Integrative multi-omic analyses identify noncoding somatic driver mutations for pancreatic cancer

Background: The identification and characterization of somatic cancer driver mutations in the noncoding genome remains challenging. Objective: To broadly characterize noncoding driver mutations for pancreatic ductal adenocarcinoma (PDAC). Design: Using mutation calls from whole-genome sequence (WGS) data in PDACs and genome-scale maps of accessible gene regulatory regions in normal- and tumor- derived pancreatic samples, we analyzed enrichment of noncoding mutations in gene regulatory regions relevant to normal- and tumor- 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 noncoding somatic mutations. 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 3,614 noncoding somatic mutations (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 (CRISPRi) 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 = 6.0x10-4 - 3.2x10-3) implicates a possible tumor suppressor function. Conclusion: Our integrative approach provides a catalog of potential noncoding driver mutations and nominates ZFP36L2 as a novel PDAC driver gene with a likely tumor suppressor function.