# Patent

## Title
Diagnostic and treatment methods in subjects having or at risk of developing resistance to cancer therapy

## Abstract

The invention relates to methods of treatment and diagnosis of subjects with cancer. In some aspects, the invention relates to methods of treatment and diagnosis of subjects with cancer, wherein the cancer is characterized by a Notch pathway activation mutation or by resistance to a Notch pathway inhibitor.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a national stage filing under 35 U.S.C. §371 of International Application No. PCT/US2013/046485, filed Jun. 19, 2013, which was published under PCT Article 21(2) in English and which claims the benefit of U.S. Provisional Application No. 61/661,772, filed Jun. 19, 2012, U.S. Provisional Application No. 61/661,884, filed Jun. 20, 2012, and U.S. Provisional Application No. 61/780,665, filed Mar. 13, 2013. The entire contents of each of these referenced applications are incorporated by reference herein.


GOVERNMENT SUPPORT
This invention was made with government support under 5U01ES017155 awarded by the National Institutes of Health. The Government has certain rights in the invention.


FIELD OF INVENTION
The invention relates to treatment of certain cancers, including cancers that are resistant to the standard of care, and to methods of diagnosing the resistance phenotype.
BACKGROUND OF INVENTION
T-cell acute lymphoblastic leukemia (T-ALL) is a devastating form of cancer characterized by malignant, immature white blood cells that continuously multiply and are overproduced in the bone marrow. T-ALL leads to pain and damage throughout the body and eventually death due to the crowding out of normal cells in the bone marrow and the spreading of tumor cells to other organs. 50% of T-ALL cases harbor a mutation in the Notch signaling pathway. As a result, gamma secretase inhibitors (GSI) that inhibit cleavage of the activated form of Notch have been developed. Unfortunately, early relapse and refractory disease are common in T-ALL cases due to the transient response of the cancer to a GSI. Additionally, GSI treatment is also associated with toxicity, especially damage to the gastrointestinal tract.
SUMMARY OF INVENTION
The invention provides new therapies to treat certain cancers, including those having Notch pathway activation mutations, those having observed resistance to Notch inhibitors, and those likely to manifest resistance to Notch inhibitors. The invention also provides methods for identifying subjects to be treated with the new therapies provided herein.
Thus, in one aspect, the invention provides a method comprising administering to a subject having cancer (i) a bromodomain inhibitor and/or (ii) a Bcl-2 inhibitor, and a Notch pathway inhibitor, in an effective amount to treat the cancer.
In some embodiments, the cancer is resistant to a previously-administered Notch pathway inhibitor. In some embodiments, the cancer is characterized by the presence of a Notch pathway activation mutation. In some embodiments, the cancer is characterized by abnormal increased HPI-alpha, HPI-beta, and/or HPI-gamma level. In some embodiments, the cancer is characterized by a chromatin compactness or a marker thereof.
In some embodiments, the bromodomain inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially. In some embodiments, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially. In some embodiments, the bromodomain inhibitor, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered. In some embodiments, the bromodomain inhibitor, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially.
In another aspect, the invention provides a method comprising: administering to a subject having cancer (i) a bromodomain inhibitor and/or (ii) a Bcl-2 inhibitor, in an effective amount to treat the cancer, wherein the cancer is characterized by the presence of a Notch pathway activation mutation.
In some embodiments, the method further comprises identifying the subject having cancer characterized by the presence of a Notch pathway activation mutation. In some embodiments, the method further comprises administering to the subject a Notch pathway inhibitor in an effective amount to treat the cancer.
In some embodiments, the bromodomain inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially. In some embodiments, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially. In some embodiments, the bromodomain inhibitor, the Bcl-2 inhibitor, and the Notch pathway inhibitor are administered. In some embodiments, the bromodomain inhibitor, the Bcl-2 inhibitor, and the Notch pathway inhibitor are administered concurrently or sequentially.
In another aspect, the invention provides a method comprising: administering to a subject having cancer (i) a bromodomain inhibitor and/or (ii) a Bcl-2 inhibitor in an effective amount to treat the cancer, wherein the cancer is resistant to treatment with a Notch pathway inhibitor.
In some embodiments, the method further comprises administering to the subject a Notch pathway inhibitor in an effective amount to treat the cancer. In some embodiments, the bromodomain inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially. In some embodiments, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially. In some embodiments, the bromodomain inhibitor, the Bcl-2 inhibitor, and the Notch pathway inhibitor are administered. In some embodiments, the bromodomain inhibitor, the Bcl-2 inhibitor, and the Notch pathway inhibitor are administered concurrently or sequentially.
In another aspect, the invention provides a method comprising: administering to a subject having cancer (i) a bromodomain inhibitor and/or (ii) a Bcl-2 inhibitor in an effective amount to treat the cancer, wherein the cancer is characterized by abnormal increased HPI level, wherein the HPI level is HPI-alpha level, HPI-beta level and/or HPI-gamma level.
In some embodiments, the method further comprises identifying a subject having cancer characterized by the abnormal increased HPI level. In some embodiments, the method further comprises administering to the subject a Notch pathway inhibitor in an effective amount to treat the cancer.
In some embodiments, the bromodomain inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially. In some embodiments, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially. In some embodiments, the bromodomain inhibitor, the Bcl-2 inhibitor, and the Notch pathway inhibitor are administered. In some embodiments, the bromodomain inhibitor, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially.
In embodiments of any of the aspects of the invention, the bromodomain inhibitor, the Bcl-2 inhibitor and/or the Notch pathway inhibitor is a small compound or inhibitory nucleic acid molecule. In some embodiments, the inhibitory nucleic acid molecule is an siRNA, shRNA, or antisense nucleic acid molecule. In some embodiments, the bromodomain inhibitor is a BET inhibitor. In some embodiments, the bromodomain inhibitor is JQ1 or a derivative thereof including those compounds described in WO 2011/143660. In some embodiments, the Bcl-2 inhibitor is G3139, GX15-070, ABT-737 or ABT-199, or a derivative thereof. In some embodiments, the Notch pathway inhibitor is a gamma secretase inhibitor.
In another aspect, the invention provides a method comprising: administering to a subject having cancer an inhibitor of ARID3B, EZH2, PRMT2, SND1, BRD1, SUV39H1, PRMT5, SS18, BRD4, KDM5D, PRMT7, STAG3L1, CD2BP2, MLL5, SUDS3, CHD1, MINA, CHD8, MORF4L1, or CHRAC1, wherein the cancer is resistant to a Notch pathway inhibitor.
In some embodiments, the method further comprises administering to the subject a Notch pathway inhibitor. In some embodiments, the method further comprises administering to the subject a bromodomain inhibitor and/or a Bcl-2 inhibitor in an effective amount to treat the cancer. In some embodiments, the inhibitor is an shRNA, an siRNA, or an antisense nucleic acid molecule.
In another aspect, the invention provides a method comprising: (a) measuring nucleus size in a tumor sample from a subject; and (b) comparing nucleus size in the tumor sample to a control, wherein a decreased nucleus size in the tumor sample compared to the control identifies a subject to be treated with a bromodomain inhibitor and/or Bcl-2 inhibitor. In some embodiments, the nucleus size is nucleus diameter or nucleus volume.
In another aspect, the invention provides a method comprising: (a) measuring HPI level in a tumor sample from a subject; and (b) comparing the HPI level in the tumor sample to a control, wherein an increased HPI level in the tumor sample compared to the control identifies a subject to be treated with a bromodomain inhibitor and/or Bcl-2 inhibitor, wherein the HPI level is HPI-alpha level, HPI-beta level, and/or HPI-gamma level.
In another aspect, the invention provides a method comprising: (a) measuring level of a chromatin state biomarker (CSB) in a tumor sample from a subject, the CSB selected from: (i) a first CSB group consisting of NPM1, NARG1, RCC1, SSRP1, PRMT3, SAP30, CBX6, CHMP2B, UBE2M, WDR77, HMGB1, CARM1, USP13, HDAC4, COQ3, SET, GATAD2A, PRMT6, HMG20B, DNMT1, ADA, SS18, UBE3A, ZMYND11, and NOC2LL (“Group I CSB”); and (ii) a second CSB group consisting of UTX, SIN3A, SAP30L, FLJ20309, RCOR2, ARID5A, UBE2Q2, TRIM24, BAZ2B, SMYD3, EZH2, PHF1, PHF2, BCR, SMARCD3, BMI1, CHD6, FBXL11, SIRT7, ASF1A, RCOR3, CBX4, EPC1, BRD1, and BNF11 (“Group II CSB”); (b) comparing the Group I and/or Group II CSB level with a control, wherein a Group I CSB level that is reduced in the tumor sample compared to a control and/or a Group II CSB level that is elevated in the tumor sample compared to a control identifies a subject to be treated with a bromodomain inhibitor and/or Bcl-2 inhibitor.
In another aspect, the invention provides a method comprising: (a) measuring a level of a biomarker in a tumor sample from a subject, the biomarker selected from DTX1, HES4, CD1d, ETS1, ETV6, Runx1, Bcl-2, MYC and CD52; and (b) comparing the biomarker level with a control, wherein a level of DTX1, HES4, or CD1d that is reduced in the tumor sample compared to the control and/or a level of ETS1, ETV6, Runx1, CD52, MYC or Bcl-2 that is elevated in the tumor sample compared to the control identifies a subject to be treated with a bromodomain inhibitor and/or Bcl-2 inhibitor.
In another aspect, the invention provides a method comprising: (a) measuring a level of histone modification in a tumor sample from a subject, the histone modification selected from H3K27me3 and H3K9me3; and (b) comparing the histone modification level with a control, wherein a level of histone modification that is elevated in the tumor sample compared to the control identifies a subject to be treated with a bromodomain inhibitor and/or Bcl-2 inhibitor.
In another aspect, the invention provides a method comprising: (a) measuring a level of H3K27Ac histone modification in a tumor sample from a subject; and (b) comparing the H3K27Ac histone modification level with a control, wherein a level of H3K27Ac histone modification that is reduced in the tumor sample compared to the control identifies a subject to be treated with a bromodomain inhibitor and/or Bcl-2 inhibitor.
In another aspect, the invention provides a method comprising: (a) measuring a level of H3K4me1 histone modification at a site of elevated H3K27Ac histone modification; and (b) comparing the H3K4me1 histone modification level with a control, wherein a level of H3K4me1 histone modification at a site of elevated H3K27Ac histone modification that is elevated in the tumor sample compared to the control identifies a subject to be treated with a bromodomain inhibitor and/or Bcl-2 inhibitor.
In some embodiments of the foregoing methods, the level is an mRNA level or a protein level. In some embodiments, the control is a nucleus size, an HPI-alpha level, an HPI-beta level, an HPI-gamma level, a CSB level, a histone modification level or a biomarker level selected from DTX1, HES4, CD1d, ETS1, ETV6, Runx1, Bcl-2, MYC and CD52 in a non-tumor sample. In some embodiments, the control is a predetermined threshold. In some embodiments, the methods further comprise identifying the subject to be treated with a bromodomain inhibitor and/or Bcl-2 inhibitor. In some embodiments, the methods further comprise administering to the identified subject a bromodomain inhibitor and/or Bcl-2 inhibitor in an effective amount. In some embodiments, the methods further comprise further comprising administering to the identified subject a Notch pathway inhibitor in an effective amount. In some embodiments, the cancer or tumor is a T-ALL. In some embodiments, the T-ALL is resistant to a Notch pathway inhibitor.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1 is a line graph depicting Gene Set Enrichment Analysis (GSEA) for leukemia cells resistant to a gamma secretase inhibitor (GSI) and naïve leukemia cells (not treated with a GSI).
FIG. 2 is a bar graph depicting the ratio of lactate production to glucose consumption and the ratio of glutamate production to glutamine consumption in resistant leukemia cells versus naïve leukemia cells.
FIG. 3 depicts cell and nucleus size changes in resistant leukemia cells compared to naïve leukemia cells. FIG. 3A is a line graph depicting the forward scatter of naïve leukemia cells and resistant leukemia cells. FIG. 3B is a photograph of a nuclear stain (DAPI) and a cytoplasmic stain (Actin) in naïve leukemia cells and resistant leukemia cells. FIG. 3C is a bar graph showing nuclear size (by DAPI) for naïve and persister cells.
FIG. 4 is an analysis of the chromatin state of naïve leukemia cells and resistant leukemia cells. FIG. 4A is a Western blot showing the levels of HP1-gamma in naïve, short-term GSI treated, and resistant leukemia cells. FIG. 4B is a DNA gel showing partial MNase digestion in naïve and resistant leukemia cells.
FIG. 5 depicts the chromatin compaction state in naïve and resistant leukemia cells. FIG. 5A is a bar graph depicting the levels of chromatin marks H3K27me3 and H3K9me3 in naïve and resistant cells. FIG. 5B is a heat map of expression levels of chromatin state biomarkers in naïve and resistant leukemia cells.
FIG. 6 is a Western blot depicting the protein levels of BRD4 in naïve, short-term GSI treated, and resistant leukemia cells.
FIG. 7 is two line graphs depicting proliferation of naïve and resistant leukemia cells after 7 days in specific concentrations of JQ1 (left) and apoptosis of naïve and resistant leukemia cells after 4 days in specific concentrations of JQ1 (right).
FIG. 8 is an example ChIP-SEQ readout of a genomic location where BRD4, H3K4me1, and H3K27ac all bind in the same place. Peaks indicate potential binding locations. Pie charts depict the number of “active” enhancers occupied by BRD4 in naïve and resistant leukemia cells.
FIG. 9 depicts the presence of BRD4 near the Bcl-2 gene. FIG. 9A is a ChIP-Seq readout of the location of BRD4, H3K4me1, and H3K27ac near the Bcl-2 gene. Peaks indicate potential binding locations. FIG. 9B is a Western blot depicting the protein levels of Bcl-2 in naïve and resistant cells treated with JQ1.
FIG. 10 is a line graph depicting the bioluminescence of luciferized leukemia cells, which is a readout of tumor burden, in mice treated with vehicle, DBZ (a GSI), JQ1, and JQ1+DBZ.
FIG. 11 is a photograph of Periodic acid-Schiff (PAS) staining of a section of the gastrointestinal tract from a mouse treated with vehicle, DBZ, JQ1, or JQ1+DBZ.
FIG. 12 is an analysis of Notch signaling in naïve (N), short-term treated (ST, 5 days), persister (P), reversed (Rev) and re-treated (Rev tx) cells. FIG. 12A is a pair of line graphs showing DTX1 and HES4 mRNA expression. FIG. 12B is a photograph of a western blot showing expression of activated intracellular NOTCH1 (ICN) and MYC.
FIG. 13 is a line graph depicting cell proliferative response to the AKT inhibitor MK-2206 in naïve and persister cells.
FIG. 14 shows a western blot of Phospho-mTOR (p2481), a marker of activated mTOR signaling, total mTOR and Tubulin for naïve (N), short-term treated (ST) and persister (R) cells and a line graph depicting cell proliferative response to Rapamycin in naïve and persister cells.
FIG. 15 is a graphical depiction of the shRNA screen for chromatin regulators preferentially required for naïve or persister cell survival. Top hits for each cell state are shown in boxes (left box and right box, naïve and persister cells, respectively).
FIG. 16 shows that ETS and Runx transcription factors are targets of BRD4. FIG. 16A shows the motifs enriched at BRD4 binding sites. FIG. 16B shows mRNA levels of ETS1, ETV6, and Runx1 in naïve and persister cells.
FIG. 17A is two photographs of western blots show MYC expression in naïve and persister cells after 3 day treatment with 2 μM AKT inhibitor, MK-2206, or 10 nM mTOR inhibitor, Rapamycin. FIG. 17B depicts graphs showing BRD4 binding at the MYC and BCL2 promoters.
FIG. 18A is a line graph showing the proliferative response of persister cells after 6 days of treatment with the Bcl-2 inhibitor ABT-737. FIG. 18B is a bar graph depicting the proliferative response of persister cells transfected with Bcl-2 expression vector (or empty vector control) after 6 days of treatment with JQ1.
FIG. 19A is a series of photographs depicting hematoxylin and eosin (H&E) stains and immunohistochemistry for activated Notch (ICN) for bone marrow from leukemic mice treated with Notch inhibitor DBZ for 5 days (ST) or 3 weeks (LT) or treated with vehicle (Veh). FIG. 19B is a series of bar graphs showing levels of HES4, DTX1, HP1γ, and Bcl-2 for leukemia cells sorted from spleens of vehicle (Veh) or long-term (LT) treated mice.
FIG. 20 is a pair of graphs depicting the level of CD1d in in vitro naïve and persister cells. The left graph shows expression of CD in naïve or persister populations. The right graph depicts quantification of CD1d expression for clones originating from single naïve cells that proliferated in the presence of GSI (n=7) or control conditions (n=7)(p<0.002).
FIG. 21 is a pair of graphs depicting data from primary human T-ALL cells. The left graph shows the proliferative response of primary human T-ALL cells from 6 different patients after 5 days of treatment with 1 micromolar GSI and the indicated JQ1 doses, relative to no JQ1 control. The right graphs shows the relative expression of intracellular BCL2 measured by flow cytometry in primary T-ALL cells after 3 days of treatment with 1 micromolar GSI and 0.5 micromolar JQ1, normalized to untreated.



It is to be understood that the Figures are not required for enablement of the invention.
DETAILED DESCRIPTION OF INVENTION
The invention provides methods to diagnose and treat subjects using single or combination therapy. Certain methods of the invention relate to treatment of cancers that are resistant to therapy with a Notch pathway inhibitor or that are likely to become resistant to therapy with a Notch pathway inhibitor.
It has been found, in accordance with the invention, that a Notch inhibitor resistant phenotype (also referred to herein as a resister or persister phenotype) correlated with changes in chromatin structure of the cancer cells, resulting in more compact chromatin and smaller cell size, and with changes in expression of heterochromatin markers such as HPI-alpha, beta and gamma and various chromatin regulatory markers, such as histone modifications, or chromatin state biomarkers such as but not limited to BRD4. It was also found that changes in biomarkers selected from DTX1, HES4, CD1d, ETS1, ETV6, Runx1, Bcl-2, MYC and CD52 correlated with resistance to a Notch pathway inhibitor. Significantly, it has also been found, in accordance with the invention, that the resistance to the Notch pathway inhibitor could be reversed by using the Notch pathway inhibitor with a bromodomain inhibitor such as a BRD4 inhibitor. Without intending to be bound by any particular mechanism or theory, it is believed that the bromodomain inhibitor reverses the observed changes in chromatin structure, thereby reversing the resistance to the Notch pathway inhibitor. The invention further contemplates that a bromodomain inhibitor may be administered before resistance to a Notch pathway inhibitor is even manifest, thereby preventing the resistant phenotype from developing altogether or delaying its onset. The invention therefore contemplates treating subjects having certain cancers with a Notch pathway inhibitor and a bromodomain inhibitor. It has also been found, in accordance with the invention, that Notch pathway inhibitor resistant cells were sensitive to treatment with an mTOR or AKT inhibitor. The invention therefore contemplates treating subjects having certain cancers with a Notch pathway inhibitor and an mTOR and/or AKT inhibitor. The inhibitors may be administered before or after resistance to the Notch pathway inhibitor is observed. The cancers to be treated in this manner may be those that would be treated with a Notch pathway inhibitor, such as for example T-ALL, and those that are characterized by the presence of a Notch pathway activation mutation.
The invention further contemplates use of a bromodomain inhibitor alone or in combination with other anti-cancer agents in the treatment of cancers characterized by chromatin compaction or abnormal expression of chromatin regulatory markers or chromatin state biomarkers. Such cancers may manifest a reduced nucleus or cell size (or diameter) relative to normal, non-cancerous cells and/or they may have an increased expression level of HPI-alpha, beta and/or gamma mRNA and/or proteins relative to normal, non-cancerous cells, inter alia. In some embodiments, the cancer is (a) characterized by a compact nucleus or smaller cell size compared to a normal control, (b) characterized by abnormal increased (mRNA or protein) levels of HPI-alpha, beta and/or gamma, (c) characterized by abnormal increased (mRNA or protein) levels of certain chromatin regulatory proteins or chromatin state biomarkers such as but not limited to BRD4 and/or abnormal decreased (mRNA or protein) levels of other chromatin regulatory proteins or chromatin state biomarkers, (d) characterized by decreased expression of DTX1, HES4, and/or CD1d and/or by increased expression of ETS1, ETV6, Runx1, CD52, MYC or Bcl-2, (e) characterized by increased levels of repressive chromatin markers such as H3K27me3, or H3K9me2/3 and/or decreased levels of other chromatin markers such as H3K27Ac. and/or (f) characterized by resistance to a previously administered anti-cancer agent such as a Notch pathway inhibitor.
It has also been found, in accordance with the invention, that bromodomain inhibition, such as BRD4 inhibition, inhibits expression of Bcl-2, a known anti-apoptotic mediator. It is therefore contemplated by the invention that bromodomain inhibition may mediate its effects via Bcl-2 inhibition. This suggests that Bcl-2 inhibitors may be used instead of bromodomain inhibitors in certain methods of the invention, including those that involve combination therapy with a Notch pathway inhibitor.
In addition to treatment methods, the invention also provides methods of identifying subjects to be treated with bromodomain inhibitors alone or in combination with another anti-cancer such as but not limited to a Notch pathway inhibitor. Such subjects will be identified based on the presence of a cancer that is (a) characterized by the presence of a Notch pathway activation mutation, (b) characterized by a compact nucleus or smaller cell size compared to a normal control, (c) characterized by abnormal increased (mRNA or protein) levels of HPI-alpha, beta and/or gamma, (d) characterized by abnormal increased (mRNA or protein) levels of certain chromatin regulatory proteins or chromatin state biomarkers such as but not limited to BRD4 and/or abnormal decreased (mRNA or protein) levels of other chromatin regulatory proteins or chromatin state biomarkers, (e) characterized by decreased expression of DTX1, HES4, and/or CD1d and/or by increased expression of ETS1, ETV6, Runx1, CD52, MYC or Bcl-2, (f) characterized by increased levels of repressive chromatin markers such as H3K27me3, or H3K9me2/3 and/or decreased levels of other chromatin markers such as H3K27Ac. and/or (g) characterized by resistance to a previously administered anti-cancer agent such as a Notch pathway inhibitor.
In still other aspects, the invention provides methods for treating a subject having a cancer that is resistant to a Notch pathway inhibitor using inhibitors of a number of chromatin regulatory proteins such as ARID3B, EZH2, PRMT2, SND1, BRD1, SUV39H1, PRMT5, SS18, BRD4, KDM5D, PRMT7, STAG3L1, CD2BP2, MLL5, SUDS3, CHD1, MINA, CHD8, MORF4L1, or CHRAC1.
As shown in the Examples, shRNA based knock-down of any of these chromatin regulatory proteins caused cell death in cell lines that were resistant to Notch pathway inhibition.
These and other aspects of the invention will be described in greater detail herein.
Bromodomain-Containing Proteins
As described herein, various methods of the invention involve the use of a bromodomain inhibitor. Bromodomain inhibitors are compounds that inhibit the activity of bromodomain-containing proteins. Bromodomain-containing proteins, as their name implies, are proteins that comprise a bromodomain. Bromodomains (BRDs) function by detecting lysine acetylation (i.e., detecting ε-N-acetyl lysine, also known as Kac) on other proteins. Lysine acetylation neutralizes charge and can therefore alter protein conformation and protein-protein interactions. Lysine acetylation involves histone acetyltransferases (or HATs) and lysine deacetylation involves histone deactylases (or HDACs).
Bromodomains (BRDs) are a diverse family of evolutionarily conserved protein-interaction modules. One family of bromodomain-containing proteins, the BET (bromodomain and extra-terminal) family, is represented by six members in humans (BRD1, BRD2, BRD3, BRD4, BRD7 and the testis-specific isoform BRDT), with each containing two N-terminal BRDs. BRD4 and BRD2 mediate transcriptional elongation by recruiting the positive transcription elongation factor complex (P-TEFb). The P-TEFb core complex is composed of cyclin-dependent kinase-9 (CDK9) and its activator cyclin T. CDK9 phosphorylates the RNA polymerase II (RNAPII)C-terminal domain. RNAPII undergoes sequential phosphorylation at Ser5 during promoter clearance and at Ser2 by P-TEFb at the start of elongation. It has been shown that BRD4 couples P-TEFb to acetylated chromatin through its BRDs.
Examples of BRD-containing proteins include, but are not limited to, ASH1L, ATAD2A/B, BAZ1A/B, BAZ2A/B, BRD1, BRD2, BRD3, BRD4, BRDT, BRD7, BRD8A/B, BRD9, BRPF1A/B, BRPF3A, BRWD3, CECR2, CREBBP, EP300, FALZ, GCN5L2, MLL, PB1, PCAF, PHIP, PRKCBP1, SMARCA2A/B, SMARCA4, SP100/SP110/SP140, TAF1/TAF1L, TRIM24/TRIM28/TRIM33/TRIM66, WDR9, and ZMYND11.
As described herein, a novel role for BRD-containing proteins and other chromatin regulatory proteins in cancer has been elucidated in accordance with the invention. Tumor cells resistant to Notch pathway inhibitor treatment were found to have globally compact chromatin and altered expression of certain chromatin regulatory proteins with some having increased expression levels and some having decreased expression levels compared to a normal control. Knock-down of several chromatin regulatory proteins, including BRD4, in Notch pathway inhibitor-resistant tumor cells, using shRNA, resulted in decreased proliferation and increased cell death. Accordingly, aspects of the invention provide methods comprising administering to a subject having cancer a bromodomain inhibitor in an effective amount to treat the cancer, wherein the cancer is characterized by a Notch Activation mutation or by resistance to a Notch pathway inhibitor.
As described herein, use of a BRD inhibitor in combination with a Notch pathway inhibitor was found to result in reduction of tumor burden in a mouse model that was greater than treatment with the BRD inhibitor or the Notch pathway inhibitor alone. Additionally, use of the BRD inhibitor in combination with the Notch pathway inhibitor reduces the side effects associated with treatment using either agent alone. In particular, the side effects observed with the BRD inhibitor, JQ1, are reduced when the inhibitor is used in combination with a Notch pathway inhibitor. Such side effects include without limitation gastrointestinal side effects. The invention therefore contemplates a combination therapy that is associated with a lower frequency of side effects and/or less severe side effects. Accordingly, aspects of the invention provide methods comprising administering to a subject having cancer a BRD inhibitor and a Notch pathway inhibitor in an effective amount to treat the cancer.
Bromodomain Inhibitors
Bromodomain inhibitors are known in the art. A bromodomain inhibitor is any molecule or compound that can prevent or inhibit, in part or in whole, the binding of at least one bromodomain to acetyl-lysine residues of proteins (e.g., to the acetyl-lysine residues of histones). The bromodomain inhibitor may be any molecule or compound that inhibits a bromodomain as described above, including nucleic acids such as DNA and RNA aptamers, antisense oligonucleotides, siRNA and shRNA, small peptides, antibodies or antibody fragments, and small molecules such as small chemical compounds. It is to be understood that the bromodomain inhibitor may inhibit only one bromo-domain-containing protein or it may inhibit more than one or all bromodomain-containing proteins.
Examples of bromodomain inhibitors are described in JP 2009028043, JP 2009183291, WO 2011054843, WO 2011054848, WO2009/084693A1, WO2009084693, WO 2011054844, WO 2011054846, US 2012028912, Filippakopoulos et al. Bioorg Med Chem. 20(6): 1878-1886, 2012; Chung et al. J Med Chem. 54(11):3827-38, 2011; and Chung et al. J Biomol Screen. 16(10):1170-85, 2011, which are incorporated herein by reference.
In some embodiments, the bromodomain inhibitor is 1-[2-(1/-/-benzimidazol-2-ylthio)ethyl]-1,3-dihydro-3-methyl-2H-benzinidazole-2-thione (JP2008-156311), Alprazolam (Sigma-Aldrich), Midazolam (Sigma-Aldrich, GW841819X (BZD, GlaxoSmithKline), a compound in Table 1 (WO 2011054843), or any other bromodomain inhibitor compound described herein.







TABLE 1







Examples of Bromodomain inhibitors










Name
Structure





Example 1
1-methylethyl((2S,4R)-1-acetyl-2- methyl-6-{4- [(methylamino)methyl]phenyl}-1,2,3,4- tetrahydro-4-quinolinyl)carbamate






 


Example 2
2-[(4S)-6-(4-Chlorophenyl)-1-methyl-8- (methyloxy)-4H-[1,2,4]triazolo[4,3- a][1,4]benzodiazepin-4-yll-N- ethylacetamide






 


Example 3
7-(3,5-dimethyl-4-isoxazolyl)-8- (methoxy)-1-[(1R)-1-(2-pyridinyl)ethyl]- 1,3-dihydro-2H-imidazo[4,5-c]quinolin- 2-one






 


Example 4
7-(3,5-dimethyl-4-isoxazolyl)-8- (methoxy)-1-[(1R)-1-phenylethyl]-2- (tetrahydro-2H-pyran-4-yl)-1H- imidazo[4,5-c]quinoline






 


Example 5
4-{(2S,4R)-1-acetyl-4-[(4- chlorophenyl)amino]-2-methyl-1,2,3,4- tetrahydro-6-quinolinyl}benzoic acid






 


Example 6
N-{1-methyl-7-[4-(1- piperidinylmethyl)phenyl][1,2,4]triazolo [4,3-a]quinolin-4-yl}urea













In some embodiments, the bromodomain inhibitor is a BET inhibitor. A BET inhibitor is any molecule or compound that can prevent or inhibit the binding of the bromodomain of at least one BET family member to acetyl-lysine residues of proteins. The BET inhibitor may be any molecule or compound that inhibits a BET as described above, including nucleic acids such as DNA and RNA aptamers, antisense oligonucleotides, siRNA and shRNA, small peptides, antibodies or antibody fragments, and small molecules such as small chemical compounds.
Examples of BET inhibitors are described in US 2011143651, WO2009/084693A1, WO 2011143669, WO 2011143660, WO 2011054851, and JP 2008156311, which are incorporated herein by reference. It is to be understood that a BET inhibitor may inhibit only one BET family member or it may inhibit more than one or all BET family members. Examples of BET inhibitors known in the art include, but are not limited to, RVX-208 (Resverlogix), PFI-1 (Structural Genomics Consortium), OTX015 (Mitsubishi Tanabe Pharma Corporation), BzT-7, GSK525762A (iBET, GlaxoSmithKline), and the compounds below (WO 2011054851, GlaxoSmithKline):




In some embodiments, the BET inhibitor is a small molecule compound (e.g., JQ1 or derivatives thereof and compounds of formulas I-XXII or any other compound described herein) that binds to the binding pocket of the first bromodomain of a BET family member (e.g., BRD1, BRD2, BRD3, BRD4, BRD7, BRDT; see WO 2011143669).
In some important embodiments, the BET inhibitor is JQ1 and has the formula below:




In some embodiments, the BET inhibitor has the structures of Formulas I-XXII or any other compound as described below. These structures are known in the art (WO 2011143660, which is incorporated herein by reference).
In some embodiments, a bromodomain or BET inhibitor is a compound of Formula I:




wherein X is N or CR5; R5 is H, alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; RB is H, alkyl, hydroxylalkyl, aminoalkyl, alkoxyalkyl, haloalkyl, hydroxy, alkoxy, or —COO—R3, each of which is optionally substituted; ring A is aryl or heteroaryl; each RA is independently alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; or any two RA together with the atoms to which each is attached, can form a fused aryl or heteroaryl group; R is alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl; each of which is optionally substituted;

Ri is —(CH2)n-L, in which n is 0-3 and L is H, —COO—R3, —CO—R3, —CO— N(R3R4), —S(O)2—R3, —S(O)2—N(R3R4), N(R3R4), N(R4)C(O)R3, optionally substituted aryl, or optionally substituted heteroaryl;
R2 is H, D (deuterium), halogen, or optionally substituted alkyl;
each R3 is independently selected from the group consisting of:

    
    
        (i) H, aryl, substituted aryl, heteroaryl, or substituted heteroaryl;
        (ii) heterocycloalkyl or substituted heterocycoalkyl;
        (iii) —C1-C8 alkyl, —C2-C8 alkenyl or —C2-C8 alkynyl, each containing 0, 1, 2, or 3 heteroatoms selected from O, S, or N; —C3-Ci2 cycloalkyl, substituted —C3-Ci2 cycloalkyl, —C3-Ci2 cycloalkenyl, or substituted —C3-Ci2 cycloalkenyl, each of which may be optionally substituted; and
        (iv) NH2, N═CR4R6;
    
    


each R4 is independently H, alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl,
each of which is optionally substituted;
or R3 and R4 are taken together with the nitrogen atom to which they are attached to form a 4-10-membered ring;
R6 is alkyl, alkenyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; or R4 and R6 are taken together with the carbon atom to which they are attached to form a 4-10-membered ring;
m is 0, 1, 2, or 3;
provided that
(a) if ring A is thienyl, X is N, R is phenyl or substituted phenyl, R2 is H, RB is methyl, and Ri is —(CH2)n-L, in which n is 1 and L is —CO— N(R3R4), then R3 and R4 are not taken together with the nitrogen atom to which they are attached to form a morpholino ring;
(b) if ring A is thienyl, X is N, R is substituted phenyl, R2 is H, RB is methyl, and Ri is —(CH2)n-L, in which n is 1 and L is —CO—N(R3R4), and one of R3 and R4 is H, then the other of R3 and R4 is not methyl, hydroxyethyl, alkoxy, phenyl, substituted phenyl, pyridyl or substituted pyridyl; and
(c) if ring A is thienyl, X is N, R is substituted phenyl, R2 is H, RB is methyl, and Ri is —(CH2)n-L, in which n is 1 and L is —COO—R3 then R3 is not methyl or ethyl; or a salt, solvate or hydrate thereof.
In certain embodiments, R is aryl or heteroaryl, each of which is optionally substituted.
In certain embodiments, L is H, —COO—R3, —CO—N(R3R4), —S(O)2—R3, —S(O)2—N(R3R4), N(R3R4), N(R4)C(O)R3 or optionally substituted aryl. In certain embodiments, each R3 is independently selected from the group consisting of: H, —Ci-C8 alkyl, which is optionally substituted, containing 0, 1, 2, or 3 heteroatoms selected from O, S, or N; or NH2, N═CR4R6.
In certain embodiments, R2 is H, D, halogen or methyl.
In certain embodiments, RB is alkyl, hydroxyalkyl, haloalkyl, or alkoxy; each of which is optionally substituted.
In certain embodiments, RB is methyl, ethyl, hydroxy methyl, methoxymethyl, trifluoromethyl, COOH, COOMe, COOEt, or COOCH2OC(O)CH3.
In certain embodiments, ring A is a 5 or 6-membered aryl or heteroaryl. In certain embodiments, ring A is thiofuranyl, phenyl, naphthyl, biphenyl, tetrahydronaphthyl, indanyl, pyridyl, furanyl, indolyl, pyrimidinyl, pyridizinyl, pyrazinyl, imidazolyl, oxazolyl, thienyl, thiazolyl, triazolyl, isoxazolyl, quinolinyl, pyrrolyl, pyrazolyl, or 5,6,7,8-tetrahydroisoquinolinyl.
In certain embodiments, ring A is phenyl or thienyl.
In certain embodiments, m is 1 or 2, and at least one occurrence of RA is methyl.
In certain embodiments, each RA is independently H, an optionally substituted alkyl, or any two RA together with the atoms to which each is attached, can form an aryl.
In some embodiments, a bromodomain or BET inhibitor is a compound of Formula II:




wherein X is N or CR5; R5 is H, alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; RB is H, alkyl, hydroxylalkyl, aminoalkyl, alkoxyalkyl, haloalkyl, hydroxy, alkoxy, or —COO—R3, each of which is optionally substituted;
each RA is independently alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; or any two RA together with the atoms to which each is attached, can form a fused aryl or heteroaryl group;
R is alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted;
R′ i is H, —COO—R3, —CO—R3, optionally substituted aryl, or optionally substituted heteroaryl;
each R3 is independently selected from the group consisting of:

    
    
        (i) H, aryl, substituted aryl, heteroaryl, substituted heteroaryl;
        (ii) heterocycloalkyl or substituted heterocycloalkyl;
        (iii) —C1-C8 alkyl, —C2-C8 alkenyl or —C2-C8 alkynyl, each containing 0, 1, 2, or 3 heteroatoms selected from O, S, or N; —C3-C12 cycloalkyl, substituted —C3-C12 cycloalkyl; —C3-C12 cycloalkenyl, or substituted —C3-C12 cycloalkenyl; each of which may be optionally substituted;
    
    


m is 0, 1, 2, or 3;
provided that if R′ 1 is —COO—R3, X is N, R is substituted phenyl, and RB is methyl, then R3 is not methyl or ethyl;
or a salt, solvate or hydrate thereof.
In certain embodiments, R is aryl or heteroaryl, each of which is optionally substituted. In certain embodiments, R is phenyl or pyridyl, each of which is optionally substituted. In certain embodiments, R is p-Cl-phenyl, o-Cl-phenyl, m-Cl-phenyl, p-F-phenyl, o-F-phenyl, m-F-phenyl or pyridinyl.
In certain embodiments, R′ i is —COO—R3, optionally substituted aryl, or optionally substituted heteroaryl; and R3 is —C3-C8 alkyl, which contains 0, 1, 2, or 3 heteroatoms selected from O, S, or N, and which may be optionally substituted. In certain embodiments, R′ i is —COO—R3, and R3 is methyl, ethyl, propyl, i-propyl, butyl, sec-butyl, or t-butyl; or R′i is H or optionally substituted phenyl.
In certain embodiments, RB is methyl, ethyl, hydroxy methyl, methoxymethyl, trifluoromethyl, COOH, COOMe, COOEt, COOCH2OC(O)CH3.
In certain embodiments, RB is methyl, ethyl, hydroxy methyl, methoxymethyl, trifluoromethyl, COOH, COOMe, COOEt, or COOCH2OC(O)CH3.
In certain embodiments, each RA is independently an optionally substituted alkyl, or any two RA together with the atoms to which each is attached, can form a fused aryl.
In certain embodiments, each RA is methyl.
In some embodiments, a bromodomain or BET inhibitor is a compound of formula III:




wherein

X is N or CR5; R5 is H, alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; RB is H, alkyl, hydroxylalkyl, aminoalkyl, alkoxyalkyl, haloalkyl, hydroxy, alkoxy, or —COO—R3, each of which is optionally substituted; ring A is aryl or heteroaryl; each RA is independently alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; or any two RA together with the atoms to which each is attached, can form a fused aryl or heteroaryl group;
R is alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted;
each R3 is independently selected from the group consisting of:

    
    
        (i) H, aryl, substituted aryl, heteroaryl, or substituted heteroaryl;
        (ii) heterocycloalkyl or substituted heterocycloalkyl;
        (iii) —C1-C8 alkyl, —C2-C8 alkenyl or —C2-C8 alkynyl, each containing 0, 1, 2, or 3 heteroatoms selected from O, S, or N; —C3-Ci2 cycloalkyl, substituted —C3-Ci2 cycloalkyl, —C3-Ci2 cycloalkenyl, or substituted —C3-Ci2 cycloalkenyl, each of which may be optionally substituted; and
        (iv) NH2, N═CR4R6;
    
    


each R4 is independently H, alkyl, alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; or R3 and R4 are taken together with the nitrogen atom to which they are attached to form a 4-10-membered ring;
R6 is alkyl, alkenyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; or R4 and R6 are taken together with the carbon atom to which they are attached to form a 4-10-membered ring;
m is 0, 1, 2, or 3;
provided that:
(a) if ring A is thienyl, X is N, R is phenyl or substituted phenyl, RB is methyl, then R3 and R4 are not taken together with the nitrogen atom to which they are attached to form a morpholino ring; and
(b) if ring A is thienyl, X is N, R is substituted phenyl, R2 is H, RB is methyl, and one of R3 and R4 is H, then the other of R3 and R4 is not methyl, hydroxyethyl, alkoxy, phenyl, substituted phenyl, pyridyl or substituted pyridyl;
or a salt, solvate or hydrate thereof.
In certain embodiments, R is aryl or heteroaryl, each of which is optionally substituted.
In certain embodiments, R is phenyl or pyridyl, each of which is optionally substituted.
In certain embodiments, R is p-Cl-phenyl, o-Cl-phenyl, m-Cl-phenyl, p-F-phenyl, o-F-phenyl, m-F-phenyl or pyridinyl. In certain embodiments, R3 is H, NH2, or N═CR4R6.
In certain embodiments, each R4 is independently H, alkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl; each of which is optionally substituted.
In certain embodiments, R6 is alkyl, alkenyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted.
In some embodiments, a bromodomain or BET inhibitor is a compound of formula IV:




wherein X is N or CR5; R5 is H, alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted;

RB is H, alkyl, hydroxylalkyl, aminoalkyl, alkoxyalkyl, haloalkyl, hydroxy, alkoxy, or —COO—R3, each of which is optionally substituted;
ring A is aryl or heteroaryl;
each RA is independently alkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; or any two RA together with the atoms to which each is attached, can form a fused aryl or heteroaryl group;
Ri is —(CH2)n-L in which n is 0-3and L is H, —COO—R3, —CO—R3, —CO— N(R3R4), —S(O)2—R3, —S(O)2—N(R3R4), N(R3R4), N(R4)C(O)R3, optionally substituted aryl, or optionally substituted heteroaryl;
R2 is H, D, halogen, or optionally substituted alkyl;
each R3 is independently selected from the group consisting of:

    
    
        (i) H, aryl, substituted aryl, heteroaryl, or substituted heteroaryl;
        (ii) heterocycloalkyl or substituted heterocycloalkyl;
        (iii) —C1-C8 alkyl, —C2-C8 alkenyl or —C2-C8 alkynyl, each containing 0, 1, 2, or 3 heteroatoms selected from O, S, or N; —C3-C12 cycloalkyl, substituted —C3-C12 cycloalkyl, —C3-C12 cycloalkenyl, or substituted —C3-C12 cycloalkenyl, each of which may be optionally substituted; and
        (iv) NH2, N═CR4R6;
    
    


each R4 is independently H, alkyl, alkyl, cycoloalkyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted;
or R3 and R4 are taken together with the nitrogen atom to which they are attached to form a 4-10-membered ring;
R6 is alkyl, alkenyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, aryl, or heteroaryl, each of which is optionally substituted; or R4 and R6 are taken together with the carbon atom to which they are attached to form a 4-10-membered ring;
m is 0, 1, 2, or 3;
provided that
(a) if ring A is thienyl, X is N, R2 is H, RB is methyl, and Ri is —(CH2)n-L, in which n is 0 and L is —CO—N(R3R4), then R3 and R4 are not taken together with the nitrogen atom to which they are attached to form a morpholino ring;
(b) if ring A is thienyl, X is N, R2 is H, RB is methyl, and Ri is —(CH2)n-L, in which n is 0 and L is —CO—N(R3R4), and one of R3 and R4 is H, then the other of R3 and R4 is not methyl, hydroxyethyl, alkoxy, phenyl, substituted phenyl, pyridyl or substituted pyridyl; and
(c) if ring A is thienyl, X is N, R2 is H, RB is methyl, and Ri is —(CH2)n-L, in which n is 0 and L is —COO—R3, then R3 is not methyl or ethyl; or a salt, solvate or hydrate thereof.
In certain embodiments, Ri is —(CH2)n-L, in which n is 0-3 and L is —COO—R3, optionally substituted aryl, or optionally substituted heteroaryl; and R3 is —C1-C8 alkyl, which contains 0, 1, 2, or 3 heteroatoms selected from O, S, or N, and which may be optionally substituted. In certain embodiments, n is 1 or 2 and L is alkyl or —COO—R3, and R3 is methyl, ethyl, propyl, i-propyl, butyl, sec-butyl, or t-butyl; or n is 1 or 2 and L is H or optionally substituted phenyl.
In certain embodiments, R2 is H or methyl.
In certain embodiments, RB is methyl, ethyl, hydroxy methyl, methoxymethyl, trifluoromethyl, COOH, COOMe, COOEt, COOCH2OC(O)CH3.
In certain embodiments, ring A is phenyl, naphthyl, biphenyl, tetrahydronaphthyl, indanyl, pyridyl, furanyl, indolyl, pyrimidinyl, pyridizinyl, pyrazinyl, imidazolyl, oxazolyl, thienyl, thiazolyl, triazolyl, isoxazolyl, quinolinyl, pyrrolyl, pyrazolyl, or 5,6,7,8-tetrahydroisoquinolinyl.
In certain embodiments, each RA is independently an optionally substituted alkyl, or any two RA together with the atoms to which each is attached, can form an aryl.
The invention also provides compounds of Formulae V-XXII, and any compound described herein.
In some embodiments, a bromodomain or BET inhibitor is:




a salt, solvate or hydrate thereof.

In certain embodiments, the compound is (+)-JQ1:




or a salt, solvate or hydrate thereof.

In some embodiments, a bromodomain or BET inhibitor is a compound represented by the formula:




a salt, solvate or hydrate thereof.

In some embodiments, a bromodomain or BET inhibitor is a compound represented by the formula:




a salt, solvate or hydrate thereof.

In some embodiments, a bromodomain or BET inhibitor is a compound represented by any following formulae:










or a salt, solvate or hydrate thereof. In some embodiments, a bromodomain or BET inhibitor is a compound represented by any one of the following formulae:





a salt, solvate or hydrate thereof. In some embodiments, a bromodomain or BET inhibitor is a compound represented by any following structures:
































or a salt, solvate or hydrate thereof. In some embodiments, a bromodomain or BET inhibitor can be one of the following structures:























a salt, solvate or hydrate thereof.

In some embodiments, a bromodomain or BET inhibitor is a compound represented by the following structure:




or a salt, solvate or hydrate thereof. In some embodiments, a bromodomain or BET inhibitor is a compound represented by the following structure:





or a salt, solvate or hydrate thereof. In some embodiments, a bromodomain or BET inhibitor is a compound represented by the following structure:





or a salt, solvate or hydrate thereof. In some embodiments, a bromodomain or BET inhibitor is a compound with the opposite chirality of any compound shown herein. In some embodiments, a bromodomain or BET inhibitor is a compound represented by Formula (V), (VI), or (VII):





in which R, Ri, and R2 and RB have the same meaning as in Formula (I); Y is O, N, S, or CR5, in which R5 has the same meaning as in Formula (I); n is 0 or 1; and the dashed circle in Formula (VII) indicates an aromatic or non-aromatic ring; or a salt, solvate or hydrate thereof.
In certain embodiments of any of the Formulae I-IV and VI (or any formula herein), R6 represents the non-carbonyl portion of an aldehyde shown in Table A, below (i.e., for an aldehyde of formula R6CHO, R6 is the non-carbonyl portion of the aldehyde). In certain embodiments, R4 and R6 together represent the non-carbonyl portion of a ketone shown in Table A (i.e., for a ketone of formula R6C(O)R4, R4 and R6 are the non-carbonyl portion of the ketone).







TABLE A





(Plates 1 to 4)







Plate 1

















01
02
03
04
05
06





A























 


B


























 


C























 


D


























 


E


























 


F


























 


G


























 


H






























07
08
09
10
11
12





A


























 


B


























 


C


























 


D























 


E


























 


F























 


G























 


H


































Plate 2

















01
02
03
04
05
06





A























 


B


























 


C























 


D


























 


E


























 


F


























 


G


























 


H






























07
08
09
10
11
12





A


























 


B


























 


C


























 


D























 


E


























 


F























 


G























 


H


































Plate 3

















01
02
03
04
05
06





A























 


B


























 


C























 


D


























 


E


























 


F


























 


G


























 


H






























07
08
09
10
11
12





A


























 


B


























 


C


























 


D























 


E


























 


F























 


G























 


H


































Plate 4

















01
02
03
04
05
06





A























 


B


























 


C























 


D


























 


E


























 


F


























 


G






























07
08
09
10
11
12





A


























 


B


























 


C


























 


D























 


E


























 


F























 


G


























In some embodiments, a bromodomain or BET inhibitor is a compound represented by the formula:




or a salt, solvate, or hydrate thereof. In some embodiments, a bromodomain or BET inhibitor is (racemic) JQ1; in certain embodiments, the compound is (+)-JQ1. In some embodiments, a bromodomain or BET inhibitor is a compound selected from the group consisting of:





or a salt, solvate, or hydrate thereof.

Additional examples of compounds include compounds according to any of the following formulae:













or a salt, solvate or hydrate thereof.

In Formulae IX-XXII, R and R′ can be, e.g., H, aryl, substituted aryl, heteroaryl, heteroaryl, heterocycloalkyl, —C1-C8 alkyl, —C2-C8 alkenyl, —C2-C8 alkynyl, —C3-Ci2 cycloalkyl, substituted —C3-Ci2 cycloalkyl, —C3-Ci2 cycloalkenyl, or substituted —C3-Ci2 cycloalkenyl, each of which may be optionally substituted. In Formulae XIV, X can be any substituent for an aryl group as described herein.
The compounds described in herein can be prepared using methods well known in the prior art (see, e.g., WO 011143669, the entirety which is incorporated by reference herein).
As used herein, the term an “aromatic ring” or “aryl” means a monocyclic or polycyclic-aromatic ring or ring radical comprising carbon and hydrogen atoms. Examples of suitable aryl groups include, but are not limited to, phenyl, tolyl, anthacenyl, fluorenyl, indenyl, azulenyl, and naphthyl, as well as benzo-fused carbocyclic moieties such as 5,6,7,8-tetrahydronaphthyl. An aryl group can be unsubstituted or optionally is substituted with one or more substituents, e.g., substituents as described herein for alkyl groups (including without limitation alkyl (preferably, lower alkyl or alkyl substituted with one or more halo), hydroxy, alkoxy (preferably, lower alkoxy), alkylthio, cyano, halo, amino, boronic acid (—B(OH)2, and nitro). In certain embodiments, the aryl group is a monocyclic ring, wherein the ring comprises 6 carbon atoms.
As used herein, the term “alkyl” means a saturated straight chain or branched non-cyclic hydrocarbon typically having from 1 to 10 carbon atoms. Representative saturated straight chain alkyls include methyl, ethyl, n-propyl, n-butyl, n-pentyl, n-hexyl, n-heptyl, n-octyl, n-nonyl and n-decyl; while saturated branched alkyls include isopropyl, sec-butyl, isobutyl, tert-butyl, isopentyl, 2-methylbutyl, 3-methylbutyl, 2-methylpentyl, 3-methylpentyl, 4-methylpentyl, 2-methylhexyl, 3-methylhexyl, 4-methylhexyl, 5-methylhexyl, 2,3-dimethylbutyl, 2,3-dimethylpentyl, 2,4-dimethylpentyl, 2,3-dimethylhexyl, 2,4-dimethylhexyl, 2,5-dimethylhexyl, 2,2-dimethylpentyl, 2,2-dimethylhexyl, 3,3-dimethylpentyl, 3,3-dimethylhexyl, 4,4-dimethylhexyl, 2-ethylpentyl, 3-ethylpentyl, 2-ethylhexyl, 3-ethylhexyl, 4-ethylhexyl, 2-methyl-2-ethylpentyl, 2-methyl-3-ethylpentyl, 2-methyl-4-ethylpentyl, 2-methyl-2-ethylhexyl, 2-methyl-3-ethylhexyl, 2-methyl-4-ethylhexyl, 2,2-diethylpentyl, 3,3-diethylhexyl, 2,2-diethylhexyl, 3,3-diethylhexyl and the like. Alkyl groups included in compounds of this invention may be unsubstituted, or optionally substituted with one or more substituents, such as amino, alkylamino, arylamino, heteroarylamino, alkoxy, alkylthio, oxo, halo, acyl, nitro, hydroxyl, cyano, aryl, heteroaryl, alkylaryl, alkylheteroaryl, aryloxy, heteroaryloxy, arylthio, heteroarylthio, arylamino, heteroarylamino, carbocyclyl, carbocyclyloxy, carbocyclylthio, carbocyclylamino, heterocyclyl, heterocyclyloxy, heterocyclylamino, heterocyclylthio, and the like. Lower alkyls are typically preferred for the compounds of this invention.
The term “diastereomers” refers to stereoisomers with two or more centers of dissymmetry and whose molecules are not mirror images of one another.
The term “enantiomers” refers to two stereoisomers of a compound which are non-superimposable mirror images of one another. An equimolar mixture of two enantiomers is called a “racemic mixture” or a “racemate.”
The term “halogen” designates —F, —Cl, —Br or —I.
The term “haloalkyl” is intended to include alkyl groups as defined above that are mono-, di- or polysubstituted by halogen, e.g., fluoromethyl and trifluoromethyl.
The term “hydroxyl” means —OH.
The term “heteroatom” as used herein means an atom of any element other than carbon or hydrogen. Preferred heteroatoms are nitrogen, oxygen, sulfur and phosphorus.
The term “heteroaryl” refers to an aromatic 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system having 1-4 ring heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, said heteroatoms selected from O, N, or S, and the remainder ring atoms being carbon. Heteroaryl groups may be optionally substituted with one or more substituents as for aryl groups. Examples of heteroaryl groups include, but are not limited to, pyridyl, furanyl, benzodioxolyl, thienyl, pyrrolyl, oxazolyl, oxadiazolyl, imidazolyl thiazolyl, isoxazolyl, quinolinyl, pyrazolyl, isothiazolyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, triazolyl, thiadiazolyl, isoquinolinyl, indazolyl, benzoxazolyl, benzofuryl, indolizinyl, imidazopyridyl, tetrazolyl, benzimidazolyl, benzothiazolyl, benzothiadiazolyl, benzoxadiazolyl, and indolyl.
The term “heterocyclic” as used herein, refers to organic compounds that contain at least at least one atom other than carbon (e.g., S, O, N) within a ring structure. The ring structure in these organic compounds can be either aromatic or non-aromatic. Some examples of heterocyclic moeities include, are not limited to, pyridine, pyrimidine, pyrrolidine, furan, tetrahydrofuran, tetrahydrothiophene, and dioxane.
The term “isomers” or “stereoisomers” refers to compounds which have identical chemical constitution, but differ with regard to the arrangement of the atoms or groups in space.
The term “isotopic derivatives” includes derivatives of compounds in which one or more atoms in the compounds are replaced with corresponding isotopes of the atoms. For example, an isotopic derivative of a compound containing a carbon atom (C 112′′) would be one in which the carbon atom of the compound is replaced with the C 13 isotope.
The term “optical isomers” as used herein includes molecules, also known as chiral molecules, that are exact non-superimposable mirror images of one another.
The terms “polycyclyl” or “polycyclic radical” refer to the radical of two or more cyclic rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls) in which two or more carbons are common to two adjoining rings, e.g., the rings are “fused rings”. Rings that are joined through non-adjacent atoms are termed “bridged” rings. Each of the rings of the polycycle can be substituted with such substituents as described above, as for example, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkyl, alkylaryl, or an aromatic or heteroaromatic moiety.
The term “sulfhydryl” or “thiol” means —SH.
The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof
In some embodiments, the bromodomain inhibitor is any molecule or compound that reduces or prevents expression of BRD-containing proteins. Examples of such inhibitors include siRNA, shRNA, dsRNA, oligomimics, and proteases that target one or more BRD-containing protein.
Methods for producing inhibitors as described above are well known in the art (See e.g., Sambrook, Fritsch and Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL, (Current Edition); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel et al. eds., (Current Edition)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICAL APPROACH (Current Edition) ANTIBODIES, A LABORATORY MANUAL and ANIMAL CELL CULTURE (R. I. Freshney, ed. (1987)). DNA Cloning: A Practical Approach, vol. I & II (D. Glover, ed.); Oligonucleotide Synthesis (N. Gait, ed., Current Edition); Nucleic Acid Hybridization (B. Hames & S. Higgins, eds., Current Edition); Transcription and Translation (B. Hames & S. Higgins, eds., Current Edition); Fundamental Virology, 2nd Edition, vol. I & II (B. N. Fields and D. M. Knipe, eds.).
Examples of bromodomain-containing proteins are shown in Table 2.







TABLE 2







Bromodomain-containing proteins










Gene
Ensembl gene ID
Ensembl transcript ID
Ensembl protein ID





ASH1L
ENSG00000116539
ENST00000548830,
ENSP00000449283,




ENST00000492987,
ENSP00000448820,




ENST00000392403,
ENSP00000376204,




ENST00000368346
ENSP00000357330


ATAD2
ENSG00000156802
ENST00000521903,
ENSP00000429213,




ENST00000519124,
ENSP00000429617,




ENST00000517666,
ENSP00000429331,




ENST00000287394
ENSP00000287394


BAZ1A/B
ENSG00000198604
ENST00000555331 (A),
ENSP00000450902 (A),



(A),
ENST00000554865 (A),
ENSP00000450923 (A),



ENSG00000009954
ENST00000553573 (A),
ENSP00000451896 (A),



(B)
ENST00000543083 (A),
ENSP00000445562 (A),




ENST00000382422 (A),
ENSP00000371859 (A),




ENST00000360310 (A),
ENSP00000353458 (A),




ENST00000358716 (A),
ENSP00000351555 (A),




ENST00000404251 (B),
ENSP00000385442 (B),




ENST00000339594 (B)
ENSP00000342434 (B)


BAZ2A/B
ENSG00000076108
ENST00000551996 (A),
ENSP00000447591 (A),



(A),
ENST00000551812 (A),
ENSP00000446880 (A),



ENSG00000123636
ENST00000549884 (A),
ENSP00000447941 (A),



(B)
ENST00000549787 (A),
ENSP00000448760 (A),




ENST00000549506 (A),
ENSP00000447248 (A),




ENST00000547650 (A),
ENSP00000449473 (A),




ENST00000547453 (A),
ENSP00000447314 (A),




ENST00000546695 (A),
ENSP00000449496 (A),




ENST00000379441 (A),
ENSP00000368754 (A),




ENST00000179765 (A),
ENSP00000179765 (A),




ENST00000546335 (A),
ENSP00000437619 (B),




ENST00000541068 (B),
ENSP00000441341 (B),




ENST00000441143 (B),
ENSP00000393565 (B),




ENST00000437839 (B),
ENSP00000415613 (B),




ENST00000426648 (B),
ENSP00000400505 (B),




ENST00000392783 (B),
ENSP00000376534 (B),




ENST00000392782 (B),
ENSP00000376533 (B),




ENST00000355831 (B),
ENSP00000348087 (B),




ENST00000343439 (B),
ENSP00000339670 (B),




ENST00000294905 (B)
ENSP00000294905 (B)


BRD1
ENSG00000100425
ENST00000542442,
ENSP00000437514,




ENST00000457780,
ENSP00000410042,




ENST00000438393,
ENSP00000388027,




ENST00000419212,
ENSP00000399110,




ENST00000404760,
ENSP00000385858,




ENST00000404034,
ENSP00000384076,




ENST00000342989,
ENSP00000345886,




ENST00000216267
ENSP00000216267


BRD2
ENSG00000234704,
ENST00000550598,
ENSP00000447012,



ENSG00000236227,
ENST00000547286,
ENSP00000448429,



ENSG00000230678,
ENST00000546777,
ENSP00000449979,



ENSG00000204256,
ENST00000479699,
ENSP00000434155,



ENSG00000234507,
ENST00000450320,
ENSP00000413845,



ENSG00000235307,
ENST00000449118,
ENSP00000399009,



ENSG00000215077
ENST00000433783,
ENSP00000416399,




ENST00000427021,
ENSP00000400737,




ENST00000414731
ENSP00000391246


BRD3
ENSG00000169925
ENST00000540795,
ENSP00000442302,




ENST00000433041,
ENSP00000406749,




ENST00000371842,
ENSP00000360908,




ENST00000371834,
ENSP00000360900,




ENST00000357885,
ENSP00000350557,




ENST00000303407
ENSP00000305918


BRD4
ENSG00000141867
ENST00000371835,
ENSP00000360901,




ENST00000360016,
ENSP00000353112,




ENST00000263377,
ENSP00000263377


BRDT
ENSG00000137948
ENST00000552654,
ENSP00000446599,




ENST00000548992,
ENSP00000447394,




ENST00000539070,
ENSP00000441862,




ENST00000457265,
ENSP00000408138,




ENST00000450792,
ENSP00000414349,




ENST00000449584,
ENSP00000408625,




ENST00000448194,
ENSP00000410587,




ENST00000440509,
ENSP00000416714,




ENST00000427104,
ENSP00000400002,




ENST00000426141,
ENSP00000404969,




ENST00000423434,
ENSP00000396351,




ENST00000402388,
ENSP00000384051,




ENST00000399546,
ENSP00000387822,




ENST00000394530,
ENSP00000378038,




ENST00000370389,
ENSP00000359416,




ENST00000362005,
ENSP00000354568,




ENST00000355011
ENSP00000400199


BRD7
ENSG00000166164
ENST00000569774,
ENSP00000461556,




ENST00000562383,
ENSP00000458430,




ENST00000394689,
ENSP00000378181,




ENST00000394688
ENSP00000378180


BRD8
ENSG00000112983
ENST00000512140,
ENSP00000427475,




ENST00000511898,
ENSP00000426385,




ENST00000506167,
ENSP00000427126,




ENST00000472478,
ENSP00000420884,




ENST00000455658,
ENSP00000408396,




ENST00000454473,
ENSP00000398067,




ENST00000453824,
ENSP00000407129,




ENST00000450756,
ENSP00000396487,




ENST00000441656,
ENSP00000398084,




ENST00000432618,
ENSP00000398676,




ENST00000430331, 
ENSP00000407414,




ENST00000428808,
ENSP00000414625,




ENST00000427976,
ENSP00000392646,




ENST00000418329,
ENSP00000398873,




ENST00000411594,
ENSP00000394330,




ENST00000402931,
ENSP00000384845,




ENST00000254900,
ENSP00000254900,




ENST00000239899,
ENSP00000239899,




ENST00000230901
ENSP00000230901


BRD9
ENSG00000028310
ENST00000523139,
ENSP00000430170,




ENST00000519112,
ENSP00000429353,




ENST00000518251,
ENSP00000428194,




ENST00000518250,
ENSP00000430510,




ENST00000495265,
ENSP00000420080,




ENST00000490814,
ENSP00000417431,




ENST00000489816,
ENSP00000419752,




ENST00000489093,
ENSP00000420722,




ENST00000487688,
ENSP00000420492,




ENST00000483173,
ENSP00000419845,




ENST00000467963,
ENSP00000419765,




ENST00000466684,
ENSP00000420397,




ENST00000435709,
ENSP00000402984,




ENST00000388890,
ENSP00000373542,




ENST00000323547,
ENSP00000325200,




ENST00000323510
ENSP00000323557


BRPF1
ENSG00000156983
ENST00000457855,
ENSP00000410210,




ENST00000433861,
ENSP00000402485,




ENST00000426583,
ENSP00000404235,




ENST00000424362,
ENSP00000398863,




ENST00000420291,
ENSP00000416728,




ENST00000383829,
ENSP00000373340,




ENST00000302054
ENSP00000306297


BRPF3
ENSG00000096070
ENST00000543502,
ENSP00000445352,




ENST00000534694,
ENSP00000434501,




ENST00000534400,
ENSP00000436504,




ENST00000532330,
ENSP00000437087,




ENST00000527657,
ENSP00000431894,




ENST00000454960,
ENSP00000413655,




ENST00000449261,
ENSP00000416842,




ENST00000446974,
ENSP00000410669,




ENST00000443324,
ENSP00000387368,




ENST00000441730,
ENSP00000413022,




ENST00000441123,
ENSP00000411558,




ENST00000394572,
ENSP00000378073,




ENST00000357641,
ENSP00000350267,




ENST00000339717
ENSP00000345419


BRWD3
ENSG00000165288
ENST00000373275
ENSP00000362372


CECR2
ENSG00000099954
ENST00000400585,
ENSP00000383428,




ENST00000400573,
ENSP00000383417,




ENST00000355219,
ENSP00000347357,




ENST00000342247,
ENSP00000341219,




ENST00000262608
ENSP00000262608


CREBBP
ENSG00000005339
ENST00000573517,
ENSP00000460474,




ENST00000572134,
ENSP00000458254,




ENST00000571826,
ENSP00000459490,




ENST00000570939,
ENSP00000461002,




ENST00000382070,
ENSP00000371502,




ENST00000323508,
ENSP00000323550,




ENST00000262367
ENSP00000262367


EP300
ENSG00000100393
ENST00000263253
ENSP00000263253


FALZ
aka BPTF:
ENST00000544778,
ENSP00000440854,



ENSG00000262858,
ENST00000544491,
ENSP00000443949,



ENSG00000171634
ENST00000424123,
ENSP00000388405,




ENST00000342579,
ENSP00000343837,




ENST00000335221,
ENSP00000334351,




ENST00000321892,
ENSP00000315454,




ENST00000306378,
ENSP00000307208,




ENST00000576412,
ENSP00000461707,




ENST00000575874,
ENSP00000459656,




ENST00000574652,
ENSP00000459309,




ENST00000574648,
ENSP00000459251,




ENST00000573838,
ENSP00000458864,




ENST00000573834,
ENSP00000461014,




ENST00000571054
ENSP00000460704


GCN5L2
aka KAT2A:
ENST00000564173,
ENSP00000456712,



ENSG00000259958,
ENST00000225916
ENSP00000225916



ENSG00000108773




MLL
ENSG00000118058
ENST00000534358,
ENSP00000436786,




ENST00000533790,
ENSP00000436700,




ENST00000532204,
ENSP00000434618,




ENST00000531904,
ENSP00000432391,




ENST00000529852,
ENSP00000436564,




ENST00000527869,
ENSP00000432652,




ENST00000392873,
ENSP00000376612,




ENST00000389507,
ENSP00000374158,




ENST00000389506,
ENSP00000374157,




ENST00000359313,
ENSP00000352262,




ENST00000354520,
ENSP00000346516,




ENST00000328469
ENSP00000333556


PB1
ENSG00000163939
ENST00000458294,
ENSP00000411895,




ENST00000450271,
ENSP00000416851,




ENST00000449505,
ENSP00000412401,




ENST00000446103,
ENSP00000397662,




ENST00000439181,
ENSP00000404635,




ENST00000431678,
ENSP00000409939,




ENST00000424867,
ENSP00000397399,




ENST00000423351,
ENSP00000387775,




ENST00000420148,
ENSP00000389390,




ENST00000412587,
ENSP00000404579,




ENST00000410007,
ENSP00000386529,




ENST00000409767,
ENSP00000386601,




ENST00000409114,
ENSP00000386643,




ENST00000409057,
ENSP00000386593,




ENST00000394830,
ENSP00000378307,




ENST00000356770,
ENSP00000349213,




ENST00000337303,
ENSP00000338302,




ENST00000296302
ENSP00000296302


PCAF
ENSG00000114166
ENST00000263754
ENSP00000263754


PHIP
ENSG00000146247
ENST00000355098,
ENSP00000347215,




ENST00000275034
ENSP00000275034


PRKCBP1
ENSG00000101040
ENST00000540497,
ENSP00000443086,




ENST00000536340,
ENSP00000439800,




ENST00000471951,
ENSP00000420095,




ENST00000467200,
ENSP00000418495,




ENST00000461685,
ENSP00000418210,




ENST00000458360,
ENSP00000392964,




ENST00000446994,
ENSP00000396725,




ENST00000446894,
ENSP00000394379,




ENST00000441977,
ENSP00000393806,




ENST00000435836,
ENSP00000413727,




ENST00000396281,
ENSP00000379577,




ENST00000372023,
ENSP00000361093,




ENST00000360911,
ENSP00000354166,




ENST00000355972,
ENSP00000348246,




ENST00000352431,
ENSP00000335537,




ENST00000311275,
ENSP00000312237,




ENST00000262975
ENSP00000262975


SMARCA2
ENSG00000080503
ENST00000457226,
ENSP00000415218,




ENST00000452193,
ENSP00000401096,




ENST00000450198,
ENSP00000392081,




ENST00000439732,
ENSP00000409398,




ENST00000423555,
ENSP00000413057,




ENST00000417599,
ENSP00000387486,




ENST00000416751,
ENSP00000412242,




ENST00000382203,
ENSP00000371638,




ENST00000382194,
ENSP00000371629,




ENST00000382186,
ENSP00000371621,




ENST00000382185,
ENSP00000371620,




ENST00000382183,
ENSP00000371618,




ENST00000382182,
ENSP00000371617,




ENST00000357248,
ENSP00000349788,




ENST00000349721,
ENSP00000265773,




ENST00000324954,
ENSP00000324770,




ENST00000302401
ENSP00000305411


SMARCA4
ENSG00000127616
ENST00000541122,
ENSP00000445036,




ENST00000538456,
ENSP00000443848,




ENST00000450717,
ENSP00000397783,




ENST00000444061,
ENSP00000392837,




ENST00000429416,
ENSP00000395654,




ENST00000421844,
ENSP00000403803,




ENST00000413806,
ENSP00000414727,




ENST00000358026,
ENSP00000350720,




ENST00000344626
ENSP00000343896


SP100
ENSG00000067066
ENST00000452345,
ENSP00000416563,




ENST00000432979,
ENSP00000391616,




ENST00000431952,
ENSP00000393679,




ENST00000427101,
ENSP00000399389,




ENST00000414648,
ENSP00000412837,




ENST00000413284,
ENSP00000400277,




ENST00000409897,
ENSP00000386998,




ENST00000409824,
ENSP00000387311,




ENST00000409341,
ENSP00000386404,




ENST00000409112,
ENSP00000386427,




ENST00000341950,
ENSP00000342729,




ENST00000340126,
ENSP00000343023,




ENST00000264052
ENSP00000264052


SP110
ENSG00000135899
ENST00000540870,
ENSP00000439558,




ENST00000455674,
ENSP00000393992,




ENST00000416610,
ENSP00000399978,




ENST00000409815,
ENSP00000387172,




ENST00000392048,
ENSP00000375902,




ENST00000358662,
ENSP00000351488,




ENST00000338556,
ENSP00000344049,




ENST00000258382,
ENSP00000258382,




ENST00000258381
ENSP00000258381


SP140
ENSG00000079263
ENST00000537563,
ENSP00000445084,




ENST00000486687,
ENSP00000440107,




ENST00000420434,
ENSP00000398210,




ENST00000417495,
ENSP00000393618,




ENST00000392045,
ENSP00000375899,




ENST00000392044,
ENSP00000375898,




ENST00000373645,
ENSP00000362749,




ENST00000350136,
ENSP00000345846,




ENST00000343805
ENSP00000342096


TAF1
ENSG00000147133
ENST00000538124,
ENSP00000441908,




ENST00000483985,
ENSP00000424526,




ENST00000463163,
ENSP00000421611,




ENST00000449580,
ENSP00000389000,




ENST00000437147,
ENSP00000406517,




ENST00000423759,
ENSP00000406549,




ENST00000395779,
ENSP00000379125,




ENST00000373790,
ENSP00000362895,




ENST00000373775,
ENSP00000362880,




ENST00000276072
ENSP00000276072


TAF1L
ENSG00000122728
ENST00000242310
ENSP00000418379


TRIM24
ENSG00000122779
ENST00000536822,
ENSP00000440535,




ENST00000452999,
ENSP00000402079,




ENST00000439939,
ENSP00000403347,




ENST00000415680,
ENSP00000390829,




ENST00000378381,
ENSP00000367632,




ENST00000343526
ENSP00000340507


TRIM28
ENSG00000130726
ENST00000341753,
ENSP00000342232,




ENST00000253024
ENSP00000253024


TRIM33
ENSG00000197323
ENST00000450349,
ENSP00000412077,




ENST00000448034,
ENSP00000402333,




ENST00000369543,
ENSP00000358556,




ENST00000358465
ENSP00000351250


TRIM66
ENSG00000166436
ENST00000530502,
ENSP00000437234,




ENST00000402157,
ENSP00000384876,




ENST00000299550
ENSP00000299550


WDR9
ENSG00000185658
ENST00000455867,
ENSP00000389882,




ENST00000446924,
ENSP00000391014,




ENST00000445668,
ENSP00000395575,




ENST00000445245,
ENSP00000390684,




ENST00000430093,
ENSP00000393702,




ENST00000424441,
ENSP00000415066,




ENST00000412604,
ENSP00000398900,




ENST00000380800,
ENSP00000370178,




ENST00000380783,
ENSP00000370160,




ENST00000342449,
ENSP00000344333,




ENST00000341322,
ENSP00000342106,




ENST00000333229
ENSP00000330753


ZMYND11
ENSG00000015171,
ENST00000545619,
ENSP00000438461,



ENSG00000260150
ENST00000535374,
ENSP00000439587,




ENST00000509513,
ENSP00000424205,




ENST00000439456,
ENSP00000397072,




ENST00000403354,
ENSP00000385484,




ENST00000402736,
ENSP00000386010,




ENST00000397962,
ENSP00000381053,




ENST00000397959,
ENSP00000381050,




ENST00000397955,
ENSP00000381046,




ENST00000381607,
ENSP00000371020,




ENST00000381604,
ENSP00000371017,




ENST00000381602,
ENSP00000371015,




ENST00000381591,
ENSP00000371003,




ENST00000381584,
ENSP00000370996,




ENST00000309776,
ENSP00000309992,




ENST00000568927,
ENSP00000458138,




ENST00000568174,
ENSP00000457204,




ENST00000565311,
ENSP00000457248,




ENST00000564303,
ENSP00000456325,




ENST00000563851,
ENSP00000456634,




ENST00000562898,
ENSP00000454775,




ENST00000562457
ENSP00000455330









In some embodiments, “inhibit”, “block”, “suppress” or “prevent” means that the activity being inhibited, blocked, suppressed, or prevented is reduced by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% as compared to the activity of a control (e.g., activity in the absence of the inhibitor). In some embodiments, “inhibit”, “block”, “suppress” or “prevent” means that the expression of the target of the inhibitor (e.g. a bromodomain-containing protein) is reduced by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% as compared to a control (e.g., the expression in the absence of the inhibitor).
Notch Pathway Inhibitors
A Notch pathway inhibitor prevents or inhibits, in part or in whole, the activity of components of the Notch pathway. It is to be understood that the activity of components of the Notch pathway may include one or more activities, such as cell fate specification, differentiation, proliferation, apoptosis, adhesion, epithelial-mesenchymal transition, migration, or angiogenesis. In some embodiments, a Notch pathway inhibitor suppresses or inhibits a Notch pathway activation mutation. Examples of Notch pathway activation mutations are described below. Notch pathway inhibitors are known in the art. In some embodiments, a Notch pathway inhibitor is a gamma secretase inhibitor (GSI). Gamma secretase is a multi-subunit protease complex that cleaves Notch. This cleavage releases Notch from the cell membrane, allowing Notch to enter the nucleus and modify gene expression. Examples of gamma secretase inhibitors include, but are not limited to, DBZ (Axon Medchem, Cat. No. 1488), BMS-906024 (Bristol-Myers Squibb), RO4929097 (Roche/Genentech), LY450139 (Eli Lilly), BMS-708163 (Bristol-Myers Squibb), MK-0752 (University of Michigan), PF-03084014 (Pfizer), IL-X (also referred to as cbz-IL-CHO, Calbiochem), z-Leu-leu-Nle-CHO (EMD Millipore), N—[N-(3,5-difluorophenacetyl)-L-alanyl]-Sphenylglycine t-butyl ester (DAPT), BH589 (Panobinostat, Novartis), MEDI0639 (MedImmune LLC), Choline magnesium trisalicylate (e.g., Trilisate), and Curcumin (a curcuminoid of turmeric).
Other Notch pathway inhibitors include antibodies and antibody fragments. Examples include monoclonal antibodies against extracellular Notch receptors (developed by Genentech and described by Wu et al. Nature 2010). Another example is a stapled peptide inhibitor of the intracellular Notch transcriptional complex (SAHM1) described by Moellering et al. Nature, 2009 (being developed by Aileron Therapeutics).
In some embodiments, a Notch pathway inhibitor is any molecule or compound that reduces or prevents (mRNA or protein) expression of any component of the Notch pathway (e.g. Notch, Notch ligands, downstream effectors, and the like). Examples of such inhibitors include siRNA, shRNA, dsRNA, oligomimics, and proteases that target one or more components of the Notch pathway. Components of the Notch pathway include, but are not limited to, those in Table 3.







TABLE 3







Notch pathway components










Gene
Ensembl gene ID
Ensembl transcript ID
Ensembl protein ID





ADAM17
ENSG00000151694
ENST00000310823,
ENSP00000309968,




ENST00000497134,
ENSP00000418728,




ENST00000538558,
ENSP00000439780




ENST00000478059



AKT1
ENSG00000142208
ENST00000349310,ENS
ENSP00000270202,E




T00000407796,ENST00
NSP00000384293,EN




000402615,ENST00000
SP00000385326,ENS




554848,ENST00000554
P00000451166,ENSP




581,ENST00000555528,
00000451828,ENSP0




ENST00000544168,EN 
0000450688,ENSP00




ST00000554192,ENST0
000443897,ENSP000




0000555380,ENST0000
00450681,ENSP0000




0555926,ENST0000055
0451290,ENSP00000




5458
451824,ENSP000004





51470


APH1A
ENSG00000117362
ENST00000360244,ENS
ENSP00000353380,E




T00000369109,ENST00
NSP00000358105,EN




000236017,ENST00000 
SP00000236017,ENS




414276
P00000397473


APH1B
ENSG00000138613
ENST00000261879,ENS
ENSP00000261879,E




T00000380343,ENST00 
NSP00000369700,EN




000560353,ENST00000
SP00000453327,ENS




560890,ENST00000380 
P00000453002,ENSP




340,ENST00000559971
00000369697,ENSP0





0000453516


CDKN1A
ENSG00000124762
ENST00000244741,ENS
ENSP00000244741,E




T00000373711,ENST00
NSP00000362815,EN




000405375,ENST00000
SP00000384849,ENS




448526
P00000409259


CIR1
ENSG00000138433
ENST00000342016,ENS
ENSP00000339723,E




T00000377973,ENST00
NSP00000367211,EN




000414336,ENST00000
SP00000395036,ENS




362053,ENST00000425
P00000355034,ENSP




101
00000405693


CUL1
ENSG00000055130
ENST00000409469,ENS
ENSP00000387160,E




T00000325222,ENST00
NSP00000326804,EN




000433865,ENST00000
SP00000396011,ENS




543583
P00000441340


DLL1
ENSG00000198719
ENST00000366756
ENSP00000355718


DLL3
ENSG00000090932
ENST00000205143,
ENSP00000205143,




ENST00000356433
ENSP00000348810


DLL4
ENSG00000128917
ENST00000249749
ENSP00000249749


DTX1
ENSG00000135144
ENST00000257600
ENSP00000257600


EP300
ENSG00000100393
ENST00000263253
ENSP00000263253


FBXW7
ENSG00000109670
ENST00000263981,ENS
ENSP00000263981,E




T00000281708,ENST00
NSP00000281708,EN




000296555,ENST00000
SP00000296555,ENS




393956
P00000377528


FHL1
ENSG00000022267
ENST00000370690,ENS
ENSP00000359724,E




T00000345434,ENST00
NSP00000071281,EN




000370676,ENST00000
SP00000359710,ENS




370683,ENST00000420
P00000359717,ENSP




362,ENST00000370674,
00000391779,ENSP0




ENST00000452016,EN
0000359708,ENSP00




ST00000434885,ENST0
000408038,ENSP000




0000458357,ENST0000
00413798,ENSP0000




0456445,ENST0000044
0389920,ENSP00000




9474,ENST0000039415
412642,ENSP000004




3, ENST00000394155,E
14604,ENSP0000037




NST00000456218,ENST
7709,ENSP00000377




00000535737,ENST000
710,ENSP000003928




00536581,ENST000005
13,ENSP0000044481




39015,ENST000005427
5, ENSP00000445335,




04,ENST00000543669
ENSP00000437673,E





NSP00000446441,EN





SP00000443333


GATA3
ENSG00000107485
ENST00000379328,ENS
ENSP00000368632,E




T00000346208,ENST00
NSP00000341619,EN




000544011
SP00000439641


GSK3B
ENSG00000082701
ENST00000264235,ENS
ENSP00000264235,E




T00000316626,ENST00
NSP00000324806,EN




000539838
SP00000437981


HAT1
ENSG00000128708
ENST00000264108,ENS
ENSP00000264108,E




T00000392584,ENST00
NSP00000376363,EN




000412731,ENST00000
SP00000407921,ENS




457761
P00000403466


HDAC1
ENSG00000116478
ENST00000373548,
ENSP00000362649,




ENST00000428704,
ENSP00000407859,




ENST00000373541
ENSP00000362642


HDAC10
ENSG00000100429
ENST00000216271,ENS
ENSP00000216271,E




T00000448072,ENST00
NSP00000397542,EN




000349505,ENST00000
SP00000343540,ENS




415993,ENST00000429
P00000397517,ENSP




374,ENST00000454936
00000407640,ENSP0





0000406150


HDAC11
ENSG00000163517
ENST00000295757,ENS
ENSP00000295757,E




T00000433119,ENST00
NSP00000412514,EN




000402259,ENST00000
SP00000384706,ENS




402271,ENST00000404
P00000384123,ENSP




040,ENST00000404548,
00000385475,ENSP0




ENST00000405025,EN
0000385528,ENSP00




ST00000405478,ENST0
000384019,ENSP000




0000458642,ENST0000
00385252,ENSP0000




0418189,ENST0000043
0405403,ENSP00000




4848,ENST0000041624
411792,ENSP000003




8, ENST00000455904,E
98651,ENSP0000040




NST00000437379,ENST
2298,ENSP00000396




00000522202,ENST000
122,ENSP000003951




00446613,ENST000004
88,ENSP0000042979




25430
4,ENSP00000401487,





ENSP00000399792


HDAC2
ENSG00000196591
ENST00000519065,ENS
ENSP00000430432,E




T00000425835,ENST00
NSP00000417026,EN




000368632,ENST00000
SP00000357621,ENS




519108,ENST00000518
P00000430008,ENSP




690,ENST00000523240,
00000428653,ENSP0




ENST00000521610,EN
0000429236,ENSP00




ST00000524334,ENST0
000429901,ENSP000




0000520895,ENST0000
00428989,ENSP0000




0523628,ENST0000052
0428861,ENSP00000




2371,ENST0000052116
427861,ENSP000004




3, ENST00000398283
28599,ENSP0000042





8024,ENSP00000381





331


HDAC3
ENSG00000171720
ENST00000305264,ENS
ENSP00000302967,E




T00000523088,ENST00
NSP00000429099,EN




000523353,ENST00000
SP00000430667,ENS




519474
P00000430782


HDAC4
ENSG00000068024
ENST00000345617,ENS
ENSP00000264606,E




T00000446876,ENST00
NSP00000392912,EN




000454542,ENST00000
SP00000405226,ENS




445704,ENST00000430
P00000391226,ENSP




200,ENST00000544989,
00000410551,ENSP0




ENST00000393621,EN
0000438111,ENSP00




ST00000456922,ENST0
000377243,ENSP000




0000541256,ENST0000
00406618,ENSP0000




0543185
0443057,ENSP00000





440481


HDAC5
ENSG00000108840
ENST00000225983,ENS
ENSP00000225983,E




T00000336057,ENST00
NSP00000337290,EN




000393622
SP00000377244


HDAC6
ENSG00000094631
ENST00000334136,ENS
ENSP00000334061,E




T00000376643,ENST00
NSP00000365831,EN




000426196,ENST00000 
SP00000402189,ENS




430858,ENST00000376
P00000397697,ENSP




619,ENST00000423941,
00000365804,ENSP0




ENST00000438518,EN
0000392815,ENSP00




ST00000376610,ENST0
000403370,ENSP000




0000441703,ENST0000
00365795,ENSP0000




0443563,ENST0000044
0393916,ENSP00000




0653,ENST0000041316
402751,ENSP000003




3, ENST00000436813,E
94377,ENSP0000039




NST00000444343
8801,ENSP00000405





449,ENSP000003985





66


HDAC7
ENSG00000061273
ENST00000080059,ENS
ENSP00000080059,E




T00000354334,ENST00
NSP00000351326,EN




000417107,ENST00000
SP00000387792,ENS




450805,ENST00000433
P00000397236,ENSP




685,ENST00000447463,
00000403149,ENSP0




ENST00000427332,EN
0000389501,ENSP00




ST00000434070,ENST0
000404394,ENSP000




0000445237,ENST0000
00388561,ENSP0000




0421231,ENST0000041
0390415,ENSP00000




7902,ENST0000043067
412155,ENSP000004




0, ENST00000440293,E
00811,ENSP0000039




NST00000422254,ENST
6159,ENSP00000411




00000552960,ENST000
058,ENSP000004100




00380610,ENST000005
68,ENSP0000044853




48080,ENST000005489
2,ENSP00000369984,




38,ENST00000547259,E
ENSP00000446538,E




NST00000425451,ENST
NSP00000448305,EN




00000485796,ENST000
SP00000447191,ENS




00551602,ENST000004
P00000401872,ENSP




77203
00000448448,ENSP0





0000449193,ENSP00





000449171


HDAC8
ENSG00000147099
ENST00000373573,ENS
ENSP00000362674,E




T00000439122,ENST00
NSP00000414486,EN




000373556,ENST00000
SP00000362657,ENS




373571,ENST00000373
P00000362672,ENSP




554,ENST00000373568,
00000362655,ENSP0




ENST00000373560,EN
0000362669,ENSP00




ST00000373559,ENST0
000362661,ENSP000




0000421523,ENST0000
00362660,ENSP0000




0373583,ENST0000041
0398997,ENSP00000




5409,ENST0000037356
362685,ENSP000003




1, ENST00000373589,E
96424,ENSP0000036




NST00000429103,ENST
2662,ENSP00000362




00000412342,ENST000
691,ENSP000003884




00444609,ENST000004
59,ENSP0000040018




36675
0,ENSP00000409778,





ENSP00000416489


HDAC9
ENSG00000048052
ENST00000406451,ENS
ENSP00000384657,E




T00000405010,ENST00
NSP00000384382,EN




000406072,ENST00000
SP00000384017,ENS




417496,ENST00000433
P00000401669,ENSP




709,ENST00000413509,
00000409003,ENSP0




ENST00000430454,EN
0000412497,ENSP00




ST00000413380,ENST0
000411422,ENSP000




0000441986,ENST0000
00392564,ENSP0000




0456174,ENST0000040
0404763,ENSP00000




1921,ENST0000044154
388568,ENSP000003




2,ENST00000524023,E
83912,ENSP0000040




NST00000432645,ENST
8617,ENSP00000430




00000428307,ENST000
036,ENSP000004103




00262069,ENST000003
37,ENSP0000039565




41009,ENST000004466
5,EN5P00000262069,




46
ENSP00000339165,E





NSP00000415095


HES1
ENSG00000114315
ENST00000232424
ENSP00000232424


HES5
ENSG00000197921
ENST00000378453
ENSP00000367714


HES6
ENSG00000144485
ENST00000272937,ENS
ENSP00000272937,E




T00000409002,ENST00
NSP00000387155,EN




000409160,ENST00000
SP00000387215,ENS




436051,ENST00000409
P00000392596,ENSP




574,ENST00000409182,
00000387008,ENSP0




ENST00000409356,EN
0000387343,ENSP00




ST00000450098,ENST0
000387107,ENSP000




0000417803
00390870,ENSP0000





0401797


HEY1
ENSG00000164683
ENST00000354724,ENS
ENSP00000346761,E




T00000523976,ENST00
NSP00000429792,EN




000518733,ENST00000
SP00000429705,ENS




337919,ENST00000542
P00000338272,ENSP




205
00000445025


HEY2
ENSG00000135547
ENST00000368364,
ENSP00000357348,




ENST00000368365
ENSP00000357349


HIF1A
ENSG00000100644
ENST00000337138,ENS
ENSP00000338018,E




T00000323441,ENST00
NSP00000323326,EN




000394997,ENST00000
SP00000378446,ENS




557538,ENST00000394
P00000451696,ENSP




988,ENST00000539097,
00000378439,ENSP0




ENST00000539494
0000437955,ENSP00





000446436


ITCH
ENSG00000078747
ENST00000374864,ENS
ENSP00000363998,E




T00000262650,ENST00
NSP00000262650,EN




000535650
SP00000445608


JAG1
ENSG00000101384
ENST00000254958,
ENSP00000254958,




ENST00000423891
ENSP00000389519


JAG2
ENSG00000184916
ENST00000331782,
ENSP00000328169,




ENST00000347004
ENSP00000328566


JAK2
ENSG00000096968
ENST00000381652,ENS
ENSP00000371067,E




T00000539801,ENST00
NSP00000440387,EN




000544510
SP00000443103


LCK
ENSG00000182866
ENST00000336890,ENS
ENSP00000337825,E




T00000482949,ENST00
NSP00000431517,EN




000333070,ENST00000
SP00000328213,ENS




495610,ENST00000373
P00000435605,ENSP




557,ENST00000477031,
00000362658,ENSP0




ENST00000461712,EN
0000436554,ENSP00




ST00000373562,ENST0
000434525,ENSP000




0000373564,ENST0000
00362663,ENSP0000




0398345,ENST0000043
0362665,ENSP00000




6824
381387,ENSP000004





00092


LFNG
ENSG00000106003
ENST00000222725,ENS
ENSP00000222725,E




T00000359574,ENST00
NSP00000352579,EN




000402506,ENST00000
SP00000385764,ENS




402045,ENST00000338
P00000384786,ENSP




732
00000343095


MAGEA1
ENSG00000198681
ENST00000356661
ENSP00000349085


MAML1
ENSG00000161021
ENST00000292599,
ENSP00000292599,




ENST00000376951
ENSP00000366150


MAML2
ENSG00000184384
ENST00000524717,
ENSP00000434552,




ENST00000440572
ENSP00000412394


MAML3
ENSG00000196782
ENST00000509479,ENS
ENSP00000421180,E




T00000502696,ENST00
NSP00000422783,EN




000327122,ENST00000
SP00000313316,ENS




398940,ENST00000538
P00000381913,ENSP




400
00000444397


MFNG
ENSG00000100060
ENST00000356998,ENS
ENSP00000349490,E




T00000442496,ENST00
NSP00000389274,EN




000436341,ENST00000
SP00000394081,ENS




424765,ENST00000454
P00000407110,ENSP




291,ENST00000416983,
00000407094,ENSP0




ENST00000450946,EN
0000413855,ENSP00




ST00000430411,ENST0
000396605,ENSP000




0000438891
00414342,ENSP0000





0414222


MTOR
ENSG00000198793
ENST00000361445,ENS
ENSP00000354558,E




T00000376838,ENST00
NSP00000366034,EN




000455339,ENST00000
SP00000398745,ENS




539766
P00000440730


MYC
ENSG00000136997
ENST00000377970,ENS
ENSP00000367207,E




T00000259523,ENST00
NSP00000259523,EN




000517291,ENST00000
SP00000429441,ENS




524013,ENST00000520
P00000430235,ENSP




751,ENST00000454617
00000430226,ENSP0





0000405312


NCOR1
ENSG00000141027
ENST00000268712,ENS
ENSP00000268712,E




T00000436828,ENST00
NSP00000387727,EN




000395851,ENST00000
SP00000379192,ENS




395849,ENST00000436
P00000379190,ENSP




068,ENST00000395848,
00000389839,ENSP0




ENST00000411510,EN
0000379189,ENSP00




ST00000430577,ENST0
000407998,ENSP000




0000395857,ENST0000
00410784,ENSP0000




0458113
0379198,ENSP00000





395091


NCOR2
ENSG00000196498
ENST00000429285,ENS
ENSP00000400281,E




T00000404621,ENST00
NSP00000384202,EN




000458234,ENST00000
SP00000402808,ENS




420698,ENST00000405
P00000405367,ENSP




201,ENST00000448614,
00000384018,ENSP0




ENST00000453428,EN
0000408247,ENSP00




ST00000440187,ENST0
000400687,ENSP000




0000440337,ENST0000
00396044,ENSP0000




0418829,ENST0000041
0398963,ENSP00000




3172,ENST0000044800
391389,ENSP000004




8,ENST00000443451,E
07357,ENSP0000040




NST00000542927,ENST
3034,ENSP00000405




00000356219,ENST000
246,ENSP000004436




00397355,ENST000004
89,ENSP0000034855




04121,ENST000004470
1, ENSP00000380513,




11,ENST00000447675
ENSP00000385618,E





NSP00000396746,EN





SP00000401058


NCSTN
ENSG00000162736
ENST00000294785,ENS
ENSP00000294785,E




T00000368063,ENST00
NSP00000357042,EN




000438008,ENST00000
SP00000389370,ENS




421914,ENST00000437
P00000390409,ENSP




169,ENST00000424645,
00000415442,ENSP0




ENST00000435149,EN
0000388118,ENSP00




ST00000424754,ENST0
000407849,ENSP000




0000368065,ENST0000
00410124,ENSP0000




0368067,ENST0000039
0357044,ENSP00000




2212,ENST0000053585
357046,ENSP000003




7
76047,ENSP0000044





2605


NFKB1
ENSG00000109320
ENST00000226574,ENS
ENSP00000226574,E




T00000394820,ENST00
NSP00000378297,EN




000505458,ENST00000
SP00000424790,ENS




507079,ENST00000511
P00000426147,ENSP




926,ENST00000509165,
00000420904,ENSP0




ENST00000508584
0000423877,ENSP00





000424815


NOTCH1
ENSG00000148400
ENST00000277541
ENSP00000277541


NOTCH2
ENSG00000134250
ENST00000256646,ENS
ENSP00000256646,E




T00000369342,ENST00
NSP00000358348,EN




000401649,ENST00000
SP00000384752,ENS




538680,ENST00000539
P00000439516,ENSP




617
00000438937


NOTCH3
ENSG00000074181
ENST00000263388,
ENSP00000263388,




ENST00000539383
ENSP00000446150


NOTCH4
ENSG00000204301
ENST00000375023,
ENSP00000364163,




ENST00000443903
ENSP00000398123


NUMB
ENSG00000133961
ENST00000554546,ENS
ENSP00000452416,E




T00000555394,ENST00
NSP00000451625,EN




000557597,ENST00000
SP00000451117,ENS




555238,ENST00000356
P00000451300,ENSP




296,ENST00000556772,
00000348644,ENSP0




ENST00000559312,EN
0000451513,ENSP00




ST00000554521,ENST0
000452888,ENSP000




0000560335,ENST0000
00450817,ENSP0000




0555738,ENST0000055
0453209,ENSP00000




4818,ENST0000055530
452069,ENSP000004




7,ENST00000555987,E
51959,ENSP0000045




NST00000555859,ENST
2357,ENSP00000451




00000554394,ENST000
559,ENSP000004513




00326018,ENST000003
26,ENSP0000045137




55058,ENST000003595
4, ENSP00000315193,




60,ENST00000454166,E
ENSP00000347169,E




NST00000535282,ENST
NSP00000352563,EN




00000544991
SP00000394025,ENS





P00000441258,ENSP





00000446001


NUMBL
ENSG00000105245
ENST00000252891,
ENSP00000252891,




ENST00000540131
ENSP00000442759


PSENEN
ENSG00000205155
ENST00000222266
ENSP00000222266


PSEN1
ENSG00000080815
ENST00000324501,ENS
ENSP00000326366,E




T00000357710,ENST00
NSP00000350342,EN




000394164,ENST00000
SP00000377719,ENS




394157,ENST00000406
P00000377712,ENSP




768,ENST00000556864,
00000385948,ENSP0




ENST00000557037,EN
0000451588,ENSP00




ST00000556533,ENST0
000451347,ENSP000




0000556066,ENST0000
00452128,ENSP0000




0553599,ENST0000055
0452267,ENSP00000




7356,ENST0000055695
452477,ENSP000004




1,ENST00000557293,E
51498,ENSP0000045




NST00000553719,ENST
0551,ENSP00000451




00000554131,ENST000
880,ENSP000004516




00555254,ENST000005
74,ENSP0000045191




56011,ENST000005575
5,ENSP00000450652,




11,ENST00000560005,E
ENSP00000451662,E




NST00000261970,ENST
NSP00000451429,EN




00000344094,ENST000
SP00000453466,ENS




00555386,ENST000005
P00000261970,ENSP




53855,ENST000005593
00000339523,ENSP0




61
0000450845,ENSP00





000452242,ENSP000





00454156


PSEN2
ENSG00000143801
ENST00000366783,ENS
ENSP00000355747,E




T00000366782,ENST00
NSP00000355746,EN




000495488,ENST00000
SP00000429682,ENS




460775,ENST00000472
P00000427912,ENSP




139,ENST00000422240,
00000427806,ENSP0




ENST00000524196,EN
0000403737,ENSP00




ST00000340188,ENST0
000429036,ENSP000




0000391872,ENST0000
00339860,ENSP0000




0496965
0375745,ENSP00000





430647


PTCRA
ENSG00000171611
ENST00000304672,ENS
ENSP00000304447,E




T00000418903,ENST00
NSP00000407061,EN




000441198,ENST00000
SP00000409550,ENS




446507
P00000392288


RBPJ
ENSG00000168214
ENST00000345843,ENS
ENSP00000305815,E




T00000361572,ENST00
NSP00000354528,EN




000342320,ENST00000
SP00000340124,ENS




512351,ENST00000512
P00000424789,ENSP




671,ENST00000505958,
00000423644,ENSP0




ENST00000507561,EN
0000426872,ENSP00




ST00000504907,ENST0
000423907,ENSP000




0000506956,ENST0000
00423703,ENSP0000




0514807,ENST0000050
0425750,ENSP00000




9158,ENST0000051473
424989,ENSP000004




0,ENST00000507574,E
24804,ENSP0000042




NST00000514675,ENST
5061,ENSP00000422




00000515573,ENST000
617,ENSP000004235




00511546,ENST000005
75,ENSP0000042340




04938,ENST000005044
6,ENSP00000422838,




23,ENST00000510778,E
ENSP00000424459,E




NST00000348160,ENST
NSP00000421804,EN




00000342295,ENST000
SP00000427170,ENS




00355476,ENST000005
P00000339699,ENSP




13182,,ENST00000510
00000345206,ENSP0




778,ENST00000348160,
0000347659,ENSP00




ENST00000342295,EN
000427344,ENSP000




ST00000355476,ENST0
00427170,ENSP0000




0000513182
0339699,ENSP00000





345206,ENSP000003





47659,ENSP0000042





7344


RFNG
ENSG00000169733
ENST00000310496,
ENSP00000307971,




ENST00000429557
ENSP00000402931


RING1
ENSG00000204227
ENST00000374656
ENSP00000363787


SKP1
ENSG00000113558
ENST00000353411,ENS
ENSP00000231487,E




T00000522552,ENST00
NSP00000429472,EN




000519321,ENST00000
SP00000429415,ENS




517625,ENST00000522
P00000429961,ENSP




855,ENST00000520417,
00000429686,ENSP0




ENST00000523359,EN
0000429996,ENSP00




ST00000328392,ENST0
000428962,ENSP000




0000521216,ENST0000
00331708,ENSP0000




0519718,ENST0000052
0431067,ENSP00000




3966,ENST0000051905
430774,ENSP000004




4
29995,ENSP0000043





0885


SNW1
ENSG00000100603
ENST00000261531,ENS
ENSP00000261531,E




T00000555761,ENST00
NSP00000451129,EN




000554775,ENST00000
SP00000452059,ENS




554324,ENST00000416
P00000452473,ENSP




259,ENST00000556428
00000387847,ENSP0





0000451741


STAT3
ENSG00000168610
ENST00000264657,ENS
ENSP00000264657,E




T00000404395,ENST00
NSP00000384943,EN




000389272
SP00000373923


TLE1
ENSG00000196781
ENST00000376499,ENS
ENSP00000365682,E




T00000418319,ENST00
NSP00000391347,EN




000376484,ENST00000
SP00000365667,ENS




376463,ENST00000355
P00000365646,ENSP




002,ENST00000376472
00000347102,ENSP0





0000365655









Bcl-2 Inhibitors

As shown in the Examples, Bcl-2 expression is inhibited in the presence of the bromodomain inhibitor (JQ1). Accordingly, certain aspects of the invention contemplate treatment using Bcl-2 inhibitors alone or in combination with Notch pathway inhibitors to treat certain cancers.
Members of the Bcl-2 family control the integrity of the outer mitochondrial membrane (OMM) and thus are involved in determining the susceptibility of cells to apoptosis induced by the intrinsic pathway. The Bcl-2 family comprises anti-apoptotic members, such as Bcl-2, Mcl-1, Bcl-XL, Bcl-w and Bcl-2A1 (Bfl-1/A1), multidomain proapoptotic members, such as Bax and Bak, and proapoptotic BH3-only proteins, including Bad, Bim, Puma, Bid, Bik, Noxa and Bmf.
A Bcl-2 inhibitor is any molecule or compound that can prevent or inhibit the activity, in part or in whole, of Bcl-2 family members (e.g., Bcl-2, Bcl-X, Bcl-w, Mcl-1 or Bcl-2A1). It is to be understood that the activity of Bcl-2 family members may include one or more activities, such as cell survival or apoptosis. Inhibitors of Bcl-2 family members are known in the art. Examples of Bcl-2 inhibitors include, but are not limited to, HA14-1(Tocris Bioscience), BH3I-1 (Sigma-Aldrich), antimycin A (Sigma-Aldrich), chelerythrine (Fermentek), gossypol (NSC19048, NCI—Developmental Therapeutics Program), apogossypol (NSC736630, NCI—Developmental Therapeutics Program), TW-37 (Selleckchem), 4-(3-methoxy-phenylsulfonyl)-7-nitro-benzofurazan-3-oxide (MNB), TM12-06, obatoclax (GX15-070, Cephalon), ABT-737 (Selleckchem) and a related orally-active derivative, ABT-263 (Navitoclax, Genentech), AT-101 (Ascenta Therapeutics), pyrogallol-based molecules (Tang et al. J Med Chem. 2007, 50(8):1723-6), and ABT-199 (Abbott and Genentech).
In some embodiments, a Bcl-2 inhibitor is any molecule or compound that reduces or prevents expression of Bcl-2 family members. Examples of such inhibitors include siRNA, shRNA, dsRNA, oligomimics, and proteases that target one or more Bcl-2 family members. In some embodiments, the Bcl-2 inhibitor is the antisense oligonucleotide drug Genasense (G3139, Genta).
Examples of Bcl-2 family members are shown in Table 4.







TABLE 4







Examples of Bcl-2 family members










Gene
Ensembl gene ID
Ensembl transcript ID
Ensembl protein ID





Bcl-
ENSG00000171791
ENST00000444484,
ENSP00000404214,


2

ENST00000398117,
ENSP00000381185,




ENST00000333681
ENSP00000329623


Bcl-
ENSG00000171552
ENST00000456404,
ENSP00000395545,


X

ENST00000450273,
ENSP00000406203,




ENST00000439267,
ENSP00000389688,




ENST00000434194,
ENSP00000401173,




ENST00000422920,
ENSP00000411252,




ENST00000420653,
ENSP00000405563,




ENST00000420488,
ENSP00000390760,




ENST00000376062,
ENSP00000365230,




ENST00000376055,
ENSP00000365223,




ENST00000307677
ENSP00000302564


Bcl-
ENSG00000129473
ENST00000557579,
ENSP00000452265,


w

ENST00000557236,
ENSP00000451701,




ENST00000556599,
ENSP00000451197,




ENST00000554635,
ENSP00000451234,




ENST00000553824,
ENSP00000451148,




ENST00000250405
ENSP00000250405


Mcl-
ENSG00000143384
ENST00000439749,
ENSP00000411395,


1

ENST00000369026,
ENSP00000358022,




ENST00000307940
ENSP00000309973


Bcl-
ENSG00000140379
ENST00000335661,
ENSP00000335250,


2A1

ENST00000267953
ENSP00000267953









AKT and mTOR Inhibitors

As shown in the Examples, persister cells were found to be sensitive to treatment with an AKT inhibitor or treatment with a mammalian target of rapamycin (mTOR) inhibitor. Accordingly, certain aspects of the invention contemplate treatment using mTOR or AKT inhibitors alone or in combination with Notch pathway inhibitors to treat certain cancers.
An mTOR inhibitor is any molecule or compound that can prevent or inhibit, in part or in whole, the activity of mTOR. It is to be understood that the activity of mTOR may include one or more activities, such as cell growth, cell proliferation, cell motility, cell survival, protein synthesis, or transcription. mTOR gene, mRNA, and protein sequence identifiers are provided in Table 5. Inhibitors of mTOR are known in the art. Examples of mTOR inhibitors include, but are not limited to, rapamycin (sirolimus, Pfizer), temsirolimus (CCI-779, Wyeth), everolimus (Novartis), deforolimus (AP23573, MK-8669, Merck and ARIAD Pharmaceuticals), NVP-BEZ235 (Novartis), BGT226 (Novartis), SF1126 (Semafore Pharmaceuticals), PKI-587 (Selleckchem), PF-04691502 (Selleckchem), INK128 (Intellikine), AZD8055 (Selleckchem), and AZD2014 (AstraZeneca).
In some embodiments, an mTOR inhibitor is any molecule or compound that reduces or prevents expression of mTOR. Examples of such inhibitors include siRNA, shRNA, dsRNA, and oligomimics with complementarity to mTOR mRNA, and proteases that target mTOR protein.
An AKT inhibitor is any molecule or compound that can prevent or inhibit, in part or in whole, the activity of an AKT family member (AKT1, AKT2, or AKT3). It is to be understood that the activity of AKT may include one or more activities, such as glucose metabolism, apoptosis, cell proliferation, transcription and cell migration. AKT family member gene, mRNA, and protein sequence identifiers are provided in Table 5. Inhibitors of AKT are known in the art. Examples of AKT inhibitors include, but are not limited to, MK-2206 (Selleckchem), GDC-0068 (Genetech), Perifosine (Selleckchem), GSK690693 (Selleckchem), AT7867 (Selleckchem), CCT128930 (Selleckchem), PF-04691502 (Selleckchem), INK128 (Selleckchem), RX-0201 (Rexahn Pharmaceuticals), PBI-05204 (Phoenix Biotechnology, Inc.), GSK2141795 (GlaxoSmithKline), Erucylphosphocholine (ErPC, AEterna Zentaris Inc.), and XL-418 (Exelixis).
In some embodiments, an AKT inhibitor is any molecule or compound that reduces or prevents expression of an AKT family member (AKT1, AKT2, or AKT3). Examples of such inhibitors include siRNA, shRNA, dsRNA, oligomimics, and proteases that target AKT.







TABLE 5







mTOR and AKT family members










Gene
Ensembl gene ID
Ensembl transcript ID
Ensembl protein ID





FRAP1/
ENSG00000198793
ENST00000361445,
ENSP00000354558,


mTOR

ENST00000376838,
ENSP00000366034,




ENST00000455339,
ENSP00000398745




ENST00000495435,





ENST00000476768,





ENST00000490931,





ENST00000473471



AKT1
ENSG00000142208
ENST00000349310,
ENSP00000270202,




ENST00000407796,
ENSP00000384293,




ENST00000402615,
ENSP00000385326,




ENST00000554848,
ENSP00000451166,




ENST00000554581,
ENSP00000451828,




ENST00000555528,
ENSP00000450688,




ENST00000544168,
ENSP00000443897,




ENST00000554192,
ENSP00000450681,




ENST00000555380,
ENSP00000451290,




ENST00000555926,
ENSP00000451824,




ENST00000555458,
ENSP00000451470




ENST00000553797,





ENST00000557494,





ENST00000554585,





ENST00000557552,





ENST00000553506,





ENST00000556836,





ENST00000554826



AKT2
ENSG00000105221
ENST00000392038,
ENSP00000375892,




ENST00000452077,
ENSP00000404083,




ENST00000456441,
ENSP00000396532,




ENST00000423127,
ENSP00000403842,




ENST00000416994,
ENSP00000392458,




ENST00000416362,
ENSP00000407999,




ENST00000427375,
ENSP00000403890,




ENST00000441941,
ENSP00000396968,




ENST00000392037,
ENSP00000375891,




ENST00000497948,
ENSP00000472382,




ENST00000579047,
ENSP00000471369,




ENST00000311278,
ENSP00000309428,




ENST00000578123,
ENSP00000462022,




ENST00000583859,
ENSP00000462715,




ENST00000580747,
ENSP00000463806,




ENST00000486368,
ENSP00000463686,




ENST00000578615,
ENSP00000463262,




ENST00000578310,
ENSP00000462919,




ENST00000476247,
ENSP00000463368,




ENST00000358335,
ENSP00000351095,




ENST00000596634,
ENSP00000470604,




ENST00000424901,
ENSP00000399532,




ENST00000492463,
ENSP00000462776,




ENST00000489375,
ENSP00000470822,




ENST00000584288,
ENSP00000462469,




ENST00000391844,
ENSP00000375719,




ENST00000491778,
ENSP00000463086,




ENST00000601166,
ENSP00000472371




ENST00000498350,





ENST00000391845,





ENST00000486647,





ENST00000581582,





ENST00000480878,





ENST00000476266,





ENST00000483166,





ENST00000487537,





ENST00000537834,





ENST00000496089,





ENST00000580878,





ENST00000579345,





ENST00000578282,





ENST00000578975



AKT3
ENSG00000117020
ENST00000366539,
ENSP00000355497,




ENST00000336199,
ENSP00000336943,




ENST00000366540,
ENSP00000355498,




ENST00000552631,
ENSP00000447820,




ENST00000263826,
ENSP00000263826




ENST00000463991,





ENST00000490018,





ENST00000491219,





ENST00000492957,





ENST00000550388









Treatment Methods

The invention provides methods of treatment of a patient having cancer. In some embodiments, the patient is identified as one who has cancer associated with or characterized by a Notch pathway activation mutation. The methods may comprise administration of one or more BRD inhibitors in the absence of a second therapy.
Other methods of the invention comprise administration of a first inhibitor and a second inhibitor. The designation of “first” and “second” inhibitors is used to distinguish between the two and is not intended to refer to a temporal order of administration of the inhibitors.
The first inhibitor may be a bromodomain inhibitor. The bromodomain inhibitor may target the gene, mRNA expression, protein expression, and/or activity of any member of the bromodomain family, in all instances reducing the level and/or activity of one or more bromodomain-containing proteins (e.g., Brd1, Brd2, Brd3, Brd4, Brd7, or BrdT). Inhibitors may be nucleic acids such as DNA and RNA aptamers, antisense oligonucleotides, siRNA and shRNA, small peptides, antibodies or antibody fragments, and small molecules such as small chemical compounds. The bromodomain inhibitor may be a pan-bromodomain inhibitor or a selective bromodomain inhibitor.
In some embodiments, the first inhibitor may be a BET inhibitor. The BET inhibitor may target the gene, mRNA expression, protein expression, and/or activity of any member of the BET family, in all instances reducing the level and/or activity of one or more BET (e.g., Brd1, Brd2, Brd3, Brd4, Brd7, or BrdT). Inhibitors may be nucleic acids such as DNA and RNA aptamers, antisense oligonucleotides, siRNA and shRNA, small peptides, antibodies or antibody fragments, and small molecules such as small chemical compounds.
The BET inhibitor may be a pan-BET inhibitor or a selective BET inhibitor. BET inhibitors include but are not limited to, RVX-208, PFI-1, OTX015, GSK525762A, JQ1 and Formulas I-XXII and any other compounds as outlined in herein. In some embodiments, the BET inhibitor is JQ1.
The first inhibitor may be a Bcl-2 inhibitor. The Bcl-2 inhibitor may target the gene, mRNA expression, protein expression, and/or activity of any member of the Bcl-2 family, in all instances reducing the level and/or activity of one or more Bcl-2 family member (e.g. Bcl-2, Bcl-X, Bcl-w, Mcl-1 or Bcl-2A1). Inhibitors may be nucleic acids such as DNA and RNA aptamers, antisense oligonucleotides, siRNA and shRNA, small peptides, antibodies or antibody fragments, and small molecules such as small chemical compounds.
The Bcl-2 inhibitor may be a pan-Bcl-2 inhibitor or a selective Bcl-2 inhibitor. In some embodiments, the Bcl-2 inhibitor selectively inhibits one or more of: Bcl-2, Bcl-X, Bcl-w, Mcl-1 or Bcl-2A1. Examples of pan- and selective-Bcl-2 inhibitors include but are not limited to HA14-1, BH3I-1, antimycin A, chelerythrine, gossypol (NSC19048), apogossypol (NSC736630), TW-37, 4-(3-methoxy-phenylsulfonyl)-7-nitro-benzofurazan-3-oxide (MNB), TM12-06, obatoclax (GX15-070), ABT-737, ABT-263, AT-101, pyrogallol-based molecules, ABT-199, and Genasense (G3139).
In some embodiments, the first inhibitor may be an AKT or mTOR inhibitor. In some embodiments, an AKT inhibitor and mTOR inhibitor may be administered together.
The second inhibitor may be an inhibitor of the Notch signaling pathway. It is to be understood that the inhibitor can act on any part of the Notch signaling pathway as described herein. The Notch pathway inhibitor may target a gene, mRNA expression, protein expression, and/or activity in the Notch pathway or associated with the Notch pathway, in all instances reducing the level and/or activity of the Notch signaling pathway. Inhibitors may be nucleic acids such as DNA and RNA aptamers, antisense oligonucleotides, siRNA and shRNA, small peptides, antibodies or antibody fragments, and small molecules such as small chemical compounds.
In some embodiments, the Notch pathway inhibitor is a gamma secretase inhibitor (GSI). In some embodiments the GSI is DBZ, BMS-906024, RO4929097, LY450139, BMS-708163, MK-0752, PF-03084014, IL-X, z-Leu-leu-Nle-CHO, or N—[N-(3,5-difluorophenacetyl)-L-alanyl]-Sphenylglycine t-butyl ester (DAPT). Other Notch pathway inhibitors are provided herein such as in but not limited to LBH589 (Panobinostat), MEDI0639, Choline magnesium trisalicylate (e.g., Trilisate), or Curcumin (a curcuminoid of turmeric).
In some embodiments, the invention contemplates the use of a BRD inhibitor, a Notch pathway inhibitor, and a Bcl-2 inhibitor.
Other aspects of the invention provide methods for treating subjects with cancer with an inhibitor of one or more chromatin regulatory proteins selected from ARID3B, EZH2, PRMT2, SND1, BRD1, SUV39H1, PRMT5, SS18, BRD4, KDM5D, PRMT7, STAG3L1, CD2BP2, MLL5, SUDS3, CHD1, MINA, CHD8, MORF4L1, or CHRAC1. In some embodiments, the one or more chromatin regulatory proteins are selected from BRD4 or PRMT7.
When two or more inhibitors or agents are administered to a subject, these can be administered simultaneously (e.g., where they are pre-mixed and administered together), substantially simultaneously (e.g., where they are administered one after another in the time it would take a medical practitioner to administer two agents to a subject), or sequentially with a period of time lapsing between the inhibitor administrations. The two or more inhibitors can also be administered by the same route or by a different route. For example, the inhibitors may be all administered by injection (e.g., intravenous injection) or orally. As another example, one inhibitor may be administered by injection and another may be administered orally.
The term “treat”, “treated,” “treating” or “treatment” is used herein to mean to relieve, reduce or alleviate at least one symptom of a disease such as cancer in a subject. For example, treatment can be diminishment of one or several symptoms of a disorder or complete eradication of a disorder, such as cancer. Within the meaning of the present invention, the term “treat” also denotes to arrest, delay the onset (i.e., the period prior to clinical manifestation of a disease) and/or reduce the risk of developing or worsening a disease. The term “protect” is used herein to mean prevent delay or treat, or all, as appropriate, development or continuance or aggravation of a disease in a subject. Within the meaning of the present invention, the disease is typically a cancer.
The term “effective amount” is used herein to mean the amount of an agent or inhibitor required to ameliorate the symptoms of a disease relative to an untreated patient. The effective amount of active compound(s) used to practice the present invention for therapeutic treatment of a disease varies depending upon the manner of administration, the age, body weight, and general health of the subject. Ultimately, the attending physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an “effective” amount.
Where two or more inhibitors are administered to the subject, the effective amount may be a combined effective amount. The effective amount of a first inhibitor may be different when it is used with a second and optionally a third inhibitor. When two more inhibitors are used together, the effective amounts of each may be the same as when they are used alone. Alternatively, the effective amounts of each may be less than the effective amounts when they are used alone because the desired effect is achieved at lower doses. Alternatively, again, the effective amount of each may be greater than the effective amounts when they are used alone because the subject is better able to tolerate one or more of the inhibitors which can then be administered at a higher dose provided such higher dose provides more therapeutic benefit.
Subjects
The term “subject” or “patient” is intended to include humans and animals that are capable of suffering from or afflicted with a cancer or any disorder involving, directly or indirectly, a cancer. Examples of subjects include mammals, e.g., humans, dogs, cows, horses, pigs, sheep, goats, cats, mice, rabbits, rats, and transgenic non-human animals. In some embodiments, subjects include companion animals, e.g. dogs, cats, rabbits, and rats. In some embodiments, subjects include livestock, e.g., cows, pigs, sheep, goats, and rabbits. In some embodiments, subjects include Thoroughbred or show animals, e.g. horses, pigs, cows, and rabbits. In important embodiments, the subject is a human, e.g., a human having, at risk of having, or potentially capable of having cancer.
Cancer
The term “cancer” is used herein to mean malignant solid tumors as well as hematological malignancies. Examples of cancer include but are not limited to leukemias, lymphomas, myelomas, carcinomas, metastatic carcinomas, sarcomas, adenomas, nervous system cancers and genito-urinary cancers. In certain embodiments, the cancer is acute lymphoblastic leukemia. In other embodiments, the foregoing methods are useful in treating adult and pediatric acute lymphoblastic leukemia, acute myeloid leukemia, adrenocortical carcinoma, AIDS-related cancers, anal cancer, cancer of the appendix, astrocytoma, basal cell carcinoma, bile duct cancer, bladder cancer, bone cancer, osteosarcoma, fibrous histiocytoma, brain cancer, brain stem glioma, cerebellar astrocytoma, malignant glioma, ependymoma, medulloblastoma, supratentorial primitive neuroectodermal tumors, hypothalamic glioma, breast cancer, male breast cancer, bronchial adenomas, Burkitt lymphoma, carcinoid tumor, carcinoma of unknown origin, central nervous system lymphoma, cerebellar astrocytoma, malignant glioma, cervical cancer, childhood cancers, chronic lymphocytic leukemia, chronic myelogenous leukemia, chronic myeloproliferative disorders, colorectal cancer, cutaneous T-cell lymphoma, endometrial cancer, ependymoma, esophageal cancer, Ewing family tumors, extracranial germ cell tumor, extragonadal germ cell tumor, extrahepatic bile duct cancer, intraocular melanoma, retinoblastoma, gallbladder cancer, gastric cancer, gastrointestinal stromal tumor, extracranial germ cell tumor, extragonadal germ cell tumor, ovarian germ cell tumor, gestational trophoblastic tumor, glioma, hairy cell leukemia, head and neck cancer, hepatocellular cancer, Hodgkin lymphoma, non-Hodgkin lymphoma, hypopharyngeal cancer, hypothalamic and visual pathway glioma, intraocular melanoma, islet cell tumors, Kaposi sarcoma, kidney cancer, renal cell cancer, laryngeal cancer, lip and oral cavity cancer, small cell lung cancer, non-small cell lung cancer, primary central nervous system lymphoma, Waldenstrom macroglobulinema, malignant fibrous histiocytoma, medulloblastoma, melanoma, Merkel cell carcinoma, malignant mesothelioma, squamous neck cancer, multiple endocrine neoplasia syndrome, multiple myeloma, mycosis fungoides, myelodysplastic syndromes, myeloproliferative disorders, chronic myeloproliferative disorders, nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, neuroblastoma, oropharyngeal cancer, ovarian cancer, pancreatic cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pheochromocytoma, pineoblastoma and supratentorial primitive neuroectodermal tumors, pituitary cancer, plasma cell neoplasms, pleuropulmonary blastoma, prostate cancer, rectal cancer, rhabdomyosarcoma, salivary gland cancer, soft tissue sarcoma, uterine sarcoma, Sezary syndrome, non-melanoma skin cancer, small intestine cancer, squamous cell carcinoma, squamous neck cancer, supratentorial primitive neuroectodermal tumors, testicular cancer, throat cancer, thymoma and thymic carcinoma, thyroid cancer, transitional cell cancer, trophoblastic tumors, urethral cancer, uterine cancer, uterine sarcoma, vaginal cancer, vulvar cancer, and Wilms tumor.
In some embodiments, the cancer is a resistant to a Notch pathway inhibitor. A cancer that is resistant to a Notch pathway inhibitor means that the cancer does not respond to such inhibitor, for example as evidenced by continued proliferation and increasing tumor growth and burden. In some instances, the cancer may have initially responded to treatment with such inhibitor (referred to herein as a previously administered therapy) but may have grown resistant after a time. In some instances, the cancer may have never responded to treatment with such inhibitor at all.
Notch Pathway Activation Mutations
In some embodiments, the cancer is associated with or is characterized by a Notch pathway activation mutation. A cancer that is associated with or is characterized by a Notch pathway activation mutation is a cancer that carries such a mutation, as detected by any number of diagnostic assays and methods including fluorescence in situ hybridization (FISH), genomic sequencing, whole exome sequencing, whole genome sequencing, and the like. For example, a mutation in the Notch1 gene can be detected by Notch1 exon sequencing which can be done using a variety of methods as described above including, for example Sanger sequencing. In some embodiments, tumorigenesis, tumor progression, and/or metastasis is increased or enhanced by a Notch pathway activation mutation. Such tumorigenesis, tumor progression and/or metastasis processes that may be increased or enhanced by a Notch pathway activation mutation include, but is not limited to: the epithelial-to-mesenchymal transition (EMT), angiogenesis, and bone metastasis (Sethi et al. British Journal of Cancer, 105; 1805-1810, 2011). In some embodiments, the cancer is sensitive to a Notch pathway inhibitor.
The term “Notch pathway” as used herein encompasses Notch, Notch ligands, and upstream and downstream effectors of the Notch signaling pathway. The term “activation mutation” as used herein refers to mutations (e.g. a mutation in the coding region of a downstream effector of the Notch pathway or chromosomal translocation, point mutations, and chromosomal amplification at the Notch receptor loci) or epigenetic modifications within Notch, Notch ligands, upstream and/or downstream effectors of the Notch pathway.
Examples of cancers that are associated with a Notch pathway activation mutation, are characterized by a Notch pathway activation mutation, or are sensitive to a Notch pathway inhibitor include, but are not limited to: hematological tumors, T-cell acute lymphoblastic leukemia, B-cell malignancies, breast cancer, gut cancer, skin cancer, keratinocyte-derived carcinoma, melanocyte-derived carcinoma, primary melanoma, basal cell carcinoma, squamous cell carcinoma, cervical cancer, prostate cancer, non-small cell lung adenocarcinoma, ovarian carcinoma, medulloblastoma, Kaposi's sarcoma, pancreatic cancer, colorectal cancer, and glioma (see, e.g., Bolós et. al., Notch Signaling in Development and Cancer, Endocrine Reviews, 28(3):339-363, 2007; Sethi et al., British Journal of Cancer, 105; 1805-1810, 2011). In some embodiments, the cancer that has or is characterized by a Notch pathway activation mutation is acute lymphoblastic leukemia. In certain embodiments, the cancer that has or is characterized by a Notch pathway activation mutation is T-cell acute lymphoblastic leukemia.
Other cancers associated with or are characterized by a Notch pathway activation mutation may be identified by detecting mutations or epigenetic modifications within Notch, Notch ligands, upstream and/or downstream effectors of the Notch pathway using methods well known in the art (e.g., genomic and/or proteomic means to identify regions or factors that affect the expression of any gene within the Notch pathway).
Pharmaceutical Formulations, Administration and Dosages
Provided herein are pharmaceutical formulations comprising single agents, such as bromodomain inhibitors and/or pharmacologically active metabolites, salts, solvates and racemates thereof, or a combination of agents which can be, for example, a combination of two types of agents comprising: (1) a bromodomain inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof and (2) Notch pathway inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof.
In another embodiment, the combination of agents comprises (1) a Bcl-2 inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof and (2) Notch pathway inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof. In still another embodiment, the combination of agents comprises (1) a bromodomain inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof, (2) a Bcl-2 inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof and (3) Notch pathway inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof.
In another embodiment, the combination of agents comprises (1) an MTOR inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof and (2) a Notch pathway inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof.
In another embodiment, the combination of agents comprises (1) an AKT inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof and (2) Notch pathway inhibitor and/or pharmacologically active metabolites, salts, solvates and racemates thereof.
For therapeutic uses, the inhibitors described herein may be administered systemically, for example, formulated in a pharmaceutically-acceptable buffer such as physiological saline. Preferable routes of administration include, for example, subcutaneous, intravenous, intraperitoneally, intramuscular, or intradermal injections that provide continuous, sustained levels of the drug in the subject.
Treatment of human patients or other animals will be carried out using a therapeutically effective amount of a therapeutic identified herein in a physiologically-acceptable carrier. Suitable carriers and their formulation are described, for example, in Remington's Pharmaceutical Sciences by E. W. Martin. The amount of the therapeutic agent to be administered varies depending upon the manner of administration, the age and body weight of the patient, and with the clinical symptoms of the cancer. Generally, amounts will be in the range of those used for other agents used in the treatment of other diseases associated with such diseases or states, although in certain instances lower amounts will be needed because of the increased specificity of the compound. A compound is administered at a dosage that is cytotoxic to a neoplastic cell, that reduces the biological activity of a bromodomain, Notch pathway, or Bcl-2 family member, or that reduces the proliferation, survival, or invasiveness of a neoplastic cell as determined by a method known to one skilled in the art
Human dosage amounts can initially be determined by extrapolating from the amount of compound used in mice, as a skilled artisan recognizes it is routine in the art to modify the dosage for humans compared to animal models. In certain embodiments it is envisioned that the dosage may vary from between about 1 μg compound/Kg body weight to about 5000 mg compound/Kg body weight; or from about 5 mg/Kg body weight to about 4000 mg/Kg body weight or from about 10 mg/Kg body weight to about 3000 mg/Kg body weight; or from about 50 mg/Kg body weight to about 2000 mg/Kg body weight; or from about 100 mg/Kg body weight to about 1000 mg/Kg body weight; or from about 150 mg/Kg body weight to about 500 mg/Kg body weight. In other embodiments this dose may be about 1, 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, 2000, 2500, 3000, 3500, 4000, 4500, or 5000 mg/Kg body weight. In other embodiments, it is envisaged that doses may be in the range of about 5 mg compound/Kg body to about 20 mg compound/Kg body. In other embodiments the doses may be about 8, 10, 12, 14, 16 or 18 mg/Kg body weight. Of course, this dosage amount may be adjusted upward or downward, as is routinely done in such treatment protocols, depending on the results of the initial clinical trials and the needs of a particular patient.
The formulation of a compound for the treatment of a cancer may be by any suitable means that results in a concentration of the therapeutic that, combined with other components, is effective in ameliorating, reducing, or stabilizing cancer. The compound may be contained in any appropriate amount in any suitable carrier substance, and is generally present in an amount of 1-95% by weight of the total weight of the composition. The composition may be provided in a dosage form that is suitable for parenteral (e.g., subcutaneously, intravenously, intramuscularly, or intraperitoneally) administration route. The pharmaceutical compositions may be formulated according to conventional pharmaceutical practice (see, e.g., Remington: The Science and Practice of Pharmacy (20th ed.), ed. A. R. Gennaro, Lippincott Williams & Wilkins, 2000 and Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York).
Pharmaceutical compositions according to the invention may be formulated to release the active compound substantially immediately upon administration or at any predetermined time or time period after administration. The latter types of compositions are generally known as controlled release formulations, which include (i) formulations that create a substantially constant concentration of the drug within the body over an extended period of time; (ii) formulations that after a predetermined lag time create a substantially constant concentration of the drug within the body over an extended period of time; (iii) formulations that sustain action during a predetermined time period by maintaining a relatively, constant, effective level in the body with concomitant minimization of undesirable side effects associated with fluctuations in the plasma level of the active substance (sawtooth kinetic pattern); (iv) formulations that localize action by, e.g., spatial placement of a controlled release composition adjacent to or in contact with the thymus; (v) formulations that allow for convenient dosing, such that doses are administered, for example, once every one or two weeks; and (vi) formulations that target a neoplasia or inflammatory disease by using carriers or chemical derivatives to deliver the therapeutic agent to a particular cell type (e.g., neoplastic cell). For some applications, controlled release formulations obviate the need for frequent dosing during the day to sustain the plasma level at a therapeutic level.
Any of a number of strategies can be pursued in order to obtain controlled release in which the rate of release outweighs the rate of metabolism of the compound in question. In one example, controlled release is obtained by appropriate selection of various formulation parameters and ingredients, including, e.g., various types of controlled release compositions and coatings. Thus, the therapeutic is formulated with appropriate excipients into a pharmaceutical composition that, upon administration, releases the therapeutic in a controlled manner. Examples include single or multiple unit tablet or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, molecular complexes, nanoparticles, patches, and liposomes.
Parenteral Compositions
The pharmaceutical composition may be administered parenterally by injection, infusion or implantation (subcutaneous, intravenous, intramuscular, intraperitoneal, or the like) in dosage forms, formulations, or via suitable delivery devices or implants containing conventional, non-toxic pharmaceutically acceptable carriers and adjuvants. The formulation and preparation of such compositions are well known to those skilled in the art of pharmaceutical formulation. Formulations can be found in Remington: The Science and Practice of Pharmacy, supra. Compositions for parenteral use may be provided in unit dosage forms (e.g., in single-dose ampoules), or in vials containing several doses and in which a suitable preservative may be added (see below). The composition may be in the form of a solution, a suspension, an emulsion, an infusion device, or a delivery device for implantation, or it may be presented as a dry powder to be reconstituted with water or another suitable vehicle before use. Apart from the active agent that reduces or ameliorates cancer, the composition may include suitable parenterally acceptable carriers and/or excipients. The active therapeutic agent(s) may be incorporated into microspheres, microcapsules, nanoparticles, liposomes, or the like for controlled release. Furthermore, the composition may include suspending, solubilizing, stabilizing, pH-adjusting agents, tonicity adjusting agents, and/or dispersing, agents.
As indicated above, the pharmaceutical compositions according to the invention may be in the form suitable for sterile injection. To prepare such a composition, the suitable active anticancer therapeutic(s) are dissolved or suspended in a parenterally acceptable liquid vehicle. Among acceptable vehicles and solvents that may be employed are water, water adjusted to a suitable pH by addition of an appropriate amount of hydrochloric acid, sodium hydroxide or a suitable buffer, 1,3-butanediol, Ringer's solution, and isotonic sodium chloride solution and dextrose solution. The aqueous formulation may also contain one or more preservatives (e.g., methyl, ethyl or n-propyl p-hydroxybenzoate). In cases where one of the compounds is only sparingly or slightly soluble in water, a dissolution enhancing or solubilizing agent can be added, or the solvent may include 10-60% w/w of propylene glycol or the like.
Controlled Release Parenteral Compositions
Controlled release parenteral compositions may be in form of aqueous suspensions, microspheres, microcapsules, magnetic microspheres, oil solutions, oil suspensions, or emulsions. Alternatively, the active drug may be incorporated in biocompatible carriers, liposomes, nanoparticles, implants, or infusion devices.
Materials for use in the preparation of microspheres and/or microcapsules are, e.g., biodegradable/bioerodible polymers such as polygalactia poly-(isobutyl cyanoacrylate), poly(2-hydroxyethyl-L-glutaminine) and, poly(lactic acid).
Biocompatible carriers that may be used when formulating a controlled release parenteral formulation are carbohydrates (e.g., dextrans), proteins (e.g., albumin), lipoproteins, or antibodies. Materials for use in implants can be non-biodegradable (e.g., polydimethyl siloxane) or biodegradable (e.g., poly(caprolactone), poly(lactic acid), poly(glycolic acid) or poly(ortho esters) or combinations thereof).
Solid Dosage Forms for Oral Use
Formulations for oral use include tablets containing the active ingredient(s) in a mixture with non-toxic pharmaceutically acceptable excipients. Such formulations are known to the skilled artisan. Excipients may be, for example, inert diluents or fillers (e.g., sucrose, sorbitol, sugar, mannitol, microcrystalline cellulose, starches including potato starch, calcium carbonate, sodium chloride, lactose, calcium phosphate, calcium sulfate, or sodium phosphate); granulating and disintegrating agents (e.g., cellulose derivatives including microcrystalline cellulose, starches including potato starch, croscarmellose sodium, alginates, or alginic acid); binding agents (e.g., sucrose, glucose, sorbitol, acacia, alginic acid, sodium alginate, gelatin, starch, pregelatinized starch, microcrystalline cellulose, magnesium aluminum silicate, carboxymethylcellulose sodium, methylcellulose, hydroxypropyl methylcellulose, ethylcellulose, polyvinylpyrrolidone, or polyethylene glycol); and lubricating agents, glidants, and antiadhesives (e.g., magnesium stearate, zinc stearate, stearic acid, silicas, hydrogenated vegetable oils, or talc). Other pharmaceutically acceptable excipients can be colorants, flavoring agents, plasticizers, humectants, buffering agents, and the like.
The tablets may be uncoated or they may be coated by known techniques, optionally to delay disintegration and absorption in the gastrointestinal tract and thereby providing a sustained action over a longer period. The coating may be adapted to release the active drug in a predetermined pattern (e.g., in order to achieve a controlled release formulation) or it may be adapted not to release the active drug until after passage of the stomach (enteric coating). The coating may be a sugar coating, a film coating (e.g., based on hydroxypropyl methylcellulose, methylcellulose, methyl hydroxyethylcellulose, hydroxypropylcellulose, carboxymethylcellulose, acrylate copolymers, polyethylene glycols and/or polyvinylpyrrolidone), or an enteric coating (e.g., based on methacrylic acid copolymer, cellulose acetate phthalate, hydroxypropyl methylcellulose phthalate, hydroxypropyl methylcellulose acetate succinate, polyvinyl acetate phthalate, shellac, and/or ethylcellulose). Furthermore, a time delay material, such as, e.g., glyceryl monostearate or glyceryl distearate may be employed.
The solid tablet compositions may include a coating adapted to protect the composition from unwanted chemical changes, (e.g., chemical degradation prior to the release of the active therapeutic substance). The coating may be applied on the solid dosage form in a similar manner as that described in Encyclopedia of Pharmaceutical Technology, supra.
At least two therapeutics may be mixed together in the tablet, or may be partitioned. In one example, the first active anti-neoplasia therapeutic is contained on the inside of the tablet, and the second active therapeutic is on the outside, such that a substantial portion of the second therapeutic is released prior to the release of the first therapeutic.
Formulations for oral use may also be presented as chewable tablets, or as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent (e.g., potato starch, lactose, microcrystalline cellulose, calcium carbonate, calcium phosphate or kaolin), or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example, peanut oil, liquid paraffin, or olive oil. Powders and granulates may be prepared using the ingredients mentioned above under tablets and capsules in a conventional manner using, e.g., a mixer, a fluid bed apparatus or a spray drying equipment.
Controlled Release Oral Dosage Forms
Controlled release compositions for oral use may, e.g., be constructed to release the active anti-neoplasia or anti-inflammatory therapeutic by controlling the dissolution and/or the diffusion of the active substance. Dissolution or diffusion controlled release can be achieved by appropriate coating of a tablet, capsule, pellet, or granulate formulation of compounds, or by incorporating the compound into an appropriate matrix. A controlled release coating may include one or more of the coating substances mentioned above and/or, e.g., shellac, beeswax, glycowax, castor wax, carnauba wax, stearyl alcohol, glyceryl monostearate, glyceryl distearate, glycerol palmitostearate, ethylcellulose, acrylic resins, dl-polylactic acid, cellulose acetate butyrate, polyvinyl chloride, polyvinyl acetate, vinyl pyrrolidone, polyethylene, polymethacrylate, methylmethacrylate, 2-hydroxymethacrylate, methacrylate hydrogels, 1,3 butylene glycol, ethylene glycol methacrylate, and/or polyethylene glycols. In a controlled release matrix formulation, the matrix material may also include, e.g., hydrated metylcellulose, carnauba wax and stearyl alcohol, carbopol 934, silicone, glyceryl tristearate, methyl acrylate-methyl methacrylate, polyvinyl chloride, polyethylene, and/or halogenated fluorocarbon.
A controlled release composition containing one or more therapeutic compounds may also be in the form of a buoyant tablet or capsule (i.e., a tablet or capsule that, upon oral administration, floats on top of the gastric content for a certain period of time). A buoyant tablet formulation of the compound(s) can be prepared by granulating a mixture of the compound(s) with excipients and 20-75% w/w of hydrocolloids, such as hydroxyethylcellulose, hydroxypropylcellulose, or hydroxypropylmethylcellulose. The obtained granules can then be compressed into tablets. On contact with the gastric juice, the tablet forms a substantially water-impermeable gel barrier around its surface. This gel barrier takes part in maintaining a density of less than one, thereby allowing the tablet to remain buoyant in the gastric juice.
Combination Therapies
Optionally, one or more inhibitors of the invention may be administered in combination with any other standard anti-cancer therapy known in the art; such methods are known to the skilled artisan and described in Remington's Pharmaceutical Sciences by E. W. Martin. If desired, agents of the invention (e.g., bromodomain inhibitors, Notch pathway inhibitors, and Bcl-2 inhibitors) are administered in combination with any conventional cancer therapy, including but not limited to, surgery, radiation therapy, or chemotherapy.
In preferred embodiments, a compound of the invention is administered in combination with an epigenetic or transcriptional modulator (e.g., DNA methyltransferase inhibitor, histone deacetylase inhibitor (HDAC inhibitor), lysine methyltransferase inhibitor), with antimitotic drugs (e.g., taxanes, vinca alkaloids), hormone receptor modulators (e.g., estrogen receptor modulators, androgen receptor modulators), cell signaling pathway inhibitors (e.g., tyrosine kinase inhibitors), modulators of protein stability (proteasome inhibitors), hsp90 inhibitors, conventional chemotherapeutics, glucocorticoids, all-trans retinoic acid or other agents that promote differentiation.
Diagnostic/Prognostic Methods
In one aspect, the invention provides methods of detecting the presence of one or more predictive, diagnostic or prognostic markers in a sample (e.g., a biological sample from a cancer patient). A variety of screening methods known to one of skill in the art may be used to detect the presence and the level of the marker in the sample including DNA, RNA and protein detection. The techniques described herein can be used to determine the presence or absence of a target in a sample obtained from a patient.
Identification of one or more markers (including identification of elevated levels of one or more markers) in a patient assists a physician or other medical professional in determining a treatment protocol for the patient. For example, in a patient having one or more markers, the physician may treat the patient with a combination therapy as described in more detail above.
Detection Methods
The methods invention may be protein or mRNA based. Examples of protein-based assays include immunoassays (also referred to herein as immune-based assays), Western blots, Western immunoblotting, multiplex bead-based assays, and assays involving aptamers (such as SOMAmerTM technology) and related affinity agents. Examples of mRNA-based assays include Northern analysis, quantitative RT-PCR, microarray hybridization, RNA sequencing, and multiplex bead-based assays. These assays are well known in the art and generally and commonly detect and measure the level of the marker of interest. The level of the marker may then be compared to a control level. The control level may be a level of the same marker in a control tissue, control subject, or a population of control subjects. The “control” may be (or may be derived from) a normal subject (or normal subjects). Normal may refer to a subject that is apparently cancer-free. It is to be understood however that the methods provided herein do not require that a control level be measured every time a subject is tested. Rather, it is contemplated that control levels of markers are obtained and recorded and that any test level is compared to such a pre-determined level. Such pre-determined control levels may also be referred to herein as pre-determined threshold levels.
Chromatin Compaction
In some aspects, the invention relates to methods for diagnosing a subject in need of treatment with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor. In some embodiments, the method comprises measuring the global level of chromatin compaction. Chromatin compaction can be measured, for example, (a) by partial micrococcal nuclease (MNase) or DNase digestion, (b) by increased expression of heterochromatin associated proteins, such as HP1 alpha, beta and/or gamma, (c) by measuring nucleus size, (d) by decreased expression of DTX1, HES4, and/or CD1d and/or by increased expression of ETS1, ETV6, Runx1, CD52, MYC or Bcl-2, and/or (d) by measuring increased levels of repressive chromatin markers such as H3K27me3, H3K9me2/3 and/or decreased levels of other chromatin markers such as H3K27Ac.
In some embodiments, the method comprises measuring nucleus size, nucleosomal repeat length, or cell size in a sample. The nucleus or cell size may be the nucleus or cell diameter or the nucleus or cell volume. Methods for measuring nucleus size are known in the art and may involve staining nuclei (e.g. with DAPI), fluorescently labeling nuclei (e.g. with green fluorescent protein), or May-Grunwald giemsa staining (particularly for hematopoietic cells). Methods for measuring cell size are known in the art and may involve forward and side scatter analysis using fluorescent activated cell sorting (FACS). Methods for measuring nucleosomal repeat length are known in the art and may involve a micrococcal nuclease (MNase) digestion assay. In some embodiments, a decreased nucleus size or cell size, or an increased nucleosomal repeat length, in a tumor sample compared to a control identifies a subject to be treated with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor.
In some embodiments the methods for diagnosing comprise measuring the expression level of HPI-alpha, beta, or gamma. The expression level may be an mRNA level or a protein level. Methods for measuring mRNA and protein levels in a cell population are known in the art. In some embodiments, an increased HPI level in a tumor sample compared to a control identifies a subject to be treated with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor.
In some embodiments, the methods for diagnosing comprise measuring expression levels of at least one chromatin state biomarker (CSB). The CSB may be selected from NPM1, NARG1, RCC1, SSRP1, PRMT3, SAP30, CBX6, CHMP2B, UBE2M, WDR77, HMGB1, CARM1, USP13, HDAC4, COQ3, SET, GATAD2A, PRMT6, HMG20B, DNMT1, ADA, SS18, UBE3A, ZMYND11, NOC2LL, UTX, SIN3A, SAP30L, FLJ20309, RCOR2, ARID5A, UBE2Q2, TRIM24, BAZ2B, SMYD3, EZH2, PHF1, PHF2, BCR, SMARCD3, BMI1, CHD6, FBXL11, SIRT7, ASF1A, RCOR3, CBX4, EPC1, BRD1, and BNF11.
In some embodiments, decreased levels in a tumor sample of a CSB from the group consisting of NPM1, NARG1, RCC1, SSRP1, PRMT3, SAP30, CBX6, CHMP2B, UBE2M, WDR77, HMGB1, CARM1, USP13, HDAC4, COQ3, SET, GATAD2A, PRMT6, HMG20B, DNMT1, ADA, SS18, UBE3A, ZMYND11, and/or NOC2LL (“Group I CSB”) compared to a control identifies a subject to be treated with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor.
In some embodiments, increased levels in a tumor sample of a CSB from the group consisting of UTX, SIN3A, SAP30L, FLJ20309, RCOR2, ARID5A, UBE2Q2, TRIM24, BAZ2B, SMYD3, EZH2, PHF1, PHF2, BCR, SMARCD3, BMI1, CHD6, FBXL11, SIRT7, ASF1A, RCOR3, CBX4, EPC1, BRD1, and/or BNF11 (“Group II CSB”) compared to a control identifies a subject to be treated with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor.
In some embodiments, more than one CSB expression level is measured. The more than one CSB may be chosen from Group I, Group II, or both Group I and Group II.
Chromatin state biomarkers of the invention include those in Table 6.







TABLE 6







Chromatin state biomarkers










Gene
Ensembl gene ID
Ensembl transcript ID
Ensembl protein ID





NPM1
ENSG00000181163
ENST00000523622,
ENSP00000428647,




ENST00000521672,
ENSP00000429485,




ENST00000517671,
ENSP00000428755,




ENST00000393820,
ENSP00000377408,




ENST00000351986,
ENSP00000341168,




ENST00000296930
ENSP00000296930


NARG1
ENSG00000164134
ENST00000544077,
ENSP00000443524,




ENST00000515576,
ENSP00000421839,




ENST00000398947,
ENSP00000381920,




ENST00000296543
ENSP00000296543


RCC1
ENSG00000180198
ENST00000434290,
ENSP00000405258,




ENST00000430407,
ENSP00000394650,




ENST00000429051,
ENSP00000416220,




ENST00000427469,
ENSP00000402740,




ENST00000419074,
ENSP00000402260,




ENST00000411533,
ENSP00000413644,




ENST00000398958,
ENSP00000381931,




ENST00000373833,
ENSP00000362939,




ENST00000373832,
ENSP00000362938,




ENST00000373831
ENSP00000362937


SSRP1
ENSG00000149136
ENST00000529002,
ENSP00000434546,




ENST00000526696,
ENSP00000431154,




ENST00000278412
ENSP00000278412


PRMT3
ENSG00000185238
ENST00000541255,
ENSP00000440367,




ENST00000526583,
ENSP00000434260,




ENST00000525188,
ENSP00000435151,




ENST00000437750,
ENSP00000397766,




ENST00000331079,
ENSP00000331879,




ENST00000330796
ENSP00000329586


SAP30
ENSG00000164105
ENST00000296504
ENSP00000296504


CBX6
ENSG00000183741
ENST00000407418,
ENSP00000384490,




ENST00000216083
ENSP00000216083


CHMP2B
ENSG00000083937
ENST00000494980,
ENSP00000418920,




ENST00000471660,
ENSP00000419998,




ENST00000263780
ENSP00000263780


UBE2M
ENSG00000130725
ENST00000253023
ENSP00000253023


WDR77
ENSG00000116455
ENST00000449340, 
ENSP00000409300,




ENST00000411751,
ENSP00000400321,




ENST00000235090
ENSP00000235090


HMGB1
ENSG00000189403
ENST00000426225,
ENSP00000411269,




ENST00000405805,
ENSP00000384678,




ENST00000399494,
ENSP00000382417,




ENST00000399489,
ENSP00000382412,




ENST00000398908,
ENSP00000410465,




ENST00000341423,
ENSP00000345347,




ENST00000339872,
ENSP00000343040,




ENST00000326004
ENSP00000369904


CARM1
ENSG00000142453
ENST00000344150,
ENSP00000340934,




ENST00000327064
ENSP00000325690


USP13
ENSG00000058056
ENST00000497380,
ENSP00000418651,




ENST00000497155,
ENSP00000420057,




ENST00000496897,
ENSP00000417146,




ENST00000263966
ENSP00000263966


HDAC4
ENSG00000068024
ENST00000544989,
ENSP00000438111,




ENST00000543185, 
ENSP00000440481,




ENST00000541256,
ENSP00000443057,




ENST00000456922, 
ENSP00000406618,




ENST00000454542, 
ENSP00000405226,




ENST00000446876, 
ENSP00000392912,




ENST00000445704, 
ENSP00000391226,




ENST00000430200, 
ENSP00000410551,




ENST00000393621,
ENSP00000377243,




ENST00000345617
ENSP00000264606


COQ3
ENSG00000132423
ENST00000369242,
ENSP00000358245,




ENST00000369240,
ENSP00000358243,




ENST00000254759
ENSP00000254759


SET
ENSG00000119335
ENST00000454747,
ENSP00000410806,




ENST00000409104, 
ENSP00000387321,




ENST00000372692, 
ENSP00000361777,




ENST00000372688,
ENSP00000361773,




ENST00000372686,
ENSP00000361771,




ENST00000322030
ENSP00000318012


GATAD2A
ENSG00000167491
ENST00000537887,
ENSP00000442588,




ENST00000457895, 
ENSP00000404212,




ENST00000448576, 
ENSP00000416452,




ENST00000444839, 
ENSP00000407293,




ENST00000432704, 
ENSP00000390495,




ENST00000429563, 
ENSP00000388416,




ENST00000429242, 
ENSP00000414252,




ENST00000418032, 
ENSP00000411869,




ENST00000417582, 
ENSP00000403703,




ENST00000404158, 
ENSP00000384899,




ENST00000360315, 
ENSP00000353463,




ENST00000358713, 
ENSP00000351552,




ENST00000252577
ENSP00000252577


PRMT6
ENSG00000198890
ENST00000540389,
ENSP00000440829,




ENST00000370078,
ENSP00000359095,




ENST00000361318
ENSP00000355145


HMG20B
ENSG00000064961
ENST00000453933,
ENSP00000402877,




ENST00000435022, 
ENSP00000393481,




ENST00000417382,
ENSP00000393904,




ENST00000416526,
ENSP00000410924,




ENST00000402569,
ENSP00000385987,




ENST00000333651,
ENSP00000328269,




ENST00000262949
ENSP00000262949


DNMT1
ENSG00000130816
ENST00000541266,
ENSP00000437951,




ENST00000540357,
ENSP00000440457,




ENST00000359526,
ENSP00000352516,




ENST00000340748
ENSP00000345739


ADA
ENSG00000196839
ENST00000539235,
ENSP00000446464,




ENST00000537820,
ENSP00000441818,




ENST00000536532,
ENSP00000440946,




ENST00000372874
ENSP00000361965


SS18
ENSG00000141380
ENST00000545952,
ENSP00000443097,




ENST00000542743,
ENSP00000444551,




ENST00000542420,
ENSP00000438066,




ENST00000539849,
ENSP00000444647,




ENST00000539244,
ENSP00000441760,




ENST00000415083,
ENSP00000414516,




ENST00000269138,
ENSP00000269138,




ENST00000269137
ENSP00000269137


UBE3A
ENSG00000114062
ENST00000566215,
ENSP00000457771,




ENST00000438097,
ENSP00000411258,




ENST00000428984,
ENSP00000401265,




ENST00000397954,
ENSP00000381045,




ENST00000356465,
ENSP00000348850,




ENST00000232165
ENSP00000232165


NOC2L
ENSG00000188976
ENST00000327044
ENSP00000317992


UTX
ENSG00000147050
ENST00000543216,
ENSP00000443078,




ENST00000542299,
ENSP00000444873,




ENST00000536777,
ENSP00000437405,




ENST00000535688,
ENSP00000444629,




ENST00000451692,
ENSP00000399980,




ENST00000433797,
ENSP00000398929,




ENST00000431196,
ENSP00000408230,




ENST00000414389,
ENSP00000405910,




ENST00000382899,
ENSP00000372355,




ENST00000377967,
ENSP00000367203,




ENST00000334516
ENSP00000334340


SIN3A
ENSG00000169375
ENST00000570115,
ENSP00000455662,




ENST00000568431,
ENSP00000454750,




ENST00000568309,
ENSP00000455644,




ENST00000568190,
ENSP00000456997,




ENST00000567289,
ENSP00000455834,




ENST00000565264,
ENSP00000454296,




ENST00000564778,
ENSP00000455204,




ENST00000562776,
ENSP00000455072,




ENST00000394949,
ENSP00000378403,




ENST00000394947,
ENSP00000378402,




ENST00000360439
ENSP00000353622


SAP3OL
ENSG00000164576
ENST00000440364,
ENSP00000390927,




ENST00000426761,
ENSP00000416393,




ENST00000297109
ENSP00000297109


FU20309
ENSG00000114933
ENST00000424117,
ENSP00000402369,




ENST00000414320,
ENSP00000409031,




ENST00000403263,
ENSP00000384198,




ENST00000233270
ENSP00000233270


RCOR2
ENSG00000167771
ENST00000301459
ENSP00000301459


ARID5A
ENSG00000196843
ENST00000454558,
ENSP00000400785,




ENST00000412735,
ENSP00000397286,




ENST00000359765,
ENSP00000352808,




ENST00000357485
ENSP00000350078


UBE2Q2
ENSG00000140367
ENST00000569423,
ENSP00000456324,




ENST00000567921,
ENSP00000454742,




ENST00000561851,
ENSP00000456229,




ENST00000561723,
ENSP00000458006,




ENST00000426727,
ENSP00000400960,




ENST00000338677,
ENSP00000340187,




ENST00000267938
ENSP00000267938


TRIM24
ENSG00000122779
ENST00000536822,
ENSP00000440535,




ENST00000452999,
ENSP00000402079,




ENST00000439939,
ENSP00000403347,




ENST00000415680,
ENSP00000390829,




ENST00000378381,
ENSP00000367632,




ENST00000343526
ENSP00000340507


BAZ2B
ENSG00000123636
ENST00000546335,
ENSP00000437619,




ENST00000541068,
ENSP00000441341,




ENST00000441143,
ENSP00000393565,




ENST00000437839,
ENSP00000415613,




ENST00000426648,
ENSP00000400505,




ENST00000392783,
ENSP00000376534,




ENST00000392782,
ENSP00000376533,




ENST00000355831,
ENSP00000348087,




ENST00000343439,
ENSP00000339670,




ENST00000294905
ENSP00000294905


SMYD3
ENSG00000185420
ENST00000544586,
ENSP00000443400,




ENST00000541742,
ENSP00000444184,




ENST00000490107,
ENSP00000419184,




ENST00000455277,
ENSP00000394281,




ENST00000453676,
ENSP00000408122,




ENST00000403792,
ENSP00000385380,




ENST00000391836,
ENSP00000375712,




ENST00000388985
ENSP00000373637


EZH2
ENSG00000106462
ENST00000541220,
ENSP00000443219,




ENST00000536783,
ENSP00000439305,




ENST00000492143,
ENSP00000417377,




ENST00000483967,
ENSP00000419856,




ENST00000483012,
ENSP00000417704,




ENST00000478654,
ENSP00000417062,




ENST00000476773,
ENSP00000419050,




ENST00000460911,
ENSP00000419711,




ENST00000350995,
ENSP00000223193,




ENST00000320356
ENSP00000320147


PHF1
ENSG00000239756,
ENST00000495185,
ENSP00000433516,



ENSG00000225553,
ENST00000475137,
ENSP00000434774,



ENSG00000112511
ENST00000454914,
ENSP00000407295,




ENST00000447305,
ENSP00000396023,




ENST00000427869,
ENSP00000391901,




ENST00000423868,
ENSP00000399226,




ENST00000421466,
ENSP00000395839,




ENST00000419154,
ENSP00000413510,




ENST00000495509,
ENSP00000434347,




ENST00000487667,
ENSP00000432419,




ENST00000428274,
ENSP00000392697,




ENST00000427826,
ENSP00000404788,




ENST00000427004,
ENSP00000410494,




ENST00000374516,
ENSP00000363640,




ENST00000374512
ENSP00000363636


PHF2
ENSG00000197724
ENST00000375376,
ENSP00000364525,




ENST00000359246
ENSP00000352185


BCR
ENSG00000186716
ENST00000427791,
ENSP00000396531,




ENST00000420248,
ENSP00000445910,




ENST00000398512,
ENSP00000381524,




ENST00000359540,
ENSP00000352535,




ENST00000334149,
ENSP00000335450,




ENST00000305877,
ENSP00000303507,




ENST00000292697,
ENSP00000292697,




ENST00000290956
ENSP00000290956


SMARCD3
ENSG00000082014
ENST00000491651,
ENSP00000419886,




ENST00000485592,
ENSP00000417145,




ENST00000469154,
ENSP00000417908,




ENST00000392811,
ENSP00000376558,




ENST00000356800,
ENSP00000349254,




ENST00000347683,
ENSP00000173385,




ENST00000262188
ENSP00000262188


BMI1
ENSG00000168283
ENST00000456675,
ENSP00000401773,




ENST00000443519,
ENSP00000390768,




ENST00000442508,
ENSP00000397912,




ENST00000417470,
ENSP00000398759,




ENST00000416820,
ENSP00000399220,




ENST00000376691,
ENSP00000365881,




ENST00000376663
ENSP00000365851


CHD6
ENSG00000124177
ENST00000440697,
ENSP00000404637,




ENST00000440647,
ENSP00000392503,




ENST00000373233,
ENSP00000362330,




ENST00000373222,
ENSP00000362319,




ENST00000309279
ENSP00000308684


FBXL11
ENSG00000173120
ENST00000530342,
ENSP00000435776,




ENST00000529006,
ENSP00000432786,




ENST00000446134,
ENSP00000392902,




ENST00000398645,
ENSP00000381640,




ENST00000308783
ENSP00000309302


SIRT7
ENSG00000187531
ENST00000576971,
ENSP00000458897,




ENST00000576004,
ENSP00000458737,




ENST00000575360,
ENSP00000459524,




ENST00000572902,
ENSP00000461044,




ENST00000328666
ENSP00000329466


ASF1A
ENSG00000111875
ENST00000229595
ENSP00000229595


RCOR3
ENSG00000117625
ENST00000534478,
ENSP00000436057,




ENST00000534460,
ENSP00000433441,




ENST00000533469,
ENSP00000436838,




ENST00000529763,
ENSP00000437048,




ENST00000529572,
ENSP00000434605,




ENST00000528926,
ENSP00000432779,




ENST00000485186,
ENSP00000434181,




ENST00000452621,
ENSP00000398558,




ENST00000419091,
ENSP00000413929,




ENST00000367006,
ENSP00000355973,




ENST00000367005
ENSP00000355972


CBX4
ENSG00000141582
ENST00000495122,
ENSP00000461198,




ENST00000448310,
ENSP00000415348,




ENST00000343048,
ENSP00000345967,




ENST00000269397
ENSP00000269397


EPC1
ENSG00000120616
ENST00000375110,
ENSP00000364251,




ENST00000319778,
ENSP00000318559,




ENST00000263062
ENSP00000263062


BRD1
ENSG00000100425
ENST00000542442,
ENSP00000437514,




ENST00000457780,
ENSP00000410042,




ENST00000438393,
ENSP00000388027,




ENST00000419212,
ENSP00000399110,




ENST00000404760,
ENSP00000385858,




ENST00000404034,
ENSP00000384076,




ENST00000342989,
ENSP00000345886,




ENST00000216267
ENSP00000216267


BNF11
ENSG00000054938
ENST00000534276,
ENSP00000432055,




ENST00000529912,
ENSP00000432345,




ENST00000528789,
ENSP00000431380,




ENST00000528471,
ENSP00000434589,




ENST00000525413,
ENSP00000434257,




ENST00000393519,
ENSP00000377154,




ENST00000376332,
ENSP00000365510,




ENST00000376324,
ENSP00000365502,




ENST00000376323,
ENSP00000365501,




ENST00000263671
ENSP00000263671


HP1A
ENSG00000094916
ENST00000550489,
ENSP00000448452,


(CBX5)

ENST00000209875,
ENSP00000209875,




ENST00000550411,
ENSP00000449207,




ENST00000439541,
ENSP00000401009,




ENST00000552562
ENSP00000450190


HP1B
ENSG00000108468
ENST00000225603,
ENSP00000225603,


(CBX1)

ENST00000393408,
ENSP00000377060,




ENST00000444685,
ENSP00000393179,




ENST00000402583
ENSP00000385413


HP1G
ENSG00000122565
ENST00000337620,
ENSP00000336687,


(CBX3)

ENST00000396386,
ENSP00000379670,




ENST00000409747,
ENSP00000387348,




ENST00000456948
ENSP00000408672









In some embodiments, the methods for diagnosing comprise measuring expression levels of at least one biomarker selected from DTX1, HES4, CD1d, ETS1, ETV6, Runx1, Bcl-2, MYC and CD52. In some embodiments, decreased levels in a tumor sample of DTX1, HES4, and/or CD1d compared to a control identifies a subject to be treated with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor. In some embodiments, increased levels in a tumor sample of a biomarker selected from the group consisting of ETS1, ETV6, Runx1, CD52, MYC or Bcl-2 compared to a control identifies a subject to be treated with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor. Expression levels of biomarkers could be, for example, mRNA and/or protein levels.
In some embodiments, more than one biomarker selected from DTX1, HES4, CD1d, ETS1, ETV6, Runx1, Bcl-2, MYC and CD52 is measured and the diagnosis or identification of a subject is made based on 2 or more biomarkers. These biomarkers are found in Table 7.







TABLE 7







DTX1, HES4, CD1d, ETS1, ETV6, Runx1, Bcl-2, MYC and CD52 Biomarkers










Gene
Ensembl gene ID
Ensembl transcript ID
Ensembl protein ID





DTX1
ENSG00000135144
ENST00000257600,
ENSP00000257600




ENST00000547974,





ENST00000553140,





ENST00000547730,





ENST00000548759



HES4
ENSG00000188290
ENST00000304952,
ENSP00000304595,




ENST00000428771,
ENSP00000393198,




ENST00000484667,
ENSP00000425085




ENST00000481869



CD1d
ENSG00000158473
ENST00000368171
ENSP00000357153


ETS1
ENSG00000134954
ENST00000392668,
ENSP00000376436,




ENST00000319397,
ENSP00000324578,




ENST00000531611,
ENSP00000435666,




ENST00000526145,
ENSP00000433500,




ENST00000345075,
ENSP00000340485,




ENST00000535549,
ENSP00000441430




ENST00000525404,





ENST00000527676,





ENST00000530924



ETV6
ENSG00000139083
ENST00000396373,
ENSP00000379658,




ENST00000545027,
ENSP00000441463,




ENST00000266427,
ENSP00000266427




ENST00000544715,





ENST00000541426



Runx1
ENSG00000159216
ENST00000344691
ENSP00000340690,




ENST00000300305
ENSP00000300305,




ENST00000416754
ENSP00000405158,




ENST00000358356
ENSP00000351123,




ENST00000399240
ENSP00000382184,




ENST00000455571
ENSP00000388189,




ENST00000399237
ENSP00000382182,




ENST00000325074
ENSP00000319459,




ENST00000437180
ENSP00000409227,




ENST00000486278
ENSP00000438019




ENST00000482318





ENST00000479325





ENST00000467577





ENST00000475045





ENST00000468726





ENST00000494829





ENST00000467692





ENST00000460207





ENST00000469087



Bcl-2
ENSG00000171791
ENST00000398117,
ENSP00000381185,




ENST00000333681,
ENSP00000329623,




ENST00000589955,
ENSP00000466417,




ENST00000444484,
ENSP00000404214




ENST00000590515



MYC
ENSG00000136997
ENST00000377970,
ENSP00000367207,




ENST00000259523,
ENSP00000259523,




ENST00000517291,
ENSP00000429441,




ENST00000524013,
ENSP00000430235,




ENST00000520751
ENSP00000430226


CD52
ENSG00000169442
ENST00000374213,
ENSP00000363330




ENST00000470468,





ENST00000492808









In some embodiments, the methods for diagnosing comprise measuring a level of histone modification. Histone modifications can be detected, e.g., using chromatin immunoprecipitation sequencing (ChIP-Seq). In some embodiments, the histone modification is selected from H3K27me3, H3K9me3, and H3K27Ac. In some embodiments, decreased levels in a tumor sample of H3K27Ac histone modification compared to a control identifies a subject to be treated with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor. In some embodiments, increased levels in a tumor sample of a histone modification from the group consisting of H3K27me3 and H3K9me3 compared to a control identifies a subject to be treated with a bromodomain inhibitor and or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor.
In some embodiments, the histone modification is H3K4me1. In some embodiments, elevated levels of H3K4me1 histone modification at a site of elevated H3K27Ac histone modification in the tumor sample compared to the control identifies a subject to be treated with a bromodomain inhibitor or a combination of agents as described herein, including, but not limited to, a bromodomain inhibitor and/or a Bcl-2 inhibitor.
EXAMPLES
Example 1
Modeling and Characterization of Drug Resistance in T-ALL
Methods:
Notch inhibitor sensitive T-ALL cell lines were cultured in the presence of 1 μM GSI in vitro. Cells were plated at 0.25×106/ml in 20 mL and split every 3-4 days. Cell viability, cell size and cell cycle were measured every 3-4 days. GSI treated cells demonstrated decreased proliferation as measured by decreased fold expansion after 7 to 14 days. GSI-treated cells stopped proliferating between day 14 to 30 of culture, but eventually started proliferating again despite the presence of GSI with subsequent growth rates being equal or similar to untreated cells.
For RNA expression profiles, cells were washed once in PBS and then snap frozen. RNA was isolated using the Qiagen RNeasy kit. Expression profiles were obtained with the Affymetrix HU133+2 array.
To measure metabolites, cell culture supernatant was taken on day 1, 2, 3, 4, 5 of culture and frozen. Metabolites were measured by mass spectrometry and results were adjusted to input metabolites in media and fold expansion over time.
Cell size was determined by measuring the forward/side scatter on a FACS Calibur (BD Biosciences). To determine nuclear size, cells were spun on slides using a Cytospin centrifuge, then fixed and permeabilized prior to staining with DAPI or anti-Actin antibody. Staining intensity was measured by fluorescent microscopy.
HP1 protein expression was measured by performing Western Blot analysis using the iblot® system (Invitrogen) and enhanced chemiluminescence (ECL) for visualization.
To measure chromatin compaction, naïve or resistant cells were washed once in PBS, lysed and nuclei were isolated using a sucrose gradient. Samples were adjusted for equal nuclear size prior to digestion with MNase. Digests were done for increasing time intervals. DNA was isolated by phenol/chloroform extraction and nucleosomes run on a gel and visualized by SYBR® Safe DNA gel stain (Invitrogen).
Global histone levels were measured by enzyme-linked immunosorbent assay (ELISA) after acid extraction of histones.
For ChIP-Seq, cells were crosslinked in 1% formaldehyde for 15 minutes. Cells were lysed and sonicated with a Branson 250 to a size range of 200 to 700 bp. Chromatin was immunoprecipitated with antibody against K4me1, H3K27ac or BRD4.
Libraries were prepared from  ̃5 nanograms of ChIP DNA, loaded onto flow cells and sequenced on the Illumina HiSeq Genome Analyzer by standard procedures. Reads were aligned to the reference (hg19) human genome. For data analysis, enrichment profiles were generated for each histone modification. Briefly, aligned reads were extended to 300 bases to approximate the average ChIP fragment. Signal was then estimated at any given position (25 bp resolution) as the number of sequenced ChIP fragments that overlap that position. A sliding window approach was used to identify significantly enriched intervals or ‘peaks’ from each dataset.
Results:
A gamma secretase inhibitor (GSI)-resistant leukemia cell population was produced using the methods above. Several biological parameters were compared between the GSI-resistant leukemia cells and naïve leukemia cells (those not treated with a GSI).
Firstly, RNA expression profiles of naïve cells and resistant cells were compared using the methods described above. Gene set enrichment analysis (GSEA) was performed and revealed a shift from Myc-dependent signaling to JNK/Map kinase dependent signaling (FIG. 1).
Secondly, the metabolic state of resistant versus naïve cells was compared as described above. The ratio of lactate production to glucose consumption was found to be higher in naïve cells than in resistant cells whereas the ratio of glutamate production to glutamine consumption was found to be lower in naïve cells than in resistant cells (FIG. 2).
Thirdly, the nuclear and cellular morphology of resistant versus naïve cells was compared as described above. Forward-scatter FACS analysis revealed that resistant cells were smaller than naïve cells (FIG. 3A). DAPI staining showed that resistant cells contained smaller nuclei than naïve cells (FIG. 3B).
The smaller nuclear size of resistant cells prompted an investigation of the chromatin status in naïve versus resistant cells. HP1-gamma, a marker of global chromatin compaction was measured using Western blot analysis as described above. A higher level of HP1-gamma was found in resistant cells and those treated for a short period of time with a GSI indicating a higher level of chromatin compaction compared to naïve cells (FIG. 4A). Additionally, a partial MNase digestion was performed as described above and showed that resistant cells are protected from MNase digestion, indicating a higher level of chromatin compaction compared to naïve cells (FIG. 4B).
To further analyze the chromatin state in naïve versus resistant cells, the methylation status of certain histone residues that are indicative of the level of chromatin compaction were examined. Tri-methylation of lysine 9 and lysine 27 of histone 3 (H3K9me3 and H3K27me3, respectively) are markers of compacted heterochromatin (a repressed chromatin state). As depicted in FIG. 5A, when assessing global levels of these repressive chromatin marks, both H3K9me3 and H3K27me3 levels were found to be elevated in resistant cells as compared to naïve cells, indicating that resistant had more compacted heterochromatin than naïve cells.
Differences in the chromatin regulatory network between naïve and resistant cells were assessed by determining relative expression levels of chromatin state biomarkers. As depicted in FIG. 5B, expression levels of certain chromatin state biomarkers were increased in resistant cells as compared to naïve cells. The chromatin state biomarkers with increased expression levels were UTX, SIN3A, SAP30L, FLJ20309, RCOR2, ARID5A, UBE2Q2, TRIM24, BAZ2B, SMYD3, EZH2, PHF1, PHF2, BCR, SMARCD3, BMI1, CHD6, FBXL11, SIRT7, ASF1A, RCOR3, CBX4, EPC1, BRD1, and BNF11. Such chromatin state biomarkers may be associated with a repressed heterochromatin state.
Conversely, relative expression levels of certain chromatin state biomarkers were decreased in resistant cells as compared to naïve cells. These chromatin state biomarkers included NPM1, NARG1, RCC1, SSRP1, PRMT3, SAP30, CBX6, CHMP2B, UBE2M, WDR77, HMGB1, CARM1, USP13, HDAC4, COQ3, SET, GATAD2A, PRMT6, HMG20B, DNMT1, ADA, SS18, UBE3A, ZMYND11, and NOC2LL. Such chromatin state biomarkers may be associated with promoting an active, open chromatin state.
Example 2
A BRD Inhibitor Blocks Proliferation of and Kills Resistant Leukemia Cells In Vitro and In Vivo
Methods:
Notch inhibitor sensitive and resistant T-ALL cell lines were plated in 96 well plates and treated with vehicle, 1 uM GSI and/or increasing concentrations of the bet inhibitor JQ1. Cell viability was determined by measuring luminescence after Celltiterglo® (Promega) addition on day 6. Apoptosis was measured using Caspaseglo® (Promega) on day 4.
Luciferized KOPTK1 cells were injected into NOD/SCID mice by tail vein injection. Tumor burden was measured by following the bioluminescence signal in the mouse body. Following KOPTK1 cell engraftment, mice were treated with a GSI called dibenzazepine (DBZ), JQ1, DBZ+JQ1, or a vehicle control.
Balb/c mice were treated with DBZ+JQ1, DBZ, or vehicle alone. Hyperproliferation of globlet cells was measured by Periodic acid-Schiff (PAS) stain.
Results:
One gene from Example 3, BRD4, was chosen as an example chromatin regulatory factor for further analysis in vitro and in vivo. BRD4 was found to be upregulated in leukemia cells that were resistant to a GSI and leukemia cells that underwent short-term treatment with a GSI compared to naïve leukemia cells (FIG. 6). Treatment with a bromodomain inhibitor, JQ1, resulted in a decrease in proliferation and an increase in apoptosis in resistant leukemia cells compared to naïve leukemia cells (FIG. 7).
Chromatin Immunoprecipitation (ChIP) with sequencing (Seq) was performed using a BRD4 antibody to identify regions of the genome that were associated with BRD4. BRD4 was found to be associated with enhancers that were also shown to have histone marks H3K4me1 and H3K27ac (FIG. 8). Of interest, BRD4 was found to be associated with the enhancer region of BCL-2, a known anti-apoptotic gene (FIG. 9A). Bcl-2 protein was found to be upregulated in GSI resistant leukemia cells compared to naïve leukemia cells (FIG. 9B). Treatment with the bromodomain inhibitor JQ1 resulted in a decreased level of Bcl-2 protein in resistant cells (FIG. 9B).
Lastly, in vivo animal studies were performed on preclinical model of T-ALL using NOD/SCID mice. Mice were injected via tail-vein with luciferized KOPTK1 cells and engraftment was monitored by bioluminescence. Following leukemia cell engraftment, mice were treated with a GSI dibenzazepine (DBZ), JQ1, DBZ+JQ1, or a vehicle control. As shown in FIG. 10, the combination of DBZ+JQ1 greatly reduced the tumor burden compared to either drug alone or the control. Additionally, side effects normally associated with GSI treatment, namely gastrointestinal damage, were reduced in normal BALB/c mice with the combination of DBZ+JQ1 compared to use of DBZ alone. Mice treated with DBZ showed significant disruption of intestinal villi architecture caused by hyperproliferation of globlet cells, as shown by Periodic acid-Schiff (PAS) stain (FIG. 11). Addition of JQ1 largely ameliorated villi architecture by partially restoring proper enterocyte differentiation.
The results indicate that bromodomain inhibitors and Bcl-2 inhibitors are a useful treatment for cancers with a Notch pathway activation mutation or cancers that are resistant to treatment with a Notch pathway inhibitor.
Example 3
An Epigenetic Mechanism of Resistance to Targeted Therapy in T-cell Acute Lymphoblastic Leukemia
T-ALL is an aggressive malignancy with significant rates of therapy failure that is frequently associated with activating mutations in NOTCH1, a critically important oncogene in this disease. Gamma secretase inhibitors (GSIs) that inhibit NOTCH1 cleavage and activation have been tested in clinical trials and mouse models, but responses have been modest and transient (Palomero, T. & Ferrando, A. Therapeutic targeting of NOTCH1 signaling in T-cell acute lymphoblastic leukemia. Clin Lymphoma Myeloma 9 Suppl 3, S205-210 (2009)). To understand mechanisms by which T-ALL cells overcome chronic Notch1 inhibition, GSI-resistance was modeled in vitro and in vivo, and the functional and molecular characteristics of resistant cells were investigated. When Notch-dependent T-ALL cells were treated with GSI in vitro a majority of cells stopped proliferating over the course of two weeks, but a fraction persisted and recovered their growth capacity. These ‘persister’ cells tolerated concentrations of GSI (compound E) more than 50-fold higher than the IC50, suggesting that they have become resistant to Notch inhibition. In order to address the mechanism of drug resistance, it was determined whether acquired resistance is fixed or reversible. It was found that, upon removal of GSI, the persisters re-express Notch target genes within a week (FIG. 12). Retreatment of these reversed cells with GSI leads to cell cycle arrest in a pattern similar to that seen for naïve T-ALL cells. Furthermore, the re-treated cells eventually acquired resistance with similar kinetics as the naïve population. The reversibility of acquired GSI tolerance in this model suggests that the resistance phenotype is mediated epigenetically.
To characterize the drug tolerant cells, the active intracellular form of NOTCH1 (ICN) (Guruharsha, K. G., Kankel, M. W. & Artavanis-Tsakonas, S. The Notch signalling system: recent insights into the complexity of a conserved pathway. Nat Rev Genet 13, 654-666 (2012)). ICN was examined and found to be present at high levels in naïve T-ALL cells, but is essentially undetectable in the persisters (FIG. 12). The persisters re-expressed ICN when GSI was removed, consistent with their reversible phenotype. Expression of Notch target genes followed a similar pattern: DTX1 and HES4 were profoundly down-regulated in the persisters (FIG. 12), but gradually recover after removal of GSI. Induction of MYC is thought to be a major mechanism by which constitutive Notch activation leads to malignancy in T-ALL (Weng, A. P. et al. c-Myc is an important direct target of Notch1 in T-cell acute lymphoblastic leukemia/lymphoma. Genes Dev 20, 2096-2109 (2006) and Palomero, T. et al. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci USA 103, 18261-18266 (2006)). Although MYC levels are dramatically reduced by short term GSI treatment, expression of this oncoprotein recovers modestly in the persisters (FIG. 12). Nonetheless, gene expression profiles indicated that the persisters had lost the predominating MYC transcriptional signature of naïve T-ALL cells. These data suggest that the persisters had acquired the ability to proliferate in the absence of Notch signaling, but maintained modest MYC activity through alternative means.
In contrast to the reduced MYC signature, gene expression profiles revealed enhanced signatures for MAPK, JNK, PI3K and MTOR signaling in the persisters. Genetic alterations of PTEN resulting in increased AKT pathway activity have been associated with Notch resistance (Gutierrez, A. et al. High frequency of PTEN, PI3K, and AKT abnormalities in T-cell acute lymphoblastic leukemia. Blood 114, 647-650 (2009) and Palomero, T. et al. Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nat Med 13, 1203-1210 (2007)). Although the T-ALL cell lines modeled here do not harbor PTEN mutations, the persisters have increased levels of phosphorylated PTEN and, accordingly, are more sensitive to treatment with an AKT inhibitor (FIG. 13). mTOR has been demonstrated to be active in leukemia, including Notch-dependent T-ALL (Chan, S. M., Weng, A. P., Tibshirani, R., Aster, J. C. & Utz, P. J. Notch signals positively regulate activity of the mTOR pathway in T-cell acute lymphoblastic leukemia. Blood 110, 278-286 (2007) and Kalaitzidis, D. et al. mTOR complex 1 plays critical roles in hematopoiesis and Pten-loss-evoked leukemogenesis. Cell Stem Cell 11, 429-439 (2012)). The persisters showed increased levels of the phosphorylated form p2481 of mTOR and sensitivity to the mTOR inhibitor Rapamycin (FIG. 14). These alterations in cytoplasmic signaling were accompanied by changes in the metabolic profiles indicative of a shift from a predominantly glycolytic state in naïve T-ALL cells to a greater reliance on oxidative phosphorylation in the persisters (FIG. 2). These data suggest that rewired signaling and metabolic programs in the persister cells are critical for proliferation in the absence of Notch signaling.
The persistence phenotype was also notable for morphologic changes, including a profound decrease in cell and nuclear size, which was reversible after removal of GSI (FIGS. 3A-C). It was postulated that these changes might reflect global chromatin compaction associated with exposure and subsequent tolerance to Notch inhibition. In support of this view, it was found that the persisters up-regulate heterochromatin-associated HP1 proteins and have high global levels of repressive chromatin modifications (FIG. 4A). To evaluate global compaction more directly, chromatin was digested from naïve and persister cells with micrococcal nuclease. It was found that chromatin in the persisters is relatively inaccessible and has a longer average nucleosomal repeat length indicative of linker histone H1 incorporation (FIG. 4B), as is consistent with a more compact chromatin state. Recent links drawn between metabolism and chromatin regulation (Lu, C. & Thompson, C. B. Metabolic regulation of epigenetics. Cell Metab 16, 9-17 (2012)) prompted evaluation of the relationships between metabolic changes and chromatin compaction. It was found that glucose restriction led to increased chromatin compaction in naïve T-ALL cells. It was also found that chromatin compaction was an early consequence of Notch inhibition, with rapid up-regulation of HP1 protein expression upon GSI exposure (FIG. 4A). The functional significance of chromatin state changes in T-ALL persister cells was then investigated further.
First, histone modifications were profiled in naïve and persister T-ALL cells by ChIP-seq. Marks associated with promoters (H3K4me3), transcripts (H3K36me3), enhancers (H3K4me1, H3K27ac) and Polycomb-repressed loci (H3K27me3) were surveyed (Zhou, V. W., Goren, A. & Bernstein, B. E. Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet 12, 7-18 (2011) and Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012)). Striking differences in chromatin state were evident within loci encoding Notch target genes, including CD300A and DELTEX1. Promoter, transcript and enhancer chromatin signals in these loci were markedly reduced in the persisters, consistent with reduced gene expressions17. Conversely, chromatin activity was increased within certain loci, such as MAP3K5, that are induced in the persisters. In addition, the persisters exhibited a modest increase in H3K27me3 levels over euchromatic loci and a reduction in bulk H3K27ac levels (FIG. 5A). Thus, acquisition of GSI tolerance is associated with focal chromatin changes at differentially-regulated loci and a genome-wide reduction of accessible euchromatin.
It was postulated that their altered chromatin state might uncover new susceptibilities in the persister cells that could be targeted by emerging epigenetic therapies. To test this, a lentiviral short-hairpin RNA (shRNA) knockdown screen was designed that targeted  ̃350 chromatin regulators with an average of 5 independent hairpins per gene (FIG. 15). About 15 genes were identified for which knockdown compromised survival in both naïve and persister cells, and thus presumed to be generally required for T-ALL cells. Riger analysis was then used to identify genes preferentially required for survival of either naïve or persister cells. Naïve cells were found to be preferentially dependent on several histone deactylase (HDACs) enzymes, while the persister cells showed a greater dependence on other genes, including several arginine methyltransferases (FIG. 15). The chromatin regulatory proteins identified for the persister cells include: ARID3B, EZH2, PRMT2, SND1, BRD1, SUV39H1, PRMT5, SS18, BRD4, KDM5D, PRMT7, STAG3L1, CD2BP2, MLL5, SUDS3, CHD1, MINA, CHD8, MORF4L1, or CHRAC1. The gene name and transcript IDs provided in Table 8 can be used to identify the shRNA sequences used by searching the RNAi Consortium (TRC) Portal (Broad Institute, Cambridge, Mass.).







TABLE 8







Chromatin Regulatory Proteins for which the persister


cells showed a greater dependence










GENE NAME
GENE ID
TRANSCRIPT ID
PROTEIN ID





ARID3B
ENSG00000179361
ENST00000346246,
ENSP00000343126,




ENST00000566147,
ENSP00000455668




ENST00000563567,





ENST00000569680,





ENST00000566468



EZH2
ENSG00000106462
ENST00000483967,
ENSP00000419856,




ENST00000320356,
ENSP00000320147,




ENST00000478654,
ENSP00000417062,




ENST00000476773,
ENSP00000419050,




ENST00000460911,
ENSP00000419711,




ENST00000350995,
ENSP00000223193,




ENST00000536783,
ENSP00000439305,




ENST00000541220,
ENSP00000443219,




ENST00000492143,
ENSP00000417377,




ENST00000483012,
ENSP00000417704




ENST00000498186,





ENST00000469631



PRMT2
ENSG00000160310
ENST00000355680
ENSP00000347906




ENST00000334494
ENSP00000335490




ENST00000397637
ENSP00000380759




ENST00000397638
ENSP00000380760




ENST00000455177
ENSP00000406127




ENST00000397628
ENSP00000380752




ENST00000440086
ENSP00000397266




ENST00000291705
ENSP00000291705




ENST00000451211
ENSP00000411984




ENST00000458387
ENSP00000407463




ENST00000498151





ENST00000491389





ENST00000482508





ENST00000481861





ENST00000486520



SND1
ENSG00000197157
ENST00000354725,
ENSP00000346762,




ENST00000486037,
ENSP00000419327




ENST00000461056,





ENST00000468621,





ENST00000483503,





ENST00000492772,





ENST00000468166,





ENST00000465900,





ENST00000467238,





ENST00000470723,





ENST00000470463,





ENST00000485871,





ENST00000484767,





ENST00000492840,





ENST00000489417,





ENST00000463020



BRD1
ENSG00000100425
ENST00000542442,
ENSP00000437514,




ENST00000457780,
ENSP00000410042,




ENST00000438393,
ENSP00000388027,




ENST00000419212,
ENSP00000399110,




ENST00000404760,
ENSP00000385858,




ENST00000404034,
ENSP00000384076,




ENST00000342989,
ENSP00000345886,




ENST00000216267
ENSP00000216267


SUV39H1
ENSG00000101945
ENST00000376687,
ENSP00000365877,




ENST00000337852,
ENSP00000337976,




ENST00000453214,
ENSP00000410686




ENST00000482260,





ENST00000462786



PRMT5
ENSG00000100462
ENST00000324366,
ENSP00000319169,




ENST00000397440,
ENSP00000380582,




ENST00000557443,
ENSP00000452501,




ENST00000397441,
ENSP00000380583,




ENST00000216350,
ENSP00000216350,




ENST00000553897,
ENSP00000452555,




ENST00000553550,
ENSP00000450737,




ENST00000554910,
ENSP00000452411,




ENST00000553502,
ENSP00000450956,




ENST00000556043,
ENSP00000452509,




ENST00000555530,
ENSP00000452409,




ENST00000555454,
ENSP00000451245,




ENST00000454731,
ENSP00000387663,




ENST00000421938,
ENSP00000409482,




ENST00000556616,
ENSP00000450919,




ENST00000554867,
ENSP00000452218,




ENST00000538452,
ENSP00000444915,




ENST00000556426,
ENSP00000451127,




ENST00000553915,
ENSP00000450633,




ENST00000557415,
ENSP00000452102




ENST00000553787,





ENST00000476175,





ENST00000554716,





ENST00000553641,





ENST00000557015,





ENST00000557758,





ENST00000553417,





ENST00000556032



SS18
ENSG00000141380
ENST00000269137,
ENSP00000269137,




ENST00000542420,
ENSP00000438066,




ENST00000415083,
ENSP00000414516,




ENST00000581021,
ENSP00000463586,




ENST00000584083,
ENSP00000463943,




ENST00000579061,
ENSP00000462766,




ENST00000539849,
ENSP00000444647,




ENST00000542743,
ENSP00000444551,




ENST00000545952,
ENSP00000443097,




ENST00000579640,
ENSP00000462363,




ENST00000585121,
ENSP00000462838,




ENST00000539244,
ENSP00000441760,




ENST00000269138,
ENSP00000269138,




ENST00000582448,
ENSP00000464609,




ENST00000578700,
ENSP00000464673,




ENST00000577572,
ENSP00000463802,




ENST00000578954,
ENSP00000464664,




ENST00000581570,
ENSP00000464556,




ENST00000582792,
ENSP00000463928,




ENST00000580751,
ENSP00000464049,




ENST00000580642,
ENSP00000462104,




ENST00000577636,
ENSP00000463933




ENST00000577751,





ENST00000583595,





ENST00000578595,





ENST00000585241,





ENST00000582092,





ENST00000580003,





ENST00000580958



BRD4
ENSG00000141867
ENST00000371835,
ENSP00000360901,




ENST00000360016,
ENSP00000353112,




ENST00000263377,
ENSP00000263377


KDM5D
ENSG00000012817
ENST00000317961,
ENSP00000322408,




ENST00000382806,
ENSP00000372256,




ENST00000447300,
ENSP00000416377,




ENST00000440077,
ENSP00000398543,




ENST00000415360,
ENSP00000389433,




ENST00000535647,
ENSP00000445530,




ENST00000541639,
ENSP00000444293




ENST00000492117,





ENST00000469599,





ENST00000485154,





ENST00000478891



PRMT7
ENSG00000132600
ENST00000339507,
ENSP00000343103,




ENST00000563562,
ENSP00000455238,




ENST00000449359,
ENSP00000414716,




ENST00000565745,
ENSP00000456190,




ENST00000566657,
ENSP00000454980,




ENST00000569571,
ENSP00000455538,




ENST00000569047,
ENSP00000456848,




ENST00000348497,
ENSP00000345775,




ENST00000441236,
ENSP00000409324,




ENST00000568975,
ENSP00000454776,




ENST00000562050,
ENSP00000457381,




ENST00000566341,
ENSP00000455705,




ENST00000562381 
ENSP00000456364


STAG3L1
ENSG00000205583
ENST00000404291,





ENST00000487154,





ENST00000402225,





ENST00000456374,





ENST00000338421





ENST00000339898,





ENST00000436837,



CD2BP2
ENSG00000169217
ENST00000305596,
ENSP00000304903,




ENST00000569466,
ENSP00000456935




ENST00000564525



MLL5
ENSG00000005483
ENST00000311117,
ENSP00000312379,




ENST00000476671,
ENSP00000417888,




ENST00000473063,
ENSP00000417156,




ENST00000495267,
ENSP00000420415,




ENST00000478990,
ENSP00000419883,




ENST00000474203,
ENSP00000420206,




ENST00000257745,
ENSP00000257745,




ENST00000334877,
ENSP00000335599,




ENST00000334914,
ENSP00000333986,




ENST00000334884,
ENSP00000335398,




ENST00000482560,
ENSP00000417193,




ENST00000478079,
ENSP00000419525




ENST00000480368,





ENST00000485619,





ENST00000468607,





ENST00000496191,





ENST00000479838



SUDS3
ENSG00000111707
ENST00000543473,
ENSP00000443988,




ENST00000397564,
ENSP00000380695




ENST00000541591,





ENST00000541280,





ENST00000360286



CHD1
ENSG00000153922
ENST00000284049,
ENSP00000284049,




ENST00000512844,
ENSP00000422589,




ENST00000505657,
ENSP00000422225




ENST00000511067,





ENST00000514344,





ENST00000512392,





ENST00000511628,





ENST00000513064,





ENST00000508756,





ENST00000414220,





ENST00000505982



MINA
ENSG00000170854
ENST00000394198,
ENSP00000377748,




ENST00000333396,
ENSP00000328251,




ENST00000360258,
ENSP00000353395,




ENST00000507612,
ENSP00000424530,




ENST00000503097
ENSP00000421347,




ENST00000506099,
ENSP00000423816,




ENST00000330299,
ENSP00000327424,




ENST00000514314,
ENSP00000424955




ENST00000506682,





ENST00000503517



CHD8
ENSG00000100888
ENST00000430710,
ENSP00000406288,




ENST00000557364,
ENSP00000451601,




ENST00000553622,
ENSP00000450957,




ENST00000555935,
ENSP00000451442,




ENST00000553283,
ENSP00000450860,




ENST00000553870,
ENSP00000451071,




ENST00000399982,
ENSP00000382863




ENST00000553651,





ENST00000555962,





ENST00000556833,





ENST00000557727,





ENST00000557329,





ENST00000554384,





ENST00000555301



MORF4L1
ENSG00000185787
ENST00000331268,
ENSP00000331310,




ENST00000426013,
ENSP00000408880,




ENST00000559345,
ENSP00000452717,




ENST00000379535,
ENSP00000368850,




ENST00000560422,
ENSP00000453625,




ENST00000559690,
ENSP00000453351,




ENST00000559158,
ENSP00000453432,




ENST00000559930,
ENSP00000454191,




ENST00000559244,
ENSP00000454030,




ENST00000559751,
ENSP00000453972,




ENST00000558746,
ENSP00000453231,




ENST00000558830,
ENSP00000453738,




ENST00000558502,
ENSP00000452808




ENST00000559697,





ENST00000558539,





ENST00000561171,





ENST00000558893,





ENST00000558522,





ENST00000559258,





ENST00000557961,





ENST00000559619,





ENST00000558923,





ENST00000560710



CHRAC1
ENSG00000104472
ENST00000220913,
ENSP00000220913,




ENST00000519533,
ENSP00000428697,




ENST00000518971,
ENSP00000430484,




ENST00000519618,
ENSP00000430003




ENST00000523569









BRD4 was identified as a top hit in the screen, with 3 shRNAs significantly reducing persister cell proliferation without affecting the naïve population. BRD4 is a member of the BET family of bromodomains that selectively bind acetylated histones and mediate epigenetic gene regulation (Dawson, M. A. & Kouzarides, T. Cancer epigenetics: from mechanism to therapy. Cell 150, 12-27 (2012) and Zhao, R., Nakamura, T., Fu, Y., Lazar, Z. & Spector, D. L. Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nat Cell Biol 13, 1295-1304 (2011)). BRD4 has been implicated in several malignancies, including acute myeloid leukemia and lymphoma (Blobel, G. A., Kalota, A., Sanchez, P. V. & Carroll, M. Short hairpin RNA screen reveals bromodomain proteins as novel targets in acute myeloid leukemia. Cancer Cell 20, 287-288 (2011) and Zuber, J. et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukemia. Nature 478, 524-528 (2011)). It was confirmed that the shRNAs silence BRD4 at protein levels and also replicated their selective effect on persister cell survival. The exquisite dependency of GSI tolerant persister cells on BRD4 is of particular interest given the recent development of small molecule BET inhibitors, such as JQ1 (Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067-1073 (2010) and Nicodeme, E. et al. Suppression of inflammation by a synthetic histone mimic. Nature 468, 1119-1123 (2010)). Indeed, it was found that the persisters undergo proliferation arrest in response to JQ1 concentrations that are well tolerated by naïve T-ALL cells (FIG. 7), whereas a JQ1 enantiomer had no effect. Thus, chromatin state changes in the persister cells are accompanied by markedly increased sensitivity to inhibition of BRD4, a ‘reader’ of acetylated chromatin.
To investigate its regulatory functions, BRD4 was mapped genome-wide in persister cells. BRD4 bound mainly to promoters ( ̃30% of sites) and putative enhancers enriched for H3K4me1 and H3K27ac ( ̃60%), consistent with its biochemical affinity for acetylated histones. In contrast, sites of open chromatin marked exclusively by H3K4me1 were rarely bound by BRD4. BRD4-bound enhancers were enriched near genes with functions related to phosphoprotein signaling (539/989 genes; 53%), including many in the AKT and mTOR pathways. The binding sites were also found to be enriched for consensus motifs for ETS family and RUNX transcription factors (FIG. 16). Consistently, RT-PCR revealed increased expression of ETS1, ETV6 and RUNX1 in the persister cells (FIG. 16B). Our analysis suggests that BRD4 mediates gene regulatory programs required for the proliferation of drug tolerant T-ALL cells. The global chromatin compaction in the persister cells may render enhancers and their gene targets particularly reliant on BRD4 for their epigenetic maintenance.
Next, individual genes that might account for the BRD4 dependency of the persister cells were examined. MYC was focused on first, as it is a known BRD4 target (Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067-1073 (2010)), whose expression is sustained in the persister cells, albeit at a lower level compared to the naïve. It was postulated that increased AKT and mTOR signaling might maintain MYC expression in these cells. Indeed, a small molecule inhibitor of the mTOR pathway markedly reduce MYC expression in persister cells, but have essentially no effect in naïve cells (FIG. 17A). BRD4 bound several putative enhancers in the MYC locus (FIG. 17B). JQ1 significantly reduced MYC expression in the persisters at doses that did not alter MYC in naïve cells (FIG. 17A). Thus, altered mechanisms of MYC activation appear to sensitize persister cells to BRD4 inhibition.
The anti-apoptosis regulator BCL2 is an established BRD4-dependent gene in mixed lineage leukemia (Dawson, M. A. et al Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukemia. Nature 478, 529-533 (2011)). Intense BRD4 binding is evident throughout the BCL2 locus (FIGS. 9A and 17B), which is highly expressed in the drug tolerant T-ALL cells. JQ1 treatment significantly reduced Bcl-2 expression in these cells, but had little effect on the naïve population (FIG. 9B). It was reasoned that loss of Bcl-2 might account for the apoptosis seen in persisters treated with JQ1 (FIG. 7). In support of this model, the Bcl-2 inhibitor ABT-737 effectively killed persister cells (FIG. 18A). Furthermore, Bcl-2 over-expression partially rescues persister cells from JQ1 treatment (FIG. 18B). Hence, down-regulation of this survival gene is critical for JQ1-induced cell death in drug tolerant T-ALL cells.
To investigate the in vivo relevance of the GSI resistance and associated epigenetic changes, KOPT-K1 T-ALL cells with a mcherry marker were injected orthotopically into NOD-SCID mice and the bioluminescence was followed over time. GSI resistance developed rapidly in vivo after a short period of slowed tumor growth. ICN levels were drastically reduced in bone marrow of GSI-treated mice and Notch target genes were down-regulated in the corresponding leukemia cells, indicating that resistance is not due to Notch reactivation (FIG. 19A). The ‘in vivo persisters’ also share other phenotypic characteristics with their in vitro counterparts, including increased HP1γ, Bcl-2 and CD52 expression and decreased CD1d expression, suggestive of a common mechanism (FIG. 19B). Primary T-ALL cells were also examined for their sensitivity to the combination of GSI and JQ1. Growth arrest was observed in two-thirds of cases, and this was associated with marked reduction in BCL2 expression (FIG. 20). These data support the in vivo relevance of GSI drug tolerance and a shared mechanism of BET inhibitor sensitivity in primary T-ALL.
Finally, the population level dynamics of naïve T-ALL cells exposed to GSI were considered. The initial response to drug appears relatively homogeneous, with near complete loss of activated Notch, rapid chromatin compaction and a marked reduction in the size distribution of the population. However, striking cell-to-cell variability was observed in terms of the efficiency with which naïve cells acquire resistance. Specifically, when single cell clones were isolated and treated with GSI, it was found that  ̃3% of clones in the starting population could resume growth in the presence of drug. The single cell persister clones shared phenotypic markers with persisters derived by treating naïve T-ALL populations (FIG. 21). The reversibility of the persister phenotype indicates that these clones are distinguished by epigenetic as opposed to genetic alterations. This suggests that while Notch inhibition elicits a relatively uniform response, GSI resistance may depend on a pre-existing population of epigenetically distinct T-ALL cells able to engage requisite resistance mechanisms.
Therapeutic resistance plagued early GSI trials in humans (Palomero, T. & Ferrando, A. Therapeutic targeting of NOTCH1 signaling in T-cell acute lymphoblastic leukemia. Clin Lymphoma Myeloma 9 Suppl 3, S205-210 (2009)) and is a major challenge in cancer treatment today, pertinent to conventional chemotherapy and targeted therapy alike (Haber, D. A., Gray, N. S. & Baselga, J. The evolving war on cancer. Cell 145, 19-24 (2011)). As shown herein, T-ALL cells can acquire GSI resistance by a fully reversible epigenetic mechanism reminiscent of a previously established model of drug tolerant lung cancer cells (Sharma, S. V. et al. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 141, 69-80 (2010)). GSI resistance in T-ALL is mediated through rewired signaling and metabolic pathways, and a dramatic chromatin state transition that uncovers a new therapeutic sensitivity to BET inhibition. The data shown herein suggests that the heightened sensitivity of persister cells to BET inhibition reflects a stringent requirement for BRD4 to sustain the activity of distal gene enhancers, as is consistent with previously established bookmarking functions at promoters (Zhao, R., Nakamura, T., Fu, Y., Lazar, Z. & Spector, D. L. Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nat Cell Biol 13, 1295-1304 (2011)). The study described herein provides a framework for understanding epigenetic alterations that underlie tumor pathogenesis, and suggests the potential of combination therapy that incorporates new classes of epigenetic therapies as a means to avert resistance phenotypes.
Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present invention to its fullest extent. The specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. All publications, patent application, and patents cited herein are incorporated by reference for the purposes or subject matter referenced herein.
The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.”
From the above description, one skilled in the art can easily ascertain the essential characteristics of the present invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions. Thus, other embodiments are also within the claims.

## Claims

1. A method comprising administering to a subject having cancer a bromodomain inhibitor, with or without a Bcl-2 inhibitor, and a Notch pathway inhibitor, in an effective amount to treat the cancer, wherein the cancer is characterized by the presence of a Notch pathway activation mutation.

2. The method of claim 1, wherein the bromodomain inhibitor, without the Bcl-2 inhibitor, and the Notch pathway inhibitor are administered.

3. The method of claim 1, wherein the bromodomain inhibitor, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered.

4. The method of claim 3, wherein the bromodomain inhibitor, the Bcl-2 inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially.

5. The method of claim 1, further comprising identifying the subject as a subject having cancer characterized by the presence of a Notch pathway activation mutation.

6. The method of claim 2, wherein the bromodomain inhibitor and the Notch pathway inhibitor are administered concurrently or sequentially.

7. The method of claim 3, wherein the bromodomain inhibitor and the Bcl-2 inhibitor are administered concurrently or sequentially.

8. The method of claim 3, wherein the Bcl-2 inhibitor is G3139, GX15-070, ABT-737 or ABT-199.

9. The method of claim 1, wherein the bromodomain inhibitor is a BET inhibitor.

10. The method of claim 1, wherein the bromodomain inhibitor is JQ1 or a derivative thereof.

11. The method of claim 1, wherein the Notch pathway inhibitor is a gamma secretase inhibitor.

12. The method of claim 3, wherein the bromodomain inhibitor, the Bcl-2 inhibitor and/or the Notch pathway inhibitor is an siRNA, shRNA, or antisense nucleic acid molecule.