BET inhibitors reduce tumor growth in preclinical models of gastrointestinal gene signature–positive castration-resistant prostate cancer
Shipra Shukla, Dan Li, Woo Hyun Cho, Dana M. Schoeps, Holly M. Nguyen, Jennifer L. Conner, Marjorie L. Roskes, Anisha Tehim, Gabriella Bayshtok, Mohini R. Pachai, Juan Yan, Nicholas A. Teri, Eric Campeau, Sarah Attwell, Patrick Trojer, Irina Ostrovnaya, Anuradha Gopalan, Ekta Khurana, Eva Corey, Ping Chi, Yu Chen
Shipra Shukla, Dan Li, Woo Hyun Cho, Dana M. Schoeps, Holly M. Nguyen, Jennifer L. Conner, Marjorie L. Roskes, Anisha Tehim, Gabriella Bayshtok, Mohini R. Pachai, Juan Yan, Nicholas A. Teri, Eric Campeau, Sarah Attwell, Patrick Trojer, Irina Ostrovnaya, Anuradha Gopalan, Ekta Khurana, Eva Corey, Ping Chi, Yu Chen
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Research Article Cell biology Genetics Oncology

BET inhibitors reduce tumor growth in preclinical models of gastrointestinal gene signature–positive castration-resistant prostate cancer

Abstract

A subgroup (~20%–30%) of castration-resistant prostate cancer (CRPC) aberrantly expresses a gastrointestinal (GI) transcriptome governed by 2 GI-lineage-restricted transcription factors, HNF1A and HNF4G. In this study, we found that expression of GI transcriptome in CRPC correlated with adverse clinical outcomes to androgen receptor (AR) signaling inhibitor treatment and shorter overall survival. Bromo- and extraterminal domain inhibitors (BETi) downregulated HNF1A, HNF4G, and the GI transcriptome in multiple CRPC models, including cell lines, patient-derived organoids, and patient-derived xenografts, whereas AR and the androgen-dependent transcriptome were largely spared. Accordingly, BETi selectively inhibited growth of GI transcriptome-positive preclinical models of prostate cancer. Mechanistically, BETi inhibited BRD4 binding at enhancers globally, including both AR and HNF4G bound enhancers, while gene expression was selectively perturbed. Restoration of HNF4G expression in the presence of BETi rescued target gene expression without rescuing BRD4 binding. This suggests that inhibition of master transcription factors expression underlies the selective transcriptional effects of BETi.

Authors

Shipra Shukla, Dan Li, Woo Hyun Cho, Dana M. Schoeps, Holly M. Nguyen, Jennifer L. Conner, Marjorie L. Roskes, Anisha Tehim, Gabriella Bayshtok, Mohini R. Pachai, Juan Yan, Nicholas A. Teri, Eric Campeau, Sarah Attwell, Patrick Trojer, Irina Ostrovnaya, Anuradha Gopalan, Ekta Khurana, Eva Corey, Ping Chi, Yu Chen

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Figure 2

BETis downregulate the expression of HNF4G and HNF1A and their transcriptional signature.

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BETis downregulate the expression of HNF4G and HNF1A and their transcrip...
(A) qRT-PCR showing expression of HNF1A after 4 hours of treatment with ABBV-075 and JQ1 at indicated doses. (B) qRT-PCR showing expression of HNF4G after 4 hours of treatment with ABBV-075 and JQ1 at indicated doses. (C) A representative immunoblot of 22Rv1 cells treated with JQ (0.5 μM), ABBV-075 (50 nM), and DMSO control for 24 hours against the indicated proteins (top). Bar graph (bottom) showing fold change in β-actin normalized band intensities of JQ1- and ABBV-075–treated samples over DMSO controls (n = 2). (D) Heat map of RNA-Seq expression of HNF signature genes in 22Rv1 cells after treatment with 25 nM ABBV-075 for 24 hours (top). (Bottom) The 2 heat maps show the modulation of AR target genes with ABBV-075 treatment using 2 different AR gene signatures. Data are plotted as the log2 difference in gene expression between ABBV-075– and DMSO-treated cells. Unadjusted P values are shown: *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001. (E) Global representation of GSEA analysis of RNA-Seq gene expression data set of 22RV1 cells treated with 25 nM ABBV-075 for 24 hours. The x-axis shows the normalized enrichment score, and y-axis is the FDR q-value (q-val). The PCa_GI and the HNF1A- and HNF4G-regulated gene sets are indicated in red. A GSEA plot of PCa_GI gene signature is shown (middle). (Right) A bar diagram shows the expression of AR, HNF1A, and HNF4G. NES, normalized enrichment score. (F) Modulation of HNF and AR scores by BETi ZEN-3694 in paired tumor biopsy specimens of patient 101047. (G) GSEA plots of PCa_GI gene signature in ZEN-3694–treated tumors compared with pretreated tumor. NES, normalized enrichment score.