 amino acid sequence, with the exception of the 12th and 13th amino acids. These two positions are highly variable, showing a strong correlation with specific nucleotide recognition. They can thus be engineered to bind to a desired DNA sequence.

To produce a TALEN, a TALE protein is fused to a nuclease (N), which is a wild-type or mutated Fokl endonuclease. Several mutations to Fokl have been made for its use in TALENs; these, for example, improve cleavage specificity or activity. Cermak et al. 2011 Nucl. Acids Res. 39: e82; Miller et al. 2011 Nature Biotech. 29: 143-8; Hockemeyer et al. 2011 Nature Biotech. 29: 731-734; Wood et al. 2011 Science 333: 307; Doyon et al. 2010 Nature Methods 8: 74-79; Szczepek et al. 2007 Nature Biotech. 25: 786-793; and Guo et al. 2010 J. Mol. Biol. 200: 96.

The Fokl domain functions as a dimer, requiring two constructs with unique DNA binding domains for sites in the target genome with proper orientation and spacing. Both the number of amino acid residues between the TALE DNA binding domain and the Fokl cleavage domain and the number of bases between the two individual TALEN binding sites appear to be important parameters for achieving high levels of activity. Miller et al. 2011 Nature Biotech. 29: 143-8.

A TALEN to a target can be used inside a cell to produce a double-stranded break (DSB). A mutation can be introduced at the break site if the repair mechanisms improperly repair the break via non-homologous end joining. For example, improper repair may introduce a frame shift mutation. Alternatively, foreign DNA can be introduced into the cell along with the TALEN; depending on the sequences of the foreign DNA and chromosomal sequence, this process can be used to correct a defect in the target gene or introduce such a defect into a wildtype (WT) target gene, thus decreasing expression of target gene.

TALENs specific to sequences in a target gene, e.g., a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), can be constructed using any method known in the art, including various schemes using modular components. Zhang et al. 2011 Nature Biotech. 29: 149-53; Geibler et al. 2011 PLoS ONE 6: el9509.

The present disclosure thus provides use of a TALEN for a target gene, e.g., a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), for the treatment of cancer, such as a cancer described herein.

(c) Zinc Finger Nucleases

In some embodiments, the gene-editing system comprises a zinc finger nuclease. By “ZFN”, or “Zinc Finger Nuclease” or “ZFN to a target gene” or “ZFN to inhibit target gene” and the like is meant a zinc finger nuclease, an artificial nuclease which can be used to edit a target gene, e.g., a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM).

Like a TALEN, a ZFN comprises a Fokl nuclease domain (or derivative thereof) fused to a DNA-binding domain. In the case of a ZFN, the DNA-binding domain comprises one or more zinc fingers. Carroll et al. 2011. Genetics Society of America 188: 773-782; and Kim et al. Proc. Natl. Acad. Sci. USA 93: 1156-1160.

A zinc finger is a small protein structural motif stabilized by one or more zinc ions. A zinc finger can comprise, for example, Cys2His2, and can recognize an approximately 3 -bp sequence. Various zinc fingers of known specificity can be combined to produce multi-finger polypeptides which recognize about 6, 9, 12, 15 or 18-bp sequences. Various selection and modular assembly techniques are available to generate zinc fingers (and combinations thereof) recognizing specific sequences, including phage display, yeast one-hybrid systems, bacterial one-hybrid and two-hybrid systems, and mammalian cells.

Like a TALEN, a ZFN must dimerize to cleave DNA. Thus, a pair of ZFNs is required to target non-palindromic DNA sites. The two individual ZFNs must bind opposite strands of the DNA with their nucleases properly spaced apart. Bitinaite et al. 1998 Proc. Natl. Acad. Sci. USA 95: 10570-5.

Il l Also like a TALEN, a ZFN can create a double-stranded break in the DNA, which can create a frame-shift mutation if improperly repaired, leading to a decrease in the expression and amount of a target in a cell. ZFNs can also be used with homologous recombination to mutate, or repair defects, in the target gene.

ZFNs specific to sequences in a target gene, e.g., a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM), can be constructed using any method known in the art. Cathomen et al. Mol. Ther. 16: 1200-7; and Guo et al. 2010. J. Mol. Biol. 400: 96.

The present disclosure thus provides use of a ZFN specific to sequences in a target gene, e.g., a target gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRIM), for the treatment of cancer.

(ii) Small Molecule Inhibitors

In some embodiments, the one or more therapeutic agents comprises a small molecule inhibitor (e.g., a molecule having a molecular weight of less than 900 Daltons). In some embodiments, the therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises a small molecule inhibitor (e.g., a molecule having a molecular weight of less than 900 Daltons). In some embodiments, the small molecule is configured to decrease the expression level and/or activity level of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the small molecule inhibits the normal cellular function of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the small molecule inhibitor comprises a BET inhibitor. In some embodiments, the BET inhibitor binds to the bromodomain of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the BET inhibitor prevents protein-protein interactions between a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) and one or more histones and/or transcription factors. In some embodiments, the small molecule inhibitor is an allosteric therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4).

Methods to identify a small molecule inhibitor of a target protein (e.g., a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)) are known in the art. In some embodiments, the method comprises screening a library of small molecule compounds (e.g., a library of synthetic organic compounds and/or natural products) for a compound that decreases the activity of the target protein (e.g., a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)). In some embodiments, the method comprises a computational docking program to identify a small molecule compound that interacts with one or more binding sites (e.g., DNA binding sites and/or transactivation sites) of the target protein (e.g., a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)). In some embodiments, the computational docking program uses the 3D structure of the target protein identified using a crystallography approach or generated using homology modeling to identify a small molecule compound that interacts with the one or more binding sites. 3D structures of a BET polypeptide are known in the art (see, e.g., protein structures identifiable via the protein database (world wide web: rcsb.org) for BRD1 (4Z02), BRD2 (7ENZ), BRD3 (7R8R), and BRD4 (7WWZ)).

Methods to test small molecule inhibitors for blocking activity of a target protein (e.g., a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)) are also known in the art. In some embodiments, the method comprises determining the half maximal inhibitory concentration (IC50) of the small molecule inhibitor. As used herein, the “IC50,” “IC50,” or “half maximal inhibitory concentration” refers to the in vitro concentration of a test compound that inhibits a biological process by half. In some embodiments, the IC50 is the concentration of a test compound that reduces the activity of the target protein (e.g., the DNA binding activity and/or transactivating cofactor binding activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)) by half. In some embodiments, the IC50 is the concentration of a test compound that reduces the binding between the target protein and a substrate (e.g., binding between a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) and DNA and/or a transactivating cofactor) by half. Methods to measure IC50 are known in the art. In some embodiments, the measurement comprises constructing a dose-response curve (e.g., a plot of activity of the target protein versus concentration of the test compound) and determining the concentration of the test compound that yields half the maximum biological response (e.g., activity of the target protein). In some embodiments, IC50 is determined by generating a dose response of activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) versus concentration of the test compound. In some embodiments, activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) is measured using a functional assay. In some embodiments, the functional assay is an enzymatic assay. In some embodiments, the function assay is a cell proliferation assay. In some embodiments, the cell proliferation uses an enzyme inherent to living cells to turn over a substrate, thereby producing a luminescence of fluorescence signal that can be quantified. In some embodiments, the functional assay is selected from Cell Titer Gio and PrestoBlue.

In some embodiments, the small molecule inhibitor inhibits a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) with a sub-micromolar IC50 (e.g., less than about 500 nM, about 400 nM, about 300 nM, about 200 nM or about 100 nM). In some embodiments, the small molecule inhibitor inhibits a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) with a nanomolar IC50 (e.g., about 1 nM to about 10 nM, about 1 nM to about 20 nM, about 1 nM to about 30 nM, about 1 nM to about 40 nM, about 1 nM to about 50 nM, about 1 nM to about 60 nM, about 1 nM to about 70 nM, about 1 nM to about 80 nM, about 1 nM to about 90 nM, or about 1 nM to about 100 nM). In some embodiments, the small molecule inhibitor inhibits a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) with a sub-nanomolar IC50 (e.g., less than about 1 nM).

Non-limiting examples of a BET inhibitor are GSK-2820151, GSK525762 (molibresib), GSK046, GSK778, RG-6146 (also known as “pelabresib”), birabresib dihydrate (also known as “OTX-015” and “MK-8628”), BAY-1238097, BMS-986158, BMS-986378, CC-90010, CC- 95775, Apabetalone, RVX-208, RVX-000222, INCB054329, INCB057643, AZ-5153, ABBV- 744, ABBV-075 (also known as “Mivabresib”). In some embodiments, the BET inhibitor is any one identified in Table 1.

In some embodiments, the BET inhibitor is birabresib. Birabresib is a thienotriazolodiazepine BET inhibitor that competitively occupies the acetyl-binding pockets of BRD2/3/4, resulting in their release from active chromatin and suppression of downstream signaling to RNA polymerases (see, e.g., Noel et al (2013) Mol Cancer Ther 12:C244; Boi et al (2015) Clin Cancer Res 21 :1628; Henssen et al (2016) Clin Cancer Res 22:2470). Birabresib has the structure of Compound 1 (see, e.g., US9757385, herein incorporated by reference. Birabresib is commercially available (see, e.g., CAS Number 202590-98-5; PubChem Substance ID 329825491; Sigma Aldrich SML1605).

In some embodiments, the BET inhibitor is CPI-203. CPI-203 is a thi enodiazepine derivative that inhibits BRD4 (see, e.g., Devaiah, et al (2012) PNAS 109:6927; Shao, et al (2016) Cell 16:3138). CPI-203 has the structure of Compound 2. CPI-203 is commercially available (see, e.g., CAS Number 1446144-04-2; PubChem Substance ID 329825722; Sigma Aldrich SML1212). In some embodiments, the BET inhibitor is BAY 1238079. BAY 1238079 is a BET inhibitor that binds to BRD 2, BRD3, and BRD4 (see, e.g., Lejeune, et al (2015) Cancer Research 75(15 Suppl), 884; Postel-Vinay et al (2016) Eur J Cancer 68:S7-S8; Gaudio, et al (2017) British J Haematology 178:936). BAY 1238079 has the structure of Compound 3. The synthesis of BAY 1238097 is described in patent application WO 2014/026997 as example 127.

In some embodiments, the BET inhibitor is PLX51107. PLX51107 is a 7-azaindole derivative that inhibits BRD2, BRD3, and BRD4 (see, e.g., Tsai, et al (2008) PNAS 105:3041; Ozer, et al (2018) Cancer Discov. 8:458). PLX51107 has the structure of Compound 4. PLX51107 is commercially available (see, e.g., CAS No. 1627929-55-8; Selleckchem Catalog No. S8739).

Table 1. BET Small Molecule Inhibitors

In some embodiments, the small molecule inhibitor is a proteolysis targeting chimera (PROTAC). PROTACs are heterobifunctional molecules comprising a first active domain operably linked to a second active domain, wherein the first active domain binds to the target protein (e.g., a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)) and the second active domain mediates the degradation of the target protein. Methods and compositions related to PROTACs are further described in US2019/0210996, US10899768, US20190175612, Wang, et al (2020) Acta Pharm Sin B 10:207, Toure, et al (2016) ACIE 55:1966, Bondeson et al (2018) Cell Chem Biol 25:78, Crews et al (2016) J Med Chem 59:5129, each of which are herein incorporated by reference). In some embodiments, the PROTAC comprises a first active domain that binds a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) and a second active domain that mediates degradation of the target protein upon binding, wherein the first active domain and second active domain are operably linked via a linker. In some embodiments, the second active domain binds to a ubiquitin ligase. In some embodiments, the second active domain binds to an E3 ubiquitin ligase.

In some embodiments, the small molecule inhibitor comprises a combination of small molecule inhibitors or derivatives thereof. In some embodiments, a combination of small molecule inhibitors (e.g., a small molecule “cocktail”) is used to decrease expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4).

In some embodiments, the small molecule inhibitor is administered at a dosage to have a therapeutic effect. In some embodiments, the small molecule inhibitor is administered at the maximum tolerated dose. As used herein, the term “maximum tolerated dose” or “MTD” refers to the highest dose of a drug that does not cause unacceptable adverse effects. In some embodiments, the MTD is determined by clinical testing, e.g., in a Phase I clinical trial.

In some embodiments, the administration of the one or more therapeutic agents in a subject having a cancer with a mutation or deficiency in a biomarker described herein requires a lower concentration or dosage to achieve therapeutic efficacy. For example, in some embodiments, a lower dosage of BET inhibitor is sufficient to kill cancer cells comprising a deficiency and/or mutation in a gene encoding a biomarker described herein that is a synthetic lethal pair with a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), as compared to control cells (e.g., non-cancer cells) that do not have the biomarker deficiency and/or mutation. Without being bound by theory, as higher dosages of BET inhibition in a subject may increase toxicity, administration of a lower dosage of a BET inhibitor in selected or pre-screened cancer types (e.g., cancers comprising the deficiency and/or mutation in a biomarker described herein that is a synthetic lethal pair with a BET polypeptide) is advantageous to reduce toxicity and side effects to the subject.

(iii) Polypeptides

In some embodiments, the one or more therapeutic agents comprises a protein or peptide. In some embodiments, the therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises a protein or peptide. For example, in some embodiments, the one or more therapeutic agents comprises an antibody, an antibody fragment, a hormone, a ligand, or an immunoglobulin. In some embodiments, the protein or peptide is naturally occurring or is synthetic. In some embodiments, the protein comprises an engineered variant of a protein (e.g., recombinant protein), or fragment thereof. In some embodiments, the protein is subjected to other modifications, e.g., post-translational modifications, including but not limited to: glycosylation, acylation, prenylation, lipoylation, alkylation, amidation, acetylation, methylation, formylation, butyrylation, carboxylation, phosphorylation, malonylation, hydroxylation, iodination, propionylation, S-nitrosylation, S-glutationylation, succinylation, sulfation, glycation, carbamylation, carbonylation, biotinylation, carbamylation, oxidation, pegylation, sumoylation, ubiquitination, ubiquitylation, racemization, etc. One or more modifications may be made to the protein or peptide.

In some embodiments, the therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises an antibody or antigen binding fragment thereof. In some embodiments, the antibody or antigen binding fragment thereof specifically binds a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), wherein binding blocks an activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) (e.g., a DNA binding and/or transactivation cofactor binding activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4).

As used herein, the term “antibody” refers to whole antibodies that interact with (e.g., by binding, steric hindrance, stabilizing/destabilizing, spatial distribution) an epitope of the target (e.g., an epitope on a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)). The term encompasses monoclonal antibodies, human antibodies, humanized antibodies, camelized antibodies, and chimeric antibodies. Additionally, the term encompasses any isotype (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgGl, IgG2, IgG3, IgG4, IgAl and IgA2) or subclass.

The term “antigen binding fragment” refers to a portion of an antibody that specifically interacts with (e.g., by binding, steric hindrance, stabilizing/destabilizing, spatial distribution) an epitope of the target (e.g., an epitope on a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)). Examples of antigen binding fragments include, but are not limited to, an scFv, a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHI domains; a F(ab).sub.2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; a Fd fragment consisting of the VH and CHI domains; a Fv fragment consisting of the VL and VH domains of a single arm of an antibody; a dAb fragment (Ward et al., (1989) Nature 341 : 544-546), which consists of a VH domain; and an isolated complementarity determining region (CDR).

In some embodiments, the therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises an antibody drug conjugate. The term “antibody drug conjugate” as used herein refers to the linkage of an antibody or an antigen binding fragment thereof with another agent, such as a chemotherapeutic agent, a toxin, an immunotherapeutic agent, an imaging probe, and the like. The linkage can be covalent bonds, or non-covalent interactions such as through electrostatic forces. Various linkers, known in the art, can be employed in order to form the immunoconjugate. Additionally, the immunoconjugate can be provided in the form of a fusion protein that may be expressed from a polynucleotide encoding the immunoconjugate.

As used herein, “fusion protein” refers to proteins created through the joining of two or more genes or gene fragments which originally coded for separate proteins (including peptides and polypeptides). Translation of the fusion gene results in a single protein with functional properties derived from each of the original proteins. In some embodiments, the antibody or antigen binding fragment is operably linked to a biophysical probe, a fluorophore, a spin label, an infrared probe, an affinity probe, a chelator, a spectroscopic probe, a radioactive probe, a lipid molecule, a polyethylene glycol, a polymer, a spin label, DNA, RNA, a protein, a peptide, a surface, an antibody, an antibody fragment, a nanoparticle, a quantum dot, a liposome, a PLGA particle, a saccharide or a polysaccharide or a drug moiety.

In some embodiments, the therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises an intrabody (a single chain antibody expressed in a cell). In some embodiments, the intrabody blocks a cytoplasmic antigen (e.g., a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)) and inhibits its biological activity. (Beerli et al., 1994 J Biol Chem, 269, 23931-6; Biocca et al., 1994 Bio/Technology, 12, 396-9; Duan et al., 1994 Proceedings of the National Academy of Sciences of the United States of America, 91, 5075-9; Gargano and Cattaneo, 1997 FEBS Lett, 414, 537-40; Greenman et al., 1996 J Immunol Methods, 194, 169-80; Martineau et al., 1998 Journal of Molecular Biology, 280, 117-27; Mhashilkar et al., 1995 EMBO Journal, 14, 1542-51; Tavladoraki et al., 1993 Nature, 366, 469- 72). In some embodiments, the intrabody comprises a Fab fragment or scFv fragment (see, e.g., Lecerf et al., Proc. Natl. Acad. Sci. USA 98:4764-49 (2001). The framework regions flanking the CDR regions can be modified to improve expression levels and solubility of an intrabody in an intracellular reducing environment (see, e.g., Worn et al., J. Biol. Chem. 275:2795-803 (2000). An intrabody may be directed to a particular cellular location or organelle, for example by constructing a vector that comprises a polynucleotide sequence encoding the variable regions of an intrabody that may be operatively fused to a polynucleotide sequence that encodes a particular target antigen within the cell (see, e.g., Graus-Porta et al., Mol. Cell Biol. 15:1182-91 (1995); Lener et al., Eur. J. Biochem. 267: 1196-205 (2000)). An intrabody may be introduced into a cell by a variety of techniques available to the skilled artisan including via a gene therapy vector, or a lipid mixture (e.g., Provectin™ manufactured by Imgenex Corporation, San Diego, Calif), or according to photochemical internalization methods. Intrabodies can be derived from monoclonal antibodies which were first selected with classical techniques (e.g., phage display) and subsequently tested for their biological activity as intrabodies within the cell (Visintin et al., 1999 Proceedings of the National Academy of Sciences of the United States of America, 96, 11723-11728). For additional information, see: Cattaneo, 1998 Bratisl Lek Listy, 99, 413-8; Cattaneo and Biocca, 1999 Trends In Biotechnology, 17, 115-21. The solubility of an intrabody can be modified by either changes in the framework (Knappik and Pluckthun, 1995 Protein Engineering, 8, 81-9) or the CDRs (Kipriyanov et al., 1997; Ulrich et al., 1995 Protein Engineering, 10, 445-53). Additional methods for producing intrabodies are described in the art, e.g., U.S. Pat. Nos. 7,258,985 and 7,258,986.

(iv) Nucleic Acids

In some embodiments, the one or more therapeutic agents comprises a nucleic acid molecule, e.g., an RNA molecule. In some embodiments, the RNA molecule comprises any suitable RNA molecule and size sufficient to decrease the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the RNA molecule comprises a small hairpin RNA (shRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA), or other useful RNA molecule. In some embodiments, the RNA molecule comprises a messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNAs (rRNA), small nuclear RNA (snRNA), piwi-interacting RNA (piRNA), non-coding RNA (ncRNA), long non-coding RNA, (IncRNA), and fragments of any of the foregoing. In some embodiments, the RNA molecule is single-stranded, double-stranded, or partially single- or double-stranded.

In some embodiments, the therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises an oligonucleotide comprising a region of complementarity to a target sequence in an RNA transcript encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) (e.g., an mRNA encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)). As used herein, the term “oligonucleotide” refers to a molecule comprising at least one strand of two or more covalently linked nucleosides and/or nucleotides. The nucleosides and/or nucleotides can be modified or unmodified independent of each other. In some embodiments, an oligonucleotide comprises at least one strand of 10-100 covalently linked nucleosides. In some embodiments, an oligonucleotide comprises at least one strand of 10-50 nucleosides. In some embodiments, the oligonucleotide comprises a single-stranded RNA, a single-stranded DNA, a single-stranded modified RNA, a single-stranded modified DNA, or a single-stranded hybrid of RNA, DNA, modified RNA, and/or modified DNA. In some embodiments, the single-strand comprises one or more secondary structures, e.g., a stem-loop structure. In some embodiments, the oligonucleotide comprises two or more strands. In some embodiments, the oligonucleotide is double-stranded. In some embodiments, the oligonucleotide comprises a two-stranded DNA/DNA duplex, a two-stranded DNA/RNA duplex, or a two- stranded RNA/RNA duplex, including modified oligonucleotides thereof. In some embodiments, the oligonucleotide inhibits or reduces expression and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) by any known mechanism for an RNA interference nucleotide, aptamer, or antisense oligonucleotide, e.g., by inhibiting transcription, promoting cleavage of a transcript, or disrupting translation.

In some embodiments, the oligonucleotide comprises a region of contiguous nucleosides having substantial complementary to a target sequence present in an RNA transcript encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) (e.g., there is a sufficient degree of complementarity between the oligonucleotide and the target sequence so that they bind and expression and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) is reduced or inhibited).

In some embodiments, the oligonucleotide is an aptamer. As used herein, an “aptamer” refers to a synthetic nucleic acid polymer of about 25-80 nucleotides in length that contains RNA nucleotides, DNA nucleotides, or combinations thereof, and/or modified nucleotides or modified nucleoside linkages, and which comprises a region of recognition to a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or an RNA transcript (e g., pre-mRNA or mRNA) encoding a polypeptide intended for inhibition. In some embodiments, the aptamer associates with the BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or an RNA transcript encoding a BET polypeptide in a structure-specific manner (e.g., binds to or forms shapedependent interactions). In some embodiments, the association functions to modulate the activity of the gene product or RNA transcript by one or more processes to inhibit, interfere, disrupt, degrade, or block normal function. This interference with or modulation of the function of the target gene product or RNA transcript by an aptamer described herein is referred to as “aptamer inhibition.” Aptamers as described herein mediate a variety of effects including, for example, binding to a target structure in a pre-mRNA encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) and block an activity/effect (e.g., splicing pattern) that facilitates expression; interact with a gene product encoding a BET polypeptide to inhibit normal activity; and/or interact with a target structure in an RNA transcript encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) to mediate translational inhibition and/or degradation.

In some embodiments, an aptamer for inhibition of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) or RNA transcript encoding a BET polypeptide is selected by any process known in the art: Colin Cox et al., Nuc. Acid Res., 2002, 30(20), e80. For additional information, see: U.S. Patent No. 7,329,742.

In some embodiments, the oligonucleotide is an antisense oligonucleotide. As used herein, an “antisense oligonucleotide” refers to a synthetic, single-stranded nucleic acid polymer of about 10-50 nucleotides in length that contains RNA nucleotides, DNA nucleotides, or combinations thereof, and/or modified nucleotides or modified nucleoside linkages, and which comprises a region of complementarity to a target sequence in a gene or an RNA transcript (e.g., pre-mRNA or mRNA) encoding a polypeptide intended for inhibition. In some embodiments, the antisense oligonucleotide comprises a region of complementarity to a target sequence in a gene or RNA transcript (e.g., pre-mRNA or mRNA) encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the antisense oligonucleotide associates with the gene or RNA transcript in a sequence-specific manner (e.g., binds to or hybridizes with the target sequence). In some embodiments, the association functions to modulate expression of the gene or RNA transcript by one or more processes to inhibit, interfere, disrupt, cleave, degrade, and/or alter, activate or block normal function and/or expression. This interference with or modulation of the function of the target nucleic acid by an antisense oligonucleotide described herein is referred to as “antisense inhibition.” Antisense oligonucleotides as described herein mediate a variety of effects including, for example, bind to a target sequence in a pre-mRNA encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) and block an activity/effect (e.g., splicing pattern) necessary for expression; interact with a target gene described herein to modulate transcriptional inhibition; and/or interact with a target sequence in an RNA transcript encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) to mediate translational inhibition and/or degradation.

In some embodiments, the therapeutic agent targeting a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises an RNAi oligonucleotide. In some embodiments, the RNAi oligonucleotide functions to reduce or inhibit expression and/or activity of a gene or an RNA transcript thereof encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). Herein, the term “RNA interference (RNAi) molecule” refers to any molecule inhibiting RNA expression or translation via the RNA reducing silencing complex (RISC) in a cell's cytoplasm, where the RNAi molecule interact with the catalytic RISC component argonaute. In some embodiments, the RNAi oligonucleotide is a double-stranded RNA. The term “double-stranded RNA” or “dsRNA”, as used herein, refers to a complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary, as defined above, nucleic acid strands. The two strands forming the duplex structure may be different portions of one larger RNA molecule, or they may be separate RNA molecules. Where separate RNA molecules, such dsRNA are often referred to as siRNA (“short interfering RNA”) or DsiRNA (“Dicer substrate siRNAs”). Where the two strands are part of one larger molecule, and therefore are connected by an uninterrupted chain of nucleotides between the 3 '-end of one strand and the 5' end of the respective other strand forming the duplex structure, the connecting RNA chain is referred to as a “hairpin loop”, “short hairpin RNA” or “shRNA”. Where the two strands are connected covalently by means other than an uninterrupted chain of nucleotides between the 3'- end of one strand and the 5'end of the respective other strand forming the duplex structure, the connecting structure is referred to as a “linker”. The RNA strands may have the same or a different number of nucleotides. The maximum number of base pairs is the number of nucleotides in the shortest strand of the dsRNA minus any overhangs that are present in the duplex. In addition to the duplex structure, a dsRNA may comprise one or more nucleotide overhangs. In addition, as used herein, “dsRNA” may include chemical modifications to ribonucleotides, internucleoside linkages, end- groups, caps, and conjugated moieties, including substantial modifications at multiple nucleotides and including all types of modifications disclosed herein or known in the art.

In some embodiments, an antisense oligonucleotide or RNAi agent for inhibition of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) is selected by any process known in the art. In some embodiments, the selection criteria includes one or more of the following steps: (i) initial analysis of the target gene sequence (e.g., gene encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4)) and design of RNAi agents; this design can take into consideration sequence similarity across species (human, cynomolgus, mouse, etc.) and dissimilarity to other (non-target) genes; screening of RNAi agents in vitro (e.g., at 10 nM in cells); (ii) determination of EC50 in cell culture expressing a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4); (iii) determination of viability of various cells treated with the RNAi agents, wherein it is desired that the RNAi agent to a target not inhibit the viability of these cells; (iv) testing with human PBMC (peripheral blood mononuclear cells), e.g., to test levels of TNF-alpha to estimate immunogenicity, wherein immunostimulatory sequences are less desired; (v) testing in human whole blood assay, wherein fresh human blood is treated with an RNAi agent and cytokine/chemokine levels are determined (e.g., TNF-alpha (tumor necrosis factor-alpha) and/or MCPI (monocyte chemotactic protein 1)), wherein immunostimulatory sequences are less desired; (vi) determination of gene knockdown in vivo in test animals; (vii) target gene modulation analysis, e.g., using a pharmacodynamic (PD) marker, and optimization of specific modifications of the RNAi agents.

In some embodiments, the RNAi agent for inhibition of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) comprises a sense strand and an antisense strand, wherein the antisense strand comprises a contiguous nucleotide sequence of at least 10 nucleotides having complementarity (e.g., full or partial complementarity) to a target sequence in a gene or transcript thereof encoding a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), wherein the contiguous nucleotide sequence has no more than 1, 2, or 3 mismatches relative to the target sequence. In some embodiments, the antisense and sense strand are physically separated strands (e.g., an siRNA). In some embodiments, the antisense and sense strand are components of a single strand or molecule, e.g., they are linked by a loop of nucleotides or nonnucleotide linker (e.g., an shRNA). In some embodiments, the sense strand comprises a nick. In some embodiments, the antisense and sense strands comprise one or more mismatches. In some embodiments, the antisense strand is about 30 or fewer nucleotides in length. In one embodiment, the antisense strand forms a duplex region with a sense strand, wherein the duplex region is about 15 to 30 nucleotide pairs in length. In one embodiment, the antisense strand is about 15 to about 30 nucleotides in length (e.g., about 9 to about 23 nucleotides in length). In one embodiment, the antisense strand has a length of about 15 nucleotides, about 16 nucleotides, about 17 nucleotides, about 18 nucleotides, about 19 nucleotides, about 20 nucleotides, about 21 nucleotides, about 22 nucleotides, about 23 nucleotides, about 24 nucleotides, about 25 nucleotides, about 26 nucleotides, about 27 nucleotides, about 28 nucleotides, about 29 nucleotides or about 30 nucleotides.

In some embodiments, the RNAi agent, aptamer, or antisense oligonucleotide comprises a modification that increases stability in a biological sample or environment. In some embodiments, the RNAi agent or antisense oligonucleotide comprises a modification of one or more internucleoside linkages (e.g., a modification of a phosphoester linkage with a phosphorothioate linkage). In some embodiments, the RNAi agent, aptamer or antisense oligonucleotide comprises one or more 2'modified nucleosides. In some embodiments, one or more nucleosides are substituted with a locked nucleic acid, a deoxynucleoside, a morpholino nucleoside, a peptide nucleoside, a cyclohexene nucleoside, a glycol nucleoside, a threose nucleoside, an arabinose nucleoside, an anhydrohexitol nucleoside, a 2'-fluoroarabinose nucleoside, or a combination thereof.

In some embodiments the RNAi agent comprises at least one blunt end. In some embodiments, the RNAi agent comprises at least one overhang of 1, 2, 3, or 4 nucleosides/nucleotides in length. In some embodiments, the RNAi agent comprises an overhang at the 3 'end or the 5 'end of the antisense strand.

In some embodiments, the antisense oligonucleotide is a gapmer. A “gapmer” refers to an antisense oligonucleotide comprising a central DNA segment flanked by nucleotides composed of ribonucleosides or modified nucleosides. Gapmers comprise a region of complementarity to a target sequence in a transcript targeted for downregulation and recruit ribonuclease H to promote degradation of the transcript.

In some embodiments, the RNAi agent, aptamer, or the antisense oligonucleotide comprises one or more nucleosides ligated to one or more diagnostic compound, reporter group, cross-linking agent, nuclease-resistance conferring moiety, natural or unusual nucleobase, lipophilic molecule, cholesterol, lipid, lectin, steroid, uvaol, hecigenin, diosgenin, terpene, triterpene, sarsasapogenin, Friedelin, epifriedelanol-derivatized lithocholic acid, vitamin, carbohydrate, dextran, pullulan, chitin, chitosan, synthetic carbohydrate, oligo lactate 15-mer, natural polymer, low- or medium-molecular weight polymer, inulin, cyclodextrin, hyaluronic acid, protein, protein-binding agent, integrin-targeting molecule, polycationic, peptide, polyamine, peptide mimic, and/or transferrin.

Oligonucleotides and aptamers are commonly made in the laboratory by solid-phase chemical synthesis followed by purification. In some embodiments, the oligonucleotides described herein are chemically synthesized and purified or isolated. In some embodiments, the oligonucleotide comprises ribonucleosides, and optionally, one or more non-ribonucleosides, e.g., a deoxyribonucleoside. In some embodiments, the oligonucleotide comprises one or more chemically modified nucleosides (e.g., one or more chemically-modified ribonucleosides or deoxyribonucleosides). Chemically modified nucleosides are known in the art.

RNAi and aptamers nucleic acid molecules may be synthesized chemically (typical for siRNA complexes), by in vitro transcription, or expressed from a vector. shRNA molecules are generally between 40 and 70 nucleotides in length, such as between 45 and 65 nucleotides in length, such as 50 and 60 nucleotides in length, and interacts with the endonuclease known as Dicer which is believed to processes dsRNA into 19-23 base pair short interfering RNAs with characteristic two base 3' overhangs which are then incorporated into an RNA-induced silencing complex (RISC). In some embodiments, the guide (antisense) strand of an siRNA (or antisense region of a shRNA) is 17 to 25 nucleotide in length, such as 19 - 23 nucleotides in length and complementary to the target sequence. In an siRNA complex, the guide (antisense) strand and passenger (sense) strand form a double stranded duplex, which may comprise 3 ’ terminal overhangs of e.g. 1-3 nucleotides (resembles the product produced by Dicer), or may be blunt ended (no overhang at one or both ends of the duplex). In some embodiments, an aptamer is between 10 and 80 nucleotides in length, such as between 15 and 70 nucleotides, and such as between 20 and 60 nucleotides in length.

In some embodiments, the disclosure further provides methods for delivery of an RNAi agent or antisense oligonucleotide described herein. Methods known in the art include, but are not limited to, viral delivery (retrovirus, adenovirus, lentivirus, baculovirus, AAV); liposomes (Lipofectamine, cationic DOTAP, neutral DOPC) or lipid nanoparticles (cationic polymer, PEI), bacterial delivery (tkRNAi), and also chemical modification to improve stability (see, e.g., Xia et al. 2002 Nat. Biotechnol. 20 and Devroe et al. 2002. BMC Biotechnol. 21: 15). In some embodiments, the method of delivery comprises a stable nucleic acid-lipid particle (SNALP) comprising the RNAi agent or antisense oligonucleotide. SNALP represents a vesicle of lipids coating a reduced aqueous interior comprising the RNAi agent or antisense oligonucleotide or a nucleic acid (e.g., plasmid) encoding the RNAi agent or antisense oligonucleotide. SNALPs are described, e.g., in U.S. 2006/0240093, US 2007/0135372, and US9006191, each of which are incorporated herein by reference.

In some embodiments, the method of delivery comprises chemical transfection, e.g., using a lipid-based, amine-based and polymer-based techniques (see, e.g., products from Ambion Inc., Austin, Tex. and Novagen, EMD Biosciences, Inc; Ovcharenko D (2003) Ambion TechNotes 10 (5): 15-16; Song et al. Nat Med. (2003) doi: 10.1038/nm828; Caplen et al. 2001 Proc. Natl. Acad. Sci. (USA), 98: 9742-9747; and McCaffrey et al. Nature 414: 34-39. In some embodiments, the method of delivery comprises a lipid nanoparticle (LNP); neutral liposome (NL); polymer nanoparticle; double-stranded RNA binding motifs (dsRBM); or modification of the RNAi agent or antisense oligonucleotide (e.g., by covalent attachment to a targeting moiety). Lipid nanoparticles (LNP) are self-assembling cationic lipid based systems. In some embodiments, the LNP comprises a neutral lipid, a cationic lipid, cholesterol, and PEG-lipid. Neutral liposomes (NL) are non-cationic lipid based particles. Polymer nanoparticles are selfassembling polymer-based particles. Double-stranded RNA binding motifs (dsRBMs) are selfassembling RNA binding proteins, which will need modifications.

(v) Combinations

It will be appreciated that one or more therapeutic agents (e.g., peptides, RNA molecules, protein-nucleic acid complexes) are listed as examples and that a combination of therapeutic agent types may be used to treat the subject. For example, in some embodiments, administering one or more different types of therapeutic agents may be used to alter (e.g., increase or decrease) the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). For example, in some embodiments, a protein or peptide co-administered with a small molecule (e.g., a molecule having a molecular weight of less than 900 Daltons), an RNA molecule, a DNA molecule, or a complexed molecule (e.g., protein-nucleic acid molecule) is used to alter (e.g., increase or decrease) the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, an RNA molecule is coadministered with a small molecule, a DNA molecule, or a complexed molecule to alter (e.g., increase or decrease) the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, a small molecule is co-administered with a DNA molecule or a complexed molecule to alter (e.g., increase or decrease) the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). Any of these combinations may be used to alter (e.g., increase or decrease) the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) in a cell comprising a mutation and/or deficiency in a biomarker described herein (e.g., a biomarker forming a synthetic lethal pair with a BET polypeptide). These combinations are non-limiting examples of different combinations of agents that may be used to treat the subject having or suspected of having cancer (e.g., liver or ovarian cancer).

Administration

In some embodiments, the present disclosure provides methods and compositions for delivery, administration of, or exposure to one or more therapeutic agents described herein. In some embodiments, one or more therapeutic agents are delivered to a subject (e.g., in vivo), or to a cell or population of cells from a subject (e.g., ex vivo or in vivo). In some embodiments, the one or more therapeutic agents are delivered to a subject in one or more delivery vesicles, such as a nanoparticle. In some embodiments, the nanoparticle is any suitable nanoparticle and may be a solid, semi-solid, semi-liquid or a gel. In some embodiments, the nanoparticle is a lipophilic or amphiphilic particle. For example, a nanoparticle may comprise a micelle, liposome, exosome, or other lipid-containing vesicle. In some embodiments, the nanoparticle is configured for targeted delivery to a certain cell or cell type (e.g., cancer cell). In such cases, the nanoparticle is decorated with any number of ligands, e.g., antibodies, nucleic acid molecules (e.g., ribonucleic acid (RNA) molecules or deoxyribonucleic acid (DNA) molecules), proteins, peptides, which may specifically bind to a certain cell or cell type (e.g., cancer cell).

In some embodiments, the one or more therapeutic agents are delivered using viral approaches. For example, in some embodiments, the one or more therapeutic agents is administered using a viral vector. In such cases, the one or more therapeutic agents is encapsulated in a virus for delivery to a cell, population of cells, or the subject. In some embodiments, the virus is an adeno-associated virus (AAV), a retrovirus, a lentivirus, a herpes simplex virus, or other useful virus. In some embodiments, the virus is engineered or naturally occurring.

In some embodiments, the one or more therapeutic agents is delivered to a subject (e.g., human patient) systemically or locally (e.g., at the tumor site) using a single or variety of approaches. For example, in some embodiments, the one or more therapeutic agents is delivered or administered orally, intravenously, intraperitoneally, intratumorally, subcutaneously, topically, transdermally, transmucosally, or through another administration approach.

In some embodiments, the one or more therapeutic agents is delivered to the subject enterally. For example, in some embodiments, the one or more therapeutic agents is administered to the subject orally, nasally, rectally, sublingually, sub-labially, buccally, topically, or through an enema. In some embodiments, the one or more therapeutic agents is formulated into a tablet, capsule, drop or other formulation. In some embodiments, the formulation is configured to be delivered enterally.

In some embodiments, the one or more therapeutic agents is delivered to the subject parenterally. For example, in some embodiments, the one or more therapeutic agents is administered via systemic or local injection. In some embodiments, the local injection comprises administration to the central nervous system (e.g., epidurally, intracerebrally, intracer ebroventricularly). In some embodiments, the local injection comprise administration to the skin (e.g., epicutaneously). In some embodiments, the one or more therapeutic agents are formulated in a transdermal patch, wherein the one or more therapeutic agents are delivered to the skin of the subject. In some embodiments, the one or more therapeutic agents is delivered sublingually and/or bucally, extra-amniotically, nasally, intra-arterially, intra-articularly, intravavernously, intracardiacally, intradermally, intralesionally, intramuscularly, intraocularly, intraosseously, intraperitoneally, intrathecally, intrauterinely, intravaginally, intravenously, intravesically, intravitreally, subcutaneously, trans-dermally, perivascularly, transmucosally, or through another route of administration. In some embodiments, the one or more therapeutic agents is delivered topically.

In some embodiments, the one or more therapeutic agents is delivered to the subject using a targeted delivery approach (e.g., for targeted delivery to the tumor site) or using a delivery approach to increase uptake of a cell of the one or more therapeutic agents. In some embodiments, the delivery approach comprises magnetic drug delivery (e.g., magnetic nanoparticle-based drug delivery), an acoustic targeted drug delivery approach, a selfmicroemulsifying drug delivery system, or other delivery approach.

Pharmaceutical Compositions

In some embodiments, the disclosure provides a pharmaceutical composition for treating a cancer (e.g., liver or ovarian cancer), comprising (i) one or more therapeutic agents and (ii) a pharmaceutically acceptable carrier. In some embodiments, the one or more therapeutic agents is present in an amount that is effective to alter (e.g., increase or decrease) expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4) following administration or exposure to the subject. In some embodiments, the pharmaceutically acceptable carrier stabilizes the one or more therapeutic agents or provides therapeutic enhancement of the one or more therapeutic agents following administration to the subject as compared to the one or more therapeutic agents administered in the absence of the pharmaceutically acceptable carrier.

In some embodiments, pharmaceutically acceptable carrier comprises a substance, which substance may be used to confer a property to the one or more therapeutic agents used to alter (e.g., increase or decrease) the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). For example, in some embodiments, the pharmaceutically acceptable carrier comprises a substance for stabilization of the one or more therapeutic agents. In some embodiments, the pharmaceutically acceptable carrier comprises a substance for bulking up a solid, liquid, or gel formulation of the one or more therapeutic agents. In some embodiments, the substance confers a therapeutic enhancement to the one or more therapeutic agents (e.g., by enhancing solubility). In some embodiments, the substance is used to alter a property of the pharmaceutical composition, such as the viscosity. In some embodiments, the substance is used to alter a property of the one or more therapeutic agent, e.g., bioavailability, absorption, hydrophilicity, hydrophobicity, pharmacokinetics, etc.

In some embodiments, the pharmaceutically acceptable carrier comprises a binding agent, anti-adherent agent, a coating, a disintegrant, a glidant (e.g., silica gel, talc, magnesium carbonate), a lubricant, a preservative, a sorbent, a sweetener, a vehicle, or a combination thereof. For example, in some embodiments, the pharmaceutically acceptable carrier comprises a powder, a mineral, a metal, a sugar (e.g. saccharide or polysaccharide), a sugar alcohol, a naturally occurring polymer (e.g., cellulose, methylcellulose) synthetic polymer (e.g., polyethylene glycol or polyvinylpyrrolidone), an alcohol, a thickening agent, a starch, a macromolecule (e.g., lipid, protein, carbohydrate, nucleic acid molecule), etc.

In some embodiments, the one or more therapeutic agents is formulated into an aerosol, pill, tablet, capsule (e.g., asymmetric membrane capsule), pastille, elixir, emulsion, powder, solution, suspension, tincture, liquid, gel, dry powder, vapor, droplet, ointment, patch, or a combination thereof. In some embodiments, the one or more therapeutic agents is formulated in a gel or polymer and delivered via a thin film.

In some embodiments, the one or more therapeutic agents is formulated for targeted delivery or for increased uptake by a cell. For example, in some embodiments, the one or more therapeutic agents is formulated with another agent, which may improve the solubility, hydrophobicity, hydrophilicity, absorbability, half-life, bioavailability, release profile, or other property of the one or more therapeutic agents. For example, in some embodiments, the one or more therapeutic agents is formulated with a polymer which enables a controlled release profile (e.g., slow release). In some embodiments, the one or more therapeutic agents is formulated as a coating or with a coating (e.g., bovine submaxillary mucin coatings, polymer coatings, etc.) to alter a property of the one or more therapeutic agents (e.g., bioavailability, pharmacokinetics, etc.).

In some embodiments, the one or more therapeutic agents is formulated using a retro- metabolic drug design. In such embodiments, the one or more therapeutic agents is assessed for metabolic effects in a cell, and a new formulation comprising a derivative (e.g., chemically synthesized alternative or engineered variant) is prepared to change a property of the one or more therapeutic agents (e.g., to increase efficacy, minimize undesirable side effects, alter bioavailability, etc.). Kits

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agent described herein. In some embodiments, the kit further comprises a package insert comprising instructions for using the one or more therapeutic agents described herein for treating or delaying progression of cancer in a subject. In some embodiments, the kit further comprises a package insert comprising instructions for using the one or more therapeutic agents described herein for treating or delaying progression of cancer in a subject, wherein the cancer has altered (e.g., increased or decreased) expression level and/or activity of a biomarker described herein. In some embodiments, the kit further comprises a package insert comprising instructions for using the one or more therapeutic agents described herein for treating or delaying progression of cancer in a subject, wherein the cancer comprises a mutation in a biomarker described herein (e.g., loss of function mutation resulting a decreased expression level and/or activity of the biomarker). In some embodiments, the kit further comprises materials desirable from a commercial and user standpoint, such as other buffers, diluents, filters, needles, and syringes. Suitable containers for the one or more therapeutic agent include, for example, bottles, vials, bags and syringes.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for treating or delaying progression of cancer in a subject, wherein the cancer has one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity a biomarker described herein (e.g., TNKS and/or a biomarker selected from Table 2), wherein the biomarker forms a synthetic lethal pair with the target gene encoding a BET polypeptide.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for reducing tumor burden in a subject, wherein the cancer has one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity a biomarker described herein (e.g., TNKS and/or a biomarker selected from Table 2), wherein the biomarker forms a synthetic lethal pair with the target gene encoding a BET polypeptide. In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for treating or delaying progression of cancer in a subject, wherein the cancer has one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of one or more biomarkers described herein (e.g., a biomarker selected from Table 2). In some embodiments, the one or more biomarkers forms a synthetic lethal pair with the one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the instructions further comprise administering the one or more therapeutic agents to a subject having a mutation in, a decreased expression level of, and/or decreased activity level of the one or more biomarkers. In some embodiments, the instructions further comprise administering an effective amount of the one or more therapeutic agents to a subject having a mutation in, a decreased expression level of, and/or decreased activity level of the one or more biomarkers.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for reducing tumor burden in a subject, wherein the tumor has one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of one or more biomarkers described herein (e.g., a biomarker selected from Table 2). In some embodiments, the one or more biomarkers form a synthetic lethal pair with the one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the instructions further comprise administering the one or more therapeutic agents to a subject having a mutation in, a decreased expression level of, and/or decreased activity level of the one or more biomarkers. In some embodiments, the instructions further comprise administering an effective amount of the one or more therapeutic agents to a subject having a mutation in, a decreased expression level of, and/or decreased activity level of the one or more biomarkers.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for treating or delaying progression of cancer in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of one or more biomarkers in a cancer sample obtained from the subject, wherein the one or more biomarkers are selected from Table 2, and (ii) administering an effective dose of the one or more therapeutic agents to the subject based upon the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of the one or more biomarkers in the cancer sample as compared to a reference sample.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for treating or delaying progression of cancer in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of one or more biomarkers in a cancer sample obtained from the subject, wherein the one or more biomarkers are selected from Table 2, and (ii) administering an effective dose of the one or more therapeutic agents to the subject based upon the presence of an inactivating mutation in, a decreased expression level of, and/or a decreased activity level of the one or more biomarkers in the cancer sample as compared to a reference sample.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers are selected from Table 2, and (ii) administering an effective dose of the one or more therapeutic agents to the subject based upon the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of the one or more biomarkers in the tumor sample as compared to a reference sample. In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of one or more biomarkers in a tumor sample obtained from the subject, wherein the one or more biomarkers are selected from Table 2, and (ii) administering an effective dose of the one or more therapeutic agents to the subject based upon the presence of an inactivating mutation in, a decreased expression level of, and/or a decreased activity level of the one or more biomarkers in the tumor sample as compared to a reference sample.

In some embodiments, the one or more biomarkers selected from Table 2 is TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and/or MBP. In some embodiments, the one or more biomarkers selected from Table 2 is TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and/or CHD8. In some embodiments, the one or more biomarkers selected from Table 2 is TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and/or MBP. In some embodiments, the one or more biomarkers comprises TNKS. In some embodiments, the one or more biomarkers comprises PTEN. In some embodiments, the one or more biomarkers comprises JAK1. In some embodiments, the one or more biomarkers comprises RBI.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRIM), and a package insert comprising instructions for reducing tumor burden in a subject, wherein the tumor has one or more mutations in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level in at least one biomarker selected from a panel of biomarkers (e.g., a panel comprising one or more biomarkers selected from Table 2) in a tumor sample obtained from a subject. In some embodiments, the panel of biomarkers comprises one or more biomarkers that forms a synthetic lethal pair a BET polypeptide (e.g., BRD1, BRD2, BRD3, and/or BRD4). In some embodiments, the panel of biomarkers comprises one or more biomarkers selected from Table 2. In some embodiments, the panel of biomarkers comprises one or more biomarkers selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP. In some embodiments, the panel of biomarkers comprises one or more biomarkers selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8. In some embodiments, the panel of biomarkers comprises one or more biomarkers selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP. In some embodiments, the instructions further comprise administering the one or more therapeutic agents to a subject having an inactivating mutation in, a decreased expression level of, and/or decreased activity level in the at least one biomarker in the panel. In some embodiments, the at least one biomarker is selected from Table 2. In some embodiments, the at least one biomarker is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, APC, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP. In some embodiments, the at least one biomarker is selected from TP53, SMAD4, PTEN, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, MBP, CHD4, and CHD8. In some embodiments, the at least one biomarker is selected from TP53, SMAD4, CREBBP, SMARCA4, PBRM1, VHL, JAK1, RBI, MLH1, STAG2, LTK, CTCF, ADAMTS12, B2M, BRAF, CDCA2, CDH13, CDK7, CHD3, TNKS, TENM3, THSD7B, SETDB2, TUSC3, PCLO, PLK2, PSD3, REV3L, JAK2, KRAS, DNAH3, ERBB2, FGFR1, GRM2, IKBKB, KAT6A, KMT2C, MAST4, and MBP.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRIM), and a package insert comprising instructions for treating or delaying progression of cancer in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of a panel of biomarkers in a cancer sample obtained from the subject, wherein the panel of biomarkers comprises one or more biomarkers described herein (e.g., one or more biomarkers selected from Table 2), and (ii) administering an effective dose of the one or more therapeutic agents to the subject based upon the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level in at least one biomarker of the panel (e.g., a biomarker described herein that forms a synthetic lethal pair with a BET protein, e.g., a biomarker selected from Table 2) in the cancer sample as compared to a reference sample.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRIM), and a package insert comprising instructions for reducing tumor burden in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of a panel of biomarkers in a tumor sample obtained from the subject, wherein the panel of biomarkers comprises one or more biomarkers described herein (e.g., one or more biomarkers selected from Table 2), and (ii) administering an effective dose of the one or more therapeutic agents to the subject based upon the presence of an inactivating mutation in, a decreased expression level of, and/or a decreased activity level of at least one biomarker of the panel (e.g., a biomarker described herein that forms a synthetic lethal pair with a BET protein, e.g., a biomarker selected from Table 2) in the tumor sample as compared to a reference sample.

In some embodiments, the disclosure provides a kit comprising one or more therapeutic agents described herein for altering the expression level and/or activity of one or more BET polypeptides (e.g., BRD1, BRD2, BRD3, and/or BRD4), and a package insert comprising instructions for treating or delaying progression of cancer in a subject, wherein the instructions comprise (i) determining the presence of a mutation in, an altered (e.g., increased or decreased) expression level of, and/or an altered (e.g., increased or decreased) activity level of a panel of biomarkers in a cancer sample obtained from the subject, wherein the panel of biomarkers comprises one or more biomarkers described herein (e.g., one or more biomarkers selected from Table 2), and (ii) administering an effective dose of the one or more therapeutic agents to the subject based upon the presence of an inactivating mutation in, a decreased expression level of, and/or a decreased activity level of at least one biomarker of the panel (e.g., a biomarker described herein that forms a synthetic lethal pair with a BET protein, e.g., a biomarker selected from Table 2) in the cancer sample as compared to a reference sample.

Definitions

While various embodiments of the invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions may occur to those skilled in the art without departing from the invention. It will be understood that various alternatives to the embodiments of the invention described herein may be employed.

Whenever the term “at least,” “greater than,” or “greater than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “at least,” “greater than” or “greater than or equal to” applies to each of the numerical values in that series of numerical values. For example, greater than or equal to 1, 2, or 3 is equivalent to greater than or equal to 1, greater than or equal to 2, or greater than or equal to 3.

Whenever the term “no more than,” “less than,” or “less than or equal to” precedes the first numerical value in a series of two or more numerical values, the term “no more than,” “less than,” or “less than or equal to” applies to each of the numerical values in that series of numerical values. For example, less than or equal to 3, 2, or 1 is equivalent to less than or equal to 3, less than or equal to 2, or less than or equal to l.The term “subject,” as used herein, generally refers to an animal, such as a mammal (e.g., human), reptile, or avian (e.g., bird), or other organism, such as a plant. For example, the subject can be a vertebrate, a mammal, a rodent (e.g., a mouse), a primate, a simian or a human. The subject can be a healthy individual, an individual that is asymptomatic with respect to a disease (e.g., liver or ovarian cancer), an individual that has or is suspected of having the disease (e.g., liver or ovarian cancer) or a predisposition to the disease, or an individual that is symptomatic with respect to the disease. The subject may be in need of therapy. The subject can be a patient undergoing monitoring or treatment by a healthcare provider, such as a treating physician.

As used herein, the term “patient” refers to a human subject having a disease or condition in need of treatment. In some embodiments, a patient to be treated or tested for responsiveness to a treatment according to the methods described herein is one who has been diagnosed with a cancer, such as any cancer described herein. Diagnosis may be performed by any method or technique known in the art, such as x-ray, MRI, or biopsy, and may also be confirmed by a physician. To minimize exposure of a patient to drug treatments that may not be therapeutic, the patient may be determined to be either responsive or non-responsive to a cancer treatment, such as a BET therapeutic agent described herein, according to the methods described herein prior to treatment.

The term “genome,” as used herein, generally refers to genomic information from a subject, which may be, for example, at least a portion or an entirety of a subject’s hereditary information. A genome can be encoded in a deoxyribonucleic acid (DNA) molecule (s) and may be expressed in a ribonucleic acid (RNA) molecule(s). A genome can comprise coding regions (e.g., that code for proteins) as well as non-coding regions. A genome can include the sequence of all chromosomes together in an organism. For example, the human genome ordinarily has a total of 46 chromosomes. The sequence of all of these together may constitute a human genome.

The term “contacting” as used herein means establishing a physical connection between two or more entities. Methods of contacting cells with external entities both in vivo, in vitro, and ex vivo are well known in the biological arts. In exemplary embodiments of the disclosure, the step of contacting a mammalian cell with a composition (e.g., a composition comprising a therapeutic agent described herein) is performed in vivo. For example, contacting a composition and a cell (for example, a mammalian cell) which may be disposed within an organism (e.g., a mammal) may be performed by any suitable administration route (e.g., parenteral administration to the organism, including intravenous, intramuscular, intradermal, and subcutaneous administration). For a cell present in vitro, a composition (e.g., a composition comprising a therapeutic agent described herein) and a cell may be contacted, for example, by adding the composition to the culture medium of the cell and may involve or result in transfection.

Moreover, more than one cell may be contacted by the composition.

As used herein the terms “cancer” and “cancerous” refer to or describe the physiological condition in mammals (e.g., humans) that is typically characterized by unregulated cell proliferation. Examples of cancer include, but are not limited to, brain cancer (e.g., astrocytoma, glioblastoma multiforme, and craniopharyngioma), metastatic cancer (e.g., breast cancer that has metastasized to the brain), breast cancer (e.g., an estrogen receptor-positive (ERpos) breast cancer or a metastatic form of breast cancer), prostate cancer, ovarian cancer (e.g., ovarian adenocarcinoma or embryonal carcinoma), liver cancer (e.g., hepatocellular carcinoma (HCC) or hepatoma), myeloma (e.g., multiple myeloma), colorectal cancer (e.g., colon cancer and rectal cancer), leukemia (e.g., acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, and chronic leukemia), myelodysplastic syndrome, lymphoma (e.g., diffuse large B-cell lymphoma, cutaneous T-cell lymphoma, peripheral T-cell lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, Waldenstrom's macroglobulinemia, and lymphocytic lymphoma), cervical cancer, esophageal cancer, melanoma, glioma (e.g., oligodendroglioma), pancreatic cancer (e.g., adenosquamous carcinoma, signet ring cell carcinoma, hepatoid carcinoma, colloid carcinoma, islet cell carcinoma, and pancreatic neuroendocrine carcinoma), gastrointestinal stromal tumor, sarcoma (e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, leiomyosarcoma, Ewing's sarcoma, and rhabdomyosarcoma), breast cancer (e.g., medullary carcinoma), bladder cancer, head and neck cancer (e.g., squamous cell carcinoma of the head and neck), lung cancer (e.g., non-small cell lung carcinoma, large cell carcinoma, bronchogenic carcinoma, and papillary adenocarcinoma), oral cavity cancer, uterine cancer, testicular cancer (e.g., seminoma and embryonal carcinoma), skin cancer (e.g., squamous cell carcinoma and basal cell carcinoma), thyroid cancer (e.g., papillary carcinoma and medullary carcinoma), stomach cancer, intra-epithelial cancer, bone cancer, biliary tract cancer, eye cancer, larynx cancer, kidney cancer (e.g., renal cell carcinoma and Wilms tumor), gastric cancer, blastoma (e.g., nephroblastoma, medulloblastoma, hemangioblastoma, neuroblastoma, and retinoblastoma), polycythemia vera, chordoma, synovioma, mesothelioma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, cystadenocarcinoma, bile duct carcinoma, choriocarcinoma, epithelial carcinoma, ependymoma, pinealoma, acoustic neuroma, schwannoma, meningioma, pituitary adenoma, nerve sheath tumor, cancer of the small intestine, cancer of the endocrine system, cancer of the penis, cancer of the urethra, cutaneous or intraocular melanoma, a gynecologic tumor, solid tumors of childhood, and neoplasms of the central nervous system. The term cancer includes solid tumors (e.g., breast cancer or brain cancer) and hematological cancers (e.g., cancer of the blood, such as lymphoma (e.g., diffuse large B-cell lymphoma (DLBCL), cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), and Hodgkin's lymphoma)).

The term “microarray” as used herein refers to a method to quantify one or more subject oligonucleotides, e.g., RNA, DNA, cDNA, or analogues thereof, at a time. For example, many DNA microarrays, including those made by Affymetrix (e.g., an Affymetrix HG-U133A or HG- U133_Plus_2 array), use several probes for determining the level of a single biomarker. The DNA microarray may contain oligonucleotide probes that may be, e.g., full-length cDNAs complementary to an RNA or cDNA fragments that hybridize to part of an RNA. The DNA microarray may also contain modified versions of DNA or RNA, such as locked nucleic acids or LNA. Exemplary RNAs include mRNA, miRNA, and miRNA precursors.

Examples

Example 1 - Identification of TNKS as a Biomarker Forming a Synthetic Lethal Pair with BRD2/4

This example is based on prediction of biomarkers that function as synthetic lethal pairs with BET proteins and associated protein kinases (e.g., BRD1, BRD2, BRD3, or BRD4) A computational approach was used to identify genes that are inactivated (e.g., via mutation or deletion) in tumor cells that when combined with loss of function of a gene encoding a BET protein (e.g., by genetic knockout using CRISPR/Cas9 or by pharmacological inhibition) generate a synthetic lethal phenotype.

The approach allowed for identification of biomarkers that are inactivated by deletion or mutation (e.g., homozygous deletion, missense mutation that is deleterious to protein function, or missense mutation rendering an open reading frame that encodes a truncated protein) in a human cancer that have little effect on cell viability alone, but when combined with loss of function of a gene encoding a BET protein results in synthetic lethality. The computational approaches taken to identify the biomarkers involved mining public and proprietary datasets using unbiased, orthogonal algorithms. A first algorithm (referred to herein as “algorithm A”) was developed to evaluate one or more publicly available databases. Suitable databases catalog data generated from genetic knockout-libraries (e.g., RNAi or CRISPR/Cas9 libraries) screened for lethality across many genetic contexts. Algorithm A enabled analysis of the lethality of gene knockouts of BET proteins (BRD2, BRD3, and BRD4) across different genetic backgrounds to identify potential synthetic lethal pairs. For example, algorithm A considers gene mutations present in a given genetic background and the effect of suppression of the target gene on cell fitness (e.g., using a gene-knockout tool such as CRISPR/Cas9 or an inhibitory drug). The second algorithm (referred to herein as “algorithm B”) used was based on a machine-learning model. A large database featuring synthetic lethal pairs was developed from internally-generated functional genomic and experimental data and externally sourced and/or publicly-available datasets. The database was used to train the machine learning model to identify gene interactions that could function as synthetic lethal pairs. Algorithm B was used to predict biomarkers that form a synthetic lethal pair with a BET protein (e.g., BRD2 and BRD4).

Based on inferences made using these algorithms, a selection of genes predicted to form synthetic lethal pairs with one or more members of the BET protein family were identified and provided in Table 2. The biomarkers are prioritized based upon their prevalence in human cancers, such as those listed in the TCGA. Selection criteria included prevalence of at least 3% in two cancer types and at least 5% in one cancer type.

Table 2: Synthetic Lethality Gene Predictions for Biomarkers to BET inhibition Proves the gene reference number as used in the National Library of Medicine National Center for Biotechnology Information (NCBI) Gene Database (accessible via the world wide web: ncbi.nlm.nih.gov/)

Bioinformatic analysis was performed for TNKS, which was predicted to form a synthetic lethal pair with one or more members of the BET protein family (e.g., it was predicted that a loss of function mutation in the TNKS gene would render a cancer cell susceptible to inhibition of a member of the BET protein family). The frequency of mutations (e.g., homozygous deletion, missense mutation, a protein truncating variation) in TNKS across different human cancers was evaluated. As shown in FIG. 1, the frequency of mutation of TNKS is as high as about 11% in certain types of cancers (e.g., prostate adenocarcinoma) or about 7% in other cancer types (e.g., colon adenocarcinoma, ovarian adenocarcinoma). The deficiencies in TNKS that were identified as resulting in loss of function include: deep deletion or mutation in the TNKS gene.

Example 2 - Validation of TNKS and BRD2/3/4 as a Synthetic Lethal Pair

It was further evaluated whether a genetic knockout of TNKS in combination with pharmacological inhibition of BRD2, BRD3, and BRD4 would produce a synthetic lethal phenotype in cancer cells.

CRISPR-Cas9 gene-editing was used to knock-down expression of TNKS in the HT29 cancer cell line. Cancer cells were transduced with lentiviral particles containing two guide RNAs (gRNAs) directed to the TNKS gene. Control cancer cells were generated using a non- TNKS specific (NTC) sgRNA. Expression of tankyrase was measured in TNKS-knockout HT29 cells compared to control cells by Western blot. As shown in FIG. 2, expression of tankyrase was substantially decreased in TNKS-knockout HT29 cells as compared to control cells.

At 5 days following transduction, test plates were seeded with 4,000 TNKS-knockout cells or control cells per well in a 96 well plate format. After 24 hours, the cells were treated with a dilution series of BRD inhibitors. The BET inhibitors evaluated are identified in Table 3, which further includes the targeted BET family members. Each treatment was performed in triplicate. After 72 hours post-treatment with inhibitor, the cell viability was measured in each well using the Cell Titer Gio assay.

Table 3: BET Protein Small Molecule Inhibitors

Shown in FIGs 3A-3D is the percentage of total cells that were viable across different concentrations of the BET inhibitors. Shown is the increased sensitivity to birabresib, CPI-203, BAY1238079, and PLX51107 respectively in HT29 cancer cells having a knockout of the TNKS gene compared to control cells. The IC50 for each inhibitor in TNKS-knockout cells and control cells was evaluated and provided in Table 4. As shown in FIG. 4, the fold-change decrease in IC50 value in TNKS-knockout cells relative to control cells was about 48-fold for Birabresib, about 125-fold for PLX51107, about 180-fold for CPI-203, and about 20-fold for BAY123897. Together, these results demonstrate that decreased expression of TNKS renders cancer cells susceptible to pharmacological inhibition of BET proteins.

Table 4: IC50 of Small Molecule Inhibitors in Control Cancer Cells vs Cancer Cells having a TNKS Knockout

Example 3 - Knockout of JAK1, PTEN, or RBI increases sensitivity to PLX51107 in HT29 and OVCAR3 cell lines

In this example, the BET protein (BRD2/3/4) small molecule inhibitor PLX51107 was further evaluated with single gene knockouts of PTEN, JAK1, or RBI for inducing a synthetic lethal phenotype in HT29 and OVCAR3 cell lines.

PTEN, JAK1, and RBI are prevalent in various cancers (Table 5) and were selected for further validation. The method used in Example 2 for genetic knockout via CRISPR-Cas9 was used to knockout (KO) PTEN, JAK1, and RBI in HT29 and OVCAR3 cell lines. Control cell lines were generated using CRISRP/Cas with a non-specific gRNA. Cells were then seeded as described in Example 2. After 24 hours, both KO and NTC cells were treated with log dilutions of PLX51107 (0.001 uM to 100 uM). Each treatment was performed in triplicate. After 72 hours post-treatment with inhibitor, the cell viability was measured in each well using the Cell Titer Gio assay.

Shown in FIGs. 5A-5F is the normalized cell density (i.e., cells per unit volume normalized to control) for HT29 cells having a PTEN-KO (FIG. 5A), HT29 cells having an RBI -KO (FIG. 5B), HT29 cells having a JAK1-KO (FIG. 5C), OVCAR3 cells having a PTEN- KO (FIG. 5D), OVCAR3 cells having a RBI -KO (FIG. 5E), and OVCAR3 cells having a JAK1-KO (FIG. 5F). The IC50 for PLX51107 was calculated for both the NTC and KO cells. The NTC cells treated with PLX51107 were calculated to have an IC50 >10 uM whereas the KO cells treated with PLX51107 were calculated to have IC50s ranging from 0.4 uM to 1.69 uM. The fold-change sensitization (KO relative to NTC) is summarized in Table 6. Together, these results demonstrate that decreased expression of PTEN, JAK1, or RBI renders cancer cells susceptible to pharmacological inhibition of BET proteins (BRD2/3/4) by PLX51107.

Table 5: Exemplary prevalence of biomarkers in various cancers a Data from The Cancer Genome Atlas (TCGA; see world wide web: cancer.gov/tcga).

Table 6: Fold-change sensitization of PLX51107 in HT29 and OVCAR3 cancer cell lines with various biomarker knockouts