The contributions of coding mutations to tumorigenesis are relatively well known; however, little is known about somatic alterations in noncoding DNA. Here we describe GECCO (Genomic Enrichment Computational Clustering Operation) to analyze somatic noncoding alterations in 308 pancreatic ductal adenocarcinomas (PDAs) and identify commonly mutated regulatory regions. We find recurrent noncoding mutations to be enriched in PDA pathways, including axon guidance and cell adhesion, and newly identified processes, including transcription and homeobox genes. We identified mutations in protein binding sites correlating with differential expression of proximal genes and experimentally validated effects of mutations on expression. We developed an expression modulation score that quantifies the strength of gene regulation imposed by each class of regulatory elements, and found the strongest elements were most frequently mutated, suggesting a selective advantage. Our detailed single-cancer analysis of noncoding alterations identifies regulatory mutations as candidates for diagnostic and prognostic markers, and suggests new mechanisms for tumor evolution.
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We thank the members of the Tuveson laboratory, C. Vakoc and A. Siepel for discussions. D.A.T. is a distinguished scholar of the Lustgarten Foundation and Director of the Lustgarten Foundation-designated Laboratory of Pancreatic Cancer Research. D.A.T. is also supported by the Cold Spring Harbor Laboratory Association, the V Foundation, PCUK and the David Rubinstein Center for Pancreatic Cancer Research at MSKCC. In addition, we are grateful for support from the following: the STARR Foundation (I7-A718 for D.A.T.), DOD (W81XWH-13-PRCRP-IA for D.A.T.), Louis Morin Charitable Trust (M.E.F.) and NIH (5P30CA45508-26, 5P50CA101955-07, 1U10CA180944-03, 5U01CA168409-5, 1R01CA188134-01A1 and 1R01CA190092-03 for D.A.T. and R01HG006677 for M.C.S.).
The authors declare no competing financial interests.
Integrated supplementary information
Distribution of SNV rates across the patient cohort.
Distribution of SNVs across the patient cohort, with common coding mutations (colored bars) in PDA genes.
Distribution of CRR mutation rates across the patient cohort, with common coding mutations (colored bars) in PDA genes.
(a) A G→A mutation in a regulatory site on chromosome 15 at position 25,200,056 alters a critical nucleotide in an NRF1 binding site. The regulatory site lies in the promoter of SNRPN. At the bottom, the heat map displays the predicted change in binding, considered here as ChIP-seq signal for NRF1 in H1-hESCs. The line plots above measure the maximum (gain) and minimum (loss) predicted change; the loss highlights nucleotides that significantly alter the overall signal upon mutation as this mutation does. (b) A G→T mutation in a regulatory site on chromosome 3 at position 115,757,580 introduces a GATA factor binding site nearby an established PU.1 binding site. The heat map displays the predicted change in accessibility, considered here as DNase-seq signal in K562. In other cells, such as monocytes, the model predicts reduced accessibility, suggesting that GATA binding here may alter the combinatorial logic of the regulatory element in a complex fashion.
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Feigin, M., Garvin, T., Bailey, P. et al. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nat Genet 49, 825–833 (2017). https://doi.org/10.1038/ng.3861
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