Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13

Abstract

The constitutively active androgen receptor (AR) splice variant 7 (AR-V7) plays an important role in the progression of castration-resistant prostate cancer (CRPC). Although biomarker studies established the role of AR-V7 in resistance to AR-targeting therapies, how AR-V7 mediates genomic functions in CRPC remains largely unknown. Using a ChIP-exo approach, we show AR-V7 binds to distinct genomic regions and recognizes a full-length androgen-responsive element in CRPC cells and patient tissues. Remarkably, we find dramatic differences in AR-V7 cistromes across diverse CRPC cells and patient tissues, regulating different target gene sets involved in CRPC progression. Surprisingly, we discover that HoxB13 is universally required for and colocalizes with AR-V7 binding to open chromatin across CRPC genomes. HoxB13 pioneers AR-V7 binding through direct physical interaction, and collaborates with AR-V7 to up-regulate target oncogenes. Transcriptional coregulation by HoxB13 and AR-V7 was further supported by their coexpression in tumors and circulating tumor cells from CRPC patients. Importantly, HoxB13 silencing significantly decreases CRPC growth through inhibition of AR-V7 oncogenic function. These results identify HoxB13 as a pivotal upstream regulator of AR-V7-driven transcriptomes that are often cell context-dependent in CRPC, suggesting that HoxB13 may serve as a therapeutic target for AR-V7-driven prostate tumors.

Androgen receptor enhancer usage and the chromatin regulatory landscape in human prostate cancers

“…While hereditary HOXB13 mutations have been extensively reported in tissue, it remains to be determined whether this mutation affects HOXB13 and/or AR chromatin binding in vitro. Especially since HOXB13 functions as a key upstream regulator of AR signaling, both for the full-length (Pomerantz et al 2015) and AR-V7 splice variant (Chen et al 2018) (Fig. 2C), deeper mechanistic understanding of HOXB13 action in the AR signaling axis would be highly instrumental for designing novel therapeutics that would perturb this route.…”

Chromatin reprogramming as an adaptation mechanism in advanced prostate cancer

“…Endocrine-Related Cancer , Antonarakis et al 2014, Sharp et al 2019 and to contribute to resistance to enzalutamide and abiraterone (Sharp et al 2019). Interestingly, evidence of a distinct ligand-independent chromatin-binding profile of constitutively active AR splice variants (Lu et al 2015, Chen et al 2018 could be the result of the chromatin being incidentally more relaxed in CRPC. Moreover, recently, Chen and colleagues showed that HOXB13 directly interacted and pioneered binding of one of the most abundant AR splice variants, AR-V7, thereby suggesting cooperation in upregulating target oncogenes (Chen et al 2018).…”

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells

“…In summary, we have shown that HOXC4 and HOXC6 regulate critical genes affecting prostate cancer proliferation. In addition, we showed colocalization of HOXC4 and HOXC6 at HOXB13 sites that are also bound by FOXA1 and AR, which have been previously linked to regulation of prostate cancer cell proliferation [9,15,21,32,33]. We suggest that the Fig 5.…”

“…To ensure high quality of our FOXA1 ChIP-seq data, we used two different FOXA1 antibodies and confirmed, using IDR, that similar sets of binding sites were detected by both antibodies. We used published ChIP-seq datasets from 22Rv1 cells for AR [21]. We found that there is a striking correlation between the strength of the HOXC4 or HOXC6 binding sites and the strength of the binding sites for the key prostate cancer transcription factors HOXB13, FOXA1, and AR ( Fig 5A).…”