Abstract LB196: An atlas of accessible chromatin in advanced prostate cancer
Authors: Raunak Shrestha, Lisa N. Chesner, Meng Zhang, Stanley Zhou, Adam Foye, Arian Lundberg, Alana S. Weinstein, Martin Sjöström, Xiaolin Zhu, Thaidy Moreno-Rodriguez, Haolong Li, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Mathieu Lupien, David A. Quigley, Felix Y. Feng
Journal: Cancer Research (2024)

Abstract Although androgen deprivation therapy (ADT) and second-generation Androgen Receptor (AR) signaling inhibitors (ARSIs) extend the survival of patients with metastatic castration-resistant prostate cancer (mCRPC), these tumors almost inevitably progress on these therapies. Prolonged usage of ADT and/or ARSI is associated with the development of treatment-associated transcriptional subtypes distinguished by alterations that affect the activity of the AR and neuroendocrine (NE) genes. Genomic and transcriptomic distinctions between the mCRPC subtypes are emerging. However, relatively little is known about the epigenome of the mCRPC transcriptional subtypes. We hypothesized that epigenetic mechanisms drive lineage plasticity in mCRPC by changing chromatin accessibility at regulatory loci for transcription factors (TFs) that affect downstream gene activity. In this study, we produced high-resolution chromatin accessibility maps linked to lineage-specific TF binding by performing Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on 70 mCRPC tissue biopsy samples from the SU2C/PCF West Coast Prostate Cancer Dream Team cohort. Here, we demonstrate that the global chromatin accessibility profile of mCRPC is unique and primarily correlated with the functional activity of AR. We comprehensively examined genome-wide TF occupancy signals in accessible chromatin regions and identified 203 TFs associated with mCRPC subtypes. Our findings indicated that different mCRPC subtypes exhibit a specific preference for certain TFs. The AR+NE- subtype showed a greater dependence on TFs, such as FOXA1, AR, and HOXB13, while the AR-NE+ subtype was more addicted to ASCL1 and NEUROD1. We found that a group of TFs including SP1, KLF5, and ZNF263 that bind to GC-rich sequences, are likely to play a major role in the regulation of the AR-NE- subtype. Most notably, we identified a potentially novel TF in prostate cancer, ZNF263, which is estimated to have a significant impact on gene activity in the AR-NE- subtype and may play a role in activating the targets of the MYC signaling pathway. Overall, our analysis of chromatin accessibility in mCRPC provides valuable insights into epigenetic changes that occur during mCRPC progression. Citation Format: Raunak Shrestha, Lisa N. Chesner, Meng Zhang, Stanley Zhou, Adam Foye, Arian Lundberg, Alana S. Weinstein, Martin Sjöström, Xiaolin Zhu, Thaidy Moreno-Rodriguez, Haolong Li, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Mathieu Lupien, David A. Quigley, Felix Y. Feng. An atlas of accessible chromatin in advanced prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB196.