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Olazagoitia-Garmendia A, Zhang L, Mera P, Godbout JK, Sebastian-DelaCruz M, Garcia-Santisteban I, Mendoza LM, Huerta A, Irastorza I, Bhagat G, Green PH, Herrero L, Serra D, Rodriguez JA, Verdu EF, He C, Bilbao JR, Castellanos-Rubio A. Gluten-induced RNA methylation changes regulate intestinal inflammation via allele-specific XPO1 translation in epithelial cells. Gut 2022; 71:68-76. [PMID: 33526437 PMCID: PMC8666699 DOI: 10.1136/gutjnl-2020-322566] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/23/2020] [Accepted: 01/17/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Coeliac disease (CD) is a complex autoimmune disorder that develops in genetically susceptible individuals. Dietary gluten triggers an immune response for which the only available treatment so far is a strict, lifelong gluten free diet. Human leucocyte antigen (HLA) genes and several non-HLA regions have been associated with the genetic susceptibility to CD, but their role in the pathogenesis of the disease is still essentially unknown, making it complicated to develop much needed non-dietary treatments. Here, we describe the functional involvement of a CD-associated single-nucleotide polymorphism (SNP) located in the 5'UTR of XPO1 in the inflammatory environment characteristic of the coeliac intestinal epithelium. DESIGN The function of the CD-associated SNP was investigated using an intestinal cell line heterozygous for the SNP, N6-methyladenosine (m6A)-related knock-out and HLA-DQ2 mice, and human samples from patients with CD. RESULTS Individuals harbouring the risk allele had higher m6A methylation in the 5'UTR of XPO1 RNA, rendering greater XPO1 protein amounts that led to downstream nuclear factor kappa B (NFkB) activity and subsequent inflammation. Furthermore, gluten exposure increased overall m6A methylation in humans as well as in in vitro and in vivo models. CONCLUSION We identify a novel m6A-XPO1-NFkB pathway that is activated in CD patients. The findings will prompt the development of new therapeutic approaches directed at m6A proteins and XPO1, a target under evaluation for the treatment of intestinal disorders.
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Affiliation(s)
- Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Linda Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Paula Mera
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie K Godbout
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Maialen Sebastian-DelaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iraia Garcia-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Luis Manuel Mendoza
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Alain Huerta
- Enfermedades Digestivas, Hospital de Galdakao-Usansolo, Galdacano, Spain
| | - Iñaki Irastorza
- Department of Pediatrics, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Govind Bhagat
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Peter H Green
- Celiac Disease Center, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Laura Herrero
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Dolors Serra
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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Liang W, Feng Z, Rao S, Xiao C, Xue X, Lin Z, Zhang Q, Qi W. Diarrhoea may be underestimated: a missing link in 2019 novel coronavirus. Gut 2020; 69:1141-1143. [PMID: 32102928 DOI: 10.1136/gutjnl-2020-320832] [Citation(s) in RCA: 251] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Weicheng Liang
- Cell-gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, China
| | - Zhijie Feng
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Shijiazhuang, China
| | - Shitao Rao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Cuicui Xiao
- Cell-gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, China
| | - Xingyang Xue
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Zexiao Lin
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, China.,Department of Medical Oncology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qi Zhang
- Cell-gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China .,Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, China
| | - Wei Qi
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Shijiazhuang, China
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Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M. DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development. Gut 2019; 68:49-61. [PMID: 29141958 PMCID: PMC6839835 DOI: 10.1136/gutjnl-2017-314817] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/06/2017] [Accepted: 10/15/2017] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited. DESIGN We performed genome-wide DNA methylation and transcriptomic profiling of human IEOs derived from paediatric/adult and fetal small and large bowel as well as matching purified human gut epithelium. Furthermore, organoids were subjected to in vitro differentiation and genome editing using CRISPR/Cas9 technology. RESULTS We discovered stable epigenetic signatures which define regional differences in gut epithelial function, including induction of segment-specific genes during cellular differentiation. Established DNA methylation profiles were independent of cellular environment since organoids retained their regional DNA methylation over prolonged culture periods. In contrast to paediatric and adult organoids, fetal gut-derived organoids showed distinct dynamic changes of DNA methylation and gene expression in culture, indicative of an in vitro maturation. By applying CRISPR/Cas9 genome editing to fetal organoids, we demonstrate that this process is partly regulated by TET1, an enzyme involved in the DNA demethylation process. Lastly, generating IEOs from a child diagnosed with gastric heterotopia revealed persistent and distinct disease-associated DNA methylation differences, highlighting the use of organoids as disease-specific research models. CONCLUSIONS Our study demonstrates striking similarities of epigenetic signatures in mucosa-derived IEOs with matching primary epithelium. Moreover, these results suggest that intestinal stem cell-intrinsic DNA methylation patterns establish and maintain regional gut specification and are involved in early epithelial development and disease.
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Affiliation(s)
- Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
| | - Komal M Nayak
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
| | - Kate J Howell
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Alexander Ross
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK,Anne McLaren Laboratory & Department of Surgery, Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jessica Forbester
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, UK
| | - Roxana Mustata
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK,Department of Genetics, University of Cambridge, Cambridge, UK
| | - Sally Perkins
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, UK
| | - Amanda Andersson-Rolf
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK,Department of Genetics, University of Cambridge, Cambridge, UK
| | - Esther Leenen
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
| | - Anke Liebert
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
| | - Ludovic Vallier
- Anne McLaren Laboratory & Department of Surgery, Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Philip C Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, UK
| | - Bon-Kyoung Koo
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK,Department of Genetics, University of Cambridge, Cambridge, UK
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK,Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, UK,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
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