Advances and applications of gut organoids: modeling intestinal diseases and therapeutic development

Abstract

Gut organoids are 3D cellular structures derived from adult or pluripotent stem cells, capable of closely replicating the physiological properties of the gut. These organoids serve as powerful tools for studying gut development and modeling the pathogenesis of intestinal diseases. This review provides an in-depth exploration of technological advancements and applications of gut organoids, with a focus on their construction methods. Additionally, the potential applications of gut organoids in disease modeling, microenvironmental simulation, and personalized medicine are summarized. This review aims to offer perspectives and directions for understanding the mechanisms of intestinal health and disease as well as for developing innovative therapeutic strategies.

Keywords

organoid / intestinal disease / personalized medicine / therapeutic strategy / microenvironment

References

[1] Chelakkot C , Ghim J , Ryu SH . Mechanisms regulating intestinal barrier integrity and its pathological implications. Exp Mol Med 2018; 50: 1- 9.

[2] Nyström EEL , Martinez-Abad B , Arike L , et al. An intercrypt subpopulation of goblet cells is essential for colonic mucus barrier function. Science (New York, N.Y.) 2021; 372: eabb1590.

[3] Clevers HC , Bevins CL . Paneth cells: maestros of the small intestinal crypts. Annu Rev Physiol 2013; 75: 289- 311.

[4] Beumer J , Clevers H . Cell fate specification and differentiation in the adult mammalian intestine. Nat Rev Mol Cell Biol 2021; 22: 39- 53.

[5] Gehart H , Clevers H . Tales from the crypt: new insights into intestinal stem cells. Nat Rev Gastroenterol Hepatol 2019; 16: 19- 34.

[6] Yu Q , Kilik U , Holloway EM , et al. Charting human development using a multi-endodermal organ atlas and organoid models,. Cell 2021; 184: 3281- 98.e22.

[7] Barker N . Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration. Nat Rev Mol Cell Biol 2014; 15: 19- 33.

[8] Rossi G , Manfrin A , Lutolf MP . Progress and potential in organoid research. Nat Rev Genet 2018; 19: 671- 87.

[9] Corrò C , Novellasdemunt L , Li VSW . A brief history of organoids. Am J Physiol Cell Physiol 2020; 319: C151- 65.

[10] Wilson HV . A new method by which sponges may be artificially reared. Science (New York, N.Y.) 1907; 25: 912- 5.

[11] Barker N , van Es JH , Kuipers J , et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 2007; 449: 1003- 7.

[12] Sato T , Vries RG , Snippert HJ , et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 2009; 459: 262- 5.

[13] Hung SSC , Khan S , Lo CY , et al. Drug discovery using induced pluripotent stem cell models of neurodegenerative and ocular diseases. Pharmacol Ther 2017; 177: 32- 43.

[14] Palasantzas V , Tamargo-Rubio I , Le K , et al. iPSC-derived organon-a-chip models for personalized human genetics and pharmacogenomics studies. Trends Genet 2023; 39: 268- 84.

[15] Chen L , Vasoya RP , Toke NH , et al. HNF4 regulates fatty acid oxidation and is required for renewal of intestinal stem cells in mice. Gastroenterology 2020; 158: 985- 99.e9.

[16] Chen L , Toke NH , Luo S , et al. A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity. Nat Genet 2019; 51: 777- 85.

[17] Chen L , Qiu X , Dupre A , et al. TGFB1 induces fetal reprogramming and enhances intestinal regeneration. Cell Stem Cell 2023; 30: 1520- 37.e8.

[18] Almeqdadi M , Mana MD , Roper J , et al. Gut organoids: mini-tissues in culture to study intestinal physiology and disease. Am J Physiol Cell Physiol 2019; 317: C405- 19.

[19] Artegiani B , Clevers H . Use and application of 3D-organoid technology. Hum Mol Genet 2018; 27: R99- R107.

[20] Fujii M , Matano M , Nanki K , et al. Efficient genetic engineering of human intestinal organoids using electroporation. Nat Protocols 2015; 10: 1474- 85.

[21] Tsakmaki A , Fonseca Pedro P , Bewick GA . 3D intestinal organoids in metabolic research: virtual reality in a dish. Curr Opin Pharmacol 2017; 37: 51- 8.

[22] Spence JR , Mayhew CN , Rankin SA , et al. Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature 2011; 470: 105- 9.

[23] McCracken KW , Howell JC , Wells JM , et al. Generating human intestinal tissue from pluripotent stem cells in vitro. Nat Protocols 2011; 6: 1920- 8.

[24] Wells JM , Spence JR . How to make an intestine. Development (Cambridge, England) 2014; 141: 752- 60.

[25] Hynds RE , Bonfanti P , Janes SM . Regenerating human epithelia with cultured stem cells: feeder cells, organoids and beyond. EMBO Mol Med 2018; 10: 139- 50.

[26] Broguiere N , Isenmann L , Hirt C , et al. Growth of epithelial organoids in a defined hydrogel. Advanced Materials (Deerfield Beach, Fla.) 2018; 30: e1801621.

[27] Jee J , Jeong SY , Kim HK , et al. In vivo evaluation of scaffolds compatible for colonoid engraftments onto injured mouse colon epithelium. FASEB J 2019; 33: 10116- 25.

[28] Capeling MM , Czerwinski M , Huang S , et al. Nonadhesive alginate hydrogels support growth of pluripotent stem cell-derived intestinal organoids. Stem Cell Rep 2019; 12: 381- 94.

[29] Rastogi P , Kandasubramanian B . Review of alginate-based hydrogel bioprinting for application in tissue engineering. Biofabrication 2019; 11: 042001.

[30] Varadarajan A , Kearney LT , Keum JK , et al. Effects of salt on phase behavior and rheological properties of Alginate-Chitosan polyelectrolyte complexes. Biomacromolecules 2023; 24: 2730- 40.

[31] Curvello R , Kerr G , Micati DJ , et al. Engineered plant-based nanocellulose hydrogel for small intestinal organoid growth. Advanced Sci (Weinheim, Baden-Wurttemberg, Germany) 2020; 8: 2002135.

[32] Ogawa I , Onozato D , Anno S , et al. Suspension culture of human induced pluripotent stem cell-derived intestinal organoids using natural polysaccharides. Biomaterials 2022; 288: 121696.

[33] Ma W , Zheng Y , Yang G , et al. A bioactive calcium silicate nanowire-containing hydrogel for organoid formation and functionalization. Mater Horiz 2024; 11: 2957- 73.

[34] Gjorevski N , Sachs N , Manfrin A , et al. Designer matrices for intestinal stem cell and organoid culture. Nature 2016; 539: 560- 4.

[35] Cruz-Acuña R , Quirós M , Huang S , et al. PEG-4MAL hydrogels for human organoid generation, culture, and in vivo delivery. Nat Protocols 2018; 13: 2102- 19.

[36] Bergenheim F , Fregni G , Buchanan CF , et al. A fully defined 3D matrix for ex vivo expansion of human colonic organoids from biopsy tissue. Biomaterials 2020; 262: 120248.

[37] Yokota J , Yamashita T , Inui T , et al. Comparison of culture media for human intestinal organoids from the viewpoint of pharmacokinetic studies. Biochem Biophys Res Commun 2021; 566: 115- 22.

[38] Hogenson TL , Xie H , Phillips WJ , et al. Culture media composition influences patient-derived organoid ability to predict therapeutic responses in gastrointestinal cancers. JCI Insight 2022; 7: e158060.

[39] He S , Lei P , Kang W , et al. Stiffness restricts the stemness of the intestinal stem cells and skews their differentiation toward goblet cells. Gastroenterology 2023; 164: 1137- 51.e15.

[40] Garreta E , Moya-Rull D , Marco A , et al. Natural hydrogels support kidney organoid generation and promote in vitro angiogenesis. Advanced Materials (Deerfield Beach, Fla.) 2024; 36: e2400306.

[41] Kim S , Min S , Choi YS , et al. Tissue extracellular matrix hydrogels as alternatives to Matrigel for culturing gastrointestinal organoids. Nat Commun 2022; 13: 1692.

[42] Curvello R , Alves D , Abud HE , et al. A thermo-responsive collagen-nanocellulose hydrogel for the growth of intestinal organoids. Mater Sci Eng C Mater Biol Appl 2021; 124: 112051.

[43] Yavitt FM , Brown TE , Hushka EA , et al. The effect of thiol structure on allyl sulfide photodegradable hydrogels and their application as a degradable scaffold for organoid passaging. Adv Mater 2020; 32: e1905366.

[44] Elomaa L , Gerbeth L , Almalla A , et al. Bioactive photocrosslinkable resin solely based on refined decellularized small intestine submucosa for vat photopolymerization of in vitro tissue mimics. Addit Manuf 2023; 64: 103439.

[45] Xie D , Chen B , Xue Y , et al. Printable and biocompatible hydrogels for residual-free and high-throughput printing patient-derived organoid biochips,. Sci China Mater 2024; 67: 2505- 14.

[46] Min S , Kim S , Cho SW . Gastrointestinal tract modeling using organoids engineered with cellular and microbiota niches. Exp Mol Medi 2020; 52: 227- 37.

[47] Magré L , Verstegen MMA , Buschow S , et al. Emerging organoid-immune co-culture models for cancer research: from oncoimmunology to personalized immunotherapies. J ImmunoTher Cancer 2023; 11: e006290.

[48] Schuth S , Le Blanc S , Krieger TG , et al. Patient-specific modeling of stroma-mediated chemoresistance of pancreatic cancer using a three-dimensional organoid-fibroblast co-culture system. J Exp Clin Cancer Res 2022; 41: 312.

[49] Jiang S , Deng T , Cheng H , et al. Macrophage-organoid co-culture model for identifying treatment strategies against macrophagerelated gemcitabine resistance. J Exp Clin Cancer Res 2023; 42: 199.

[50] Lago C , Gianesello M , Santomaso L , et al. Medulloblastoma and high-grade glioma organoids for drug screening, lineage tracing, co-culture and in vivo assay. Nat Protocols 2023; 18: 2143- 80.

[51] Kasendra M , Tovaglieri A , Sontheimer-Phelps A , et al. Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids. Sci Rep 2018; 8: 2871.

[52] Trapecar M , Wogram E , Svoboda D , et al. Human physiomimetic model integrating microphysiological systems of the gut, liver, and brain for studies of neurodegenerative diseases. Sci Adv 2021; 7: eabd1707.

[53] Subtil B , Iyer KK , Poel D , et al. Dendritic cell phenotype and function in a 3D co-culture model of patient-derived metastatic colorectal cancer organoids. Front Immunol 2023; 14: 1105244.

[54] Hammoudi N , Hamoudi S , Bonnereau J , et al. Autologous organoid co-culture model reveals T cell-driven epithelial cell death in Crohn's disease. Front Immunol 2022; 13: 1008456.

[55] Orge ID , Nogueira Pinto H , Silva MA , et al. Vascular units as advanced living materials for bottom-up engineering of perfusable 3D microvascular networks. Bioact Mater 2024; 38: 499- 511.

[56] Lin M , Hartl K , Heuberger J , et al. Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche. Nat Commun 2023; 14: 3025.

[57] Yetkin-Arik B , Jansen SA , Varderidou-Minasian S , et al. Mesenchymal stromal/stem cells promote intestinal epithelium regeneration after chemotherapy-induced damage. Stem Cell Res Therapy 2024; 15: 125.

[58] Chen J , Horiuchi S , Kuramochi S , et al. Human intestinal organoid-derived PDGFRα + mesenchymal stroma enables proliferation and maintenance of LGR4 + epithelial stem cells. Stem Cell Res Therapy 2024; 15: 16.

[59] Xu Y , Ren Z , Zeng F , et al. Cancer-associated fibroblast-derived WNT5A promotes cell proliferation, metastasis, stemness and glycolysis in gastric cancer via regulating HK2. World J Surg Oncol 2024; 22: 193.

[60] Calon A , Lonardo E , Berenguer-Llergo A , et al. Stromal gene expression defines poor-prognosis subtypes in colorectal cancer. Nat Genet 2015; 47: 320- 9.

[61] Isella C , Terrasi A , Bellomo SE , et al. Stromal contribution to the colorectal cancer transcriptome. Nat Genet 2015; 47: 312- 9.

[62] Takahashi Y , Sato S , Kurashima Y , et al. A refined culture system for human induced pluripotent stem cell-derived intestinal epithelial organoids. Stem Cell Rep 2018; 10: 314- 28.

[63] Luo X , Fong ELS , Zhu C , et al. Hydrogel-based colorectal cancer organoid co-culture models. Acta Biomater 2021; 132: 461- 72.

[64] Verhulsel M , Simon A , Bernheim-Dennery M , et al. Developing an advanced gut on chip model enabling the study of epithelial cell/fibroblast interactions. Lab Chip 2021; 21: 365- 77.

[65] Jowett GM , Norman MDA , Yu TTL , et al. ILC1 drive intestinal epithelial and matrix remodelling. Nat Mater 2021; 20: 250- 9.

[66] Lindemans CA , Calafiore M , Mertelsmann AM , et al. Interleukin-22 promotes intestinal-stem-cell-mediated epithelial regeneration. Nature 2015; 528: 560- 4.

[67] Hernández PP , Mahlakoiv T , Yang I , et al. Interferon-λ and interleukin 22 act synergistically for the induction of interferon-stimulated genes and control of rotavirus infection. Nat Immunol 2015; 16: 698- 707.

[68] Brice DP , Murray GI , Wilson HM , et al. Interleukin-27 regulates the function of the gastrointestinal epithelial barrier in a human tissue-derived organoid model. Biology 2022; 11: 427.

[69] Kumar BV , Connors TJ , Farber DL . Human T cell development, localization, and function throughout life. Immunity 2018; 48: 202- 13.

[70] Lee CZW , Ginhoux F . Biology of resident tissue macrophages. Development (Cambridge, England) 2022; 149: dev200270.

[71] Staab JF , Lemme-Dumit JM , Latanich R , et al. Co-culture system of human enteroids/colonoids with innate immune cells. Curr Protocols Immunol 2020; 131: e113.

[72] Neal JT , Li X , Zhu J , et al. Organoid modeling of the tumor immune microenvironment. Cell 2018; 175: 1972- 88.e16.

[73] Múnera JO , Kechele DO , Bouffi C , et al. Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon. Cell Stem Cell 2023; 30: 1434- 51. e9.

[74] Hentschel V , Govindarajan D , Seufferlein T , et al. An adaptable protocol to generate a murine enteroid-macrophage co-culture system. Int J Mol Sci 2024; 25: 7944.

[75] Kakni P , Truckenmüller R , Habibović P , et al. A microwell-based intestinal organoid-macrophage co-culture system to study intestinal inflammation. Int J Mol Sci 2022; 23: 15364.

[76] Bouffi C , Wikenheiser-Brokamp KA , Chaturvedi P , et al. In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice. Nat Biotechnol 2023; 41: 824- 31.

[77] Sharkey KA , Mawe GM . The enteric nervous system. Physiol Rev 2023; 103: 1487- 564.

[78] Workman MJ , Mahe MM , Trisno S , et al. Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system. Nat Med 2017; 23: 49- 59.

[79] Llorente C . Isolation of myenteric and submucosal plexus from mouse gastrointestinal tract and subsequent co-culture with small intestinal organoids. Cells 2024; 13: 820.

[80] Cortez AR , Poling HM , Brown NE , et al. Transplantation of human intestinal organoids into the mouse mesentery: A more physiologic and anatomic engraftment site. Surgery 2018; 164: 643- 50.

[81] Huang J , Xu Z , Jiao J , et al. Microfluidic intestinal organoid-on-a-chip uncovers therapeutic targets by recapitulating oxygen dynamics of intestinal IR injury. Bioact Mater 2023; 30: 1- 14.

[82] Rajasekar S , Lin DSY , Abdul L , et al. IFlowPlate-A customized 384- well plate for the culture of perfusable vascularized colon organoids. Adv Mater 2020; 32: e2002974.

[83] Park SE , Kang S , Paek J , et al. Geometric engineering of organoid culture for enhanced organogenesis in a dish. Nat Methods 2022; 19: 1449- 60.

[84] Palikuqi B , Nguyen DT , Li G , et al. Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. Nature 2020; 585: 426- 32.

[85] Wen Z , Orduno M , Liang Z , et al. Optimization of vascularized intestinal organoid model. Adv Healthcare Mater 2024; 13: e2400977.

[86] Puschhof J , Pleguezuelos-Manzano C , Martinez-Silgado A , et al. Intestinal organoid cocultures with microbes. Nat Protocols 2021; 16: 4633- 49.

[87] Andersson-Rolf A , Fink J , Mustata RC , et al. A video protocol of retroviral infection in primary intestinal organoid culture. J Vis Exp 2014: e51765.

[88] Holthaus D , Delgado-Betancourt E , Aebischer T , et al. Harmonization of protocols for multi-species organoid platforms to study the intestinal biology of toxoplasma gondii and other protozoan infections. Front Cell Infect Microbiol 2020; 10: 610368.

[89] Huang J , Zhou C , Zhou G , et al. Effect of Listeria monocytogenes on intestinal stem cells in the co-culture model of small intestinal organoids. Microb Pathog 2021; 153: 104776.

[90] Iftekhar A , Berger H , Bouznad N , et al. Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells. Nat Commun 2021; 12: 1003.

[91] Nickerson KP , Llanos-Chea A , Ingano L , et al. A versatile human intestinal organoid-derived epithelial monolayer model for the study of enteric pathogens. Microbiol Spectrum 2021; 9: e0000321.

[92] Sasaki N , Miyamoto K , Maslowski KM , et al. Development of a scalable coculture system for gut anaerobes and human colon epithelium. Gastroenterology 2020; 159: 388- 90.e5.

[93] Co JY , Margalef-Català M , Li X , et al. Controlling epithelial polarity: a human enteroid model for host-pathogen interactions. Cell Reports 2019; 26: 2509- 20.e4.

[94] Horvath TD , Haidacher SJ , Engevik MA , et al. Interrogation of the mammalian gut-brain axis using LC-MS/MS-based targeted metabolomics with in vitro bacterial and organoid cultures and in vivo gnotobiotic mouse models. Nat Protocols 2023; 18: 490- 529.

[95] Zhang YG , Wu S , Xia Y , et al. Salmonella-infected crypt-derived intestinal organoid culture system for host-bacterial interactions. Physiological Reports 2014; 2: e12147.

[96] Bozzetti V , Senger S . Organoid technologies for the study of intestinal microbiota-host interactions. Trends Mol Med 2022; 28: 290- 303.

[97] Zhang J , Hernandez-Gordillo V , Trapecar M , et al. Coculture of primary human colon monolayer with human gut bacteria. Nat Protocols 2021; 16: 3874- 900.

[98] Kim R , Attayek PJ , Wang Y , et al. An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface. Biofabrication 2019; 12: 015006.

[99] Li T , Ding N , Guo H , et al. A gut microbiota-bile acid axis promotes intestinal homeostasis upon aspirin-mediated damage. Cell Host Microbe 2024; 32: 191- 208.e9.

[100] Ahmad V , Yeddula SGR , Telugu BP , et al. Development of polarity-reversed endometrial epithelial organoids. Reproduction 2024; 167: e230478.

[101] Joo SS , Gu BH , Park YJ , et al. Porcine intestinal apical-out organoid model for gut function study. Animals 2022; 12: 372.

[102] Csukovich G , Wagner M , Walter I , et al. Polarity reversal of canine intestinal organoids reduces proliferation and increases cell death. Cell Prolif 2024; 57: e13544.

[103] Dinteren SV , Araya-Cloutier C , Robaczewska E , et al. Switching the polarity of mouse enteroids affects the epithelial interplay with prenylated phenolics from licorice (Glycyrrhiza) roots. Food Function 2024; 15: 1852- 66.

[104] Kakni P , Jutten B , Teixeira Oliveira Carvalho D , et al. Hypoxia-tolerant apical-out intestinal organoids to model host-microbiome interactions. J Tissue Eng 2023; 14: 20417314221149208.

[105] Recaldin T , Steinacher L , Gjeta B , et al. Human organoids with an autologous tissue-resident immune compartment. Nature 2024; 633: 165- 73.

[106] Wallisch S , Neef SK , Denzinger L , et al. Protocol for establishing a coculture with fibroblasts and colorectal cancer organoids,. STAR Protocols 2023; 4: 102481.

[107] Fattahi F , Steinbeck JA , Kriks S , et al. Deriving human ENS lineages for cell therapy and drug discovery in Hirschsprung disease. Nature 2016; 531: 105- 9.

[108] Leslie JL , Huang S , Opp JS , et al. Persistence and toxin production by Clostridium difficile within human intestinal organoids result in disruption of epithelial paracellular barrier function. Infect Immun 2015; 83: 138- 45.

[109] Li J , Ma X , Chakravarti D , et al. Genetic and biological hallmarks of colorectal cancer. Genes Development 2021; 35: 787- 820.

[110] Vlachogiannis G , Hedayat S , Vatsiou A , et al. Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science (New York, N.Y.) 2018; 359: 920- 6.

[111] Li H , Feng H , Zhang T , et al. CircHAS2 activates CCNE2 to promote cell proliferation and sensitizes the response of colorectal cancer to anlotinib. Mol Cancer 2024; 23: 59.

[112] Dong C , Meng X , Zhang T , et al. Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome. Nat Methods 2024; 21: 1624- 33.

[113] Xu T , Li X , Zhao W , et al. SF3B3-regulated mTOR alternative splicing promotes colorectal cancer progression and metastasis. J Exp Clin cancer Res 2024; 43: 126.

[114] Kim N , Kwon J , Shin US , et al. Fisetin induces the upregulation of AKAP12 mRNA and anti-angiogenesis in a patient-derived organoid xenograft model. Biomed Pharmacother 2023; 167: 115613.

[115] Pilat JM , Brown RE , Chen Z , et al. SELENOP modifies sporadic colorectal carcinogenesis and WNT signaling activity through LRP5/6 interactions. J Clin Invest 2023; 133: e165988.

[116] Sane S , Srinivasan R , Potts RA , et al. UBXN2A suppresses the Rictor-mTORC2 signaling pathway, an established tumorigenic pathway in human colorectal cancer. Oncogene 2023; 42: 1763- 76.

[117] Jiang T , Qi J , Xue Z , et al. The m(6)A modification mediated-lncRNA POU6F2-AS1 reprograms fatty acid metabolism and facilitates the growth of colorectal cancer via upregulation of FASN. Mol Cancer 2024; 23: 55.

[118] Goto N , Westcott PMK , Goto S , et al. SOX17 enables immune evasion of early colorectal adenomas and cancers. Nature 2024; 627: 636- 45.

[119] Pennel KAF , Hatthakarnkul P , Wood CS , et al. JAK/STAT3 represents a therapeutic target for colorectal cancer patients with stromal-rich tumors. J Exp Clin Cancer Res 2024; 43: 64.

[120] Mosa MH , Michels BE , Menche C , et al. A Wnt-Induced phenotypic switch in cancer-associated fibroblasts inhibits EMT in colorectal cancer. Cancer Res 2020; 80: 5569- 82.

[121] Noben M , Verstockt B , Bruyn M . de, et al. Epithelial organoid cultures from patients with ulcerative colitis and Crohn's disease: a truly long-term model to study the molecular basis for inflammatory bowel disease? Gut 2017; 66: 2193- 5.

[122] Limanskiy V , Vyas A , Chaturvedi LS , et al. Harnessing the potential of gene editing technology using CRISPR in inflammatory bowel disease. World J Gastroenterol 2019; 25: 2177- 87.

[123] Geng Z , Zuo L , Li J , et al. Ginkgetin improved experimental colitis by inhibiting intestinal epithelial cell apoptosis through EGFR/PI3K/AKT signaling. FASEB J 2024; 38: e23817.

[124] Dong Y , Johnson BA , Ruan L , et al. Disruption of epithelium integrity by inflammation-associated fibroblasts through prostaglandin signaling. Sci Adv 2024; 10: eadj7666.

[125] Pavlidis P , Tsakmaki A , Treveil A , et al. Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease. Cell Reports 2022; 40: 111439.

[126] Chiriac MT , Hracsko Z , Günther C , et al. IL-20 controls resolution of experimental colitis by regulating epithelial IFN/STAT2 signalling. Gut 2024; 73: 282- 97.

[127] He GW , Lin L , DeMartino J , et al. Optimized human intestinal organoid model reveals interleukin-22-dependency of paneth cell formation. Cell Stem Cell 2022; 29: 1333- 45.e6.

[128] Lee C , Song JH , Cha YE , et al. Intestinal epithelial responses to IL-17 in adult stem cell-derived human intestinal organoids. J Crohns Colitis 2022; 16: 1911- 23.

[129] Choi EK , Rajendiran TM , Soni T , et al. The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease. Nat Commun 2024; 15: 4775.

[130] Liang X , Li C , Song J , et al. HucMSC-Exo promote mucosal healing in experimental colitis by accelerating intestinal stem cells and epithelium regeneration via Wnt signaling pathway. Int J Nanomedicine 2023; 18: 2799- 818.

[131] Deleu S , Arnauts K , Deprez L , et al. High acetate concentration protects intestinal barrier and exerts anti-inflammatory effects in organoid-derived epithelial monolayer cultures from patients with ulcerative colitis. Int J Mol Sci 2023; 24: 768.

[132] Ye J , Haskey N , Dadlani H , et al. Deletion of mucin 2 induces colitis with concomitant metabolic abnormalities in mice. Am J Physiol Gastrointest Liver Physiol 2021; 320: G791- 803.

[133] Jurickova I , Bonkowski E , Angerman E , et al. Eicosatetraynoic acid and butyrate regulate human intestinal organoid mitochondrial and extracellular matrix pathways implicated in Crohn's disease strictures. Inflamm Bowel Dis 2022; 28: 988- 1003.

[134] Gallagher K , Catesson A , Griffin JL , et al. Metabolomic analysis in inflammatory bowel disease: a systematic review. J Crohns Colitis 2021; 15: 813- 26.

[135] Sorrentino G , Perino A , Yildiz E , et al. Bile acids signal via TGR5 to activate intestinal stem cells and epithelial regeneration. Gastroenterology 2020; 159: 956- 68.e8.

[136] Lavelle A , Sokol H . Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatoly 2020; 17: 223- 37.

[137] Park JH , Lee JM , Lee EJ , et al. Indole-3-carbinol promotes goblet-cell differentiation regulating Wnt and Notch signaling pathways AhR-dependently. Mol Cells 2018; 41: 290- 300.

[138] Yang Q , Bermingham NA , Finegold MJ , et al. Requirement of Math1 for secretory cell lineage commitment in the mouse intestine. Science (New York, N.Y.) 2001; 294: 2155- 8.

[139] Giri R , Hoedt EC , Khushi S , et al. Secreted NF-κB suppressive microbial metabolites modulate gut inflammation. Cell Reports 2022; 39: 110646.

[140] Zhu Y , Wang Y , Xia G , et al. Oral delivery of bioactive glass-loaded core-shell hydrogel microspheres for effective treatment of inflammatory bowel disease. Advanced Sci (Weinheim, Baden-Wurttemberg, Germany) 2023; 10: e2207418.

[141] Kim MR , Cho SY , Lee HJ , et al. Schisandrin C improves leaky gut conditions in intestinal cell monolayer, organoid, and nematode models by increasing tight junction protein expression. Phytomedicine 2022; 103: 154209.

[142] Qu M , Xiong L , Lyu Y , et al. Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration. Cell Res 2021; 31: 259- 71.

[143] Lukonin I , Serra D , Challet Meylan L , et al. Phenotypic landscape of intestinal organoid regeneration. Nature 2020; 586: 275- 80.

[144] Yui S , Nakamura T , Sato T , et al. Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5⁺ stem cell. Nat Med 2012; 18: 618- 23.

[145] Teng L , Dedousis N , Adeshirlarijaney A , et al. Impaired intestinal free fatty acid transport followed by chylomicron malformation, not pancreatic insufficiency, cause metabolic defects in cystic fibrosis. J Lipid Res 2024; 65: 100551.

[146] Bierlaagh MC , Ramalho AS , Silva IAL , et al. Repeatability and reproducibility of the Forskolin-induced swelling (FIS) assay on intestinal organoids from people with Cystic Fibrosis. J Cyst Fibros 2024; 23: 693- 702.

[147] Cuyx S , Ramalho AS , Fieuws S , et al. Rectal organoid morphology analysis (ROMA) as a novel physiological assay for diagnostic classification in cystic fibrosis. Thorax 2024; 79: 834- 41.

[148] Bulcaen M , Kortleven P , Liu RB , et al. Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells. Cell Rep Med 2024; 5: 101544.

[149] Finkbeiner SR , Zeng XL , Utama B , et al. Stem cell-derived human intestinal organoids as an infection model for rotaviruses. mBio 2012; 3: e00159- 00112.

[150] Yin Y , Bijvelds M , Dang W , et al. Modeling rotavirus infection and antiviral therapy using primary intestinal organoids. Antiviral Res 2015; 123: 120- 31.

[151] Drummond CG , Bolock AM , Ma C , et al. Enteroviruses infect human enteroids and induce antiviral signaling in a cell lineage-specific manner. Proc Natl Acad Sci USA 2017; 114: 1672- 7.

[152] Holthaus D , Kraft MR , Krug SM , et al. Dissection of barrier dysfunction in organoid-derived human intestinal epithelia induced by giardia duodenalis. Gastroenterology 2022; 162: 844- 58.

[153] Catassi C , Verdu EF , Bai JC , et al. Coeliac disease. Lancet (London, England) 2022; 399: 2413- 26.

[154] Iversen R , Sollid LM . The immunobiology and pathogenesis of celiac disease. Annu Rev Pathol 2023; 18: 47- 70.

[155] Fais S , Maiuri L , Pallone F , et al. Gliadin induced changes in the expression of MHC-class II antigens by human small intestinal epithelium. Organ culture studies with coeliac disease mucosa. Gut 1992; 33: 472- 5.

[156] Dotsenko V , Sioofy-Khojine AB , Hyöty H , et al. Human intestinal organoid models for celiac disease research. Methods Cell Biol 2023; 179: 173- 93.

[157] Ribeiro M , Sousa T . de, Sabença C, et al. Advances in quantification and analysis of the celiac-related immunogenic potential of gluten. Compr Rev Food Sci Food Saf 2021; 20: 4278- 98.

[158] Verdu EF , Schuppan D . Co-factors, microbes, and immunogenetics in celiac disease to guide novel approaches for diagnosis and treatment. Gastroenterology 2021; 161: 1395- 411.e4.

[159] Conte M , Nigro F , Porpora M , et al. Gliadin peptide P31-43 induces mTOR/NFkβ activation and reduces autophagy: the role of lactobacillus paracasei CBA L74 postbiotc. Int J Mol Sci 2022; 23: 3655.

[160] Barone MV , Auricchio R , Nanayakkara M , et al. Pivotal role of inflammation in celiac disease. Int J Mol Sci 2022; 23: 7177.

[161] Santos AJM , van Unen V , Lin Z , et al. A human autoimmune organoid model reveals IL-7 function in coeliac disease. Nature 2024; 632: 401- 410.

[162] Day CP , Merlino G , Van Dyke T . Preclinical mouse cancer models: a maze of opportunities and challenges. Cell 2015; 163: 39- 53.

[163] Cekanova M , Rathore K . Animal models and therapeutic molecular targets of cancer: utility and limitations. Drug Design Dev Ther 2014; 8: 1911- 21.

[164] Bleijs M , van de Wetering M , Clevers H , et al. Xenograft and organoid model systems in cancer research. EMBO J 2019; 38: e101654.

[165] Kenny PA , Lee GY , Myers CA , et al. The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression. Mol Oncol 2007; 1: 84- 96.

[166] Stock K , Estrada MF , Vidic S , et al. Capturing tumor complexity in vitro: comparative analysis of 2D and 3D tumor models for drug discovery. Sci Rep 2016; 6: 28951.

[167] Porter RJ , Murray GI , McLean MH . Current concepts in tumourderived organoids. Br J Cancer 2020; 123: 1209- 18.

[168] Schutgens F , Clevers H . Human organoids: tools for understanding biology and treating diseases. Annu Rev Pathol 2020; 15: 211- 34.

[169] Wetering M . van de, Francies HE, Francis JM, et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell 2015; 161: 933- 45.

[170] Toden S , Ravindranathan P , Gu J , et al. Oligomeric proanthocyanidins (OPCs) target cancer stem-like cells and suppress tumor organoid formation in colorectal cancer. Sci Rep 2018; 8: 3335.

[171] Luo Z , Wang B , Luo F , et al. Establishment of a large-scale patient-derived high-risk colorectal adenoma organoid biobank for high-throughput and high-content drug screening. BMC Med 2023; 21: 336.

[172] Cartry J , Bedja S , Boilève A , et al. Implementing patient derived organoids in functional precision medicine for patients with advanced colorectal cancer. J Exp Clin Cancer Res 2023; 42: 281.

[173] Mao Y , Wang W , Yang J , et al. Drug repurposing screening and mechanism analysis based on human colorectal cancer organoids. Protein Cell 2024; 15: 285- 304.

[174] Zhang K , Xi J , Wang Y , et al. A microfluidic chip-based automated system for whole-course monitoring the drug responses of organoids. Anal Chem 2024; 96: 10092- 101.

[175] Inui T , Uraya Y , Yokota J , et al. Functional intestinal monolayers from organoids derived from human iPS cells for drug discovery research. Stem Cell Res Ther 2024; 15: 57.

[176] Mertens S , Huismans MA , Verissimo CS , et al. Drug-repurposing screen on patient-derived organoids identifies therapy-induced vulnerability in KRAS-mutant colon cancer. Cell Reports 2023; 42: 112324.

[177] Hao M , Cao Z , Wang Z , et al. Patient-derived organoid model in the prediction of chemotherapeutic drug response in colorectal cancer. ACS Biomater Sci Eng 2022; 8: 3515- 25.

[178] Toshimitsu K , Takano A , Fujii M , et al. Organoid screening reveals epigenetic vulnerabilities in human colorectal cancer. Nat Chem Biol 2022; 18: 605- 14.

[179] Zheng R , Yang W , Wen Y , et al. Dnah9 mutant mice and organoid models recapitulate the clinical features of patients with PCD and provide an excellent platform for drug screening. Cell Death Disease 2022; 13: 559.

[180] Tebon PJ , Wang B , Markowitz AL , et al. Drug screening at singleorganoid resolution via bioprinting and interferometry. Nat Commun 2023; 14: 3168.

[181] Zhu Y , Jiang D , Qiu Y , et al. Dynamic microphysiological system chip platform for high-throughput, customizable, and multi-dimensional drug screening. Bioact Mater 2024; 39: 59- 73.

[182] Deben C , Hoz E . C. De La, Compte ML, et al. OrBITS: label-free and time-lapse monitoring of patient derived organoids for advanced drug screening. Cellular Oncol (Dordrecht, Netherlands) 2023; 46: 299- 314.

[183] Lin L , Clevers H . Decoding endocrine cell differentiation: insights from high-throughput CRISPR screening in human gut organoids. Clin Translational Med 2024; 14: e1526.

[184] Brandenberg N , Hoehnel S , Kuttler F , et al. High-throughput automated organoid culture via stem-cell aggregation in microcavity arrays. Nat Biomed Eng 2020; 4: 863- 74.

[185] Li X , Fu G , Zhang L , et al. Assay establishment and validation of a high-throughput organoid-based drug screening platform. Stem Cell Res Ther 2022; 13: 219.

[186] Cai X , Li Y , Zheng J , et al. Modeling of senescence-related chemoresistance in ovarian cancer using data analysis and patient-derived organoids. Front Oncol 2023; 13: 1291559.

[187] Watson CL , Mahe MM , Múnera J , et al. An in vivo model of human small intestine using pluripotent stem cells. Nat Med 2014; 20: 1310- 4.

[188] Singh A , Poling HM , Sundaram N , et al. Evaluation of transplantation sites for human intestinal organoids. PLoS One 2020; 15: e0237885.

[189] Singh A , Poling HM , Chaturvedi P , et al. Transplanted human intestinal organoids: a resource for modeling human intestinal development. Development (Cambridge, England) 2023; 150: dev201416.

[190] Watanabe S , Kobayashi S , Ogasawara N , et al. Transplantation of intestinal organoids into a mouse model of colitis. Nat Protocols 2022; 17: 649- 71.

[191] Watanabe S , Ogasawara N , Kobayashi S , et al. Organoids transplantation as a new modality to design epithelial signature to create a membrane-protective sulfomucin-enriched segment. J Gastroenterol 2023; 58: 379- 93.

[192] Nash A , Lokhorst N , Veiseh O . Localized immunomodulation technologies to enable cellular and organoid transplantation. Trends Mol Med 2023; 29: 635- 45.

[193] Zhang FL , Hu Z , Wang YF , et al. Organoids transplantation attenuates intestinal ischemia/reperfusion injury in mice through L-Malic acid-mediated M2 macrophage polarization. Nat Commun 2023; 14: 6779.

[194] Cruz-Acuña R , Quirós M , Farkas AE , et al. Synthetic hydrogels for human intestinal organoid generation and colonic wound repair. Nat Cell Biol 2017; 19: 1326- 35.

[195] Huang J , Xu Z , Ren J . Small intestinalization of colon using ileum organoids. Trends Cell Biol 2021; 31: 517- 9.

[196] Sugimoto S , Kobayashi E , Fujii M , et al. An organoid-based organ-repurposing approach to treat short bowel syndrome. Nature 2021; 592: 99- 104.

RIGHTS & PERMISSIONS

The Author(s). Published by Oxford University Press on behalf of Higher Education Press.