Review Article | Published:

Progress and potential in organoid research

Nature Reviews Geneticsvolume 19pages671687 (2018) | Download Citation


Tissue and organ biology are very challenging to study in mammals, and progress can be hindered, particularly in humans, by sample accessibility and ethical concerns. However, advances in stem cell culture have made it possible to derive in vitro 3D tissues called organoids, which capture some of the key multicellular, anatomical and even functional hallmarks of real organs at the micrometre to millimetre scale. Recent studies have demonstrated that organoids can be used to model organ development and disease and have a wide range of applications in basic research, drug discovery and regenerative medicine. Researchers are now beginning to take inspiration from other fields, such as bioengineering, to generate organoids that are more physiologically relevant and more amenable to real-life applications.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Additional information

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


  1. 1.

    Murry, C. E. & Keller, G. Differentiation of embryonic stem cells to clinically relevant populations: lessons from embryonic development. Cell 132, 661–680 (2008).

  2. 2.

    Clevers, H. Modeling development and disease with organoids. Cell 165, 1586–1597 (2016).

  3. 3.

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

  4. 4.

    Sasai, Y. Cytosystems dynamics in self-organization of tissue architecture. Nature 493, 318–326 (2013).This article is an inspiring review on self-organization.

  5. 5.

    Rheinwald, J. G. & Green, H. Serial cultivation of strains of human epidermal keratinocytes: the formation of keratinizing colonies from single cells. Cell 6, 331–343 (1975).

  6. 6.

    Ehrmann, R. L. & Gey, G. O. The growth of cells on a transparent gel of reconstituted rat-tail collagen. J. Natl Cancer Inst. 16, 1375–1403 (1956).

  7. 7.

    Orkin, R. W. et al. A murine tumor producing a matrix of basement membrane. J. Exp. Med. 145, 204–220 (1977).

  8. 8.

    Harrison, R. G., Greenman, M. J., Mall, F. P. & Jackson, C. M. Observations of the living developing nerve fiber. Anat. Rec. 1, 116–128 (1907).

  9. 9.

    Michalopoulos, G. & Pitot, H. C. Primary culture of parenchymal liver cells on collagen membranes. Morphological and biochemical observations. Exp. Cell Res. 94, 70–78 (1975).

  10. 10.

    Barcellos-Hoff, M. H., Aggeler, J., Ram, T. G. & Bissell, M. J. Functional differentiation and alveolar morphogenesis of primary mammary cultures on reconstituted basement membrane. Development 105, 223–235 (1989).

  11. 11.

    Petersen, O. W., Rønnov-Jessen, L., Howlett, A. R. & Bissell, M. J. Interaction with basement membrane serves to rapidly distinguish growth and differentiation pattern of normal and malignant human breast epithelial cells. Proc. Natl Acad. Sci. USA 89, 9064–9068 (1992).

  12. 12.

    Eiraku, M. et al. Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature 472, 51–56 (2011). This landmark study reports the capacity of PSCs to self-organize into the complex structure of an optic cup.

  13. 13.

    Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009). This landmark study reports the derivation of intestinal organoids from single adult ISCs.

  14. 14.

    Eiraku, M. et al. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell 3, 519–532 (2008). This work highlights the self-organization properties of stem cells and describes the derivation of cerebral organoids from PSCs.

  15. 15.

    Fata, J. E. et al. The MAPKERK-1,2 pathway integrates distinct and antagonistic signals from TGFα and FGF7 in morphogenesis of mouse mammary epithelium. Dev. Biol. 306, 193–207 (2007).

  16. 16.

    Guibert, C., Savineau, J. P., Crevel, H., Marthan, R. & Rousseau, E. Effect of short-term organoid culture on the pharmaco-mechanical properties of rat extra- and intrapulmonary arteries. Br. J. Pharmacol. 146, 692–701 (2005).

  17. 17.

    Simian, M. et al. The interplay of matrix metalloproteinases, morphogens and growth factors is necessary for branching of mammary epithelial cells. Development 128, 3117–3131 (2001).

  18. 18.

    Zhang, Y. S. et al. Multisensor-integrated organs-on-chips platform for automated and continual in situ monitoring of organoid behaviors. Proc. Natl Acad. Sci. USA 114, E2293–E2302 (2017).

  19. 19.

    Simian, M. & Bissell, M. J. Organoids: a historical perspective of thinking in three dimensions. J. Cell Biol. 216, 31–40 (2016).

  20. 20.

    Langer, R. & Vacanti, J. P. Tissue engineering. Science 260, 920–926 (1993).

  21. 21.

    Drost, J. et al. Organoid culture systems for prostate epithelial and cancer tissue. Nat. Protoc. 11, 347–358 (2016).

  22. 22.

    Kelava, I. & Lancaster, M. A. Dishing out mini-brains: current progress and future prospects in brain organoid research. Dev. Biol. 420, 199–209 (2016).

  23. 23.

    Kretzschmar, K. & Clevers, H. Organoids: modeling development and the stem cell niche in a dish. Dev. Cell 38, 590–600 (2016).

  24. 24.

    Simunovic, M. & Brivanlou, A. H. Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis. Development 144, 976–985 (2017).

  25. 25.

    Takasato, M. & Little, M. H. A strategy for generating kidney organoids: recapitulating the development in human pluripotent stem cells. Dev. Biol. 420, 210–220 (2016).

  26. 26.

    Yin, X. et al. Engineering stem cell organoids. Cell Stem Cell 18, 25–38 (2016).

  27. 27.

    Turner, D. A., Baillie-Johnson, P. & Martinez Arias, A. Organoids and the genetically encoded self-assembly of embryonic stem cells. BioEssays 38, 181–191 (2016).

  28. 28.

    Green, J. B. A. & Sharpe, J. Positional information and reaction-diffusion: two big ideas in developmental biology combine. Development 142, 1203–1211 (2015).

  29. 29.

    Turing, A. M. The chemical basis of morphogenesis. Phil. Trans. R. Soc. Lond. 237, 37–72 (1952).

  30. 30.

    Ferrell, J. E. Bistability, bifurcations, and Waddington’s epigenetic landscape. Curr. Biol. 22, R458–R466 (2012).

  31. 31.

    Mori, H., Gjorevski, N., Inman, J. L., Bissell, M. J. & Nelson, C. M. Self-organization of engineered epithelial tubules by differential cellular motility. Proc. Natl Acad. Sci. USA 106, 14890–14895 (2009).

  32. 32.

    Lancaster, M. A. et al. Cerebral organoids model human brain development and microcephaly. Nature 501, 373–379 (2013). This pioneering work reports the derivation of human cerebral organoids featuring coexisting, discrete brain regions. This work is also among the first to use an organoid to model a pathological condition.

  33. 33.

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

  34. 34.

    Linnemann, J. R. et al. Quantification of regenerative potential in primary human mammary epithelial cells. Development 142, 3239–3251 (2015).

  35. 35.

    Sachs, N., Tsukamoto, Y., Kujala, P., Peters, P. J. & Clevers, H. Intestinal epithelial organoids fuse to form self-organizing tubes in floating collagen gels. Development 144, 1107–1112 (2017).

  36. 36.

    Gjorevski, N. et al. Designer matrices for intestinal stem cell and organoid culture. Nature 539, 560–564 (2016).

  37. 37.

    Lindborg, B. A. et al. Rapid induction of cerebral organoids from human induced pluripotent stem cells using a chemically defined hydrogel and defined cell culture medium. Stem Cells Transl Med. 5, 970–979 (2016).

  38. 38.

    Muguruma, K., Nishiyama, A., Kawakami, H., Hashimoto, K. & Sasai, Y. Self-organization of polarized cerebellar tissue in 3D culture of human pluripotent stem cells. Cell Rep. 10, 537–550 (2015).

  39. 39.

    Sakaguchi, H. et al. Generation of functional hippocampal neurons from self-organizing human embryonic stem cell-derived dorsomedial telencephalic tissue. Nat. Commun. 6, 8896 (2015).

  40. 40.

    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).

  41. 41.

    Takasato, M. et al. Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis. Nature 536, 238 (2016).

  42. 42.

    McCracken, K. W. et al. Wnt/β-catenin promotes gastric fundus specification in mice and humans. Nature 541, 182–187 (2017).

  43. 43.

    Takebe, T. et al. Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature 499, 481–484 (2013). This work reports the formation of vascularized hPSC-derived liver organoids, demonstrating the possibility to obtain vascularized organoids by co-culturing stem cells and endothelial cells.

  44. 44.

    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).

  45. 45.

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

  46. 46.

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

  47. 47.

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

  48. 48.

    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). References 40 and 48 are among the first reports of organoids of mesodermal origin (kidney organoids).

  49. 49.

    Jamieson, P. R. et al. Derivation of a robust mouse mammary organoid system for studying tissue dynamics. Development 144, 1065–1071 (2017).

  50. 50.

    Maimets, M. et al. Long-term in vitro expansion of salivary gland stem cells driven by Wnt signals. Stem Cell Rep. 6, 150–162 (2016).

  51. 51.

    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).

  52. 52.

    Panciera, T. et al. Induction of expandable tissue-specific stem/progenitor cells through transient expression of YAP/TAZ. Cell Stem Cell 19, 725–737 (2016).

  53. 53.

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

  54. 54.

    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).

  55. 55.

    Bartfeld, S. et al. In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. Gastroenterology 148, 126–136.e6 (2015).

  56. 56.

    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).

  57. 57.

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

  58. 58.

    Azzolin, L. et al. YAP/TAZ incorporation in the β-catenin destruction complex orchestrates the Wnt response. Cell 158, 157–170 (2014).

  59. 59.

    Xinaris, C., Brizi, V. & Remuzzi, G. Organoid models and applications in biomedical research. Nephron 130, 191–199 (2015).

  60. 60.

    McCauley, H. A. & Wells, J. M. Pluripotent stem cell-derived organoids: using principles of developmental biology to grow human tissues in a dish. Development 144, 958–962 (2017).

  61. 61.

    Rivron, N. C. et al. Blastocyst-like structures generated solely from stem cells. Nature 557, 106–111 (2018).

  62. 62.

    Harrison, S. E., Sozen, B., Christodoulou, N., Kyprianou, C. & Zernicka-Goetz, M. Assembly of embryonic and extraembryonic stem cells to mimic embryogenesis in vitro. Science 356, eaal1810 (2017).

  63. 63.

    Shao, Y. et al. Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche. Nat. Mater. 16, 419–425 (2017).

  64. 64.

    Shao, Y. et al. A pluripotent stem cell-based model for post-implantation human amniotic sac development. Nat. Commun. 8, 208 (2017).

  65. 65.

    Baillie-Johnson, P., van den Brink, S. C., Balayo, T., Turner, D. A. & Martinez Arias, A. Generation of aggregates of mouse embryonic stem cells that show symmetry breaking, polarization and emergent collective behaviour in vitro. J. Vis. Exp. 105, e53252 (2015).

  66. 66.

    van den Brink, S. C. et al. Symmetry breaking, germ layer specification and axial organisation in aggregates of mouse embryonic stem cells. Development 141, 4231–4242 (2014). This work shows the capacity of mouse PSCs to recapitulate, in 3D, complex gastrulation-like processes that resemble those occurring in the early embryo.

  67. 67.

    Etoc, F. et al. A balance between secreted inhibitors and edge sensing controls gastruloid self-organization. Dev. Cell 39, 302–315 (2016).

  68. 68.

    Martyn, I., Kanno, T. Y., Ruzo, A., Siggia, E. D. & Brivanlou, A. H. Self-organization of a human organizer by combined Wnt and Nodal signalling. Nature 558, 132–135 (2018).

  69. 69.

    Morgani, S. M., Metzger, J. J., Nichols, J., Siggia, E. D. & Hadjantonakis, A. K. Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning. elife 7, e32839 (2018).

  70. 70.

    Tewary, M. et al. A stepwise model of reaction-diffusion and positional-information governs self-organized human peri-gastrulation-like patterning. Development 144, 4298–4312 (2017).

  71. 71.

    Warmflash, A., Sorre, B., Etoc, F., Siggia, E. D. & Brivanlou, A. H. A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nat. Methods 11, 847–854 (2014). This work highlights the capacity of human ESCs to self-organize into patterned germ layers.

  72. 72.

    Meinhardt, A. et al. 3D reconstitution of the patterned neural tube from embryonic stem cells. Stem Cell Rep. 3, 987–999 (2014).

  73. 73.

    Ranga, A. et al. Neural tube morphogenesis in synthetic 3D microenvironments. Proc. Natl Acad. Sci. USA 113, E6831–E6839 (2016).

  74. 74.

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

  75. 75.

    Sato, T. & Clevers, H. Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications. Science 340, 1190–1194 (2013).

  76. 76.

    Farin, H. F. et al. Visualization of a short-range Wnt gradient in the intestinal stem-cell niche. Nature 530, 340–343 (2016).

  77. 77.

    Snippert, H. J. et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143, 134–144 (2010).

  78. 78.

    Nakano, T. et al. Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell 10, 771–785 (2012).

  79. 79.

    Dekkers, J. F. et al. A functional CFTR assay using primary cystic fibrosis intestinal organoids. Nat. Med. 19, 939–945 (2013). This article provides one of the first examples of the development of an organoid-based functional assay for drug discovery and/or screening.

  80. 80.

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

  81. 81.

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

  82. 82.

    Castellanos-Gonzalez, A., Cabada, M. M., Nichols, J., Gomez, G. & White, A. C. Human primary intestinal epithelial cells as an improved in vitro model for Cryptosporidium parvum infection. Infect. Immun. 81, 1996–2001 (2013).

  83. 83.

    Cugola, F. R. et al. The Brazilian Zika virus strain causes birth defects in experimental models. Nature 534, 267–271 (2016).

  84. 84.

    Dang, J. et al. Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3. Cell Stem Cell 19, 258–265 (2016).

  85. 85.

    Farin, H. F. et al. Paneth cell extrusion and release of antimicrobial products is directly controlled by immune cell–derived IFN-γ. J. Exp. Med. 211, 1393–1405 (2014).

  86. 86.

    Finkbeiner, S. R. et al. Stem cell-derived human intestinal organoids as an infection model for rotaviruses. mBio 3, e00159–12 (2012).

  87. 87.

    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).

  88. 88.

    Garcez, P. P. et al. Zika virus impairs growth in human neurospheres and brain organoids. Science 352, 816–818 (2016).

  89. 89.

    Leslie, J. L. et al. Persistence and toxin production by Clostridium difficile within human intestinal organoids result in disruption of epithelial paracellular barrier function. Infect. Immun. 83, 138–145 (2015).

  90. 90.

    Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016).

  91. 91.

    Tao, L. et al. Frizzled proteins are colonic epithelial receptors for C. difficile toxin B. Nature 538, 350–355 (2016).

  92. 92.

    Wilson, S. S., Tocchi, A., Holly, M. K., Parks, W. C. & Smith, J. G. A small intestinal organoid model of non-invasive enteric pathogen–epithelial cell interactions. Mucosal Immunol. 8, 352–361 (2014).

  93. 93.

    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).

  94. 94.

    Zomer-van Ommen, D. D. et al. Functional characterization of cholera toxin inhibitors using human intestinal organoids. J. Med. Chem. 59, 6968–6972 (2016).

  95. 95.

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

  96. 96.

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

  97. 97.

    Hubert, C. G. et al. A three-dimensional organoid culture system derived from human glioblastomas recapitulates the hypoxic gradients and cancer stem cell heterogeneity of tumors found in vivo. Cancer Res. 76, 2465–2477 (2016).

  98. 98.

    Yeung, T. M., Gandhi, S. C., Wilding, J. L., Muschel, R. & Bodmer, W. F. Cancer stem cells from colorectal cancer-derived cell lines. Proc. Natl Acad. Sci. USA 107, 3722–3727 (2010).

  99. 99.

    Zhou, T. et al. High-content screening in hPSC-neural progenitors identifies drug candidates that inhibit zika virus infection in fetal-like organoids and adult brain. Cell Stem Cell 21, 274–283 (2017).

  100. 100.

    Davies, J. C., Alton, E. W. F. W. & Bush, A. Cystic fibrosis. BMJ 335, 1255–1259 (2007).

  101. 101.

    Saini, A. Cystic fibrosis patients benefit from mini guts. Cell Stem Cell 19, 425–427 (2016).

  102. 102.

    Czerniecki, S. M. et al. High-throughput screening enhances kidney organoid differentiation from human pluripotent stem cells and enables automated multidimensional phenotyping. Cell Stem Cell 22, 929–940.e4 (2018).

  103. 103.

    Dekkers, J. F. et al. Characterizing responses to CFTR-modulating drugs using rectal organoids derived from subjects with cystic fibrosis. Sci. Transl Med. 8, 344ra84 (2016).

  104. 104.

    Fujii, M. et al. A colorectal tumor organoid library demonstrates progressive loss of niche factor requirements during tumorigenesis. Cell Stem Cell 18, 827–838 (2016).

  105. 105.

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

  106. 106.

    Vlachogiannis, G. et al. Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science 359, 920–926 (2018).

  107. 107.

    Lee, S. H. et al. Tumor evolution and drug response in patient-derived organoid models of bladder cancer. Cell 173, 515–528.e17 (2018).

  108. 108.

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

  109. 109.

    Tannenbaum, J. & Bennett, B. T. Russell and Burch’s 3Rs then and now: the need for clarity in definition and purpose. J. Am. Assoc. Lab. Anim. Sci. 54, 120–132 (2015).

  110. 110.

    Assawachananont, J. et al. Transplantation of embryonic and induced pluripotent stem cell-derived 3D retinal sheets into retinal degenerative mice. Stem Cell Rep. 2, 662–674 (2014).

  111. 111.

    Mandai, M. et al. iPSC-derived retina transplants improve vision in rd1 end-stage retinal-degeneration mice. Stem Cell Rep. 8, 69–83 (2017).

  112. 112.

    Shirai, H. et al. Transplantation of human embryonic stem cell-derived retinal tissue in two primate models of retinal degeneration. Proc. Natl Acad. Sci. USA 113, E81–E90 (2016).

  113. 113.

    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).

  114. 114.

    Schwank, G. et al. Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell 13, 653–658 (2013).

  115. 115.

    Camp, J. G. et al. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc. Natl Acad. Sci. USA 112, 15672–15677 (2015).

  116. 116.

    Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48–53 (2017).

  117. 117.

    Camp, J. G. et al. Multilineage communication regulates human liver bud development from pluripotency. Nature 546, 533–538 (2017).

  118. 118.

    Scialdone, A. et al. Resolving early mesoderm diversification through single-cell expression profiling. Nature 535, 289–293 (2016).

  119. 119.

    Junker, J. P. et al. Genome-wide RNA tomography in the zebrafish embryo. Cell 159, 662–675 (2014).

  120. 120.

    Grubb, M. S. & Thompson, I. D. The influence of early experience on the development of sensory systems. Curr. Opin. Neurobiol. 14, 503–512 (2004).

  121. 121.

    Martin, I., Wendt, D. & Heberer, M. The role of bioreactors in tissue engineering. Trends Biotechnol. 22, 80–86 (2004).

  122. 122.

    Zhao, J. et al. Bioreactors for tissue engineering: an update. Biochem. Eng. J. 109, 268–281 (2016).

  123. 123.

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

  124. 124.

    Miller, J. S. et al. Rapid casting of patterned vascular networks for perfusable engineered three-dimensional tissues. Nat. Mater. 11, 768–774 (2012).

  125. 125.

    Tocchio, A. et al. Versatile fabrication of vascularizable scaffolds for large tissue engineering in bioreactor. Biomaterials 45, 124–131 (2015).

  126. 126.

    Wang, X. Y. et al. Engineering interconnected 3D vascular networks in hydrogels using molded sodium alginate lattice as the sacrificial template. Lab. Chip 14, 2709–2716 (2014).

  127. 127.

    Brandenberg, N. & Lutolf, M. P. In situ patterning of microfluidic networks in 3D cell-laden hydrogels. Adv. Mater. 28, 7450–7456 (2016).

  128. 128.

    Zhang, Y. S. et al. Bioprinting 3D microfibrous scaffolds for engineering endothelialized myocardium and heart-on-a-chip. Biomaterials 110, 45–59 (2016).

  129. 129.

    Zhu, W. et al. Direct 3D bioprinting of prevascularized tissue constructs with complex microarchitecture. Biomaterials 124, 106–115 (2017).

  130. 130.

    Pham, M. T. et al. Generation of human vascularized brain organoids. Neuroreport 29, 588–593 (2018).

  131. 131.

    Mansour, A. A. et al. An in vivo model of functional and vascularized human brain organoids. Nat. Biotechnol 36, 432–441 (2018).

  132. 132.

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

  133. 133.

    Dye, B. R. et al. A bioengineered niche promotes in vivo engraftment and maturation of pluripotent stem cell derived human lung organoids. eLife 5, e19732 (2016).

  134. 134.

    Miller, J. D. et al. Human iPSC-based modeling of late-onset disease via progerin-induced aging. Cell Stem Cell 13, 691–705 (2013).

  135. 135.

    Wang, Y. et al. Formation of human colonic crypt array by application of chemical gradients across a shaped epithelial monolayer. Cell. Mol. Gastroenterol. Hepatol. 5, 113–130 (2018).

  136. 136.

    Wang, Y. et al. A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium. Biomaterials 128, 44–55 (2017).

  137. 137.

    Ehrbar, M. et al. Biomolecular hydrogels formed and degraded via site-specific enzymatic reactions. Biomacromolecules 8, 3000–3007 (2007).

  138. 138.

    Kim, S., Chung, E. H., Gilbert, M. & Healy, K. E. Synthetic MMP-13 degradable ECMs based on poly(N-isopropylacrylamide-co-acrylic acid) semi-interpenetrating polymer networks. I. Degradation and cell migration. J. Biomed. Mater. Res. A 75, 73–88 (2005).

  139. 139.

    Kloxin, A. M., Kasko, A. M., Salinas, C. N. & Anseth, K. S. Photodegradable hydrogels for dynamic tuning of physical and chemical properties. Science 324, 59–63 (2009).

  140. 140.

    Lutolf, M. P. & Hubbell, J. A. Synthesis and physicochemical characterization of end-linked poly(ethylene glycol)-co-peptide hydrogels formed by Michael-type addition. Biomacromolecules 4, 713–722 (2003).

  141. 141.

    Mann, B. K., Gobin, A. S., Tsai, A. T., Schmedlen, R. H. & West, J. L. Smooth muscle cell growth in photopolymerized hydrogels with cell adhesive and proteolytically degradable domains: synthetic ECM analogs for tissue engineering. Biomaterials 22, 3045–3051 (2001).

  142. 142.

    Peyton, S. R., Raub, C. B., Keschrumrus, V. P. & Putnam, A. J. The use of poly(ethylene glycol) hydrogels to investigate the impact of ECM chemistry and mechanics on smooth muscle cells. Biomaterials 27, 4881–4893 (2006).

  143. 143.

    Phelps, E. A. et al. Maleimide cross-linked bioactive PEG hydrogel exhibits improved reaction kinetics and cross-linking for cell encapsulation and in situ delivery. Adv. Mater. 24, 64–70 (2012).

  144. 144.

    Tsurkan, M. V. et al. Defined polymer–peptide conjugates to form cell-instructive starPEG–heparin matrices in situ. Adv. Mater. 25, 2606–2610 (2013).

  145. 145.

    Wylie, R. G. et al. Spatially controlled simultaneous patterning of multiple growth factors in three-dimensional hydrogels. Nat. Mater. 10, 799–806 (2011).

  146. 146.

    Cruz-Acuña, R. et al. Synthetic hydrogels for human intestinal organoid generation and colonic wound repair. Nat. Cell Biol. 19, 1326–1335 (2017).

  147. 147.

    DeForest, C. A., Polizzotti, B. D. & Anseth, K. S. Sequential click reactions for synthesizing and patterning three-dimensional cell microenvironments. Nat. Mater. 8, 659–664 (2009).

  148. 148.

    Mosiewicz, K. A. et al. In situ cell manipulation through enzymatic hydrogel photopatterning. Nat. Mater. 12, 1072–1078 (2013).

  149. 149.

    Dankers, P. Y., Harmsen, M. C., Brouwer, L. A., van Luyn, M. J. & Meijer, E. W. A modular and supramolecular approach to bioactive scaffolds for tissue engineering. Nat. Mater. 4, 568–574 (2005).

  150. 150.

    Gelain, F., Bottai, D., Vescovi, A. & Zhang, S. Designer self-assembling peptide nanofiber scaffolds for adult mouse neural stem cell 3-dimensional cultures. PLOS ONE 1, e119 (2006).

  151. 151.

    Silva, G. A. et al. Selective differentiation of neural progenitor cells by high-epitope density nanofibers. Science 303, 1352–1355 (2004).

  152. 152.

    Bajaj, P., Schweller, R. M., Khademhosseini, A., West, J. L. & Bashir, R. 3D biofabrication strategies for tissue engineering and regenerative medicine. Annu. Rev. Biomed. Eng. 16, 247–276 (2014).

  153. 153.

    Todhunter, M. E. et al. Programmed synthesis of three-dimensional tissues. Nat. Methods 12, 975–981 (2015).

  154. 154.

    Hughes, A. J. et al. Engineered tissue folding by mechanical compaction of the mesenchyme. Dev. Cell 44, 165–178.e6 (2018).

  155. 155.

    Demers, C. J. et al. Development-on-chip: in vitro neural tube patterning with a microfluidic device. Development 143, 1884–1892 (2016).

  156. 156.

    Keenan, T. M. & Folch, A. Biomolecular gradients in cell culture systems. Lab. Chip 8, 34–57 (2008).

  157. 157.

    Tabata, Y. & Lutolf, M. P. Multiscale microenvironmental perturbation of pluripotent stem cell fate and self-organization. Sci. Rep. 7, 44711 (2017).

  158. 158.

    Carpenedo, R. L. et al. Homogeneous and organized differentiation within embryoid bodies induced by microsphere-mediated delivery of small molecules. Biomaterials 30, 2507–2515 (2009).

  159. 159.

    Morsut, L. et al. Engineering customized cell sensing and response behaviors using synthetic notch receptors. Cell 164, 780–791 (2016).

  160. 160.

    Toda, S., Blauch, L. R., Tang, S. K. Y., Morsut, L. & Lim, W. A. Programming self-organizing multicellular structures with synthetic cell-cell signaling. Science 361, 156–162 (2018).

  161. 161.

    Workman, M. J. et al. Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system. Nat. Med. 23, 49–59 (2017).

  162. 162.

    Zhang, C., Zhao, Z., Abdul Rahim, N. A., van Noort, D. & Yu, H. Towards a human-on-chip: culturing multiple cell types on a chip with compartmentalized microenvironments. Lab. Chip 9, 3185–3192 (2009).

  163. 163.

    Zhang, L. et al. Establishing estrogen-responsive mouse mammary organoids from single Lgr5+ cells. Cell. Signal. 29, 41–51 (2017).

  164. 164.

    Pera, M. F. et al. What if stem cells turn into embryos in a dish? Nat. Methods 12, 917 (2015).

  165. 165.

    Shen, H. Embryo assembly 101. Nature 559, 19–22 (2018).

  166. 166.

    Hyun, I. Engineering ethics and self-organizing models of human development: opportunities and challenges. Cell Stem Cell 21, 718–720 (2017).

  167. 167.

    Kuwahara, A. et al. Generation of a ciliary margin-like stem cell niche from self-organizing human retinal tissue. Nat. Commun. 6, 6286 (2015).

  168. 168.

    Wahlin, K. J. et al. Photoreceptor outer segment-like structures in long-term 3D retinas from human pluripotent stem cells. Sci. Rep. 7, 766 (2017).

  169. 169.

    Zhong, X. et al. Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs. Nat. Commun. 5, 4047 (2014).

  170. 170.

    Otani, T., Marchetto, M. C., Gage, F. H., Simons, B. D. & Livesey, F. J. 2D and 3D stem cell models of primate cortical development identify species-specific differences in progenitor behavior contributing to brain size. Cell Stem Cell 18, 467–480 (2016).

  171. 171.

    Lancaster, M. A. et al. Guided self-organization and cortical plate formation in human brain organoids. Nat. Biotechnol. 35, 659–666 (2017).

  172. 172.

    Suga, H. et al. Self-formation of functional adenohypophysis in three-dimensional culture. Nature 480, 57–62 (2011).

  173. 173.

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

  174. 174.

    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).

  175. 175.

    von Furstenberg, R. J. et al. Sorting mouse jejunal epithelial cells with CD24 yields a population with characteristics of intestinal stem cells. Am. J. Physiol. Gastrointest. Liver Physiol. 300, G409–G417 (2011).

  176. 176.

    Gracz, A. D., Ramalingam, S. & Magness, S. T. Sox9 expression marks a subset of CD24-expressing small intestine epithelial stem cells that form organoids in vitro. Am. J. Physiol. Gastrointest. Liver Physiol. 298, G590–G600 (2010).

  177. 177.

    Hannan, N. R. F. et al. Generation of multipotent foregut stem cells from human pluripotent stem cells. Stem Cell Rep. 1, 293–306 (2013).

  178. 178.

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

  179. 179.

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

  180. 180.

    Broutier, L. et al. Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation. Nat. Protoc. 11, 1724–1743 (2016).

  181. 181.

    Rock, J. R. et al. Basal cells as stem cells of the mouse trachea and human airway epithelium. Proc. Natl Acad. Sci. USA 106, 12771–12775 (2009).

  182. 182.

    Tadokoro, T. et al. IL-6/STAT3 promotes regeneration of airway ciliated cells from basal stem cells. Proc. Natl Acad. Sci. USA 111, E3641–E3649 (2014).

  183. 183.

    Wong, A. P. et al. Directed differentiation of human pluripotent stem cells into mature airway epithelia expressing functional CFTR protein. Nat. Biotechnol. 30, 876–882 (2012).

  184. 184.

    Huang, S. X. L. et al. Highly efficient generation of airway and lung epithelial cells from human pluripotent stem cells. Nat. Biotechnol. 32, 84–91 (2014).

  185. 185.

    Jain, R. et al. Plasticity of Hopx(+) type I alveolar cells to regenerate type II cells in the lung. Nat. Commun. 6, 6727 (2015).

  186. 186.

    Barkauskas, C. E. et al. Type 2 alveolar cells are stem cells in adult lung. J. Clin. Invest. 123, 3025–3036 (2013).

  187. 187.

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

  188. 188.

    Kurmann, A. A. et al. Regeneration of thyroid function by transplantation of differentiated pluripotent stem cells. Cell Stem Cell 17, 527–542 (2015).

  189. 189.

    DeWard, A. D., 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).

  190. 190.

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

  191. 191.

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

  192. 192.

    Kessler, M. et al. The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids. Nat. Commun. 6, 8989 (2015).

  193. 193.

    Morizane, R. et al. Nephron organoids derived from human pluripotent stem cells model kidney development and injury. Nat. Biotechnol. 33, 1193–1200 (2015).

  194. 194.

    Freedman, B. S. et al. Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids. Nat. Commun. 6, 8715 (2015).

  195. 195.

    Sachs, N. et al. A living biobank of breast cancer organoids captures disease heterogeneity. Cell 172, 373–386.e10 (2018).

  196. 196.

    Jardé, T. et al. Wnt and Neuregulin1/ErbB signalling extends 3D culture of hormone responsive mammary organoids. Nat. Commun. 7, 13207 (2016).

  197. 197.

    Lombaert, I. M. A. et al. Rescue of salivary gland function after stem cell transplantation in irradiated glands. PLOS ONE 3, e2063 (2008).

  198. 198.

    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).

  199. 199.

    Feng, J., van der Zwaag, M., Stokman, M. A., van Os, R. & Coppes, R. P. Isolation and characterization of human salivary gland cells for stem cell transplantation to reduce radiation-induced hyposalivation. Radiother. Oncol. 92, 466–471 (2009).

Download references


The work of M.P.L. in the area of organoid biology and technology is supported by the Swiss National Science Foundation, the European Union’s Horizon 2020 research and innovation programme (INTENS 668294), the Personalized Health and Related Technologies Initiative from the ETH Board, the Vienna Science and Technology Fund and École Polytechnique Fédérale de Lausanne (EPFL). The authors are grateful to their collaborators in the organoid field, including J. Briscoe, H. Clevers, D. Duboule, A. Grapin-Botton, A. Kitcheva, J. Knoblich, A. Martinez-Arias and E. Tanaka. The authors thank the members of their laboratory for helpful discussions and apologize to all the scientists whose work they could not cite owing to space restrictions.

Reviewer information

Nature Reviews Genetics thanks P. Arlotta, J. Wells and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Author information

Author notes

  1. These authors contributed equally: Giuliana Rossi, Andrea Manfrin.


  1. Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

    • Giuliana Rossi
    • , Andrea Manfrin
    •  & Matthias P. Lutolf
  2. Institute of Chemical Sciences and Engineering, School of Basic Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

    • Matthias P. Lutolf


  1. Search for Giuliana Rossi in:

  2. Search for Andrea Manfrin in:

  3. Search for Matthias P. Lutolf in:


G.R., A.M. and M.P.L. researched data for the article, made substantial contributions to discussions of the content and wrote the article. M.P.L. reviewed and/or edited the manuscript before submission.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Matthias P. Lutolf.



Stem cell-derived or progenitor cell-derived 3D structures that, on much smaller scales, re-create important aspects of the 3D anatomy and multicellular repertoire of their physiological counterparts and that can recapitulate basic tissue-level functions.

Adult stem cells

(ASCs). Somatic stem cells with the capacity to give rise to the terminally differentiated cells of the tissue in which they reside.

Pluripotent stem cells

(PSCs). Stem cells that have the capacity to give rise to all the cell types of the embryo proper. PSCs include embryonic stem cells and induced PSCs.


Microfluidic cell culture device that contains perfused chambers in which living cells are arranged to simulate tissue-level and organ-level physiology.


The first identifiable event that triggers the formation of an asymmetric system from an initially homogeneous (symmetric) state.

Reaction-diffusion mechanisms

Mathematical models that describe the dynamics of pattern formation in terms of local production and diffusion of activators and inhibitors and their interactions.

Bistability of regulatory networks

The behaviour of biological systems in which positive and negative feedback between networks of regulatory elements results in only one of two mutually exclusive outcomes.

Asymmetric cell division

The mechanism of cellular division by which the mother cell produces two daughter cells with different cell fates.

Air–liquid interface

A method for cell culture that is typically used for epithelial cells and in which a porous filter is used to expose basal cell layers to the cell culture medium and external cell layers to the air.


Biomolecules that act in a concentration-dependent manner to determine cell fate choices and tissue patterning in vivo.


(NE). Derived from neuroectoderm, the ectodermal embryonic compartment that will give rise to the nervous system. From this epithelium, components of the sensory organs are also formed, as in the case of the eye. Can be considered a synonym of neuroectoderm.

Neural retina

(NR). A multi-layered structure of the eye formed by the neuronal types responsible for light acquisition and conversion into neural signals.

Retinal pigmented epithelium

(RPE). A pigmented epithelium attached to the outside of the neural retina in the eye. It provides nutritional support to neural retina cells.

Ureteric epithelium

Derivative of the intermediate mesoderm that contributes to the formation of the renal collecting ducts.

Metanephric mesenchyme

Derivative of the intermediate mesoderm that substantially contributes to the formation of the renal nephrons.


The identity of the gastric epithelium in the most distal part of the stomach, pertaining to an anatomical region that connects to the intestinal duodenum called the pyloric antrum.


The identity of the gastric epithelium in the upper curvature of the stomach, pertaining to an anatomical region called the fundus of the stomach.


Derived from the mesoderm, the middle embryonic germ layer that is formed upon gastrulation and will give rise to different adult tissues such as skeletal and cardiac muscle, smooth muscle, blood, cartilage, bones and dermis.

Surface ectoderm

The part of the embryonic ectoderm that lines the exterior of the embryo (the surface). Derivatives of the surface ectoderm include the epidermis with associated glands (including the mammary glands), sensory receptors, the epithelium of the oral and nasal cavity with associated glands and the cornea and the lens of the eye, among others.

Glandular tissues

Epithelial tissues that produce and release biomolecules (hormones and growth factors, among others) into the bloodstream, in external or internal body cavities.


Derived from the endoderm, the most inner embryonic germ layer formed upon gastrulation, that will give rise to internal structures such as the epithelial lining of the respiratory and gastrointestinal tracts and of the urinary system.


A process that occurs during mammalian embryonic development in which the three germ layers (ectoderm, mesoderm and endoderm) form from the epiblast and arrange in space to generate a more defined body plan of the organism.


Spherical epithelial cysts of fetal intestinal progenitors.


Invaginations of the intestinal epithelium at the base of villi, which typically host self-renewing LGR5+ intestinal stem cells and Paneth cells at their bottom.

Optic vesicles

Embryonic epithelial vesicles evaginating from the forebrain neuroepithelium that will give rise to the optic cup. In organoids, they are the vesicular structures forming at early stages of organoid development, before the morphological changes that will give rise to the final optic cup structure.

Personalized medicine

A medical procedure in which the therapy and/or treatment is tailored to a specific patient.

Organoid biobanks

Collections of organoid samples, typically of human origin, that are stored for research purposes and aim to encompass a wide range of population genetic variance.

3R principles

A framework for more humane animal research aimed at replacing, reducing and refining animal experimentation.


Devices for the large-scale expansion of cells under controlled culture conditions.

Sacrificial moulds

Templates used to form a structure; they are dissolved after the moulding process.

Laser ablation

The controlled removal of portions of a material through irradiation with a laser beam.


The use of specialized 3D printing technologies to combine cells, biomolecules and biomaterials in 3D assemblies.


Devices comprising biological components (such as antibodies and enzymes, among others) and electrochemical components for the measurement of biological parameters.

About this article

Publication history