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Acquired genetic changes in human pluripotent stem cells: origins and consequences

Nature Reviews Molecular Cell Biology volume 21, pages 715–728 (2020)Cite this article

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Abstract

In the 20 years since human embryonic stem cells, and subsequently induced pluripotent stem cells, were first described, it has become apparent that during long-term culture these cells (collectively referred to as ‘pluripotent stem cells’ (PSCs)) can acquire genetic changes, which commonly include gains or losses of particular chromosomal regions, or mutations in certain cancer-associated genes, especially TP53. Such changes raise concerns for the safety of PSC-derived cellular therapies for regenerative medicine. Although acquired genetic changes may not be present in a cell line at the start of a research programme, the low sensitivity of current detection methods means that mutations may be difficult to detect if they arise but are present in only a small proportion of the cells. In this Review, we discuss the types of mutations acquired by human PSCs and the mechanisms that lead to their accumulation. Recent work suggests that the underlying mutation rate in PSCs is low, although they also seem to be particularly susceptible to genomic damage. This apparent contradiction can be reconciled by the observations that, in contrast to somatic cells, PSCs are programmed to die in response to genomic damage, which may reflect the requirements of early embryogenesis. Thus, the common genetic variants that are observed are probably rare events that give the cells with a selective growth advantage.

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Fig. 1: Cultured human pluripotent stem cells can acquire a variety of mutations.
Fig. 2: Nature of tumours derived from pluripotent stem cells.
Fig. 3: Mechanisms of variant growth advantage.
Fig. 4: Overview of the origins of mutation in human pluripotent stem cells.

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References

  1. Thomson, J. A. et al. Embryonic stem cell lines derived from human blastocysts. Science 282, 1145–1147 (1998).

    CAS  PubMed  Google Scholar 

  2. Reubinoff, B. E., Pera, M. F., Fong, C. Y., Trounson, A. & Bongso, A. Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro. Nat. Biotechnol. 18, 399–404 (2000).

    CAS  PubMed  Google Scholar 

  3. Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872 (2007).

    CAS  PubMed  Google Scholar 

  4. Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917–1920 (2007).

    CAS  PubMed  Google Scholar 

  5. da Cruz, L. et al. Phase 1 clinical study of an embryonic stem cell-derived retinal pigment epithelium patch in age-related macular degeneration. Nat. Biotechnol. 36, 328–337 (2018).

    PubMed  Google Scholar 

  6. Schwartz, S. D. et al. Embryonic stem cell trials for macular degeneration: a preliminary report. Lancet 379, 713–720 (2012).

    CAS  PubMed  Google Scholar 

  7. Song, W. K. et al. Treatment of macular degeneration using embryonic stem cell-derived retinal pigment epithelium: preliminary results in Asian patients. Stem Cell Rep. 4, 860–872 (2015).

    CAS  Google Scholar 

  8. Mandai, M., Kurimoto, Y. & Takahashi, M. Autologous induced stem-cell-derived retinal cells for macular degeneration. N. Engl. J. Med. 377, 792–793 (2017).

    PubMed  Google Scholar 

  9. Barker, R. A., Parmar, M., Studer, L. & Takahashi, J. Human trials of stem cell-derived dopamine neurons for Parkinson’s disease: dawn of a new era. Cell Stem Cell 21, 569–573 (2017).

    CAS  PubMed  Google Scholar 

  10. Bar, S. & Benvenisty, N. Epigenetic aberrations in human pluripotent stem cells. EMBO J. https://doi.org/10.15252/embj.2018101033 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Yasuda, S. et al. Tumorigenicity-associated characteristics of human iPS cell lines. PLoS ONE 13, e0205022 (2018).

    PubMed  PubMed Central  Google Scholar 

  12. Sato, Y. et al. Tumorigenicity assessment of cell therapy products: the need for global consensus and points to consider. Cytotherapy 21, 1095–1111 (2019).

    CAS  PubMed  Google Scholar 

  13. Andrews, P. W. From teratocarcinomas to embryonic stem cells. Philos. Trans. R. Soc. Lond. B Biol. Sci. 357, 405–417 (2002).

    PubMed  PubMed Central  Google Scholar 

  14. Garber, K. RIKEN suspends first clinical trial involving induced pluripotent stem cells. Nat. Biotechnol. 33, 890–891 (2015).

    CAS  PubMed  Google Scholar 

  15. Hussein, S. M. et al. Copy number variation and selection during reprogramming to pluripotency. Nature 471, 58–62 (2011).

    CAS  PubMed  Google Scholar 

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

    PubMed  PubMed Central  Google Scholar 

  17. Steichen, C., Hannoun, Z., Luce, E., Hauet, T. & Dubart-Kupperschmitt, A. Genomic integrity of human induced pluripotent stem cells: reprogramming, differentiation and applications. World J. Stem Cell 11, 729–747 (2019).

    Google Scholar 

  18. Amps, K. et al. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat. Biotechnol. 29, 1132–1144 (2011). Amps et al. report a study of a large panel of cells lines by an international consortium, using karyotype and SNP array analyses to survey the range of genetic variants commonly recurring in human PSCs.

    CAS  PubMed  Google Scholar 

  19. Merkle, F. T. et al. Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature 545, 229–233 (2017). The work by Merkle et al. provides the first demonstration of point mutations that occur recurrently in a single gene in human PSCs, resulting in variants of a tumour suppressor that provide a growth advantage by reducing sensitivity to apoptosis.

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Olariu, V. et al. Modeling the evolution of culture-adapted human embryonic stem cells. Stem Cell Res. 4, 50–56 (2010).

    PubMed  Google Scholar 

  21. Thompson, O. et al. Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions. Nat. Commun. 11, 1528 (2020). Using a clonogenic strategy, Thompson et al. report the low mutation rate in human PSCs and show that this rate is reduced by growth under low-oxygen conditions.

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Draper, J. S. et al. Recurrent gain of chromosomes 17q and 12 in cultured human embryonic stem cells. Nat. Biotechnol. 22, 53–54 (2004).

    CAS  PubMed  Google Scholar 

  23. Taapken, S. M. et al. Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells. Nat. Biotechnol. 29, 313–314 (2011).

    CAS  PubMed  Google Scholar 

  24. Baker, D. et al. Detecting genetic mosaicism in cultures of human pluripotent stem cells. Stem Cell Rep. 7, 998–1012 (2016). Baker et al. provide a comprehensive comparison of the sensitivity of commonly used methods for detection of genetic changes in PSCs, providing the basis for interpreting genetic tests used for assessment of PSC cultures.

    CAS  Google Scholar 

  25. Torres, E. M., Williams, B. R. & Amon, A. Aneuploidy: cells losing their balance. Genetics 179, 737–746 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Assou, S. et al. Recurrent genetic abnormalities in human pluripotent stem cells: definition and routine detection in culture supernatant by targeted droplet digital PCR. Stem Cell Rep. 14, 1–8 (2020).

    CAS  Google Scholar 

  27. Baker, D. E. et al. Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat. Biotechnol. 25, 207–215 (2007).

    CAS  PubMed  Google Scholar 

  28. Nguyen, H. T., Geens, M. & Spits, C. Genetic and epigenetic instability in human pluripotent stem cells. Hum. Reprod. Update 19, 187–205 (2013).

    CAS  PubMed  Google Scholar 

  29. Lefort, N. et al. Human embryonic stem cells reveal recurrent genomic instability at 20q11.21. Nat. Biotechnol. 26, 1364–1366 (2008).

    CAS  PubMed  Google Scholar 

  30. Spits, C. et al. Recurrent chromosomal abnormalities in human embryonic stem cells. Nat. Biotechnol. 26, 1361–1363 (2008).

    CAS  PubMed  Google Scholar 

  31. Enver, T. et al. Cellular differentiation hierarchies in normal and culture-adapted human embryonic stem cells. Hum. Mol. Genet. 14, 3129–3140 (2005).

    CAS  PubMed  Google Scholar 

  32. Ben-David, U. et al. Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells. Nat. Commun. 5, 4825 (2014). Ben-David et al. provide a detailed analysis of how gains of chromosome 12, one of the common chromosomal variants seen in human PSCs and in germ cell tumours, affect the transcriptome and the growth patterns of human PSCs.

    CAS  PubMed  Google Scholar 

  33. Avior, Y., Eggan, K. & Benvenisty, N. Cancer-related mutations identified in primed and naive human pluripotent stem cells. Cell Stem Cell 25, 456–461 (2019).

    CAS  PubMed  Google Scholar 

  34. Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333–339 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Malkin, D. et al. Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science 250, 1233–1238 (1990).

    CAS  PubMed  Google Scholar 

  36. Srivastava, S., Zou, Z. Q., Pirollo, K., Blattner, W. & Chang, E. H. Germ-line transmission of a mutated p53 gene in a cancer-prone family with Li-Fraumeni syndrome. Nature 348, 747–749 (1990).

    CAS  PubMed  Google Scholar 

  37. Nichols, J. & Smith, A. Naive and primed pluripotent states. Cell Stem Cell 4, 487–492 (2009).

    CAS  PubMed  Google Scholar 

  38. Mostofi, F. K. & Price, E. B. Tumors of the Male Genital System, Atlas of Tumor Pathology, Second Series. (Armed Forces Institute of Pathology, 1973).

  39. Damjanov, I. & Solter, D. Experimental teratoma. Curr. Top. Pathol. 59, 69–130 (1974).

    CAS  PubMed  Google Scholar 

  40. Damjanov, I. & Andrews, P. W. The terminology of teratocarcinomas and teratomas. Nat. Biotechnol. 25, 1212 (2007).

    CAS  PubMed  Google Scholar 

  41. Damjanov, I. & Andrews, P. W. Teratomas produced from human pluripotent stem cells xenografted into immunodeficient mice - a histopathology atlas. Int. J. Dev. Biol. 60, 337–419 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Einhorn, L. H. & Donohue, J. Cis-diamminedichloroplatinum, vinblastine, and bleomycin combination chemotherapy in disseminated testicular cancer. Ann. Intern. Med. 87, 293–298 (1977).

    CAS  PubMed  Google Scholar 

  43. Oosterhuis, J. W., Andrews, P. W., Knowles, B. B. & Damjanov, I. Effects of cis-platinum on embryonal carcinoma cell lines in vitro. Int. J. Cancer 34, 133–139 (1984).

    CAS  PubMed  Google Scholar 

  44. Einhorn, L. H., Nagy, C., Furnas, B. & Williams, S. D. Nabilone: an effective antiemetic in patients receiving cancer chemotherapy. J. Clin. Pharmacol. 21, 64S–69S (1981).

    CAS  PubMed  Google Scholar 

  45. Williams, S. D. et al. Treatment of disseminated germ-cell tumors with cisplatin, bleomycin, and either vinblastine or etoposide. N. Engl. J. Med. 316, 1435–1440 (1987).

    CAS  PubMed  Google Scholar 

  46. Andrews, P. W. et al. Embryonic stem (ES) cells and embryonal carcinoma (EC) cells: opposite sides of the same coin. Biochem. Soc. Trans. 33, 1526–1530 (2005).

    CAS  PubMed  Google Scholar 

  47. Allison, T. F. et al. Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells. Nat. Commun. 9, 1925 (2018).

    Google Scholar 

  48. Cunningham, J. J., Ulbright, T. M., Pera, M. F. & Looijenga, L. H. Lessons from human teratomas to guide development of safe stem cell therapies. Nat. Biotechnol. 30, 849–857 (2012).

    CAS  PubMed  Google Scholar 

  49. Plantaz, D. et al. Gain of chromosome 17 is the most frequent abnormality detected in neuroblastoma by comparative genomic hybridization. Am. J. Pathol. 150, 81–89 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Avery, S. et al. BCL-XL mediates the strong selective advantage of a 20q11.21 amplification commonly found in human embryonic stem cell cultures. Stem Cell Rep. 1, 379–386 (2013). Avery et al. report the identification of BCL2L1 as the driver gene on chromosome band 20q11.21, which is commonly amplified in PSCs.

    CAS  Google Scholar 

  51. Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Hainaut, P. & Hollstein, M. in Advances in Cancer Research Vol. 77 (eds Vande Woude, G. F. & Klein, G.) 81–137 (Academic Press, 1999).

  53. Andrews, P. W. et al. Assessing the safety of human pluripotent stem cells and their derivatives for clinical applications. Stem Cell Rep. 9, 1–4 (2017).

    Google Scholar 

  54. Technologies, S. Challenges in Ensuring hPSC Quality. Stemcell.com, https://www.stemcell.com/nature-research-roundtable-hPSC-quality (2018).

  55. Ministry of Health, Labour and Welfare. English translation of Annex of Notification 0613-3. http://www.nihs.go.jp/cbtp/sispsc/pdf/Eg.ver.Annex_0613-3_2016.pdf (2016).

  56. Catalina, P. et al. Human ESCs predisposition to karyotypic instability: is a matter of culture adaptation or differential vulnerability among hESC lines due to inherent properties? Mol. Cancer 7, 76 (2008).

    PubMed  PubMed Central  Google Scholar 

  57. Imreh, M. P. et al. In vitro culture conditions favoring selection of chromosomal abnormalities in human ES cells. J. Cell Biochem. 99, 508–516 (2006).

    CAS  PubMed  Google Scholar 

  58. Andrews, P. W., Bronson, D. L., Benham, F., Strickland, S. & Knowles, B. B. A comparative study of eight cell lines derived from human testicular teratocarcinoma. Int. J. Cancer 26, 269–280 (1980).

    CAS  PubMed  Google Scholar 

  59. Andrews, P. W., Goodfellow, P. N., Shevinsky, L. H., Bronson, D. L. & Knowles, B. B. Cell-surface antigens of a clonal human embryonal carcinoma cell line: morphological and antigenic differentiation in culture. Int. J. Cancer 29, 523–531 (1982).

    CAS  PubMed  Google Scholar 

  60. Fazeli, A. et al. Altered patterns of differentiation in karyotypically abnormal human embryonic stem cells. Int. J. Dev. Biol. 55, 175–180 (2011).

    CAS  PubMed  Google Scholar 

  61. Werbowetski-Ogilvie, T. E. et al. Characterization of human embryonic stem cells with features of neoplastic progression. Nat. Biotechnol. 27, 91–97 (2009). The study by Werbowetski-Ogilvie et al. demonstrates a profound effect of some of the recurrent genetic changes on PSC growth rates and the ability of PSCs to differentiate to specific lineages.

    CAS  PubMed  Google Scholar 

  62. Lee, C. T. et al. Functional consequences of 17q21.31/WNT3-WNT9B amplification in hPSCs with respect to neural differentiation. Cell Rep. 10, 616–632 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Markouli, C. et al. Gain of 20q11.21 in human pluripotent stem cells impairs TGF-β-dependent neuroectodermal commitment. Stem Cell Rep. 13, 163–176 (2019). Markouli et al. show that altered transforming growth factor-β signalling in PSCs harbouring a 20q11.21 copy number variant impairs their neuroectodermal differentiation.

    CAS  Google Scholar 

  64. Laurent, L. C. et al. Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture. Cell Stem Cell 8, 106–118 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Ohgushi, M. et al. Molecular pathway and cell state responsible for dissociation-induced apoptosis in human pluripotent stem cells. Cell Stem Cell 7, 225–239 (2010).

    CAS  PubMed  Google Scholar 

  66. Barbaric, I. et al. Time-lapse analysis of human embryonic stem cells reveals multiple bottlenecks restricting colony formation and their relief upon culture adaptation. Stem Cell Rep. 3, 142–155 (2014).

    CAS  Google Scholar 

  67. Liu, J. C. et al. High mitochondrial priming sensitizes hESCs to DNA-damage-induced apoptosis. Cell Stem Cell 13, 483–491 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Dumitru, R. et al. Human embryonic stem cells have constitutively active Bax at the Golgi and are primed to undergo rapid apoptosis. Mol. Cell 46, 573–583 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Price, C. J. et al. Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition. bioRxiv https://doi.org/10.1101/854430 (2019).

  70. Bowling, S., Lawlor, K. & Rodríguez, T. A. Cell competition: the winners and losers of fitness selection. Development https://doi.org/10.1242/dev.167486 (2019).

  71. Haupt, S., Mejía-Hernández, J. O., Vijayakumaran, R., Keam, S. P. & Haupt, Y. The long and the short of it: the MDM4 tail so far. J. Mol. Cell Biol. 11, 231–244 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Blum, B., Bar-Nur, O., Golan-Lev, T. & Benvenisty, N. The anti-apoptotic gene survivin contributes to teratoma formation by human embryonic stem cells. Nat. Biotechnol. 27, 281–287 (2009).

    CAS  PubMed  Google Scholar 

  73. Mesri, M., Wall, N. R., Li, J., Kim, R. W. & Altieri, D. C. Cancer gene therapy using a survivin mutant adenovirus. J. Clin. Invest. 108, 981–990 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Ma, X. et al. High-level expression, purification and pro-apoptosis activity of HIV-TAT-survivin (T34A) mutant to cancer cells in vitro. J. Biotechnol. 123, 367–378 (2006).

    CAS  PubMed  Google Scholar 

  75. Yang, D., Welm, A. & Bishop, J. M. Cell division and cell survival in the absence of survivin. Proc. Natl Acad. Sci. USA 101, 15100–15105 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Atkin, N. B. & Baker, M. C. Specific chromosome change, i(12p), in testicular tumours? Lancet 2, 1349 (1982).

    CAS  PubMed  Google Scholar 

  77. Rodriguez, S. et al. Expression profile of genes from 12p in testicular germ cell tumors of adolescents and adults associated with i(12p) and amplification at 12p11.2-p12.1. Oncogene 22, 1880–1891 (2003).

    CAS  PubMed  Google Scholar 

  78. Korkola, J. E. et al. Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13.31, is associated with in vivo differentiation of human male germ cell tumors. Cancer Res. 66, 820–827 (2006).

    CAS  PubMed  Google Scholar 

  79. Chambers, I. et al. Nanog safeguards pluripotency and mediates germline development. Nature 450, 1230–1234 (2007).

    CAS  PubMed  Google Scholar 

  80. Darr, H., Mayshar, Y. & Benvenisty, N. Overexpression of NANOG in human ES cells enables feeder-free growth while inducing primitive ectoderm features. Development 133, 1193–1201 (2006).

    CAS  PubMed  Google Scholar 

  81. Singh, R., Letai, A. & Sarosiek, K. Regulation of apoptosis in health and disease: the balancing act of BCL-2 family proteins. Nat. Rev. Mol. Cell Biol. 20, 175–193 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Madden, D. T., Davila-Kruger, D., Melov, S. & Bredesen, D. E. Human embryonic stem cells express elevated levels of multiple pro-apoptotic BCL-2 family members. PLoS ONE 6, e28530 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Zhang, J. et al. Anti-apoptotic mutations desensitize human pluripotent stem cells to mitotic stress and enable aneuploid cell survival. Stem Cell Rep. 12, 557–571 (2019).

    CAS  Google Scholar 

  84. Ardehali, R. et al. Overexpression of BCL2 enhances survival of human embryonic stem cells during stress and obviates the requirement for serum factors. Proc. Natl Acad. Sci. USA 108, 3282–3287 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Watanabe, K. et al. A ROCK inhibitor permits survival of dissociated human embryonic stem cells. Nat. Biotechnol. 25, 681–686 (2007).

    CAS  PubMed  Google Scholar 

  86. Milholland, B. et al. Differences between germline and somatic mutation rates in humans and mice. Nat. Commun. 8, 15183 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Kuijk, E. et al. Mutational impact of culturing human pluripotent and adult stem cells. Nat. Commun. 11, 2493 (2018).

    Google Scholar 

  88. Cervantes, R. B., Stringer, J. R., Shao, C., Tischfield, J. A. & Stambrook, P. J. Embryonic stem cells and somatic cells differ in mutation frequency and type. Proc. Natl Acad. Sci. USA 99, 3586–3590 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Petljak, M. et al. Characterizing mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis. Cell 176, 1282–1294.e1220 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Kucab, J. E. et al. A compendium of mutational signatures of environmental agents. Cell 177, 821–836.e816 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    PubMed  PubMed Central  Google Scholar 

  92. Bartkova, J. et al. DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis. Nature 434, 864–870 (2005).

    CAS  PubMed  Google Scholar 

  93. Gorgoulis, V. G. et al. Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature 434, 907–913 (2005).

    CAS  PubMed  Google Scholar 

  94. Cannan, W. J. & Pederson, D. S. Mechanisms and consequences of double-strand DNA break formation in chromatin. J. Cell Physiol. 231, 3–14 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Becker, K. A. et al. Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase. J. Cell Physiol. 209, 883–893 (2006).

    CAS  PubMed  Google Scholar 

  96. Becker, K. A. et al. Cyclin D2 and the CDK substrate p220NPAT are required for self-renewal of human embryonic stem cells. J. Cell Physiol. 222, 456–464 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Filipczyk, A. A., Laslett, A. L., Mummery, C. & Pera, M. F. Differentiation is coupled to changes in the cell cycle regulatory apparatus of human embryonic stem cells. Stem Cell Res. 1, 45–60 (2007).

    CAS  PubMed  Google Scholar 

  98. Halliwell, J. A. et al. Nucleosides rescue replication-mediated genome instability of human pluripotent stem cells. Stem Cell Rep. 14, 1009–1017 (2020). Halliwell et al. show that human PSCs are subject to DNA replication stress that leads to DNA damage, mitotic errors and reduced population growth rates, but that these effects can be greatly reduced by culture in medium supplemented with nucleosides.

    CAS  Google Scholar 

  99. Simara, P. et al. DNA double-strand breaks in human induced pluripotent stem cell reprogramming and long-term in vitro culturing. Stem Cell Res. Ther. 8, 73 (2017).

    PubMed  PubMed Central  Google Scholar 

  100. Vallabhaneni, H. et al. High basal levels of γH2AX in human induced pluripotent stem cells are linked to replication-associated DNA damage and repair. Stem Cell 36, 1501–1513 (2018).

    CAS  Google Scholar 

  101. Akli, S. & Keyomarsi, K. Cyclin E and its low molecular weight forms in human cancer and as targets for cancer therapy. Cancer Biol. Ther. 2, S38–S47 (2003).

    CAS  PubMed  Google Scholar 

  102. Bester, A. C. et al. Nucleotide deficiency promotes genomic instability in early stages of cancer development. Cell 145, 435–446 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  103. Burrell, R. A. et al. Replication stress links structural and numerical cancer chromosomal instability. Nature 494, 492–496 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. Frame, F. M., Rogoff, H. A., Pickering, M. T., Cress, W. D. & Kowalik, T. F. E2F1 induces MRN foci formation and a cell cycle checkpoint response in human fibroblasts. Oncogene 25, 3258–3266 (2006).

    CAS  PubMed  Google Scholar 

  105. Pickering, M. T. & Kowalik, T. F. Rb inactivation leads to E2F1-mediated DNA double-strand break accumulation. Oncogene 25, 746–755 (2006).

    CAS  PubMed  Google Scholar 

  106. Ahuja, A. K. et al. A short G1 phase imposes constitutive replication stress and fork remodelling in mouse embryonic stem cells. Nat. Commun. 7, 10660 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Halazonetis, T. D., Gorgoulis, V. G. & Bartek, J. An oncogene-induced DNA damage model for cancer development. Science 319, 1352–1355 (2008).

    CAS  PubMed  Google Scholar 

  108. Jones, R. M. et al. Increased replication initiation and conflicts with transcription underlie cyclin E-induced replication stress. Oncogene 32, 3744–3753 (2013).

    CAS  PubMed  Google Scholar 

  109. Cimini, D. et al. Merotelic kinetochore orientation is a major mechanism of aneuploidy in mitotic mammalian tissue cells. J. Cell Biol. 153, 517–527 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Chan, K. L., Palmai-Pallag, T., Ying, S. & Hickson, I. D. Replication stress induces sister-chromatid bridging at fragile site loci in mitosis. Nat. Cell Biol. 11, 753–760 (2009).

    CAS  PubMed  Google Scholar 

  111. Naim, V., Wilhelm, T., Debatisse, M. & Rosselli, F. ERCC1 and MUS81-EME1 promote sister chromatid separation by processing late replication intermediates at common fragile sites during mitosis. Nat. Cell Biol. 15, 1008–1015 (2013).

    CAS  PubMed  Google Scholar 

  112. Lukas, C. et al. 53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress. Nat. Cell Biol. 13, 243–253 (2011).

    CAS  PubMed  Google Scholar 

  113. Lamm, N. et al. Genomic instability in human pluripotent stem cells arises from replicative stress and chromosome condensation defects. Cell Stem Cell 18, 253–261 (2016).

    CAS  PubMed  Google Scholar 

  114. Maynard, S. et al. Human embryonic stem cells have enhanced repair of multiple forms of DNA damage. Stem Cell 26, 2266–2274 (2008).

    Google Scholar 

  115. Momcilović, O. et al. Ionizing radiation induces ataxia telangiectasia mutated-dependent checkpoint signaling and G2 but not G1 cell cycle arrest in pluripotent human embryonic stem cells. Stem Cell 27, 1822–1835 (2009).

    Google Scholar 

  116. Luo, L. Z. et al. DNA repair in human pluripotent stem cells is distinct from that in non-pluripotent human cells. PLoS ONE 7, e30541 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Hyka-Nouspikel, N. et al. Deficient DNA damage response and cell cycle checkpoints lead to accumulation of point mutations in human embryonic stem cells. Stem Cell 30, 1901–1910 (2012).

    CAS  Google Scholar 

  118. Adams, B. R., Golding, S. E., Rao, R. R. & Valerie, K. Dynamic dependence on ATR and ATM for double-strand break repair in human embryonic stem cells and neural descendants. PLoS ONE 5, e10001 (2010).

    PubMed  PubMed Central  Google Scholar 

  119. Adams, B. R., Hawkins, A. J., Povirk, L. F. & Valerie, K. ATM-independent, high-fidelity nonhomologous end joining predominates in human embryonic stem cells. Aging 2, 582–596 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. Saretzki, G. et al. Downregulation of multiple stress defense mechanisms during differentiation of human embryonic stem cells. Stem Cell 26, 455–464 (2008).

    CAS  Google Scholar 

  121. Desmarais, J. A. et al. Human embryonic stem cells fail to activate CHK1 and commit to apoptosis in response to DNA replication stress. Stem Cell 30, 1385–1393 (2012). The study by Desmarais et al. demonstrates that human PSCs respond differently to DNA replication stress compared with somatic cells, as PSCs fail to activate the CHK1 checkpoint and, instead of arresting and repairing the DNA, PSCs undergo apoptosis.

    CAS  Google Scholar 

  122. Desmarais, J. A., Unger, C., Damjanov, I., Meuth, M. & Andrews, P. Apoptosis and failure of checkpoint kinase 1 activation in human induced pluripotent stem cells under replication stress. Stem Cell Res. Ther. 7, 17 (2016).

    PubMed  PubMed Central  Google Scholar 

  123. Hong, Y. & Stambrook, P. J. Restoration of an absent G1 arrest and protection from apoptosis in embryonic stem cells after ionizing radiation. Proc. Natl Acad. Sci. USA 101, 14443–14448 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. van Echten-Arends, J. et al. Chromosomal mosaicism in human preimplantation embryos: a systematic review. Hum. Reprod. Update 17, 620–627 (2011).

    PubMed  Google Scholar 

  125. Munné, S. et al. First PGT-A using human in vivo blastocysts recovered by uterine lavage: comparison with matched IVF embryo controls. Hum. Reprod. 35, 70–80 (2019).

    PubMed Central  Google Scholar 

  126. Starostik, M. R., Sosina, O. A. & McCoy, R. C. Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism. bioRxiv https://doi.org/10.1101/2020.01.06.894287 (2020).

  127. Brezina, P. et al. Genetic normalization of differentiating aneuploid human embryos. Nat. Preced. https://doi.org/10.1038/npre.2011.6045.1 (2011).

  128. Kops, G. J., Foltz, D. R. & Cleveland, D. W. Lethality to human cancer cells through massive chromosome loss by inhibition of the mitotic checkpoint. Proc. Natl Acad. Sci. USA 101, 8699–8704 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. Bolton, H. et al. Mouse model of chromosome mosaicism reveals lineage-specific depletion of aneuploid cells and normal developmental potential. Nat. Commun. 7, 11165 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  130. Hardy, K. Cell death in the mammalian blastocyst. Mol. Hum. Reprod. 3, 919–925 (1997).

    CAS  PubMed  Google Scholar 

  131. Haouzi, D. & Hamamah, S. Pertinence of apoptosis markers for the improvement of in vitro fertilization (IVF). Curr. Med.Chem. 16, 1905–1916 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. Ihry, R. J. et al. p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat. Med. 24, 939–946 (2018).

    CAS  PubMed  Google Scholar 

  133. Schiroli, G. et al. Precise gene editing preserves hematopoietic stem cell function following transient p53-mediated DNA damage response. Cell Stem Cell 24, 551–565.e558 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  134. Enache, O. M. et al. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat. Genet. https://doi.org/10.1038/s41588-020-0623-4 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  135. Chagtai, T. et al. Gain of 1q as a prognostic biomarker in Wilms tumors (WTs) treated with preoperative chemotherapy in the International Society of Paediatric Oncology (SIOP) WT 2001 trial: a SIOP renal tumours biology consortium study. J. Clin. Oncol. 34, 3195–3203 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. Walker, B. A. et al. A compendium of myeloma-associated chromosomal copy number abnormalities and their prognostic value. Blood 116, e56–e65 (2010).

    CAS  PubMed  Google Scholar 

  137. Kilday, J. P. et al. Copy number gain of 1q25 predicts poor progression-free survival for pediatric intracranial ependymomas and enables patient risk stratification: a prospective European clinical trial cohort analysis on behalf of the Children’s Cancer Leukaemia Group (CCLG), Societe Francaise d’Oncologie Pediatrique (SFOP), and International Society for Pediatric Oncology (SIOP). Clin. Cancer Res. 18, 2001–2011 (2012).

    CAS  PubMed  Google Scholar 

  138. Kraggerud, S. M. et al. Genome profiles of familial/bilateral and sporadic testicular germ cell tumors. Genes Chromosomes Cancer 34, 168–174 (2002).

    CAS  PubMed  Google Scholar 

  139. Bown, N. et al. 17q gain in neuroblastoma predicts adverse clinical outcome. U.K. Cancer Cytogenetics Group and the U.K. Children’s Cancer Study Group. Med. Pediatr. Oncol. 36, 14–19 (2001).

    CAS  PubMed  Google Scholar 

  140. Nguyen, H. T. & Duong, H. Q. The molecular characteristics of colorectal cancer: Implications for diagnosis and therapy. Oncol. Lett. 16, 9–18 (2018).

    PubMed  PubMed Central  Google Scholar 

  141. Robertson, G. P., Herbst, R. A., Nagane, M., Huang, H. J. & Cavenee, W. K. The chromosome 10 monosomy common in human melanomas results from loss of two separate tumor suppressor loci. Cancer Res. 59, 3596–3601 (1999).

    CAS  PubMed  Google Scholar 

  142. Kimmelman, A. C., Ross, D. A. & Liang, B. C. Loss of heterozygosity of chromosome 10p in human gliomas. Genomics 34, 250–254 (1996).

    CAS  PubMed  Google Scholar 

  143. Popat, S. & Houlston, R. S. A systematic review and meta-analysis of the relationship between chromosome 18q genotype, DCC status and colorectal cancer prognosis. Eur. J. Cancer 41, 2060–2070 (2005).

    CAS  PubMed  Google Scholar 

  144. Damjanov, I. & Andrews, P. W. The terminology of teratocarcinomas and teratomas. Nat. Biotechnol. 25, 1212 (2007).

    CAS  PubMed  Google Scholar 

  145. Steinemann, D., Göhring, G. & Schlegelberger, B. Genetic instability of modified stem cells - a first step towards malignant transformation? Am. J. Stem Cell 2, 39–51 (2013).

    CAS  Google Scholar 

  146. Valli, R. et al. Comparative genomic hybridization on microarray (a-CGH) in constitutional and acquired mosaicism may detect as low as 8% abnormal cells. Mol. Cytogenet. 4, 13 (2011).

    PubMed  PubMed Central  Google Scholar 

  147. Mayshar, Y. et al. Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell 7, 521–531 (2010).

    CAS  PubMed  Google Scholar 

  148. Weissbein, U., Schachter, M., Egli, D. & Benvenisty, N. Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq. Nat. Commun. 7, 12144 (2016).

    PubMed  PubMed Central  Google Scholar 

  149. Jackson, S. P. & Bartek, J. The DNA-damage response in human biology and disease. Nature 461, 1071–1078 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  150. Bartek, J. & Lukas, J. Chk1 and Chk2 kinases in checkpoint control and cancer. Cancer Cell 3, 421–429 (2003).

    CAS  PubMed  Google Scholar 

  151. Krokan, H. E. & Bjørås, M. Base excision repair. Cold Spring Harb. Perspect. Biol. 5, a012583 (2013).

    PubMed  PubMed Central  Google Scholar 

  152. Hoeijmakers, J. H. Genome maintenance mechanisms for preventing cancer. Nature 411, 366–374 (2001).

    CAS  PubMed  Google Scholar 

  153. Lieber, M. R. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu. Rev. Biochem. 79, 181–211 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  154. San Filippo, J., Sung, P. & Klein, H. Mechanism of eukaryotic homologous recombination. Annu. Rev. Biochem. 77, 229–257 (2008).

    CAS  PubMed  Google Scholar 

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Acknowledgements

This work was funded in part by grants from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 668724 and from the UK Regenerative Medicine Platform, MRC reference MR/R015724/1.

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  1. Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, UK

    Jason Halliwell, Ivana Barbaric & Peter W. Andrews

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  1. Jason Halliwell
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  2. Ivana Barbaric
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  3. Peter W. Andrews
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The authors contributed equally to the writing and revisions of the article.

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Correspondence to Ivana Barbaric or Peter W. Andrews.

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Glossary

Age-related macular degeneration

A common cause of blindness in elderly people due to degeneration of the retinal pigment epithelium underlying the retina.

Mosaic culture

A culture containing two or more genetically distinct cell types; for example, an original cell type and a genetic variant derived from it.

Population bottleneck

A situation occurring during successive passaging of cell cultures in which a culture is derived from a very small number of cells from the preceding culture.

Driver genes

Genes whose altered expression provides the main selective growth advantage associated with a particular genomic variant.

Clonogenic assays

Assays in which clones of cells are grown out from isolated single cells to assess the properties of the different cells composing a mosaic culture.

Aneuploidy

An unbalanced genome caused by the presence of an abnormal number of chromosomes or fragments of chromosomes in a cell; it does not include abnormal numbers of chromosomes that are exact multiples of the haploid set of chromosomes (that is, 23 in human cells).

Interstitial duplications

A type of chromosomal aberration in which a duplicated DNA segment is inserted in the same chromosome.

Whole-exome sequencing

A method of sequencing all of the protein-coding regions (exome) in the genome.

Epiblast

Embryonic tissue that gives rise to all of the fetal tissues, including the germ line.

Xenograft tumours

Tumours developing from cells transplanted to a host of a different species; in this Review, typically tumours produced by human cells in an immunodeficient mouse host.

Primitive endoderm

Cells found in teratomas and closely resembling cells of the extraembryonic endoderm found in the pre-implantation embryo.

Amplicon

A discrete region of the genome that has been duplicated one or more times.

Hitchhiker genes

Genes present on amplified or deleted chromosome segments with no effect on the growth advantage of the variant cell.

Cell competition

Cell–cell interaction mechanism leading to elimination of cells that are viable in their homotypic environment in the presence of comparatively fitter cells.

Isochromosome

A chromosomal rearrangement in which one whole arm of a chromosome is replaced by a complete copy of the other arm, resulting in a loss of the genes located on the first arm and duplication of the genes located on the other arm.

Clinical grade

A loose and ill-defined term that identifies cell lines that have been developed and maintained in ways that will satisfy regulatory authorities for clinical application; it is commonly applied to pluripotent stem cell lines that have been derived according to good manufacturing practice.

Indels

Genomic changes involving the insertion or deletion of a sequence of one or more nucleotides.

RB1–E2F checkpoint

Controls the entry into S phase and the initiation of DNA replication during the cell cycle; dependent on the retinoblastoma tumour suppressor protein, RB1, regulating expression of the transcription factor E2F.

G1/S checkpoint

Also known as the restriction point, safeguards entry into S phase during the cell cycle, where DNA synthesis occurs.

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Halliwell, J., Barbaric, I. & Andrews, P.W. Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat Rev Mol Cell Biol 21, 715–728 (2020). https://doi.org/10.1038/s41580-020-00292-z

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