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Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells

Nature Biotechnology volume 29, pages 1117–1119 (2011)Cite this article

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An Erratum to this article was published on 09 January 2012

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Abstract

We compared bona fide human induced pluripotent stem cells (iPSCs) derived from umbilical cord blood (CB) cells and neonatal keratinocytes (K). As a consequence of both incomplete erasure of tissue-specific methylation and aberrant de novo methylation, CB-iPSCs and K-iPSCs were distinct in genome-wide DNA methylation profiles and differentiation potential. Extended passage of some iPSC clones in culture did not improve their epigenetic resemblance to embryonic stem cells, implying that some human iPSCs retain a residual 'epigenetic memory' of their tissue of origin.

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Figure 1: Derivation and differentiation of iPSCs from neonatal umbilical cord blood cells and foreskin fibroblasts.
Figure 2: Analysis of methylation in CB-iPSCs, K-iPSCs, ESCs and somatic cells.

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Gene Expression Omnibus

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  • 09 January 2012

    In the version of this article initially published, the received date was incorrect. The correct received date is 17 February 2011. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Kim, K. et al. Nature 467, 285–290 (2010).

    Article  CAS  Google Scholar 

  2. Polo, J.M. et al. Nat. Biotechnol. 28, 848–855 (2010).

    Article  CAS  Google Scholar 

  3. Metallo, M.C., Ji, L., de Pablo, J.J. & Palecek, S.P. Methods Mol. Biol. 585, 83–92 (2010).

    Article  CAS  Google Scholar 

  4. Irizarry, R.A. et al. Genome Res. 18, 780–790 (2008).

    Article  CAS  Google Scholar 

  5. Doi, A. et al. Nat. Genet. 41, 1350–1353 (2009).

    Article  CAS  Google Scholar 

  6. Bhattacharya, B. et al. BMC Dev. Biol. 5, 22 (2005).

    Article  Google Scholar 

  7. Ball, M.P. et al. Nat. Biotechnol. 27, 361–368 (2009).

    Article  CAS  Google Scholar 

  8. Soshnikova, N., Montavon, T., Leleu, M., Galjart, N. & Duboule, D. Dev. Cell 19, 819–830 (2010).

    Article  CAS  Google Scholar 

  9. Stadtfeld, M. et al. Nature 465, 175–181 (2010).

    Article  CAS  Google Scholar 

  10. Lister, R. et al. Nature 471, 68–73 (2011).

    Article  CAS  Google Scholar 

  11. Bock, C. et al. Cell 144, 439–452 (2011).

    Article  CAS  Google Scholar 

  12. Boulting, G.L. et al. Nat. Biotechnol. 29, 279–286 (2011).

    Article  CAS  Google Scholar 

  13. Ohi, Y. et al. Nat. Cell Biol. 13, 541–549 (2011).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

G.Q.D. was funded by US National Institutes of Health (NIH) grants DK70055 and DK59279, special funds received by the NIH under the American Recovery and Reinvestment Act (RC2-HL102815). K.K. was supported by NIH (K99HL093212-01), Leukemia and Lymphoma Society (3567-07), and Cooley′s Anemia Foundation. A.P.F. was funded by NIH grants R37CA054358 and P50HG003233.

Author information

Author notes

  1. Kitai Kim

    Present address: Present address: Department of Cancer Biology and Genetics, Center for Cell Engineering, Sloan-Kettering Institute, New York, New York, USA.,

  2. Kitai Kim, Rui Zhao, Akiko Doi and Kitwa Ng: These authors contributed equally to this work.

Authors and Affiliations

  1. Division of Pediatric Hematology/Oncology, Stem Cell Transplantation Program, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Kitai Kim, Rui Zhao, Kitwa Ng, Juli Unternaehrer, Patrick Cahan, Huo Hongguang, Yuin-Han Loh, M William Lensch & George Q Daley

  2. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA

    Kitai Kim, Rui Zhao, Juli Unternaehrer, Patrick Cahan, Yuin-Han Loh, M William Lensch & George Q Daley

  3. Harvard Stem Cell Institute, Cambridge, Massachusetts, USA

    Kitai Kim, Rui Zhao, Kitwa Ng, Juli Unternaehrer, Patrick Cahan, Huo Hongguang, Yuin-Han Loh, M William Lensch & George Q Daley

  4. Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Akiko Doi & Andrew P Feinberg

  5. Oncology Department, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA

    Martin J Aryee

  6. Department of Biomedical Engineering and Center for BioDynamics, Boston University, Boston, Massachusetts, USA

    Hu Li & James J Collins

  7. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA.; Howard Hughes Medical Institute.,

    James J Collins

  8. Howard Hughes Medical Institute.,

    James J Collins

  9. Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts, USA

    George Q Daley

Authors
  1. Kitai Kim
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  10. M William Lensch
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  11. Hu Li
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  13. Andrew P Feinberg
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Contributions

K.K., R.Z., K.N. and G.Q.D. conceived the experimental plan. K.K., R.Z., A.D., K.N., J.U., H.H., M.W.L., Y.-H.L. and H.L. performed the experiments. K.K., A.D., P.C. and M.J.A. performed data analysis. A.D., M.J.A. and A.P.F. performed CHARM and guided analysis of methylation. K.K., R.Z., A.D., K.N., J.U., P.C., J.J.C., M.W.L., A.P.F. and G.Q.D. wrote the manuscript.

Corresponding authors

Correspondence to Andrew P Feinberg or George Q Daley.

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Competing interests

G.Q.D. is a member of the scientific advisory boards of iPierian, Verastem, Epizyme, Solasia, MPM Capital and Johnson & Johnson.

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Supplementary Tables 1–6, Supplementary Methods and Supplementary Figures 1–15 (PDF 2438 kb)

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Kim, K., Zhao, R., Doi, A. et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 29, 1117–1119 (2011). https://doi.org/10.1038/nbt.2052

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