Epigenetic disruption of the RARγ complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer

Abstract

Lineage plasticity in advanced prostate cancer (PCa) involves a corruption of differentiation programs, often regulated by the androgen receptor (AR). This study explores an under-explored cistromic mechanism: how type II nuclear receptors like RARγ may affect AR control of prodifferentiation transcriptional programs. The components of the RARγ complex are dynamic in PCa cell models and enriched for miR-96 targets, partly due to m6A-marked miR-96 recognition elements. Restoration of TACC1 and RARγ, both miR-96 repressed targets, in 22Rv1 cells augmented the AR cistrome, particularly in active enhancers and super-enhancers. In 22Rv1 cells the RARγ complex was enriched for bookmarking components, and created nucleosome-free chromatin enriched for H3K27ac, and profoundly enhanced the dihydrotestosterone (DHT)-dependent AR cistrome in G2/M cells and are all indicative of bookmarking functions. The RARγ-dependent and DHT-regulated AR cistrome-transcriptome relationships were significantly strengthened, notably in Active Enhancers, associated with AR-dependent luminal differentiation transcriptional programs. Interestingly RARγ-dependent AR cistromes significantly overlapped with ONECUT2, but the comparative transcriptional analyses supported an antagonistic function between RARγ and ONECUT2. Finally, the footprint of these data was detected in advanced tumors. For example, the miR-96 targetome and RARγ/ONECUT2 antagonized genes were significantly similar to AR signaling inhibitor-induced alternative lineages and metastatic tumors. Partial correlation analyses revealed RARγ CoAs identified by RIME, including SSRP1, significantly strengthened the correlations between AR and RARγ-TACC1-dependent DHT-regulated target genes in SU2C advanced PCa, and differentially-expressed genes between tumors with high RARγ and low ONECUT2 expression compared to the reverse was significantly associated with elevated AR score. In summary, the RARγ complex, selectively targeted by miR-96 functions as an enhancer re-programmer by bookmarking chromatin in G ₂/M cells to sustain and restrict AR transcriptional competency required for programs such as luminal differentiation, and antagonizing ONECUT2.