Androgen Receptor Cistrome Research Articles

Abstract 6285: Defining androgen receptor function and the effects of PARP inhibition in BRCA1/2-deficient vs. proficient prostate cancer

Abstract Mutation or loss of the tumor suppressor genes BRCA1 and BRCA2 promotes the development of aggressive prostate cancer with poor outcomes and a high risk of metastatic relapse. Approximately 15% of metastatic prostate tumors are BRCA1/2-deficient. These tumors are frequently resistant to standard-of-care treatments that block androgen receptor (AR) function, although the mechanisms underlying this effect remain unclear. PARP inhibitors are synthetically lethal with BRCA1/2-deficiency and are commonly used as a late-line treatment in metastatic prostate cancer; however, both preclinical and clinical data have provided conflicting results on whether PARP inhibitors can be effective in BRCA1/2-proficient prostate tumors. BRCA1, BRCA2, PARP-1, and PARP-2 all have proposed roles in regulating transcription and the chromatin landscape. We therefore hypothesized that loss of BRCA1, BRCA2, and/or inhibition of PARP modulates AR function through changes in global chromatin structure and transcriptional pathways. We used patient-derived xenograft models and next-generation sequencing techniques to profile AR function in BRCA1/2-deficient vs. proficient prostate tumors. We found that loss of BRCA1 and BRCA2 is associated with chromatin accessibility changes, and differentially accessible regions correlate with DNA binding motifs for AR and AR cofactors. ChIP-seq for AR in these tumors demonstrated that BRCA1/2-deficiency is associated with an altered AR cistrome and a global decrease in AR genomic binding. Corresponding RNA-seq data confirmed a downregulated androgen response in BRCA1/2-deficient tumors. In cell line models, inhibition of PARP1 and PARP1/2 inhibited AR-driven transcription. Combining PARP inhibition with either androgen deprivation or the AR antagonist enzalutamide dampened the growth-inhibitory effects of PARP inhibitor treatment. Together, these results indicate that BRCA1/2-deficiency and PARP inhibition modulate AR function in prostate cancer. Citation Format: Nicole A. Traphagen, Esme Wheeler, Rong Li, Xintao Qiu, Myles Brown. Defining androgen receptor function and the effects of PARP inhibition in BRCA1/2-deficient vs. proficient prostate 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 6285.

Androgen Receptor/AP-1 Activates UGT2B15 Transcription to Promote Esophageal Squamous Cell Carcinoma Invasion.

Esophageal squamous cell carcinoma (ESCC) is an aggressive epithelial malignancy with poor prognosis. Interestingly, ESCC is strongly characterized by a male-predominant propensity. Our previous study showed that androgen receptor (AR) orchestrated a transcriptional repression program to promote ESCC growth, but it remains unclear whether AR can also activate oncogenic signaling during ESCC progression. In this study, by analyzing our previous AR cistromes and androgen-regulated transcriptomes, we identified uridine diphosphate glucuronosyltransferase family 2 member B15 (UGT2B15) as a bona fide target gene of AR. Mechanistically, AP-1 cofactors played important and collaborative roles in AR-mediated UGT2B15 upregulation. Functional studies have revealed that UGT2B15 promoted invasiveness in vitro and lymph node metastasis in vivo. UGT2B15 was partially responsible for the AR-induced invasive phenotype in ESCC cells. Importantly, simultaneous blocking of AP-1 and AR resulted in stronger inhibition of cell invasiveness compared to inhibiting AP-1 or AR alone. In conclusion, our study reveals the molecular mechanisms underlying the AR-driven ESCC invasion and suggests that the AR/AP1/UGT2B15 transcriptional axis can be potentially targeted in suppressing metastasis in male ESCC patients.

Abstract C061: The impact of the BRG1/BRM-associated factor (BAF) complex on the androgen receptor cistrome in African American prostate cancer

Abstract We aimed to establish in prostate cancer (PCa) how and why the androgen receptor displays differential functions in a manner driven by genomic ancestry, namely between African American (AA) and European American (EA) PCa, with the goal to assess how this may contribute to PCa health disparities. We utilized EA and AA non-malignant prostate and PCa cell models with confirmed genomic ancestry and defined the basal and dihydrotestosterone (DHT)-regulated AR and H3K27ac cistromes using CUT&RUN, and integrated these data with publicly available genomic counterparts. The DHT-dependent AR and H3K27ac cistromes significantly overlapped within AA cells and EA cells but there was significantly less overlap between AA and EA cells. For example, H3K27ac distributions were frequent (~15-20k sites) in each of non-malignant AA RC43N and EA HPr1AR, and malignant RC43T and LNCaP, and the significance of the overlaps were comparable for basal and DHT treated cells, but this was not significantly impacted by ancestry. By contrast the AR cistrome was highly DHT-dependent, with ~2k sites notably in LNCaP and RC43T, which very significantly overlapped with H3K27ac in the same cells but significantly less so across cells. Thus, although the H3K27ac cistrome was comparable across cells, the overlap with AR was driven by genomic ancestry. To investigate this, we focused on the BAF complexes as previously we identified reduced expression of a key component, SMARCA5, in AA PCa. These large multimeric complexes regulate nucleosome positioning during gene transcription and DNA repair. In PCa, the cBAF complex impacts different transcription factors, including ERG, and it is tempting to speculate that the corruption of cBAF identified in AA PCa phenocopies the impact of TMPRSS2-ETS impact observed in EA PCa. To test the possibility that the cBAF complex corrupts AR genomic functions in AA PCa we exploited scRNA-Seq data from PCa organoids from the Rb and Pten double knockout (PBCre4:Rb1f/f:Pten f/f ) to establish that expression of genes in the cBAF genes complex were collectively significantly altered in neuroendocrine PCa (NEPC) and Pouf23 androgen indifferent lineages. Secondly, knockdown of another cBAF component, SMARCC1, enhanced Enzalutamide sensitivity in same organoids. Finally, to test the impact of cBAF complex on AR signaling we have generated AA and EA PCa cell lines that stably express dCRISPR-activator (VP64) or repressor (KRAB) proteins and designed gRNAs to regulate expression of, for example, SMARCA5 and measure the impact on the AR cistrome and function. In summary, these findings identified that the shared AR and H3K27ac cistromes are driven by genomic ancestry, and that reduced expression of SMARCA5 and other components of the cBAF complex are significant in AA and advanced PCa, and impact AR signaling. Our future directions are focused on how SMARCA5 expression disrupts the balance between transcription factor functions, such as for the AR and other transcription factors, and effective DNA repair. Citation Format: Shahid S. Hussain, Debasis Nayak, David W. Goodrich, Clayton Yates, Moray Campbell. The impact of the BRG1/BRM-associated factor (BAF) complex on the androgen receptor cistrome in African American prostate cancer [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C061.

Abstract C054: Association of fatty acid synthase expression with FASN gene methylation and self-identified race in prostate cancer

Abstract Fatty acid synthase (FASN) catalyzes the synthesis of long-chain saturated fatty acids and is overexpressed during prostatic tumorigenesis; however, the mechanism of this upregulation remains unclear and could include gene amplification, epigenetic regulation or regulation by androgen receptor (AR). Though FASN is an attractive therapeutic target in prostate cancer and several clinical trials of FASN inhibitors are underway, prior studies have suggested racial disparities in FASN copy number and FASN protein expression exist in primary prostate cancer, which may have implications for the therapeutic efficacy of FASN inhibitors. FASN gene amplification may be more common in prostate cancers from self-identified Black (BL) patients than their White (WH) counterparts, and a recent study has suggested that FASN protein expression is also higher among primary prostate tumors from BL compared to WH men due to changes in the AR cistrome. Here, we examine FASN protein expression as measured by digitally quantified immunohistochemistry assay and reverse phase protein array analysis or FASN gene expression, comparing it to gene CpG methylation pattern by InfiniumEPIC profiling and whole genome bisulfite sequencing (WGBS) across multiple racially diverse primary and metastatic prostate cancer cohorts, including more than 1000 tumors. We demonstrate that the FASN gene body is hypomethylated and overexpressed in primary prostate tumors compared to benign tissue. FASN gene methylation shows a significant inverse correlation with FASN protein and gene expression in both primary and metastatic prostate cancer. However, in contrast to previous studies, we find no significant association of FASN expression or methylation with self-identified race or genetic ancestry in models that include ERG gene fusion status across two independent primary tumor cohorts. Taken together, these data support a potential epigenetic mechanism for FASN regulation in the prostate and suggest that FASN inhibitors may be equally efficacious in both BL and WH men with prostate cancer. Citation Format: Oluwademilade Dairo, Lia DePaula Oliveira, Ethan Schaffer, Thiago Vidotto, Adrianna Amaral De Aragao Mendes, Jiayun Lu, Jessica Hicks, Adam G. Sowalsky, Angelo M. De Marzo, Corrine E. Joshu, Brian Hanratty, Karen S. Sfanos, William B. Isaacs, Michael C. Haffner, Tamara L. Lotan. Association of fatty acid synthase expression with FASN gene methylation and self-identified race in prostate cancer [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C054.

Abstract B004: Genomic loss of TP53 impairs AR-targeted activity in metastatic prostate cancer

Abstract Background: Metastatic prostate cancer (mPC) is notable for a spectrum of recurrent genomic alterations, some associated with overall prognosis and others predicting response to specific therapeutics. Standard mPC interventions are designed to suppress the signaling program regulated by the androgen receptor (AR). These include androgen deprivation therapy (ADT) to reduce AR ligand levels and AR signaling inhibitors (ARSI) that directly impair AR function. While ADT and ARSI produce clinical responses in most patients, the duration and depth of response vary greatly. In addition, specific recurring genomic alterations are associated with shorter responses after ADT and ARSI therapy. Among these are mutations and/or genomic copy loss involving key tumor suppressor genes, including PTEN, RB1 and TP53. However, the mechanistic contribution of TP53 loss to AR signaling and resistance to AR pathway-directed therapy remains unresolved. Methods: Isogenic prostate cancer cell lines with intact and TP53 deletions were constructed using CRISPR/Cas9. The transcriptome profiles were determined by RNA-seq, and ChIP-seq was used to determine the chromatin landscapes of AR localization. In addition, we performed ATAC-seq to assess chromatin accessibility. Finally, to further validate the findings, we comprehensively analyzed AR-regulated gene expression and AR cistromes across a panel of patient-derived xenograft (PDX) models and clinical cohorts of mPC patient samples with respect to TP53 status. Results: Compared to TP53-wild-type (WT) cells, the transcriptional results of isogenic knockout TP53 lines showed impaired AR canonical activity. However, the downregulated AR response pathway is not caused by reduced levels of AR transcript or protein levels. Additionally, a similar trend was also found while comparing TP53-WT PDX models with TP53-loss models. We found that the loss of TP53 can shift the chromatin binding of AR, and the altered AR binding sites correlated with genes involved in neurogenesis pathways, which provide a potential mechanism of how the loss of TP53 might impact AR signaling and promote ADT and ARSI treatment resistance. We also identified additional AR chromatin binding sites that were enriched due to the loss of TP53. The targets potentially regulated by these sites are involved in multiple pathways, including cell morphogenesis involved in differentiation and response to the endogenous stimulus. Conclusions and Future Directions: Overall, the results indicate that in addition to altering DNA damage and repair pathways and contributing to cancer progression, genetic loss of TP53 in mPC may directly impair ADT and ARSI therapies, partially through alteration of AR chromatin activity. In addition, the AR cistrome reprogramming resulting from TP53 loss could also affect other pathways that could be exploited to overcome ARSI treatment resistance. Citation Format: Wanting Han, Michael D. Nyquist, Ilsa Coleman, Navonil De Sarkar, Lisa Ang, Eva Corey, Peter S. Nelson. Genomic loss of TP53 impairs AR-targeted activity in metastatic prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B004.

Grade Group 1 Prostate Cancers Exhibit Tumor-defining Androgen Receptor–driven Programs

Grade group 1 (GG1) primary prostate cancers with a pathologic Gleason score of 6 are considered indolent and generally not associated with fatal outcomes, so treatment is not indicated for most cases. These low-grade cancers have an overall negligible risk of locoregional progression and metastasis to distant organs, which is why there is an ongoing debate about whether these lesions should be reclassified as “noncancerous”. However, the underlying molecular activity of key disease drivers, such as the androgen receptor (AR), have thus far not been thoroughly characterized in low-grade tumors. Therefore, we set out to delineate the AR chromatin-binding landscape in low-grade GG1 prostate cancers to gain insights into whether these AR-driven programs are actually tumor-specific or are normal prostate epithelium-like. These analyses showed that GG1 tumors do not harbor a distinct AR cistrome and, similar to higher-grade cancers, AR preferentially binds to tumor-defining cis-regulatory elements. Furthermore, the enhancer activity of these regions and the expression of their respective target genes were not significantly different in GG1 tumors. From an epigenetic perspective, this finding supports the cancer designation currently given to these low-grade tumors and clearly distinguishes them from noncancerous benign tissue. Patient summaryWe characterized the molecular activity of the androgen receptor protein, which drives prostate cancer disease, in low-grade tumors. Our results show that these tumors are true cancers and are clearly separate from benign prostate tissue despite their low clinical aggressiveness.

Androgen receptor coordinates muscle metabolic and contractile functions.

Androgens are anabolic steroid hormones that exert their function by binding to the androgen receptor (AR). We have previously established that AR deficiency in limb muscles impairs sarcomere myofibrillar organization and decreases muscle strength in male mice. However, despite numerous studies performed in men and rodents, the signalling pathways controlled by androgens via their receptor in skeletal muscles remain poorly understood. Male ARskm-/y (n=7-12) and female ARskm-/- mice (n=9), in which AR is selectively ablated in myofibres of musculoskeletal tissue, and male AR(i)skm-/y , in which AR is selectively ablated in post-mitotic skeletal muscle myofibres (n=6), were generated. Longitudinal monitoring of body weight, blood glucose, insulin, lipids and lipoproteins was performed, alongside metabolomic analyses. Glucose metabolism was evaluated in C2C12 cells treated with 5α-dihydrotestosterone (DHT) and the anti-androgen flutamide (n=6). Histological analyses on macroscopic and ultrastructural levels of longitudinal and transversal muscle sections were conducted. The transcriptome of gastrocnemius muscles from control and ARskm-/y mice was analysed at the age of 9weeks (P<0.05, 2138 differentially expressed genes) and validated by RT-qPCR analysis. The AR (4691 peaks with false discovery rate [FDR]<0.1) and H3K4me2 (47225 peaks with FDR<0.05) cistromes in limb muscles were determined in 11-week-old wild-type mice. We show that disrupting the androgen/AR axis impairs in vivo glycolytic activity and fastens the development of type 2 diabetes in male, but not in female mice. In agreement, treatment with DHT increases glycolysis in C2C12 myotubes by 30%, whereas flutamide has an opposite effect. Fatty acids are less efficiently metabolized in skeletal muscles of ARskm-/y mice and accumulate in cytoplasm, despite increased transcript levels of genes encoding key enzymes of beta-oxidation and mitochondrial content. Impaired glucose and fatty acid metabolism in AR-deficient muscle fibres is associated with 30% increased lysine and branched-chain amino acid catabolism, decreased polyamine biosynthesis and disrupted glutamate transamination. This metabolic switch generates ammonia (2-fold increase) and oxidative stress (30% increased H2 O2 levels), which impacts mitochondrial functions and causes necrosis in <1% fibres. We unravel that AR directly activates the transcription of genes involved in glycolysis, oxidative metabolism and muscle contraction. Our study provides important insights into diseases caused by impaired AR function in musculoskeletal system and delivers a deeper understanding of skeletal muscle pathophysiological dynamics that is instrumental to develop effective treatment for muscle disorders.

Abstract 3859: Alterations in hormone receptors regulome following response to kinase inhibitors in lethal prostate cancer

Abstract The androgen receptor (AR) signaling axis is critical for prostate cancer (PCa) pathogenesis and all subsequent phases of disease progression. Although initial success with androgen deprivation therapy and AR-targeted agents such as enzalutamide or abiraterone, most patients inevitably relapse due to therapeutic resistance. Previous studies have shown that genomic AR is unchanged despite resistance to AR antagonists, and its gene expression is unaltered. Therapeutic resistance is broadly classified into two categories; restoration of AR activity and tumor progression despite AR blockade. Indeed, others have noted an extensive reprogramming of the AR cistrome in clinical and preclinical specimens, where a shift in canonical to non-canonical AR cistrome is associated with an increase in Gleason grade. In previous studies, we observed increases in known AR target genes following exposure to kinase inhibitors which was marked by a decrease in tumor growth. We hypothesized that restoration of canonical AR cistrome can be mediated through kinase inhibition and is associated with re-sensitization to AR-targeted therapy. In addition, we treated cell lines and patient-derived xenograft models of advanced prostate cancer with kinase signaling pathway inhibitors, AR signaling inhibitors, or a combination of both for 24 hours (in vitro) or five days (in vivo). In addition, samples were collected and processed for RNA-seq and ChIP-seq. Our transcriptomic analysis showed enrichment of previously published non-canonical AR target genes in cells resistant to AR-targeted agents. When resistant cells were exposed to kinase inhibitors, we observed an enrichment of canonical AR target genes. In addition, we identified unique AR-enriched peaks at active sites associated with resistance. Through GSEA of gene annotated peaks, we found unique regulatory transcription factor targets, some of which are associated with cell proliferation and differentiation and may play a functional role in AR cistrome adaptation to resistance and survival. Overall, our data suggest that AR transcription adapts to the therapeutic resistance of AR antagonists via the enrichment of non-canonical AR cistrome. Furthermore, restoration of canonical AR cistrome is achieved following kinase signaling pathway inhibition and is associated with re-sensitization to AR-targeted therapy. Citation Format: Remi M. Adelaiye-Ogala, Surendra Gulla, Jonathan E. Bard, David J. VanderWeele, Kathleen Kelly. Alterations in hormone receptors regulome following response to kinase inhibitors in lethal prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3859.

Abstract 3989: EVI1 oncogenic role in non-canonical AR driven lethal prostate cancer

Abstract Background: Androgen receptor (AR) remains active in castration-resistant prostate cancer (CRPC), and AR cistrome can become extensively reprogrammed with disease progression. Recent findings from our group and others have shown an association with non-canonical AR signature with resistance to enzalutamide. However, the complete mechanism is not fully revealed. EVI1 belongs to the zinc-finger transcription factor family, and overexpression of EVI1 is associated with poor patient outcomes. However, its role in the context of resistance to AR-targeted therapy remains unclear. Our preliminary data from ChIP-seq and GSEA analysis shows a significant enrichment of EVI1 target gene-set captured from annotated enzalutamide-resistant AR binding sites. Hypothesis: EVI1 cooperates in regulating the non-canonical AR activity associated with resistance to AR targeted therapy and blocking EVI1 may overcome resistance to target therapy. Methods: Using a PDX model of advanced enzalutamide-resistant CRPC, we performed single-cell ATAC-seq + gene expression multi-omic assay. Next, we determined the enrichment of canonical vs. non-canonical AR signatures across cell populations. Using motif analysis and transcription factor foot printing, we determine EVI1 (MECOM) motif z score and enrichment. Results: Our findings demonstrate enrichment of non-canonical AR signatures in distinct population of cells following exposure to enzalutamide. In addition, the subpopulation of cells enriched for non-canonical AR cistrome also exhibited high EVI1 (MECOM) motif z-scores. Conclusion: Our data suggests a potential link between EVI1 and non-canonical AR signaling. Ongoing mechanistic studies will provide insight mechanism by which EVI1 controls non canonical AR activity and its vulnerabilities. Citation Format: Surendra Gulla, Jonathan E. Bard, David J. VanderWeele, Kathleen Kelly, Remi Adelaiye-Ogala. EVI1 oncogenic role in non-canonical AR driven lethal prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3989.

LSD1 inhibition disrupts super-enhancer driven oncogenic transcriptional programs in castration-resistant prostate cancer.

The lysine demethylase LSD1 (also called KDM1A) plays important roles in promoting multiple malignancies including both hematologic cancers and solid tumors. LSD1 targets histone and non-histone proteins and can function as a transcriptional corepressor and coactivator. LSD1 has been reported to act as a coactivator of androgen receptor (AR) in prostate cancer (PCa) and to regulate the AR cistrome via demethylation of its pioneer factor FOXA1. A deeper understanding of the key oncogenic programs targeted by LSD1 could help stratify PCa patients for treatment with LSD1 inhibitors, which are currently under clinical investigation. In this study, we performed transcriptomic profiling in an array of castration-resistant PCa (CRPC) xenograft models that are sensitive to LSD1 inhibitor treatment. Impaired tumor growth by LSD1 inhibition was attributed to significantly decreased MYC signaling, and MYC was found to be a consistent target of LSD1. Moreover, LSD1 formed a network with BRD4 and FOXA1 and was enriched at super-enhancer (SE) regions exhibiting liquid-liquid phase separation. Combining LSD1 inhibitors with BET inhibitors exhibited strong synergy in disrupting the activities of multiple drivers in CRPC, thereby inducing significant growth repression of tumors. Importantly, the combination treatment showed superior effects than either inhibitor alone in disrupting a subset of newly identified CRPC-specific SEs. These results provide mechanistic and therapeutic insights for co-targeting two key epigenetic factors and could be rapidly translated in the clinic for CRPC patients.

To bind or not to bind: Cistromic reprogramming in prostate cancer.

The term “cistrome” refers to the genome-wide location of regulatory elements associated with transcription factor binding-sites. The cistrome of key regulatory factors in prostate cancer etiology are substantially reprogrammed and altered during prostatic transformation and disease progression. For instance, the cistrome of the androgen receptor (AR), a ligand-inducible transcription factor central in normal prostate epithelium biology, is directly impacted and substantially reprogrammed during malignant transformation. Accumulating evidence demonstrates that additional transcription factors that are frequently mutated, or aberrantly expressed in prostate cancer, such as the pioneer transcription factors Forkhead Box A1 (FOXA1), the homeobox protein HOXB13, and the GATA binding protein 2 (GATA2), and the ETS-related gene (ERG), and the MYC proto-oncogene, contribute to the reprogramming of the AR cistrome. In addition, recent findings have highlighted key roles for the SWI/SNF complex and the chromatin-modifying helicase CHD1 in remodeling the epigenome and altering the AR cistrome during disease progression. In this review, we will cover the role of cistromic reprogramming in prostate cancer initiation and progression. Specifically, we will discuss the impact of key prostate cancer regulators, as well as the role of epigenetic and chromatin regulators in relation to the AR cistrome and the transformation of normal prostate epithelium. Given the importance of chromatin-transcription factor dynamics in normal cellular differentiation and cancer, an in-depth assessment of the factors involved in producing these altered cistromes is of great relevance and provides insight into new therapeutic strategies for prostate cancer.

FOXA1 regulates alternative splicing in prostate cancer.

SummaryDysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1. By controlling trans-acting factor expression, FOXA1 exploits an “exon definition” mechanism calibrating alternative splicing toward dominant isoform production. This regulation especially impacts splicing factors themselves and leads to a reduction of nonsense-mediated decay (NMD)-targeted isoforms. Inclusion of the NMD-determinant FLNA exon 30 by FOXA1-controlled oncogene SRSF1 promotes cell growth in vitro and predicts disease recurrence. Overall, we report a role for FOXA1 in rewiring the alternative splicing landscape in prostate cancer through a cascade of events from chromatin access, to splicing factor regulation, and, finally, to alternative splicing of exons influencing patient survival.

The Prostate Cancer Androgen Receptor Cistrome in African American Men Associates with Upregulation of Lipid Metabolism and Immune Response.

With immunotherapies and inhibitors of metabolic enzymes in clinical development, the altered lipid metabolism and immune response in African-American men provides potential therapeutic opportunities to attenuate racial disparities in prostate cancer.

Response to supraphysiological testosterone is predicted by a distinct androgen receptor cistrome.

The androgen receptor (AR) is a master transcription factor that regulates prostate cancer (PC) development and progression. Inhibition of AR signaling by androgen deprivation is the first-line therapy with initial efficacy for advanced and recurrent PC. Paradoxically, supraphysiological levels of testosterone (SPT) also inhibit PC progression. However, as with any therapy, not all patients show a therapeutic benefit, and responses differ widely in magnitude and duration. In this study, we evaluated whether differences in the AR cistrome before treatment can distinguish between SPT-responding (R) and -nonresponding (NR) tumors. We provide the first preclinical evidence to our knowledge that SPT-R tumors exhibit a distinct AR cistrome when compared with SPT-NR tumors, indicating a differential biological role of the AR. We applied an integrated analysis of ChIP-Seq and RNA-Seq to the pretreatment tumors and identified an SPT-R signature that distinguishes R and NR tumors. Because transcriptomes of SPT-treated clinical specimens are not available, we interrogated available castration-resistant PC (CRPC) transcriptomes and showed that the SPT-R signature is associated with improved survival and has the potential to identify patients who would respond to SPT. These findings provide an opportunity to identify the subset of patients with CRPC who would benefit from SPT therapy.

Genomic Insights into Non-steroidal Nuclear Receptors in Prostate and Breast Cancer.

Alterations in transcriptional programs are a fundamental feature of prostate (PCa) and breast cancer (BrCa), and frequently target the actions of the principal steroidal nuclear receptors (NRs), namely the androgen receptor (AR) and the estrogen receptor alpha (ERα), respectively. Indeed, the functions of AR and ERα are central to both prostate and mammary gland biology. The genomic interactions of these NRs become highly distorted in part by changing how they functionally interact with a cohort of non-steroidal Type II NRs, which are by contrast relatively understudied compared to their steroidal cousins. For example, the AR cistrome overlaps with cistromes of different Type II NRs, which suggests a high potential for integrated NR functions to tailor transcriptional signals. Over recent years the cistromes of these Type II NRs, including HNF4s, RARs, PPARs and VDR, have been studied in PCa and BrCa revealing convergence and functional consequences, and are reviewed in the current chapter.

Abstract P192: Comprehensive preclinical characterization of the mechanism of action of EPI-7386, an androgen receptor N-terminal domain inhibitor

Abstract Background: Androgen receptor (AR) signaling is a main driver of prostate cancer progression and remains a crucial target for therapeutic intervention even in late stages of the disease. While current anti-androgen therapies targeting directly or indirectly the AR ligand binding domain (LBD) are initially effective, resistance ultimately develops, and new methods of inhibiting the AR pathway are needed. The selective targeting of the N-terminal domain (NTD) of the AR represents a novel method of blocking AR signaling to by-pass LBD-related resistance. EPI-7386 is a potent and metabolically stable NTD inhibitor (aniten) currently in a phase 1 dose-escalation study in mCRPC patients (NCT04421222). Here we further characterized the binding to AR NTD and the mechanism of action of EPI-7386. Methods: Target engagement was measured by Cellular Thermal Shift Assay (CETSA) and two-dimensional Nuclear Magnetic Resonance (2D NMR) spectroscopy. The potency and selectivity of EPI-7386 was determined in cellular models expressing different forms of AR using reporter and cell viability assays. qPCR, NanoString, and RNA sequencing were used to explore the activity of EPI-7386 on the AR transcriptome. To determine the effect of EPI-7386 on AR genomic occupancy, Chromatin immunoprecipitation sequencing (ChIP-seq) was performed. Results: We confirmed target engagement of EPI-7386 with an LBD truncated AR variant by CETSA using a cell line which expresses only AR-V567es, suggesting the interaction of EPI-7386 with AR NTD. In the same cell line, AR antagonist enzalutamide that binds to AR LBD showed no target engagement with AR-V567es. Furthermore, 2D NMR study results demonstrate an interaction of EPI-7386 with amino acid residues located in the transcription activation unit 5 (Tau-5) region of the AR NTD, a region which has been described to be involved in interactions with transcriptional cofactors such as CBP/p300. EPI-7386 strongly impaired the transcriptional activity and gene expression driven exclusively by LBD truncated AR variants including AR-V567es and AR-V7 and decreased cell viability. EPI-7386 has been shown to suppress the AR regulated transcriptome and the combination of EPI-7386 with lutamides resulted in broader and deeper inhibition of AR-regulated gene expression. The analysis of the AR cistrome by ChIP-seq showed that EPI-7386 displaces genome-wide androgen induced AR binding and the combination with enzalutamide completely abrogated AR binding. Conclusion: EPI-7386 is a potent AR NTD inhibitor that has the capacity to by-pass AR LBD resistance mechanisms to current anti-androgen therapies by uniquely inhibiting AR-mediated signaling. The agent has the potential for providing clinical benefit as a single agent in patients whose tumors are progressing on anti-androgens or in combination with current anti-androgens in earlier line patients. Citation Format: Nan Hyung Hong, Shihua Sun, Peter Virsik, Alessandra Cesano, Elahe A. Mostaghel, Stephen R. Plymate, Berenger Biannic, Han-Jie Zhou, Ronan Le Moigne. Comprehensive preclinical characterization of the mechanism of action of EPI-7386, an androgen receptor N-terminal domain inhibitor [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P192.

An androgen receptor switch underlies lineage infidelity in treatment-resistant prostate cancer.

Cancers adapt to increasingly potent targeted therapies by reprogramming their phenotype. Here we investigated such a phenomenon in prostate cancer, in which tumours can escape epithelial lineage confinement and transition to a high-plasticity state as an adaptive response to potent androgen receptor (AR) antagonism. We found that AR activity can be maintained as tumours adopt alternative lineage identities, with changes in chromatin architecture guiding AR transcriptional rerouting. The epigenetic regulator enhancer of zeste homologue 2 (EZH2) co-occupies the reprogrammed AR cistrome to transcriptionally modulate stem cell and neuronal gene networks-granting privileges associated with both fates. This function of EZH2 was associated with T350 phosphorylation and establishment of a non-canonical polycomb subcomplex. Our study provides mechanistic insights into the plasticity of the lineage-infidelity state governed by AR reprogramming that enabled us to redirect cell fate by modulating EZH2 and AR, highlighting the clinical potential of reversing resistance phenotypes.

Somatic Alterations Impact AR Transcriptional Activity and Efficacy of AR-Targeting Therapies in Prostate Cancer.

Simple SummaryFor patients whose prostate cancer spreads beyond the confines of the prostate, treatment options continue to increase. However, we are missing the information that is needed to choose for each patient the best treatment at each step of his cancer progression so we can ensure that maximal remissions and prolonged survival are achieved. In this review, we examine whether a better understanding of how the activity of the target for the default first treatment, the androgen receptor, is regulated in prostate cancer tissues can improve prostate cancer treatment plans. We consider the evidence for variability of androgen receptor activity among patients and examine the molecular basis for this variable action. We summarize clinical evidence supporting that information on a prostate cancer’s genomic composition may inform on its level of androgen receptor action, which may facilitate choice for the most effective first-line therapy and ultimately improve prostate cancer treatment plans overall.Inhibiting the activity of the ligand-activated transcription factor androgen receptor (AR) is the default first-line treatment for metastatic prostate cancer (CaP). Androgen deprivation therapy (ADT) induces remissions, however, their duration varies widely among patients. The reason for this heterogeneity is not known. A better understanding of its molecular basis may improve treatment plans and patient survival. AR’s transcriptional activity is regulated in a context-dependent manner and relies on an interplay between its associated transcriptional regulators, DNA recognition motifs, and ligands. Alterations in one or more of these factors induce shifts in the AR cistrome and transcriptional output. Significant variability in AR activity is seen in both castration-sensitive (CS) and castration-resistant CaP (CRPC). Several AR transcriptional regulators undergo somatic alterations that impact their function in clinical CaPs. Some alterations occur in a significant fraction of cases, resulting in CaP subtypes, while others affect only a few percent of CaPs. Evidence is emerging that these alterations may impact the response to CaP treatments such as ADT, radiation therapy, and chemotherapy. Here, we review the contribution of recurring somatic alterations on AR cistrome and transcriptional output and the efficacy of CaP treatments and explore strategies to use these insights to improve treatment plans and outcomes for CaP patients.

Abstract 2317: Targeting prostate cancer super enhancers by co-inhibiting LSD1 and BRD4

Abstract In prostate cancer (PCa) cells, “pioneer” factor FOXA1 resides at distal enhancers enriched with histone 3 lysine 4 methylation (H3K4me) and lysine 27 acetylation (H3K27ac). FOXA1 is capable of remodeling the compact chromatin to facilitate androgen receptor (AR) recruitment. Recent studies revealed overexpression of FOXA1 caused by frequent structural alterations in the lethal stage of PCa, namely castration-resistant PCa(CRPC), suggesting FOXA1 as a critical target in CRPC. However, a lack of targetable domain hinders the effective targeting of FOXA1. Our recent (epi)genomic profiling study revealed that lysine-specific demethylase (LSD1) and FOXA1 co-occupy at active enhancers in PCa cells and LSD1 demethylase activity is required for FOXA1 chromatin binding. LSD1 inhibition can quickly and drastically reduce FOXA1 global binding and concurrently impair the “openness” of enhancers, leading to disrupted AR cistrome. Mechanistically, we demonstrated that this activator function of LSD1 is mediated through directly demethylating K270 of FOXA1. By testing an array of adenocarcinoma CRPC in vivo models, we further showed that the efficacy of LSD1 inhibitors may be correlated with FOXA1 levels. Collectively, these results provide the molecular reasoning on co-targeting the epigenetic regulators that are important for promoting AR activity in treating CRPC. Furthermore, we have found that LSD1, FOXA1, and BRD4 (a Bromodomain and Extra-Terminal motif (BET) protein) co-occupy the super enhancers characterized by distinguishable high levels of H3K4me2 and H3K27ac in PCa cells. Super enhancers have been found to drive oncogenic transcription program in PCa. As an active enhancer marker and an important AR coactivator, BRD4 recognizes H3K27ac signal and promotes the initiation and elongation steps in gene transcription process. Herein, we focus on the potential synergism of combined targeting of LSD1 and BRD4. We found that FOXA1 interacted with BRD4 in different cell lines and patient-derived xenograft (PDX) tumor tissues. In line with this association, either LSD1 inhibitors or BET inhibitors could decrease FOXA1 and BRD4 chromatin binding. Characterization of the physical interaction is an ongoing study. We found that the combinational treatment lead to a more effective reduction of AR transcriptional activity than either single treatment. The PCa cell proliferation in vitro was also more profoundly inhibited by combined therapy. More importantly, we demonstrated this synergism in both 22RV1 xenograft and PDX LuCaP35CR in the castrated mice, with a lower dose of LSD1 inhibitor and BET inhibitor (both in clinical trials) which did not induce overt toxicity in the animals. Currently, we are performing RNA-seq studies to identify the convergent downstream pathways by this co-treatment. In summary, our study provides important pre-clinical insights for targeting the CRPC enhancers by combining inhibitors of LSD1 and BRD4. Citation Format: Shuai Gao, Muqing Li, Mingyu Liu, Dong Han, Zifeng Wang, Wanting Han, Changmeng Cai. Targeting prostate cancer super enhancers by co-inhibiting LSD1 and BRD4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2317.

Selective androgen receptor modulators activate the canonical prostate cancer androgen receptor program and repress cancer growth.

Prostate cancer (PC) is driven by androgen receptor (AR) activity, a master regulator of prostate development and homeostasis. Frontline therapies for metastatic PC deprive the AR of the activating ligands testosterone (T) and dihydrotestosterone (DHT) by limiting their biosynthesis or blocking AR binding. Notably, AR signaling is dichotomous, inducing growth at lower activity levels, while suppressing growth at higher levels. Recent clinical studies have exploited this effect by administration of supraphysiological concentrations of T, resulting in clinical responses and improvements in quality of life. However, the use of T as a therapeutic agent in oncology is limited by poor drug-like properties as well as rapid and variable metabolism. Here, we investigated the antitumor effects of selective AR modulators (SARMs), which are small-molecule nonsteroidal AR agonists developed to treat muscle wasting and cachexia. Several orally administered SARMs activated the AR program in PC models. AR cistromes regulated by steroidal androgens and SARMs were superimposable. Coregulatory proteins including HOXB13 and GRHL2 comprised AR complexes assembled by both androgens and SARMs. At bioavailable concentrations, SARMs repressed MYC oncoprotein expression and inhibited the growth of castration-sensitive and castration-resistant PC in vitro and in vivo. These results support further clinical investigation of SARMs for treating advanced PC.