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Epigenetic memory in induced pluripotent stem cells

Abstract

Somatic cell nuclear transfer and transcription-factor-based reprogramming revert adult cells to an embryonic state, and yield pluripotent stem cells that can generate all tissues. Through different mechanisms and kinetics, these two reprogramming methods reset genomic methylation, an epigenetic modification of DNA that influences gene expression, leading us to hypothesize that the resulting pluripotent stem cells might have different properties. Here we observe that low-passage induced pluripotent stem cells (iPSCs) derived by factor-based reprogramming of adult murine tissues harbour residual DNA methylation signatures characteristic of their somatic tissue of origin, which favours their differentiation along lineages related to the donor cell, while restricting alternative cell fates. Such an ‘epigenetic memory’ of the donor tissue could be reset by differentiation and serial reprogramming, or by treatment of iPSCs with chromatin-modifying drugs. In contrast, the differentiation and methylation of nuclear-transfer-derived pluripotent stem cells were more similar to classical embryonic stem cells than were iPSCs. Our data indicate that nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin that may influence efforts at directed differentiation for applications in disease modelling or treatment.

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Figure 1: Pluripotent stem cells and their characterization.
Figure 2: Differentiation of cell lines.
Figure 3: Analysis of methylation in stem cell lines.
Figure 4: Stringently defined pluripotent stem cells and their characterization.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

CHARM microarray data are deposited at the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession number GSE22851.

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Acknowledgements

G.Q.D is an investigator of the Howard Hughes Medical Institute and was supported by NIH grants RO1-DK70055 and RO1-DK59279, and special funds received under the American Recovery and Reinvestment Act (RC2-HL102815). K.K. was supported by NIH (K99HL093212-01), LLS (3567-07) and Cooley’s Anemia Foundation. A.P.F was funded by NIH grants R37CA054358 and P50HG003233. I.L.W. was funded by NIH grants R01AI047457, R01AI047458, CA86065 and HL099999, and the Thomas and Stacey Siebel Foundation. L.I.R.E. was supported by a Special Fellow Career Development award from the Leukemia and Lymphoma Society. J.S. is supported by a fellowship from the California Institute for Regenerative Medicine (T1-00001). We acknowledge K. Hochedlinger for sharing his manuscript before publication.

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K.K. and G.Q.D. conceived the experimental plan. K.K., A.D., B.W., K.N., Z.R., H.J., L.I.R.E., A.Y., A.T., K.C.C., H.H., S.M.-F., O.N., T.J.Y., R.A.I., N.J., J.S., J.H. and P.M. performed the experiments. P.C., J.K. and M.J.A. performed statistical analysis. A.D., B.W. and A.P.F. performed CHARM and guided analysis of methylation. K.K., A.D., B.W., K.N., R.Z., P.C., J.K., M.J.A., H.J., T.J.Y., R.J., R.W., S.H.O., I.L.W., A.P.F. and G.Q.D. wrote the manuscript.

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Correspondence to A. P. Feinberg or G. Q. Daley.

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Competing interests

G.Q.D. is a member of the Scientific Advisory Boards of MPM Capital, Inc., Epizyme, Inc., and iPierian, Inc. R.J. is a member of the Scientific Advisory Boards of Fate Therapeutics, Inc. and StemGent, Inc. I.L.W is a member of the Scientific Advisory Boards of Cellerant, Inc, and Stem Cells, Inc.

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Kim, K., Doi, A., Wen, B. et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290 (2010). https://doi.org/10.1038/nature09342

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