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Grave-to-cradle: human embryonic lineage tracing from the postmortem body

Choi Seock Hwan|Ku Eu Jeong|Choi Yujin Angelina|Oh Ji Won
생화학분자생물학회 (Korean Society Of Biochemistry And Molecular Biology)|2023.12|Experimental and Molecular Medicine|제55권 |pp. 13-21|DOI 10.1038/s12276-022-00912-y

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주제분류생화학

초록

Curiosity concerning the process of human creation has been around for a long time. Relevant questions seemed to be resolved with the knowledge of how cells divide after fertilization obtained through in vitro fertilization experiments. However, we still do not know how human life is created at the cellular level. Recently, the value of cadavers as a resource from which to obtain “normal” cells and tissues has been established, and human research using postmortem bodies has attracted growing scientific attention. As the human genome can be analyzed at the level of nucleotides through whole-genome sequencing, individual cells in a postmortem body can be traced back to determine what developmental processes have transpired from fertilization. These retrospective lineage tracing studies have answered several unsolved questions on how humans are created. This review covers the methodologies utilized in lineage tracing research in a historical context and the conceptual basis for reconstructing the division history of cells in a retrospective manner using postzygotic somatic variants in postmortem tissue. We further highlight answers that postmortem research could potentially address and discuss issues that wait to be solved in the future.

Abstract

Curiosity concerning the process of human creation has been around for a long time. Relevant questions seemed to be resolved with the knowledge of how cells divide after fertilization obtained through in vitro fertilization experiments. However, we still do not know how human life is created at the cellular level. Recently, the value of cadavers as a resource from which to obtain “normal” cells and tissues has been established, and human research using postmortem bodies has attracted growing scientific attention. As the human genome can be analyzed at the level of nucleotides through whole-genome sequencing, individual cells in a postmortem body can be traced back to determine what developmental processes have transpired from fertilization. These retrospective lineage tracing studies have answered several unsolved questions on how humans are created. This review covers the methodologies utilized in lineage tracing research in a historical context and the conceptual basis for reconstructing the division history of cells in a retrospective manner using postzygotic somatic variants in postmortem tissue. We further highlight answers that postmortem research could potentially address and discuss issues that wait to be solved in the future.

참고문헌 (90)

  1. His, W, "Anatomie menschlicher Embryonen" (1880), Vogel
  2. Streeter, G. L., "Developmental horizons in human embryos", Contrib. Embryol, 30, pp.213~230 (1942)
  3. Müller, F., "Developmental Stages in Human Embryos" (1987), Carnegie Institution of Washington
  4. Steptoe, P. C., "Birth after the reimplantation of a human embryo", Lancet, 2, pp.366~ (1978)
  5. Cavaliere, G., "A 14-day limit for bioethics : the debate over human embryo research", BMC Med. Ethics, 18, pp.38~ (2017)
  6. Kretzschmar, K., "Lineage tracing", Cell, 148, pp.33~45 (2012)
  7. Conklin, E. G., "The Organization and Cell-lineage of the Ascidian Egg" (1905), Academy of Natural Sciences
  8. Jeffery, W. R., "Molecular Aspects of Early Development", pp.1~38 (1984), Springer US
  9. Wilson, E. B., "The cell-lineage of Nereis. A contribution to the cytogeny of the annelid body", J. Morphol, 6, pp.361~480 (1892)
  10. Sulston, J. E., "The embryonic cell lineage of the nematode Caenorhabditis elegans", Dev. Biol, 100, pp.64~119 (1983)
  11. Sulston, J. E., "Post-embryonic cell lineages of the nematode, Caenorhabditis elegans", Dev. Biol, 56, pp.110~156 (1977)
  12. Vogelstein, B., "Cancer genome landscapes", Science, 339, pp.1546~1558 (2013)
  13. James, C. D., "Mitotic recombination of chromosome 17 in astrocytomas", Proc. Natl Acad. Sci. USA, 86, pp.2858~2862 (1989)
  14. McFarland, C. D., "The damaging effect of passenger mutations on cancer progression", Cancer Res, 77, pp.4763~4772 (2017)
  15. Gerlinger, M., "Intratumor heterogeneity and branched evolution revealed by multiregion sequencing", N. Engl. J. Med, 366, pp.883~892 (2012)
  16. Kreso, A., "Evolution of the cancer stem cell model", Cell Stem Cell, 14, pp.275~291 (2014)
  17. Landau, D. A., "Evolution and impact of subclonal mutations in chronic lymphocytic leukemia", Cell, 152, pp.714~726 (2013)
  18. Sottoriva, A., "Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics", Proc. Natl Acad. Sci. U. S. A, 110, pp.4009~4014 (2013)
  19. Aceto, N., "Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis", Cell, 158, pp.1110~1122 (2014)
  20. Wang, Y., "Clonal evolution in breast cancer revealed by single nucleus genome sequencing", Nature, 512, pp.155~160 (2014)
  21. Ortmann, C. A., "Effect of mutation order on myeloproliferative neoplasms", N. Engl. J. Med, 372, pp.601~612 (2015)
  22. Li, Y., "Single-cell sequencing analysis characterizes common and celllineage-specific mutations in a muscle-invasive bladder cancer", Gigascience, 1, pp.12~ (2012)
  23. Xu, X., "Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor", Cell, 148, pp.886~895 (2012)
  24. Humphries, A., "Lineage tracing reveals multipotent stem cells maintain human adenomas and the pattern of clonal expansion in tumor evolution", Proc. Natl Acad. Sci. USA, 110, pp.E2490~E2499 (2013)
  25. McGranahan, N., "Clonal heterogeneity and tumor evolution : past, present, and the future", Cell, 168, pp.613~628 (2017)
  26. Garraway, L. A., "Lessons from the cancer genome", Cell, 153, pp.17~37 (2013)
  27. Vogelstein, B., "Cancer genes and the pathways they control", Nat. Med, 10, pp.789~799 (2004)
  28. Forsberg, L. A., "Mosaicism in health and disease—clones picking up speed", Nat. Rev. Genet, 18, pp.128~142 (2017)
  29. van den Hurk, J. A., "L1 retrotransposition can occur early in human embryonic development", Hum. Mol. Genet, 16, pp.1587~1592 (2007)
  30. Coufal, N. G., "L1 retrotransposition in human neural progenitor cells", Nature, 460, pp.1127~1131 (2009)
  31. Piotrowski, A., "Somatic mosaicism for copy number variation in differentiated human tissues", Hum. Mutat, 29, pp.1118~1124 (2008)
  32. Bielanska, M., "Chromosomal mosaicism throughout human preimplantation development in vitro : incidence, type, and relevance to embryo outcome", Hum. Reprod, 17, pp.413~419 (2002)
  33. Vanneste, E., "Chromosome instability is common in human cleavage-stage embryos", Nat. Med, 15, pp.577~583 (2009)
  34. De, S., "Somatic mosaicism in healthy human tissues", Trends Genet, 27, pp.217~223 (2011)
  35. Thorpe, J., "Mosaicism in human health and disease", Annu. Rev. Genet, 54, pp.487~510 (2020)
  36. "Tumor mutational landscape is a record of the pre-malignant state" (2019)[URL]
  37. Lynch, M., "Rate, molecular spectrum, and consequences of human mutation", Proc. Natl Acad. Sci. USA, 107, pp.961~968 (2010)
  38. Park, S., "Clonal dynamics in early human embryogenesis inferred from somatic mutation", Nature, 597, pp.393~397 (2021)
  39. Ju, Y. S., "Somatic mutations reveal asymmetric cellular dynamics in the early human embryo", Nature, 543, pp.714~718 (2017)
  40. Brunner, S. F., "Somatic mutations and clonal dynamics in healthy and cirrhotic human liver", Nature, 574, pp.538~542 (2019)
  41. Blokzijl, F., "Tissue-specific mutation accumulation in human adult stem cells during life", Nature, 538, pp.260~264 (2016)
  42. Osorio, F. G., "Somatic mutations reveal lineage relationships and age-related mutagenesis in human hematopoiesis", Cell Rep, 25, pp.2308~2316 (2018)
  43. Lee-Six, H., "The landscape of somatic mutation in normal colorectal epithelial cells", Nature, 574, pp.532~537 (2019)
  44. Woodworth, M. B., "Building a lineage from single cells : genetic techniques for cell lineage tracking", Nat. Rev. Genet, 18, pp.230~244 (2017)
  45. Behjati, S., "Genome sequencing of normal cells reveals developmental lineages and mutational processes", Nature, 513, pp.422~425 (2014)
  46. Bae, T., "Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis", Science, 359, pp.550~555 (2018)
  47. Lodato, M. A., "Aging and neurodegeneration are associated with increased mutations in single human neurons", Science, 359, pp.555~559 (2018)
  48. Coorens, T. H. H., "Extensive phylogenies of human development inferred from somatic mutations", Nature, 597, pp.387~392 (2021)
  49. Fasching, L., "Early developmental asymmetries in cell lineage trees in living individuals", Science, 371, pp.1245~1248 (2021)
  50. Bizzotto, S., "Landmarks of human embryonic development inscribed in somatic mutations", Science, 371, pp.1249~1253 (2021)
  51. Coorens, T. H. H., "Inherent mosaicism and extensive mutation of human placentas", Nature, 592, pp.80~85 (2021)
  52. Ferreira, P. G., "The effects of death and post-mortem cold ischemia on human tissue transcriptomes", Nat. Commun, 9, pp.490~ (2018)
  53. Palmer, T. D., "Cell culture", Progenitor cells from human brain after death. Nature, 411, pp.42~43 (2001)
  54. Lonsdale, J., "The Genotype-Tissue Expression(GTEx)project", Nat. Genet, 45, pp.580~585 (2013)
  55. GTEx Consortium, "The GTEx Consortium atlas of genetic regulatory effects across human tissues", Science, 369, pp.1318~1330 (2020)
  56. Zhu, Y., "Systematic analysis of gene expression patterns associated with postmortem interval in human tissues", Sci. Rep, 7, pp.5435~ (2017)
  57. Wall, J. D., "Estimating genotype error rates from high-coverage next-generation sequence data", Genome Res, 24, pp.1734~1739 (2014)
  58. Paskov, K., "Estimating sequencing error rates using families", BioData Min, 14, pp.27~ (2021)
  59. Kwack, M. H., "Establishment and characterization of five immortalized human scalp dermal papilla cell lines", Biochem. Biophys. Res. Commun, 496, pp.346~351 (2018)
  60. Mitchell, E., "Clonal dynamics of haematopoiesis across the human lifespan", Nature, 606, pp.343~350 (2022)
  61. Lee-Six, H., "Population dynamics of normal human blood inferred from somatic mutations", Nature, 561, pp.473~478 (2018)
  62. Jager, M., "Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures", Nat. Protoc, 13, pp.59~78 (2018)
  63. Drost, J., "Organoid culture systems for prostate epithelial and cancer tissue", Nat. Protoc, 11, pp.347~358 (2016)
  64. Espina, V., "Laser-capture microdissection", Nat. Protoc, 1, pp.586~603 (2006)
  65. Ellis, P., "Reliable detection of somatic mutations in solid tissues by lasercapture microdissection and low-input DNA sequencing", Nat. Protoc, 16, pp.841~871 (2021)
  66. Ng, S. W. K., "Convergent somatic mutations in metabolism genes in chronic liver disease", Nature, 598, pp.473~478 (2021)
  67. Olafsson, S., "Somatic evolution in non-neoplastic IBD-affected colon", Cell, 182, pp.e611~ (2020)
  68. Moore, L., "The mutational landscape of normal human endometrial epithelium", Nature, 580, pp.640~646 (2020)
  69. Spencer Chapman, M., "Lineage tracing of human development through somatic mutations", Nature, 595, pp.85~90 (2021)
  70. Moore, L., "The mutational landscape of human somatic and germline cells", Nature, 597, pp.381~386 (2021)
  71. Blanpain, C., "Unravelling stem cell dynamics by lineage tracing", Nat. Rev. Mol. Cell Biol, 14, pp.489~502 (2013)
  72. Simons, B. D., "Strategies for homeostatic stem cell self-renewal in adult tissues", Cell, 145, pp.851~862 (2011)
  73. Snippert, H. J., "Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells", Cell, 143, pp.134~144 (2010)
  74. Lodato, M. A., "Somatic mutation in single human neurons tracks developmental and transcriptional history", Science, 350, pp.94~98 (2015)
  75. Biezuner, T., "Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing", Sci. Rep, 11, pp.17171~ (2021)
  76. Gawad, C., "Single-cell genome sequencing : current state of the science", Nat. Rev. Genet, 17, pp.175~188 (2016)
  77. Huang August, Y., "Parallel RNA and DNA analysis after deep sequencing(PRDD-seq)reveals cell type-specific lineage patterns in human brain", Proc. Natl Acad. Sci. USA, 117, pp.13886~13895 (2020)
  78. Bae, T., "Analysis of somatic mutations in 131 human brains reveals agingassociated hypermutability", Science, 377, pp.511~517 (2022)
  79. Breuss, M. W., "Somatic mosaicism reveals clonal distributions of neocortical development", Nature, 604, pp.689~696 (2022)
  80. Wang, Y., "Comprehensive identification of somatic nucleotide variants in human brain tissue", Genome Biol, 22, pp.92~ (2021)
  81. Huang, A. Y., "Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs", PLoS Genet, 14, pp.e1007395~ (2018)
  82. Valecha, M., "Somatic variant calling from single-cell DNA sequencing data", Comput. Struct. Biotechnol. J, 20, pp.2978~2985 (2022)
  83. Gonzalez-Pena, V., "Accurate genomic variant detection in single cells with primary template-directed amplification", Proc. Natl. Acad. Sci. USA, 118, pp.e2024176118~ (2021)
  84. "Ultraspecific somatic SNV and indel detection in single neurons using primary template-directed amplification" (2021)[URL]
  85. Miller, M. B., "Somatic genomic changes in single Alzheimer’s disease neurons", Nature, 604, pp.714~722 (2022)
  86. Sadler, T. W., "Langman’s Medical Embryology" (2018), Wolters Kluwer
  87. Barresi, M. J. F., "Developmental Biology" (2019), Sinauer Associates, Inc., Publishers
  88. Kwon, G. S., "The endoderm of the mouse embryo arises by dynamic widespread intercalation of embryonic and extraembryonic lineages", Dev. Cell, 15, pp.509~520 (2008)
  89. Stern, C. D., "Aptly named visceral endoderm", Dev. Cell, 15, pp.493~494 (2008)
  90. Martincorena, I., "Somatic mutant clones colonize the human esophagus with age", Science, 362, pp.911~917 (2018)

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