Abstract

Induced pluripotent stem cells (iPSCs), which are used to produce transplantable tissues, may particularly benefit older patients, who are more likely to suffer from degenerative diseases. However, iPSCs generated from aged donors (A-iPSCs) exhibit higher genomic instability, defects in apoptosis and a blunted DNA damage response compared with iPSCs generated from younger donors. We demonstrated that A-iPSCs exhibit excessive glutathione-mediated reactive oxygen species (ROS) scavenging activity, which blocks the DNA damage response and apoptosis and permits survival of cells with genomic instability. We found that the pluripotency factor ZSCAN10 is poorly expressed in A-iPSCs and addition of ZSCAN10 to the four Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) during A-iPSC reprogramming normalizes ROS–glutathione homeostasis and the DNA damage response, and recovers genomic stability. Correcting the genomic instability of A-iPSCs will ultimately enhance our ability to produce histocompatible functional tissues from older patients’ own cells that are safe for transplantation.

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References

  1. 1.

    et al. Mitochondrial-associated cell death mechanisms are reset to an embryonic-like state in aged donor-derived iPS cells harboring chromosomal aberrations. PLoS ONE 6, e27352 (2011).

  2. 2.

    et al. Age-related accumulation of somatic mitochondrial DNA mutations in adult-derived human iPSCs. Cell Stem Cell 18, 625–636 (2016).

  3. 3.

    et al. Influence of donor age on induced pluripotent stem cells. Nat. Biotechnol. 35, 69–74 (2016).

  4. 4.

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

  5. 5.

    Unexpected mutations put stem cell trial on hold. New Sci. 227, 9 (2015).

  6. 6.

    et al. Mitochondrial replacement in human oocytes carrying pathogenic mitochondrial DNA mutations. Nature 540, 270–275 (2016).

  7. 7.

    et al. Autologous induced stem-cell-derived retinal cells for macular degeneration. New Engl. J. Med. 376, 1038–1046 (2017).

  8. 8.

    & Cellular mechanisms and physiological consequences of redox-dependent signalling. Nat. Rev. Mol. Cell Biol. 15, 411–421 (2014).

  9. 9.

    , & Stem cells and the impact of ROS signaling. Development 141, 4206–4218 (2014).

  10. 10.

    Reactive oxygen species and the free radical theory of aging. Free Radic. Biol. Med. 60, 1–4 (2013).

  11. 11.

    & The evolving concept of cancer and metastasis stem cells. J. Cell Biol. 198, 281–293 (2012).

  12. 12.

    & Reactive oxygen species in health and disease. J. Biomed. Biotechnol. 2012, 936486 (2012).

  13. 13.

    The mechanism of DNA breakage by phleomycin in vitro. Nucl. Acids Res. 3, 891–901 (1976).

  14. 14.

    & Apoptosis and glutathione: beyond an antioxidant. Cell Death Differ. 16, 1303–1314 (2009).

  15. 15.

    et al. Glutathione and thioredoxin antioxidant pathways synergize to drive cancer initiation and progression. Cancer Cell 27, 211–222 (2015).

  16. 16.

    , , , & ATM activation by oxidative stress. Science 330, 517–521 (2010).

  17. 17.

    & Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).

  18. 18.

    , & Pluripotency: toward a gold standard for human ES and iPS cells. J. Cell Physiol. 220, 21–29 (2009).

  19. 19.

    et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290 (2010).

  20. 20.

    , & Stem cells: balancing resistance and sensitivity to DNA damage. Trends Cell Biol. 24, 268–274 (2014).

  21. 21.

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

  22. 22.

    & Apoptosis and genomic instability. Nat. Rev. Mol. Cell Biol. 5, 752–762 (2004).

  23. 23.

    & Nuclear transfer to eggs and oocytes. Cold Spring Harb. Perspect. Biol. 3, 1–14 (2011).

  24. 24.

    et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511, 177–183 (2014).

  25. 25.

    , , & Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science 309, 1369–1373 (2005).

  26. 26.

    , , , & An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061 (2008).

  27. 27.

    , , & Zfp206, Oct4, and Sox2 are integrated components of a transcriptional regulatory network in embryonic stem cells. J. Biol. Chem. 284, 31327–31335 (2009).

  28. 28.

    et al. Zfp206 regulates ES cell gene expression and differentiation. Nucl. Acids Res. 34, 4780–4790 (2006).

  29. 29.

    , , , & JNK2-dependent regulation of SIRT1 protein stability. Cell Cycle 7, 3091–3097 (2008).

  30. 30.

    et al. Zscan4 promotes genomic stability during reprogramming and dramatically improves the quality of iPS cells as demonstrated by tetraploid complementation. Cell Res. 23, 92–106 (2013).

  31. 31.

    et al. Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nat. Biotechnol. 27, 1033–1037 (2009).

  32. 32.

    , & Establishment of hypoxanthine phosphoribosyltransferase(HPRT)-locus mutation assay system in mouse ES cells. Altern. Anim. Test. Exp. 11, 118–128 (2005).

  33. 33.

    , & The role of glutathione in cancer. Cell Biochem. Funct. 22, 343–352 (2004).

  34. 34.

    , & Glutathione in cancer biology and therapy. Crit. Rev. Clin. Lab. Sci. 43, 143–181 (2006).

  35. 35.

    et al. Role of glutathione in cancer progression and chemoresistance. Oxid. Med. Cell. Longev. 2013, 972913 (2013).

  36. 36.

    et al. Human iPSC-based modeling of late-onset disease via progerin-induced aging. Cell Stem Cell 13, 691–705 (2013).

  37. 37.

    et al. Genetic variability overrides the impact of parental cell type and determines iPSC differentiation potential. Stem Cell Rep. 6, 200–212 (2016).

  38. 38.

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

  39. 39.

    et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat. Biotechnol. 26, 101–106 (2008).

  40. 40.

    et al. Crucial role of c-Myc in the generation of induced pluripotent stem cells. Stem Cells 29, 1362–1370 (2011).

  41. 41.

    et al. A more efficient method to generate integration-free human iPS cells. Nat. Methods 8, 409–412 (2011).

  42. 42.

    et al. The epithelial-mesenchymal transition factor SNAIL paradoxically enhances reprogramming. Stem Cell Rep. 3, 691–698 (2014).

  43. 43.

    et al. Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Res. 25, 714–724 (2015).

  44. 44.

    et al. Rapid selection of XO embryonic stem cells using Y chromosome-linked GFP transgenic mice. Transgenic Res. 23, 757–765 (2014).

  45. 45.

    et al. Separation and maintenance of normal cells from human embryonic stem cells with trisomy 12 mosaicism. Chromosome Res. 16, 1075–1084 (2008).

  46. 46.

    et al. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 546, 370–375 (2017).

  47. 47.

    & Oxidants, oxidative stress and the biology of ageing. Nature 408, 239–247 (2000).

  48. 48.

    , & Oxidative stress and aging diseases. Oxid. Med. Cell. Longev. 2014, 569146 (2014).

  49. 49.

    et al. Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature 496, 101–105 (2013).

  50. 50.

    & Nonparametric Statistical Methods (Wiley, 1973).

  51. 51.

    et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat. Biotechnol. 29, 1117–1119 (2011).

  52. 52.

    Mammalian cell HPRT gene mutation assay: test methods. Methods Mol. Biol. 817, 55–67 (2012).

  53. 53.

    , , , & Ataxia telangiectasia mutated (ATM) is dispensable for endonuclease I-SceI-induced homologous recombination in mouse embryonic stem cells. J. Biol. Chem. 288, 7086–7095 (2013).

  54. 54.

    , & Establishment and characterization of two human cell lines with amplified dihydrofolate reductase genes. Exp. Cell Res. 168, 89–94 (1987).

  55. 55.

    , & Two-step cross-linking for analysis of protein–chromatin interactions. Methods Mol. Biol. 809, 105–120 (2012).

  56. 56.

    , , & Karyotype of human ES cells during extended culture. Nat. Biotechnol. 22, 381–382 (2004).

  57. 57.

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

  58. 58.

    et al. Characterization and gene expression profiling of five new human embryonic stem cell lines derived in Taiwan. Stem Cells Dev. 15, 532–555 (2006).

  59. 59.

    et al. Characterization of a new NIH-registered variant human embryonic stem cell line, BG01V: a tool for human embryonic stem cell research. Stem Cells 24, 531–546 (2006).

  60. 60.

    et al. Homozygous/compound heterozygous triadin mutations associated with autosomal-recessive long-QT syndrome and pediatric sudden cardiac arrest: elucidation of the triadin knockout syndrome. Circulation 131, 2051–2060 (2015).

  61. 61.

    et al. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat. Methods 12, 966–968 (2015).

  62. 62.

    et al. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat. Genet. 42, 969–972 (2010).

  63. 63.

    The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).

  64. 64.

    The 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012).

  65. 65.

    et al. The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. Bioinformatics 30, 1920–1922 (2014).

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Acknowledgements

K.K. is supported by the NIH (R00HL093212), NIH (R01AG043531), TriStem-Star Foundation (2013-049), Louis V. Gerstner, Jr. Young Investigators awards, Geoffrey Beene Junior Chair Award, Sidney Kimmel Scholar Award, Alfred W. Bressler Scholars Endowment Fund and MSKCC Society Fund. MSKCC Core Facilities are supported by NIH Cancer Center support grant P30 CA008748. R.Z. is supported by the UAB Development Fund. H.L. is supported by the NIH (CA196631-01A1) and Mayo Clinic Center for Individualized Medicine. C.-W.L. is supported by the NIH (R21HD081682). J.J.C. is supported by the HHMI and NIH (R24DK092760). S.L. is supported by the HHMI and NIH (P01CA087497). J.K. is supported by the NIH (R01GM112722). H.F. is supported by the TriStem-Star Foundation (2013-049). J.A. acknowledges support from the medical faculty of Heinrich Heine University, Düsseldorf. T.B. is supported by the MSKCC Single Cell Sequencing Initiative, William and Joyce O’Neil Research Fund and STARR visiting fellows programme. S.G. is supported by the American Italian Cancer Foundation and a Women in Science Rockefeller fellowship.

Author information

Affiliations

  1. Cancer Biology and Genetics Program, Center for Cell Engineering, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, USA

    • Maria Skamagki
    • , Lam Dang
    • , Tzu-Pei Chang
    • , Joye Wang
    • , Aparna Ananthanarayanan
    •  & Kitai Kim
  2. Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55904, USA

    • Cristina Correia
    • , Cheng Zhang
    • , Christian A. Ross
    •  & Hu Li
  3. Department of Obstetrics, Gynecology and Reproductive Sciences, Child Health Institute of New Jersey, New Brunswick, New Jersey 08901, USA

    • Percy Yeung
    •  & Chi-Wei Lu
  4. Howard Hughes Medical Institute, Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute for Cancer Research, and Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA

    • Timour Baslan
    • , Benedikt Bosbach
    •  & Scott Lowe
  5. Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA

    • Samuel Beck
    •  & Jonghwan Kim
  6. Department of Biochemistry and Molecular Genetics, Stem Cell Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA

    • Zhong Liu
    •  & Rui Zhao
  7. Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, New York 10065, USA

    • Simona Giunta
    •  & Hironori Funabiki
  8. Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University, Düsseldorf D-40225, Germany

    • Martina Bohndorf
    •  & James Adjaye
  9. Department of Biological Engineering, Massachusetts Institute of Technology, Broad Institute of MIT and Harvard, and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02118, USA

    • James J. Collins

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Contributions

M.S., R.Z., and K.K. conceived the experimental plan. M.S., P.Y., T.B., L.D., J.W., S.G., Z.L., M.B., R.Z. and K.K. carried out the experiments. C.C., T.B., S.B., C.Z., C.A.R., J.K. and H.L. carried out computational analysis. M.S., C.C., P.Y., T.B., C.A.R., S.B., J.A., H.F., J.K., S.L., J.J.C., C.-W.L., H.L., R.Z. and K.K. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Rui Zhao or Kitai Kim.

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https://doi.org/10.1038/ncb3598

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