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Somatic mutation landscapes at single-molecule resolution

Abascal, Federico, Harvey, Luke M. R., Mitchell, Emily, Lawson, Andrew R. J., Lensing, Stefanie V., Ellis, Peter, Russell, Andrew J. C., Alcantara, Raul E., Baez-Ortega, Adrian, Wang, Yichen, Kwa, Eugene Jing, Lee-Six, Henry, Cagan, Alex, Coorens, Tim H. H., Chapman, Michael Spencer, Olafsson, Sigurgeir, Leonard, Steven, Jones, David, Machado, Heather E., Davies, Megan, Øbro, Nina F., Mahubani, Krishnaa T., Allinson, Kieren, Gerstung, Moritz, Saeb-Parsy, Kourosh, Kent, David G., Laurenti, Elisa, Stratton, Michael R., Rahbari, Raheleh, Campbell, Peter J., Osborne, Robert J., Martincorena, Iñigo·2021·Nature
DOI 10.1038/s41586-021-03477-4
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Crossref · 10.1038/s41586-021-03477-4

Cites

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  • The same three signatures that dominate somatic mutagenesis in the human colon are dominant in other mammals: SBS1, SBSB (SBS5), and SBSC (SBS18).

    “This analysis suggests that the same three signatures that dominate somatic mutagenesis in the human colon are dominant in other mammals: SBS1, which is believed to result from the spontaneous deamination of 5-methylcytosine8,32; SBSB (SBS5), a common signature across human tissues that may result from endogenous damage and repair18,33; and SBSC (SBS18), which is dominated by C>A substitutions and”

    From Somatic mutation rates scale with lifespan across mammals (2022) · cites this paper as [18]

    The section on stem and differentiated cells in blood and colon reports that SBS1 and SBS5 dominate mutations in human colonic epithelium. It does not identify SBS18 as a dominant colonic signature, and the passages on mutational signature analysis concern human tissues, not dominance of these signatures in other mammals (no page numbers are available in our copy). (LLM, conf=0.87)

    Experimental — accuracy not yet measured

  • These observations are consistent with the hypothesis that SBS5 and SBS40 result from a combination of correlated mutational processes, with some variation across human tissues and across species.

    “These observations are consistent with the hypothesis that SBS5 and SBS40 result from a combination of correlated mutational processes, with some variation across human tissues18,33 and across species.”

    From Somatic mutation rates scale with lifespan across mammals (2022) · cites this paper as [18]

    In “Lifelong mutagenesis in post-mitotic neurons and polyclonal smooth muscle” (page not provided), the paper proposes that SBS5 may reflect co-occurring processes that differ across human tissues. It does not make that proposal about SBS40. The across-species phrase follows the citations in the citing sentence, so it is not treated as attributed to this source. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • SBS1 is more common in fast-proliferating tissues, such as colon and embryonic or foetal tissues, and SBS5 dominates in post-mitotic cells in the absence of cell division.

    “They also appear to differ in their association with the rate of cell division in humans, with SBS1 being more common in fast-proliferating tissues, such as colon and embryonic or foetal tissues, and SBS5 dominating in post-mitotic cells in the absence of cell division14,18,20.”

    From Somatic mutation rates scale with lifespan across mammals (2022) · cites this paper as [18]

    The section ‘Lifelong mutagenesis in post-mitotic neurons and polyclonal smooth muscle’ reports that an SBS5-like signature occurs in neurons without cell division, while SBS1 accumulates there at a low rate. The colon section reports SBS1 among the dominant signatures in colonic epithelium. Our copy does not establish that SBS1 is more common in embryonic or foetal tissues, or that SBS5 specifically dominates post-mitotic cells; the neuronal analysis also identifies an SBS16-like signature. Page numbers were not available in the indexed passages. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • SBS1, SBSB/5 and SBSC/18 are believed to result from different forms of DNA damage and are expected to be subject to different DNA repair pathways.

    “SBS1, SBSB/5 and SBSC/18 are believed to result from different forms of DNA damage and are expected to be subject to different DNA repair pathways18,33.”

    From Somatic mutation rates scale with lifespan across mammals (2022) · cites this paper as [18]

    The section ‘Lifelong mutagenesis in post-mitotic neurons and polyclonal smooth muscle’ (page unavailable) links SBS1-like C>T mutations to 5-methylcytosine deamination, supporting a DNA-damage origin for one signature. It says the aetiology of SBS5-like processes remains poorly understood; our copy does not establish distinct damage forms for all three cited signatures or predict different DNA repair pathways for them. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • In humans, somatic mutation rates show variability across cell types.

    “somatic mutation rates in humans are 10–20 times higher than germline mutation rates, show variability across cell types and are influenced by additional mutational processes18,20.”

    From Somatic mutation rates scale with lifespan across mammals (2022) · cites this paper as [18]

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Citations

Cites

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Research works printed but not linked: 41

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  3. Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019). · DOI · Paper page
  4. Brunner, S. F. et al. Somatic mutations and clonal dynamics in healthy and cirrhotic human liver. Nature 574, 538–542 (2019). · DOI · Paper page
  5. Franco, I. et al. Somatic mutagenesis in satellite cells associates with human skeletal muscle aging. Nat. Commun. 9, 800 (2018). · DOI
  6. Xing, D., Tan, L., Chang, C. H., Li, H. & Xie, X. S. Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands. Proc. Natl Acad. Sci. USA 118, e2013106118 (2021). · DOI
  7. Petljak, M. et al. Characterizing mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis. Cell 176, 1282–1294.e20 (2019). · DOI
  8. Salk, J. J., Schmitt, M. W. & Loeb, L. A. Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations. Nat. Rev. Genet. 19, 269–285 (2018). · DOI
  9. Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA 109, 14508–14513 (2012). · DOI · Paper page
  10. 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 · Paper page
  11. You, X. et al. Detection of genome-wide low-frequency mutations with paired-end and complementary consensus sequencing (PECC-seq) revealed end-repair-derived artifacts as residual errors. Arch. Toxicol. 94, 3475–3485 (2020). · DOI
  12. Costello, M. et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res. 41, e67 (2013). · DOI
  13. Rahbari, R. et al. Timing, rates and spectra of human germline mutation. Nat. Genet. 48, 126–133 (2016). · DOI
  14. Wyles, S. P., Brandt, E. B. & Nelson, T. J. Stem cells: the pursuit of genomic stability. Int. J. Mol. Sci. 15, 20948–20967 (2014). · DOI
  15. Nicholson, A. M. et al. Fixation and spread of somatic mutations in adult human colonic epithelium. Cell Stem Cell 22, 909–918.e8 (2018). · DOI
  16. Poduri, A., Evrony, G. D., Cai, X. & Walsh, C. A. Somatic mutation, genomic variation, and neurological disease. Science 341, 1237758 (2013). · DOI · Paper page
  17. Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020). · DOI · Paper page
  18. Rheinbay, E. et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578, 102–111 (2020). · DOI
  19. Gabella, G. Cells of visceral smooth muscles. J. Smooth Muscle Res. 48, 65–95 (2012). · DOI
  20. Yoshida, K. et al. Tobacco smoking and somatic mutations in human bronchial epithelium. Nature 578, 266–272 (2020). · DOI
  21. Gao, Z., Wyman, M. J., Sella, G. & Przeworski, M. Interpreting the dependence of mutation rates on age and time. PLoS Biol. 14, e1002355 (2016). · DOI
  22. Kucab, J. E. et al. A compendium of mutational signatures of environmental agents. Cell 177, 821–836 (2019). · DOI · Paper page
  23. Matsumura, S. et al. Genome-wide somatic mutation analysis via Hawk-seq™ reveals mutation profiles associated with chemical mutagens. Arch. Toxicol. 93, 2689–2701 (2019). · DOI
  24. Ellis, P. et al. Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing. Nat. Protocols 16, 841–871 (2021). · DOI
  25. Olafsson, S. et al. Somatic evolution in non-neoplastic IBD-affected colon. Cell 182, 672–684 (2020). · DOI
  26. Krishnaswami, S. R. et al. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat. Protocols 11, 499–524 (2016). · DOI · Paper page
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Metadata

Authors
Abascal, F., Harvey, L. M. R., Mitchell, E., Lawson, A. R. J., Lensing, S. V., Ellis, P., Russell, A. J. C., Alcantara, R. E., Baez-Ortega, A., Wang, Y., Kwa, E. J., Lee-Six, H., Cagan, A., Coorens, T. H. H., Chapman, M. S., Olafsson, S., Leonard, S., Jones, D., Machado, H. E., Davies, M., Øbro, N. F., Mahubani, K. T., Allinson, K., Gerstung, M., Saeb-Parsy, K., Kent, D. G., Laurenti, E., Stratton, M. R., Rahbari, R., Campbell, P. J., Osborne, R. J., & Martincorena, I.
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2021-04-28
Volume
593
Issue
7859
Pages
405-410
ISSN
  • 0028-0836
  • 1476-4687
DOI
10.1038/s41586-021-03477-4
Cited by
546
References
18
Language
en
Licence

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