BET Bromodomain Inhibitor JQ1 Research Articles

Abstract 4737: The combination of the BET inhibitor JQ1 and gemcitabine induces regressions in gemcitabine resistant patient-derived xenograft models of pancreatic cancer

Abstract Efforts to develop targeted therapies for drug resistant tumors have been relatively unsuccessful. The 5-year survival for patients with advanced pancreatic cancer is ~3%. Gemcitabine is usually combined with nab-paclitaxel as a standard of care for treatment of locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). However, no chemotherapeutic regimens thus far evaluated have been curative. We developed the first PDAC patient-derived xenograft (PDX) models in which resistance against gemcitabine was acquired in vivo. We used RNA-seq and ingenuity pathway analysis to compare expression profiles of paired parent vs gemcitabine resistant PDX models. This comparison suggested a previously unreported mechanism for gemcitabine resistance, involving aberrations of cholesterol biosynthesis and lipid metabolism pathways. We also made the unexpected observation that gemcitabine-resistant PDAC models derived from primary tumors have high levels of 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), an enzyme essential to cholesterol biosynthesis and rate limiting in ketogenesis. Notably, the BET bromodomain inhibitor JQ1 decreases HMGCS2 levels; and BET inhibitors + gemcitabine exert synergistic cytotoxicity in gemcitabine-resistant PDAC cells. We determined that the BET bromodomain inhibitor JQ1 + gemcitabine induces regressions of two in vivo gemcitabine-resistant tumor models which we developed directly from primary human tumor tissue. These mechanism-based studies suggest that inhibiting HMGCS2 represents a novel approach to therapy for PDAC. We propose that combining gemcitabine with agents that decrease levels of HMGCS2 comprises effective treatment for patients with drug resistant PDAC. Citation Format: Aubrey L. Miller, Samuel C. Fehling, Eric Josh Brown, Eric O. Heard, Tracy L. Gamblin, Rebecca B. Vance, Karina J. Yoon. The combination of the BET inhibitor JQ1 and gemcitabine induces regressions in gemcitabine resistant patient-derived xenograft models of pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4737.

Rapid-Kinetics Degron Benchmarking Reveals Off-Target Activities and Mixed Agonism-Antagonism of MYB Inhibitors

The transcription factor (TF) MYB is a critical transcriptional dependency of acute myeloid leukemia (AML) where it has been a long-term focus of drug development efforts. However, development of transcriptional inhibitors is hampered by the lack of a generally accepted functional cellular readout to characterize their target specificity and on-target activity. We reasoned that the specificity and on-target activity of MYB inhibitors would be best evaluated in a rapid kinetics system where their immediate transcriptional effects are benchmarked against targeted MYB degradation. We began by engineering a chemical degron model and established the direct gene-regulatory functions of MYB in a nascent transcriptomics assay. We fused the C-terminus of MYB with an FKBP12 F36V (dTAG) domain and a fluorescent tag by a homozygous knock-in of the FKBP12 F36V-coding DNA sequence into the endogenous MYB locus in MV411 cells. The resulting fusion protein was nearly completely degraded after a 1-hour treatment with dTAG V-1, a highly specific VHL-engaging PROTAC. As expected, degradation of MYB resulted in a profound loss of cell viability, consistent with the effects of a genetic MYB knockout in AML cells. To establish MYB's direct gene-regulatory functions, we measured genome-wide rates of nascent mRNA synthesis by thiol (SH)-linked alkylation metabolic sequencing of RNA (SLAM-seq) after a 1-hour MYB degradation. Defining direct targets as those genes which displayed significant changes in transcription rates (FDR<0.0), we detected 450 genes directly regulated by MYB. Of these, 319 genes were downregulated and 131 genes were upregulated, indicating that MYB acts as a transcriptional activator and repressor of these genes, respectively. In parallel, we performed SLAM-seq in AML cells treated with six agents reported as MYB inhibitors: MYBMIM, celastrol, naphthol AS-E phosphate, mebendazole, plumbagin and all-trans retinoic acid (ATRA). For comparison, we treated MV411 cells with the BET bromodomain inhibitor JQ1, which has been reported to indirectly inhibit MYB by interfering with its expression and function. The MYB inhibitors displayed a dramatic variability in the number of dysregulated genes, varying from 19 (naphthol) to 1123 (MYBMIM). In contrast, JQ1 caused widespread and bimodal effects, altering the transcription rates of >2000 genes in both directions. On pairwise overlap, the MYB inhibitors captured a relatively minor portion of the direct MYB program (between 5-155, or 1-34%, of the 450 direct MYB targets), compared with 43% of the MYB program captured by JQ1. Nonetheless, the MYB inhibitors displayed a stronger specificity for MYB target genes compared to JQ1, because they elicited much narrower responses. Thus, while MYB inhibitors displayed strong enrichments for primary MYB targets, they did not attenuate the entire MYB transcriptional program, and significant portions of their activities appeared to be off-target. In addition, the inhibitors displayed bimodal effects on the transcription of MYB-regulated genes, further activating subsets of genes that were repressed by MYB degradation, and vice versa. These observations uncovered unexpected activities of MYB inhibitors as context-dependent mixed agonists-antagonists. We conclude that MYB has a narrow direct transcriptional program in AML cells, which is only partially captured by the existing MYB inhibitors, which display partial specificity for MYB targets and act as mixed agonists-antagonists. Our work will serve as a proof-of-principle demonstration of the use of rapid kinetic resolution of TF degron models for a more precise characterization of the target specificity and efficacy of TF-directed inhibitors. Benchmarking of TF modulators against degron models in nascent transcriptomics assays should be considered as an important criterion in their functional characterization.

Reclassification of ETS Family Transcription Factor Fusions in Pediatric AML Based on Molecular Drivers

Pediatric Acute Myeloid Leukemia (pAML) patients with a fusion involving an E26 transformation-specific (ETS) transcription factor have traditionally been considered high-risk. The most common fusions include ETV6::MNX1 t(7;12)(q36;p13) and FUS::ERG t(16;21)(p11;q22), yet primary fusion alone has proven incapable of predicting response to treatment. Indeed, within the 60 pAML patients with ETS fusions from the Children's Oncology Group (COG) trials AAML0531 and AAML1031, there were 25 unique fusions and diverse outcomes between patients who did share a primary fusion. A molecular based reclassification of ETS fused pAML could prove beneficial in the development of novel therapeutic additions to standard induction. Here, using genetic and RNAseq data from over 1,400 pediatric patients from AAML0531 and AAML1031, we reclassified ETS patients based on oncogenic transcriptional profiles as well as access to hematopoietic stem cell transplant (HSCT) ( Figure 1A). (19/60) patients presented with an enhanced MYC transcriptional signature (p-val < 0.00) independent of fusion partners [EP300::ETV6, ETV6::CCND3, ETV6::FAM133B, ETV6::FOXO1, ETV6::INO80D, ETV6::LMBR1, ETV6::MNX1, EWSR1::FEV, FLI1::IFIT2, FUS::ERG, FUS::FEV, FUS::FLI1]. Median event-free survival (EFS) was 293.5 days; median overall survival (OS) was 620.5 days. Notably, 100% (19/19) of patients with a MYC-driven signature relapsed; of the six patients who received HCST, five died within 3 years of diagnosis. Preliminary in vitro data in ETS cell lines with an enhanced MYC transcriptional signature (YNH-1, TSU-1621) suggests that the BET bromodomain inhibitor JQ1 may dampen MYC and induce anti-proliferative effects. (7/60) patients were defined by an EZH2-driven “immune-cold” signature characterized by global loss of immune receptors. Patients presented at diagnosis with significantly elevated EZH2 and low levels of MHC I and II receptors typically observed at relapse; additionally, there was significant downregulation in T cell and natural killer cell ligands and a 100% failure rate for HSCT. Median EFS was 255 days and median OS was 339 days. We have previously discussed the mechanism of leukemogenesis as well as proposed therapeutic interventions for this subset (Buteyn, ASH 2021). (34/60) patients did not possess either a MYC-driven or EZH2-driven signature. These “other” ETS were instead defined by whether or not the patient underwent HCST. (21/34) patients did not receive HCST and had median EFS and OS of 429 and 1194 days, respectively. The relapsed or refractory rate in this population was still 75%; (8/14) of R/R patients were deceased within three years. The remaining (13/60) ETS patients did receive HSCT in first remission. (11/13) are still alive and at a rate higher than the general pAML population post-HSCT (62.6%). Despite a survival rate at approximately 85%, ‘Other ETS +HSCT’ patients were all still categorized as ‘High Risk’ at the end of AAML1031. Overall, reclassification based on molecular drivers appears to not only be more accurate in predicting relapse and final outcome, but also in proposing novel agents for pAML patients who overwhelmingly do not respond to standard regimens. Reinvigoration of immune recognition by inhibition of EZH2 and/or inhibition of MYC-driven proliferation via BET inhibitors may prove an essential step in setting the stage for successful HSCT for a significant portion of pAML ETS patients.

Quantitative Proteomics of the CDK9 Interactome Reveals a Function of the HSP90-CDC37-P-TEFb Complex for BETi-Induced HIV-1 Latency Reactivation.

Brd4 has been intensively investigated as a promising drug target because of its implicated functions in oncogenesis, inflammation, and HIV-1 transcription. The formation of the Brd4-P-TEFb (CDK9/Cyclin T1) complex and its regulation of transcriptional elongation are critical for HIV latency reactivation and expression of many oncogenes. To further investigate the mechanism of the Brd4-P-TEFb complex in controlling elongation, mass spectrometry-based quantitative proteomics of the CDK9 interactome was performed. Upon treatment with the selective BET bromodomain inhibitor JQ1, 352 proteins were successfully identified with high confidence as CDK9-interacting proteins. Among them, increased bindings of HSP90 and CDC37 to CDK9 were particularly striking, and our data suggest that the HSP90-CDC37-P-TEFb complex is involved in controlling the dynamic equilibrium of the P-TEFb complex during BETi-induced reactivation of HIV-1 latency. Furthermore, the HSP90-CDC37-P-TEFb complex directly regulates HIV-1 transcription and relies on recruitment by heat shock factor 1 (HSF1) for binding to the HIV-1 promoter. These results advance the understanding of HSP90-CDC37-P-TEFb in HIV-1 latency reversal and enlighten the development of potential strategies to eradicate HIV-1 using a combination of targeted drugs.

IL32 overexpression is driven by DNA hypomethylation and contributes to an extracellular matrix (ECM) remodeling phenotype in EpCAM‐/CD49f‐enriched breast cancer cells

Basal‐like breast cancers typically correspond with increased enrichment of EpCAM‐/CD49f‐ cancer stem cells (CSC) and a propensity toward metastasis. However, the molecular mechanisms underlying these general characteristics are not well understood. To provide further insight concerning CSCs and their intrinsic metastatic mechanisms, we compared the 450K DNA methylation profile of EpCAM‐/CD49f‐ poor breast cancer cell lines to that of EpCAM‐/CD49f‐ enriched breast cancer cell lines. From our results, we were able to determine and highlight IL32 as a gene whose promoter is hypomethylated in EpCAM‐/CD49f‐ enriched cell lines. The hypomethylated IL32 promoter corresponded with increased IL32 expression in both cell lines and basal‐like breast cancer patients from The Cancer Genome Atlas (TCGA) database. Interestingly, increased IL32 expression preferentially occurred for the IL32‐beta transcript and corresponds with previous reports demonstrating that IL32‐beta is not secreted from the cell like other canonical interleukins and preferentially localizes to the mitochondria in breast cancer cells. Additionally, expression of the beta‐transcript could be suppressed when CSC‐enriched cells were treated with the BET‐bromodomain inhibitor JQ1. Because of this phenomenon, we sought to determine the effects of suppressing IL32 in the EpCAM‐/CD49f‐ enriched cell line SUM159PT via siRNA‐mediated knockdown and subsequent RNAseq differential expression analysis. From our results, we determined that transcripts involved in extracellular matrix (ECM) organization and collagen/integrin interaction were preferentially affected by IL32 silencing. Additionally, IL32 suppression decreased the invasiveness of SUM159PT based on an ECM‐matrix cell invasion assay. Collectively, our results reflect the notion that differential IL32 expression by promoter hypomethylation in breast CSCs plays a role in ECM remodeling for purposes of breast cancer cell invasion and metastasis.

BET-bromodomain and EZH2 inhibitor–treated chronic GVHD mice have blunted germinal centers with distinct transcriptomes

AbstractDespite advances in the field, chronic graft-versus-host-disease (cGVHD) remains a leading cause of morbidity and mortality following allogenic hematopoietic stem cell transplant. Because treatment options remain limited, we tested efficacy of anticancer, chromatin-modifying enzyme inhibitors in a clinically relevant murine model of cGVHD with bronchiolitis obliterans (BO). We observed that the novel enhancer of zeste homolog 2 (EZH2) inhibitor JQ5 and the BET-bromodomain inhibitor JQ1 each improved pulmonary function; impaired the germinal center (GC) reaction, a prerequisite in cGVHD/BO pathogenesis; and JQ5 reduced EZH2-mediated H3K27me3 in donor T cells. Using conditional EZH2 knockout donor cells, we demonstrated that EZH2 is obligatory for the initiation of cGVHD/BO. In a sclerodermatous cGVHD model, JQ5 reduced the severity of cutaneous lesions. To determine how the 2 drugs could lead to the same physiological improvements while targeting unique epigenetic processes, we analyzed the transcriptomes of splenic GCB cells (GCBs) from transplanted mice treated with either drug. Multiple inflammatory and signaling pathways enriched in cGVHD/BO GCBs were reduced by each drug. GCBs from JQ5- but not JQ1-treated mice were enriched for proproliferative pathways also seen in GCBs from bone marrow-only transplanted mice, likely reflecting their underlying biology in the unperturbed state. In conjunction with in vivo data, these insights led us to conclude that epigenetic targeting of the GC is a viable clinical approach for the treatment of cGVHD, and that the EZH2 inhibitor JQ5 and the BET-bromodomain inhibitor JQ1 demonstrated clinical potential for EZH2i and BETi in patients with cGVHD/BO.

Discovery of a Covalent FEM1B Recruiter for Targeted Protein Degradation Applications.

Proteolysis-targeting chimeras (PROTACs), heterobifunctional compounds that consist of protein-targeting ligands linked to an E3 ligase recruiter, have arisen as a powerful therapeutic modality for targeted protein degradation (TPD). Despite the popularity of TPD approaches in drug discovery, only a small number of E3 ligase recruiters are available for the >600 E3 ligases that exist in human cells. Here, we have discovered a cysteine-reactive covalent ligand, EN106, that targets FEM1B, an E3 ligase recently discovered as the critical component of the cellular response to reductive stress. By targeting C186 in FEM1B, EN106 disrupts recognition of the key reductive stress substrate of FEM1B, FNIP1. We further establish that EN106 can be used as a covalent recruiter for FEM1B in TPD applications by demonstrating that a PROTAC linking EN106 to the BET bromodomain inhibitor JQ1 or the kinase inhibitor dasatinib leads to the degradation of BRD4 and BCR-ABL, respectively. Our study showcases a covalent ligand that targets a natural E3 ligase-substrate binding site and highlights the utility of covalent ligand screening in expanding the arsenal of E3 ligase recruiters suitable for TPD applications.

Transcriptional Reprogramming of Super-Enhancer Associated Oncogenes Following Inhibition of Cyclin-Dependent Kinase-9 (CDK9) in Aggressive Non-Hodgkin Lymphoma (NHL)

Introduction. CDKs are Ser/Thr kinases that associate with specific cyclins during the cell cycle to regulate its progression. We and others have shown that selective targeting of CDK9, a component of the positive transcription elongation factor b (pTEFb) complex which facilitates RNA transcription, is a promising approach in NHL leading to downmodulation of MYC and MCL1 (Hashiguchi et al, 2019). However, cells also exhibited resistance to CDK9i in vitro and in vivo. Here we studied the transcriptional and epigenetic effects of CDK9 inhibition using the novel selective CDK9 inhibitor AZD4573 which is under evaluation in clinical trials.Methods. A panel of NHL cell lines with variable sensitivity to CDK9i (OCI-LY3/19, SUDHL4/10/16, VAL, U2932) and primary NHL cells were employed. Response to CDK9i was characterized using RNA-Seq, ChIP-Seq and ATAC-Seq.Results. Treatment with AZD4573 potently inhibited proliferation of NHL cell lines and primary cells (IC 50 range 5-30 nM). RNA-Seq of cells treated with CDK9i demonstrated that up to 6,000 genes were significantly downregulated in NHL cells treated with CDK9i for 3 h, leading to downregulation of MAPK, PI3K, NFκB and TNFR signaling. However, following the initial nadir at 3 h, a subset of genes recovered transcription to at least baseline level (e.g., PIM1, MYC, IRF8, BCL6, BCL2L1, CXCR4 etc.), confirmed by RT-PCR and immunoblotting. Recovery was more prominent in less sensitive cells (OCI-LY3; by 6-8 h) and occurred despite continued p-RNAPII Ser2 blockade. ChIP-Seq analysis confirmed increased global RNAPII pausing at promoters in cells treated with AZD4573, including at recovery genes.Next, we conducted ChIP-Seq for H3K4me3 and H3K27ac in OCI-LY3 and VAL cells. We observed a global decrease in H3K4me3 signal across the promoters and gene bodies with AZD4573 treatment. Meanwhile, H3K27ac enhancer analysis showed a global decrease in VAL cells, but was stable/increased in OCI-LY3 cells, including at certain recovery genes (e.g., MYC and BCL2L1).BRD4 was previously shown to compensate for loss of CDK9 function to recover transcription of the MYC oncogene in HeLa cells, thereby compensating for loss of pTEFb activity. We observed increased interaction between BRD4 and RNAPII in OCI-LY3 cells treated with AZD4573 (by IP) and increased global BRD4 binding at transcription start sites (ChIP-Seq). Combination of BET bromodomain inhibitor JQ1 and CDK9i reduced expression of recovery genes including MYC and synergistically restricted proliferation of NHL cells.BRD4 inhibition leads to preferential loss of transcription at super enhancer (SE)-associated genes. Therefore we leveraged our H3K27ac ChIP-Seq data to elucidate the SE landscape in NHL cells. Enhancers were ranked by signal density and amplitude, followed by assignment of the closest gene. SE domains were identified near to genes known to contribute to lymphomagenesis. Notably the majority of the recovery genes had highly ranked SE association in the tested cell lines.Next, ATAC-Seq analysis of NHL cells revealed a significant number of genes with differential accessibility following CDK9i. Upon an 8 h treatment with AZD4573, 11121 and 4367 hyper-accessible chromatin regions were identified in VAL and OCI-LY3 cells, respectively, including MYC and BCL2L1 loci. E-box motif was found accessible across many genes at this timepoint.To investigate recovery genes as targets, we used PIM kinase inhibitors SGI1776 (PIM1) and AZD1208 (pan-PIM). Both drugs demonstrated synergy with AZD4573 in a panel of 4 cell lines and primary samples.Finally, to further elucidate genes and pathways which mediate susceptibility to CDK9i, we conducted a genome-wide loss of function CRISPR-Cas9 library screen. Cas9-expressing OCI-LY3 cells were transduced with a lentivirus encoding a CRISPR library comprised of ~5 unique sgRNA per gene. Knockout of genes in the PI3K/mTOR and DNA repair pathways sensitized cells to AZD4573. Confirming this result, combination treatment with AZD8835 (PI3K inhibitor) synergistically suppressed proliferation of the NHL cell lines and primary cells treated with AZD4573.Conclusions. CDK9i leads to transcriptional reprogramming including the upregulation of a subset of SE-associated oncogenes. Targeting recovery oncogenes may enhance sensitivity to CDK9i. DisclosuresDanilov: Gilead Sciences: Research Funding; Bristol-Meyers-Squibb: Honoraria, Research Funding; Bayer Oncology: Consultancy, Honoraria, Research Funding; SecuraBio: Research Funding; Abbvie: Consultancy, Honoraria; Beigene: Consultancy, Honoraria; Pharmacyclics: Consultancy, Honoraria; TG Therapeutics: Consultancy, Research Funding; Takeda Oncology: Research Funding; Genentech: Consultancy, Honoraria, Research Funding; Astra Zeneca: Consultancy, Honoraria, Research Funding; Rigel Pharm: Honoraria.

Comprehensive Analysis to Identify Enhancer-Regulated Inflammation-Associated Genes in Lung Adenocarcinoma.

ObjectiveThe purpose of this study was to identify prognostic inflammatory markers regulated by enhancers in lung adenocarcinoma (LUAD).MethodsInflammatory indices of 490 LUAD patients in TCGA database were calculated using genomic variation analysis (GSVA). Patients were divided into high- and low-inflammatory index groups. Fraction of 22 infiltrating immune cells was estimated using the Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT). Gene set enrichment analysis (GSEA) was used to analyze gene enrichment. Differentially expressed genes were screened based on TCGA database. The H3K27ac ChIP-seq of A549 cells in GEO database (GSE42374) was analyzed to identify super enhancers. Kaplan–Meier method and multivariate Cox proportional hazards models were used for survival analysis. CCK8 and RT-qPCR were used for cellular level verification.ResultsInflammation was associated with better outcome in LUAD patients. Anti-cancer immune cell fractions were upregulated in high-inflammatory index group. Genes enriched in inflammation-related signaling pathways were positively correlated with high-inflammatory index group. A total of 146 upregulated genes regulated by enhancers were screened, of which five genes including GDF10, HPGDS, ABCA8, SLIT3 and ADAMTS8 had significant influence on prognosis. ChIP-seq analysis showed that TGFβ+TNFα treatment promoted the enhancer activation of the five genes. Cellular experiments revealed that there was no significant effect of TGFβ treatment on the five genes expression. TNFα treatment upregulated the five genes expression, while the BET-bromodomain inhibitor JQ1 restored the effect of TNFα. Overexpression of the five genes significantly inhibited the proliferation of A549 and H1299 cells.ConclusionGDF10, HPGDS, ABCA8, SLIT3 and ADAMTS8 were identified as enhancer-regulated prognostic inflammation-related biomarkers, and the expression of these genes inhibited proliferation of LUAD cells.

BET bromodomain inhibitor JQ1 regulates spermatid development by changing chromatin conformation in mouse spermatogenesis

As a BET bromodomain inhibitor, JQ1 has been proven have efficacy against a number of different cancers. In terms of male reproduction, JQ1 may be used as a new type of contraceptive, since JQ1 treatment in male mice could lead to germ cell defects and a decrease of sperm motility, moreover, this effect is reversible. However, the mechanism of JQ1 acting on gene regulation in spermatogenesis remains unclear. Here, we performed single-cell RNA sequencing (scRNA-seq) on mouse testes treated with JQ1 or vehicle control to determine the transcriptional regulatory function of JQ1 in spermatogenesis at the single cell resolution. We confirmed that JQ1 treatment could increase the numbers of somatic cells and spermatocytes and decrease the numbers of spermatid cells. Gene Ontology (GO) analysis demonstrated that differentially expressed genes which were down-regulated after JQ1 injection were mainly enriched in “DNA conformation change” biological process in early developmental germ cells and “spermatid development” biological process in spermatid cells. ATAC-seq data further confirmed that JQ1 injection could change the open state of chromatin. In addition, JQ1 could change the numbers of accessible meiotic DNA double-stranded break sites and the types of transcription factor motif that functioned in pachytene spermatocytes and round spermatids. The multi-omics analysis revealed that JQ1 had the ability to regulate gene transcription by changing chromatin conformation in mouse spermatogenesis, which would potentiate the availability of JQ1 in male contraceptive.

Abstract D116: Glucocorticoid receptor interacts with beta-catenin to promote stemness and therapy resistance in prostate cancer cells

Abstract Prostate cancer (PCa) is the most commonly diagnosed male cancer, with men of African ancestry showing a disproportionately high incidence and mortality. There is increasing evidence that glucocorticoid signaling through glucocorticoid receptor (GR) is amplified in African American men due to cumulative life stress, and that GR signaling is a key driver of resistance to androgen-targeted therapy, radiotherapy, and taxane chemotherapy in advanced PCa. Recent studies indicate that GR also promotes in PCa cells the formation of tumorspheres, a property of cancer stem cells (CSC); however, the mechanisms remain unclear. CSCs are intrinsically resistant to therapies due to their low-frequency, expression of transporters and efflux pumps, quiescent cell cycle and metabolic profile. Our previous studies demonstrated that docetaxel (DTX)-resistant PCa cells exhibit increased capacity for CSC-like properties, suggesting that these properties contribute to chemoresistance. Like GR, beta-catenin is overexpressed in metastatic and therapy-resistant tumors, and is considered a key regulator of cancer stemness and androgen-targeted therapy resistance. Thus, we hypothesized that GR may interact with beta-catenin in PCa cells to support stemness and chemoresistance. Using whole-cell and nuclear co-immunoprecipitation, we demonstrated the interaction between GR and beta-catenin in several DTX-sensitive and -resistant PCa cell line pairs. Pharmacological inhibition of GR using the selective inhibitor CORT-108297 with concomitant inhibition of beta-catenin using the small molecule inhibitor MSAB significantly enhanced DTX cytotoxicity in resistant PCa cells grown in both adherent and spheroid cultures. The BET bromodomain inhibitor JQ1, an antagonist of enhancer-mediated GR upregulation, also significantly reduced tumorsphere formation and stemness in DTX-resistant PCa cells. In order to gain insights into transcriptomic profiles activated by GR signaling that may contribute to stemness and therapy resistance, we performed RNA sequencing in a racially diverse panel of PCa cell lines (MDA-PCa-2b, VCaP, 22RV1, and PC3) treated with and without dexamethasone, a potent glucocorticoid. We observed that the African American cell line MDA-PCa-2b yielded the largest number of differentially regulated genes, perhaps due to the ability of dexamethasone to signal through both AR and GR in this particular cell line. RNAseq data is currently being mined and validated in cellular models treated with glucocorticoids or androgens, in the presence or absence of anti-GR or anti-androgen inhibitors, in order to identify GR-regulated genes. Our results offer novel insights into mechanisms by which GR signaling may influence tumorsphere formation and stemness, and suggest that combinatorial targeting of GR and beta-catenin could be a promising therapeutic strategy to overcome PCa therapy resistance and consequently reduce PCa mortality and its racial disparities. Citation Format: Shannalee R Martinez, Evelyn S Sanchez-Hernandez, Xin Chen, Alfonso M Duran, Charles H Wang, Carlos A Casiano. Glucocorticoid receptor interacts with beta-catenin to promote stemness and therapy resistance in prostate cancer cells [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr D116.

Abstract A141: Computational models of synergy contribute to efficient combination screening

Abstract Introduction: Combination drug treatment in cancer therapy aims to improve response rate and decrease the development of drug resistance. The discovery of novel drug combinations is constrained by the cost and effort of carrying out large unbiased screens and is hampered by poor translation towards the clinic. We investigate if computational models combined with screening can more efficiently reveal synergistic combinations and improve translation towards the clinic. The models are based on three different biological views of synergy. First, compounds that exploit similar vulnerabilities in cancer cells frequently show synergy in a particular genetic context (targeted synergy, model 1) [1,2]. Secondly, drugs with non-overlapping resistance mechanisms often yield clinically relevant drug combinations (model 2) [3]. Finally, drugs that mimic synthetic lethal interactions will often act synergistically (model 3) [4]. Experimental procedures Oncolines™ is a panel of 102 genetically characterized cell lines from diverse tumor origins, on which proliferation assays are run in parallel in nine-point dose-response curves. In this cell panel we profiled 162 different cancer therapeutics, including many standard of care, chemotherapeutic agents, epigenetic modulators, and approved and pre-clinical drugs such as CDK4/6, ALK and PI3K-inhibitors [5]. Cancer hotspot mutations and gene expression data were downloaded from the DepMap and CCLE databases. ANOVA and Pearson correlations were used to analyze the single agent response and genetic data in the statistical software R, to determine gene mutation (model 1) and resistance markers (model 2). For model 3, clinically relevant synthetic lethal pairs were combined with gene expression data [4]. The methods were used to predict results from published synergy screens, e.g. DREAM [6] and results from an independent experiment (NTRC SynergyScreen™) in which fixed concentrations of the poly-ADP ribose polymerase (PARP) inhibitor niraparib and the BET bromodomain inhibitor JQ1, were combined with nine-point dose-response curves of 150 anticancer agents. Synergies were quantified using curve-shift and CI-index. Results: Using a cancer cell line IC50 profile of a compound (such as Oncolines™), all three computational models of synergy prediction can be applied. Method 1 is successful in predicting combinations that augment a targeted effect, such as combining BRAF and MEK inhibitors in BRAF-mutant cancer [1]. Method 2 does not distinguish between additive or synergistic combinations but can identify clinically relevant combinations [3]. For method 3, a tool was developed that computationally assesses if drug pairs can pharmacologically mimic clinically validated synthetic lethal interactions [4]. This can predict DREAM data with a high AUC of 0.67 in a ROC curve. The tool successfully predicts synergy between niraparib and the SUMO inhibitor 2-D08, and niraparib and BCL2 inhibitors, which we observed in our screen. Conclusions: Computational tools for synergy have predictive value and can be useful to prioritize libraries for empirical combination screening.

Pharmacological Targeting of BET Bromodomains Inhibits Lens Fibrosis via Downregulation of MYC Expression.

Lens fibrosis involves aberrant growth, migration, and transforming growth factorβ (TGFβ)-induced epithelial-mesenchymal transition (EMT) of lens epithelial cells (LECs). In this study, we investigated the role of the bromo- and extra-terminal domain (BET) inhibitor in lens fibrotic disorder to identify drug-based therapies. Rat lens explants, rabbit primary lens epithelial cells (rLECs), human lens explants and human SRA01/04 cells were treated with TGFβ2 in the presence or absence of the BET bromodomain inhibitor JQ1 or the MYC inhibitor 10058-F4. Proliferation was determined by MTS assay. Cell migration was measured by wound healing and transwell assays. The expression levels of fibronectin (FN), α-smooth muscle actin (α-SMA), E-cadherin, and phosphorylated downstream Smads were analyzed by Western blot, qRT-PCR, and immunocytochemical experiments. Transcriptome analysis was conducted to explore the molecular mechanism. Blockage of BET bromodomains with JQ1 significantly suppressed rLECs proliferation by inducing G1 cell cycle arrest. Furthermore, JQ1 attenuated TGFβ2-dependent upregulation of mesenchymal gene expression and phosphorylation of Smad2/3 during the progression of EMT, whereas E-cadherin expression was preserved. JQ1 repressed MYC expression, which was dose- and time-dependently upregulated by TGFβ2. Inhibiting MYC with either the small-molecule inhibitor 10058-F4 or genetic knockdown phenocopied the effects of JQ1 treatment. MYC overexpression partially reversed the JQ1-regulated EMT-related alteration of gene expression. Both JQ1 and 10058-F4 blocked the expression of TGFβ receptor II and integrin αv in rLECs and abolished TGFβ2-induced opacification and subcapsular plaque formation in rat lens explants. Our results demonstrate the antifibrotic role of JQ1 in maintaining the epithelial characteristics of LECs and blocking TGFβ2-induced EMT, possibly by downregulating MYC, thereby providing new avenues for treating lens fibrosis.

Synthetic Lethality-Based Approach Identified EED and BRD4 As Critical Survival Factorsin Acte Myeloid Leukemia with Monosomy 7

Backgrounds: Monosomy of chromosome 7 (monosomy 7) is observed in about 9% of acute myeloid leukemia (AML) patients and related to resistance to conventional chemotherapy and poor prognosis. It is required to establish an effective treatment strategy based on the specific molecular pathogenesis associated with the chromosomal abnormality. In this study, we aimed to find a novel therapeutic target in AML with monosomy 7. Methods and Results: Chromosome 7 encodes multiple genes regulating histone methylation such as EZH2, KTM2C and KTM2E. Although loss of these genes is considered to contribute to the development of AML with monosomy 7, it may also be required for some leukemia cell functions. We hypothesized that haploinsufficiency of the epigenetic modifiers in the chromosome 7 is compensated by other epigenetic molecules in different chromosomes, and the AML cells with monosomy 7 are vulnerable to inhibition of those molecules. Based on this notion, we performed an RNA-interference (RNAi)-based screening by targeting 53 genes encoding epigenetic enzymes regulating histone methylation by using AML cell lines with monosomy 7: KG-1 and F-36P cells. We found that the siRNA-mediated knockdown of EED, BRD4 or BRDT significantly decreased cell viability in AML cells with monosomy 7 compared to K562 cells as the control without monosomy 7. Stable knockdown of EED expression by retroviral transduction of shRNA markedly attenuated proliferation as well as increased apoptosis specifically in leukemia cells with monosomy 7. Surprisingly, pharmacologic inhibition of EED, which blocks the binding of EED to the polycomb repressive complex 2 (PRC2), was only marginally effective for the monosomy 7 leukemia cells. These results suggest that EED supports survival of the monosomy 7 leukemia cells in a PRC2-independent manner. Recent studies showed that EED is not only a component of PRC2 but also interacts with the polycomb repressive complex 1 (PRC1). In contrast to modest effects of PRC2 inhibition, inhibition of PRC1 activity showed marked efficacy specifically in leukemia cells with monosomy 7. Co-inhibition of PRC1 and PRC2 synergistically suppressed proliferation of the monosomy 7-AML cells. These results collectively suggest that while both PRC1 and PRC2 cooperatively function, the PRC1 rather than PRC2 has a predominant role in the survival of monosomy 7 leukemia cells. In addition to EED, we identified BRD4 as an essential survival factors in AML with monosomy 7. Although inhibition of BET bromodomain proteins have already shown to be effective for a variety of AML, we showed that blockade of bromodomain proteins preferentially affected cellular proliferation of AML cells with monosomy 7. We then explored whether the deletion of specific genes within the chromosome 7 was responsible for increased sensitivity to BET bromodomain protein inhibition. K562 cells were individually treated with the siRNAs against 22 genes in the presence of a BET bromodomain inhibitor JQ1. We found that knockdown of MLL3 or MLL5 resulted in increased apoptosis of the JQ1-treated K562 cells. We also confirmed that pharmacological inhibition of histone methyltransferase activity of MLL3 and MLL5 showed synergistic effects with JQ1 treatment in the leukemia cells. Conclusion: We identified EED and BRD4 as novel promising therapeutic targets in AML with monosomy 7. Disclosures Kagoya: Kyowa Kirin: Speakers Bureau; Nihon Shinyaku: Research Funding. Miyauchi:kyowa Kirin: Research Funding. Kurokawa:Novartis Pharma K.K.: Research Funding; Celgene K.K.: Consultancy, Speakers Bureau; Astellas Pharma Inc.: Research Funding, Speakers Bureau; Kyowa Hakko Kirin Co., Ltd.: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Eisai Co., Ltd.: Research Funding, Speakers Bureau; Sumitomo Dainippon Pharma Co.,Ltd.: Research Funding, Speakers Bureau; Teijin Limited: Research Funding; Boehringer Ingelheim: Speakers Bureau; Yakult Honsha Company: Speakers Bureau; Nippon Shinyaku Co., Ltd.: Research Funding; Shionogi & Co., Ltd: Consultancy, Honoraria; Bioverativ Japan ltd.: Consultancy; Otsuka Pharmaceutical Co., Ltd.: Research Funding, Speakers Bureau; Daiichi Sankyo Conpany: Speakers Bureau; Bristol-Myers Squibb: Speakers Bureau; Chugai Pharmaceutical Company: Consultancy, Research Funding, Speakers Bureau; Pfizer Japan Inc.: Research Funding; MSD K.K.: Consultancy, Research Funding, Speakers Bureau; Takeda Pharmaceutical Company Limited.: Research Funding, Speakers Bureau; ONO PHARMACEUTICAL CO., LTD.: Speakers Bureau; Shire Japan K.K.: Speakers Bureau; Janssen Pharmaceutical K.K.: Speakers Bureau.

BET bromodomain inhibitor JQ1 promotes immunogenic cell death in tongue squamous cell carcinoma

Drug resistance substantially limits the curative capability of chemotherapy in head and neck cancers such as oral squamous cell carcinoma. Immunosuppression is considered a potential cause of drug resistance. A key discovery in the past decade is that chemotherapeutics can alter tumor cell immunogenicity via inducing release of damage-associated molecular patterns (DAMPs), including ecto-calreticulin (ecto-CALR), high mobility group box 1 (HMGB1) and ATP, causing tumor cells to die in a manner known as bona fide immunogenic apoptosis or immunogenic cell death (ICD). Intriguingly, JQ1 was found in this study to exhibit therapeutic potential in tongue squamous cell carcinoma (TSCC) by inducing ICD. JQ1 induced significant release of calreticulin (CALR), HMGB1 and ATP from Cal27 and SCC7 cells in vitro. Immature dendritic cells (Im-DCs) cocultured with JQ1-pretreated Cal27 cells exhibited significant upregulation of mature markers on their surface and an increase in the secretion of cytokines. In vivo experiments demonstrated that JQ1-pretreated dying SCC7 cells protected immunocompetent mice from rechallenge of SCC7 cells. Intravenous injection of JQ1 efficiently reduced tumor growth and increased tumor-infiltration of CD3+/CD8+ T cells in C3H mice.

Synergy between arsenic trioxide and JQ1 on autophagy in pancreatic cancer.

Pancreatic cancer is a deadliest type of malignancy and lacks effective intervention. We here report a potential strategy for treatment of this malignancy by the combination of arsenic trioxide (ATO) and BET bromodomain inhibitor JQ1. These two agents synergistically modulate multistages of autophagy and thus induce apoptosis effectively in pancreatic cancer cells. Our genomic and biochemical data have demonstrated that crosstalks between ER stress and autophagy play crucial roles during ATO-induced apoptosis, in which NRF2 may stand at the crossroad between cell death and survival. This has been further strengthened by our finding that NRF2 depletion renders insensitive cells into sensitive ones in regard to ATO treatment-caused cell death. The knockdown of NRF2 and the addition of JQ1 result in similar molecular/cellular effects in promoting effective ATO-induced apoptosis in cells that are insensitive to ATO treatment alone. Thus, the combination of ATO and JQ1 may represent a new treatment strategy for pancreatic cancer.

Abstract 2158: Combining cell panel profiling and synthetic lethality data to efficiently screen for synergistic combinations

Abstract In cancer therapy, combination drug treatment aims to improve response rate and decrease the development of drug resistance. The discovery of new effective drug combinations is constrained by the cost and effort of carrying out large unbiased screens and by poor translation of results towards the clinic. Here we describe how focusing on the biological mechanisms underlying the activity of drug candidates may aid a priori selection of promising synergy candidates and help in translate synergistic combinations towards a clinical situation. We have previously shown [1] that curve shift analysis as developed by Straetemans et al. [2] is a better method than combination-matrix screening. Also a dose based score such as the isobologram or the CI-index more robustly assesses synergy than an effect-based score such as the Bliss-additivity [1]. On this basis, we developed a two-step synergy screening approach, called SynergyScreen™. By distinguishing separate synergy screening and synergy confirmation stages, this setup capitalizes on insights from high throughput screening to discover robust and reproducible pharmacologically synergistic pairs. To further improve the efficiency of synergy screening, we focused on pre-selecting compounds in our screening library according to their biological mechanism. We profiled a library of more than 160 anti-cancer agents in a cell panel of 102 cell lines from diverse tumor origins [3]. Agents were clustered according to response and so-called exemplars were collected into a focused library that represents the spectrum of biological mechanisms of current cancer therapy. This synergy screening library includes many standard of care chemotherapeutic agents, approved and pre-clinical kinase inhibitors, epigenetic modulators and compounds acting by other mechanisms. Finally, we harnassed recent insights into the biology of synergy to understand and predict synergistic pairs. A tool was developed that uses the response of a compound in a 102 cell line panel to pick potential synergistic partners from the database of preprofiled compounds. It does this by computationally assessing if pairs can pharmacologically mimick clinically validated synthetic lethal interactions [4]. We optimized prediction accuracy using the results of internal and external synergy screens. The tool was applied to specifically enrich test libraries and to predict synergies at clinically relevant doses, including the results of a SynergyScreen™ with the poly-ADP ribose polymerase (PARP) inhibitor niraparib and the BET bromodomain inhibitor JQ1.

BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer.

BET bromodomain inhibitors block prostate cancer cell growth at least in part through c-Myc and androgen receptor (AR) suppression. However, little is known about other transcriptional regulators whose suppression contributes to BET bromodomain inhibitor anti-tumor activity. Moreover, the anti-tumor activity of BET bromodomain inhibition in AR-independent castration-resistant prostate cancers (CRPC), whose frequency is increasing, is also unknown. Herein, we demonstrate that BET bromodomain inhibition blocks growth of a diverse set of CRPC cell models, including those that are AR-independent or in which c-Myc is not suppressed. To identify transcriptional regulators whose suppression accounts for these effects, we treated multiple CRPC cell lines with the BET bromodomain inhibitor JQ1 and then performed RNA-sequencing followed by Master Regulator computational analysis. This approach identified several previously unappreciated transcriptional regulators that are highly expressed in CRPC and whose suppression, via both transcriptional or post-translational mechanisms, contributes to the anti-tumor activity of BET bromodomain inhibitors.

The BET-bromodomain inhibitor JQ1 renders neuroblastoma cells more resistant to NK cell-mediated recognition and killing by downregulating ligands for NKG2D and DNAM-1 receptors.

Low expression of ligands for NK cell-activating receptors contributes to neuroblastoma (NB) aggressiveness. Recently, we demonstrated that the expression of MYCN, a poor prognosis marker in NB, inversely correlates with that of activating ligands. This indicates that MYCN expression level can predict the susceptibility of NB cells to NK cell-mediated immunotherapy and that its downregulation can be exploited as a novel therapeutic strategy to induce the expression of activating ligands. Here we evaluated the effect of the BET-bromodomain inhibitor JQ1 on the expression of ligands for NK cell-activating receptors in NB cell lines. Although downmodulating MYCN, JQ1 impaired the expression of ligands for NK cell-activating receptors, rendering NB cell lines more resistant to NK cell-mediated killing. The downregulation of activating ligands was due to JQ1-mediated impaired functions of both c-MYC and p53, two transcription factors known to regulate the expression of ULBP1-3 ligands for NKG2D activating receptor. Moreover JQ1 strongly downregulated the levels of ROS, a stress-induced signaling event associated with the induction of ligands for NK cell-activating receptors. These results suggest that the use of JQ1 should be discourage in combination with NK cell-based immunotherapy in a perspective chemotherapeutic treatment of NB. Thus, further investigations, exploiting molecular strategies aimed to boost the NK cell-mediated killing of NB cells, are warranted.

BET Bromodomain Inhibition Cooperates with PD-1 Blockade to Facilitate Antitumor Response in Kras-Mutant Non-Small Cell Lung Cancer.

KRAS mutation is present in approximately 30% of human lung adenocarcinomas. Although recent advances in targeted therapy have shown great promise, effective targeting of KRAS remains elusive, and concurrent alterations in tumor suppressors render KRAS-mutant tumors even more resistant to existing therapies. Contributing to the refractoriness of KRAS-mutant tumors are immunosuppressive mechanisms, such as increased presence of suppressive regulatory T cells (Treg) in tumors and elevated expression of the inhibitory receptor PD-1 on tumor-infiltrating T cells. Treatment with BET bromodomain inhibitors is beneficial for hematologic malignancies, and they have Treg-disruptive effects in a non-small cell lung cancer (NSCLC) model. Targeting PD-1-inhibitory signals through PD-1 antibody blockade also has substantial therapeutic impact in lung cancer, although these outcomes are limited to a minority of patients. We hypothesized that the BET bromodomain inhibitor JQ1 would synergize with PD-1 blockade to promote a robust antitumor response in lung cancer. In the present study, using Kras+/LSL-G12D ; Trp53L/L (KP) mouse models of NSCLC, we identified cooperative effects between JQ1 and PD-1 antibody. The numbers of tumor-infiltrating Tregs were reduced and activation of tumor-infiltrating T cells, which had a T-helper type 1 (Th1) cytokine profile, was enhanced, underlying their improved effector function. Furthermore, lung tumor-bearing mice treated with this combination showed robust and long-lasting antitumor responses compared with either agent alone, culminating in substantial improvement in the overall survival of treated mice. Thus, combining BET bromodomain inhibition with immune checkpoint blockade offers a promising therapeutic approach for solid malignancies such as lung adenocarcinoma. Cancer Immunol Res; 6(10); 1234-45. ©2018 AACR.