Cellular self-assembly and biomaterials-based organoid models of development and diseases

Duester, 2008, Retinoic acid synthesis and signaling during early organogenesis, Cell, 134, 921, 10.1016/j.cell.2008.09.002 Green, 2008, Opposing Wnt pathways orient cell polarity during organogenesis, Cell, 134, 646, 10.1016/j.cell.2008.06.026 Durdu, 2014, Luminal signalling links cell communication to tissue architecture during organogenesis, Nature, 515, 120, 10.1038/nature13852 Stephens, 1995, Deletion of beta 1 integrins in mice results in inner cell mass failure and peri-implantation lethality, Gene Dev., 9, 1883, 10.1101/gad.9.15.1883 Bader, 1998, Extensive vasculogenesis, angiogenesis, and organogenesis precede lethality in mice lacking all alpha v integrins, Cell, 95, 507, 10.1016/S0092-8674(00)81618-9 Takasato, 2016, Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis, Nature, 536, 238, 10.1038/nature17982 Takasato, 2015, Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis, Nature, 526, 564, 10.1038/nature15695 Clevers, 2015, Q&A: Hans Clevers. Banking on organoids, Nature, 521, S15, 10.1038/521S15a McCracken, 2014, Modelling human development and disease in pluripotent stem-cell-derived gastric organoids, Nature, 516, 400, 10.1038/nature13863 Lancaster, 2013, Cerebral organoids model human brain development and microcephaly, Nature, 501, 373, 10.1038/nature12517 Jo, 2016, Midbrain-like organoids from human pluripotent stem cells contain functional dopaminergic and neuromelanin-producing neurons, Cell Stem Cell, 19, 248, 10.1016/j.stem.2016.07.005 Shroyer, 2016, Tumor organoids fill the niche, Cell Stem Cell, 18, 686, 10.1016/j.stem.2016.05.020 Dang, 2016, Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3, Cell Stem Cell, 19, 258, 10.1016/j.stem.2016.04.014 Yin, 2016, Engineering stem cell organoids, Cell Stem Cell, 18, 25, 10.1016/j.stem.2015.12.005 Schwank, 2013, Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients, Cell Stem Cell, 13, 653, 10.1016/j.stem.2013.11.002 Willenbring, 2013, Transplantable liver organoids made from only three ingredients, Cell Stem Cell, 13, 139, 10.1016/j.stem.2013.07.014 Huch, 2015, Modeling mouse and human development using organoid cultures, Development, 142, 3113, 10.1242/dev.118570 Clevers, 2016, Modeling development and disease with organoids, Cell, 165, 1586, 10.1016/j.cell.2016.05.082 Lee, 2007, Three-dimensional culture models of normal and malignant breast epithelial cells, Nat. Methods, 4, 359, 10.1038/nmeth1015 Weaver, 2002, Beta4 integrin-dependent formation of polarized three-dimensional architecture confers resistance to apoptosis in normal and malignant mammary epithelium, Cancer Cell, 2, 205, 10.1016/S1535-6108(02)00125-3 Weaver, 1997, Reversion of the malignant phenotype of human breast cells in three-dimensional culture and in vivo by integrin blocking antibodies, J. Cell Biol., 137, 231, 10.1083/jcb.137.1.231 Nelson, 2006, Tissue geometry determines sites of mammary branching morphogenesis in organotypic cultures, Science, 314, 298, 10.1126/science.1131000 Kleinman, 2005, Matrigel: basement membrane matrix with biological activity, Semin. Cancer Biol., 15, 378, 10.1016/j.semcancer.2005.05.004 Jabaji, 2014, Type I collagen as an extracellular matrix for the in vitro growth of human small intestinal epithelium, PLoS One, 9, e107814, 10.1371/journal.pone.0107814 Shao, 2016, Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche, Nat. Mater. Sato, 2009, Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche, Nature, 459, 262, 10.1038/nature07935 Karthaus, 2014, Identification of multipotent luminal progenitor cells in human prostate organoid cultures, Cell, 159, 163, 10.1016/j.cell.2014.08.017 McCracken, 2011, Generating human intestinal tissue from pluripotent stem cells in vitro, Nat. Protoc., 6, 1920, 10.1038/nprot.2011.410 Serban, 2008, Modular extracellular matrices: solutions for the puzzle, Methods, 45, 93, 10.1016/j.ymeth.2008.01.010 Vukicevic, 1992, Identification of multiple active growth factors in basement membrane Matrigel suggests caution in interpretation of cellular activity related to extracellular matrix components, Exp. Cell Res., 202, 1, 10.1016/0014-4827(92)90397-Q Hughes, 2010, Matrigel: a complex protein mixture required for optimal growth of cell culture, Proteomics, 10, 1886, 10.1002/pmic.200900758 Prestwich, 2007, Simplifying the extracellular matrix for 3-D cell culture and tissue engineering: a pragmatic approach, J. Cell Biochem., 101, 1370, 10.1002/jcb.21386 Fatehullah, 2016, Organoids as an in vitro model of human development and disease, Nat. Cell Biol., 18, 246, 10.1038/ncb3312 Gjorevski, 2016, Designer matrices for intestinal stem cell and organoid culture, Nature, 539, 560, 10.1038/nature20168 DiMarco, 2015, Protein-engineered scaffolds for in vitro 3D culture of primary adult intestinal organoids, Biomater. Sci., 3, 1376, 10.1039/C5BM00108K Purwada, 2017, Modular immune organoids with integrin ligand specificity differentially regulate ex vivo B cell activation, ACS Biomater. Sci. Eng., 10.1021/acsbiomaterials.6b00474 Tian, 2015, Integrin-specific hydrogels as adaptable tumor organoids for malignant B and T cells, Biomaterials, 73, 110, 10.1016/j.biomaterials.2015.09.007 Wells, 2014, How to make an intestine, Development, 141, 752, 10.1242/dev.097386 Brugmann, 2013, Building additional complexity to in vitro-derived intestinal tissues, Stem Cell Res. Ther., 4, S1, 10.1186/scrt362 Hounnou, 2002, Anatomical study of the length of the human intestine, Surg. Radiol. Anat., 24, 290, 10.1007/s00276-002-0057-y Sinagoga, 2015, Generating human intestinal tissues from pluripotent stem cells to study development and disease, EMBO J., 34, 1149, 10.15252/embj.201490686 Rao, 2010, Intestinal architecture and development Barker, 2007, Identification of stem cells in small intestine and colon by marker gene Lgr5, Nature, 449, 1003, 10.1038/nature06196 Sakaguchi, 2015, Generation of functional hippocampal neurons from self-organizing human embryonic stem cell-derived dorsomedial telencephalic tissue, Nat. Commun., 6, 8896, 10.1038/ncomms9896 Muguruma, 2015, Self-organization of polarized cerebellar tissue in 3D culture of human pluripotent stem cells, Cell Rep., 10, 537, 10.1016/j.celrep.2014.12.051 Mariani, 2015, FOXG1-dependent dysregulation of GABA/glutamate neuron differentiation in autism spectrum disorders, Cell, 162, 375, 10.1016/j.cell.2015.06.034 Kadoshima, 2013, Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex, Proc. Natl. Acad. Sci. U.S.A., 110, 20284, 10.1073/pnas.1315710110 Garcez, 2016, Zika virus impairs growth in human neurospheres and brain organoids, PeerJ Preprints DeWard, 2014, Cellular heterogeneity in the mouse esophagus implicates the presence of a nonquiescent epithelial stem cell population, Cell Rep., 9, 701, 10.1016/j.celrep.2014.09.027 Sato, 2011, Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium, Gastroenterology, 141, 1762, 10.1053/j.gastro.2011.07.050 Eiraku, 2011, Self-organizing optic-cup morphogenesis in three-dimensional culture, Nature, 472, 51, 10.1038/nature09941 Nakano, 2012, Self-formation of optic cups and storable stratified neural retina from human ESCs, Cell Stem Cell, 10, 771, 10.1016/j.stem.2012.05.009 Volkner, 2016, Retinal organoids from pluripotent stem cells efficiently recapitulate retinogenesis, Stem Cell Rep., 6, 525, 10.1016/j.stemcr.2016.03.001 Shen, 2009, Number of lymph nodes examined and associated clinicopathologic factors in colorectal carcinoma, Arch. Pathol. Lab. Med., 133, 781, 10.5858/133.5.781 Gonzalez-Cordero, 2013, Photoreceptor precursors derived from three-dimensional embryonic stem cell cultures integrate and mature within adult degenerate retina, Nat. Biotechnol., 31, 741, 10.1038/nbt.2643 Busskamp, 2014, MiRNAs 182 and 183 are necessary to maintain adult cone photoreceptor outer segments and visual function, Neuron, 83, 586, 10.1016/j.neuron.2014.06.020 Koehler, 2013, Generation of inner ear sensory epithelia from pluripotent stem cells in 3D culture, Nature, 500, 217, 10.1038/nature12298 Koehler, 2014, 3D mouse embryonic stem cell culture for generating inner ear organoids, Nat. Protoc., 9, 1229, 10.1038/nprot.2014.100 Fordham, 2013, Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury, Cell Stem Cell, 13, 734, 10.1016/j.stem.2013.09.015 Mustata, 2013, Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium, Cell Rep., 5, 421, 10.1016/j.celrep.2013.09.005 Zietek, 2015, Intestinal organoids for assessing nutrient transport, sensing and incretin secretion, Sci. Rep., 5, 16831, 10.1038/srep16831 Lindemans, 2015, Interleukin-22 promotes intestinal-stem-cell-mediated epithelial regeneration, Nature, 528, 560, 10.1038/nature16460 Yui, 2012, Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5(+) stem cell, Nat. Med., 18, 618, 10.1038/nm.2695 Watson, 2014, An in vivo model of human small intestine using pluripotent stem cells, Nat. Med., 20, 1310, 10.1038/nm.3737 Zhang, 2014, Salmonella-infected crypt-derived intestinal organoid culture system for host-bacterial interactions, Physiol. Rep., 2, 10.14814/phy2.12147 Wilson, 2015, A small intestinal organoid model of non-invasive enteric pathogen-epithelial cell interactions, Mucosal Immunol., 8, 352, 10.1038/mi.2014.72 Forbester, 2015, Interaction of Salmonella enterica Serovar Typhimurium with intestinal organoids derived from human induced pluripotent stem cells, Infect. Immun., 83, 2926, 10.1128/IAI.00161-15 Rodansky, 2015, Intestinal organoids: a model of intestinal fibrosis for evaluating anti-fibrotic drugs, Exp. Mol. Pathol., 98, 346, 10.1016/j.yexmp.2015.03.033 Drost, 2015, Sequential cancer mutations in cultured human intestinal stem cells, Nature, 521, 43, 10.1038/nature14415 Matano, 2015, Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids, Nat. Med., 21, 256, 10.1038/nm.3802 van de Wetering, 2015, Prospective derivation of a living organoid biobank of colorectal cancer patients, Cell, 161, 933, 10.1016/j.cell.2015.03.053 Astashkina, 2012, A 3-D organoid kidney culture model engineered for high-throughput nephrotoxicity assays, Biomaterials, 33, 4700, 10.1016/j.biomaterials.2012.02.063 Hisha, 2013, Establishment of a novel lingual organoid culture system: generation of organoids having mature keratinized epithelium from adult epithelial stem cells, Sci. Rep., 3, 3224, 10.1038/srep03224 Huch, 2013, In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration, Nature, 494, 247, 10.1038/nature11826 Huch, 2015, Long-term culture of genome-stable bipotent stem cells from adult human liver, Cell, 160, 299, 10.1016/j.cell.2014.11.050 Takebe, 2013, Vascularized and functional human liver from an iPSC-derived organ bud transplant, Nature, 499, 481, 10.1038/nature12271 Takebe, 2014, Generation of a vascularized and functional human liver from an iPSC-derived organ bud transplant, Nat. Protoc., 9, 396, 10.1038/nprot.2014.020 Ogawa, 2015, Directed differentiation of cholangiocytes from human pluripotent stem cells, Nat. Biotechnol., 33, 853, 10.1038/nbt.3294 Sampaziotis, 2015, Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation, Nat. Biotechnol., 33, 845, 10.1038/nbt.3275 Dye, 2015, In vitro generation of human pluripotent stem cell derived lung organoids, Elife, 4, 10.7554/eLife.05098 Mondrinos, 2014, Engineering de novo assembly of fetal pulmonary organoids, Tissue Eng. Part A, 20, 2892, 10.1089/ten.tea.2014.0085 Huch, 2013, Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis, EMBO J., 32, 2708, 10.1038/emboj.2013.204 Greggio, 2013, Artificial three-dimensional niches deconstruct pancreas development in vitro, Development, 140, 4452, 10.1242/dev.096628 Boj, 2015, Organoid models of human and mouse ductal pancreatic cancer, Cell, 160, 324, 10.1016/j.cell.2014.12.021 Suga, 2011, Self-formation of functional adenohypophysis in three-dimensional culture, Nature, 480, 57, 10.1038/nature10637 Gao, 2014, Organoid cultures derived from patients with advanced prostate cancer, Cell, 159, 176, 10.1016/j.cell.2014.08.016 Nanduri, 2014, Purification and ex vivo expansion of fully functional salivary gland stem cells, Stem Cell Rep., 3, 957, 10.1016/j.stemcr.2014.09.015 Purwada, 2015, Ex vivo engineered immune organoids for controlled germinal center reactions, Biomaterials, 63, 24, 10.1016/j.biomaterials.2015.06.002 Gravelle, 2014, Cell growth in aggregates determines gene expression, proliferation, survival, chemoresistance, and sensitivity to immune effectors in follicular lymphoma, Am. J. Pathol., 184, 282, 10.1016/j.ajpath.2013.09.018 Barker, 2010, Lgr5(+ve) stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro, Cell Stem Cell, 6, 25, 10.1016/j.stem.2009.11.013 Stange, 2013, Differentiated Troy+ chief cells act as reserve stem cells to generate all lineages of the stomach epithelium, Cell, 155, 357, 10.1016/j.cell.2013.09.008 Schumacher, 2015, The use of murine-derived fundic organoids in studies of gastric physiology, J. Physiol., 593, 1809, 10.1113/jphysiol.2014.283028 Noguchi, 2015, Generation of stomach tissue from mouse embryonic stem cells, Nat. Cell Biol., 17, 984, 10.1038/ncb3200 Bertaux-Skeirik, 2015, CD44 plays a functional role in Helicobacter pylori-induced epithelial cell proliferation, PLoS Pathog., 11, e1004663, 10.1371/journal.ppat.1004663 Bartfeld, 2015, In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection, Gastroenterology, 148, 126, 10.1053/j.gastro.2014.09.042 Schlaermann, 2016, A novel human gastric primary cell culture system for modelling Helicobacter pylori infection in vitro, Gut, 65, 202, 10.1136/gutjnl-2014-307949 Wroblewski, 2015, Helicobacter pylori targets cancer-associated apical-junctional constituents in gastroids and gastric epithelial cells, Gut, 64, 720, 10.1136/gutjnl-2014-307650 Nadauld, 2014, Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer, Genome Biol., 10.1186/s13059-014-0428-9 Aihara, 2015, Characterization of stem/progenitor cell cycle using murine circumvallate papilla taste bud organoid, Sci. Rep., 5, 17185, 10.1038/srep17185 Ren, 2014, Single Lgr5- or Lgr6-expressing taste stem/progenitor cells generate taste bud cells ex vivo, Proc. Natl. Acad. Sci. U.S.A., 111, 16401, 10.1073/pnas.1409064111 Fan, 2015, Bioengineering thymus organoids to restore thymic function and induce donor-specific immune tolerance to allografts, Mol. Ther., 23, 1262, 10.1038/mt.2015.77 Lindborg, 2016, 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, 10.5966/sctm.2015-0305 Schwartz, 2015, Human pluripotent stem cell-derived neural constructs for predicting neural toxicity, Proc. Natl. Acad. Sci. U.S.A., 112, 12516, 10.1073/pnas.1516645112 Purwada, 2017, Immuno-engineered organoids for regulating the kinetics of b cell development and antibody production, Nat. Protoc., 12, 168, 10.1038/nprot.2016.157 Singh, 2013, Adhesion strength-based, label-free isolation of human pluripotent stem cells, Nat. Methods, 10, 438, 10.1038/nmeth.2437 Schlaeger, 2015, A comparison of non-integrating reprogramming methods, Nat. Biotechnol., 33, 58, 10.1038/nbt.3070 Takahashi, 2009, Human induced pluripotent stem cells on autologous feeders, PLoS One, 4, e8067, 10.1371/journal.pone.0008067 Takahashi, 2007, Induction of pluripotent stem cells from adult human fibroblasts by defined factors, Cell, 131, 861, 10.1016/j.cell.2007.11.019 Hu, 2010, Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency, Proc. Natl. Acad. Sci. U.S.A., 107, 4335, 10.1073/pnas.0910012107 Vodyanik, 2005, Human embryonic stem cell-derived CD34+ cells: efficient production in the coculture with OP9 stromal cells and analysis of lymphohematopoietic potential, Blood, 105, 617, 10.1182/blood-2004-04-1649 Yu, 2007, Induced pluripotent stem cell lines derived from human somatic cells, Science, 318, 1917, 10.1126/science.1151526 Vogelstein, 2013, Cancer genome landscapes, Science, 339, 1546, 10.1126/science.1235122 DiMarco, 2014, Engineering of three-dimensional microenvironments to promote contractile behavior in primary intestinal organoids, Integr. Biol. (Camb.), 6, 127, 10.1039/C3IB40188J Suzuki, 2015, Is this a brain which I see before me? Modeling human neural development with pluripotent stem cells, Development, 142, 3138, 10.1242/dev.120568 Eiraku, 2008, Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals, Cell Stem Cell, 3, 519, 10.1016/j.stem.2008.09.002 Mariani, 2012, Modeling human cortical development in vitro using induced pluripotent stem cells, Proc. Natl. Acad. Sci. U.S.A., 109, 12770, 10.1073/pnas.1202944109 Tang, 2016, Zika virus infects human cortical neural progenitors and attenuates their growth, Cell Stem Cell, 10.1016/j.stem.2016.02.016 Choi, 2014, A three-dimensional human neural cell culture model of Alzheimer's disease, Nature, 515, 274, 10.1038/nature13800 Bershteyn, 2013, Cerebral organoids in a dish: progress and prospects, Cell, 155, 19, 10.1016/j.cell.2013.09.010 Saha, 2008, Substrate modulus directs neural stem cell behavior, Biophys. J., 95, 4426, 10.1529/biophysj.108.132217 Keung, 2011, Rho GTPases mediate the mechanosensitive lineage commitment of neural stem cells, Stem cells, 29, 1886, 10.1002/stem.746 Keung, 2012, Soft microenvironments promote the early neurogenic differentiation but not self-renewal of human pluripotent stem cells, Integr. Biol. (Camb.), 4, 1049, 10.1039/c2ib20083j Leipzig, 2009, The effect of substrate stiffness on adult neural stem cell behavior, Biomaterials, 30, 6867, 10.1016/j.biomaterials.2009.09.002 Sun, 2014, Hippo/YAP-mediated rigidity-dependent motor neuron differentiation of human pluripotent stem cells, Nat. Mater., 13, 599, 10.1038/nmat3945 Lu, 2012, Efficient neuronal differentiation and maturation of human pluripotent stem cells encapsulated in 3D microfibrous scaffolds, Biomaterials, 33, 9179, 10.1016/j.biomaterials.2012.09.006 Willerth, 2006, Optimization of fibrin scaffolds for differentiation of murine embryonic stem cells into neural lineage cells, Biomaterials, 27, 5990, 10.1016/j.biomaterials.2006.07.036 Kuo, 2012, Material-driven differentiation of induced pluripotent stem cells in neuron growth factor-grafted poly(epsilon-caprolactone)-poly(beta-hydroxybutyrate) scaffolds, Biomaterials, 33, 5672, 10.1016/j.biomaterials.2012.04.046 Ma, 2008, Cell-extracellular matrix interactions regulate neural differentiation of human embryonic stem cells, BMC Dev. Biol., 8, 90, 10.1186/1471-213X-8-90 Tate, 2009, Laminin and fibronectin scaffolds enhance neural stem cell transplantation into the injured brain, J. Tissue Eng. Regen. Med., 3, 208, 10.1002/term.154 Raghavan, 2013, Neuroglial differentiation of adult enteric neuronal progenitor cells as a function of extracellular matrix composition, Biomaterials, 34, 6649, 10.1016/j.biomaterials.2013.05.023 Sart, 2014, Extracellular matrices decellularized from embryonic stem cells maintained their structure and signaling specificity, Tissue Eng. Part A, 20, 54, 10.1089/ten.tea.2012.0690 Pedron, 2015, Spatially gradated hydrogel platform as a 3D engineered tumor microenvironment, Adv. Mater., 27, 1567, 10.1002/adma.201404896 Kievit, 2010, Chitosan-alginate 3D scaffolds as a mimic of the glioma tumor microenvironment, Biomaterials, 31, 5903, 10.1016/j.biomaterials.2010.03.062 Ananthanarayanan, 2011, Elucidating the mechanobiology of malignant brain tumors using a brain matrix-mimetic hyaluronic acid hydrogel platform, Biomaterials, 32, 7913, 10.1016/j.biomaterials.2011.07.005 Goldrath, 1999, Selecting and maintaining a diverse T-cell repertoire, Nature, 402, 255, 10.1038/46218 Campana, 1985, Human B cell development. I. Phenotypic differences of B lymphocytes in the bone marrow and peripheral lymphoid tissue, J. Immunol., 134, 1524, 10.4049/jimmunol.134.3.1524 LeBien, 2008, B lymphocytes: how they develop and function, Blood, 112, 1570, 10.1182/blood-2008-02-078071 Allen, 2007, Germinal-center organization and cellular dynamics, Immunity, 27, 190, 10.1016/j.immuni.2007.07.009 Allen, 2007, Imaging of germinal center selection events during affinity maturation, Science, 315, 528, 10.1126/science.1136736 Randolph, 2005, Dendritic-cell trafficking to lymph nodes through lymphatic vessels, Nat. Rev. Immunol., 5, 617, 10.1038/nri1670 Schwickert, 2007, In vivo imaging of germinal centres reveals a dynamic open structure, Nature, 446, 83, 10.1038/nature05573 Swartz, 2001, The physiology of the lymphatic system, Adv. Drug Deliv. Rev., 50, 3, 10.1016/S0169-409X(01)00150-8 Klein, 2008, Germinal centres: role in B-cell physiology and malignancy, Nat. Rev. Immunol., 8, 22, 10.1038/nri2217 McHeyzer-Williams, 2012, Molecular programming of B cell memory, Nat. Rev. Immunol., 12, 24, 10.1038/nri3128 Schwickert, 2011, A dynamic T cell-limited checkpoint regulates affinity-dependent B cell entry into the germinal center, J. Exp. Med., 208, 1243, 10.1084/jem.20102477 Shulman, 2013, T follicular helper cell dynamics in germinal centers, Science, 341, 673, 10.1126/science.1241680 Liu, 1989, Mechanism of antigen-driven selection in germinal centres, Nature, 342, 929, 10.1038/342929a0 Martinez-Valdez, 1996, Human germinal center B cells express the apoptosis-inducing genes Fas, c-myc, P53, and Bax but not the survival gene bcl-2, J. Exp. Med., 183, 971, 10.1084/jem.183.3.971 Nojima, 2011, In-vitro derived germinal centre B cells differentially generate memory B or plasma cells in vivo, Nat. Commun., 2, 465, 10.1038/ncomms1475 Purwada, 2014, Engineering vaccines and niches for immune modulation, Acta Biomater., 10, 1728, 10.1016/j.actbio.2013.12.036 Singh, 2014, Hydrogels and scaffolds for immunomodulation, Adv. Mater., 26, 6530, 10.1002/adma.201402105 Muranski, 2008, Tumor-specific Th17-polarized cells eradicate large established melanoma, Blood, 112, 362, 10.1182/blood-2007-11-120998 Suematsu, 2004, Generation of a synthetic lymphoid tissue-like organoid in mice, Nat. Biotechnol., 22, 1539, 10.1038/nbt1039 Stachowiak, 2008, Inverse opal hydrogel-collagen composite scaffolds as a supportive microenvironment for immune cell migration, J. Biomed. Mater. Res. A, 85, 815, 10.1002/jbm.a.31661 Cayrol, 2015, Integrin alphavbeta3 acting as membrane receptor for thyroid hormones mediates angiogenesis in malignant T cells, Blood, 125, 841, 10.1182/blood-2014-07-587337 Vrij, 2016, 3D high throughput screening and profiling of embryoid bodies in thermoformed microwell plates, Lab Chip, 16, 734, 10.1039/C5LC01499A Mori, 2009, Self-organization of engineered epithelial tubules by differential cellular motility, Proc. Natl. Acad. Sci. U.S.A., 106, 14890, 10.1073/pnas.0901269106 Kim, 2015, Localized smooth muscle differentiation is essential for epithelial bifurcation during branching morphogenesis of the mammalian lung, Dev. Cell, 34, 719, 10.1016/j.devcel.2015.08.012 Gobaa, 2011, Artificial niche microarrays for probing single stem cell fate in high throughput, Nat. Methods, 8, 949, 10.1038/nmeth.1732 Murphy, 2014, Materials as stem cell regulators, Nat. Mater., 13, 547, 10.1038/nmat3937 Ranga, 2012, High-throughput approaches for the analysis of extrinsic regulators of stem cell fate, Curr. Opin. Cell Biol., 24, 236, 10.1016/j.ceb.2012.01.006 Fisher, 2010, Bioinspired materials for controlling stem cell fate, Acc. Chem. Res., 43, 419, 10.1021/ar900226q Pashuck, 2012, Designing regenerative biomaterial therapies for the clinic, Sci. Transl. Med., 4, 10.1126/scitranslmed.3002717 Rice, 2013, Engineering the regenerative microenvironment with biomaterials, Adv. Healthcare Mater., 2, 57, 10.1002/adhm.201200197 Vogel, 2006, Local force and geometry sensing regulate cell functions, Nat. Rev. Mol. Cell Biol., 7, 265, 10.1038/nrm1890 Lee, 2015, Light-triggered in vivo activation of adhesive peptides regulates cell adhesion, inflammation and vascularization of biomaterials, Nat. Mater., 14, 352, 10.1038/nmat4157 DeForest, 2015, A photoreversible protein-patterning approach for guiding stem cell fate in three-dimensional gels, Nat. Mater., 14, 523, 10.1038/nmat4219 Schepers, 2016, Engineering a perfusable 3D human liver platform from iPS cells, Lab Chip, 16, 2644, 10.1039/C6LC00598E Chen, 2015, Robust bioengineered 3D functional human intestinal epithelium, Sci. Rep., 5, 13708, 10.1038/srep13708 Au, 2014, Hepatic organoids for microfluidic drug screening, Lab Chip, 14, 3290, 10.1039/C4LC00531G Lee, 2013, Functionalizing calcium phosphate biomaterials with antibacterial silver particles, Adv. Mater., 25, 1173, 10.1002/adma.201203370 Lee, 2011, Mineral coatings for temporally controlled delivery of multiple proteins, Adv. Mater., 23, 4279, 10.1002/adma.201100060 Hudalla, 2011, Surfaces that sequester serum-borne heparin amplify growth factor activity, Adv. Mater., 23, 5415, 10.1002/adma.201103046 Hudalla, 2011, Harnessing endogenous growth factor activity modulates stem cell behavior, Integr. Biol. (Camb.), 3, 832, 10.1039/c1ib00021g Hudalla, 2010, Immobilization of peptides with distinct biological activities onto stem cell culture substrates using orthogonal chemistries, Langmuir, 26, 6449, 10.1021/la1008208 Benoit, 2007, Multifunctional hydrogels that promote osteogenic hMSC differentiation through stimulation and sequestering of BMP2, Adv. Funct. Mater., 17, 2085, 10.1002/adfm.200700012 Seto, 2012, Differentiation of mesenchymal stem cells in heparin-containing hydrogels via coculture with osteoblasts, Cell Tissue Res., 347, 589, 10.1007/s00441-011-1265-8 Lutolf, 2009, Designing materials to direct stem-cell fate, Nature, 462, 433, 10.1038/nature08602 Barker, 2014, Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration, Nat. Rev. Mol. Cell Biol., 15, 19, 10.1038/nrm3721 Sokol, 2016, Growth of human breast tissues from patient cells in 3D hydrogel scaffolds, Breast cancer research: BCR., 18, 19, 10.1186/s13058-016-0677-5