03976nas a2200757   4500000000100000000000100001008004100002260001500043653002000058653003100078653002600109653001600135100002300151700002000174700001900194700001900213700002500232700001900257700001800276700002200294700002000316700001900336700001900355700002400374700002000398700002000418700002000438700001900458700002000477700001800497700001700515700002500532700003000557700001400587700001800601700002200619700001800641700001400659700001900673700001700692700002800709700001700737700002100754700002500775700002400800700002400824700002000848700002600868700002100894700001600915700001400931700001600945700001600961700002200977700002300999700001601022700002101038700002201059700002201081245015301103856004201256300001401298490000701312520187401319022002503193       2024                            d  c2024/09/0110aCROHN'S DISEASE10ainflammatory bowel disease10aINTESTINAL EPITHELIUM10aMETHYLATION1 aThomas W. Dennison1 aRachel D. Edgar1 aFelicity Payne1 aKomal M. Nayak1 aAlexander D. B. Ross1 aAurelie Cenier1 aClaire Glemas1 aFederica Giachero1 aApril R. Foster1 aRebecca Harris1 aJudith Kraiczy1 aCamilla Salvestrini1 aGeorgia Stavrou1 aFranco Torrente1 aKimberley Brook1 aClaire Trayers1 aRasa Elmentaite1 aGehad Youssef1 aBálint Tél1 aDouglas James Winton1 aNefeli Skoufou-Papoutsaki1 aSam Adler1 aPhilip Bufler1 aAline Azabdaftari1 aAndreas Jenke1 aNatasha G1 aNatasha Thomas1 aErasmo Miele1 aAbdulrahman Al-Mohammad1 aGreta Guarda1 aSubra Kugathasan1 aSuresh Venkateswaran1 aMenna R. Clatworthy1 aTomas Castro-Dopico1 aOndrej Suchanek1 aCaterina Strisciuglio1 aMarco Gasparetto1 aSeokjun Lee1 aXingze Xu1 aErica Bello1 aNamshik Han1 aDaniel R. Zerbino1 aSarah A. Teichmann1 aJosquin Nys1 aRobert Heuschkel1 aFrancesca Perrone1 aMatthias Zilbauer00aPatient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn’s Disease  uhttps://gut.bmj.com/content/73/9/1464  a1464-14770 v733 aObjective Epigenetic mechanisms, including DNA methylation (DNAm), have been proposed to play a key role in Crohn’s disease (CD) pathogenesis. However, the specific cell types and pathways affected as well as their potential impact on disease phenotype and outcome remain unknown. We set out to investigate the role of intestinal epithelial DNAm in CD pathogenesis.
Design We generated 312 intestinal epithelial organoids (IEOs) from mucosal biopsies of 168 patients with CD (n=72), UC (n=23) and healthy controls (n=73). We performed genome-wide molecular profiling including DNAm, bulk as well as single-cell RNA sequencing. Organoids were subjected to gene editing and the functional consequences of DNAm changes evaluated using an organoid-lymphocyte coculture and a nucleotide-binding oligomerisation domain, leucine-rich repeat and CARD domain containing 5 (NLRC5) dextran sulphate sodium (DSS) colitis knock-out mouse model.
Results We identified highly stable, CD-associated loss of DNAm at major histocompatibility complex (MHC) class 1 loci including NLRC5 and cognate gene upregulation. Single-cell RNA sequencing of primary mucosal tissue and IEOs confirmed the role of NLRC5 as transcriptional transactivator in the intestinal epithelium. Increased mucosal MHC-I and NLRC5 expression in adult and paediatric patients with CD was validated in additional cohorts and the functional role of MHC-I highlighted by demonstrating a relative protection from DSS-mediated mucosal inflammation in NLRC5-deficient mice. MHC-I DNAm in IEOs showed a significant correlation with CD disease phenotype and outcomes. Application of machine learning approaches enabled the development of a disease prognostic epigenetic molecular signature.
Conclusions Our study has identified epigenetically regulated intestinal epithelial MHC-I as a novel mechanism in CD pathogenesis.  a0017-5749, 1468-3288