Review Article

Stem cells and genome editing: approaches to tissue regeneration and regenerative medicine

  • Journal of Human Genetics 63165178 (2018)
  • doi:10.1038/s10038-017-0348-0
  • Download Citation
Published online:


Understanding the basis of regeneration of each tissue and organ, and incorporating this knowledge into clinical treatments for degenerative tissues and organs in patients, are major goals for researchers in regenerative biology. Here we provide an overview of current work, from high-regeneration animal models, to stem cell-based culture models, transplantation technologies, large-animal chimeric models, and programmable nuclease-based genome-editing technologies. Three-dimensional culture generating organoids, which represents intact tissue/organ identity including cell fate and morphology are getting more general approaches in the fields by taking advantage of embryonic stem cells, induced pluripotent stem cells and adult stem cells. The organoid culture system potentially has profound impact on the field of regenerative medicine. We also emphasize that the large animal model, in particular pig model would be a hope to manufacture humanized organs in in vivo empty (vacant) niche, which now potentially allows not only appropriate cell fate identity but nearly the same property as human organs in size. Therefore, integrative and collaborative researches across different fields might be critical to the aims needed in clinical trial.

  • Subscribe to Journal of Human Genetics for full access:



Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.


  1. 1

    Eiraku M, Sasai Y. Self-formation of layered neural structures in three-dimensional culture of ES cells. Curr Opin Neurobiol. 2012;22:768–77.

  2. 2

    Sasai Y. Next-generation regenerative medicine: organogenesis from stem cells in 3D culture. Cell Stem Cell. 2013;12:520–30.

  3. 3

    Sato T, Clevers H. SnapShot: growing organoids from stem cells. Cell. 2015;161:1700–1700.e1.

  4. 4

    Murphy SV, Atala A. 3D bioprinting of tissues and organs. Nat Biotechnol. 2014;32:773–85.

  5. 5

    Song JJ, Ott HC. Organ engineering based on decellularized matrix scaffolds. Trends Mol Med. 2011;17:424–32.

  6. 6

    Soto-Gutierrez A, Wertheim JA, Ott HC, Gilbert TW. Perspectives on whole-organ assembly: moving toward transplantation on demand. J Clin Invest. 2012;122:3817–23.

  7. 7

    Badylak SF, Taylor D, Uygun K. Whole-Organ Tissue Engineering: Decellularization and Recellularization of Three-Dimensional Matrix Scaffolds. Annu Rev Biomed Eng. 2011;13:27–53.

  8. 8

    Ekser B, Ezzelarab M, Hara H, van der Windt DJ, Wijkstrom M, Bottino R, et al. Clinical xenotransplantation: the next medical revolution? Lancet. 2012;379:672–83.

  9. 9

    Sgroi A, Buhler LH, Morel P, Sykes M, Noel L. International human xenotransplantation inventory. Transplantation. 2010;90:597–603.

  10. 10

    Cooper, D. K. A brief history of cross-species organ transplantation. Proc (Bayl Univ Med Cent). 2012;25:49-57.

  11. 11

    Peng Y, Clark KJ, Campbell JM, Panetta MR, Guo Y, Ekker SC. Making designer mutants in model organisms. Development. 2014;141:4042–54.

  12. 12

    Cornu TI, Mussolino C, Cathomen T. Refining strategies to translate genome editing to the clinic. Nat Med. 2017;23:415–23.

  13. 13

    Blasco RB, Karaca E, Ambrogio C, Cheong TC, Karayol E, Minero VG, et al. Simple and rapid in vivo generation of chromosomal rearrangements using CRISPR/Cas9 technology. Cell Reports. 2014;9:1219–27.

  14. 14

    Li Y, Park AI, Mou H, Colpan C, Bizhanova A, Akama-Garren E, et al. A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biol. 2015;16:111.

  15. 15

    Jiang J, Zhang L, Zhou X, Chen X, Huang G, Li F, et al. Induction of site-specific chromosomal translocations in embryonic stem cells by CRISPR/Cas9. Sci Rep. 2016;6:21918.

  16. 16

    Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, et al. Editing DNA methylation in the mammalian genome. Cell. 2016;167:233–47.e217.

  17. 17

    Epigenetics: CRISPR edits gene methylation. Nature 2016;537:588,

  18. 18

    Hilton IB, D’Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015;33:510–7.

  19. 19

    Thakore PI, Black JB, Hilton IB, Gersbach CA. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat Methods. 2016;13:127–37.

  20. 20

    Xu T, Li Y, Van Nostrand JD, He Z, Zhou J. Cas9-based tools for targeted genome editing and transcriptional control. Appl Environ Microbiol. 2014;80:1544–52.

  21. 21

    Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–21.

  22. 22

    Ledford H. CRISPR, the disruptor. Nature. 2015;522:20–4.

  23. 23

    Travis J. Making the cut. Science. 2015;350:1456–7.

  24. 24

    Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide-sequence of the iap gene, responsible for alkaline-phosphatase isozyme conversion in Escherichia coli, and identification of the gene-product. J Bacteriol. 1987;169:5429–33.

  25. 25

    Sorek R, Kunin V, Hugenholtz P. CRISPR - a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol. 2008;6:181–6.

  26. 26

    Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature. 2010;468:67–+.

  27. 27

    Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol. 2014;32:347–55.

  28. 28

    Doudna JA, Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346:1258096

  29. 29

    DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013;41:4336–43.

  30. 30

    Bortesi L, Fischer R. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv. 2015;33:41–52.

  31. 31

    Dickinson DJ, Ward JD, Reiner DJ, Goldstein B. Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods. 2013;10:1028–+.

  32. 32

    Bassett AR, Tibbit C, Ponting CP, Liu JL. Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 2013;4:220–8.

  33. 33

    Awata H, Watanabe T, Hamanaka Y, Mito T, Noji S, Mizunami M. Knockout crickets for the study of learning and memory: dopamine receptor Dop1 mediates aversive but not appetitive reinforcement in crickets. Sci Rep. 2015;5:15885.

  34. 34

    Chang N, Sun C, Gao L, Zhu D, Xu X, Zhu X, et al. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res. 2013;23:465–72.

  35. 35

    Guo X, Zhang T, Hu Z, Zhang Y, Shi Z, Wang Q, et al. Efficient RNA/Cas9-mediated genome editing in Xenopus tropicalis. Development. 2014;141:707–14.

  36. 36

    Wang HY, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell. 2013;153:910–8.

  37. 37

    Yang H, Wang HY, Shivalila CS, Cheng AW, Shi LY, Jaenisch R. One-Step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell. 2013;154:1370–9.

  38. 38

    Yang H, Wang HY, Jaenisch R. Generating genetically modified mice using CRISPR/Cas-mediated genome engineering. Nat Protoc. 2014;9:1956–68.

  39. 39

    Cong L, Ran FA, Cox D, Lin SL, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819–23.

  40. 40

    Mali P, Yang LH, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339:823–6.

  41. 41

    Karl MO, Reh TA. Regenerative medicine for retinal diseases: activating endogenous repair mechanisms. Trends Mol Med. 2010;16:193–202.

  42. 42

    Ramachandran R, Zhao XF, Goldman D. Insm1a-mediated gene repression is essential for the formation and differentiation of Müller glia-derived progenitors in the injured retina. Nat Cell Biol. 2012;14:1013–+.

  43. 43

    Wan J, Ramachandran R, Goldman D. HB-EGF is necessary and sufficient for Müller Glia dedifferentiation and retina regeneration. Dev Cell. 2012;22:334–47.

  44. 44

    Nagashima M, Barthel LK, Raymond PA. A self-renewing division of zebrafish Müller glial cells generates neuronal progenitors that require N-cadherin to regenerate retinal neurons. Development. 2013;140:4510–21.

  45. 45

    Jopling C, Sleep E, Raya M, Marti M, Raya A, Belmonte JCI. Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation. Nature. 2010;464:606–9.

  46. 46

    Kikuchi K. Dedifferentiation, transdifferentiation, and proliferation: mechanisms underlying cardiac muscle regeneration in zebrafish. Curr Pathobiol Rep. 2015;3:81–8.

  47. 47

    Kikuchi K, Poss KD. Cardiac regenerative capacity and mechanisms. Annu Rev Cell Dev Biol. 2012;28:719–41.

  48. 48

    Gemberling M, Bailey TJ, Hyde DR, Poss KD. The zebrafish as a model for complex tissue regeneration. Trends Genet. 2013;29:611–20.

  49. 49

    Hata S, Namae M, Nishina H. Liver development and regeneration: From laboratory study to clinical therapy. Dev Growth Differ. 2007;49:163–70.

  50. 50

    Porrello ER, Mahmoud AI, Simpson E, Hill JA, Richardson JA, Olson EN, et al. Transient regenerative potential of the neonatal mouse heart. Science. 2011;331:1078–80.

  51. 51

    Michalopoulos GK, DeFrances MC. Liver regeneration. Science. 1997;276:60–6.

  52. 52

    Kang J, Hu J, Karra R, Dickson AL, Tornini VA, Nachtrab G, et al. Modulation of tissue repair by regeneration enhancer elements. Nature. 2016;532:201–6.

  53. 53

    Seeger T, Porteus M, Wu JC. Genome editing in cardiovascular biology. Circ Res. 2017;120:778–80.

  54. 54

    Ail D, Perron M. Retinal degeneration and regeneration-lessons from fishes and amphibians. Curr Pathobiol Rep. 2017;5:67–78.

  55. 55

    Locker M, Borday C, Perron M. Stemness or not stemness? Current status and perspectives of adult retinal stem cells. Curr Stem Cell Res Ther. 2009;4:118–30.

  56. 56

    Lamba D, Karl M, Reh T. Neural regeneration and cell replacement: a view from the eye. Cell Stem Cell. 2008;2:538–49.

  57. 57

    Stone LS, Steinitz H. Regeneration of neural retina and lens from retina pigment cell grafts in adult newts. J Exp Zool. 1957;135:301–17.

  58. 58

    Moshiri A, Close J, Reh TA. Retinal stem cells and regeneration. Int J Dev Biol. 2004;48:1003–14.

  59. 59

    Yasumuro H, Sakurai K, Toyama F, Maruo F, Chiba C. Implications of a multi-step trigger of retinal regeneration in the adult Newt. Biomedicines. 2017;5.

  60. 60

    Merrell AJ, Stanger BZ. Adult cell plasticity in vivo: de-differentiation and transdifferentiation are back in style. Nat Rev Mol Cell Biol. 2016;17:413–25.

  61. 61

    Fischer AJ, Bosse JL, El-Hodiri HM. The ciliary marginal zone (CMZ) in development and regeneration of the vertebrate eye. Exp Eye Res. 2013;116:199–204.

  62. 62

    Centanin L, Hoeckendorf B, Wittbrodt J. Fate restriction and multipotency in retinal stem cells. Cell Stem Cell. 2011;9:553–62.

  63. 63

    Tropepe V, Coles BL, Chiasson BJ, Horsford DJ, Elia AJ, McInnes RR, et al. Retinal stem cells in the adult mammalian eye. Science. 2000;287:2032–6.

  64. 64

    Coles BL, Angenieux B, Inoue T, Del Rio-Tsonis K, Spence JR, McInnes RR, et al. Facile isolation and the characterization of human retinal stem cells. Proc Natl Acad Sci USA. 2004;101:15772–7.

  65. 65

    Kuwahara A, Ozone C, Nakano T, Saito K, Eiraku M, Sasai Y. Generation of a ciliary margin-like stem cell niche from self-organizing human retinal tissue. Nat Commun. 2015;6:6286

  66. 66

    Mitashov VI. Retinal regeneration in amphibians. Int J Dev Biol. 1997;41:893–905.

  67. 67

    Goldman D. Müller glial cell reprogramming and retina regeneration. Nat Rev Neurosci. 2014;15:431–42.

  68. 68

    Young RW. Cell differentiation in the retina of the mouse. Anat Rec. 1985;212:199–205.

  69. 69

    Ooto S, Akagi T, Kageyama R, Akita J, Mandai M, Honda Y, et al. Potential for neural regeneration after neurotoxic injury in the adult mammalian retina. Proc Natl Acad Sci USA. 2004;101:13654–9.

  70. 70

    Chohan A, Singh U, Kumar A, Kaur J. Müller stem cell dependent retinal regeneration. Clin Chim Acta. 2017;464:160–4.

  71. 71

    Osakada F, Ooto S, Akagi T, Mandai M, Akaike A, Takahashi M. Wnt signaling promotes regeneration in the retina of adult mammals. J Neurosci. 2007;27:4210–9.

  72. 72

    Suga A, Sadamoto K, Fujii M, Mandai M, Takahashi M. Proliferation potential of Müller glia after retinal damage varies between mouse strains. PLoS ONE. 2014;9:e94556.

  73. 73

    Hamon A, Roger JE, Yang XJ, Perron M. Müller glial cell-dependent regeneration of the neural retina: an overview across vertebrate model systems. Dev Dyn. 2016;245:727–38.

  74. 74

    Lust K, Sinn R, Perez Saturnino A, Centanin L, Wittbrodt J. De novo neurogenesis by targeted expression of atoh7 to Müller glia cells. Development. 2016;143:1874–83.

  75. 75

    Nelson BR, Ueki Y, Reardon S, Karl MO, Georgi S, Hartman BH et al. Genome-wide analysis of Müller glial differentiation reveals a requirement for notch signaling in postmitotic cells to maintain the glial Fate. PLoS ONE. 2011;6.

  76. 76

    Zelinka CP, Volkov L, Goodman ZA, Todd L, Palazzo I, Bishop WA, et al. mTor signaling is required for the formation of proliferating Müller glia-derived progenitor cells in the chick retina. Development. 2016;143:1859–73.

  77. 77

    Powell C, Grant AR, Cornblath E, Goldman D. Analysis of DNA methylation reveals a partial reprogramming of the Müller glia genome during retina regeneration. Proc Natl Acad Sci USA. 2013;110:19814–9.

  78. 78

    Jorstad NL, Wilken MS, Grimes WN, Wohl SG, VandenBosch LS, Yoshimatsu T, et al. Stimulation of functional neuronal regeneration from Müller glia in adult mice. Nature. 2017;548:103–7.

  79. 79

    Roesch K, Jadhav AP, Trimarchi JM, Stadler MB, Roska B, Sun BB, et al. The transcriptome of retinal Müller glial cells. J Comp Neurol. 2008;509:225–38.

  80. 80

    Suzuki K, Tsunekawa Y, Hernandez-Benitez R, Wu J, Zhu J, Kim EJ, et al. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature. 2016;540:144–9.

  81. 81

    Krikorian AD, Berquam DL. Plant cell and tissue cultures - role of Haberlandt. Bot Rev. 1969;35:59–+.

  82. 82

    Thorpe TA. History of plant tissue culture. Mol Biotechnol. 2007;37:169–80.

  83. 83

    Sugiyama M. Historical review of research on plant cell dedifferentiation. J Plant Res. 2015;128:349–59.

  84. 84

    Wilson HV. A new method by which sponges may be artificially reared. Science. 1907;25:912–5.

  85. 85

    Weiss P, Taylor AC. Reconstitution of complete organs from single-cell suspensions of chick embryos in advanced stages of differentiation. Proc Natl Acad Sci USA. 1960;46:1177–85.

  86. 86

    Pierce GB Jr, Dixon FJ Jr, Verney EL. Teratocarcinogenic and tissue-forming potentials of the cell types comprising neoplastic embryoid bodies. Lab Invest. 1960;9:583–602.

  87. 87

    Rheinwald JG, Green H. Serial cultivation of strains of human epidermal keratinocytes: the formation of keratinizing colonies from single cells. Cell. 1975;6:331–43.

  88. 88

    Rheinwald JG, Green H. Formation of a keratinizing epithelium in culture by a cloned cell line derived from a teratoma. Cell. 1975;6:317–30.

  89. 89

    Lancaster MA, Knoblich JA. Organogenesis in a dish: modeling development and disease using organoid technologies. Science. 2014;345.

  90. 90

    Clevers H. Modeling development and disease with organoids. Cell. 2016;165:1586–97.

  91. 91

    Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126:663–76.

  92. 92

    Shi Y, Inoue H, Wu JC, Yamanaka S. Induced pluripotent stem cell technology: a decade of progress. Nat Rev Drug Discov. 2017;16:115–30.

  93. 93

    Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007;131:861–72.

  94. 94

    Zhou H, Martinez H, Sun B, Li A, Zimmer M, Katsanis N, et al. Rapid and efficient generation of transgene-free iPSC from a small volume of cryopreserved blood. Stem Cell Rev. 2015;11:652–65.

  95. 95

    Agu CA, Soares FAC, Alderton A, Patel M, Ansari R, Patel S, et al. Successful generation of human induced pluripotent stem cell lines from blood samples held at room temperature for up to 48 hr. Stem Cell Rep. 2015;5:660–71.

  96. 96

    Hu Q, Friedrich AM, Johnson LV, Clegg DO. Memory in induced pluripotent stem cells: reprogrammed human retinal-pigmented epithelial cells show tendency for spontaneous redifferentiation. Stem Cells. 2010;28:1981–91.

  97. 97

    Hiler D, Chen X, Hazen J, Kupriyanov S, Carroll PA, Qu C, et al. Quantification of Retinogenesis in 3D cultures reveals epigenetic memory and higher efficiency in iPSCs derived from rod photoreceptors. Cell Stem Cell. 2015;17:101–15.

  98. 98

    Hiler DJ, Barabas ME, Griffiths LM, Dyer MA. Reprogramming of mouse retinal neurons and standardized quantification of their differentiation in 3D retinal cultures. Nat Protoc. 2016;11:1955–76.

  99. 99

    Yamanaka S. A fresh look at iPS cells. Cell. 2009;137:13–7.

  100. 100

    Mandai M, Fujii M, Hashiguchi T, Sunagawa GA, Ito S, Sun JN, et al. iPSC-derived retina transplants improve vision in rd1 end-stage retinal-degeneration mice (vol 8, pg 69, 2017). Stem Cell Rep. 2017;8:1112–3.

  101. 101

    Schwartz SD, Regillo CD, Lam BL, Eliott D, Rosenfeld PJ, Gregori NZ, et al. Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies. Lancet. 2015;385:509–16.

  102. 102

    Schwartz SD, Tan G, Hosseini H, Nagiel A. Subretinal transplantation of embryonic stem cell-derived retinal pigment epithelium for the treatment of macular degeneration: an assessment at 4 years. Invest Ophth Vis Sci. 2016;57.

  103. 103

    Chiba C. The retinal pigment epithelium: an important player of retinal disorders and regeneration. Exp Eye Res. 2014;123:107–14.

  104. 104

    Mandai M, Watanabe A, Kurimoto Y, Hirami Y, Morinaga C, Daimon T, et al. Autologous induced stem-cell-derived retinal cells for macular degeneration. N Engl J Med. 2017;376:1038–46.

  105. 105

    Galdos FX, Guo YX, Paige SL, VanDusen NJ, Wu SM, Pu WT. Cardiac regeneration lessons from development. Circ Res. 2017;120:941–59.

  106. 106

    Doppler SA, Deutsch MA, Serpooshan V, Li G, Dzilic E, Lange R, et al. Mammalian heart regeneration the race to the finish line. Circ Res. 2017;120:630–2.

  107. 107

    Matsuo T, Masumoto H, Tajima S, Ikuno T, Katayama S, Minakata K, et al. Efficient long-term survival of cell grafts after myocardial infarction with thick viable cardiac tissue entirely from pluripotent stem cells. Sci Rep. 2015;5:16842.

  108. 108

    Nakane T, Masumoto H, Tinney JP, Yuan F, Kowalski WJ, Ye F, et al. Impact of cell composition and geometry on human induced pluripotent stem cells-derived engineered cardiac tissue. Sci Rep. 2017;7:45641.

  109. 109

    Yamashita JK. ES and iPS cell research for cardiovascular regeneration. Exp Cell Res. 2010;316:2555–9.

  110. 110

    Masumoto H, Yamashita JK. Human iPS cell-derived cardiac tissue sheets: a platform for cardiac regeneration. Curr Treat Options Cardiovasc Med. 2016;18:65

  111. 111

    Shkumatov A, Baek K, Kong H. Matrix rigidity-modulated cardiovascular organoid formation from embryoid bodies. PLoS ONE. 2014;9:e94764.

  112. 112

    McCracken KW, Cata EM, Crawford CM, Sinagoga KL, Schumacher M, Rockich BE, et al. Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature. 2014;516:400–4.

  113. 113

    Qian XY, Nguyen HN, Song MM, Hadiono C, Ogden SC, Hammack C, et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell. 2016;165:1238–54.

  114. 114

    Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, et al. Cerebral organoids model human brain development and microcephaly. Nature. 2013;501:373–+.

  115. 115

    Drost J, van Jaarsveld RH, Ponsioen B, Zimberlin C, van Boxtel R, Buijs A, et al. Sequential cancer mutations in cultured human intestinal stem cells. Nature. 2015;521:43–7.

  116. 116

    Soldatow VY, Lecluyse EL, Griffith LG, Rusyn I. In vitro models for liver toxicity testing. Toxicol Res. 2013;2:23–39.

  117. 117

    Nantasanti S, de Bruin A, Rothuizen J, Penning LC, Schotanus BA. Concise review: organoids are a powerful tool for the study of liver disease and personalized treatment design in humans and animals. Stem Cells Transl Med. 2016;5:325–30.

  118. 118

    Avior Y, Sagi I, Benvenisty N. Pluripotent stem cells in disease modelling and drug discovery. Nat Rev Mol Cell Biol. 2016;17:170–82.

  119. 119

    Nakano T, Ando S, Takata N, Kawada M, Muguruma K, Sekiguchi K, et al. Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell. 2012;10:771–85.

  120. 120

    Takasato M, Er PX, Chiu HS, Maier B, Baillie GJ, Ferguson C, et al. Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis. Nature. 2015;526:564–8.

  121. 121

    McCauley HA, Wells JM. Pluripotent stem cell-derived organoids: using principles of developmental biology to grow human tissues in a dish. Development. 2017;144:958–62.

  122. 122

    Fietz SA, Kelava I, Vogt J, Wilsch-Brauninger M, Stenzel D, Fish JL, et al. OSVZ progenitors of human and ferret neocortex are epithelial-like and expand by integrin signaling. Nat Neurosci. 2010;13:690–9.

  123. 123

    Hansen DV, Lui JH, Parker PR, Kriegstein AR. Neurogenic radial glia in the outer subventricular zone of human neocortex. Nature. 2010;464:554–61.

  124. 124

    Smart IH, Dehay C, Giroud P, Berland M, Kennedy H. Unique morphological features of the proliferative zones and postmitotic compartments of the neural epithelium giving rise to striate and extrastriate cortex in the monkey. Cereb Cortex. 2002;12:37–53.

  125. 125

    Shitamukai A, Konno D, Matsuzaki F. Oblique radial glial divisions in the developing mouse neocortex induce self-renewing progenitors outside the germinal zone that resemble primate outer subventricular zone progenitors. J Neurosci. 2011;31:3683–95.

  126. 126

    Eiraku M, Watanabe K, Matsuo-Takasaki M, Kawada M, Yonemura S, Matsumura M, et al. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell. 2008;3:519–32.

  127. 127

    Kadoshima T, Sakaguchi H, Nakano T, Soen M, Ando S, Eiraku M, et al. Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex. Proc Natl Acad Sci USA. 2013;110:20284–9.

  128. 128

    Nasu M, Takata N, Danjo T, Sakaguchi H, Kadoshima T, Futaki S, et al. Robust formation and maintenance of continuous stratified cortical neuroepithelium by laminin-containing matrix in mouse ES cell culture. PLoS ONE. 2012;7:e53024.

  129. 129

    Kelava I, Lancaster MA. Dishing out mini-brains: current progress and future prospects in brain organoid research. Dev Biol. 2016;420:199–209.

  130. 130

    Savic N, Schwank G. Advances in therapeutic CRISPR/Cas9 genome editing. Transl Res. 2016;168:15–21.

  131. 131

    Hockemeyer D, Jaenisch R. Induced pluripotent stem cells meet genome editing. Cell Stem Cell. 2016;18:573–86.

  132. 132

    Wataya T, Ando S, Muguruma K, Ikeda H, Watanabe K, Eiraku M, et al. Minimization of exogenous signals in ES cell culture induces rostral hypothalamic differentiation. Proc Natl Acad Sci USA. 2008;105:11796–801.

  133. 133

    Eiraku M, Takata N, Ishibashi H, Kawada M, Sakakura E, Okuda S, et al. Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature. 2011;472:51–6.

  134. 134

    Sasai Y. Grow your own eye: biologists have coaxed cells to form a retina, a step toward growing replacement organs outside the body. Sci Am. 2012;307:44–9.

  135. 135

    Suga H, Kadoshima T, Minaguchi M, Ohgushi M, Soen M, Nakano T, et al. Self-formation of functional adenohypophysis in three-dimensional culture. Nature. 2011;480:57–62.

  136. 136

    Sakaguchi H, Kadoshima T, Soen M, Narii N, Ishida Y, Ohgushi M, et al. Generation of functional hippocampal neurons from self-organizing human embryonic stem cell-derived dorsomedial telencephalic tissue. Nat Commun. 2015;6:8896

  137. 137

    Ozone C, Suga H, Eiraku M, Kadoshima T, Yonemura S, Takata N, et al. Functional anterior pituitary generated in self-organizing culture of human embryonic stem cells. Nat Commun. 2016;7:10351.

  138. 138

    Takata N, Sakakura E, Kasukawa T, Sakuma T, Yamamoto T, Sasai Y. Establishment of functional genomics pipeline in mouse epiblast-like tissue by combining transcriptomic analysis and gene knockdown/knockin/knockout, using RNA interference and CRISPR/Cas9. Hum Gene Ther. 2016;27:436–50.

  139. 139

    Takata N, Sakakura E, Sasai Y. IGF-2/IGF-1R signaling has distinct effects on Sox1, Irx3, and Six3 expressions during ES cell derived-neuroectoderm development in vitro. In Vitro Cell Dev Biol Anim. 2016;52:607–15.

  140. 140

    Nie J, Hashino E. Organoid technologies meet genome engineering. EMBO Rep. 2017;18:367–76.

  141. 141

    Brookhouser N, Raman S, Potts C, Brafman DA. May I cut in? gene editing approaches in human induced pluripotent stem cells. Cells. 2017;6.

  142. 142

    Verma N, Zhu Z, Huangfu D. CRISPR/cas-mediated knockin in human pluripotent stem cells. Methods Mol Biol. 2017;1513:119–40.

  143. 143

    Blair JD, Bateup HS, Hockemeyer DF. Establishment of genome-edited human pluripotent stem cell lines: from targeting to isolation. J Vis Exp. 2016;e53583.

  144. 144

    Sluch VM, Davis CHO, Ranganathan V, Kerr JM, Krick K, Martin R et al. Differentiation of human ESCs to retinal ganglion cells using a CRISPR engineered reporter cell line. Sci Rep. 2015;5.

  145. 145

    Homma K, Usui S, Kaneda M. Knock-in strategy at 3’-end of Crx gene by CRISPR/Cas9 system shows the gene expression profiles during human photoreceptor differentiation. Genes Cells. 2017;22:250–64.

  146. 146

    Sasai Y. Cytosystems dynamics in self-organization of tissue architecture. Nature. 2013;493:318–26.

  147. 147

    Sasai Y, Eiraku M, Suga H. In vitro organogenesis in three dimensions: self-organising stem cells. Development. 2012;139:4111–21.

  148. 148

    Sakakura E, Eiraku M, Takata N. Specification of embryonic stem cell-derived tissues into eye fields by Wnt signaling using rostral diencephalic tissue-inducing culture. Mech Develop. 2016;141:90–9.

  149. 149

    Eiraku M, Adachi T, Sasai Y. Relaxation-expansion model for self-driven retinal morphogenesis: a hypothesis from the perspective of biosystems dynamics at the multi-cellular level. Bioessays. 2012;34:17–25.

  150. 150

    Hasegawa Y, Takata N, Okuda S, Kawada M, Eiraku M, Sasai Y. Emergence of dorsal-ventral polarity in ESC-derived retinal tissue. Development. 2016;143:3895–906.

  151. 151

    Andrabi M, Kuraku S, Takata N, Sasai Y, Love NR. Comparative, transcriptome analysis of self-organizing optic tissues. Sci Data. 2015;2.

  152. 152

    Drost J, Clevers H. Translational applications of adult stem cell-derived organoids. Development. 2017;144:968–75.

  153. 153

    Huch M, Boj SF, Clevers H. Lgr5(+) liver stem cells, hepatic organoids and regenerative medicine. Regen Med. 2013;8:385–7.

  154. 154

    Huch M, Koo BK. Modeling mouse and human development using organoid cultures. Development. 2015;142:3113–25.

  155. 155

    Boj SF, Hwang CI, Baker LA, Chio IIC, Engle DD, Corbo V, et al. Organoid models of human and mouse ductal pancreatic. Cancer Cell. 2015;160:324–38.

  156. 156

    Huch M, Bonfanti P, Boj SF, Sato T, Loomans CJM, van de Wetering M, et al. Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis. EMBO J. 2013;32:2708–21.

  157. 157

    Barker N, Huch M, Kujala P, van de Wetering M, Snippert HJ, van Es JH, et al. Lgr5(+ve) stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell Stem Cell. 2010;6:25–36.

  158. 158

    Bartfeld S, Bayram T, van de Wetering M, Huch M, Begthel H, Kujala P, et al. In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. Gastroenterology. 2015;148:126–136.e6.

  159. 159

    Kessler M, Hoffmann K, Brinkmann V, Thieck O, Jackisch S, Toelle B et al. The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids. Nat Commun. 2015;6.

  160. 160

    Chua CW, Shibata M, Lei M, Toivanen R, Barlow LJ, Bergren SK, et al. Single luminal epithelial progenitors can generate prostate organoids in culture. Nat Cell Biol. 2014;16:951–61.

  161. 161

    Karthaus WR, Iaquinta PJ, Drost J, Gracanin A, van Boxtel R, Wongvipat J, et al. Identification of multipotent luminal progenitor cells in human prostate organoid cultures. Cell. 2014;159:163–75.

  162. 162

    Ren W, Lewandowski BC, Watson J, Aihara E, Iwatsuki K, Bachmanov AA, et al. Single Lgr5- or Lgr6-expressing taste stem/progenitor cells generate taste bud cells ex vivo. Proc Natl Acad Sci USA. 2014;111:16401–6.

  163. 163

    Maimets M, Rocchi C, Bron R, Pringle S, Kuipers J, Giepmans BN, et al. Long-term in vitro expansion of salivary gland stem cells driven by Wnt signals. Stem Cell Rep. 2016;6:150–62.

  164. 164

    Clevers H. What is an adult stem cell? Science. 2015;350:1319–20.

  165. 165

    Dutta D, Heo I, Clevers H. Disease modeling in stem cell-derived 3D organoid systems. Trends Mol Med. 2017.

  166. 166

    Schwank G, Koo BK, Sasselli V, Dekkers JF, Heo I, Demircan T, et al. Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell. 2013;13:653–8.

  167. 167

    Yui S, Nakamura T, Sato T, Nemoto Y, Mizutani T, Zheng X, et al. Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5(+) stem cell. Nat Med. 2012;18:618–23.

  168. 168

    Fordham RP, Yui S, Hannan NR, Soendergaard C, Madgwick A, Schweiger PJ, et al. Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury. Cell Stem Cell. 2013;13:734–44.

  169. 169

    Fukuda M, Mizutani T, Mochizuki W, Matsumoto T, Nozaki K, Sakamaki Y, et al. Small intestinal stem cell identity is maintained with functional Paneth cells in heterotopically grafted epithelium onto the colon. Gene Dev. 2014;28:1752–7.

  170. 170

    Nakamura T, Watanabe M. Intestinal stem cell transplantation. J Gastroenterol. 2017;52:151–7.

  171. 171

    Takebe T, Sekine K, Enomura M, Koike H, Kimura M, Ogaeri T, et al. Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature. 2013;499:481–4.

  172. 172

    Takebe T, Zhang RR, Koike H, Kimura M, Yoshizawa E, Enomura M, et al. Generation of a vascularized and functional human liver from an iPSC-derived organ bud transplant. Nat Protoc. 2014;9:396–409.

  173. 173

    Takebe T, Enomura M, Yoshizawa E, Kimura M, Koike H, Ueno Y, et al. Vascularized and complex organ buds from diverse tissues via mesenchymal cell-driven condensation. Cell Stem Cell. 2015;16:556–65.

  174. 174

    Ottone C, Krusche B, Whitby A, Clements M, Quadrato G, Pitulescu ME, et al. Direct cell-cell contact with the vascular niche maintains quiescent neural stem cells. Nat Cell Biol. 2014;16:1045–+.

  175. 175

    Goldberg JS, Hirschi KK. Diverse roles of the vasculature within the neural stem cell niche. Regen Med. 2009;4:879–97.

  176. 176

    Tavazoie M, Van der Veken L, Silva-Vargas V, Louissaint M, Colonna L, Zaidi B, et al. A specialized vascular niche for adult neural stem cells. Cell Stem Cell. 2008;3:279–88.

  177. 177

    Rafii S, Butler JM, Ding BS. Angiocrine functions of organ-specific endothelial cells. Nature. 2016;529:316–25.

  178. 178

    Whitelaw CB, Sheets TP, Lillico SG, Telugu BP. Engineering large animal models of human disease. J Pathol. 2016;238:247–56.

  179. 179

    Le Douarin NM. The ontogeny of the neural crest in avian embryo chimaeras. Nature. 1980;286:663–9.

  180. 180

    Gardner RL, Johnson MH. Investigation of early mammalian development using interspecific chimaeras between rat and mouse. Nat New Biol. 1973;246:86–9.

  181. 181

    Fehilly CB, Willadsen SM, Tucker EM. Interspecific chimaerism between sheep and goat. Nature. 1984;307:634–6.

  182. 182

    Williams TJ, Munro RK, Shelton JN. Production of interspecies chimeric calves by aggregation of Bos indicus and Bos taurus demi-embryos. Reprod Fertil Dev. 1990;2:385–94.

  183. 183

    Rossant J, Frels WI. Interspecific chimeras in mammals - successful production of live chimeras between mus-musculus and mus-caroli. Science. 1980;208:419–21.

  184. 184

    Rossant J, Croy BA, Chapman VM, Siracusa L, Clark DA. Interspecific chimeras in mammals: a new experimental system. J Anim Sci. 1982;55:1241–8.

  185. 185

    Rossant J, Mauro VM, Croy BA. Importance of trophoblast genotype for survival of interspecific murine chimaeras. J Embryol Exp Morphol. 1982;69:141–9.

  186. 186

    Suchy F, Nakauchi H. Lessons from interspecies mammalian chimeras. Annu Rev Cell Dev Biol. 2017.

  187. 187

    Aigner B, Renner S, Kessler B, Klymiuk N, Kurome M, Wunsch A, et al. Transgenic pigs as models for translational biomedical research. J Mol Med. 2010;88:653–64.

  188. 188

    Prather RS, Lorson M, Ross JW, Whyte JJ, Walters E. Genetically engineered pig models for human diseases. Annu Rev Anim Biosci. 2013;1:203–19.

  189. 189

    Flisikowska T, Kind A, Schnieke A. Genetically modified pigs to model human diseases. J Appl Genet. 2014;55:53–64.

  190. 190

    Feng W, Dai Y, Mou L, Cooper DK, Shi D, Cai Z. The potential of the combination of CRISPR/Cas9 and pluripotent stem cells to provide human organs from chimaeric pigs. Int J Mol Sci. 2015;16:6545–56.

  191. 191

    Kobayashi T, Yamaguchi T, Hamanaka S, Kato-Itoh M, Yamazaki Y, Ibata M, et al. Generation of rat pancreas in mouse by interspecific blastocyst injection of pluripotent stem cells. Cell. 2010;142:787–99.

  192. 192

    Usui J, Kobayashi T, Yamaguchi T, Knisely AS, Nishinakamura R, Nakauchi H. Generation of kidney from pluripotent stem cells via blastocyst complementation. Am J Pathol. 2012;180:2417–26.

  193. 193

    Yamaguchi T, Sato H, Kato-Itoh M, Goto T, Hara H, Sanbo M, et al. Interspecies organogenesis generates autologous functional islets. Nature. 2017;542:191–6.

  194. 194

    Matsunari H, Nagashima H, Watanabe M, Umeyama K, Nakano K, Nagaya M, et al. Blastocyst complementation generates exogenic pancreas in vivo in apancreatic cloned pigs. Proc Natl Acad Sci USA. 2013;110:4557–62.

  195. 195

    Wu J, Platero-Luengo A, Sakurai M, Sugawara A, Gil MA, Yamauchi T, et al. Interspecies chimerism with mammalian pluripotent stem cells. Cell. 2017;168:473–486.e415.

  196. 196

    Lee K, Kwon DN, Ezashi T, Choi YJ, Park C, Ericsson AC, et al. Engraftment of human iPS cells and allogeneic porcine cells into pigs with inactivated RAG2 and accompanying severe combined immunodeficiency. Proc Natl Acad Sci USA. 2014;111:7260–5.

  197. 197

    Rashid T, Kobayashi T, Nakauchi H. Revisiting the flight of Icarus: making human organs from PSCs with large animal chimeras. Cell Stem Cell. 2014;15:406–9.

  198. 198

    Sheets TP, Park CH, Park KE, Powell A, Donovan DM, Telugu BP. Somatic cell nuclear transfer followed by CRIPSR/Cas9 microinjection results in highly efficient genome editing in cloned pigs. Int J Mol Sci. 2016;17.

  199. 199

    Hai T, Teng F, Guo R, Li W, Zhou Q. One-step generation of knockout pigs by zygote injection of CRISPR/Cas system. Cell Res. 2014;24:372–5.

  200. 200

    Whitworth KM, Lee K, Benne JA, Beaton BP, Spate LD, Murphy SL, et al. Use of the CRISPR/Cas9 system to produce genetically engineered pigs from in vitro-derived oocytes and embryos. Biol Reprod. 2014;91. doi:ARTN 7810.1095/biolreprod.114.121723.

  201. 201

    Casal M, Haskins M. Large animal models and gene therapy. Eur J Hum Genet. 2006;14:266–72.

  202. 202

    Camus S, Ko WK, Pioli E, Bezard E. Why bother using non-human primate models of cognitive disorders in translational research? Neurobiol Learn Mem. 2015;124:123–9.

  203. 203

    Yao J, Huang J, Zhao J. Genome editing revolutionize the creation of genetically modified pigs for modeling human diseases. Hum Genet. 2016;135:1093–105.

  204. 204

    Yum SY, Yoon KY, Lee CI, Lee BC, Jang G. Transgenesis for pig models. J Vet Sci. 2016;17:261–8.

  205. 205

    Butler JR, Ladowski JM, Martens GR, Tector M, Tector AJ. Recent advances in genome editing and creation of genetically modified pigs. Int J Surg. 2015;23:217–22.

  206. 206

    Zhou X, Xin J, Fan N, Zou Q, Huang J, Ouyang Z, et al. Generation of CRISPR/Cas9-mediated gene-targeted pigs via somatic cell nuclear transfer. Cell Mol Life Sci. 2015;72:1175–84.

  207. 207

    Tan WS, Carlson DF, Walton MW, Fahrenkrug SC, Hackett PB. Precision editing of large animal genomes. Adv Genet. 2012;80:37–97.

  208. 208

    Tanihara F, Takemoto T, Kitagawa E, Rao S, Do LT, Onishi A, et al. Somatic cell reprogramming-free generation of genetically modified pigs. Sci Adv. 2016;2:e1600803.

  209. 209

    Shaw D, Dondorp W, Geijsen N, de Wert G. Creating human organs in chimaera pigs: an ethical source of immunocompatible organs? J Med Ethics. 2015;41:970–4.

Download references


We thank Dr. G. Oliver for the informative knowledge. We also thank M. Oxendine for his careful English proofreading. This work was supported by JSPS KAKENHI Grant Number 26112723 (to M.E.).

Author information


  1. Center for Vascular and Developmental Biology, Feinberg Cardiovascular Research Institute, Northwestern University, 303 East Superior Street, Chicago, IL, 60611, USA

    • Nozomu Takata
  2. Laboratory for In Vitro Histogenesis, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan

    • Nozomu Takata
    •  & Mototsugu Eiraku
  3. Laboratory of Developmental Systems, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, Kyoto, 606-8507, Japan

    • Mototsugu Eiraku


  1. Search for Nozomu Takata in:

  2. Search for Mototsugu Eiraku in:


N.T. prepared the figures and wrote the manuscript. M.E. supervised the figure preparation and the manuscript writing.

Conflict of interest

The authors declare that they have no competing interests.

Corresponding authors

Correspondence to Nozomu Takata or Mototsugu Eiraku.