参考文献
[1]Rosekrans S L,Baan B,Muncan V,et al.Esophageal development and epithelial homeostasis.Am J Physiol Gastrointest Liver Physiol,2015,309:G216-228.
[2]Nakagawa H,Whelan K,Lynch J P.Mechanisms of Barrett's oesophagus:intestinal differentiation,stem cells,and tissue models.Best Pract Res Clin Gastroenterol,2015,29:3-16.
[3]Quante M,Abrams J A,Lee Y,et al.Barrett esophagus:what a mouse model can teach us about human disease.Cell Cycle,2012,11:4328-4338.
[4]DoupéD P,Alcolea M P,Roshan A,et al.A single progenitor population switches behavior to maintain and repair esophageal epithelium.Science,2012,337:1091-1093.
[5]Blevins C H,Iyer P G,Vela M F,et al.The esophageal epithelial barrier in health and disease.Clin Gastroenterol Hepatol,2018,16:608-617.
[6]Karam S M.Lineage commitment and maturation of epithelial cells in the gut.Front Biosci,1999,4:D286-D298.
[7]Arnold K,Sarkar A,Yram M A,et al.Sox2(+)adult stem and progenitor cells are important for tissue regeneration and survival of mice.Cell Stem Cell,2011,9:317-329.
[8]Karam S M,Leblond C P.Identifying and counting epithelial cell types in the“corpus”of the mouse stomach.Anat Rec,1992,232:231-246.
[9]Barker N,Huch M,Kujala P,et al.Lgr5(+ve)stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro.Cell Stem Cell,2010,6:25-36.
[10]Willet S G,Mills J C.Stomach organ and cell lineage differentiation:from embryogenesis to adult homeostasis.Cell Mol Gastroenterol Hepatol,2016,2:546-559.
[11]Barker N,van de Wetering M,Clevers H.The intestinal stem cell.Genes Dev,2008,22:1856-1864.
[12]Barker N.Adult intestinal stem cells:critical drivers of epithelial homeostasis and regeneration.Nat Rev Mol Cell Biol,2014,15:19-33.
[13]Clevers H.The intestinal crypt,a prototype stem cell compartment.Cell,2013,154:274-284.
[14]Muñoz J,Stange D E,Schepers A G,et al.The Lgr5 intestinal stem cell signature:robust expression of proposed quiescent“+4”cell markers.Embo J,2012,31:3079-3091.
[15]de Sousa E M F,de Sauvage F J.Cellular plasticity in intestinal homeostasis and disease.Cell Stem Cell,2019,24:54-64.
[16]Wang Y,Song W,Wang J,et al.Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine.J Exp Med,2020,217:e20191130.
[17]Sato T,Vries R G,Snippert H J,et al.Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche.Nature,2009,459:262-265.
[18]Romito A,Cobellis G.Pluripotent stem cells:Current understanding and future directions.Stem Cells Int,2016,2016:9451492.
[19]Clevers H.Modeling Development and disease with organoids.Cell,2016,165:1586-1597.
[20]Kretzschmar K,Clevers H.Organoids:modeling development and the stem cell niche in a dish.Dev Cell,2016,38:590-600.
[21]Yin X,Mead B E,Safaee H,et al.Engineering stem cell organoids.Cell Stem Cell,2016,18:25-38.
[22]Osada S I,Wright C V.Xenopus nodal-related signaling is essential for mesendodermal patterning during early embryogenesis.Development,1999,126:3229-3240.
[23]McCracken K W,Aihara E,Martin B,et al.Wnt/beta-catenin promotes gastric fundus specification in mice and humans.Nature,2017,541:182-187.
[24]McCracken K W,Cata E M,Crawford C M,et al.Modelling human development and disease in pluripotent stem-cell-derived gastric organoids.Nature,2014,516:400-404.
[25]Munera J O,Sundaram N,Rankin S A,et al.Differentiation of human pluripotent stem cells into colonic organoids via transient activation of BMP signaling.Cell Stem Cell,2017,21:51-64.
[26]Spence J R,Mayhew C N,Rankin S A,et al.Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro.Nature,2011,470:105-109.
[27]Zhang Y,Yang Y,Jiang M,et al.3D Modeling of esophageal development using human PSCderived basal progenitors reveals a critical role for notch signaling.Cell Stem Cell,2018,23:516-529.
[28]Zorn A M,Wells J M.Vertebrate endoderm development and organ formation.Annu Rev Cell Dev Biol,2009,25:221-251.
[29]McCracken K W,Wells J M.Mechanisms of embryonic stomach development.Semin Cell Dev Biol,2017,66:36-42.
[30]Spence J R,Lauf R,Shroyer N F.Vertebrate intestinal endoderm development.Dev Dyn,2011,240:501-520.
[31]Koike H,Iwasawa K,Ouchi R,et al.Modelling human hepato-biliary-pancreatic organogenesis from the foregut-midgut boundary.Nature,2019,574:112-116.
[32]McCracken K W,Howell J C,Wells J M,et al.Generating human intestinal tissue from pluripotent stem cells in vitro.Nat Protoc,2011,6:1920-1928.
[33]Rustgi A K.3D human esophageal epithelium steps out from h PSCs.Cell Stem Cell,2018,23:460-462.
[34]Trisno S L,Philo K E D,McCracken K W,et al.Esophageal organoids from human pluripotent stem cells delineate Sox2 functions during esophageal specification.Cell Stem Cell,2018,23:501-515.
[35]Leushacke M,Barker N.Ex vivo culture of the intestinal epithelium:strategies and applications.Gut,2014,63:1345-1354.
[36]Yu Q,Kilik U,Holloway E M,et al.Charting human development using a multi-endodermal organ atlas and organoid models.Cell,2021,184:3281-3298.
[37]Zhang M,Liu Y,Chen Y G.Generation of 3D human gastrointestinal organoids:principle and applications.Cell Regen,2020,9:6.
[38]Li X,Ootani A,Kuo C.An air-liquid interface culture system for 3D organoid culture of diverse primary gastrointestinal tissues.Methods Mol Biol,2016,1422:33-40.
[39]Whelan K A,Muir A B,Nakagawa H.Esophageal 3D culture systems as modeling tools in esophageal epithelial pathobiology and personalized medicine.Cell Mol Gastroenterol Hepatol,2018,5:461-478.
[40]DeWard A D,Cramer J,Lagasse E.Cellular heterogeneity in the mouse esophagus implicates the presence of a nonquiescent epithelial stem cell population.Cell Rep,2014,9:701-711.
[41]Jeong Y,Rhee H,Martin S,et al.Identification and genetic manipulation of human and mouse oesophageal stem cells.Gut,2016,65:1077-1086.
[42]Giroux V,Lento A A,Islam M,et al.Long-lived keratin 15+esophageal progenitor cells contribute to homeostasis and regeneration.J Clin Invest,2017,127:2378-2391.
[43]Kim T H,Shivdasani R A.Stomach development,stem cells and disease.Development,2016,143:554-565.
[44]Leushacke M,Tan S H,Wong A,et al.Lgr5-expressing chief cells drive epithelial regeneration and cancer in the oxyntic stomach.Nat Cell Biol,2017,19:774-786.
[45]Stange D E,Koo B K,Huch M,et al.Differentiated Troy+chief cells act as reserve stem cells to generate all lineages of the stomach epithelium.Cell,2013,155:357-368.
[46]Burclaff J,Willet S G,Sáenz J B,et al.Proliferation and differentiation of gastric mucous neck and chief cells during homeostasis and injury-induced metaplasia.Gastroenterology,2020,158:598-609.
[47]Busslinger G A,Weusten B L A,Bogte A,et al.Human gastrointestinal epithelia of the esophagus,stomach,and duodenum resolved at single-cell resolution.Cell Rep,2021,34:108819.
[48]Barker N,van Es J H,Kuipers J,et al.Identification of stem cells in small intestine and colon by marker gene Lgr5.Nature,2007,449:1003-1007.
[49]Sato T,Clevers H.Growing self-organizing mini-guts from a single intestinal stem cell:mechanism and applications.Science,2013,340:1190-1194.
[50]Jung P,Sato T,Merlos-Suárez A,et al.Isolation and in vitro expansion of human colonic stem cells.Nat Med,2011,17:1225-1227.
[51]Wang H,Yang Y,Liu J,et al.Direct cell reprogramming:approaches,mechanisms and progress.Nat Rev Mol Cell Biol,2021,22:410-424.
[52]Takahashi K,Tanabe K,Ohnuki M,et al.Induction of pluripotent stem cells from adult human fibroblasts by defined factors.Cell,2007,131:861-872.
[53]Takahashi K,Yamanaka S.Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.Cell,2006,126:663-676.
[54]Rony I K,Baten A,Bloomfield J A,et al.Inducing pluripotency in vitro:recent advances and highlights in induced pluripotent stem cells generation and pluripotency reprogramming.Cell Prolif,2015,48:140-156.
[55]Hou P,Li Y,Zhang X,et al.Pluripotent stem cells induced from mouse somatic cells by smallmolecule compounds.Science,2013,341:651-654.
[56]Spurrier R G,Speer A L,Hou X,et al.Murine and human tissue-engineered esophagus form from sufficient stem/progenitor cells and do not require microdesigned biomaterials.Tissue Eng Part A,2015,21:906-915.
[57]Nakagawa H,Kasagi Y,Karakasheva T A,et al.Modeling epithelial homeostasis and reactive epithelial changes in human and murine three-dimensional esophageal organoids.Curr Protoc Stem Cell Biol,2020,52:e106.
[58]Sachdeva U M,Shimonosono M,Flashner S,et al.Understanding the cellular origin and progression of esophageal cancer using esophageal organoids.Cancer Lett,2021,509:39-52.
[59]Dong J,Wu X,Zhou X,et al.Spatially-resolved expression landscape and gene-regulatory network of human gastric corpus epithelium.Protein&Cell,2022:pwac059.
[60]团体标准.人肠道类器官.T/CSCB,2022,2022:0013.
[61]团体标准.人肠癌类器官.T/CSCB,2022,2022:0014.
[62]Sato T,van Es J H,Snippert H J,et al.Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts.Nature,2011,469:415-418.
[63]Forbester J L,Goulding D,Vallier L,et al.Interaction of salmonella enterica serovar typhimurium with intestinal organoids derived from human induced pluripotent stem cells.Infect Immun,2015,83:2926-2934.
[64]Simmini S,Bialecka M,Huch M,et al.Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2.Nat Commun,2014,5:5728.
[65]Gu W,Wang H,Huang X,et al.SATB2 preserves colon stem cell identity and mediates ileumcolon conversion via enhancer remodeling.Cell Stem Cell,2022,29:101-115.
[66]Dekkers J F,van Vliet E J,Sachs N,et al.Long-term culture,genetic manipulation and xenotransplantation of human normal and breast cancer organoids.Nat Protoc,2021,16:1936-1965.
[67]Bartfeld S,Bayram T,van de Wetering M,et al.In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection.Gastroenterology,2015,148:126-136.
[68]Le Guen L,Marchal S,Faure S,et al.Mesenchymal-epithelial interactions during digestive tract development and epithelial stem cell regeneration.Cell Mol Life Sci,2015,72:3883-3896.(https://www.daowen.com)
[69]Loe A K H,Rao-Bhatia A,Kim J E,et al.Mesenchymal niches for digestive organ development,homeostasis,and disease.Trends Cell Biol,2021,31:152-165.
[70]Eicher A K,Kechele D O,Sundaram N,et al.Functional human gastrointestinal organoids can be engineered from three primary germ layers derived separately from pluripotent stem cells.Cell Stem Cell,2022,29:36-51.
[71]Workman M J,Mahe M M,Trisno S,et al.Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system.Nat Med,2017,23:49-59.
[72]Yui S,Azzolin L,Maimets M,et al.YAP/TAZ-dependent reprogramming of colonic epithelium links ECM remodeling to tissue regeneration.Cell Stem Cell,2018,22:35-49.
[73]Nusse Y M,Savage A K,Marangoni P,et al.Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche.Nature,2018,559:109-113.
[74]Wang Y,Chiang I L,Ohara T E,et al.Long-term culture captures injury-repair cycles of colonic stem cells.Cell,2019,179:1144-1159.
[75]Qu M,Xiong L,Lyu Y,et al.Establishment of intestinal organoid cultures modeling injuryassociated epithelial regeneration.Cell Res,2021,31:259-271.
[76]Castillo-Azofeifa D,Fazio E N,Nattiv R,et al.Atoh1(+)secretory progenitors possess renewal capacity independent of Lgr5(+)cells during colonic regeneration.EMBO J,2019,38:e99984.
[77]Sprangers J,Zaalberg I C,Maurice M M.Organoid-based modeling of intestinal development,regeneration,and repair.Cell Death Differ,2021,28:95-107.
[78]Dekkers J F,Wiegerinck C L,de Jonge H R,et al.A functional CFTR assay using primary cystic fibrosis intestinal organoids.Nat Med,2013,19:939-945.
[79]Dekkers J F,Berkers G,Kruisselbrink E,et al.Characterizing responses to CFTR-modulating drugs using rectal organoids derived from subjects with cystic fibrosis.Sci Transl Med,2016,8:344ra84.
[80]Min J,Vega P N,Engevik A C,et al.Heterogeneity and dynamics of active Kras-induced dysplastic lineages from mouse corpus stomach.Nat Commun,2019,10:5549.
[81]Soutto M,Chen Z,Bhat A A,et al.Activation of STAT3 signaling is mediated by TFF1 silencing in gastric neoplasia.Nat Commun,2019,10:3039.
[82]Bigorgne A E,Farin H F,Lemoine R,et al.TTC7A mutations disrupt intestinal epithelial apicobasal polarity.J Clin Invest,2014,124:328-337.
[83]Schwerd T,Bryant R V,Pandey S,et al.NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.Mucosal Immunol,2018,11:562-574.
[84]Wiegerinck C L,Janecke A R,Schneeberger K,et al.Loss of syntaxin 3 causes variant microvillus inclusion disease.Gastroenterology,2014,147:65-68.
[85]Drubin D G,Hyman A A.Stem cells:the new“model organism”.Mol Biol Cell,2017,28:1409-1411.
[86]Jiang M,Li H,Zhang Y,et al.Transitional basal cells at the squamous-columnar junction generate Barrett's oesophagus.Nature,2017,550:529-533.
[87]Kasagi Y,Chandramouleeswaran P M,Whelan K A,et al.The esophageal organoid system reveals functional interplay between notch and cytokines in reactive epithelial changes.Cell Mol Gastroenterol Hepatol,2018,5:333-352.
[88]Yeshi K,Ruscher R,Hunter L,et al.Revisiting inflammatory bowel disease:Pathology,treatments,challenges and emerging therapeutics including drug leads from natural products.J Clin Med,2020,9:1273.
[89]Dotti I,Mora-Buch R,Ferrer-Picón E,et al.Alterations in the epithelial stem cell compartment could contribute to permanent changes in the mucosa of patients with ulcerative colitis.Gut,2017,66:2069-2079.
[90]Howell K J,Kraiczy J,Nayak K M,et al.DNA methylation and transcription patterns in intestinal epithelial cells from pediatric patients with inflammatory bowel diseases differentiate disease subtypes and associate with outcome.Gastroenterology,2018,154:585-598.
[91]Wehkamp J,Schmid M,Stange E F.Defensins and other antimicrobial peptides in inflammatory bowel disease.Curr Opin Gastroenterol,2007,23:370-378.
[92]Bartfeld S.Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids.Dev Biol,2016,420:262-270.
[93]Bertaux-Skeirik N,Feng R,Schumacher M A,et al.CD44 plays a functional role in Helicobacter pylori-induced epithelial cell proliferation.PLoS Pathog,2015,11:e1004663.
[94]Sebrell T A,Hashimi M,Sidar B,et al.A novel gastric spheroid co-culture model reveals chemokine-dependent recruitment of human dendritic cells to the gastric epithelium.Cell Mol Gastroenterol Hepatol,2019,8:157-171.
[95]Holokai L,Chakrabarti J,Broda T,et al.Increased programmed death-ligand 1 is an early epithelial cell response to Helicobacter pylori infection.PLoS Pathog,2019,15:e1007468.
[96]Morey P,Pfannkuch L,Pang E,et al.Helicobacter pylori depletes cholesterol in gastric glands to prevent interferon gamma signaling and escape the inflammatory response.Gastroenterology,2018,154:1391-1404.
[97]Ettayebi K,Crawford S E,Murakami K,et al.Replication of human noroviruses in stem cellderived human enteroids.Science,2016,353:1387-1393.
[98]Finkbeiner S R,Zeng X L,Utama B,et al.Stem cell-derived human intestinal organoids as an infection model for rotaviruses.mBio,2012,3:e00159-12.
[99]Yin Y,Bijvelds M,Dang W,et al.Modeling rotavirus infection and antiviral therapy using primary intestinal organoids.Antiviral Res,2015,123:120-131.
[100]Leslie J L,Huang S,Opp J S,et al.Persistence and toxin production by Clostridium difficile within human intestinal organoids result in disruption of epithelial paracellular barrier function.Infect Immun,2015,83:138-145.
[101]Engevik M A,Engevik K A,Yacyshyn M B,et al.Human Clostridium difficile infection:inhibition of NHE3 and microbiota profile.Am J Physiol Gastrointest Liver Physiol,2015,308:G497-509.
[102]Lamers M M,Beumer J,van der Vaart J,et al.SARS-Co V-2 productively infects human gut enterocytes.Science,2020,369:50-54.
[103]Zhou J,Li C,Liu X,et al.Infection of bat and human intestinal organoids by SARS-Co V-2.Nat Med,2020,26:1077-1083.
[104]Bray F,Ferlay J,Soerjomataram I,et al.Global cancer statistics 2018:GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.CA Cancer J Clin,2018,68:394-424.
[105]Lau H C H,Kranenburg O,Xiao H,et al.Organoid models of gastrointestinal cancers in basic and translational research.Nat Rev Gastroenterol Hepatol,2020,17:203-222.
[106]Mc Millin D W,Negri J M,Mitsiades C S.The role of tumour-stromal interactions in modifying drug response:challenges and opportunities.Nat Rev Drug Discov,2013,12:217-228.
[107]Hay M,Thomas D W,Craighead J L,et al.Clinical development success rates for investigational drugs.Nat Biotechnol,2014,32:40-51.
[108]Ben-David U,Siranosian B,Ha G,et al.Genetic and transcriptional evolution alters cancer cell line drug response.Nature,2018,560:325-330.
[109]Barbachano A,Fernandez-Barral A,Bustamante-Madrid P,et al.Organoids and colorectal cancer.Cancers(Basel),2021,13:2657.
[110]Fujii M,Shimokawa M,Date S,et al.A colorectal tumor organoid library demonstrates progressive loss of niche factor requirements during tumorigenesis.Cell Stem Cell,2016,18:827-838.
[111]van de Wetering M,Francies H E,Francis J M,et al.Prospective derivation of a living organoid biobank of colorectal cancer patients.Cell,2015,161:933-945.
[112]Sachdeva U M,Shimonosono M,Flashner S,et al.Understanding the cellular origin and progression of esophageal cancer using esophageal organoids.Cancer Lett,2021,509:39-52.
[113]Smyth E C,Lagergren J,Fitzgerald R C,et al.Oesophageal cancer.Nat Rev Dis Primers,2017,3:17048.
[114]Zheng B,Ko K P,Fang X,et al.A new murine esophageal organoid culture method and organoid-based model of esophageal squamous cell neoplasia.iScience,2021,24:103440.
[115]Wroblewski L E,Piazuelo M B,Chaturvedi R,et al.Helicobacter pylori targets cancerassociated apical-junctional constituents in gastroids and gastric epithelial cells.Gut,2015,64:720-730.
[116]Sebrell T A,Hashimi M,Sidar B,et al.A novel gastric spheroid co-culture model reveals chemokine-dependent recruitment of human dendritic cells to the gastric epithelium.Cell Mol Gastroenterol Hepatol,2019,8:157-171.
[117]Matano M,Date S,Shimokawa M,et al.Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids.Nat Med,2015,21:256-262.
[118]Drost J,van Jaarsveld R H,Ponsioen B,et al.Sequential cancer mutations in cultured human intestinal stem cells.Nature,2015,521:43-47.
[119]Kawasaki K,Fujii M,Sugimoto S,et al.Chromosome engineering of human colon-derived organoids to develop a model of traditional serrated adenoma.Gastroenterology,2020,158:638-651.
[120]Xu P,Becker H,Elizalde M,et al.Intestinal organoid culture model is a valuable system to study epithelial barrier function in IBD.Gut,2018,67:1905-1906.
[121]Pleguezuelos-Manzano C,Puschhof J,Rosendahl Huber A,et al.Mutational signature in colorectal cancer caused by genotoxic pks(+)E.coli.Nature,2020,580:269-273.
[122]Dekkers R,Vijftigschild LA,Vonk A M,et al.A bioassay using intestinal organoids to measure CFTR modulators in human plasma.J Cyst Fibros,2015,14:178-181.
[123]Vijftigschild L A,Berkers G,Dekkers J F,et al.β2-Adrenergic receptor agonists activate CFTR in intestinal organoids and subjects with cystic fibrosis.Eur Respir J,2016,48:768-779.
[124]Sayoc-Becerra A,Krishnan M,Fan S,et al.The JAK-inhibitor tofacitinib rescues human intestinal epithelial cells and colonoids from cytokine-induced barrier dysfunction.Inflamm Bowel Dis,2020,26:407-422.
[125]Lloyd K,Papoutsopoulou S,Smith E,et al.Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease.Dis Model Mech,2020,13:dmm044040.
[126]Tullie L,Jones B C,De Coppi P,et al.Building gut from scratch—progress and update of intestinal tissue engineering.Nat Rev Gastroenterol Hepatol,2022,19:417-431.
[127]Jensen T,Blanchette A,Vadasz S,et al.Biomimetic and synthetic esophageal tissue engineering.Biomaterials,2015,57:133-141.
[128]Fordham R P,Yui S,Hannan N R,et al.Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury.Cell Stem Cell,2013,13:734-744.
[129]Sugimoto S,Kobayashi E,Fujii M,et al.An organoid-based organ-repurposing approach to treat short bowel syndrome.Nature,2021,592:99-104.
[130]Nikolaev M,Mitrofanova O,Broguiere N,et al.Homeostatic mini-intestines through scaffoldguided organoid morphogenesis.Nature,2020,585:574-578.
[131]Meran L,Massie I,Campinoti S,et al.Engineering transplantable jejunal mucosal grafts using patient-derived organoids from children with intestinal failure.Nat Med,2020,26:1593-1601.
[132]Grikscheit T C,Ogilvie J B,Ochoa E R,et al.Tissue-engineered colon exhibits function in vivo.Surgery,2002,132:200-204.
[133]Cromeens B P,Liu Y,Stathopoulos J,et al.Production of tissue-engineered intestine from expanded enteroids.J Surg Res,2016,204:164-175.
[134]Purnell B A.Ethics of organoid research.Science,2017,355:257-259.
[135]Bredenoord A L,Clevers H,Knoblich J A.Human tissues in a dish:The research and ethical implications of organoid technology.Science,2017,355:eaaf9414.
[136]Arjmand B,Rabbani Z,Soveyzi F,et al.Advancement of organoid technology in regenerative medicine.Regen Eng Transl Med,2022:1-14.