Elucidating alternative polyadenylation regulation during prostate cancer progression to castration-resistance

Project Summary/Abstract Alternative polyadenylation (APA) is a major mechanism of posttranscriptional regulation that generates distinct 3′ untranslated regions (3′UTR) on RNA transcripts from most human genes. Mechanistically, APA is mainly regulated in trans through APA regulators and in cis by single-nucleotide variants (SNVs) enriched in 3′UTRs and downstream gene regions. Several reported examples indicate that APA can regulate the activity of oncogenes and tumor suppressor genes. However, the upstream regulatory mechanism and downstream function of APA in the cancer progression within clinical cohorts, particularly in prostate cancer, remains largely uncharacterized. Prostate cancer presentation is frequently stratified into groups: highly treatable androgen- dependent prostate cancer (ADPC), followed by the lethal castration-resistant prostate adenocarcinoma (CRPC), and ultimately progressing to the most aggressive form, neuroendocrine prostate cancer (NEPC). While significant efforts have been made to characterize gene expression changes during prostate cancer progression, a link between APA and prostate cancer progression has not previously been established. Our preliminary studies found that 3′UTR lengths are significantly shortened in CRPC patients compared with ADPC patients and are significantly lengthened in NEPC patients compared with CRPC patients. We further found that APA factor-regulated genes with altered 3′UTRs can function as novel oncogenes for CRPC or NEPC. Importantly, manipulating 3′UTR lengths of selected novel oncogenes by our developed 3′UTR CRISPR-dCas13 Engineering System (3′UTRCES) generates distinct molecular outcomes, leading to decreased prostate cancer growth in vitro and in vivo. We thus hypothesize that APA drives prostate cancer progression and can potentially be reversed in a clinically meaningful manner. In Aim 1, we will identify APA target genes during prostate cancer progression to castration resistance through multi-omics analyses in prostate clinical samples and cell models. In Aim 2, we will develop a computational model, namely MARS3'aQTL, to infer upstream APA regulators. In Aim 3, we will characterize the molecular regulations, biological functions, and clinical relevance of inferred APA regulators and will use 3′UTRCES to precisely interfere with APA of novel oncogenes. Our proposed studies' successful completion will establish APA as an important targetable posttranscriptional regulatory mechanism, contributing to a more complete understanding of prostate cancer progression.