Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

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Induced pluripotent stem cells (iPSCs) have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPSCs generated from different cell types are molecularly and functionally similar. Here we show that iPSCs obtained from mouse fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns. Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPSCs into embryoid bodies and different hematopoietic cell types. Notably, continuous passaging of iPSCs largely attenuates these differences. Our results suggest that early-passage iPSCs retain a transient epigenetic memory of their somatic cells of origin, which manifests as differential gene expression and altered differentiation capacity. These observations may influence ongoing attempts to use iPSCs for disease modeling and could also be exploited in potential therapeutic applications to enhance differentiation into desired cell lineages.

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Figure 1: iPSCs derived from different cell types are transcriptionally distinguishable.
Figure 2: iPSCs derived from different cell types exhibit distinguishable epigenetic signatures.
Figure 3: iPSCs derived from different cell types have distinctive in vitro differentiation potentials.
Figure 4: Continuous passaging of iPSCs abrogates transcriptional, epigenetic and functional differences.
Figure 5: Model summarizing the presented data.

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We thank N. Maherali and R. Walsh for helpful suggestions and critical reading of the manuscript, B. Wittner for statistical advice, J. LaVecchio, G. Buruzula, K. Folz-Donahue and L. Prickett for expert cell sorting and K. Coser for technical assistance. J.M.P. was supported by an MGH ECOR fellowship, E.A. by a Jane Coffin Childs fellowship, M.S. by a Schering fellowship and K.Y.T. by the Agency of Science, Technology and Research Singapore. Support to A.M. was from the Lymphoma Society, SCOR no. 7132-08; to T.E. from National Institutes of Health (NIH) grant HL056182 and NYSTEM; to A.J.W. in part from the Burroughs Wellcome Fund, Harvard Stem Cell Institute, Peabody Foundation, and NIH 1 DP2 OD004345-01, and the Joslin Diabetes Center DERC (P30DK036836); to K.H. from Howard Hughes Medical Institute, the NIH Director's Innovator Award and the Harvard Stem Cell Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

Author information

J.M.P. and K.H. conceived the study, interpreted results and wrote the manuscript; J.M.P. performed most of the experiments with help from W.K.; S.L. and T.E. performed and interpreted in vitro differentiation assays; M.E.F and A.M. performed and analyzed HELP methylation experiments; K.Y.T. and A.J.W. isolated SMPs and derived most SMP-iPSCs; T.S. and S.N. performed expression arrays; and S.E., E.A. and M.S. provided essential study material. All authors gave critical input to the manuscript draft.

Correspondence to Konrad Hochedlinger.

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Competing interests

K.H. is an advisor for iPierian.

Additional information

Note added in proof: We thank George Daley for sharing unpublished results, which show similar differences in DNA methylation patterns and differentiation propensity of iPSCs derived from distinctive cell types. Of note, this report43 also suggests that somatic cell nuclear transfer more faithfully reprograms cells to a pluripotent state than transcription factor overexpression.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–13 and Supplementary Table 1 (PDF 6276 kb)

Supplementary Table 2

Accession numbers of differentially expressed genes between indicated pairs of iPSCs. (XLS 108 kb)

Supplementary Table 3

Probe-set names and gene symbols of differentially methylated genes between SMP-iPSC and Gra-iPSC. (XLS 16 kb)

Supplementary Table 4

List of primers used for Q-PCR and Q-ChIP analyses. (XLS 20 kb)

Supplementary Table 5

List of primers used for Mass Array Epityping. (XLS 12 kb)

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