A decade of transcription factor-mediated reprogramming to pluripotency

Abstract

The past 10 years have seen great advances in our ability to manipulate cell fate, including the induction of pluripotency in vitro to generate induced pluripotent stem cells (iPSCs). This process proved to be remarkably simple from a technical perspective, only needing the host cell and a defined cocktail of transcription factors, with four factors — octamer-binding protein 3/4 (OCT3/4), SOX2, Krüppel-like factor 4 (KLF4) and MYC (collectively referred to as OSKM) — initially used. The mechanisms underlying transcription factor-mediated reprogramming are still poorly understood; however, several mechanistic insights have recently been obtained. Recent years have also brought significant progress in increasing the efficiency of this technique, making it more amenable to applications in the fields of regenerative medicine, disease modelling and drug discovery.

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Figure 1: Early studies of cell fate plasticity.
Figure 2: The timeline of reprogramming and induced pluripotency research.
Figure 3: Mechanistic insights into transcription factor-mediated reprogramming towards pluripotency.

References

  1. 1

    Weismann, A. The Germ-Plasm: A Theory of Heredity (Charles Scribner's Sons, 1893).

    Google Scholar 

  2. 2

    Waddington, C. H. The Strategy of the Genes. A Discussion of Some Aspects of Theoretical Biology (George Allen & Unwin, 1957).

    Google Scholar 

  3. 3

    Gurdon, J. B., Elsdale, T. R. & Fischberg, M. Sexually mature individuals of Xenopus laevis from the transplantation of single somatic nuclei. Nature 182, 64–65 (1958).

    CAS  Article  Google Scholar 

  4. 4

    Gurdon, J. B. The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles. J. Embryol. Exp. Morphol. 10, 622–640 (1962).

    CAS  PubMed  Google Scholar 

  5. 5

    Evans, M. J. & Kaufman, M. H. Establishment in culture of pluripotential cells from mouse embryos. Nature 292, 154–156 (1981).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  6. 6

    Martin, G. R. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl Acad. Sci. USA 78, 7634–7638 (1981).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  7. 7

    Wilmut, I., Schnieke, A. E., McWhir, J., Kind, A. J. & Campbell, K. H. Viable offspring derived from fetal and adult mammalian cells. Nature 385, 810–813 (1997).

    CAS  Article  Google Scholar 

  8. 8

    Wakayama, T., Perry, A. C., Zuccotti, M., Johnson, K. R. & Yanagimachi, R. Full-term development of mice from enucleated oocytes injected with cumulus cell nuclei. Nature 394, 369–374 (1998).

    CAS  PubMed  Article  Google Scholar 

  9. 9

    Blau, H. M., Chiu, C. P. & Webster, C. Cytoplasmic activation of human nuclear genes in stable heterocaryons. Cell 32, 1171–1180 (1983).

    CAS  PubMed  Article  Google Scholar 

  10. 10

    Takagi, N., Yoshida, M. A., Sugawara, O. & Sasaki, M. Reversal of X-inactivation in female mouse somatic cells hybridized with murine teratocarcinoma stem cells in vitro. Cell 34, 1053–1062 (1983).

    CAS  PubMed  Article  Google Scholar 

  11. 11

    Tada, M., Takahama, Y., Abe, K., Nakatsuji, N. & Tada, T. Nuclear reprogramming of somatic cells by in vitro hybridization with ES cells. Curr. Biol. 11, 1553–1558 (2001).

    CAS  PubMed  Article  Google Scholar 

  12. 12

    Cowan, C. A., Atienza, J., Melton, D. A. & Eggan, K. Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science 309, 1369–1373 (2005).

    CAS  PubMed  Article  Google Scholar 

  13. 13

    Davis, R. L., Weintraub, H. & Lassar, A. B. Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell 51, 987–1000 (1987).

    CAS  PubMed  Article  Google Scholar 

  14. 14

    Kulessa, H., Frampton, J. & Graf, T. GATA-1 reprograms avian myelomonocytic cell lines into eosinophils, thromboblasts, and erythroblasts. Genes Dev. 9, 1250–1262 (1995).

    CAS  PubMed  Article  Google Scholar 

  15. 15

    Xie, H., Ye, M., Feng, R. & Graf, T. Stepwise reprogramming of B cells into macrophages. Cell 117, 663–676 (2004).

    CAS  PubMed  Article  Google Scholar 

  16. 16

    Postlethwait, J. H. & Schneiderman, H. A. A clonal analysis of determination in Antennapedia, a homoeotic mutant of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 64, 176–183 (1969).

    CAS  PubMed  Article  Google Scholar 

  17. 17

    Schneuwly, S., Klemenz, R. & Gehring, W. J. Redesigning the body plan of Drosophila by ectopic expression of the homoeotic gene Antennapedia. Nature 325, 816–818 (1987).

    CAS  PubMed  Article  Google Scholar 

  18. 18

    Frischer, L. E., Hagen, F. S. & Garber, R. L. An inversion that disrupts the Antennapedia gene causes abnormal structure and localization of RNAs. Cell 47, 1017–1023 (1986).

    CAS  PubMed  Article  Google Scholar 

  19. 19

    Schneuwly, S., Kuroiwa, A. & Gehring, W. J. Molecular analysis of the dominant homeotic Antennapedia phenotype. EMBO J. 6, 201–206 (1987).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  20. 20

    Scott, M. P. et al. The molecular organization of the Antennapedia locus of Drosophila. Cell 35, 763–776 (1983).

    CAS  PubMed  Article  Google Scholar 

  21. 21

    Hazelrigg, T. & Kaufman, T. C. Revertants of dominant mutations associated with the Antennapedia gene complex of DROSOPHILA MELANOGASTER: cytology and genetics. Genetics 105, 581–600 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Halder, G., Callaerts, P. & Gehring, W. J. Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila. Science 267, 1788–1792 (1995).

    CAS  PubMed  Article  Google Scholar 

  23. 23

    Avior, Y., Sagi, I. & Benvenisty, N. Pluripotent stem cells in disease modelling and drug testing. Nat. Rev. Mol. Cell Biol. http://dx.doi.org/10.1038/nrm.2015.27 (2016).

  24. 24

    Mitsui, K. et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113, 631–642 (2003).

    CAS  PubMed  Article  Google Scholar 

  25. 25

    Chambers, I. et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113, 643–655 (2003).

    CAS  PubMed  Article  Google Scholar 

  26. 26

    Smith, A. G. et al. Inhibition of pluripotential embryonic stem cell differentiation by purified polypeptides. Nature 336, 688–690 (1988).

    CAS  PubMed  Article  Google Scholar 

  27. 27

    Niwa, H., Burdon, T., Chambers, I. & Smith, A. Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev. 12, 2048–2060 (1998).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  28. 28

    Matsuda, T. et al. STAT3 activation is sufficient to maintain an undifferentiated state of mouse embryonic stem cells. EMBO J. 18, 4261–4269 (1999).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  29. 29

    Niwa, H., Ogawa, K., Shimosato, D. & Adachi, K. A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells. Nature 460, 118–122 (2009).

    CAS  PubMed  Article  Google Scholar 

  30. 30

    Cartwright, P. et al. LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism. Development 132, 885–896 (2005).

    CAS  PubMed  Article  Google Scholar 

  31. 31

    Sato, N., Meijer, L., Skaltsounis, L., Greengard, P. & Brivanlou, A. H. Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nat. Med. 10, 55–63 (2004).

    CAS  PubMed  Article  Google Scholar 

  32. 32

    Burdon, T., Stracey, C., Chambers, I., Nichols, J. & Smith, A. Suppression of SHP-2 and ERK signalling promotes self-renewal of mouse embryonic stem cells. Dev. Biol. 210, 30–43 (1999).

    CAS  PubMed  Article  Google Scholar 

  33. 33

    Burdon, T., Chambers, I., Stracey, C., Niwa, H. & Smith, A. Signaling mechanisms regulating self-renewal and differentiation of pluripotent embryonic stem cells. Cells Tissues Organs 165, 131–143 (1999).

    CAS  PubMed  Article  Google Scholar 

  34. 34

    Cheng, A. M. et al. Mammalian Grb2 regulates multiple steps in embryonic development and malignant transformation. Cell 95, 793–803 (1998).

    CAS  PubMed  Article  Google Scholar 

  35. 35

    Tokuzawa, Y. et al. Fbx15 is a novel target of Oct3/4 but is dispensable for embryonic stem cell self-renewal and mouse development. Mol. Cell. Biol. 23, 2699–2708 (2003).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  36. 36

    Tomioka, M. et al. Identification of Sox-2 regulatory region which is under the control of Oct-3/4–Sox-2 complex. Nucleic Acids Res. 30, 3202–3213 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  37. 37

    Okumura-Nakanishi, S., Saito, M., Niwa, H. & Ishikawa, F. Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells. J. Biol. Chem. 280, 5307–5317 (2005).

    CAS  PubMed  Article  Google Scholar 

  38. 38

    Morita, S., Kojima, T. & Kitamura, T. Plat-E: an efficient and stable system for transient packaging of retroviruses. Gene Ther. 7, 1063–1066 (2000).

    CAS  PubMed  Article  Google Scholar 

  39. 39

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

    CAS  Article  Google Scholar 

  40. 40

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

    CAS  Article  Google Scholar 

  41. 41

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  42. 42

    Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797–801 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  43. 43

    Tanabe, K., Nakamura, M., Narita, M., Takahashi, K. & Yamanaka, S. Maturation, not initiation, is the major roadblock during reprogramming toward pluripotency from human fibroblasts. Proc. Natl Acad. Sci. USA 110, 12172–12179 (2013).

    CAS  PubMed  Article  Google Scholar 

  44. 44

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

    CAS  PubMed  Article  Google Scholar 

  45. 45

    Jiang, J. et al. A core Klf circuitry regulates self-renewal of embryonic stem cells. Nat. Cell Biol. 10, 353–360 (2008).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  46. 46

    Nakagawa, M., Takizawa, N., Narita, M., Ichisaka, T. & Yamanaka, S. Promotion of direct reprogramming by transformation-deficient Myc. Proc. Natl Acad. Sci. USA 107, 14152–14157 (2010).

    CAS  PubMed  Article  Google Scholar 

  47. 47

    Han, J. et al. Tbx3 improves the germ-line competency of induced pluripotent stem cells. Nature 463, 1096–1100 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  48. 48

    Tsubooka, N. et al. Roles of Sall4 in the generation of pluripotent stem cells from blastocysts and fibroblasts. Genes Cells 14, 683–694 (2009).

    CAS  PubMed  Article  Google Scholar 

  49. 49

    Zhao, Y. et al. Two supporting factors greatly improve the efficiency of human iPSC generation. Cell Stem Cell 3, 475–479 (2008).

    CAS  PubMed  Article  Google Scholar 

  50. 50

    Feng, B. et al. Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat. Cell Biol. 11, 197–203 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  51. 51

    Picanco-Castro, V. et al. Pluripotent reprogramming of fibroblasts by lentiviral-mediated insertion of SOX2, C-MYC and TCL-1A. Stem Cells Dev. 20, 169–180 (2010).

    PubMed  Article  CAS  Google Scholar 

  52. 52

    Heng, J. C. et al. The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell 6, 167–174 (2010).

    CAS  PubMed  Article  Google Scholar 

  53. 53

    Judson, R. L., Babiarz, J. E., Venere, M. & Blelloch, R. Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat. Biotechnol. 27, 459–461 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  54. 54

    Worringer, K. A. et al. The let-7/LIN-41 pathway regulates reprogramming to human induced pluripotent stem cells by controlling expression of prodifferentiation genes. Cell Stem Cell 14, 40–52 (2013).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  55. 55

    Festuccia, N. et al. Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells. Cell Stem Cell 11, 477–490 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  56. 56

    Dunn, S. J., Martello, G., Yordanov, B., Emmott, S. & Smith, A. G. Defining an essential transcription factor program for naive pluripotency. Science 344, 1156–1160 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  57. 57

    Buganim, Y. et al. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell 150, 1209–1222 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  58. 58

    Kawamura, T. et al. Linking the p53 tumour suppressor pathway to somatic cell reprogramming. Nature 460, 1140–1144 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  59. 59

    Li, H. et al. The Ink4/Arf locus is a barrier for iPS cell reprogramming. Nature 460, 1136–1139 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  60. 60

    Marion, R. M. et al. A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity. Nature 460, 1149–1153 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  61. 61

    Utikal, J. et al. Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. Nature 460, 1145–1148 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  62. 62

    Hong, H. et al. Suppression of induced pluripotent stem cell generation by the p53–p21 pathway. Nature 460, 1132–1135 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  63. 63

    Banito, A. et al. Senescence impairs successful reprogramming to pluripotent stem cells. Genes Dev. 23, 2134–2139 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  64. 64

    Edel, M. J. et al. Rem2 GTPase maintains survival of human embryonic stem cells as well as enhancing reprogramming by regulating p53 and cyclin D1. Genes Dev. 24, 561–573 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  65. 65

    Buganim, Y., Faddah, D. A. & Jaenisch, R. Mechanisms and models of somatic cell reprogramming. Nat. Rev. Genet. 14, 427–439 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  66. 66

    Huangfu, D. et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat. Biotechnol. 26, 795–797 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  67. 67

    Liang, G., Taranova, O., Xia, K. & Zhang, Y. Butyrate promotes induced pluripotent stem cell generation. J. Biol. Chem. 285, 25516–25521 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  68. 68

    Mali, P. et al. Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells 28, 713–720 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  69. 69

    Ang, Y. S. et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145, 183–197 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  70. 70

    Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  71. 71

    Ding, X. et al. The polycomb protein Ezh2 impacts on induced pluripotent stem cell generation. Stem Cells Dev. 23, 931–940 (2014).

    CAS  PubMed  Article  Google Scholar 

  72. 72

    Wang, T. et al. The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner. Cell Stem Cell 9, 575–587 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  73. 73

    Onder, T. T. et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature 483, 598–602 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  74. 74

    Shinagawa, T. et al. Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells. Cell Stem Cell 14, 217–227 (2014).

    CAS  PubMed  Article  Google Scholar 

  75. 75

    Pawlak, M. & Jaenisch, R. De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state. Genes Dev. 25, 1035–1040 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  76. 76

    Hu, X. et al. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 14, 512–522 (2014).

    CAS  Article  Google Scholar 

  77. 77

    Yamanaka, S. Elite and stochastic models for induced pluripotent stem cell generation. Nature 460, 49–52 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  78. 78

    Goodell, M. A., Nguyen, H. & Shroyer, N. Somatic stem cell heterogeneity: diversity in the blood, skin and intestinal stem cell compartments. Nat. Rev. Mol. Cell Biol. 16, 299–309 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  79. 79

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  80. 80

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  81. 81

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  82. 82

    Samavarchi-Tehrani, P. et al. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7, 64–77 (2010).

    CAS  Article  Google Scholar 

  83. 83

    Li, R. et al. A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell 7, 51–63 (2010).

    CAS  PubMed  Article  Google Scholar 

  84. 84

    Panopoulos, A. D. et al. The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. Cell Res. 22, 168–177 (2011).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  85. 85

    Zhang, J., Nuebel, E., Daley, G. Q., Koehler, C. M. & Teitell, M. A. Metabolic regulation in pluripotent stem cells during reprogramming and self-renewal. Cell Stem Cell 11, 589–595 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  86. 86

    Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 794 (2008).

    CAS  Article  Google Scholar 

  87. 87

    Deng, J. et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat. Biotechnol. 27, 353–360 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  88. 88

    Polo, J. M. et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 151, 1617–1632 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  89. 89

    Soufi, A., Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151, 994–1004 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  90. 90

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  91. 91

    Feng, B., Ng, J. H., Heng, J. C. & Ng, H. H. Molecules that promote or enhance reprogramming of somatic cells to induced pluripotent stem cells. Cell Stem Cell 4, 301–312 (2009).

    CAS  PubMed  Article  Google Scholar 

  92. 92

    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).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  93. 93

    Brambrink, T. et al. Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. Cell Stem Cell 2, 151–159 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  94. 94

    O'Malley, J. et al. High-resolution analysis with novel cell-surface markers identifies routes to iPS cells. Nature 499, 88–91 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  95. 95

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

    CAS  PubMed  Article  Google Scholar 

  96. 96

    Takahashi, K. et al. Induction of pluripotency in human somatic cells via a transient state resembling primitive streak-like mesendoderm. Nat. Commun. 5, 3678 (2014).

    CAS  PubMed  Article  Google Scholar 

  97. 97

    Cacchiarelli, D. et al. Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency. Cell 162, 412–424 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  98. 98

    Ohnuki, M. et al. Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential. Proc. Natl Acad. Sci. USA 111, 12426–12431 (2014).

    CAS  PubMed  Article  Google Scholar 

  99. 99

    Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  100. 100

    Grow, E. J. et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature 522, 221–225 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  101. 101

    Papapetrou, E. P. et al. Stoichiometric and temporal requirements of Oct4, Sox2, Klf4, and c-Myc expression for efficient human iPSC induction and differentiation. Proc. Natl Acad. Sci. USA 106, 12759–12764 (2009).

    CAS  PubMed  Article  Google Scholar 

  102. 102

    Yamaguchi, S., Hirano, K., Nagata, S. & Tada, T. Sox2 expression effects on direct reprogramming efficiency as determined by alternative somatic cell fate. Stem Cell Res. 6, 177–186 (2010).

    PubMed  Article  CAS  Google Scholar 

  103. 103

    Carey, B. W. et al. Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells. Cell Stem Cell 9, 588–598 (2011).

    CAS  PubMed  Article  Google Scholar 

  104. 104

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  105. 105

    Kim, S. I. et al. KLF4 N-terminal variance modulates induced reprogramming to pluripotency. Stem Cell Rep. 4, 727–743 (2015).

    CAS  Article  Google Scholar 

  106. 106

    Shu, J. et al. Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 153, 963–975 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  107. 107

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

    CAS  Article  Google Scholar 

  108. 108

    Stadtfeld, M., Nagaya, M., Utikal, J., Weir, G. & Hochedlinger, K. Induced pluripotent stem cells generated without viral integration. Science 322, 945–949 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  109. 109

    Okita, K., Nakagawa, M., Hyenjong, H., Ichisaka, T. & Yamanaka, S. Generation of mouse induced pluripotent stem cells without viral vectors. Science 322, 949–953 (2008).

    CAS  PubMed  Article  Google Scholar 

  110. 110

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  111. 111

    Jia, F. et al. A nonviral minicircle vector for deriving human iPS cells. Nat. Methods 7, 197–199 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  112. 112

    Kaji, K. et al. Virus-free induction of pluripotency and subsequent excision of reprogramming factors. Nature 458, 771–775 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  113. 113

    Woltjen, K. et al. piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature 458, 766–770 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  114. 114

    Yusa, K., Rad, R., Takeda, J. & Bradley, A. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon. Nat. Methods 6, 363–369 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  115. 115

    Fusaki, N., Ban, H., Nishiyama, A., Saeki, K. & Hasegawa, M. Efficient induction of transgene-free human pluripotent stem cells using a vector based on Sendai virus, an RNA virus that does not integrate into the host genome. Proc. Jpn Acad. Ser. B Phys. Biol. Sci. 85, 348–362 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  116. 116

    Nishimura, K. et al. Development of defective and persistent Sendai virus vector: a unique gene delivery/expression system ideal for cell reprogramming. J. Biol. Chem. 286, 4760–4771 (2010).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  117. 117

    Warren, L. et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 7, 618–630 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  118. 118

    Kim, D. et al. Generation of human induced pluripotent stem cells by direct delivery of reprogramming proteins. Cell Stem Cell 4, 472–476 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  119. 119

    Hou, P. et al. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science 341, 651–654 (2013).

    CAS  PubMed  Article  Google Scholar 

  120. 120

    Chen, G. et al. Chemically defined conditions for human iPSC derivation and culture. Nat. Methods 8, 424–429 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  121. 121

    Wang, Q. et al. A novel xeno-free and feeder-cell-free system for human pluripotent stem cell culture. Protein Cell 3, 51–59 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  122. 122

    Bergstrom, R., Strom, S., Holm, F., Feki, A. & Hovatta, O. Xeno-free culture of human pluripotent stem cells. Methods Mol. Biol. 767, 125–136 (2011).

    PubMed  Article  CAS  Google Scholar 

  123. 123

    Ross, P. J. et al. Human induced pluripotent stem cells produced under xeno-free conditions. Stem Cells Dev. 19, 1221–1229 (2009).

    Article  CAS  Google Scholar 

  124. 124

    Miyazaki, T. et al. Laminin E8 fragments support efficient adhesion and expansion of dissociated human pluripotent stem cells. Nat. Commun. 3, 1236 (2012).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  125. 125

    Nakagawa, M. et al. A novel efficient feeder-free culture system for the derivation of human induced pluripotent stem cells. Sci. Rep. 4, 3594 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  126. 126

    Rajala, K. et al. A defined and xeno-free culture method enabling the establishment of clinical-grade human embryonic, induced pluripotent and adipose stem cells. PLoS ONE 5, e10246 (2010).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  127. 127

    Hanna, J. et al. Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin. Science 318, 1920–1923 (2007).

    CAS  PubMed  Article  Google Scholar 

  128. 128

    Wernig, M. et al. Neurons derived from reprogrammed fibroblasts functionally integrate into the fetal brain and improve symptoms of rats with Parkinson's disease. Proc. Natl Acad. Sci. USA 105, 5856–5861 (2008).

    CAS  PubMed  Article  Google Scholar 

  129. 129

    Tsuji, O. et al. Therapeutic potential of appropriately evaluated safe-induced pluripotent stem cells for spinal cord injury. Proc. Natl Acad. Sci. USA 107, 12704–12709 (2010).

    CAS  PubMed  Article  Google Scholar 

  130. 130

    Kobayashi, Y. et al. Pre-evaluated safe human iPSC-derived neural stem cells promote functional recovery after spinal cord injury in common marmoset without tumorigenicity. PLoS ONE 7, e52787 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  131. 131

    Hockemeyer, D. et al. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat. Biotechnol. 27, 851–857 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  132. 132

    Nichols, J. & Smith, A. Naive and primed pluripotent states. Cell Stem Cell 4, 487–492 (2009).

    CAS  Article  Google Scholar 

  133. 133

    Weinberger, L., Ayyash, M., Novershtern, N. & Hanna, J. H. Naive and primed pluripotency. Nat. Rev. Mol. Cell Biol. http://dx.doi.org/10.1038/nrm.2015.28 (2016).

  134. 134

    Ying, Q. L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519–523 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  135. 135

    Takashima, Y. et al. Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell 158, 1254–1269 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  136. 136

    Theunissen, T. W. et al. Systematic identification of culture conditions for induction and maintenance of naive human pluripotency. Cell Stem Cell 15, 471–487 (2014).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  137. 137

    Hanna, J. et al. Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs. Proc. Natl Acad. Sci. USA 107, 9222–9227 (2010).

    CAS  Article  Google Scholar 

  138. 138

    Gafni, O. et al. Derivation of novel human ground state naive pluripotent stem cells. Nature 504, 282–286 (2013).

    CAS  Article  Google Scholar 

  139. 139

    Ware, C. B. et al. Derivation of naive human embryonic stem cells. Proc. Natl Acad. Sci. USA 111, 4484–4489 (2014).

    CAS  PubMed  Article  Google Scholar 

  140. 140

    Chan, Y. S. et al. Induction of a human pluripotent state with distinct regulatory circuitry that resembles preimplantation epiblast. Cell Stem Cell 13, 663–675 (2013).

    CAS  Article  Google Scholar 

  141. 141

    Chen, H. et al. Reinforcement of STAT3 activity reprogrammes human embryonic stem cells to naive-like pluripotency. Nat. Commun. 6, 7095 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  142. 142

    Narsinh, K. H. et al. Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells. J. Clin. Invest. 121, 1217–1221 (2011).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  143. 143

    Hough, S. R. et al. Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells. Stem Cell Rep. 2, 881–895 (2014).

    CAS  Article  Google Scholar 

  144. 144

    Kang, L., Wang, J., Zhang, Y., Kou, Z. & Gao, S. iPS cells can support full-term development of tetraploid blastocyst-complemented embryos. Cell Stem Cell 5, 135–138 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  145. 145

    Boland, M. J. et al. Adult mice generated from induced pluripotent stem cells. Nature 461, 91–94 (2009).

    CAS  PubMed  Article  Google Scholar 

  146. 146

    Zhao, X. Y. et al. iPS cells produce viable mice through tetraploid complementation. Nature 461, 86–90 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  147. 147

    Yamanaka, S. Induced pluripotent stem cells: past, present, and future. Cell Stem Cell 10, 678–684 (2012).

    CAS  Article  Google Scholar 

  148. 148

    Osafune, K. et al. Marked differences in differentiation propensity among human embryonic stem cell lines. Nat. Biotechnol. 26, 313–315 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  149. 149

    Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228–1238 (2013).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  150. 150

    Chung, Y. G. et al. Human somatic cell nuclear transfer using adult cells. Cell Stem Cell 14, 777–780 (2014).

    CAS  PubMed  Article  Google Scholar 

  151. 151

    Yamada, M. et al. Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to diploid pluripotent stem cells. Nature 510, 533–536 (2014).

    CAS  PubMed  Article  Google Scholar 

  152. 152

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  153. 153

    Johannesson, B. et al. Comparable frequencies of coding mutations and loss of imprinting in human pluripotent cells derived by nuclear transfer and defined factors. Cell Stem Cell 15, 634–642 (2014).

    CAS  PubMed  Article  Google Scholar 

  154. 154

    Choi, J. et al. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat. Biotechnol. 33, 1173–1181 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  155. 155

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

    CAS  PubMed  Article  Google Scholar 

  156. 156

    Koyanagi-Aoi, M. et al. Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells. Proc. Natl Acad. Sci. USA 110, 20569–20574 (2013).

    CAS  PubMed  Article  Google Scholar 

  157. 157

    Schwartz, S. D. et al. Embryonic stem cell trials for macular degeneration: a preliminary report. Lancet 379, 713–720 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  158. 158

    Trounson, A. & DeWitt, N. D. Pluripotent stem cells progressing to the clinic. Nat. Rev. Mol. Cell Biol. http://dx.doi.org/10.1038/nrm.2016.10 (2016).

  159. 159

    Wernig, M. et al. In vitro reprogramming of fibroblasts into a pluripotent ES cell-like state. Nature 448, 318–324 (2007).

    CAS  Article  Google Scholar 

  160. 160

    Maherali, N. et al. Directly reprogrammed fibroblasts show global epigenetic remodelling and widespread tissue contribution. Cell Stem Cell 1, 55–70 (2007).

    CAS  PubMed  Article  Google Scholar 

  161. 161

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

    CAS  PubMed  Article  Google Scholar 

  162. 162

    Hanna, J. et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462, 595–601 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  163. 163

    Yang, J. et al. Stat3 activation is limiting for reprogramming to ground state pluripotency. Cell Stem Cell 7, 319–328 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  164. 164

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

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  165. 165

    Thomson, J. A. et al. Embryonic stem cell lines derived from human blastocysts. Science 282, 1145–1147 (1998).

    CAS  Article  Google Scholar 

  166. 166

    Takahashi, K., Mitsui, K. & Yamanaka, S. Role of ERas in promoting tumour-like properties in mouse embryonic stem cells. Nature 423, 541–545 (2003).

    CAS  PubMed  Article  Google Scholar 

  167. 167

    Wernig, M., Meissner, A., Cassady, J. P. & Jaenisch, R. c-Myc is dispensable for direct reprogramming of mouse fibroblasts. Cell Stem Cell 2, 10–12 (2008).

    CAS  Article  Google Scholar 

  168. 168

    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).

    CAS  PubMed  Article  Google Scholar 

  169. 169

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

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  170. 170

    Zhou, H. et al. Generation of induced pluripotent stem cells using recombinant proteins. Cell Stem Cell 4, 381–384 (2009).

    CAS  PubMed  Article  Google Scholar 

  171. 171

    Zhou, Q., Brown, J., Kanarek, A., Rajagopal, J. & Melton, D. A. In vivo reprogramming of adult pancreatic exocrine cells to β-cells. Nature 455, 627–632 (2008).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  172. 172

    Vierbuchen, T. et al. Direct conversion of fibroblasts to functional neurons by defined factors. Nature 463, 1035–1041 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  173. 173

    Montserrat, N. et al. Reprogramming of human fibroblasts to pluripotency with lineage specifiers. Cell Stem Cell 13, 341–350 (2013).

    CAS  PubMed  Article  Google Scholar 

  174. 174

    Smith, Z. D., Sindhu, C. & Meissner, A. Molecular features of cellular reprogramming and development. Nat. Rev. Mol. Cell Biol. http://dx.doi.org/10.1038/nrm.2016.6 (2016).

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Acknowledgements

The authors would like to thank all Yamanaka laboratory members, past and present, and are also grateful to Y. Miyake, R. Kato, E. Minamitani, S. Takeshima, R. Fujiwara, H. Imagawa and Y. Uematsu for their administrative support, and P. Karagiannis for crucial reading of the manuscript. This work was supported by Grants-in-Aid for Scientific Research from the Japanese Society for the Promotion of Science (JSPS) and the Ministry of Education, Culture, Sports, Science and Technology (MEXT); a grant from the Leading Project of the MEXT; a grant from the Funding Program for World-Leading Innovative Research and Development in Science and Technology (First Program) of the JSPS; a grant from the Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine; a grant from the World Premier International Research Center Initiative (WPI), MEXT; a grant from the Japan Foundation for Applied Enzymology; and the iPS Cell Research Fund.

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Correspondence to Kazutoshi Takahashi or Shinya Yamanaka.

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Shinya Yamanaka is a scientific advisor of iPS Academia Japan without salary.

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Takahashi, K., Yamanaka, S. A decade of transcription factor-mediated reprogramming to pluripotency. Nat Rev Mol Cell Biol 17, 183–193 (2016). https://doi.org/10.1038/nrm.2016.8

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