Large-scale multiomic analysis identifies non-coding somatic driver mutations and nominates <i>ZFP36L2</i> as a driver gene for pancreatic ductal adenocarcinoma.

Abstract

The identification and characterisation of somatic cancer driver mutations in the non-coding genome remains challenging. To broadly characterise non-coding driver mutations for pancreatic ductal adenocarcinoma (PDAC). Using mutation calls from whole-genome sequence data in PDACs and genome-scale maps of accessible gene regulatory regions in normal-derived and tumour-derived pancreatic samples, we analysed enrichment of non-coding mutations in gene regulatory regions relevant to normal-derived and tumour-derived pancreatic contexts. Functional follow-up of potential driver mutations was performed using chromatin interaction analyses, massively parallel reporter assays (MPRA) and targeted analysis of selected non-coding somatic mutations (NCSMs). We first created genome-scale maps of accessible chromatin regions (ACRs) and histone modification marks (HMMs) in pancreatic cell lines and purified pancreatic acinar and duct cells. Integration with whole-genome mutation calls from 506 PDACs revealed 314 ACRs/HMMs significantly enriched with 3614 NCSMs. Chromatin interaction analysis identified 416 potential target genes and MPRA revealed 178 NCSMs impacting reporter activity (19.45% of those tested). Targeted luciferase validation confirmed negative effects on gene regulatory activity for NCSMs near <i>ZFP36L2</i> and <i>CDKN2A</i>. For the former, CRISPR interference identified <i>ZFP36L2</i> as a target gene (16.0-24.0% reduced expression, p=0.023-0.0047), and growth inhibition after overexpression of <i>ZFP36L2</i> (4.1-14.1-fold reduction, p=6.0×10^-4 - 3.2×10^-3) implicates a possible tumour suppressor function. Our integrative approach provides a catalogue of potential non-coding driver mutations and nominates <i>ZFP36L2</i> as a novel PDAC driver gene with a likely tumour suppressor function.