Whole genome and transcriptome analysis of paired metastatic biopsies identified resistance mechanisms in castration-resistant prostate cancer

Abstract Background: Androgen receptor signaling inhibitors (ARSIs), including abiraterone and enzalutamide, are widely used to treat prostate cancer. However, resistance inevitably develops, and subsequent treatment options remain limited. Prior studies of resistant tumors identified genetic mechanisms of ARSI resistance converging on AR, including its gene and enhancer amplifications, as well as mutations and structural variants involving the ligand-binding domain. Additionally, a phenotypic switch from AR-driven adenocarcinoma to AR-independent neuroendocrine carcinoma is well recognized and thought to be mediated by epigenetic reprogramming. Genomic analysis of paired metastatic biopsies before and after ARSIs offers a unique opportunity to systematically define resistance mechanisms, but such data are limited, in part due to difficulty obtaining serial biopsies. Methods: We obtained paired metastatic biopsies from patients with metastatic castration-resistant prostate cancer (mCRPC) before the initiation of an ARSI and at disease progression while on the ARSI. We performed whole-genome sequencing (WGS) and RNA-seq on these samples and conducted bioinformatic and statistical analyses contrasting pairs pre- vs. post-ARSI to search for genetic and transcriptomic alternations associated with ARSI resistance. Results: We generated WGS data for 45 paired biopsies and concurrent RNA-seq data for 35 pairs. WGS analysis identified further copy number gain in the genomic region spanning AR and its known upstream enhancer in multiple patients, driven by tandem duplications, and associated with increased AR expression. Overlaying publicly available chromatin immunoprecipitation sequencing data of transcription factors known to be important in prostate cancer (AR, FOXA1, and HOXB13) and the enhancer marker H3K27ac, we identified putative novel enhancers both upstream and downstream of AR and plan to further assess their effects on AR expression in cell lines. Paired WGS analysis also identified genes with mutations newly arising post-ARSI, yet with only limited recurrence suggesting intertumor heterogeneity. Interestingly, our paired RNA-seq analysis identified SSTR1, whose expression was consistently and significantly decreased in most ARSI-resistant samples. In a separate retrospective analysis of a cohort of 123 patients, we found that low SSTR1 expression was associated with worse overall survival, and patient survival was improved with post-biopsy ARSIs only when SSTR1 expression was high. SSTR1 encodes somatostatin receptor type 1, and its activation by endogenous somatostatin or exogenous somatostatin analogues exerts an anti-proliferative effect in cells expressing SSTR1, consistent with our observation of its downregulation in resistant tumors. Conclusions: Whole genome and transcriptome analysis of paired metastatic biopsies identified amplification of putative novel AR enhancers and decreased SSTR1 expression involved in ARSI resistance that warrant further investigation in additional patients and experimental systems. Citation Format: Xiaolin Zhu, Daniël Vis, Martin Sjöström, Raunak Shrestha, Jeroen Kneppers, Tesa Severson, Yanyun Zhu, Meng Zhang, Arian Lundberg, Thaidy Moreno Rodriguez, Alana Weinstein, Haolong Li, Adam Foye, Rahul Aggarwal, Andries M Bergman, Eric Small, Wilbert Zwart, David Quigley, Michiel van der Heijden, Felix Feng. Whole genome and transcriptome analysis of paired metastatic biopsies identified resistance mechanisms in castration-resistant prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A029.