Large-scale alternative polyadenylation (APA)-wide association studies to identify putative susceptibility genes in human common cancers

Abstract

Alternative polyadenylation (APA) modulates mRNA processing in the 3 untranslated regions (3UTR), which affect mRNA stability and translation efficiency. Here, we build genetic models to predict APA levels in multiple tissues using sequencing data of 1,337 samples from the Genotype-Tissue Expression, and apply these models to assess associations between genetically predicted APA levels and cancer risk with data from large genome-wide association studies of six common cancers, including breast, ovary, prostate, colorectum, lung, and pancreas among European-ancestry populations. At a Bonferroni-corrected P{square}<{square}0.05, we identify 58 risk genes, including seven in newly identified loci. Using luciferase reporter assays, we demonstrate that risk alleles of 3UTR variants, rs324015 (STAT6), rs2280503 (DIP2B), rs1128450 (FBXO38) and rs145220637 (LDAH), could significantly increase post-transcriptional activities of their target genes compared to reference alleles. Further gene knockdown experiments confirm their oncogenic roles. Our study provides additional insight into the genetic susceptibility of these common cancers.