SMARCA4 ablation mitigates distal-less homeobox 1 ( DLX1 )- driven oncogenicity in prostate cancer

Prostate cancer (PCa) is a molecularly heterogeneous malignancy with high prevalence and mortality rates in males across the globe. Several enhancer-driven oncogenic programs regulated by transcription factors (TFs) such as AR, FOXA1, MYC, and ERG contribute to PCa progression. Previously, elevated expression of DLX1, a homeobox TF, was reported to be oncogenic in PCa, and was established to be transcriptionally regulated by the AR/ERG/FOXA1 circuitry. While therapeutic inhibition using the BET inhibitor (BETi) and anti-androgen treatment was effective, the activation of alternate signaling cascades and bypass pathways often leads to drug resistance in PCa. To overcome BETi resistance in PCa, we employed a bottom-up approach to identify alternative therapeutic strategies. Given that the SWI/SNF chromatin remodeling complex, specifically SMARCA2/4, is a key regulator of the AR/FOXA1/ERG enhancer circuitry, here we explored the therapeutic efficacy of a dual PROTAC degrader targeting SMARCA2/4, in DLX1 -high PCa. In silico analysis of a publicly available BRG1 ChIP-seq dataset showed peak enrichment at multiple sites on the DLX1 promoter and along the DLX1 gene body, implying its direct transcriptional control. In agreement, we noted the co-expression of SMARCA4 in DLX1 -high PCa patients in the TCGA-PRAD cohort as well as in the Indian PCa cohort. Mechanistically, we show that SMARCA2/4 PROTAC degrader treatment mitigates DLX1 expression in ERG-fusion positive PCa as well as in Castration-Resistant Prostate Cancer (CRPC) models. Furthermore, cell-based functional assays using the PROTAC degrader confirmed a decrease in the proliferative, invasive, and migratory potential of PCa cells along with reduced foci formation capacity. Similarly, PROTAC degrader treatment of isogenic RWPE1 cells overexpressing DLX1 showed reduced tumorigenicity, suggesting direct inhibition of DLX1 by the PROTAC degrader. Finally, we also observed remarkable inhibition of DLX1 in BETi-resistant PCa cells, suggesting the efficacy of SMARCA4 ablation in bypassing BETi resistance and mitigating DLX1-driven PCa oncogenicity.