{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T17:46:02Z","timestamp":1790703962854,"version":"4.1.0"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T00:00:00Z","timestamp":1778112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioeng. Biotechnol."],"abstract":"<jats:p>Biliary atresia (BA), the leading cause of pediatric liver transplantation, is characterized by neonatal jaundice and progressive extrahepatic bile duct obstruction, yet its pathogenesis remains elusive. To uncover extrahepatic cholangiocyte injury, we generated patient-derived extrahepatic cholangiocyte organoids (EHCOs) from bile duct remnants of BA and controls. We performed discovery bulk RNA-seq followed by targeted molecular and functional validation. Transcriptomic profiling and pathway\/perturbation analyses revealed dysregulation of ER stress pathways, xenobiotics\/drug metabolism, and genes regulating cell adhesion and polarity. BA EHCOs exhibited altered expression of E-cadherin, RhoU, SOX17, and CFTR. ER stress markers PERK, BiP, and ATF4 were elevated, and TEM demonstrated abnormal ER morphology. Conversely, CHOP, ERO1A, WFS1, and SOD3 were downregulated, suggesting impaired ER stress resolution. Functionally, BA EHCOs were more susceptible to toxic injury, and CYP450 inhibition attenuated ER stress genes expression. Immunostaining of BA liver hilum biopsies confirmed elevated PERK and BiP. Together, these data identify unknown arms of ER stress and epithelial dysfunction as disease-relevant injury process of the extrahepatic biliary tree and potentially implicate xenobiotic metabolism as a modifiable driver.<\/jats:p>","DOI":"10.3389\/fbioe.2026.1777423","type":"journal-article","created":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T04:47:04Z","timestamp":1778129224000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Human biliary atresia extrahepatic cholangiocyte organoids express increased ER and oxidative stress, altered drug metabolism and cell polarity changes"],"prefix":"10.3389","volume":"14","author":[{"given":"Adi","family":"Har-Zahav","sequence":"first","affiliation":[{"name":"Gastroenterology, Nutrition and Liver Diseases, Schneider Children\u2019s Medical Center","place":["Petach-Tiqva, Israel"]},{"name":"Felsenstein Medical Research Center, Gray Faculty of Medical and Health Sciences, Tel-Aviv University","place":["Tel-Aviv, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yara","family":"Hamoudi","sequence":"additional","affiliation":[{"name":"Felsenstein Medical Research Center, Gray Faculty of Medical and Health Sciences, Tel-Aviv University","place":["Tel-Aviv, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keren","family":"Danan","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University","place":["Tel Aviv, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Tobar","sequence":"additional","affiliation":[{"name":"Department of Pathology, Beilinson Medical Center","place":["Petach-Tiqva, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michal","family":"Bespalchik","sequence":"additional","affiliation":[{"name":"Felsenstein Medical Research Center, Gray Faculty of Medical and Health Sciences, Tel-Aviv University","place":["Tel-Aviv, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Gurevich","sequence":"additional","affiliation":[{"name":"Pediatric Liver Transplant Unit, Schneider Children\u2019s Medical Center","place":["Petach-Tiqva, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raanan","family":"Shamir","sequence":"additional","affiliation":[{"name":"Gastroenterology, Nutrition and Liver Diseases, Schneider Children\u2019s Medical Center","place":["Petach-Tiqva, Israel"]},{"name":"Felsenstein Medical Research Center, Gray Faculty of Medical and Health Sciences, Tel-Aviv University","place":["Tel-Aviv, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irit","family":"Gat-Viks","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University","place":["Tel Aviv, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orith","family":"Waisbourd-Zinman","sequence":"additional","affiliation":[{"name":"Gastroenterology, Nutrition and Liver Diseases, Schneider Children\u2019s Medical Center","place":["Petach-Tiqva, Israel"]},{"name":"Felsenstein Medical Research Center, Gray Faculty of Medical and Health Sciences, Tel-Aviv University","place":["Tel-Aviv, Israel"]},{"name":"Children\u2019s Hospital of Philadelphia, University of Pennsylvania","place":["Philadelphia, PA, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,5,7]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1002\/hep.32107","article-title":"Biliary organoids uncover delayed epithelial development and barrier function in biliary atresia","volume":"75","author":"Amarachintha","year":"2022","journal-title":"Hepatology"},{"key":"B2","doi-asserted-by":"publisher","first-page":"1391","DOI":"10.1016\/j.jhep.2020.06.012","article-title":"Beta-amyloid deposition around hepatic bile ducts is a novel pathobiological and diagnostic feature of biliary atresia","volume":"73","author":"Babu","year":"2020","journal-title":"J. Hepatol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"e0172632","DOI":"10.1371\/journal.pone.0172632","article-title":"Englerin A induces an acute inflammatory response and reveals lipid metabolism and ER stress as targetable vulnerabilities in renal cell carcinoma","volume":"12","author":"Batova","year":"2017","journal-title":"PLoS ONE"},{"key":"B4","doi-asserted-by":"publisher","first-page":"1163","DOI":"10.1002\/hep.29905","article-title":"Biliary atresia: clinical and research challenges for the twenty-first century","volume":"68","author":"Bezerra","year":"2018","journal-title":"Hepatology"},{"key":"B5","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1038\/s41392-023-01570-w","article-title":"Endoplasmic reticulum stress: molecular mechanism and therapeutic targets","volume":"8","author":"Chen","year":"2023","journal-title":"Signal Transduct. Target Ther."},{"key":"B6","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1186\/s12894-024-01511-x","article-title":"The potential of organoids in renal cell carcinoma research","volume":"24","author":"Chen","year":"2024","journal-title":"BMC Urol."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1242\/dmm.041426","article-title":"Establishment and validation of an endoplasmic reticulum stress reporter to monitor zebrafish ATF6 activity in development and disease","volume":"13","author":"Clark","year":"2020","journal-title":"Dis. Model Mech."},{"key":"B8","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1016\/j.ydbio.2014.02.014","article-title":"The atypical rho GTPase, RhoU, regulates cell-adhesion molecules during cardiac morphogenesis","volume":"389","author":"Dickover","year":"2014","journal-title":"Dev. Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1080\/17461391.2018.1561950","article-title":"Effects of a resistance-training programme on endoplasmic reticulum unfolded protein response and mitochondrial functions in PBMCs from elderly subjects","volume":"19","author":"Est\u00e9banez","year":"2019","journal-title":"Eur. J. Sport Sci."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e00211","DOI":"10.1002\/prp2.211","article-title":"Role of endoplasmic reticulum stress in drug-induced toxicity","volume":"4","author":"Foufelle","year":"2016","journal-title":"Pharmacol. Res. Perspect."},{"key":"B11","doi-asserted-by":"publisher","first-page":"7599","DOI":"10.1038\/s41598-020-64503-5","article-title":"Extrahepatic cholangiocyte obstruction is mediated by decreased glutathione, wnt and notch signaling pathways in a toxic model of biliary atresia","volume":"10","author":"Fried","year":"2020","journal-title":"Sci. Rep."},{"key":"B12","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1038\/s41390-024-03335-9","article-title":"Biliary atresia: insights into mechanisms using a toxic model of the disease including wnt and hippo signaling pathways and microtubules","volume":"97","author":"Fried","year":"2025","journal-title":"Pediatr. Res."},{"key":"B13","doi-asserted-by":"publisher","first-page":"100552","DOI":"10.1016\/j.cophys.2022.100552","article-title":"IRE1\/XBP1 and endoplasmic reticulum signaling - from basic to translational research for cardiovascular disease","volume":"28","author":"Fu","year":"2022","journal-title":"Curr. Opin. Physiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1536","DOI":"10.1091\/mbc.E16-01-0039","article-title":"Transcription factor ATF4 directs basal and stress-induced gene expression in the unfolded protein response and cholesterol metabolism in the liver","volume":"27","author":"Fusakio","year":"2016","journal-title":"Mol. Biol. Cell"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a029181","article-title":"Cell-cell junctions organize structural and signaling networks","volume":"10","author":"Garcia","year":"2018","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1385","DOI":"10.1016\/j.jhep.2023.07.039","article-title":"Biliary atresia is associated with polygenic susceptibility in ciliogenesis and planar polarity effector genes","volume":"79","author":"Glessner","year":"2023","journal-title":"J. Hepatol."},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3390\/cells9051078","article-title":"Characterization of endoplasmic reticulum (ER) in human pluripotent stem cells revealed increased susceptibility to cell death upon ER stress","volume":"9","author":"Ha","year":"2020","journal-title":"Cells"},{"key":"B18","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1038\/ncb2738","article-title":"ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death","volume":"15","author":"Han","year":"2013","journal-title":"Nat. Cell Biol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"3787","DOI":"10.1091\/mbc.10.11.3787","article-title":"Mammalian transcription factor ATF6 is synthesized as a transmembrane protein and activated by proteolysis in response to endoplasmic reticulum stress","volume":"10","author":"Haze","year":"1999","journal-title":"Mol. Biol. Cell"},{"key":"B20","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/nrm3270","article-title":"The unfolded protein response: controlling cell fate decisions under ER stress and beyond","volume":"13","author":"Hetz","year":"2012","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1080\/21541248.2017.1362495","article-title":"Regulation and functions of RhoU and RhoV","volume":"11","author":"Hodge","year":"2020","journal-title":"Small GTPases"},{"key":"B22","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1007\/s10565-021-09689-8","article-title":"The endoplasmic reticulum participated in drug metabolic toxicity","volume":"38","author":"Huang","year":"2022","journal-title":"Cell Biol. Toxicol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1161\/CIRCRESAHA.116.310266","article-title":"ATF6 decreases myocardial ischemia\/reperfusion damage and links ER stress and oxidative stress signaling pathways in the heart","volume":"120","author":"Jin","year":"2017","journal-title":"Circ. Res."},{"key":"B24","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.3389\/fimmu.2018.01289","article-title":"IRE1\u03b1 implications in endoplasmic reticulum stress-mediated development and pathogenesis of autoimmune diseases","volume":"9","author":"Junjappa","year":"2018","journal-title":"Front. Immunol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"L27","DOI":"10.1152\/ajplung.00174.2011","article-title":"Hyperoxia-induced activation of the integrated stress response in the newborn rat lung","volume":"302","author":"Konsavage","year":"2012","journal-title":"Am. J. Physiol. Lung Cell Mol. Physiol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1038\/s41594-019-0324-9","article-title":"UPR proteins IRE1 and PERK switch BiP from chaperone to ER stress sensor","volume":"26","author":"Kopp","year":"2019","journal-title":"Nat. Struct. Mol. Biol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"101206","DOI":"10.1016\/j.xcrm.2023.101206","article-title":"Ablation of ERO1A induces lethal endoplasmic reticulum stress responses and immunogenic cell death to activate anti-tumor immunity","volume":"4","author":"Liu","year":"2023","journal-title":"Cell Rep. Med."},{"key":"B28","doi-asserted-by":"publisher","first-page":"e4170","DOI":"10.1371\/journal.pone.0004170","article-title":"Divergent effects of PERK and IRE1 signaling on cell viability","volume":"4","author":"Lin","year":"2009","journal-title":"PLoS ONE"},{"key":"B29","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1007\/s00383-024-05798-7","article-title":"Animal and organoid models to elucidate the anti-fibrotic effect of steroid on biliary atresia","volume":"40","author":"Liu","year":"2024","journal-title":"Pediatr. Surg. Int."},{"key":"B30","doi-asserted-by":"publisher","first-page":"286ra67","DOI":"10.1126\/scitranslmed.aaa1652","article-title":"Identification of a plant isoflavonoid that causes biliary atresia","volume":"7","author":"Lorent","year":"2015","journal-title":"Sci. Transl. Med."},{"key":"B31","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"5244","DOI":"10.1167\/iovs.16-19232","article-title":"The role of IRE-XBP1 pathway in regulation of retinal pigment epithelium tight junctions","volume":"57","author":"Ma","year":"2016","journal-title":"Invest Ophthalmol. Vis. Sci."},{"key":"B33","doi-asserted-by":"publisher","first-page":"e000238","DOI":"10.1161\/JAHA.113.000238","article-title":"PERK-eIF2\u03b1-ATF4-CHOP signaling contributes to TNF\u03b1-induced vascular calcification","volume":"2","author":"Masuda","year":"2013","journal-title":"J. Am. Heart Assoc."},{"key":"B34","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1161\/CIRCRESAHA.117.310577","article-title":"A new role for the ER unfolded protein response mediator ATF6: induction of a generalized antioxidant program","volume":"120","author":"McKimpson","year":"2017","journal-title":"Circ. Res."},{"key":"B35","doi-asserted-by":"publisher","first-page":"2501","DOI":"10.1038\/s41467-022-30238-2","article-title":"Stress-induced protein disaggregation in the endoplasmic reticulum catalysed by BiP","volume":"13","author":"Melo","year":"2022","journal-title":"Nat. Commun."},{"key":"B36","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1097\/MOG.0000000000000996","article-title":"Tight junction proteins and biliary diseases","volume":"40","author":"Merlen","year":"2024","journal-title":"Curr. Opin. Gastroenterol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.3390\/ijms23052688","article-title":"CFTR, cell junctions and the cytoskeleton","volume":"23","author":"Pankonien","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"B38","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.biocel.2009.07.020","article-title":"Biliary differentiation and bile duct morphogenesis in development and disease","volume":"43","author":"Raynaud","year":"2011","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"2559","DOI":"10.1016\/j.cell.2022.05.013","article-title":"Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq","volume":"185","author":"Replogle","year":"2022","journal-title":"Cell"},{"key":"B40","doi-asserted-by":"publisher","first-page":"G741","DOI":"10.1152\/ajpgi.00389.2020","article-title":"Impact of hypoxia and AMPK on CFTR-mediated bicarbonate secretion in human cholangiocyte organoids","volume":"320","author":"Roos","year":"2021","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"e0009822","DOI":"10.1128\/jvi.00098-22","article-title":"Generation of human lung organoid cultures from healthy and tumor tissue to study infectious diseases","volume":"96","author":"Salgueiro","year":"2022","journal-title":"J. Virol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"6431","DOI":"10.3390\/ijms22126431","article-title":"Superoxide dismutase 3-Transduced mesenchymal stem cells preserve epithelial tight junction barrier in murine colitis and attenuate inflammatory damage in epithelial organoids","volume":"22","author":"Tak","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"B43","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1038\/s41572-024-00533-x","article-title":"Biliary atresia","volume":"10","author":"Tam","year":"2024","journal-title":"Nat. Rev. Dis. Prim."},{"key":"B44","doi-asserted-by":"publisher","first-page":"1884","DOI":"10.1038\/s41596-019-0168-0","article-title":"Isolation and propagation of primary human cholangiocyte organoids for the generation of bioengineered biliary tissue","volume":"14","author":"Tysoe","year":"2019","journal-title":"Nat. Protoc."},{"key":"B45","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1007\/s12072-014-9582-0","article-title":"Modulation of the unfolded protein response impedes tumor cell adaptation to proteotoxic stress: a PERK for hepatocellular carcinoma therapy","volume":"9","author":"Vandewynckel","year":"2015","journal-title":"Hepatol. Int."},{"key":"B46","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1038\/ncb3070","article-title":"SOX17 links gut endoderm morphogenesis and germ layer segregation","volume":"16","author":"Viotti","year":"2014","journal-title":"Nat. Cell Biol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1002\/hep.28599","article-title":"The toxin biliatresone causes mouse extrahepatic cholangiocyte damage and fibrosis through decreased glutathione and SOX17","volume":"64","author":"Waisbourd-Zinman","year":"2016","journal-title":"Hepatology"},{"key":"B48","doi-asserted-by":"publisher","first-page":"1867","DOI":"10.1016\/j.cell.2020.10.048","article-title":"Liver immune profiling reveals pathogenesis and therapeutics for biliary atresia","volume":"183","author":"Wang","year":"2020","journal-title":"Cell"},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.16732.1","article-title":"Recent advances in understanding biliary atresia","volume":"8","author":"Wehrman","year":"2019","journal-title":"F1000Res"},{"key":"B50","doi-asserted-by":"publisher","first-page":"G545","DOI":"10.1152\/ajpgi.00211.2022","article-title":"Increased activity of epithelial Cdc42 rho GTPase and tight junction permeability in the Cftr knockout intestine","volume":"327","author":"Woode","year":"2024","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"101","DOI":"10.3892\/ijmm.2017.2985","article-title":"Silencing of both ATF4 and PERK inhibits cell cycle progression and promotes the apoptosis of differentiating chondrocytes","volume":"40","author":"Wu","year":"2017","journal-title":"Int. J. Mol. Med."},{"key":"B52","doi-asserted-by":"publisher","first-page":"e1070","DOI":"10.1002\/ctm2.1070","article-title":"Single-cell and spatial transcriptomics reveal the fibrosis-related immune landscape of biliary atresia","volume":"12","author":"Ye","year":"2022","journal-title":"Clin. Transl. Med."},{"key":"B53","doi-asserted-by":"publisher","first-page":"152","DOI":"10.3389\/fnins.2017.00152","article-title":"Endoplasmic reticulum stress PERK-ATF4-CHOP pathway is associated with hypothalamic neuronal injury in different durations of stress in rats","volume":"11","author":"Yi","year":"2017","journal-title":"Front. Neurosci."},{"key":"B54","doi-asserted-by":"publisher","first-page":"173","DOI":"10.3892\/mmr.2019.10814","article-title":"Endoplasmic reticulum stress regulates epithelial-mesenchymal transition in human lens epithelial cells","volume":"21","author":"Zhou","year":"2020","journal-title":"Mol. Med. Rep."},{"key":"B55","doi-asserted-by":"publisher","first-page":"7262","DOI":"10.7150\/thno.49116","article-title":"Congenital biliary atresia is correlated with disrupted cell junctions and polarity caused by Cdc42 insufficiency in the liver","volume":"11","author":"Zhou","year":"2021","journal-title":"Theranostics"}],"container-title":["Frontiers in Bioengineering and Biotechnology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbioe.2026.1777423\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T04:47:15Z","timestamp":1778129235000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbioe.2026.1777423\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,7]]},"references-count":55,"alternative-id":["10.3389\/fbioe.2026.1777423"],"URL":"https:\/\/doi.org\/10.3389\/fbioe.2026.1777423","relation":{},"ISSN":["2296-4185"],"issn-type":[{"value":"2296-4185","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,7]]},"article-number":"1777423"}}