Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas

Journal name:
Nature Genetics
Volume:
45,
Pages:
136–144
Year published:
DOI:
doi:10.1038/ng.2503
Received
Accepted
Published online
Corrected online

Abstract

Many individuals with multiple or large colorectal adenomas or early-onset colorectal cancer (CRC) have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple-adenoma and/or CRC cases but in no controls. The variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases ε and δ and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers were microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain.

At a glance

Figures

  1. Pedigrees of the families with POLE L424V and POLD1 S478N in the discovery phase.
    Figure 1: Pedigrees of the families with POLE L424V and POLD1 S478N in the discovery phase.

    (ac) Families SM7 (POLE) (a), SM6 (POLD1) (b) and SM4 (POLD1) (c) are shown. Filled symbol, affected; +, mutation carrier; −, wild type; S, whole genome sequenced; L, genome-wide linkage analysis. For colorectal adenomas, we show the cumulative tumor numbers from age at first presentation or screening colonoscopy to age at last contact. The diameter of the largest adenoma is also given if reported. Hyperplastic polyp (HP) numbers are also shown. For CRCs, endometrial carcinomas (ECs) and brain tumors, age at first presentation is given. The location of the CRC (colon, cecum, rectum) is also given if reported.

  2. Modeling of the germline and exonuclease domain mutations.
    Figure 2: Modeling of the germline and exonuclease domain mutations.

    (a) Composite model of the catalytic subunit of yeast Pol δ (in ternary complex with DNA and an incoming nucleotide (PDB 3IAY)) and the ssDNA component of the T4 polymerase complex (PDB 1NOY), modeled into the exonuclease active site (red). The polymerase is colored blue, the exonuclease domain is shown in green, the double-stranded DNA is shown in orange and magenta, and the ssDNA is shown in the exonuclease active site in yellow. Mutations map to the active site of the exonuclease domain (boxed). (b) Germline mutations encoding POLE L424V and POLD1 S478N map to a helix (residues 478–487) and pack against another helix, forming part of the base of the exonuclease active site. Alterations disrupt this packing of helices and distort the active site. The active site is defined by the ssDNA substrate. (c) Mapping of possibly pathogenic germline and somatic mutations to the exonuclease domain. All the POLE alterations (exonuclease domain somatic changes from TCGA colorectal cancer data) and POLD1 P327L (encoded by a germline mutation in our affected individual; same location as POLE P286H) cluster around the active site (red), whereas the POLD1 alterations S370R and G426S (encoded by germline variants from two other affected individuals) are more peripheral.

Accession codes

Change history

Corrected online 08 May 2013
In the version of this article initially published, the name of author Estrella Guarino was incorrectly listed as Estrella Guarino Almeida. The error has been corrected in the HTML and PDF versions of this article.

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Author information

  1. These authors contributed equally to this work.

    • Claire Palles &
    • Jean-Baptiste Cazier

Affiliations

  1. Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

    • Claire Palles,
    • Kimberley M Howarth,
    • Enric Domingo,
    • Angela M Jones,
    • Zoe Kemp,
    • Sarah L Spain,
    • Luis G Carvajal-Carmona,
    • Ella Barclay,
    • Maggie Gorman,
    • Lynn Martin,
    • Michal B Kovac &
    • Ian Tomlinson
  2. Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

    • Jean-Baptiste Cazier,
    • Peter Donnelly,
    • Gilean McVean,
    • John Broxholme,
    • David Buck,
    • Lorna Gregory,
    • Gerton Lunter,
    • Edouard Hatton,
    • Christopher C Holmes,
    • Linda Hughes,
    • Peter Humburg,
    • Alexander Kanapin &
    • Andy Rimmer
  3. Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK.

    • Peter Broderick,
    • Amy Sherborne,
    • Daniel Chubb,
    • Yusanne Ma,
    • Sara Dobbins &
    • Richard S Houlston
  4. Department of Zoology, University of Oxford, Oxford, UK.

    • Estrella Guarino,
    • Israel Salguero &
    • Stephen E Kearsey
  5. Oxford National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

    • Kulvinder Kaur,
    • Jenny Taylor,
    • Andrew Wilkie &
    • Ian Tomlinson
  6. Research Group Human Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland.

    • Michal B Kovac
  7. Illumina Cambridge, Ltd, Little Chesterford, UK.

    • Sean Humphray,
    • David Bentley,
    • Zoya Kingsbury,
    • Russell Grocock &
    • Lisa Murray
  8. Wessex Regional Genetics Laboratory, Princess Anne Hospital, Southampton, UK.

    • Anneke Lucassen
  9. Department of Statistics, University of Oxford, Oxford, UK.

    • Peter Donnelly &
    • Christopher C Holmes
  10. Division of Cancer Studies, NIHR Comprehensive Biomedical Research Centre, Guy's & St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London, London, UK.

    • Christos Petridis &
    • Elinor J Sawyer
  11. Institute of Cancer, Bart's and the London Medical School, Queen Mary College, University of London, London, UK.

    • Rebecca Roylance
  12. Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK.

    • David J Kerr
  13. Polyposis Registry, Imperial College School of Medicine, St. Mark's Hospital, Harrow, UK.

    • Susan Clark
  14. Wellcome Trust Centre for Human Genetics, Division of Structural Biology, University of Oxford, Oxford, UK.

    • Jonathan Grimes
  15. Science Division, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK.

    • Jonathan Grimes
  16. Family Cancer Clinic, Imperial College School of Medicine, St. Mark's Hospital, Harrow, UK.

    • Huw J W Thomas,
    • Carole Cummings &
    • Margaret Stevens
  17. Department of Clinical Genetics, University of Birmingham, Birmingham, UK.

    • Eamonn Maher
  18. Department of Clinical Genetics, University of Manchester, Manchester, UK.

    • Gareth Evans
  19. Oxford Regional Genetics Service, Churchill Hospital, Oxford, UK.

    • Lisa Walker &
    • Dorothy Halliday
  20. Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK.

    • Ruth Armstrong &
    • Joan Paterson
  21. South-West Thames Regional Genetics Service, St George's Hospital, London, UK.

    • Shirley Hodgson &
    • Tessa Homfray
  22. North-East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK.

    • Lucy Side
  23. South-East Thames Regional Genetics Service, Guy's Hospital, London, UK.

    • Louise Izatt
  24. South-West Regional Genetics Service, Bristol, UK.

    • Alan Donaldson &
    • Susan Tomkins
  25. Northern Ireland Regional Genetics Service, City Hospital, Belfast, UK.

    • Patrick Morrison
  26. Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, UK.

    • Selina Goodman &
    • Carole Brewer
  27. Northern Regional Genetics Service, International Centre for Life, Newcastle, UK.

    • Alex Henderson
  28. West of Scotland Regional Genetics Service, Yorkhill Hospital, Glasgow, UK.

    • Rosemarie Davidson &
    • Victoria Murday
  29. Sheffield Regional Genetics Service, Children's Hospital, Sheffield, UK.

    • Jaqueline Cook
  30. North of Scotland Regional Genetics Service, Foresterhill Hospital, Aberdeen, UK.

    • Neva Haites
  31. Yorkshire Regional Genetics Service, St James's Hospital, Leeds, UK.

    • Timothy Bishop &
    • Eamonn Sheridan
  32. Republic of Ireland Genetics Service, Our Lady's Hospital for Sick Children, Dublin, Ireland.

    • Andrew Green
  33. Guildford Undetected Tumour Screening Study, The Royal Surrey County Hospital, Guildford, UK.

    • Christopher Marks,
    • Sue Carpenter &
    • Mary Broughton
  34. Department of Clinical Genetics, Royal Liverpool Children's Hospital, Alderhay, Liverpool, UK.

    • Lynn Greenhalge
  35. Department of Clinical Genetics, City Hospital, Nottingham, UK.

    • Mohnish Suri
  36. Office of the Regius Professor of Medicine, Oxford, UK.

    • John Bell
  37. Centre for Cellular and Molecular Physiology, Nuffield Department of Clinical Medicine, Oxford, UK.

    • Peter Ratcliffe &
    • Richard Cornall
  38. Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK.

    • Andrew Wilkie
  39. Functional Genomics of Inflammation and Immunity, Wellcome Trust Centre for Human Genetics, Oxford, UK.

    • Julian Knight

Consortia

  1. The CORGI Consortium

    • Huw J W Thomas,
    • Eamonn Maher,
    • Gareth Evans,
    • Anneke Lucassen,
    • Carole Cummings,
    • Margaret Stevens,
    • Lisa Walker,
    • Dorothy Halliday,
    • Ruth Armstrong,
    • Joan Paterson,
    • Shirley Hodgson,
    • Tessa Homfray,
    • Lucy Side,
    • Louise Izatt,
    • Alan Donaldson,
    • Susan Tomkins,
    • Patrick Morrison,
    • Selina Goodman,
    • Carole Brewer,
    • Alex Henderson,
    • Rosemarie Davidson,
    • Victoria Murday,
    • Jaqueline Cook,
    • Neva Haites,
    • Timothy Bishop,
    • Eamonn Sheridan,
    • Andrew Green,
    • Christopher Marks,
    • Sue Carpenter,
    • Mary Broughton,
    • Lynn Greenhalge &
    • Mohnish Suri
  2. A list of contributing members is provided at the end of the manuscript

  3. The WGS500 Consortium

  4. A list of contributing members is provided at the end of the manuscript

  5. Steering Committee:

    • Peter Donnelly (Chair),
    • John Bell,
    • David Bentley,
    • Gilean McVean,
    • Peter Ratcliffe,
    • Jenny Taylor &
    • Andrew Wilkie
  6. Operations Committee:

    • Peter Donnelly (Chair),
    • John Broxholme,
    • David Buck,
    • Jean-Baptiste Cazier,
    • Richard Cornall,
    • Lorna Gregory,
    • Julian Knight,
    • Gerton Lunter,
    • Gilean McVean,
    • Jenny Taylor,
    • Ian Tomlinson &
    • Andrew Wilkie
  7. Sequencing & Experimental Follow-up:

    • David Buck (Lead),
    • Lorna Gregory,
    • Sean Humphray &
    • Zoya Kingsbury
  8. Data Analysis:

    • Gilean McVean (Lead),
    • Peter Donnelly,
    • Jean-Baptiste Cazier,
    • John Broxholme,
    • Russell Grocock,
    • Edouard Hatton,
    • Christopher C Holmes,
    • Linda Hughes,
    • Peter Humburg,
    • Alexander Kanapin,
    • Gerton Lunter,
    • Lisa Murray &
    • Andy Rimmer

Contributions

C. Palles, K.M.H., E.D., A.M.J., P.B., A.S., D.C., Z.K., S.L.S., C. Petridis, E.J.S., L.G.C.-C., Y.M., K.K., S.D., E.G., I.S. and S.H. performed laboratory experiments and/or analyzed the data. J.-B.C. analyzed whole-genome sequencing data, with assistance from M.B.K., and supervised other bioinformatics data analysis. J.T., S.E.K. and I.T. supervised laboratory experiments. G.M., P.D. and D.B. oversaw WGS500 analysis, and C.C.H. provided additional statistical advice. L.M., E.B., M.G., A.L., C. Petridis, R.R., E.J.S., D.J.K., S.C., H.J.W.T., R.S.H. and I.T. obtained samples. J.G. undertook structural analysis. R.S.H. and I.T. provided sequencing data and oversaw the study. I.T. wrote the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

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