Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma

Abstract

Alternative polyadenylation (APA) is a gene regulatory process that dictates mRNA 3’-UTR length, resulting in changes in mRNA stability and localization. APA is frequently disrupted in cancer and promotes tumorigenesis through altered expression of oncogenes and tumor suppressors. Pan-cancer analyses have revealed common APA events across the tumor landscape; however, little is known about tumor type-specific alterations that may uncover novel events and vulnerabilities. Here we integrate RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project and The Cancer Genome Atlas (TCGA) to comprehensively analyze APA events in 148 pancreatic ductal adenocarcinomas (PDAs). We report widespread, recurrent and functionally relevant 3’-UTR alterations associated with gene expression changes of known and newly identified PDA growth-promoting genes and experimentally validate the effects of these APA events on expression. We find enrichment for APA events in genes associated with known PDA pathways, loss of tumor-suppressive miRNA binding sites, and increased heterogeneity in 3’-UTR forms of metabolic genes. Survival analyses reveal a subset of 3’-UTR alterations that independently characterize a poor prognostic cohort among PDA patients. Finally, we identify and validate the casein kinase CK1α as an APA-regulated therapeutic target in PDA. Knockdown or pharmacological inhibition of CK1α attenuates PDA cell proliferation and clonogenic growth. Our single-cancer analysis reveals APA as an underappreciated driver of pro-tumorigenic gene expression in PDA via the loss of miRNA regulation.

Alternative polyadenylation characterizes epithelial and fibroblast phenotypic heterogeneity in pancreatic ductal adenocarcinoma

“…S1b). In concordance with previous findings, tumor tissues exhibited significantly higher proximal 3’ UTR-APA gene events (3’ UTR shortening) as compared to normal tissues [14,16]. In particular, tumor ductal cells showed significantly higher numbers of proximal 3’ UTR-APA events (1177 genes expressed shorter 3’ UTRs and 250 genes expressed longer 3’ UTRs) compared to normal ductal cells (Fig.…”

“…However, mechanistic drivers of such transcriptional and phenotypic heterogeneity in PDAC remain unclear. Recently, we performed an in-depth analysis of sequencing data on PDAC tumors that established 3’ UTR alternative polyadenylation (APA) as a mechanistic driver of oncogene expression [14–16]. Specific PDAC oncogenes were found to undergo proximal 3’ UTR-APA (usage of proximal 3’ UTR polyadenylation site) resulting in shorter 3’ UTRs, driving increased expression.…”

The RNA‐binding protein MEX3A is a prognostic factor and regulator of resistance to gemcitabine in pancreatic ductal adenocarcinoma

“…This regulation abolished ZEB1 translational repression by microRNAs, thus yielding higher protein levels [16]. Notably, enhanced PDAC tumorigenicity by loss of microRNA control through alternative polyadenylation has been recently observed on genome‐wide scale by analysis of a cohort of 148 PDAC patients [17], supporting the pathological relevance of this process in the disease. Lastly, control of mRNA stability by specific RBPs also contributes to PDAC growth and progression.…”