Abstract

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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Acknowledgements

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.).

Author information

Author notes

    • John D McPherson
    •  & Sean M Grimmond

    Present addresses: University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia (S.M.G.) and Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, University of California Davis, Sacramento, California, USA (J.D.M.).

    • Michael E Feigin
    •  & Tyler Garvin

    These authors contributed equally to this work.

Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

    • Michael E Feigin
    • , Michael C Schatz
    •  & David A Tuveson
  2. Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York, USA.

    • Michael E Feigin
    •  & David A Tuveson
  3. Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

    • Tyler Garvin
  4. Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, UK.

    • Peter Bailey
    • , David K Chang
    • , Sean M Grimmond
    •  & Andrew V Biankin
  5. QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.

    • Nicola Waddell
  6. Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.

    • Nicola Waddell
    •  & Sean M Grimmond
  7. The Kinghorn Cancer Centre, Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia.

    • David K Chang
  8. Department of Surgery, Bankstown Hospital, Bankstown, Sydney, New South Wales, Australia.

    • David K Chang
  9. South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales, Australia.

    • David K Chang
    •  & Andrew V Biankin
  10. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

    • David R Kelley
  11. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

    • Shimin Shuai
    •  & Lincoln D Stein
  12. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.

    • Steven Gallinger
  13. Division of General Surgery, Toronto General Hospital, Toronto, Ontario, Canada.

    • Steven Gallinger
  14. Genome Technologies Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

    • John D McPherson
  15. Sandra and Edward Meyer Cancer Center, Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York, USA.

    • Ekta Khurana
  16. Informatics and Biocomputing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

    • Lincoln D Stein
  17. Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.

    • Michael C Schatz
  18. Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.

    • Michael C Schatz
  19. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • David A Tuveson
  20. West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, Scotland, UK.

    • Andrew V Biankin

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Contributions

M.E.F., T.G., M.C.S. and D.A.T. wrote the manuscript. M.C.S. and D.A.T. supervised the study. T.G. performed FunSeq analysis and developed GECCO. M.E.F. performed pathway analysis. M.E.F., T.G., S.M.G., A.V.B., E.K., S.S., L.D.S., S.G. and J.D.M. contributed to data analysis. D.K.C. and P.B. performed patient outcome analysis. D.R.K. performed Basset analysis. N.W. performed germline sequence analysis.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Michael C Schatz or David A Tuveson.

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