Background: Androgen Receptor (AR) signaling inhibitors, including enzalutamide, are treatment options for patients with metastatic castration-resistant prostate cancer (mCRPC), but resistance inevitably develops.

Methods: Using fresh-frozen mCRPC metastases samples from a prospective phase II clinical trial, we epigenetically profiled enhancer/promoter activities with H3K27ac chromatin immunoprecipitation sequencing, before and after AR-targeted therapy.

Results: Interestingly, AR-targeted therapy in mCRPC metastases had no impact on H3K27ac profiles indicating a static epigenetic landscape that is unaffected by treatment. We identified a distinct subset of H3K27ac-differentially marked regions that associate with treatment responsiveness. These data were successfully validated in mCRPC patient-derived xenograft models (PDX), stratifying samples on response to castration. In silico analyses revealed HDAC3 as a critical factor that can drive resistance to hormonal interventions, which we validated in vitro.

Conclusions: Using cell lines and mCRPC PDX tumors in vitro, we identified drug-drug synergy between enzalutamide and the pan-HDAC inhibitor vorinostat, providing therapeutic proof-of-concept. Cumulatively, these findings demonstrate the rationale for new therapeutic strategies using a combination of AR and HDAC inhibitors to improve patient outcome in advanced stages of mCRPC.