Abstract

The gradual accumulation of genetic mutations in human adult stem cells (ASCs) during life is associated with various age-related diseases, including cancer1,2. Extreme variation in cancer risk across tissues was recently proposed to depend on the lifetime number of ASC divisions, owing to unavoidable random mutations that arise during DNA replication1. However, the rates and patterns of mutations in normal ASCs remain unknown. Here we determine genome-wide mutation patterns in ASCs of the small intestine, colon and liver of human donors with ages ranging from 3 to 87 years by sequencing clonal organoid cultures derived from primary multipotent cells3,4,5. Our results show that mutations accumulate steadily over time in all of the assessed tissue types, at a rate of approximately 40 novel mutations per year, despite the large variation in cancer incidence among these tissues1. Liver ASCs, however, have different mutation spectra compared to those of the colon and small intestine. Mutational signature analysis reveals that this difference can be attributed to spontaneous deamination of methylated cytosine residues in the colon and small intestine, probably reflecting their high ASC division rate. In liver, a signature with an as-yet-unknown underlying mechanism is predominant. Mutation spectra of driver genes in cancer show high similarity to the tissue-specific ASC mutation spectra, suggesting that intrinsic mutational processes in ASCs can initiate tumorigenesis. Notably, the inter-individual variation in mutation rate and spectra are low, suggesting tissue-specific activity of common mutational processes throughout life.

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Accessions

Primary accessions

European Nucleotide Archive

Data deposits

The human sequencing data have been deposited at the European Genome-phenome Archive (http://www.ebi.ac.uk/ega/) under accession numbers EGAS00001001682 and EGAS00001000881. The mouse sequencing data have been deposited at the European Nucleotide Archive (http://www.ebi.ac.uk/ena/) under accession number ERP005717.

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Acknowledgements

The authors would like to thank the gastroenterologists of the UMCU/Wilhelmina Children’s Hospital and Diakonessen Hospital for obtaining human duodenal and colon biopsies and R. Eijkemans for his advice on the statistical analyses. This study was financially supported by a Zenith grant of the Netherlands Genomics Initiative (935.12.003) to E.C., the NWO Zwaartekracht program Cancer Genomics.nl and funding of Worldwide Cancer Research (WCR no. 16-0193) to R.B. We declare no competing financial interests.

Author information

Author notes

    • Joep de Ligt
    • , Myrthe Jager
    • , Valentina Sasselli
    •  & Sophie Roerink

    These authors contributed equally to this work.

Affiliations

  1. Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands

    • Francis Blokzijl
    • , Joep de Ligt
    • , Myrthe Jager
    • , Sander Boymans
    • , Ewart Kuijk
    • , Edwin Cuppen
    •  & Ruben van Boxtel
  2. Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands

    • Francis Blokzijl
    • , Joep de Ligt
    • , Myrthe Jager
    • , Valentina Sasselli
    • , Nobuo Sasaki
    • , Meritxell Huch
    • , Sander Boymans
    • , Ewart Kuijk
    • , Pjotr Prins
    • , Isaac J. Nijman
    • , Toshiro Sato
    • , Gerald Schwank
    • , Marc van de Wetering
    • , Hans Clevers
    • , Edwin Cuppen
    •  & Ruben van Boxtel
  3. Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK

    • Sophie Roerink
    • , Inigo Martincorena
    •  & Michael R. Stratton
  4. Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands

    • Michal Mokry
    • , Caroline L. Wiegerinck
    • , Sabine Middendorp
    •  & Edward E. S. Nieuwenhuis
  5. Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands

    • Monique M. A. Verstegen
    • , Luc J. W. van der Laan
    • , Jeroen de Jonge
    •  & Jan N. M. IJzermans
  6. Foundation Hubrecht Organoid Technology (HUB), Uppsalalaan 8, 3584CT Utrecht, The Netherlands

    • Robert G. Vries

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Contributions

C.L.W., S.M. and E.E.S.N. obtained duodenal biopsies. N.S., M.M., E.E.S.N., M.M.A.V. and J.J. obtained colon biopsies. M.M.A.V., L.J.W.L., J.J. and J.N.M.I. obtained human liver biopsies. M.J., V.S., N.S., M.H., E.K., C.L.W., T.S., G.S. and R.B. performed ASC culturing. M.W. performed cell sorting. S.R., M.R.S., E.C. and R.B. performed sequencing. F.B., J.L., S.B., P.P., I.J.N., I.M. and R.B. performed bioinformatic analyses. F.B, R.G.V., H.C., E.C. and R.B. were involved in the conceptual design of the study. F.B., H.C., E.C. and R.B. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Edwin Cuppen.

Reviewer Information Nature thanks G. Pfeifer, L. Vermeulen, J. Vijg and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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