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Processed pseudogenes acquired somatically during cancer development

Author

Listed:
  • Susanna L. Cooke

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Adam Shlien

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • John Marshall

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Christodoulos P. Pipinikas

    (Lungs for Living Research Centre, Rayne Institute, University College London)

  • Inigo Martincorena

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Jose M.C. Tubio

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Yilong Li

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Andrew Menzies

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Laura Mudie

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Manasa Ramakrishna

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Lucy Yates

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Helen Davies

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Niccolo Bolli

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton
    University of Cambridge)

  • Graham R. Bignell

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Patrick S. Tarpey

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Sam Behjati

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton
    University of Cambridge)

  • Serena Nik-Zainal

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Elli Papaemmanuil

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Vitor H. Teixeira

    (Lungs for Living Research Centre, Rayne Institute, University College London)

  • Keiran Raine

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Sarah O’Meara

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Maryam S. Dodoran

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Jon W. Teague

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Adam P. Butler

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Christine Iacobuzio-Donahue

    (Johns Hopkins Medical Institutions)

  • Thomas Santarius

    (Addenbrooke’s NHS Foundation Trust)

  • Richard G. Grundy

    (Children’s Brain Tumour Research Centre, University of Nottingham)

  • David Malkin

    (Hospital for Sick Children, University of Toronto)

  • Mel Greaves

    (Institute for Cancer Research, Sutton)

  • Nikhil Munshi

    (Dana-Farber Cancer Institute)

  • Adrienne M. Flanagan

    (Lungs for Living Research Centre, Rayne Institute, University College London
    Royal National Orthopaedic Hospital)

  • David Bowtell

    (Peter MacCallum Cancer Centre)

  • Sancha Martin

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Denis Larsimont
  • Jorge S. Reis-Filho

    (Memorial-Sloan-Kettering Cancer Center)

  • Alex Boussioutas

    (Peter MacCallum Cancer Centre
    Royal Melbourne Hospital, University of Melbourne)

  • Jack A. Taylor

    (National Institute of Environmental Health Sciences, Research Triangle Park)

  • Neil D. Hayes

    (UNC Lineberger Comprehensive Cancer Center, University of North Carolina)

  • Sam M. Janes

    (Lungs for Living Research Centre, Rayne Institute, University College London)

  • P. Andrew Futreal

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Michael R. Stratton

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Ultan McDermott

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton
    Addenbrooke’s NHS Foundation Trust)

  • Peter J. Campbell

    (Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton
    University of Cambridge
    Addenbrooke’s NHS Foundation Trust)

Abstract

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context.

Suggested Citation

  • Susanna L. Cooke & Adam Shlien & John Marshall & Christodoulos P. Pipinikas & Inigo Martincorena & Jose M.C. Tubio & Yilong Li & Andrew Menzies & Laura Mudie & Manasa Ramakrishna & Lucy Yates & Helen , 2014. "Processed pseudogenes acquired somatically during cancer development," Nature Communications, Nature, vol. 5(1), pages 1-9, May.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4644
    DOI: 10.1038/ncomms4644
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