Zhong Jun, O'Brien Aidan, Patel Minal, Eiser Daina, Mobaraki Michael, Collins Irene, Wang Li, Guo Konnie, TruongVo ThucNhi, Jermusyk Ashley, O'Neill Maura, Dill Courtney D, Wells Andrew D, Leonard Michelle E, Pippin James A, Grant Struan F A, Zhang Tongwu, Andresson Thorkell, Connelly Katelyn E, Shi Jianxin, Arda H Efsun, Hoskins Jason W, Amundadottir Laufey T
Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
medRxiv. 2024 Sep 24:2024.09.22.24314165. doi: 10.1101/2024.09.22.24314165.
Identification of somatic driver mutations in the noncoding genome remains challenging. To comprehensively characterize noncoding driver mutations for pancreatic ductal adenocarcinoma (PDAC), 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). Functional assessment using massively parallel reporter assays (MPRA) identified 178 NCSMs impacting reporter activity (19.45% of those tested). Focused luciferase validation confirmed negative effects on gene regulatory activity for NCSMs near and . For the latter, CRISPR interference (CRISPRi) further identified as a target gene (16.0 - 24.0% reduced expression, = 0.023-0.0047) with disrupted KLF9 binding likely mediating the effect. Our integrative approach provides a catalog of potentially functional noncoding driver mutations and nominates as a PDAC driver gene.
在非编码基因组中识别体细胞驱动突变仍然具有挑战性。为了全面表征胰腺导管腺癌（PDAC）的非编码驱动突变，我们首先创建了胰腺细胞系以及纯化的胰腺腺泡细胞和导管细胞中可及染色质区域（ACR）和组蛋白修饰标记（HMM）的全基因组图谱。将这些图谱与来自506个PDAC的全基因组突变分析结果相结合，发现314个ACR/HMM显著富集了3614个非编码体细胞突变（NCSM）。使用大规模平行报告基因检测（MPRA）进行功能评估，确定了178个影响报告基因活性的NCSM（占测试总数的19.45%）。聚焦荧光素酶验证证实，靠近和处的NCSM对基因调控活性有负面影响。对于后者，CRISPR干扰（CRISPRi）进一步确定为一个靶基因（表达降低16.0 - 24.0%，P = 0.023 - 0.0047），KLF9结合的破坏可能介导了这种效应。我们的综合方法提供了一份潜在功能性非编码驱动突变的目录，并提名作为一个PDAC驱动基因。
