Organoids as an in vitro model of human development and disease

Abstract

The in vitro organoid model is a major technological breakthrough that has already been established as an essential tool in many basic biology and clinical applications. This near-physiological 3D model facilitates an accurate study of a range of in vivo biological processes including tissue renewal, stem cell/niche functions and tissue responses to drugs, mutation or damage. In this Review, we discuss the current achievements, challenges and potential applications of this technique.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Organoid generation and culture from primary tissue and ESCs/iPSCs.
Figure 2: Applications of organoid technology for studying development, homeostasis and diseases.
Figure 3: Potential therapeutic and diagnostic uses for organoid technology in personalized medicine.

References

  1. 1

    Shamir, E. R. & Ewald, A. J. Three-dimensional organotypic culture: experimental models of mammalian biology and disease. Nat. Rev. Mol. Cell Biol. 15, 647–664 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2

    Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009).

    CAS  Article  Google Scholar 

  3. 3

    Sato, T. et al. Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium. Gastroenterology 141, 1762–1772 (2011).

    CAS  Google Scholar 

  4. 4

    Dekkers, J. F. et al. A functional CFTR assay using primary cystic fibrosis intestinal organoids. Nat. Med. 19, 939–945 (2013).

    CAS  PubMed  Google Scholar 

  5. 5

    Barker, N. et al. Lgr5+ve stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell Stem Cell 6, 25–36 (2010).

    CAS  Google Scholar 

  6. 6

    Stange, D. E. et al. Differentiated Troy+ chief cells act as reserve stem cells to generate all lineages of the stomach epithelium. Cell 155, 357–368 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7

    Huch, M. et al. In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration. Nature 494, 247–250 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8

    Hisha, H. et al. Establishment of a novel lingual organoid culture system: generation of organoids having mature keratinized epithelium from adult epithelial stem cells. Sci. Rep. 3, 3224 (2013).

    PubMed  PubMed Central  Google Scholar 

  9. 9

    Aihara, E. et al. Characterization of stem/progenitor cell cycle using murine circumvallate papilla taste bud organoid. Sci. Rep. 5, 17185 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10

    Ren, W. et al. Single Lgr5- or Lgr6-expressing taste stem/progenitor cells generate taste bud cells ex vivo. Proc. Natl Acad. Sci. USA 111, 16401–16406 (2014).

    CAS  PubMed  Google Scholar 

  11. 11

    Nanduri, L. S. Y. et al. Purification and ex vivo expansion of fully functional salivary gland stem cells. Stem Cell Rep. 3, 957–964 (2014).

    CAS  Google Scholar 

  12. 12

    Cramer, J. & Lagasse, E. Cellular heterogeneity in the mouse esophagus implicates the presence of a nonquiescent epithelial stem cell population. Cell Rep. 9, 701–711 (2014).

    PubMed  PubMed Central  Google Scholar 

  13. 13

    Yin, X. et al. Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny. Nat, Methods 11, 106–112 (2014).

    CAS  Google Scholar 

  14. 14

    Huch, M. et al. Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis. EMBO J. 32, 2708–2721 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15

    Mondrinos, M. J., Jones, P. L., Finck, C. M. & Lelkes, P. I. Engineering de novo assembly of fetal pulmonary organoids. Tissue Eng. 20, 2892–2907 (2014).

    CAS  Google Scholar 

  16. 16

    Mondrinos, M.J. et al. Engineering three-dimensional pulmonary tissue constructs. Tissue Eng. 12, 717–728 (2006).

    CAS  PubMed  Google Scholar 

  17. 17

    Drost, J. et al. Sequential cancer mutations in cultured human intestinal stem cells. Nature 521, 43–47 (2015).

    CAS  PubMed  Google Scholar 

  18. 18

    Finkbeiner, S. R. et al. Transcriptome-wide analysis reveals hallmarks of human intestine development and maturation in vitro and in vivo. Stem Cell Rep. 4, 1140–1155 (2015).

    CAS  Google Scholar 

  19. 19

    Finkbeiner, S. R. et al. Stem cell-derived human intestinal organoids as an infection model for rotaviruses. MBio 3, e00159–00112 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Forbester, J. L. et al. Interaction of Salmonella enterica serovar Typhimurium with intestinal organoids derived from human induced pluripotent stem cells. Infect. Immun. 83, 2926–2934 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21

    Matano, M. et al. Modeling colorectal cancer using CRISPR–Cas9-mediated engineering of human intestinal organoids. Nat. Med. 21, 256–262 (2015).

    CAS  PubMed  Google Scholar 

  22. 22

    Jung, P. et al. Isolation and in vitro expansion of human colonic stem cells. Nat. Med. 17, 1225–1227 (2011).

    CAS  PubMed  Google Scholar 

  23. 23

    Schlaermann, P. et al. A novel human gastric primary cell culture system for modelling Helicobacter pylori infection in vitro. Gut 65, 202–213 (2016).

    CAS  Google Scholar 

  24. 24

    Bartfeld, S. et al. In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. Gastroenterology 148, 126–136 (2015).

    PubMed  PubMed Central  Google Scholar 

  25. 25

    Huch, M. et al. Long-term culture of genome-stable bipotent stem cells from adult human liver. Cell 160, 299–312 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26

    Boj, S. F. et al. Organoid models of human and mouse ductal pancreatic cancer. Cell 160, 324–338 (2015).

    CAS  Google Scholar 

  27. 27

    Karthaus, W. R. et al. Identification of multipotent luminal progenitor cells in human prostate organoid cultures. Cell 159, 163–175 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 28

    Gao, D. et al. Organoid cultures derived from patients with advanced prostate cancer. Cell 159, 176–187 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. 29

    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  PubMed  PubMed Central  Google Scholar 

  30. 30

    Cao, L. et al. Intestinal lineage commitment of embryonic stem cells. Differentiation 81, 1–10 (2011).

    CAS  PubMed  Google Scholar 

  31. 31

    Spence, J. R. et al. Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature 470, 105–109 (2011).

    PubMed  Google Scholar 

  32. 32

    Noguchi, T. A. et al. Generation of stomach tissue from mouse embryonic stem cells. Nat. Cell Biol. 17, 984–993 (2015).

    CAS  PubMed  Google Scholar 

  33. 33

    McCracken, K. W. et al. Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature 516, 400–404 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Takebe, T. et al. Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature 499, 481–484 (2013).

    CAS  PubMed  Google Scholar 

  35. 35

    Sampaziotis, F. et al. Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation. Nat. Biotech. 33, 845–852 (2015).

    CAS  Google Scholar 

  36. 36

    Ogawa, M. et al. Directed differentiation of cholangiocytes from human pluripotent stem cells. Nat. Biotechnol. 33, 853–861 (2015).

    CAS  PubMed  Google Scholar 

  37. 37

    Dye, B. R. et al. In vitro generation of human pluripotent stem cell derived lung organoids. eLife 4, e05098 (2015).

    PubMed Central  Google Scholar 

  38. 38

    Eiraku, M. et al. Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature 472, 51–56 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39

    Mariani, J. et al. Modeling human cortical development in vitro using induced pluripotent stem cells. Proc. Natl Acad. Sci. USA 109, 12770–12775 (2012).

    CAS  PubMed  Google Scholar 

  40. 40

    Lancaster, M. A. et al. Cerebral organoids model human brain development and microcephaly. Nature 501, 373–379 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41

    Koehler, K. R., Mikosz, A. M., Molosh, A. I., Patel, D. & Hashino, E. Generation of inner ear sensory epithelia from pluripotent stem cells in 3D culture. Nature 500, 217–221 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. 42

    Takasato, M. et al. Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis. Nature 526, 564–568 (2015).

    CAS  PubMed  Google Scholar 

  43. 43

    Valente, M. J. et al. A rapid and simple procedure for the establishment of human normal and cancer renal primary cell cultures from surgical specimens. PLoS ONE 6, e19337 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44

    Xia, Y. et al. Directed differentiation of human pluripotent cells to ureteric bud kidney progenitor-like cells. Nat. Cell Biol. 15, 1507–1515 (2013).

    CAS  PubMed  Google Scholar 

  45. 45

    Takasato, M. et al. Directing human embryonic stem cell differentiation towards a renal lineage generates a self-organizing kidney. Nat. Cell Biol. 16, 118–126 (2014).

    CAS  PubMed  Google Scholar 

  46. 46

    Taguchi, A. et al. Redefining the in vivo origin of metanephric nephron progenitors enables generation of complex kidney structures from pluripotent stem cells. Cell Stem Cell 14, 53–67 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47

    Ng, A. & Barker, N. Ovary and fimbrial stem cells: biology, niche and cancer origins. Nat. Rev. Mol. Cell Biol. 16, 625–638 (2015).

    CAS  PubMed  Google Scholar 

  48. 48

    Lancaster, M. A. & Knoblich, J. A. Organogenesis in a dish: modeling development and disease using organoid technologies. Science 345, 1247125–1247129 (2014).

    PubMed  Google Scholar 

  49. 49

    Murphy, W. L., McDevitt, T. C. & Engler, A. J. Materials as stem cell regulators. Nat. Mater. 13, 547–557 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50

    Soen, Y., Mori, A., Palmer, T. D. & Brown, P. O. Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments. Mol. Syst. Biol. 2, 37 (2006).

    PubMed  PubMed Central  Google Scholar 

  51. 51

    LaBarge, M. A. et al. Human mammary progenitor cell fate decisions are products of interactions with combinatorial microenvironments. Integr. Biol. 1, 70–79 (2009).

    CAS  Google Scholar 

  52. 52

    Flaim, C. J., Chien, S. & Bhatia, S. N. An extracellular matrix microarray for probing cellular differentiation. Nat. Methods 2, 119–125 (2005).

    CAS  Google Scholar 

  53. 53

    Fordham, R. P. et al. Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury. Cell Stem Cell 13, 734–744 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. 54

    Mustata, R. C. et al. Lgr4 is required for Paneth cell differentiation and maintenance of intestinal stem cells ex vivo. EMBO Rep. 12, 558–564 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. 55

    Mustata, R. C. et al. Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium. Cell Rep. 5, 421–432 (2013).

    CAS  PubMed  Google Scholar 

  56. 56

    Okamoto, R. & Watanabe, M. Role of epithelial cells in the pathogenesis and treatment of inflammatory bowel disease. J. Gastroenterol. 51, 1–11 (2015).

    Google Scholar 

  57. 57

    Sato, T. et al. Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature 469, 415–418 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. 58

    Simmini, S. et al. Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2. Nat. Commun. 5, 5728 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59

    Van Es, J. H. et al. Dll1+ secretory progenitor cells revert to stem cells upon crypt damage. Nat. Cell Biol. 14, 1099–1104 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60

    Yui, S. et al. Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5+ stem cell. Nat. Med. 18, 618–623 (2012).

    CAS  PubMed  Google Scholar 

  61. 61

    Zhang, Y. G., Wu, S., Xia, Y. & Sun, J. Salmonella-infected crypt-derived intestinal organoid culture system for host–bacterial interactions. Physiol. Rep. 2, e12147 (2014).

    PubMed  PubMed Central  Google Scholar 

  62. 62

    Horita, N. et al. Fluorescent labelling of intestinal epithelial cells reveals independent long-lived intestinal stem cells in a crypt. Biochem. Biophys. Res. Commun. 454, 493–499 (2014).

    CAS  PubMed  Google Scholar 

  63. 63

    Wang, X. et al. Cloning and variation of ground state intestinal stem cells. Nature 522, 173–178 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. 64

    Watson, C. L. et al. An in vivo model of human small intestine using pluripotent stem cells. Nat. Med. 20, 1310–1314 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65

    Van de Wetering, M. et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell 161, 933–945 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66

    Greggio, C. et al. Artificial three-dimensional niches deconstruct pancreas development in vitro. Development 140, 4452–4462 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. 67

    McCracken, K. W. et al. Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature 516, 400–404 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68

    Grun, D. et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525, 251–255 (2015).

    PubMed  Google Scholar 

  69. 69

    Kusters, J. G., van Vliet, A. H. M. & Kuipers, E. J. Pathogenesis of Helicobacter pylori infection. Clin. Microbiol. Rev. 19, 449–490 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. 70

    Wroblewski, L. E. et al. Helicobacter pylori targets cancer-associated apical-junctional constituents in gastroids and gastric epithelial cells. Gut 64, 720–730 (2015).

    CAS  PubMed  Google Scholar 

  71. 71

    DesRochers, T. M. et al. Effects of Shiga toxin type 2 on a bioengineered three-dimensional model of human renal tissue. Infect. Immun. 83, 28–38 (2015).

    PubMed  Google Scholar 

  72. 72

    Li, X. et al. Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture. Nat. Med. 20, 769–777 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. 73

    Mariani, J. et al. FOXG1-dependent dysregulation of GABA/glutamate neuron differentiation in autism spectrum disorders. Cell 162, 375–390 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. 74

    Marx, V. Cell-line authentication demystified. Nat. Methods 11, 483–488 (2014).

    CAS  PubMed  Google Scholar 

  75. 75

    Masters, J. R. & Stacey, G. N. Changing medium and passaging cell lines. Nat. Protocols 2, 2276–2284 (2007).

    CAS  PubMed  Google Scholar 

  76. 76

    Gracz, A. D. et al. A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis. Nat. Cell Biol. 17, 340–349 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. 77

    Cao, L. et al. Development of intestinal organoids as tissue surrogates: cell composition and the epigenetic control of differentiation. Mol. Carcinogen. 54, 189–202 (2015).

    CAS  Google Scholar 

  78. 78

    Meng, Q. Three-dimensional culture of hepatocytes for prediction of drug-induced hepatotoxicity. Expert Opin. Drug Metab. Toxicol. 6, 733–746 (2010).

    CAS  PubMed  Google Scholar 

  79. 79

    Fukuda, M. et al. Small intestinal stem cell identity is maintained with functional Paneth cells in heterotopically grafted epithelium onto the colon. Genes Dev. 28, 1752–1757 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. 80

    Bertaux-Skeirik, N. et al. CD44 plays a functional role in Helicobacter pylori-induced epithelial cell proliferation. PLoS Pathog. 11, e1004663 (2015).

    PubMed  PubMed Central  Google Scholar 

  81. 81

    Nadauld, L. D. et al. Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer. Genome Biol. 15, 428 (2014).

    PubMed  PubMed Central  Google Scholar 

  82. 82

    Schumacher, M. A. et al. The use of murine-derived fundic organoids in studies of gastric physiology. J. Physiol. 593, 1809–1827 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. 83

    McCracken, K. W., Howell, J. C., Wells, J. M. & Spence, J. R. Generating human intestinal tissue from pluripotent stem cells in vitro. Nat. Protoc. 6, 1920–1928 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84

    Ootani, A. et al. Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche. Nat. Med. 15, 701–706 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. 85

    Takebe, T. et al. Generation of a vascularized and functional human liver from an iPSC-derived organ bud transplant. Nat. Protoc. 9, 396–409 (2014).

    CAS  PubMed  Google Scholar 

  86. 86

    Chua, C. W. et al. Single luminal epithelial progenitors can generate prostate organoids in culture. Nat. Cell Biol. 16, 951–961 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. 87

    Koehler, K. R. & Hashino, E. 3D mouse embryonic stem cell culture for generating inner ear organoids. Nat. Protoc. 9, 1229–1244 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88

    Lancaster, M. A. & Knoblich, J. A. Generation of cerebral organoids from human pluripotent stem cells. Nat. Protoc. 9, 2329–2340 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank the members of the Barker lab for critical input on the manuscript. A.F., S.H.T. and N.B. are supported by the Agency for Science, Technology and Research (A*STAR).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Nick Barker.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Fatehullah, A., Tan, S. & Barker, N. Organoids as an in vitro model of human development and disease. Nat Cell Biol 18, 246–254 (2016). https://doi.org/10.1038/ncb3312

Download citation

Further reading

Search

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing