Identification of critical epigenetic modifiers in prostate cancer

Prostate cancer (PCa) is the second leading cause of cancer-related death in men. The introduction of potent second-generation antiandrogens such as enzalutamide (ENZA) has improved overall survival for patients with recurrent or metastatic PCa. Yet, while patients initially respond to treatment, the vast majority eventually develop resistance. ENZA-resistant PCa is almost invariably lethal, and few treatment options are available. Clinical and basic studies have demonstrated that epigenetic events play a critical role in the development of ENZA resistance by changing the genome accessibility through DNA methylation, histone modifications, and chromatin remodeling. Considering their critical function and druggability, epigenetic modifiers offer a promising pharmacological target to treat ENZA-resistant PCa. This study aims to identify critical epigenetic modifiers in late-stage ENZA-resistant PCa. Due to the availability of lysine demethylase (KDM) inhibitors, we tested the essentiality of all KDM enzymes to provide preclinical evidence that would support further drug development. We performed an arrayed screen using a KDM-focused shRNA library in multiple PCa cell lines. Despite previous literature, we observed that the knockdown of KDM enzymes largely had little effect on PCa proliferation, potentially due to genetic redundancies. To expand the focus of the project and screen all epigenetic modifiers, we, therefore, generated an epigenetic-focused CRISPR library and performed unbiased CRISPR-Cas9 dropout screens in multiple PCa and ENZA-resistant cell lines. Although shRNA screen results were inconclusive, our epigenome-wide CRISPR-Cas9 screens (EPIKOL) identified both known and novel epigenetic targets in ENZA-resistant PCa. From this, we focused on SMARCC2, a core subunit of the SWI/SNF complex as a potential candidate for ENZA-resistant prostate cancer. We confirmed SMARCC2-dependency on multiple ENZA-resistant models with orthogonal proliferation assays. We found that the SMARCC2 cistrome was significantly expanded in ENZA-resistant cells with marked differences in transcription factor occupancy. These gained binding sites correlated with increased chromatin structures in PDX and clinical CRPC samples. Collectively, these findings suggest that the SMARCC2-dependent SWI/SNF complex gains an essential role in ENZA resistance by expanding its chromatin regulation. This dependency could be exploited for the treatment of ENZA-resistant CRPC by SWI/SNF inhibitors.