Engineered materials for organoid systems

Abstract

Organoids are 3D cell culture systems that mimic some of the structural and functional characteristics of an organ. Organoid cultures provide the opportunity to study organ-level biology in models that mimic human physiology more closely than 2D cell culture systems or non-primate animal models. Many organoid cultures rely on decellularized extracellular matrices as scaffolds, which are often poorly chemically defined and allow only limited tunability and reproducibility. By contrast, the biochemical and biophysical properties of engineered matrices can be tuned and optimized to support the development and maturation of organoid cultures. In this Review, we highlight how key cell–matrix interactions guiding stem-cell decisions can inform the design of biomaterials for the reproducible generation and control of organoid cultures. We survey natural, synthetic and protein-engineered hydrogels for their applicability to different organoid systems and discuss biochemical and mechanical material properties relevant for organoid formation. Finally, dynamic and cell-responsive material systems are investigated for their future use in organoid research.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1
Fig. 2: Organoid cell sources and types.
Fig. 3: Cell–matrix interactions.
Fig. 4: Dynamic organoid niches.

References

  1. 1.

    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).

  2. 2.

    Weiss, P. & Taylor, A. C. Reconstitution of complete organs from single-cell suspensions of chick embryos in advanced stages of differentiation. Proc. Natl. Acad. Sci. USA 46, 1177–1185 (1960).

  3. 3.

    Ishii, K. Reconstruction of dissociated chick brain cells in rotation-mediated culture. Cytologia (Tokyo) 31, 89–98 (1966).

  4. 4.

    Edington, C. D. et al. Interconnected microphysiological systems for quantitative biology and pharmacology studies. Sci. Rep. 8, 4530 (2018).

  5. 5.

    Simian, M. & Bissell, M. J. Organoids: a historical perspective of thinking in three dimensions. J. Cell Biol. 216, 31–40 (2017).

  6. 6.

    Stelzner, M. et al. A nomenclature for intestinal in vitro cultures. Am. J. Physiol. Gastrointest. Liver Physiol. 302, G1359–G1363 (2012).

  7. 7.

    Pasca, A. M. et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671–678 (2015).

  8. 8.

    HogenEsch, H. & Nikitin, A. Y. Challenges in pre-clinical testing of anti-cancer drugs in cell culture and in animal models. J. Control. Release 164, 183–186 (2012).

  9. 9.

    Horrobin, D. F. Modern biomedical research: an internally self-consistent universe with little contact with medical reality? Nat. Rev. Drug Discov. 2, 151–154 (2003).

  10. 10.

    Pasca, S. P. Assembling human brain organoids. Science 363, 126–127 (2019).

  11. 11.

    Mak, I. W., Evaniew, N. & Ghert, M. Lost in translation: animal models and clinical trials in cancer treatment. Am. J. Transl. Res. 6, 114–118 (2014).

  12. 12.

    Pound, P. & Ritskes-Hoitinga, M. Is it possible to overcome issues of external validity in preclinical animal research? Why most animal models are bound to fail. J. Transl. Med. 16, 304 (2018).

  13. 13.

    Co, J. Y. et al. Controlling epithelial polarity: a human enteroid model for host-pathogen interactions. Cell Rep. 26, 2509–2520.e4 (2019).

  14. 14.

    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).

  15. 15.

    Forbes, T. A. et al. Patient-iPSC-derived kidney organoids show functional validation of a ciliopathic renal phenotype and reveal underlying pathogenetic mechanisms. Am. J. Hum. Genet. 102, 816–831 (2018).

  16. 16.

    Zhang, B. Y., Korolj, A., Lai, B. F. L. & Radisic, M. Advances in organ-on-a-chip engineering. Nat. Rev. Mat. 3, 257–278 (2018).

  17. 17.

    Ahadian, S. et al. Organ-on-a-chip platforms: a convergence of advanced materials, cells, and microscale technologies. Adv. Healthc. Mater. 7, 1700506 (2018).

  18. 18.

    Bhise, N. S. et al. A liver-on-a-chip platform with bioprinted hepatic spheroids. Biofabrication 8, 014101 (2016).

  19. 19.

    Homan, K. A. et al. Flow-enhanced vascularization and maturation of kidney organoids in vitro. Nat. Methods 16, 255–262 (2019).

  20. 20.

    Karzbrun, E., Kshirsagar, A., Cohen, S. R., Hanna, J. H. & Reiner, O. Human brain organoids on a chip reveal the physics of folding. Nat. Phys. 14, 515–522 (2018).

  21. 21.

    Kasendra, M. et al. Development of a primary human small intestine-on-a-chip using biopsy-derived organoids. Sci. Rep. 8, 2871 (2018).

  22. 22.

    Rossi, G., Manfrin, A. & Lutolf, M. P. Progress and potential in organoid research. Nat. Rev. Genet. 19, 671–687 (2018).

  23. 23.

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

  24. 24.

    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).

  25. 25.

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

  26. 26.

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

  27. 27.

    Lu, P., Takai, K., Weaver, V. M. & Werb, Z. Extracellular matrix degradation and remodeling in development and disease. Cold Spring Harb. Perspect. Biol. 3, a005058 (2011).

  28. 28.

    Levental, K. R. et al. Matrix crosslinking forces tumor progression by enhancing integrin signaling. Cell 139, 891–906 (2009).

  29. 29.

    Simao, D. et al. Recapitulation of human neural microenvironment signatures in iPSC-derived NPC 3D differentiation. Stem Cell Rep. 11, 552–564 (2018).

  30. 30.

    Sasai, Y., Eiraku, M. & Suga, H. In vitro organogenesis in three dimensions: self-organising stem cells. Development 139, 4111–4121 (2012).

  31. 31.

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

  32. 32.

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

  33. 33.

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

  34. 34.

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

  35. 35.

    Taguchi, A. & Nishinakamura, R. Higher-order kidney organogenesis from pluripotent stem cells. Cell Stem Cell 21, 730–746.e6 (2017).

  36. 36.

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

  37. 37.

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

  38. 38.

    Dorrell, C. et al. The organoid-initiating cells in mouse pancreas and liver are phenotypically and functionally similar. Stem Cell Res. 13, 275–283 (2014).

  39. 39.

    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).

  40. 40.

    Poznansky, M. C. et al. Efficient generation of human T cells from a tissue-engineered thymic organoid. Nat. Biotechnol. 18, 729–734 (2000).

  41. 41.

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

  42. 42.

    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).

  43. 43.

    Kadoshima, T. 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 110, 20284–20289 (2013).

  44. 44.

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

  45. 45.

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

  46. 46.

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

  47. 47.

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

  48. 48.

    Munera, J. O. et al. Differentiation of human pluripotent stem cells into colonic organoids via transient activation of bmp signaling. Cell Stem Cell 21, 51–64.e6 (2017).

  49. 49.

    Rankin, S. A. et al. Timing is everything: reiterative Wnt, BMP and RA signaling regulate developmental competence during endoderm organogenesis. Dev. Biol. 434, 121–132 (2018).

  50. 50.

    Carcamo-Orive, I. et al. Analysis of transcriptional variability in a large human iPSC library reveals genetic and non-genetic determinants of heterogeneity. Cell Stem Cell 20, 518–532.e9 (2017).

  51. 51.

    Graf, T. & Stadtfeld, M. Heterogeneity of embryonic and adult stem cells. Cell Stem Cell 3, 480–483 (2008).

  52. 52.

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

  53. 53.

    Wu, H. et al. Comparative analysis and refinement of human PSC-derived kidney organoid differentiation with single-cell transcriptomics. Cell Stem Cell 23, 869–881.e8 (2018).

  54. 54.

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

  55. 55.

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

  56. 56.

    Yoon, S. J. et al. Reliability of human cortical organoid generation. Nat. Methods 16, 75–78 (2019).

  57. 57.

    Sloan, S. A. et al. Human astrocyte maturation captured in 3D cerebral cortical spheroids derived from pluripotent stem cells. Neuron 95, 779–790.e6 (2017).

  58. 58.

    Birey, F. et al. Assembly of functionally integrated human forebrain spheroids. Nature 545, 54–59 (2017).

  59. 59.

    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).

  60. 60.

    Watanabe, K. et al. Directed differentiation of telencephalic precursors from embryonic stem cells. Nat. Neurosci. 8, 288–296 (2005).

  61. 61.

    Qian, X. et al. Generation of human brain region-specific organoids using a miniaturized spinning bioreactor. Nat. Protoc. 13, 565–580 (2018).

  62. 62.

    Kleinman, H. K. et al. Isolation and characterization of type IV procollagen, laminin, and heparan sulfate proteoglycan from the EHS sarcoma. Biochemistry 21, 6188–6193 (1982).

  63. 63.

    Huang, G. et al. Functional and biomimetic materials for engineering of the three-dimensional cell microenvironment. Chem. Rev. 117, 12764–12850 (2017).

  64. 64.

    Darnell, M. et al. Material microenvironmental properties couple to induce distinct transcriptional programs in mammalian stem cells. Proc. Natl. Acad. Sci. USA 115, E8368–E8377 (2018).

  65. 65.

    Caplan, A. I. Mesenchymal stem cells: time to change the name! Stem Cells Transl. Med. 6, 1445–1451 (2017).

  66. 66.

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

  67. 67.

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

  68. 68.

    Parsons, J. T., Horwitz, A. R. & Schwartz, M. A. Cell adhesion: integrating cytoskeletal dynamics and cellular tension. Nat. Rev. Mol. Cell Biol. 11, 633–643 (2010).

  69. 69.

    Hynes, R. O. The extracellular matrix: not just pretty fibrils. Science 326, 1216–1219 (2009).

  70. 70.

    Huttenlocher, A. & Horwitz, A. R. Integrins in cell migration. Cold Spring Harb. Perspect. Biol. 3, a005074 (2011).

  71. 71.

    Vicente-Manzanares, M., Choi, C. K. & Horwitz, A. R. Integrins in cell migration—the actin connection. J. Cell Sci. 122, 199–206 (2009).

  72. 72.

    Kim, S. H., Turnbull, J. & Guimond, S. Extracellular matrix and cell signalling: the dynamic cooperation of integrin, proteoglycan and growth factor receptor. J. Endocrinol. 209, 139–151 (2011).

  73. 73.

    Schwartz, M. A. Integrins and extracellular matrix in mechanotransduction. Cold Spring Harb. Perspect. Biol. 2, a005066 (2010).

  74. 74.

    Maheshwari, G., Brown, G., Lauffenburger, D. A., Wells, A. & Griffith, L. G. Cell adhesion and motility depend on nanoscale RGD clustering. J. Cell Sci. 113 (10), 1677–1686 (2000).

  75. 75.

    Chaudhuri, O. et al. Substrate stress relaxation regulates cell spreading. Nat. Commun. 6, 6364 (2015).

  76. 76.

    Chaudhuri, O. et al. Hydrogels with tunable stress relaxation regulate stem cell fate and activity. Nat. Mater. 15, 326–334 (2016).

  77. 77.

    Benitez, P. L., Mascharak, S., Proctor, A. C. & Heilshorn, S. C. Use of protein-engineered fabrics to identify design rules for integrin ligand clustering in biomaterials. Integr. Biol. (Camb.) 8, 50–61 (2016).

  78. 78.

    Kong, H. J., Polte, T. R., Alsberg, E. & Mooney, D. J. FRET measurements of cell-traction forces and nano-scale clustering of adhesion ligands varied by substrate stiffness. Proc. Natl. Acad. Sci. USA 102, 4300–4305 (2005).

  79. 79.

    Pierschbacher, M. D. & Ruoslahti, E. Cell attachment activity of fibronectin can be duplicated by small synthetic fragments of the molecule. Nature 309, 30–33 (1984).

  80. 80.

    Knight, C. G. et al. The collagen-binding A-domains of integrins alpha(1)beta(1) and alpha(2)beta(1) recognize the same specific amino acid sequence, GFOGER, in native (triple-helical) collagens. J. Biol. Chem. 275, 35–40 (2000).

  81. 81.

    Tashiro, K. et al. A synthetic peptide containing the IKVAV sequence from the A chain of laminin mediates cell attachment, migration, and neurite outgrowth. J. Biol. Chem. 264, 16174–16182 (1989).

  82. 82.

    Graf, J. et al. Identification of an amino acid sequence in laminin mediating cell attachment, chemotaxis, and receptor binding. Cell 48, 989–996 (1987).

  83. 83.

    Le Saux, G., Magenau, A., Bocking, T., Gaus, K. & Gooding, J. J. The relative importance of topography and RGD ligand density for endothelial cell adhesion. PLOS ONE 6, e21869 (2011).

  84. 84.

    Oria, R. et al. Force loading explains spatial sensing of ligands by cells. Nature 552, 219–224 (2017).

  85. 85.

    Ye, K. et al. Matrix stiffness and nanoscale spatial organization of cell-adhesive ligands direct stem cell fate. Nano Lett. 15, 4720–4729 (2015).

  86. 86.

    Wang, X. et al. Effect of RGD nanospacing on differentiation of stem cells. Biomaterials 34, 2865–2874 (2013).

  87. 87.

    Salinas, C. N. & Anseth, K. S. The influence of the RGD peptide motif and its contextual presentation in PEG gels on human mesenchymal stem cell viability. J. Tissue Eng. Regen. Med. 2, 296–304 (2008).

  88. 88.

    Koivunen, E., Wang, B. & Ruoslahti, E. Phage libraries displaying cyclic peptides with different ring sizes: ligand specificities of the RGD-directed integrins. Biotechnology (N. Y.) 13, 265–270 (1995).

  89. 89.

    Wade, R. J., Bassin, E. J., Gramlich, W. M. & Burdick, J. A. Nanofibrous hydrogels with spatially patterned biochemical signals to control cell behavior. Adv. Mater. 27, 1356–1362 (2015).

  90. 90.

    Arnold, M. et al. Activation of integrin function by nanopatterned adhesive interfaces. ChemPhysChem 5, 383–388 (2004).

  91. 91.

    Cavalcanti-Adam, E. A. et al. Cell spreading and focal adhesion dynamics are regulated by spacing of integrin ligands. Biophys. J. 92, 2964–2974 (2007).

  92. 92.

    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).

  93. 93.

    Campbell, I. D. & Humphries, M. J. Integrin structure, activation, and interactions. Cold Spring Harb. Perspect. Biol. 3, a004994 (2011).

  94. 94.

    Li, S. et al. Hydrogels with precisely controlled integrin activation dictate vascular patterning and permeability. Nat. Mater. 16, 953–961 (2017).

  95. 95.

    Lam, J., Carmichael, S. T., Lowry, W. E. & Segura, T. Hydrogel design of experiments methodology to optimize hydrogel for iPSC-NPC culture. Adv. Healthc. Mater. 4, 534–539 (2015).

  96. 96.

    Ali, S., Saik, J. E., Gould, D. J., Dickinson, M. E. & West, J. L. Immobilization of cell-adhesive laminin peptides in degradable PEGDA hydrogels influences endothelial cell tubulogenesis. BioRes. Open Access 2, 241–249 (2013).

  97. 97.

    Moshayedi, P. et al. Systematic optimization of an engineered hydrogel allows for selective control of human neural stem cell survival and differentiation after transplantation in the stroke brain. Biomaterials 105, 145–155 (2016).

  98. 98.

    Lee, J. W. & Lee, K. Y. Dual peptide-presenting hydrogels for controlling the phenotype of PC12 cells. Colloids Surf. B Biointerfaces 152, 36–41 (2017).

  99. 99.

    Huettner, N., Dargaville, T. R. & Forget, A. Discovering cell-adhesion peptides in tissue engineering: beyond RGD. Trends Biotechnol. 36, 372–383 (2018).

  100. 100.

    Seidlits, S. K. et al. Peptide-modified, hyaluronic acid-based hydrogels as a 3D culture platform for neural stem/progenitor cell engineering. J. Biomed. Mater. Res. A 107, 704–718 (2019).

  101. 101.

    Müller, C., Müller, A. & Pompe, T. Dissipative interactions in cell–matrix adhesion. Soft Matter 9, 6207–6216 (2013).

  102. 102.

    Eyckmans, J., Boudou, T., Yu, X. & Chen, C. S. A hitchhiker’s guide to mechanobiology. Dev. Cell 21, 35–47 (2011).

  103. 103.

    Vianello, S. & Lutolf, M. P. Understanding the mechanobiology of early mammalian development through bioengineered models. Dev. Cell 48, 751–763 (2019).

  104. 104.

    Butcher, D. T., Alliston, T. & Weaver, V. M. A tense situation: forcing tumour progression. Nat. Rev. Cancer 9, 108–122 (2009).

  105. 105.

    Sherratt, M. J. Tissue elasticity and the ageing elastic fibre. Age 31, 305–325 (2009).

  106. 106.

    Handorf, A. M., Zhou, Y., Halanski, M. A. & Li, W. J. Tissue stiffness dictates development, homeostasis, and disease progression. Organogenesis 11, 1–15 (2015).

  107. 107.

    Lampi, M. C. & Reinhart-King, C. A. Targeting extracellular matrix stiffness to attenuate disease: From molecular mechanisms to clinical trials. Sci. Transl. Med. 10, eaao0475 (2018).

  108. 108.

    Engler, A. J., Sen, S., Sweeney, H. L. & Discher, D. E. Matrix elasticity directs stem cell lineage specification. Cell 126, 677–689 (2006).

  109. 109.

    Saha, K. et al. Substrate modulus directs neural stem cell behavior. Biophys. J. 95, 4426–4438 (2008).

  110. 110.

    Leipzig, N. D. & Shoichet, M. S. The effect of substrate stiffness on adult neural stem cell behavior. Biomaterials 30, 6867–6878 (2009).

  111. 111.

    Gilbert, P. M., Havenstrite, K. L., Magnusson, K. & Blau, H. M. Substrate elasticity regulates skeletal muscle stem cell self-renewal in culture. Science 329, 1078–1081 (2010).

  112. 112.

    Huebsch, N. et al. Harnessing traction-mediated manipulation of the cell/matrix interface to control stem-cell fate. Nat. Mater. 9, 518–526 (2010).

  113. 113.

    Evans, N. D. et al. Substrate stiffness affects early differentiation events in embryonic stem cells. Eur. Cell. Mater. 18, 1–13; discussion 13–14 (2009).

  114. 114.

    Hadden, W. J. et al. Stem cell migration and mechanotransduction on linear stiffness gradient hydrogels. Proc. Natl. Acad. Sci. USA 114, 5647–5652 (2017).

  115. 115.

    Lee, D. A., Knight, M. M., Campbell, J. J. & Bader, D. L. Stem cell mechanobiology. J. Cell. Biochem. 112, 1–9 (2011).

  116. 116.

    Vining, K. H. & Mooney, D. J. Mechanical forces direct stem cell behaviour in development and regeneration. Nat. Rev. Mol. Cell Biol. 18, 728–742 (2017).

  117. 117.

    Wang, N. Review of cellular mechanotransduction. J. Phys. D Appl. Phys. 50, 233002 (2017).

  118. 118.

    Cameron, A. R., Frith, J. E. & Cooper-White, J. J. The influence of substrate creep on mesenchymal stem cell behaviour and phenotype. Biomaterials 32, 5979–5993 (2011).

  119. 119.

    Cameron, A. R., Frith, J. E., Gomez, G. A., Yap, A. S. & Cooper-White, J. J. The effect of time-dependent deformation of viscoelastic hydrogels on myogenic induction and Rac1 activity in mesenchymal stem cells. Biomaterials 35, 1857–1868 (2014).

  120. 120.

    Nam, S., Stowers, R., Lou, J., Xia, Y. & Chaudhuri, O. Varying PEG density to control stress relaxation in alginate-PEG hydrogels for 3D cell culture studies. Biomaterials 200, 15–24 (2019).

  121. 121.

    Rudnicki, M. S. et al. Nonlinear strain stiffening is not sufficient to explain how far cells can feel on fibrous protein gels. Biophys. J. 105, 11–20 (2013).

  122. 122.

    Storm, C., Pastore, J. J., MacKintosh, F. C., Lubensky, T. C. & Janmey, P. A. Nonlinear elasticity in biological gels. Nature 435, 191–194 (2005).

  123. 123.

    Jaspers, M. et al. Ultra-responsive soft matter from strain-stiffening hydrogels. Nat. Commun. 5, 5808 (2014).

  124. 124.

    Das, R. K., Gocheva, V., Hammink, R., Zouani, O. F. & Rowan, A. E. Stress-stiffening-mediated stem-cell commitment switch in soft responsive hydrogels. Nat. Mater. 15, 318–325 (2016).

  125. 125.

    de Almeida, P. et al. Cytoskeletal stiffening in synthetic hydrogels. Nat. Commun. 10, 609 (2019).

  126. 126.

    Kouwer, P. H. et al. Responsive biomimetic networks from polyisocyanopeptide hydrogels. Nature 493, 651–655 (2013).

  127. 127.

    Yin, Z. et al. The regulation of tendon stem cell differentiation by the alignment of nanofibers. Biomaterials 31, 2163–2175 (2010).

  128. 128.

    Cardwell, R. D., Dahlgren, L. A. & Goldstein, A. S. Electrospun fibre diameter, not alignment, affects mesenchymal stem cell differentiation into the tendon/ligament lineage. J. Tissue Eng. Regen. Med. 8, 937–945 (2014).

  129. 129.

    Silantyeva, E. A. et al. Accelerated neural differentiation of mouse embryonic stem cells on aligned GYIGSR-functionalized nanofibers. Acta Biomater. 75, 129–139 (2018).

  130. 130.

    Christopherson, G. T., Song, H. & Mao, H. Q. The influence of fiber diameter of electrospun substrates on neural stem cell differentiation and proliferation. Biomaterials 30, 556–564 (2009).

  131. 131.

    Lutolf, M. P. et al. Synthetic matrix metalloproteinase-sensitive hydrogels for the conduction of tissue regeneration: engineering cell-invasion characteristics. Proc. Natl. Acad. Sci. USA 100, 5413–5418 (2003).

  132. 132.

    Han, L. H., Lai, J. H., Yu, S. & Yang, F. Dynamic tissue engineering scaffolds with stimuli-responsive macroporosity formation. Biomaterials 34, 4251–4258 (2013).

  133. 133.

    Nih, L. R., Sideris, E., Carmichael, S. T. & Segura, T. Injection of microporous annealing particle (MAP) hydrogels in the stroke cavity reduces gliosis and inflammation and promotes NPC migration to the lesion. Adv. Mater. 29, 1606471 (2017).

  134. 134.

    Han, L. H., Tong, X. & Yang, F. Photo-crosslinkable PEG-based microribbons for forming 3D macroporous scaffolds with decoupled niche properties. Adv. Mater. 26, 1757–1762 (2014).

  135. 135.

    Darling, N. J., Hung, Y. S., Sharma, S. & Segura, T. Controlling the kinetics of thiol-maleimide Michael-type addition gelation kinetics for the generation of homogenous poly(ethylene glycol) hydrogels. Biomaterials 101, 199–206 (2016).

  136. 136.

    Wang, H., Cai, L., Paul, A., Enejder, A. & Heilshorn, S. C. Hybrid elastin-like polypeptide-polyethylene glycol (ELP-PEG) hydrogels with improved transparency and independent control of matrix mechanics and cell ligand density. Biomacromolecules 15, 3421–3428 (2014).

  137. 137.

    Zhao, H. et al. Microengineered in vitro model of cardiac fibrosis through modulating myofibroblast mechanotransduction. Biofabrication 6, 045009 (2014).

  138. 138.

    Tse, J. R. & Engler, A. J. Stiffness gradients mimicking in vivo tissue variation regulate mesenchymal stem cell fate. PLOS ONE 6, e15978 (2011).

  139. 139.

    Kharkar, P. M., Kiick, K. L. & Kloxin, A. M. Designing degradable hydrogels for orthogonal control of cell microenvironments. Chem. Soc. Rev. 42, 7335–7372 (2013).

  140. 140.

    Giambernardi, T. A. et al. Overview of matrix metalloproteinase expression in cultured human cells. Matrix Biology 16, 483–496 (1998).

  141. 141.

    Girish, K. S. & Kemparaju, K. The magic glue hyaluronan and its eraser hyaluronidase: a biological overview. Life Sci. 80, 1921–1943 (2007).

  142. 142.

    Lee, K. Y. & Mooney, D. J. Alginate: properties and biomedical applications. Prog. Polym. Sci. 37, 106–126 (2012).

  143. 143.

    Kong, H. J., Smith, M. K. & Mooney, D. J. Designing alginate hydrogels to maintain viability of immobilized cells. Biomaterials 24, 4023–4029 (2003).

  144. 144.

    Parmar, P. A. et al. Temporally degradable collagen-mimetic hydrogels tuned to chondrogenesis of human mesenchymal stem cells. Biomaterials 99, 56–71 (2016).

  145. 145.

    Stern, R., Asari, A. A. & Sugahara, K. N. Hyaluronan fragments: an information-rich system. Eur. J. Cell Biol. 85, 699–715 (2006).

  146. 146.

    Lampe, K. J., Bjugstad, K. B. & Mahoney, M. J. Impact of degradable macromer content in a poly(ethylene glycol) hydrogel on neural cell metabolic activity, redox state, proliferation, and differentiation. Tissue Eng. Part A 16, 1857–1866 (2010).

  147. 147.

    Khetan, S. et al. Degradation-mediated cellular traction directs stem cell fate in covalently crosslinked three-dimensional hydrogels. Nat. Mater. 12, 458–465 (2013).

  148. 148.

    Salinas, C. N. & Anseth, K. S. The enhancement of chondrogenic differentiation of human mesenchymal stem cells by enzymatically regulated RGD functionalities. Biomaterials 29, 2370–2377 (2008).

  149. 149.

    Ehrbar, M. et al. Elucidating the role of matrix stiffness in 3D cell migration and remodeling. Biophys. J. 100, 284–293 (2011).

  150. 150.

    Khetan, S. & Burdick, J. A. Patterning network structure to spatially control cellular remodeling and stem cell fate within 3-dimensional hydrogels. Biomaterials 31, 8228–8234 (2010).

  151. 151.

    Kloxin, A. M. et al. Responsive culture platform to examine the influence of microenvironmental geometry on cell function in 3D. Integr. Biol. (Camb.) 4, 1540–1549 (2012).

  152. 152.

    Anderson, S. B., Lin, C. C., Kuntzler, D. V. & Anseth, K. S. The performance of human mesenchymal stem cells encapsulated in cell-degradable polymer-peptide hydrogels. Biomaterials 32, 3564–3574 (2011).

  153. 153.

    Ashton, R. S., Banerjee, A., Punyani, S., Schaffer, D. V. & Kane, R. S. Scaffolds based on degradable alginate hydrogels and poly(lactide-co-glycolide) microspheres for stem cell culture. Biomaterials 28, 5518–5525 (2007).

  154. 154.

    Bryant, S. J. & Anseth, K. S. Controlling the spatial distribution of ECM components in degradable PEG hydrogels for tissue engineering cartilage. J. Biomed. Mater. Res. A 64, 70–79 (2003).

  155. 155.

    Chung, C., Beecham, M., Mauck, R. L. & Burdick, J. A. The influence of degradation characteristics of hyaluronic acid hydrogels on in vitro neocartilage formation by mesenchymal stem cells. Biomaterials 30, 4287–4296 (2009).

  156. 156.

    Madl, C. M. et al. Maintenance of neural progenitor cell stemness in 3D hydrogels requires matrix remodelling. Nat. Mater. 16, 1233–1242 (2017).

  157. 157.

    Purwada, A. et al. Ex vivo engineered immune organoids for controlled germinal center reactions. Biomaterials 63, 24–34 (2015).

  158. 158.

    Purwada, A., Shah, S. B., Beguelin, W., Melnick, A. M. & Singh, A. Modular immune organoids with integrin ligand specificity differentially regulate ex vivo B cell activation. ACS Biomater. Sci. Eng. 3, 214–225 (2017).

  159. 159.

    McGuigan, A. P. & Sefton, M. V. Vascularized organoid engineered by modular assembly enables blood perfusion. Proc. Natl. Acad. Sci. USA 103, 11461–11466 (2006).

  160. 160.

    Weber, R. J. et al. Rapid organoid reconstitution by chemical micromolding. ACS Biomater. Sci. Eng. 2, 1851–1855 (2016).

  161. 161.

    Jabaji, Z. et al. Type I collagen as an extracellular matrix for the in vitro growth of human small intestinal epithelium. PLOS ONE 9, e107814 (2014).

  162. 162.

    DiMarco, R. L. et al. Engineering of three-dimensional microenvironments to promote contractile behavior in primary intestinal organoids. Integr. Biol. (Camb.) 6, 127–142 (2014).

  163. 163.

    Takezawa, T., Ozaki, K., Nitani, A., Takabayashi, C. & Shimo-Oka, T. Collagen vitrigel: a novel scaffold that can facilitate a three-dimensional culture for reconstructing organoids. Cell Transplant. 13, 463–473 (2004).

  164. 164.

    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).

  165. 165.

    Wilkinson, D. C. et al. Development of a three-dimensional bioengineering technology to generate lung tissue for personalized disease modeling. Stem Cells Transl. Med. 6, 622–633 (2017).

  166. 166.

    Wolf, K. J. & Kumar, S. Hyaluronic acid: incorporating the bio into the material. ACS Biomater. Sci. Eng. https://doi.org/10.1021/acsbiomaterials.8b01268 (2019).

  167. 167.

    Antoine, E. E., Vlachos, P. P. & Rylander, M. N. Review of collagen I hydrogels for bioengineered tissue microenvironments: characterization of mechanics, structure, and transport. Tissue Eng. Part B Rev. 20, 683–696 (2014).

  168. 168.

    Hughes, C. S., Postovit, L. M. & Lajoie, G. A. Matrigel: a complex protein mixture required for optimal growth of cell culture. Proteomics 10, 1886–1890 (2010).

  169. 169.

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

  170. 170.

    Neal, J. T. et al. Organoid modeling of the tumor immune microenvironment. Cell 175, 1972–1988.e16 (2018).

  171. 171.

    Giandomenico, S. L. et al. Cerebral organoids at the air–liquid interface generate diverse nerve tracts with functional output. Nat. Neurosci. 22, 669–679 (2019).

  172. 172.

    Capeling, M. M. et al. Nonadhesive alginate hydrogels support growth of pluripotent stem cell-derived intestinal organoids. Stem Cell Rep. 12, 381–394 (2019).

  173. 173.

    Chen, Y., Zhou, W., Roh, T., Estes, M. K. & Kaplan, D. L. In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses. PLOS ONE 12, e0187880 (2017).

  174. 174.

    Banerjee, I., Pangule, R. C. & Kane, R. S. Antifouling coatings: recent developments in the design of surfaces that prevent fouling by proteins, bacteria, and marine organisms. Adv. Mater. 23, 690–718 (2011).

  175. 175.

    Zhu, J. Bioactive modification of poly(ethylene glycol) hydrogels for tissue engineering. Biomaterials 31, 4639–4656 (2010).

  176. 176.

    Enemchukwu, N. O. et al. Synthetic matrices reveal contributions of ECM biophysical and biochemical properties to epithelial morphogenesis. J. Cell Biol. 212, 113–124 (2016).

  177. 177.

    Sengupta, D. & Heilshorn, S. C. Protein-engineered biomaterials: highly tunable tissue engineering scaffolds. Tissue Eng. Part B Rev. 16, 285–293 (2010).

  178. 178.

    DiMarco, R. L., Dewi, R. E., Bernal, G., Kuo, C. & Heilshorn, S. C. Protein-engineered scaffolds for in vitro 3D culture of primary adult intestinal organoids. Biomater. Sci. 3, 1376–1385 (2015).

  179. 179.

    Candiello, J. et al. 3D heterogeneous islet organoid generation from human embryonic stem cells using a novel engineered hydrogel platform. Biomaterials 177, 27–39 (2018).

  180. 180.

    Sasai, Y. Cytosystems dynamics in self-organization of tissue architecture. Nature 493, 318–326 (2013).

  181. 181.

    Li, J. & Mooney, D. J. Designing hydrogels for controlled drug delivery. Nat. Rev. Mater. 1, 16071 (2016).

  182. 182.

    Liang, Y. & Kiick, K. L. Heparin-functionalized polymeric biomaterials in tissue engineering and drug delivery applications. Acta Biomater. 10, 1588–1600 (2014).

  183. 183.

    Sakiyama-Elbert, S. E. Incorporation of heparin into biomaterials. Acta Biomater. 10, 1581–1587 (2014).

  184. 184.

    Vulic, K. & Shoichet, M. S. Affinity-based drug delivery systems for tissue repair and regeneration. Biomacromolecules 15, 3867–3880 (2014).

  185. 185.

    Willerth, S. M., Rader, A. & Sakiyama-Elbert, S. E. The effect of controlled growth factor delivery on embryonic stem cell differentiation inside fibrin scaffolds. Stem Cell Res. 1, 205–218 (2008).

  186. 186.

    Guo, C. et al. Bio-orthogonal conjugation and enzymatically triggered release of proteins within multi-layered hydrogels. Acta Biomater. 56, 80–90 (2017).

  187. 187.

    Straley, K. S. & Heilshorn, S. C. Independent tuning of multiple biomaterial properties using protein engineering. Soft Matter 5, 114–124 (2009).

  188. 188.

    Patterson, J. & Hubbell, J. A. Enhanced proteolytic degradation of molecularly engineered PEG hydrogels in response to MMP-1 and MMP-2. Biomaterials 31, 7836–7845 (2010).

  189. 189.

    Kukreja, M. et al. High-throughput multiplexed peptide-centric profiling illustrates both substrate cleavage redundancy and specificity in the MMP family. Chem. Biol. 22, 1122–1133 (2015).

  190. 190.

    Kwon, M. Y. et al. Dose and timing of N-cadherin mimetic peptides regulate MSC chondrogenesis within hydrogels. Adv. Healthc. Mater. 7, 1701199 (2018).

  191. 191.

    Ruskowitz, E. R. & DeForest, C. A. Photoresponsive biomaterials for targeted drug delivery and 4D cell culture. Nat. Rev. Mater. 3, 17087–17017 (2018).

  192. 192.

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

  193. 193.

    DeForest, C. A. & Tirrell, D. A. A photoreversible protein-patterning approach for guiding stem cell fate in three-dimensional gels. Nat. Mater. 14, 523–531 (2015).

  194. 194.

    Grim, J. C. et al. A reversible and repeatable thiol–ene bioconjugation for dynamic patterning of signaling proteins in hydrogels. ACS Cent. Sci. 4, 909–916 (2018).

  195. 195.

    Jeon, O., Lee, K. & Alsberg, E. Spatial micropatterning of growth factors in 3D hydrogels for location-specific regulation of cellular behaviors. Small 14, 1800579 (2018).

  196. 196.

    Hoffmann, J. C. & West, J. L. Three-dimensional photolithographic patterning of multiple bioactive ligands in poly(ethylene glycol) hydrogels. Soft Matter 6, 5056–5063 (2010).

  197. 197.

    Shadish, J. A., Benuska, G. M. & DeForest, C. A. Bioactive site-specifically modified proteins for 4D patterning of gel biomaterials. Nat. Mater. https://doi.org/10.1038/s41563-019-0367-7 (2019).

  198. 198.

    Attayek, P. J. et al. In vitro polarization of colonoids to create an intestinal stem cell compartment. PLOS ONE 11, e0153795 (2016).

  199. 199.

    Thorne, C. A. et al. Enteroid monolayers reveal an autonomous WNT and BMP circuit controlling intestinal epithelial growth and organization. Dev. Cell 44, 624–633.e4 (2018).

  200. 200.

    Cederquist, G. Y. et al. Specification of positional identity in forebrain organoids. Nat. Biotechnol. 37, 436–444 (2019).

  201. 201.

    Nguyen, E. H., Schwartz, M. P. & Murphy, W. L. Biomimetic approaches to control soluble concentration gradients in biomaterials. Macromol. Biosci. 11, 483–492 (2011).

  202. 202.

    Foty, R. A. & Steinberg, M. S. The differential adhesion hypothesis: a direct evaluation. Dev. Biol. 278, 255–263 (2005).

  203. 203.

    Brodland, G. W. The differential interfacial tension hypothesis (DITH): a comprehensive theory for the self-rearrangement of embryonic cells and tissues. J. Biomech. Eng. 124, 188–197 (2002).

  204. 204.

    Fagotto, F. The cellular basis of tissue separation. Development 141, 3303–3318 (2014).

  205. 205.

    Canty, L., Zarour, E., Kashkooli, L., Francois, P. & Fagotto, F. Sorting at embryonic boundaries requires high heterotypic interfacial tension. Nat. Commun. 8, 157 (2017).

  206. 206.

    Knight, G. T. et al. Engineering induction of singular neural rosette emergence within hPSC-derived tissues. Elife 7, e37549 (2018).

  207. 207.

    Knight, G. T., Sha, J. & Ashton, R. S. Micropatterned, clickable culture substrates enable in situ spatiotemporal control of human PSC-derived neural tissue morphology. Chem. Commun. 51, 5238–5241 (2015).

  208. 208.

    Cerchiari, A. E. et al. A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity. Proc. Natl. Acad. Sci. USA 112, 2287–2292 (2015).

  209. 209.

    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).

  210. 210.

    Pedron, S. et al. Patterning three-dimensional hydrogel microenvironments using hyperbranched polyglycerols for independent control of mesh size and stiffness. Biomacromolecules 18, 1393–1400 (2017).

  211. 211.

    Luo, Y. & Shoichet, M. S. A photolabile hydrogel for guided three-dimensional cell growth and migration. Nat. Mater. 3, 249–253 (2004).

  212. 212.

    Lee, S. H., Moon, J. J. & West, J. L. Three-dimensional micropatterning of bioactive hydrogels via two-photon laser scanning photolithography for guided 3D cell migration. Biomaterials 29, 2962–2968 (2008).

  213. 213.

    Guvendiren, M. & Burdick, J. A. Stiffening hydrogels to probe short- and long-term cellular responses to dynamic mechanics. Nat. Commun. 3, 792 (2012).

  214. 214.

    Marklein, R. A. & Burdick, J. A. Spatially controlled hydrogel mechanics to modulate stem cell interactions. Soft Matter 6, 136–143 (2010).

  215. 215.

    Doyle, A. D., Wang, F. W., Matsumoto, K. & Yamada, K. M. One-dimensional topography underlies three-dimensional fibrillar cell migration. J. Cell Biol. 184, 481–490 (2009).

  216. 216.

    Plotnikov, S. V., Pasapera, A. M., Sabass, B. & Waterman, C. M. Force fluctuations within focal adhesions mediate ECM-rigidity sensing to guide directed cell migration. Cell 151, 1513–1527 (2012).

  217. 217.

    Brown, T. E. et al. Photopolymerized dynamic hydrogels with tunable viscoelastic properties through thioester exchange. Biomaterials 178, 496–503 (2018).

  218. 218.

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

  219. 219.

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

  220. 220.

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

  221. 221.

    Madl, C. M., Katz, L. M. & Heilshorn, S. C. Tuning bulk hydrogel degradation by simultaneous control of proteolytic cleavage kinetics and hydrogel network architecture. ACS Macro. Lett. 7, 1302–1307 (2018).

  222. 222.

    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).

  223. 223.

    Sarig-Nadir, O., Livnat, N., Zajdman, R., Shoham, S. & Seliktar, D. Laser photoablation of guidance microchannels into hydrogels directs cell growth in three dimensions. Biophys. J. 96, 4743–4752 (2009).

  224. 224.

    McKinnon, D. D., Brown, T. E., Kyburz, K. A., Kiyotake, E. & Anseth, K. S. Design and characterization of a synthetically accessible, photodegradable hydrogel for user-directed formation of neural networks. Biomacromolecules 15, 2808–2816 (2014).

  225. 225.

    Badeau, B. A., Comerford, M. P., Arakawa, C. K., Shadish, J. A. & DeForest, C. A. Engineered modular biomaterial logic gates for environmentally triggered therapeutic delivery. Nat. Chem. 10, 251–258 (2018).

  226. 226.

    Moroni, L. et al. Biofabrication strategies for 3D in vitro models and regenerative medicine. Nat. Rev. Mater. 3, 21–37 (2018).

  227. 227.

    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).

  228. 228.

    Xiang, Y. et al. hESC-derived thalamic organoids form reciprocal projections when fused with cortical organoids. Cell Stem Cell 24, 487–497.e7 (2019).

  229. 229.

    Du, Y., Lo, E., Ali, S. & Khademhosseini, A. Directed assembly of cell-laden microgels for fabrication of 3D tissue constructs. Proc. Natl. Acad. Sci. USA 105, 9522–9527 (2008).

  230. 230.

    Kang, H. W. et al. A 3D bioprinting system to produce human-scale tissue constructs with structural integrity. Nat. Biotechnol. 34, 312–319 (2016).

  231. 231.

    Groll, J. et al. A definition of bioinks and their distinction from biomaterial inks. Biofabrication 11, 013001 (2018).

  232. 232.

    Jia, W. et al. Direct 3D bioprinting of perfusable vascular constructs using a blend bioink. Biomaterials 106, 58–68 (2016).

  233. 233.

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

  234. 234.

    Mironov, V. et al. Organ printing: tissue spheroids as building blocks. Biomaterials 30, 2164–2174 (2009).

  235. 235.

    Yu, Y. et al. Three-dimensional bioprinting using self-assembling scalable scaffold-free “tissue strands” as a new bioink. Sci. Rep. 6, 28714 (2016).

  236. 236.

    Laronda, M. M. et al. A bioprosthetic ovary created using 3D printed microporous scaffolds restores ovarian function in sterilized mice. Nat. Commun. 8, 15261 (2017).

  237. 237.

    Chen, H. J., Miller, P. & Shuler, M. L. A pumpless body-on-a-chip model using a primary culture of human intestinal cells and a 3D culture of liver cells. Lab Chip 18, 2036–2046 (2018).

  238. 238.

    Chen, W. L. K. et al. Integrated gut/liver microphysiological systems elucidates inflammatory inter-tissue crosstalk. Biotechnol. Bioeng. 114, 2648–2659 (2017).

  239. 239.

    Esch, M. B., Ueno, H., Applegate, D. R. & Shuler, M. L. Modular, pumpless body-on-a-chip platform for the co-culture of GI tract epithelium and 3D primary liver tissue. Lab Chip 16, 2719–2729 (2016).

  240. 240.

    Benam, K. H. et al. Matched-comparative modeling of normal and diseased human airway responses using a microengineered breathing lung chip. Cell Systems 3, 456–466.e4 (2016).

  241. 241.

    Barrile, R. et al. Organ-on-chip recapitulates thrombosis induced by an anti-CD154 monoclonal antibody: translational potential of advanced microengineered systems. Clin. Pharmacol. Ther. 104, 1240–1248 (2018).

  242. 242.

    Figtree, G. A., Bubb, K. J., Tang, O., Kizana, E. & Gentile, C. Vascularized cardiac spheroids as novel 3D in vitro models to study cardiac fibrosis. Cells Tissues Organs 204, 191–198 (2017).

  243. 243.

    Nguyen, E. H. et al. Versatile synthetic alternatives to Matrigel for vascular toxicity screening and stem cell expansion. Nat. Biomed. Eng. 1, 0096 (2017).

  244. 244.

    Soofi, S. S., Last, J. A., Liliensiek, S. J., Nealey, P. F. & Murphy, C. J. The elastic modulus of Matrigel as determined by atomic force microscopy. J. Struct. Biol. 167, 216–219 (2009).

  245. 245.

    Chaudhuri, O. et al. Extracellular matrix stiffness and composition jointly regulate the induction of malignant phenotypes in mammary epithelium. Nat. Mater. 13, 970–978 (2014).

  246. 246.

    Villa-Diaz, L. G., Ross, A. M., Lahann, J. & Krebsbach, P. H. Concise review: the evolution of human pluripotent stem cell culture: from feeder cells to synthetic coatings. Stem Cells 31, 1–7 (2012).

  247. 247.

    Halbleib, J. M. & Nelson, W. J. Cadherins in development: cell adhesion, sorting, and tissue morphogenesis. Genes Dev. 20, 3199–3214 (2006).

  248. 248.

    Takeichi, M. Cadherins: a molecular family important in selective cell-cell adhesion. Annu. Rev. Biochem. 59, 237–252 (1990).

  249. 249.

    Steinberg, M. S. & McNutt, P. M. Cadherins and their connections: adhesion junctions have broader functions. Curr. Opin. Cell Biol. 11, 554–560 (1999).

  250. 250.

    Katsamba, P. et al. Linking molecular affinity and cellular specificity in cadherin-mediated adhesion. Proc. Natl. Acad. Sci. USA 106, 11594–11599 (2009).

  251. 251.

    Vendome, J. et al. Structural and energetic determinants of adhesive binding specificity in type I cadherins. Proc. Natl. Acad. Sci. USA 111, E4175–E4184 (2014).

  252. 252.

    le Duc, Q. et al. Vinculin potentiates E-cadherin mechanosensing and is recruited to actin-anchored sites within adherens junctions in a myosin II-dependent manner. J. Cell Biol. 189, 1107–1115 (2010).

  253. 253.

    Leckband, D. E., le Duc, Q., Wang, N. & de Rooij, J. Mechanotransduction at cadherin-mediated adhesions. Curr. Opin. Cell Biol. 23, 523–530 (2011).

  254. 254.

    Cosgrove, B. D. et al. N-cadherin adhesive interactions modulate matrix mechanosensing and fate commitment of mesenchymal stem cells. Nat. Mater. 15, 1297–1306 (2016).

  255. 255.

    Bian, L., Guvendiren, M., Mauck, R. L. & Burdick, J. A. Hydrogels that mimic developmentally relevant matrix and N-cadherin interactions enhance MSC chondrogenesis. Proc. Natl. Acad. Sci. USA 110, 10117–10122 (2013).

  256. 256.

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

  257. 257.

    Jo, J. et al. Midbrain-like organoids from human pluripotent stem cells contain functional dopaminergic and neuromelanin-producing neurons. Cell Stem Cell 19, 248–257 (2016).

  258. 258.

    Miller, A. J. et al. Generation of lung organoids from human pluripotent stem cells in vitro. Nat. Protoc. 14, 518–540 (2019).

  259. 259.

    Baptista, P. M. et al. The use of whole organ decellularization for the generation of a vascularized liver organoid. Hepatology 53, 604–617 (2011).

  260. 260.

    Finkbeiner, S. R. et al. Generation of tissue-engineered small intestine using embryonic stem cell-derived human intestinal organoids. Biol. Open 4, 1462–1472 (2015).

  261. 261.

    Astashkina, A. I., Mann, B. K., Prestwich, G. D. & Grainger, D. W. A 3-D organoid kidney culture model engineered for high-throughput nephrotoxicity assays. Biomaterials 33, 4700–4711 (2012).

  262. 262.

    Broguiere, N. et al. Growth of epithelial organoids in a defined hydrogel. Adv. Mater. 30, 1801621 (2018).

  263. 263.

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

  264. 264.

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

  265. 265.

    Drumheller, P. D. & Hubbell, J. A. Densely crosslinked polymer networks of poly(ethylene glycol) in trimethylolpropane triacrylate for cell-adhesion-resistant surfaces. J. Biomed. Mater. Res. 29, 207–215 (1995).

  266. 266.

    Rheinwald, J. G. & Green, H. Formation of a keratinizing epithelium in culture by a cloned cell line derived from a teratoma. Cell 6, 317–330 (1975).

  267. 267.

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

  268. 268.

    Li, M. L. et al. Influence of a reconstituted basement membrane and its components on casein gene expression and secretion in mouse mammary epithelial cells. Proc. Natl. Acad. Sci. USA 84, 136–140 (1987).

  269. 269.

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

  270. 270.

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

Download references

Acknowledgements

The authors acknowledge financial support from the National Institutes of Health (R21HL138042, R01HL142718, R01EB027666 (S.C.H.), U01DK085527 (C.J.K.), U19AI116484 (S.C.H., C.J.K.)), the National Science Foundation (DMR 1808415 (S.C.H.)), the Human Brain Organogenesis Program funded by the Wu Tsai Neurosciences Institute (S.C.H., S.P.P.), New York Stem Cell Foundation (NYSCF) Robertson Stem Cell Investigator Award (S.P.P.) and the Chan Zuckerberg Initiative (CZI) Ben Barres Award (S.P.P.). The authors thank D. Hunt, B. LaSavage, L. Marquardt and J. Roth for their helpful discussions.

Author information

M.J.K., A.J.S., T.L.L., S.P.P., C.J.K. and S.C.H. wrote, edited and reviewed the manuscript. All authors contributed to the discussion of the content.

Correspondence to Sarah C. Heilshorn.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note

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

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark