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

Article metrics

Abstract

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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

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.

Accession codes

Primary accessions

Gene Expression Omnibus

References

  1. 1

    Aoi, T. et al. Generation of pluripotent stem cells from adult mouse liver and stomach cells. Science 321, 699–702 (2008).

  2. 2

    Eminli, S. et al. Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells. Nat. Genet. 41, 968–976 (2009).

  3. 3

    Eminli, S., Utikal, J., Arnold, K., Jaenisch, R. & Hochedlinger, K. Reprogramming of neural progenitor cells into induced pluripotent stem cells in the absence of exogenous Sox2 expression. Stem Cells 26, 2467–2474 (2008).

  4. 4

    Hanna, J. et al. Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell 133, 250–264 (2008).

  5. 5

    Lowry, W.E. et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proc. Natl. Acad. Sci. USA 105, 2883–2888 (2008).

  6. 6

    Park, I.H. et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141–146 (2008).

  7. 7

    Stadtfeld, M., Brennand, K. & Hochedlinger, K. Reprogramming of pancreatic beta cells into induced pluripotent stem cells. Curr. Biol. 18, 890–894 (2008).

  8. 8

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

  9. 9

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

  10. 10

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

  11. 11

    Loh, Y.H. et al. Generation of induced pluripotent stem cells from human blood. Blood 113, 5476–5479 (2009).

  12. 12

    Aasen, T. et al. Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes. Nat. Biotechnol. 26, 1276–1284 (2008).

  13. 13

    Maherali, N. et al. A high-efficiency system for the generation and study of human induced pluripotent stem cells. Cell Stem Cell 3, 340–345 (2008).

  14. 14

    Utikal, J., Maherali, N., Kulalert, W. & Hochedlinger, K. Sox2 is dispensable for the reprogramming of melanocytes and melanoma cells into induced pluripotent stem cells. J. Cell Sci. 122, 3502–3510 (2009).

  15. 15

    Kim, J.B. et al. Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors. Nature 454, 646–650 (2008).

  16. 16

    Shi, Y. et al. A combined chemical and genetic approach for the generation of induced pluripotent stem cells. Cell Stem Cell 2, 525–528 (2008).

  17. 17

    Silva, J. et al. Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol. 6, e253 (2008).

  18. 18

    Miura, K. et al. Variation in the safety of induced pluripotent stem cell lines. Nat. Biotechnol. 27, 743–745 (2009).

  19. 19

    Ghosh, Z. et al. Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells. PLoS One 5, e8975 (2010).

  20. 20

    Soldner, F. et al. Parkinson's disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Cell 136, 964–977 (2009).

  21. 21

    Okita, K., Ichisaka, T. & Yamanaka, S. Generation of germline-competent induced pluripotent stem cells. Nature 448, 313–317 (2007).

  22. 22

    Stadtfeld, M. et al. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 465, 175–181 (2010).

  23. 23

    Dimos, J.T. et al. Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons. Science 321, 1218–1221 (2008).

  24. 24

    Ebert, A.D. et al. Induced pluripotent stem cells from a spinal muscular atrophy patient. Nature 457, 277–280 (2009).

  25. 25

    Park, I.H. et al. Disease-specific induced pluripotent stem cells. Cell 134, 877–886 (2008).

  26. 26

    Saha, K. & Jaenisch, R. Technical challenges in using human induced pluripotent stem cells to model disease. Cell Stem Cell 5, 584–595 (2009).

  27. 27

    Lee, G. et al. Modelling pathogenesis and treatment of familial dysautonomia using patient-specific iPSCs. Nature 461, 402–406 (2009).

  28. 28

    Wernig, M. et al. A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types. Nat. Biotechnol. 26, 916–924 (2008).

  29. 29

    Stadtfeld, M., Maherali, N., Breault, D.T. & Hochedlinger, K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell 2, 230–240 (2008).

  30. 30

    Cerletti, M. et al. Highly efficient, functional engraftment of skeletal muscle stem cells in dystrophic muscles. Cell 134, 37–47 (2008).

  31. 31

    Stadtfeld, M., Maherali, N., Borkent, M. & Hochedlinger, K. A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nat. Methods 7, 53–55 (2010).

  32. 32

    Chin, M.H. et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 5, 111–123 (2009).

  33. 33

    Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).

  34. 34

    Mikkelsen, T.S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008).

  35. 35

    Sridharan, R. et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell 136, 364–377 (2009).

  36. 36

    Marion, R.M. et al. Telomeres acquire embryonic stem cell characteristics in induced pluripotent stem cells. Cell Stem Cell 4, 141–154 (2009).

  37. 37

    Boiani, M., Eckardt, S., Scholer, H.R. & McLaughlin, K.J. Oct4 distribution and level in mouse clones: consequences for pluripotency. Genes Dev. 16, 1209–1219 (2002).

  38. 38

    Bortvin, A. et al. Incomplete reactivation of Oct4-related genes in mouse embryos cloned from somatic nuclei. Development 130, 1673–1680 (2003).

  39. 39

    Ng, R.K. & Gurdon, J.B. Epigenetic memory of active gene transcription is inherited through somatic cell nuclear transfer. Proc. Natl. Acad. Sci. USA 102, 1957–1962 (2005).

  40. 40

    Ng, R.K. & Gurdon, J.B. Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription. Nat. Cell Biol. 10, 102–109 (2008).

  41. 41

    Feng, Q. et al. Hemangioblastic derivatives from human induced pluripotent stem cells exhibit limited expansion and early senescence. Stem Cells 28, 704–712 (2010).

  42. 42

    Hu, B.Y. et al. Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc. Natl. Acad. Sci. USA 107, 4335–4340 (2010).

  43. 43

    Kim, K. et al. Epigenetic memory in induced pluripotent stem cells. Nature doi:10.1038/nature09342 (19 July 2010).

  44. 44

    Conboy, I.M., Conboy, M.J., Smythe, G.M. & Rando, T.A. Notch-mediated restoration of regenerative potential to aged muscle. Science 302, 1575–1577 (2003).

  45. 45

    Sherwood, R.I. et al. Isolation of adult mouse myogenic progenitors: functional heterogeneity of cells within and engrafting skeletal muscle. Cell 119, 543–554 (2004).

  46. 46

    Cheshier, S.H., Morrison, S.J., Liao, X. & Weissman, I.L. In vivo proliferation and cell cycle kinetics of long-term self-renewing hematopoietic stem cells. Proc. Natl. Acad. Sci. USA 96, 3120–3125 (1999).

  47. 47

    Huang, D.W. et al. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc. 4, 44–57 (2009).

  48. 48

    Figueroa, M.E., Melnick, A. & Greally, J.M. Genome-wide determination of DNA methylation by Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemias. Methods Mol. Biol. 538, 395–407 (2009).

  49. 49

    Selzer, R.R. et al. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosom. Cancer 44, 305–319 (2005).

  50. 50

    Thompson, R.F. et al. An analytical pipeline for genomic representations used for cytosine methylation studies. Bioinformatics 24, 1161–1167 (2008).

  51. 51

    Culhane, A.C., Thioulouse, J., Perriere, G. & Higgins, D.G. MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics 21, 2789–2790 (2005).

  52. 52

    Ehrich, M. et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102, 15785–15790 (2005).

Download references

Acknowledgements

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.

Ethics declarations

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)

Rights and permissions

Reprints and Permissions

About this article

Further reading