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

Background The identification and characterisation of somatic cancer driver mutations in the non-coding genome remains challenging. Objective To broadly characterise non-coding driver mutations for pancreatic ductal adenocarcinoma (PDAC). Design 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). Results 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 ZFP36L2 and CDKN2A . For the former, CRISPR interference identified ZFP36L2 as a target gene (16.0–24.0% reduced expression, p=0.023–0.0047), and growth inhibition after overexpression of ZFP36L2 (4.1–14.1-fold reduction, p=6.0×10–4 − 3.2×10–3) implicates a possible tumour suppressor function. Conclusion Our integrative approach provides a catalogue of potential non-coding driver mutations and nominates ZFP36L2 as a novel PDAC driver gene with a likely tumour suppressor function. Data are available in a public, open access repository. Data may be obtained from a third party and are not publicly available. Data are available in a public, open access repository or may be obtained from a third party and are not publicly available. All data sets created as part of this work or used in this study and available through third parties, are listed in the Online Methods section under the Data availability section.