دورية أكاديمية
أعرض في EDS

Extensive phylogenies of human development inferred from somatic mutations.

التفاصيل البيبلوغرافية
العنوان: Extensive phylogenies of human development inferred from somatic mutations.
المؤلفون: Coorens THH; Wellcome Sanger Institute, Hinxton, UK., Moore L; Wellcome Sanger Institute, Hinxton, UK.; Department of Pathology, University of Cambridge, Cambridge, UK., Robinson PS; Wellcome Sanger Institute, Hinxton, UK.; Department of Paediatrics, University of Cambridge, Cambridge, UK., Sanghvi R; Wellcome Sanger Institute, Hinxton, UK., Christopher J; Wellcome Sanger Institute, Hinxton, UK.; Department of Paediatrics, University of Cambridge, Cambridge, UK.; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK., Hewinson J; Wellcome Sanger Institute, Hinxton, UK., Przybilla MJ; Wellcome Sanger Institute, Hinxton, UK., Lawson ARJ; Wellcome Sanger Institute, Hinxton, UK., Spencer Chapman M; Wellcome Sanger Institute, Hinxton, UK.; Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK.; Department of Haematology, University of Cambridge, Cambridge, UK., Cagan A; Wellcome Sanger Institute, Hinxton, UK., Oliver TRW; Wellcome Sanger Institute, Hinxton, UK.; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK., Neville MDC; Wellcome Sanger Institute, Hinxton, UK., Hooks Y; Wellcome Sanger Institute, Hinxton, UK., Noorani A; Wellcome Sanger Institute, Hinxton, UK., Mitchell TJ; Wellcome Sanger Institute, Hinxton, UK.; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.; Department of Surgery, University of Cambridge, Cambridge, UK., Fitzgerald RC; MRC Cancer Unit, University of Cambridge, Biomedical Campus, Cambridge, UK., Campbell PJ; Wellcome Sanger Institute, Hinxton, UK., Martincorena I; Wellcome Sanger Institute, Hinxton, UK., Rahbari R; Wellcome Sanger Institute, Hinxton, UK., Stratton MR; Wellcome Sanger Institute, Hinxton, UK. mrs@sanger.ac.uk.
المصدر: Nature [Nature] 2021 Sep; Vol. 597 (7876), pp. 387-392. Date of Electronic Publication: 2021 Aug 25.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE
أسماء مطبوعة: Publication: Basingstoke : Nature Publishing Group
Original Publication: London, Macmillan Journals ltd.
مواضيع طبية MeSH: Mutation*, Cell Lineage/*genetics , Embryo, Mammalian/*cytology , Embryo, Mammalian/*metabolism , Embryonic Development/*genetics, Brain/metabolism ; Chromosomes, Human, Y/genetics ; Clone Cells/metabolism ; Germ-Line Mutation/genetics ; Humans ; Male ; Mosaicism ; Organ Specificity/genetics ; Polymorphism, Single Nucleotide/genetics
مستخلص: Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing 1,2 . Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors in the same generation of a phylogeny often contribute to different extents to the adult body. The degree of this asymmetry varies between individuals, with ratios between the two reconstructed daughter cells of the zygote ranging from 60:40 to 93:7. Asymmetries pervade subsequent generations and can differ between tissues in the same individual. The phylogenies resolve the spatial embryonic patterning of tissues, revealing contiguous patches of, on average, 301 crypts in the adult colonic epithelium derived from a most recent embryonic cell and also a spatial effect in brain development. Using data from ten additional men, we investigated the developmental split between soma and germline, with results suggesting an extraembryonic contribution to primordial germ cells. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.
(© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)
التعليقات: Comment in: Nature. 2021 Sep;597(7876):334-336. (PMID: 34433973)
Comment in: Nat Rev Genet. 2021 Nov;22(11):689. (PMID: 34522034)
References: Behjati, S. et al. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature 513, 422–425 (2014). (PMID: 10.1038/nature13448250430034227286)
Ju, Y. S. et al. Somatic mutations reveal asymmetric cellular dynamics in the early human embryo. Nature 543, 714–718 (2017). (PMID: 10.1038/nature21703283297616169740)
Sulston, J. E. & Horvitz, H. R. Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56, 110–156 (1977). (PMID: 10.1016/0012-1606(77)90158-0838129)
Keller, P. J., Schmidt, A. D., Wittbrodt, J. & Stelzer, E. H. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065–1069 (2008). (PMID: 10.1126/science.116249318845710)
Strnad, P. et al. Inverted light-sheet microscope for imaging mouse pre-implantation development. Nat. Methods 13, 139–142 (2016). (PMID: 10.1038/nmeth.369026657559)
McKenna, A. et al. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907 (2016). (PMID: 10.1126/science.aaf7907272291444967023)
Alemany, A., Florescu, M., Baron, C. S., Peterson-Maduro, J. & van Oudenaarden, A. Whole-organism clone tracing using single-cell sequencing. Nature 556, 108–112 (2018). (PMID: 10.1038/nature2596929590089)
Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719–724 (2009). (PMID: 10.1038/nature07943193600792821689)
Coorens, T. H. H. et al. Embryonal precursors of Wilms tumor. Science 366, 1247–1251 (2019). (PMID: 10.1126/science.aax1323318068146914378)
Lee-Six, H. et al. Population dynamics of normal human blood inferred from somatic mutations. Nature 561, 473–478 (2018). (PMID: 10.1038/s41586-018-0497-0301859106163040)
Coorens, T. H. H. et al. Lineage-independent tumors in bilateral neuroblastoma. N. Engl. J. Med. 383, 1860–1865 (2020). (PMID: 10.1056/NEJMoa2000962332119297611571)
Park, S. et al. Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature https://doi.org/10.1038/s41586-021-03786-8 (2021).
Coorens, T. H. H. et al. Inherent mosaicism and extensive mutation of human placentas. Nature 592, 80–85 (2021). (PMID: 10.1038/s41586-021-03345-1336925437611644)
Lodato, M. A. et al. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 350, 94–98 (2015). (PMID: 10.1126/science.aab1785264301214664477)
Lodato, M. A. et al. Aging and neurodegeneration are associated with increased mutations in single human neurons. Science 359, 555–559 (2018). (PMID: 10.1126/science.aao442629217584)
Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019). (PMID: 10.1038/s41586-019-1672-731645730)
Moore, L. et al. The mutational landscape of human somatic and germline cells. Nature https://doi.org/10.1038/s41586-021-03822-7 (2021).
Ye, A. Y. et al. A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations. Genome Res. 28, 943–951 (2018). (PMID: 10.1101/gr.230003.117298752906028137)
Spencer Chapman, M. et al. Lineage tracing of human development through somatic mutations. Nature 595, 85–90 (2021).
Kuijk, E. et al. Early divergence of mutational processes in human fetal tissues. Sci. Adv. 5, eaaw1271 (2019). (PMID: 10.1126/sciadv.aaw1271311496366541467)
Kobayashi, T. & Surani, M. A. On the origin of the human germline. Development 145, dev150433 (2018).
Aitken, S. J. et al. Pervasive lesion segregation shapes cancer genome evolution. Nature 583, 265–270 (2020). (PMID: 10.1038/s41586-020-2435-1325813617116693)
Priestley, P. et al. Pan-cancer whole-genome analyses of metastatic solid tumours. Nature 575, 210–216 (2019). (PMID: 10.1038/s41586-019-1689-y316457656872491)
Forsberg, L. A. et al. Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer. Nat. Genet. 46, 624–628 (2014). (PMID: 10.1038/ng.2966247774495536222)
Loftfield, E. et al. Predictors of mosaic chromosome Y loss and associations with mortality in the UK Biobank. Sci. Rep. 8, 12316 (2018). (PMID: 10.1038/s41598-018-30759-1301203416098142)
Voet, T., Vanneste, E. & Vermeesch, J. R. The human cleavage stage embryo is a cradle of chromosomal rearrangements. Cytogenet. Genome Res. 133, 160–168 (2011). (PMID: 10.1159/00032423521311182)
Shahbazi, M. N. et al. Developmental potential of aneuploid human embryos cultured beyond implantation. Nat. Commun. 11, 3987 (2020). (PMID: 10.1038/s41467-020-17764-7327786787418029)
Sancho, M. et al. Competitive interactions eliminate unfit embryonic stem cells at the onset of differentiation. Dev. Cell 26, 19–30 (2013). (PMID: 10.1016/j.devcel.2013.06.012238672263714589)
Moore, L. et al. The mutational landscape of normal human endometrial epithelium. Nature 580, 640–646 (2020). (PMID: 10.1038/s41586-020-2214-z32350471)
Olafsson, S. et al. Somatic evolution in non-neoplastic IBD-affected colon. Cell 182, 672–684.e11 (2020). (PMID: 10.1016/j.cell.2020.06.036326979697427325)
Robinson, P. S. et al. Elevated somatic mutation burdens in normal human cells due to defective DNA polymerases. Preprint at https://doi.org/10.1101/2020.06.23.167668 (2020).
Ellis, P. et al. Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing. Nat. Protoc. 16, 841–871 (2020). (PMID: 10.1038/s41596-020-00437-633318691)
Lawson, A. R. J. et al. Extensive heterogeneity in somatic mutation and selection in the human bladder. Science 370, 75–82 (2020). (PMID: 10.1126/science.aba834733004514)
Li, H. & Durbin, R., Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009). (PMID: 10.1093/bioinformatics/btp324194511682705234)
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). (PMID: 10.1002/cpbi.2027930805)
Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865–2871 (2009). (PMID: 10.1093/bioinformatics/btp394195610182781750)
Van Loo, P., et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA 107, 16910–16915 (2010). (PMID: 10.1073/pnas.1009843107208375332947907)
Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994–1007 (2012). (PMID: 10.1016/j.cell.2012.04.023226080833428864)
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 289–300 (1995).
Yoshida, K. et al. Tobacco smoking and somatic mutations in human bronchial epithelium. Nature 578, 266–272 (2020). (PMID: 10.1038/s41586-020-1961-1319968507021511)
Gerstung, M., Papaemmanuil, E. & Campbell, P. J. Subclonal variant calling with multiple samples and prior knowledge. Bioinformatics 30, 1198–1204 (2014). (PMID: 10.1093/bioinformatics/btt750244431483998123)
Hoang, H. T. et al. MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol. 18, 11 (2018). (PMID: 10.1186/s12862-018-1131-3293909735796505)
Nguyen, L.-T. et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2014). (PMID: 10.1093/molbev/msu300253714304271533)
Novelli, M. et al. X-inactivation patch size in human female tissue confounds the assessment of tumor clonality. Proc. Natl Acad. Sci. USA 100, 3311–3314 (2003). (PMID: 10.1073/pnas.043782510012610207152288)
Gori, K. & Baez-Ortega, A. sigfit: flexible Bayesian inference of mutational signatures. Preprint at https://doi.org/10.1101/372896 (2018).
Coorens, T. H. H. et al. Clonal hematopoiesis and therapy-related myeloid neoplasms following neuroblastoma treatment. Blood 137, 2992–2997 (2021). (PMID: 10.1182/blood.2020010150335986918160503)
معلومات مُعتمدة: United Kingdom WT_ Wellcome Trust; 27176 United Kingdom CRUK_ Cancer Research UK; 21777 United Kingdom CRUK_ Cancer Research UK; 203943/Z/16/Z United Kingdom WT_ Wellcome Trust; 27114 United Kingdom CRUK_ Cancer Research UK
تواريخ الأحداث: Date Created: 20210826 Date Completed: 20211104 Latest Revision: 20240320
رمز التحديث: 20240320
DOI: 10.1038/s41586-021-03790-y
PMID: 34433963
قاعدة البيانات: MEDLINE
الوصف
تدمد:1476-4687
DOI:10.1038/s41586-021-03790-y