Abstract A062: Alternative promoter usage is linked to transcriptional and epigenetic alterations during prostate cancer progression
Authors: Zhang Meng , Sjöström Martin , Shrestha Raunak , Lundberg Arian , Moreno-Rodriguez Thaidy , Foye Adam , Dang Ha X. , Alumkal Joshi J. , Aggarwal Rahul , Small Eric J. , Maher Christopher A. , Feng Felix Y. , Quigley David 
Published: June 2023

Abstract
Background: Prostate tumor progression is driven by transcription factors (TFs), most prominently the Androgen Receptor (AR), that drive proliferation and therapy resistance. Many genes have several promoters that can be bound by distinct TFs. It is unclear what role alternative promoter selection plays in tumor progression. We hypothesized that driver TFs target novel gene promoters during prostate tumor progression, and that understanding how this targeting occurs would reveal novel aspects of prostate tumor biology. Methods: We performed ultra-deep RNA sequencing on 104 metastatic Castration Resistant Prostate Cancer (mCRPC) biopsies, generating &gt; 450M reads/sample (10X the typical depth), in samples with matched whole genome DNA and methylation sequencing. We combined these data with published deep transcriptomes in normal prostate and localized prostate cancer for a total of 274 samples. Promoter activity was evaluated in all 274 biopsies using the proActiv tool. Differential promoter activity levels were integrated with transcription factor motif enrichment, chromatin immunoprecipitation sequencing, and previously published somatic and methylation sequencing data in the mCRPC samples. Results: Using normal prostate tissue as a baseline, we identified 463 and 3,237 APs with differential activity in localized prostate cancer and mCRPC, respectively. Increased alternative promoter (AP) usage was associated with upregulation of prostate tumor driver genes. Elevated androgen signaling in both localized and mCRPC was correlated with increased AP use. In localized prostate tumors, APs preferentially switch to promoters harboring binding sites for the AR pioneer factor FOXA1. In mCPRC, APs were further enriched for binding of MYC, E2F1, and HIF1A. Furthermore, AP usage reflects transcriptional dysregulation related to lineage plasticity in response to therapy. APs in neuroendocrine prostate cancer (NEPC) were bound by neuroendocrine TFs such as ASCL1 and HAND2. While canonical promoters are usually unmethylated, methylation levels at APs were strongly linked to AP activity. Conclusions: Our data show that transcription initiated at APs is a key contributor to increased gene activity in prostate tumors. APs that are upregulated in prostate tumors are linked to transcription factors activated by recurrent somatic alterations and lineage plasticity. Methylation at APs is an important and underappreciated driver of promoter choice in mCRPC. Understanding how somatic alterations and epigenetic reprogramming of TFs affect APs is essential to understanding how these processes impact therapy resistance.
Citation Format: Meng Zhang, Martin Sjöström, Raunak Shrestha, Arian Lundberg, Thaidy Moreno-Rodriguez, Adam Foye, Ha X. Dang, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Christopher A. Maher, Felix Y. Feng, David Quigley. Alternative promoter usage is linked to transcriptional and epigenetic alterations during prostate cancer progression [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 A062.