Review Article | Published:

Organoids as an in vitro model of human development and disease

Nature Cell Biology volume 18, pages 246254 (2016) | Download Citation

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 optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

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

  2. 2.

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

  3. 3.

    et al. Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium. Gastroenterology 141, 1762–1772 (2011).

  4. 4.

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

  5. 5.

    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).

  6. 6.

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

  7. 7.

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

  8. 8.

    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).

  9. 9.

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

  10. 10.

    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).

  11. 11.

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

  12. 12.

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

  13. 13.

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

  14. 14.

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

  15. 15.

    , , & Engineering de novo assembly of fetal pulmonary organoids. Tissue Eng. 20, 2892–2907 (2014).

  16. 16.

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

  17. 17.

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

  18. 18.

    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).

  19. 19.

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

  20. 20.

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

  21. 21.

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

  22. 22.

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

  23. 23.

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

  24. 24.

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

  25. 25.

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

  26. 26.

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

  27. 27.

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

  28. 28.

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

  29. 29.

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

  30. 30.

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

  31. 31.

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

  32. 32.

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

  33. 33.

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

  34. 34.

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

  35. 35.

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

  36. 36.

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

  37. 37.

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

  38. 38.

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

  39. 39.

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

  40. 40.

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

  41. 41.

    , , , & Generation of inner ear sensory epithelia from pluripotent stem cells in 3D culture. Nature 500, 217–221 (2013).

  42. 42.

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

  43. 43.

    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).

  44. 44.

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

  45. 45.

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

  46. 46.

    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).

  47. 47.

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

  48. 48.

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

  49. 49.

    , & Materials as stem cell regulators. Nat. Mater. 13, 547–557 (2014).

  50. 50.

    , , & Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments. Mol. Syst. Biol. 2, 37 (2006).

  51. 51.

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

  52. 52.

    , & An extracellular matrix microarray for probing cellular differentiation. Nat. Methods 2, 119–125 (2005).

  53. 53.

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

  54. 54.

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

  55. 55.

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

  56. 56.

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

  57. 57.

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

  58. 58.

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

  59. 59.

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

  60. 60.

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

  61. 61.

    , , & Salmonella-infected crypt-derived intestinal organoid culture system for host–bacterial interactions. Physiol. Rep. 2, e12147 (2014).

  62. 62.

    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).

  63. 63.

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

  64. 64.

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

  65. 65.

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

  66. 66.

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

  67. 67.

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

  68. 68.

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

  69. 69.

    , & Pathogenesis of Helicobacter pylori infection. Clin. Microbiol. Rev. 19, 449–490 (2006).

  70. 70.

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

  71. 71.

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

  72. 72.

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

  73. 73.

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

  74. 74.

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

  75. 75.

    & Changing medium and passaging cell lines. Nat. Protocols 2, 2276–2284 (2007).

  76. 76.

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

  77. 77.

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

  78. 78.

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

  79. 79.

    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).

  80. 80.

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

  81. 81.

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

  82. 82.

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

  83. 83.

    , , & Generating human intestinal tissue from pluripotent stem cells in vitro. Nat. Protoc. 6, 1920–1928 (2011).

  84. 84.

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

  85. 85.

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

  86. 86.

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

  87. 87.

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

  88. 88.

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

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

  1. A*STAR Institute of Medical Biology, 8A Biomedical Grove, 06-06 Immunos, 138648, Singapore

    • Aliya Fatehullah
    • , Si Hui Tan
    •  & Nick Barker
  2. Centre for Regenerative Medicine, 47 Little France Crescent, University of Edinburgh, Edinburgh, EH16 4TJ, UK

    • Nick Barker
  3. Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore

    • Nick Barker

Authors

  1. Search for Aliya Fatehullah in:

  2. Search for Si Hui Tan in:

  3. Search for Nick Barker in:

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nick Barker.

About this article

Publication history

Published

DOI

https://doi.org/10.1038/ncb3312

Further reading