Abstract 2778: Large-scale multi-omic analysis identifies noncoding somatic driver mutations and nominates <i>ZFP36L2</i> as a driver gene for pancreatic ductal adenocarcinoma
Authors: Jun Zhong, Aidan O’Brien, Minal Patel, Daina Eiser, Michael Mobaraki, Irene Collins, Li Wang, Konnie Guo, ThucNhi TruongVo, Ashley Jermusyk, Maura O’Neill, Courtney D. Dill, Andrew D. Wells, Michelle E. Leonard, James A. Pippin, Struan F. Grant, Tongwu Zhang, Thorkell Andresson, Katelyn E. Connelly, Jianxin Shi, H. Efsun Arda, Jason W. Hoskins, Laufey T. Amundadottir
Journal: Cancer Research (2025)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer-related mortality in the U.S. by the end of this decade. Due mainly to a late stage at diagnosis and lack of effective treatment, PDAC is a highly lethal malignancy with an overall 5-year survival rate of 13%. This highlights an urgent need for further research into the etiology of PDAC to improve outcomes for this cancer of unmet need. Cancer develops due to somatic and germline genetic factors exerting their influence within the cellular context of environmental factors. Most somatic mutations are in noncoding regions of the genome, but identification of noncoding somatic driver mutations remains challenging. To comprehensively characterize noncoding driver mutations for PDAC, we first created genome-scale maps (2,929,610 elements) of accessible chromatin regions (ACRs) (using ATAC-Seq) and histone modification marks (HMMs) (using ChIP-Seq for H3K27Ac, H3K27me3, H3K4me1 and H3K4me3 marks) 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). Although a majority of these were only observed in a single patient, using enrichment analysis, we identified 988 NCSMs located to ACRs/HMMs where at least two PDAC patients had a mutation within a 31bp window (selected as the longest ENCODE transcription factor (TF) motif). On one hand, to identify the potential target genes for the 988 NCSMs highlighted by our enrichment analysis, chromatin interactions between promoter and enhancer regions by high-resolution promoter-focused capture C (in-house datasets) and HiChIP revealed 416 target genes putatively implicated by these NCSMs, and differential expression analysis revealed six significant NCSMs/target gene pairs by RNA-seq. One the other hand, to functionally assess if the 988 NCSMs alter gene regulatory activity, the functional assessment using massively parallel reporter assays (MPRA) (in-house datasets) identified 178 NCSMs impacting reporter activity (19.45% of those tested) in one or more cell lines. Focused luciferase validation confirmed negative effects on gene regulatory activity for NCSMs near CDKN2A and ZFP36L2. For the latter, CRISPR interference (CRISPRi) further identified ZFP36L2 as a target gene (16 - 24% reduced expression, P = 0.0230-0.0047) with disrupted KLF9 binding likely mediating the effect. Our integrative analysis provides a catalog of potentially functional noncoding driver mutations, nominates ZFP36L2 as a PDAC driver gene and highlights potential therapeutic targets. Moreover, our approach provides a paradigm for employing a multi-omics approach to decipher complex noncoding mutations related to tumorigenesis. Citation Format: Jun Zhong, Aidan O’Brien, Minal Patel, Daina Eiser, Michael Mobaraki, Irene Collins, Li Wang, Konnie Guo, ThucNhi TruongVo, Ashley Jermusyk, Maura O’Neill, Courtney D. Dill, Andrew D. Wells, Michelle E. Leonard, James A. Pippin, Struan F. Grant, Tongwu Zhang, Thorkell Andresson, Katelyn E. Connelly, Jianxin Shi, H. Efsun Arda, Jason W. Hoskins, Laufey T. Amundadottir. Large-scale multi-omic analysis identifies noncoding somatic driver mutations and nominates ZFP36L2 as a driver gene for pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2778.