Tissue-specific mutation accumulation in human adult stem cells during life

Nature

Volumn 538, Issue 7624, 2016, Pages 260-264

  Blokzijl, Francis ^a   De Ligt, Joep ^a   Jager, Myrthe ^a   Sasselli, Valentina ^a   Roerink, Sophie ^b   Sasaki, Nobuo ^a   Huch, Meritxell ^a   Boymans, Sander ^a   Kuijk, Ewart ^a   Prins, Pjotr ^a   Nijman, Isaac J ^a   Martincorena, Inigo ^b   Mokry, Michal ^a   Wiegerinck, Caroline L ^a   Middendorp, Sabine ^a   Sato, Toshiro ^a   Schwank, Gerald ^a   Nieuwenhuis, Edward E S ^a   Verstegen, Monique M A ^c   Van Der Laan, Luc J W ^c   De Jonge, Jeroen ^c   Ijzermans, Jan N M ^d   Vries, Robert G ^a   Van De Wetering, Marc ^a   Stratton, Michael R ^b   Clevers, Hans ^a   Cuppen, Edwin ^a   Van Boxtel, Ruben ^a   more..

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c ERASMUS MEDICAL CENTER   (Netherlands)

^d Foundation Hubrecht Organoid Technology (HUB)   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANATOMY; CANCER; CELLS AND CELL COMPONENTS; DISEASE INCIDENCE; DNA; GENE EXPRESSION; MUTATION; PROTEIN; TUMOR;

ADOLESCENT; ADULT; ADULT STEM CELL; AGE; AGED; ANIMAL CELL; APC GENE; ARTICLE; CHILD; COLORECTAL CANCER; CONTROLLED STUDY; CTNNB1 GENE; FEMALE; HUMAN; HUMAN CELL; HUMAN TISSUE; LIVER CANCER; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; MOUSE; MUTATIONAL ANALYSIS; NONHUMAN; POINT MUTATION; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; SMAD4 GENE; SOMATIC MUTATION; TISSUE SPECIFICITY; TP53 GENE; TUMOR GENE; VERY ELDERLY; AGING; ANIMAL; ANTIBODY SPECIFICITY; COLON; CYTOPLASM; DNA MUTATIONAL ANALYSIS; GENETICS; INCIDENCE; LIVER; METABOLISM; MULTIPOTENT STEM CELL; MUTATION ACCUMULATION; MUTATION RATE; NEOPLASMS; SMALL INTESTINE; YOUNG ADULT;

ADOLESCENT; ADULT; ADULT STEM CELLS; AGED; AGED, 80 AND OVER; AGING; ANIMALS; CHILD; CHILD, PRESCHOOL; COLON; DNA MUTATIONAL ANALYSIS; FEMALE; GENES, NEOPLASM; HUMANS; INCIDENCE; INTESTINE, SMALL; LIVER; MALE; MICE; MIDDLE AGED; MULTIPOTENT STEM CELLS; MUTATION ACCUMULATION; MUTATION RATE; NEOPLASMS; ORGAN SPECIFICITY; ORGANOIDS; POINT MUTATION; YOUNG ADULT;

EID: 84991669713     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature19768     Document Type: Article

References (42)

1. Tomasetti, C., Vogelstein, B. Cancer etiology. Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Science 347, 78-81 (2015).
2. Rossi, D. J., Jamieson, C. H. M., Weissman, I. L. Stems cells and the pathways to aging and cancer. Cell 132, 681-696 (2008).
3. Huch, M. et al. Long-term culture of genome-stable bipotent stem cells from adult human liver. Cell 160, 299-312 (2015).
4. Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262-265 (2009).
5. Sato, T. et al. Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium. Gastroenterology 141, 1762-1772 (2011).
6. Stratton, M. R., Campbell, P. J., Futreal, P. A. The cancer genome. Nature 458, 719-724 (2009).
7. Barker, N. et al. Crypt stem cells as the cells-of-origin of intestinal cancer. Nature 457, 608-611 (2009).
8. Milholland, B., Auton, A., Suh, Y., Vijg, J. Age-related somatic mutations in the cancer genome. Oncotarget 6, 24627-24635 (2015).
9. Wu, S., Powers, S., Zhu, W., Hannun, Y. A. Substantial contribution of extrinsic risk factors to cancer development. Nature 529, 43-47 (2016).
10. Hou, Y. et al. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 148, 873-885 (2012).
11. Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
12. Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Campbell, P. J., Stratton, M. R. Deciphering signatures of mutational processes operative in human cancer. Cell Reports 3, 246-259 (2013).
13. Alexandrov, L. B. et al. Clock-like mutational processes in human somatic cells. Nat. Genet. 47, 1402-1407 (2015).
14. Supek, F., Lehner, B. Differential DNA mismatch repair underlies mutation rate variation across the human genome. Nature 521, 81-84 (2015).
15. Schuster-Böckler, B., Lehner, B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488, 504-507 (2012).
16. Lynch, M. Evolution of the mutation rate. Trends Genet. 26, 345-352 (2010).
17. Finette, B. A. et al. Determination of HPRT mutant frequencies in T-lymphocytes from a healthy pediatric population: statistical comparison between newborn, children and adult mutant frequencies, cloning efficiency and age. Mutat. Res. 308, 223-231 (1994).
18. Martincorena, I. et al. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science 348, 880-886 (2015).
19. Xie, M. et al. Age-related cancer mutations associated with clonal hematopoietic expansion. Nat. Med. 20, 1472-1478 (2014).
20. Genovese, G. et al. Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N. Engl. J. Med. 371, 2477-2487 (2014).
21. Jaiswal, S. et al. Age-related clonal hematopoiesis associated with adverse outcomes. N. Engl. J. Med. 371, 2488-2498 (2014).
22. Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196 (2010).
23. Dollé, M. E. T., Snyder, W. K., Dunson, D. B., Vijg, J. Mutational fingerprints of aging. Nucleic Acids Res. 30, 545-549 (2002).
24. Dollé, M. E., Snyder, W. K., Gossen, J. A., Lohman, P. H., Vijg, J. Distinct spectra of somatic mutations accumulated with age in mouse heart and small intestine. Proc. Natl Acad. Sci. USA 97, 8403-8408 (2000).
25. Behjati, S. et al. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature 513, 422-425 (2014).
26. Fearon, E. R. Molecular genetics of colorectal cancer. Annu. Rev. Pathol. 6, 479-507 (2011).
27. Li, H., Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
28. Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., Prins, P. Sambamba: fast processing of NGS alignment formats. Bioinformatics 31, 2032-2034 (2015).
29. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
30. Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311 (2001).
31. R Core Team. R: A language and environment for statistical computing; http://www. r-project. org/(2015).
32. Pinheiro J et al. nlme: Linear and Nonlinear Mixed Effects Models. https://cran. r-project. org/web/packages/nlme/nlme. pdf (2016).
33. ENCODE Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2013).
34. Rosenbloom, K. R. et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 43, D670-D681 (2015).
35. Cunningham, F. et al. Ensembl 2015. Nucleic Acids Res. 43, D662-D669 (2015).
36. Gaujoux, R., Seoighe, C. A flexible R package for nonnegative matrix factorization. BMC Bioinformatics 11, 367 (2010).
37. Lawrence, M. et al. Software for computing and annotating genomic ranges. PLOS Comput. Biol. 9, e1003118 (2013).
38. Abyzov, A., Urban, A. E., Snyder, M., Gerstein, M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974-984 (2011).
39. Boeva, V. et al. Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28, 423-425 (2012).
40. Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, 1333-1339 (2012).
41. Le Tallec, B. et al. Common fragile site profiling in epithelial and erythroid cells reveals that most recurrent cancer deletions lie in fragile sites hosting large genes. Cell Reports 4, 420-428 (2013).
42. Jurka, J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16, 418-420 (2000).