The landscape of somatic mutation in normal colorectal epithelial cells.

Adenoma / genetics Aged Axin Protein / genetics Carcinoma / genetics Cell Transformation, Neoplastic Clone Cells / cytology Colon / cytology Colorectal Neoplasms / genetics DNA Copy Number Variations DNA Mutational Analysis Epithelial Cells / cytology Female Humans Intestinal Mucosa / cytology Male Middle Aged Mutation Prodromal Symptoms Rectum / cytology Stem Cells / cytology

Journal

Nature

ISSN: 1476-4687

Titre abrégé: Nature

Pays: England

ID NLM: 0410462

Informations de publication

Date de publication:
10 2019

Historique:

received: 11 09 2018

accepted: 11 09 2019

entrez: 25 10 2019

pubmed: 28 10 2019

medline: 20 11 2019

Statut: ppublish

Résumé

The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions that lead to cancer

Identifiants

DOI: 10.1038/s41586-019-1672-7 PMID: 31645730

pubmed: 31645730

doi: 10.1038/s41586-019-1672-7

pii: 10.1038/s41586-019-1672-7

doi:

Substances chimiques

AXIN2 protein, human 0

Axin Protein 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

Pagination

532-537

Subventions

Organisme : Wellcome Trust

Pays : United Kingdom

Références

Fearon, E. R. & Vogelstein, B. A genetic model for colorectal tumorigenesis. Cell 61, 759–767 (1990).

doi: 10.1016/0092-8674(90)90186-I pubmed: 2188735 pmcid: 2188735

Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Preprint at https://www.biorxiv.org/content/10.1101/322859v2 (2019).

Sabarinathan, R. et al. The whole genome panorama of cancer drivers. Preprint at https://www.biorxiv.org/content/10.1101/190330v2 (2017).

Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).

doi: 10.1038/nature19768 pubmed: 27698416 pmcid: 5536223

Roerink, S. F. et al. Intra-tumour diversification in colorectal cancer at the single-cell level. Nature 556, 457–462 (2018).

doi: 10.1038/s41586-018-0024-3 pubmed: 29643510

Welch, J. S. et al. The origin and evolution of mutations in acute myeloid leukemia. Cell 150, 264–278 (2012).

doi: 10.1016/j.cell.2012.06.023 pubmed: 22817890 pmcid: 3407563

Bae, T. et al. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science 359, 550–555 (2018).

doi: 10.1126/science.aan8690 pubmed: 29217587

Behjati, S. et al. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature 513, 422–425 (2014).

doi: 10.1038/nature13448 pubmed: 25043003 pmcid: 4227286

Lee-Six, H. et al. Population dynamics of normal human blood inferred from somatic mutations. Nature 561, 473–478 (2018).

doi: 10.1038/s41586-018-0497-0 pubmed: 30185910 pmcid: 6163040

Martincorena, I. et al. High burden and pervasive positive selection of somatic mutations in normal human skin. Science 348, 880–886 (2015).

doi: 10.1126/science.aaa6806 pubmed: 25999502 pmcid: 4471149

Suda, K. et al. Clonal expansion and diversification of cancer-associated mutations in endometriosis and normal endometrium. Cell Rep. 24, 1777–1789 (2018).

doi: 10.1016/j.celrep.2018.07.037 pubmed: 30110635

Lodato, M. A. et al. Aging and neurodegeneration are associated with increased mutations in single human neurons. Science 359, 555–559 (2018).

doi: 10.1126/science.aao4426 pubmed: 29217584

Hoang, M. L. et al. Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing. Proc. Natl Acad. Sci. USA 113, 9846–9851 (2016).

doi: 10.1073/pnas.1607794113 pubmed: 27528664

Nicholson, A. M. et al. Fixation and spread of somatic mutations in adult human colonic epithelium. Cell Stem Cell 22, 909–918 (2018).

doi: 10.1016/j.stem.2018.04.020 pubmed: 29779891 pmcid: 5989058

Moore, L. et al. The mutational landscape of normal human endometrial epithelium. Preprint at https://www.biorxiv.org/content/10.1101/505685v1 (2018).

Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018).

doi: 10.1126/science.aau3879 pubmed: 30337457 pmcid: 6298579

Jaiswal, S. et al. Age-related clonal hematopoiesis associated with adverse outcomes. N. Engl. J. Med. 371, 2488–2498 (2014).

doi: 10.1056/NEJMoa1408617 pubmed: 25426837 pmcid: 4306669

Xie, M. et al. Age-related mutations associated with clonal hematopoietic expansion and malignancies. Nat. Med. 20, 1472–1478 (2014).

doi: 10.1038/nm.3733 pubmed: 25326804 pmcid: 4313872

McKerrell, T. et al. Leukemia-associated somatic mutations drive distinct patterns of age-related clonal hemopoiesis. Cell Rep. 10, 1239–1245 (2015).

doi: 10.1016/j.celrep.2015.02.005 pubmed: 25732814 pmcid: 4542313

Genovese, G. et al. Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N. Engl. J. Med. 371, 2477–2487 (2014).

doi: 10.1056/NEJMoa1409405 pubmed: 25426838 pmcid: 4290021

Potten, C. S., Kellett, M., Roberts, S. A., Rew, D. A. & Wilson, G. D. Measurement of in vivo proliferation in human colorectal mucosa using bromodeoxyuridine. Gut 33, 71–78 (1992).

doi: 10.1136/gut.33.1.71 pubmed: 1740282 pmcid: 1373868

Cheng, H. & Leblond, C. P. Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. V. Unitarian Theory of the origin of the four epithelial cell types. Am. J. Anat. 141, 537–561 (1974).

doi: 10.1002/aja.1001410407 pubmed: 4440635

Lopez-Garcia, C., Klein, A. M., Simons, B. D. & Winton, D. J. Intestinal stem cell replacement follows a pattern of neutral drift. Science 330, 822–825 (2010).

doi: 10.1126/science.1196236 pubmed: 20929733

Snippert, H. J. et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143, 134–144 (2010).

doi: 10.1016/j.cell.2010.09.016 pubmed: 20887898

Griffiths, D. F., Davies, S. J., Williams, D., Williams, G. T. & Williams, E. D. Demonstration of somatic mutation and colonic crypt clonality by X-linked enzyme histochemistry. Nature 333, 461–463 (1988).

doi: 10.1038/333461a0 pubmed: 3374587

Winton, D. J. & Ponder, B. A. J. Stem-cell organization in mouse small intestine. Proc. R. Soc. B 241, 13–18 (1990).

doi: 10.1098/rspb.1990.0059 pubmed: 1978330

Kozar, S. et al. Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas. Cell Stem Cell 13, 626–633 (2013).

doi: 10.1016/j.stem.2013.08.001 pubmed: 24035355

Barker, N. et al. Crypt stem cells as the cells-of-origin of intestinal cancer. Nature 457, 608–611 (2009).

doi: 10.1038/nature07602 pubmed: 19092804

Rouhani, F. J. et al. Mutational history of a human cell lineage from somatic to induced pluripotent stem cells. PLoS Genet. 12, e1005932 (2016).

doi: 10.1371/journal.pgen.1005932 pubmed: 27054363 pmcid: 4824386

Viel, A. et al. A specific mutational signature associated with DNA 8-Oxoguanine persistence in MUTYH-defective colorectal cancer. EBioMedicine 20, 39–49 (2017).

doi: 10.1016/j.ebiom.2017.04.022 pubmed: 28551381 pmcid: 5478212

Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).

doi: 10.1038/nature12477 pubmed: 23945592 pmcid: 3776390

Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012).

doi: 10.1016/j.cell.2012.04.024 pubmed: 22608084 pmcid: 3414841

Chan, K. et al. An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers. Nat. Genet. 47, 1067–1072 (2015).

doi: 10.1038/ng.3378 pubmed: 26258849 pmcid: 4594173

Boot, A. et al. Identification of novel mutational signatures in Asian oral squamous cell carcinomas associated with bacterial infections. Preprint at https://www.biorxiv.org/content/10.1101/368753v3 (2019).

Haradhvala, N. J. et al. Mutational strand asymmetries in cancer genomes reveal mechanisms of DNA damage and repair. Cell 164, 538–549 (2016).

doi: 10.1016/j.cell.2015.12.050 pubmed: 26806129 pmcid: 4753048

Wolf, J. et al. Peripheral blood mononuclear cells of a patient with advanced Hodgkin’s lymphoma give rise to permanently growing Hodgkin–Reed Sternberg cells. Blood 87, 3418–3428 (1996).

doi: 10.1182/blood.V87.8.3418.bloodjournal8783418 pubmed: 8605360

Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).

doi: 10.1038/nature11252

Bomme, L. et al. Cytogenetic analysis of colorectal adenomas: karyotypic comparisons of synchronous tumors. Cancer Genet. Cytogenet. 106, 66–71 (1998).

doi: 10.1016/S0165-4608(98)00047-8 pubmed: 9772912

Andersen, C. L. et al. Frequent occurrence of uniparental disomy in colorectal cancer. Carcinogenesis 28, 38–48 (2007).

doi: 10.1093/carcin/bgl086 pubmed: 16774939

Corley, D. A. et al. Variation of adenoma prevalence by age, sex, race, and colon location in a large population: implications for screening and quality programs. Clin. Gastroenterol. Hepatol. 11, 172–180 (2013).

doi: 10.1016/j.cgh.2012.09.010 pubmed: 22985608

Cancer Research UK. Bowel Cancer Incidence Statistics https://www.cancerresearchuk.org/health-professional/cancer-statistics/statistics-by-cancer-type/bowel-cancer/incidence#heading-Seven (accessed August 2018).

Stamp, C. et al. Predominant asymmetrical stem cell fate outcome limits the rate of niche succession in human colonic crypts. EBioMedicine 31, 166–173 (2018).

doi: 10.1016/j.ebiom.2018.04.017 pubmed: 29748033 pmcid: 6013780

Li, Y. et al. Patterns of structural variation in human cancer. Preprint at https://www.biorxiv.org/content/10.1101/181339v1 (2017).

Lugli, N. et al. Enhanced rate of acquisition of point mutations in mouse intestinal adenomas compared to normal tissue. Cell Rep. 19, 2185–2192 (2017).

doi: 10.1016/j.celrep.2017.05.051 pubmed: 28614706

Travis, L. B. Therapy-associated solid tumors. Acta Oncol. 41, 323–333 (2002).

doi: 10.1080/028418602760169361 pubmed: 12234023

Jones, D. et al. cgpCaVEManWrapper: Simple execution of CaVEMan in order to detect somatic single nucleotide variants in NGS data. Curr. Protoc. Bioinformatics 56, 15.10.1–15.10.18 (2016).

doi: 10.1002/cpbi.20

Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).

doi: 10.1093/nar/gkq603 pubmed: 20601685 pmcid: 20601685

Raine, K. M. et al. cgpPindel: Identifying somatically acquired insertion and deletion events from paired end sequencing. Curr. Protoc. Bioinformatics 52, 15.7.1–15.7.12 (2015).

Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910–16915 (2010).

doi: 10.1073/pnas.1009843107 pubmed: 20837533

Scheinin, I. et al. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 24, 2022–2032 (2014).

doi: 10.1101/gr.175141.114 pubmed: 25236618 pmcid: 4248318

Buels, R. et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 17, 66 (2016).

doi: 10.1186/s13059-016-0924-1 pubmed: 27072794 pmcid: 4830012

Martincorena, I. et al. Universal patterns of selection in cancer and somatic tissues. Cell 171, 1029–1041 (2017).

doi: 10.1016/j.cell.2017.09.042 pubmed: 29056346 pmcid: 5720395

Forbes, S. A. et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 45, D777–D783 (2017).

doi: 10.1093/nar/gkw1121 pubmed: 27899578

Felsenstein, J. PHYLIP—Phylogeny inference package (version 3.2).Cladistics 5, 164–166 (1989).

Roberts, N. Patterns of somatic genome rearrangement in human cancer. PhD thesis, Univ. Cambridge (Wellcome Trust Sanger Institute, 2018).

Farmery, J. H. R., Smith, M. L., Bioresource, N., Diseases, R. & Lynch, A. G. Telomerecat: a ploidy-agnostic method for estimating telomere length from whole genome sequencing data. Sci. Rep. 8, 1300 (2018).

doi: 10.1038/s41598-017-14403-y pubmed: 29358629 pmcid: 5778012

Nersisyan, L. & Arakelyan, A. Computel: computation of mean telomere length from whole-genome next-generation sequencing data. PLoS One 10, e0125201 (2015).

doi: 10.1371/journal.pone.0125201 pubmed: 25923330 pmcid: 4414351

Ding, Z. et al. Estimating telomere length from whole genome sequence data. Nucleic Acids Res. 42, e75 (2014).

doi: 10.1093/nar/gku181 pubmed: 24609383 pmcid: 4027178

Feuerbach, L. et al. TelomereHunter: telomere content estimation and characterization from whole genome sequencing data. Preprint at https://www.biorxiv.org/content/10.1101/065532v1 (2016).