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Dennison TW, Edgar RD, Payne F, Nayak KM, Ross ADB, Cenier A, Glemas C, Giachero F, Foster AR, Harris R, Kraiczy J, Salvestrini C, Stavrou G, Torrente F, Brook K, Trayers C, Elmentaite R, Youssef G, Tél B, Winton DJ, Skoufou-Papoutsaki N, Adler S, Bufler P, Azabdaftari A, Jenke A, G N, Thomas N, Miele E, Al-Mohammad A, Guarda G, Kugathasan S, Venkateswaran S, Clatworthy MR, Castro-Dopico T, Suchanek O, Strisciuglio C, Gasparetto M, Lee S, Xu X, Bello E, Han N, Zerbino DR, Teichmann SA, Nys J, Heuschkel R, Perrone F, Zilbauer M. Patient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn's Disease. Gut 2024:gutjnl-2024-332043. [PMID: 38857990 DOI: 10.1136/gutjnl-2024-332043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024]
Abstract
OBJECTIVE 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.
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Affiliation(s)
- Thomas W Dennison
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Rachel D Edgar
- European Bioinformatics Institute, Cambridge, Cambridgeshire, UK
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Felicity Payne
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Komal M Nayak
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Alexander D B Ross
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- University Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Aurelie Cenier
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Technische Universität München, ZIEL - Institute for Food & Health, Freising, Germany
| | - Claire Glemas
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Federica Giachero
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - April R Foster
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Rebecca Harris
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Georgia Stavrou
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Kimberley Brook
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Claire Trayers
- Department of Paediatric and Perinatal Pathology, Cambridge University Hospitals (CUH), Addenbrooke's Hospital, Cambridge, UK
| | | | - Gehad Youssef
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Bálint Tél
- Pediatric Center, MTA Center of Excellence, Semmelweis University, Budapest, Hungary
| | - Douglas James Winton
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Nefeli Skoufou-Papoutsaki
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Sam Adler
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Philip Bufler
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Aline Azabdaftari
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Jenke
- Department of Neonatology and General Pediatrics, Children's Hospital Kassel, Kassel, Germany
- Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education and Research (ZBAF), HELIOS University Hospital Wuppertal, Witten/Herdecke University, Wuppertal, Germany
| | - Natasha G
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Natasha Thomas
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Erasmo Miele
- Department of Translational Medical Science, Section of Pediatrics, University of Naples "Federico II", Naples, Italy
| | | | - Greta Guarda
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine (IRB), Università della Svizzera italiana, Bellinzona, Switzerland
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Tomas Castro-Dopico
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Caterina Strisciuglio
- Department of Woman, Child ad General and Specialistic Surgery, University of Campania " Vanvitelli", Naples, Italy
| | - Marco Gasparetto
- Norfolk and Norwich University Hospital, Jenny Lind Children's Hospital, Norwich, UK
| | - Seokjun Lee
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Xingze Xu
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Erica Bello
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Daniel R Zerbino
- European Bioinformatics Institute, Cambridge, Cambridgeshire, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- Dept Physics/Cavendish Laboratory, Theory of Condensed Matter, JJ Thomson Ave, Cambridge, UK
| | - Josquin Nys
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
| | - Francesca Perrone
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Matthias Zilbauer
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke's, Cambridge, UK
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2
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Wright AP, Harris S, Madden S, Reyes BR, Mulamula E, Gibson A, Rauch I, Constant DA, Nice TJ. Interferon regulatory factor 6 (IRF6) determines intestinal epithelial cell development and immunity. Mucosal Immunol 2024:S1933-0219(24)00032-1. [PMID: 38604478 DOI: 10.1016/j.mucimm.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024]
Abstract
Intestinal epithelial cell (IEC) responses to interferon (IFN) favor antiviral defense with minimal cytotoxicity, but IEC-specific factors that regulate these responses remain poorly understood. Interferon regulatory factors (IRFs) are a family of nine related transcription factors, and IRF6 is preferentially expressed by epithelial cells, but its roles in IEC immunity are unknown. In this study, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) screens found that Irf6 deficiency enhanced IFN-stimulated antiviral responses in transformed mouse IECs but not macrophages. Furthermore, knockout (KO) of Irf6 in IEC organoids resulted in profound changes to homeostasis and immunity gene expression. Irf6 KO organoids grew more slowly, and single-cell ribonucleic acid sequencing indicated reduced expression of genes in epithelial differentiation and immunity pathways. IFN-stimulated gene expression was also significantly different in Irf6 KO organoids, with increased expression of stress and apoptosis-associated genes. Functionally, the transcriptional changes in Irf6 KO organoids were associated with increased cytotoxicity upon IFN treatment or inflammasome activation. These data indicate a previously unappreciated role for IRF6 in IEC biology, including regulation of epithelial development and moderation of innate immune responses to minimize cytotoxicity and maintain barrier function.
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Affiliation(s)
- Austin P Wright
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Sydney Harris
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Shelby Madden
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Bryan Ramirez Reyes
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Ethan Mulamula
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Alexis Gibson
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - David A Constant
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | - Timothy J Nice
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA.
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3
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Beaumont M, Lencina C, Fève K, Barilly C, Le-Normand L, Combes S, Devailly G, Boudry G. Disruption of the primocolonizing microbiota alters epithelial homeostasis and imprints stem cells in the colon of neonatal piglets. FASEB J 2023; 37:e23149. [PMID: 37671857 DOI: 10.1096/fj.202301182r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/07/2023]
Abstract
The gut microbiota plays a key role in the postnatal development of the intestinal epithelium. However, the bacterial members of the primocolonizing microbiota driving these effects are not fully identified and the mechanisms underlying their long-term influence on epithelial homeostasis remain poorly described. Here, we used a model of newborn piglets treated during the first week of life with the antibiotic colistin in order to deplete specific gram-negative bacteria that are transiently dominant in the neonatal gut microbiota. Colistin depleted Proteobacteria and Fusobacteriota from the neonatal colon microbiota, reduced the bacterial predicted capacity to synthetize lipopolysaccharide (LPS), and increased the concentration of succinate in the colon. The colistin-induced disruption of the primocolonizing microbiota was associated with altered gene expression in the colon epithelium including a reduction of toll-like receptor 4 (TLR4) and lysozyme (LYZ). Our data obtained in porcine colonic organoid cell monolayers suggested that these effects were not driven by the variation of succinate or LPS levels nor by a direct effect of colistin on epithelial cells. The disruption of the primocolonizing microbiota imprinted colon epithelial stem cells since the expression of TLR4 and LYZ remained lower in organoids derived from colistin-treated piglet colonic crypts after several passages when compared to control piglets. Finally, the stable imprinting of LYZ in colon organoids was independent of the H3K4me3 level in its transcription start site. Altogether, our results show that disruption of the primocolonizing gut microbiota alters epithelial innate immunity in the colon and imprints stem cells, which could have long-term consequences for gut health.
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Affiliation(s)
- Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Corinne Lencina
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Katia Fève
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Céline Barilly
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | - Gaëlle Boudry
- Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint-Gilles, France
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4
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Kelly C, Jawahar J, Davey L, Everitt JI, Galanko JA, Anderson C, Avendano JE, McCann JR, Sartor RB, Valdivia RH, Rawls JF. Spontaneous episodic inflammation in the intestines of mice lacking HNF4A is driven by microbiota and associated with early life microbiota alterations. mBio 2023; 14:e0150423. [PMID: 37526424 PMCID: PMC10470520 DOI: 10.1128/mbio.01504-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 08/02/2023] Open
Abstract
The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals who mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. Whereas IBD clinical presentation is well described, how interactions between microbiota and host genotype impact early subclinical stages of the disease remains unclear. The transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has been associated with human IBD, and deletion of Hnf4a in intestinal epithelial cells (IECs) in mice (Hnf4aΔIEC) leads to spontaneous colonic inflammation by 6-12 mo of age. Here, we tested if pathology in Hnf4aΔIEC mice begins earlier in life and if microbiota contribute to that process. Longitudinal analysis revealed that Hnf4aΔIEC mice reared in specific pathogen-free (SPF) conditions develop episodic elevated fecal lipocalin 2 (Lcn2) and loose stools beginning by 4-5 wk of age. Lifetime cumulative Lcn2 levels correlated with histopathological features of colitis at 12 mo. Antibiotic and gnotobiotic tests showed that these phenotypes in Hnf4aΔIEC mice were dependent on microbiota. Fecal 16S rRNA gene sequencing in SPF Hnf4aΔIEC and control mice disclosed that genotype significantly contributed to differences in microbiota composition by 12 mo, and longitudinal analysis of the Hnf4aΔIEC mice with the highest lifetime cumulative Lcn2 revealed that microbial community differences emerged early in life when elevated fecal Lcn2 was first detected. These microbiota differences included enrichment of a novel phylogroup of Akkermansia muciniphila in Hnf4aΔIEC mice. We conclude that HNF4A functions in IEC to shape composition of the gut microbiota and protect against episodic inflammation induced by microbiota throughout the lifespan. IMPORTANCE The inflammatory bowel diseases (IBD), characterized by chronic inflammation of the intestine, affect millions of people around the world. Although significant advances have been made in the clinical management of IBD, the early subclinical stages of IBD are not well defined and are difficult to study in humans. This work explores the subclinical stages of disease in mice lacking the IBD-associated transcription factor HNF4A in the intestinal epithelium. Whereas these mice do not develop overt disease until late in adulthood, we find that they display episodic intestinal inflammation, loose stools, and microbiota changes beginning in very early life stages. Using germ-free and antibiotic-treatment experiments, we reveal that intestinal inflammation in these mice was dependent on the presence of microbiota. These results suggest that interactions between host genotype and microbiota can drive early subclinical pathologies that precede the overt onset of IBD and describe a mouse model to explore those important processes.
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Affiliation(s)
- Cecelia Kelly
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jayanth Jawahar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jeffrey I. Everitt
- Department of Pathology, Research Animal Pathology Core, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph A. Galanko
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chelsea Anderson
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan E. Avendano
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - R. Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
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Bootz-Maoz H, Simon A, Del Mare-Roumani S, Bennet Y, Toister E, Romano H, Zheng D, Amidror S, Elinav E, Yissachar N. Ex vivo intestinal permeability assay (X-IPA) for tracking barrier function dynamics. NPJ Biofilms Microbiomes 2023; 9:44. [PMID: 37400593 DOI: 10.1038/s41522-023-00409-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/09/2023] [Indexed: 07/05/2023] Open
Abstract
The intestinal epithelial barrier facilitates homeostatic host-microbiota interactions and immunological tolerance. However, mechanistic dissections of barrier dynamics following luminal stimulation pose a substantial challenge. Here, we describe an ex vivo intestinal permeability assay, X-IPA, for quantitative analysis of gut permeability dynamics at the whole-tissue level. We demonstrate that specific gut microbes and metabolites induce rapid, dose-dependent increases to gut permeability, thus providing a powerful approach for precise investigation of barrier functions.
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Affiliation(s)
- Hadar Bootz-Maoz
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Ariel Simon
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Sara Del Mare-Roumani
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yifat Bennet
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Einat Toister
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Hadar Romano
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Danping Zheng
- Systems Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
| | - Sivan Amidror
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
- Microbiome & Cancer Division, Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Nissan Yissachar
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
- Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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6
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Wei X, Tan X, Chen Q, Jiang Y, Wu G, Ma X, Fu J, Li Y, Gang K, Yang Q, Ni R, He J, Luo L. Extensive jejunal injury is repaired by migration and transdifferentiation of ileal enterocytes in zebrafish. Cell Rep 2023; 42:112660. [PMID: 37342912 DOI: 10.1016/j.celrep.2023.112660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/07/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
A major cause of intestinal failure (IF) is intestinal epithelium necrosis and massive loss of enterocytes, especially in the jejunum, the major intestinal segment in charge of nutrient absorption. However, mechanisms underlying jejunal epithelial regeneration after extensive loss of enterocytes remain elusive. Here, we apply a genetic ablation system to induce extensive damage to jejunal enterocytes in zebrafish, mimicking the jejunal epithelium necrosis that causes IF. In response to injury, proliferation and filopodia/lamellipodia drive anterior migration of the ileal enterocytes into the injured jejunum. The migrated fabp6+ ileal enterocytes transdifferentiate into fabp2+ jejunal enterocytes to fulfill the regeneration, consisting of dedifferentiation to precursor status followed by redifferentiation. The dedifferentiation is activated by the IL1β-NFκB axis, whose agonist promotes regeneration. Extensive jejunal epithelial damage is repaired by the migration and transdifferentiation of ileal enterocytes, revealing an intersegmental migration mechanism of intestinal regeneration and providing potential therapeutic targets for IF caused by jejunal epithelium necrosis.
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Affiliation(s)
- Xiangyong Wei
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Xinmiao Tan
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Qi Chen
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Yan Jiang
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Guozhen Wu
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Xue Ma
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Jialong Fu
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Yongyu Li
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Kai Gang
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Qifen Yang
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Ni
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Jianbo He
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Lingfei Luo
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, Chongqing 400715, China.
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7
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Massaquoi MS, Kong GL, Chilin-Fuentes D, Ngo JS, Horve PF, Melancon E, Hamilton MK, Eisen JS, Guillemin K. Cell-type-specific responses to the microbiota across all tissues of the larval zebrafish. Cell Rep 2023; 42:112095. [PMID: 36787219 PMCID: PMC10423310 DOI: 10.1016/j.celrep.2023.112095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/22/2022] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
Animal development proceeds in the presence of intimate microbial associations, but the extent to which different host cells across the body respond to resident microbes remains to be fully explored. Using the vertebrate model organism, the larval zebrafish, we assessed transcriptional responses to the microbiota across the entire body at single-cell resolution. We find that cell types across the body, not limited to tissues at host-microbe interfaces, respond to the microbiota. Responses are cell-type-specific, but across many tissues the microbiota enhances cell proliferation, increases metabolism, and stimulates a diversity of cellular activities, revealing roles for the microbiota in promoting developmental plasticity. This work provides a resource for exploring transcriptional responses to the microbiota across all cell types of the vertebrate body and generating new hypotheses about the interactions between vertebrate hosts and their microbiota.
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Affiliation(s)
- Michelle S Massaquoi
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Thermo Fisher Scientific, 29851 Willow Creek Road, Eugene, OR 97402, USA; Thermo Fisher Scientific, 22025 20th Avenue SE, Bothell, WA 98021, USA
| | - Garth L Kong
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
| | - Daisy Chilin-Fuentes
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
| | - Julia S Ngo
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
| | - Patrick F Horve
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
| | - Ellie Melancon
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
| | - M Kristina Hamilton
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA; Thermo Fisher Scientific, 29851 Willow Creek Road, Eugene, OR 97402, USA
| | - Judith S Eisen
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Humans and the Microbiome Program, CIFAR, Toronto, ON M5G 1M1, Canada.
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8
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Yang J, van Dijk TH, Koehorst M, Havinga R, de Boer JF, Kuipers F, van Zutphen T. Intestinal Farnesoid X Receptor Modulates Duodenal Surface Area but Does Not Control Glucose Absorption in Mice. Int J Mol Sci 2023; 24:ijms24044132. [PMID: 36835544 PMCID: PMC9961586 DOI: 10.3390/ijms24044132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/18/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Bile acids facilitate the intestinal absorption of dietary lipids and act as signalling molecules in the maintenance of metabolic homeostasis. Farnesoid X receptor (FXR) is a bile acid-responsive nuclear receptor involved in bile acid metabolism, as well as lipid and glucose homeostasis. Several studies have suggested a role of FXR in the control of genes regulating intestinal glucose handling. We applied a novel dual-label glucose kinetic approach in intestine-specific FXR-/- mice (iFXR-KO) to directly assess the role of intestinal FXR in glucose absorption. Although iFXR-KO mice showed decreased duodenal expression of hexokinase 1 (Hk1) under obesogenic conditions, the assessment of glucose fluxes in these mice did not show a role for intestinal FXR in glucose absorption. FXR activation with the specific agonist GS3972 induced Hk1, yet the glucose absorption rate remained unaffected. FXR activation increased the duodenal villus length in mice treated with GS3972, while stem cell proliferation remained unaffected. Accordingly, iFXR-KO mice on either chow, short or long-term HFD feeding displayed a shorter villus length in the duodenum compared to wild-type mice. These findings indicate that delayed glucose absorption reported in whole-body FXR-/- mice is not due to the absence of intestinal FXR. Yet, intestinal FXR does have a role in the small intestinal surface area.
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Affiliation(s)
- Jiufang Yang
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Theo H. van Dijk
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Martijn Koehorst
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Rick Havinga
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Jan Freark de Boer
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
- Correspondence: (F.K.); (T.v.Z.); Tel.: +31-58-288-2132 (F.K.)
| | - Tim van Zutphen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
- Faculty Campus Fryslân, University of Groningen, 8911CE Leeuwarden, The Netherlands
- Correspondence: (F.K.); (T.v.Z.); Tel.: +31-58-288-2132 (F.K.)
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9
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Jiang Q, Palombo V, Sherlock DN, Vailati-Riboni M, D’Andrea M, Yoon I, Loor JJ. Alterations in ileal transcriptomics during an intestinal barrier challenge in lactating Holstein cows fed a Saccharomyces cerevisiae fermentation product identify potential regulatory processes. J Anim Sci 2023; 101:skad277. [PMID: 37616596 PMCID: PMC10576520 DOI: 10.1093/jas/skad277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
Stressors such as lack of access to feed, hot temperatures, transportation, and pen changes can cause impairment of ruminal and intestinal barrier function, also known as "leaky gut". Despite the known benefits of some nutritional approaches during periods of stress, little is understood regarding the underlying mechanisms, especially in dairy cows. We evaluated the effect of feeding a Saccharomyces cerevisiae fermentation product (SCFP; NutriTek, Diamond V, Cedar Rapids, IA) on the ileal transcriptome in response to feed restriction (FR), an established model to induce intestinal barrier dysfunction. Multiparous cows [97.1 ± 7.6 days in milk (DIM); n = 5/group] fed a control diet or control plus 19 g/d SCFP for 9 wk were subjected to an FR challenge for 5 d during which they were fed 40% of their ad libitum intake from the 7 d before FR. All cows were slaughtered at the end of FR, and ileal scrapping RNA was used for RNAseq (NovaSeq 6000, 100 bp read length). Statistical analysis was performed in R and bioinformatics using the KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO databases. One thousand six hundred and ninety-six differentially expressed genes (DEG; FDR-adjusted P ≤ 0.10) were detected in SCFP vs. control, with 451 upregulated and 1,245 downregulated. "Mucin type O-glycan biosynthesis" was the top downregulated KEGG pathway due to downregulation of genes catalyzing glycosylation of mucins (GCNT3, GALNT5, B3GNT3, GALNT18, and GALNT14). An overall downregulation of cell and tissue structure genes (e.g., extracellular matrix proteins) associated with collagen (COL6A1, COL1A1, COL4A1, COL1A2, and COL6A2), laminin (LAMB2), and integrins (ITGA8, ITGA2, and ITGA5) also were detected with SCFP. A subset of DEG enriched in the GO term "extracellular exosome" and "extracellular space". Chemokines within "Cytokine-cytokine receptor interaction pathways" such as CCL16, CCL21, CCL14, CXCL12, and CXCL14 were downregulated by SCFP. The "Glutathione metabolism" pathway was upregulated by SCFP, including GSTA1 and RRM2B among the top upregulated genes, and GSTM1 and GPX8 as top downregulated genes. There were 9 homeobox transcription factors among the top 50 predicted transcription factors using the RNAseq DEG dataset, underscoring the importance of cell differentiation as a potential target of dietary SCFP. Taken together, SCFP downregulated immune-, ECM-, and mucin synthesis-related genes during FR. Homeobox transcription factors appear important for the transcriptional response of SCFP.
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Affiliation(s)
- Qianming Jiang
- Department of Animal Sciences, University of Illinois, Urbana 61801, IL, USA
| | | | - Danielle N Sherlock
- Department of Animal Sciences, University of Illinois, Urbana 61801, IL, USA
| | | | | | | | - Juan J Loor
- Department of Animal Sciences, University of Illinois, Urbana 61801, IL, USA
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10
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Meran L, Tullie L, Eaton S, De Coppi P, Li VSW. Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds. Nat Protoc 2023; 18:108-135. [PMID: 36261633 DOI: 10.1038/s41596-022-00751-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/30/2022] [Indexed: 01/14/2023]
Abstract
Tissue engineering is an interdisciplinary field that combines stem cells and matrices to form functional constructs that can be used to repair damaged tissues or regenerate whole organs. Tissue stem cells can be expanded and functionally differentiated to form 'mini-organs' resembling native tissue architecture and function. The choice of the scaffold is also pivotal to successful tissue reconstruction. Scaffolds may be broadly classified into synthetic or biological depending upon the purpose of the engineered organ. Bioengineered intestinal grafts represent a potential source of transplantable tissue for patients with intestinal failure, a condition resulting from extensive anatomical and functional loss of small intestine and therefore digestive and absorptive capacity. Prior strategies in intestinal bioengineering have predominantly used either murine or pluripotent cells and synthetic or decellularized rodent scaffolds, thus limiting their translation. Microscale models of human intestinal epithelium on shaped hydrogels and synthetic scaffolds are more physiological, but their regenerative potential is limited by scale. Here we present a protocol for bioengineering human intestinal grafts using patient-derived materials in a bioreactor culture system. This includes the isolation, expansion and biobanking of patient-derived intestinal organoids and fibroblasts, the generation of decellularized human intestinal scaffolds from native human tissue and providing a system for recellularization to form transplantable grafts. The duration of this protocol is 12 weeks, and it can be completed by scientists with prior experience of organoid culture. The resulting engineered mucosal grafts comprise physiological intestinal epithelium, matrix and surrounding niche, offering a valuable tool for both regenerative medicine and the study of human gastrointestinal diseases.
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Affiliation(s)
- Laween Meran
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
- Stem Cell and Regenerative Medicine Section, DBC, Great Ormond Street Institute of Child Health, University College London, London, UK
- Medical Research Council Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lucinda Tullie
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
- Stem Cell and Regenerative Medicine Section, DBC, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Simon Eaton
- Stem Cell and Regenerative Medicine Section, DBC, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Paolo De Coppi
- Stem Cell and Regenerative Medicine Section, DBC, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Specialist Neonatal and Paediatric Surgery Unit, Great Ormond Street Hospital, London, UK.
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK.
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11
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Heppert JK, Lickwar CR, Tillman MC, Davis BR, Davison JM, Lu HY, Chen W, Busch-Nentwich EM, Corcoran DL, Rawls JF. Conserved roles for Hnf4 family transcription factors in zebrafish development and intestinal function. Genetics 2022; 222:iyac133. [PMID: 36218393 PMCID: PMC9713462 DOI: 10.1093/genetics/iyac133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 12/13/2022] Open
Abstract
Transcription factors play important roles in the development of the intestinal epithelium and its ability to respond to endocrine, nutritional, and microbial signals. Hepatocyte nuclear factor 4 family nuclear receptors are liganded transcription factors that are critical for the development and function of multiple digestive organs in vertebrates, including the intestinal epithelium. Zebrafish have 3 hepatocyte nuclear factor 4 homologs, of which, hnf4a was previously shown to mediate intestinal responses to microbiota in zebrafish larvae. To discern the functions of other hepatocyte nuclear factor 4 family members in zebrafish development and intestinal function, we created and characterized mutations in hnf4g and hnf4b. We addressed the possibility of genetic redundancy amongst these factors by creating double and triple mutants which showed different rates of survival, including apparent early lethality in hnf4a; hnf4b double mutants and triple mutants. RNA sequencing performed on digestive tracts from single and double mutant larvae revealed extensive changes in intestinal gene expression in hnf4a mutants that were amplified in hnf4a; hnf4g mutants, but limited in hnf4g mutants. Changes in hnf4a and hnf4a; hnf4g mutants were reminiscent of those seen in mice including decreased expression of genes involved in intestinal function and increased expression of cell proliferation genes, and were validated using transgenic reporters and EdU labeling in the intestinal epithelium. Gnotobiotics combined with RNA sequencing also showed hnf4g has subtler roles than hnf4a in host responses to microbiota. Overall, phenotypic changes in hnf4a single mutants were strongly enhanced in hnf4a; hnf4g double mutants, suggesting a conserved partial genetic redundancy between hnf4a and hnf4g in the vertebrate intestine.
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Affiliation(s)
- Jennifer K Heppert
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew C Tillman
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Briana R Davis
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - James M Davison
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hsiu-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wei Chen
- Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - David L Corcoran
- Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA
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12
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Kopacz A, Kloska D, Fichna J, Klimczyk D, Kopec M, Jozkowicz A, Piechota-Polanczyk A. The lack of transcriptionally active Nrf2 triggers colon dysfunction in female mice - The role of estrogens. Free Radic Biol Med 2022; 192:141-151. [PMID: 36155082 DOI: 10.1016/j.freeradbiomed.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIM The proper functioning of the gastrointestinal system relies on an intricate crosstalk between a plethora of cell types and signaling pathways. Recently we identified that the lack of NRF2 transcriptional activity (NRF2 tKO) triggers significant colon microscopical alterations, still they do not affect the general functioning of mice. Therefore, in this study, we aimed to address the gender-dependent impact of NRF2 transcriptional deficiency on colon function, and relate them to an established model of inflammatory bowel disease (IBD). METHODS In the study we subjected 3- and 6-month old mice deficient in IL-10 and NRF2 transcriptional activity and wild-type counterparts to tests assessing colon functionality, and histological analyses. To address the role of estrogens, we attempted to rescue the phenotype by the delivery of 17β-estradiol through subcutaneous implants. RESULTS In females, NRF2 transcriptional abrogation, like IL-10 deficiency, triggers a functional and microscopic phenotype, that resembles IBD. The females are significantly more affected by the dysfunctional phenotype, and the functional impairmentdecreases with age. We found that NRF2 transcriptional activity influences 17β-estradiol level and the estrogen receptors expression and location. Exogenous delivery of 17β-estradiol normalized colon motility in the NRF2 tKO mice, which is related to enhanced ERβ signaling. CONCLUSIONS Summing up, in this study, we underline that NRF2 transcriptional deficiency or the lack of IL-10 results in pronounced GI functional decline in young females. Mechanistically, we show that the impaired distal colon motility is dependent on ERβ signaling. Targeting estrogen signaling seems a promising therapeutic strategy to counteract colonic dysfunction.
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Affiliation(s)
- Aleksandra Kopacz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Damian Kloska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jakub Fichna
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Poland
| | - Dominika Klimczyk
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Magdalena Kopec
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alicja Jozkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Piechota-Polanczyk
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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13
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Fei Y, Ma Y, Zhang H, Li H, Feng G, Fang J. Nanotechnology for research and treatment of the intestine. J Nanobiotechnology 2022; 20:430. [PMID: 36175955 PMCID: PMC9523975 DOI: 10.1186/s12951-022-01517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
The establishment of intestinal in vitro models is crucial for elucidating intestinal cell-microbe intrinsic connections and interaction mechanisms to advance normalized intestinal diagnosis and precision therapy. This review discusses the application of nanomaterials in mucosal therapy and mechanism research in combination with the study of nanoscaffold in vitro models of the gut. By reviewing the original properties of nanomaterials synthesized by different physicochemical principles and modifying the original properties, the contribution of nanomaterials to solving the problems of short survival period, low cell differentiation rate, and poor reduction ability in traditional intestinal models is explored. According to nanomaterials’ different diagnostic mediators and therapeutic targets, the current diagnostic principles in inflammatory bowel disease, intestinal cancer, and other diseases are summarized inductively. In addition, the mechanism of action of nanomedicines in repairing mucosa, inhibiting inflammation, and alleviating the disease process is also discussed. Through such systematic elaboration, it offers a basis for nanomaterials to help advance in vitro research on the intestine and provide precision treatments in the clinic.
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Affiliation(s)
- Yanquan Fei
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China
| | - Yong Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China
| | - Huaizu Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China
| | - Hao Li
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Guangfu Feng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China.
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha, 410128, Hunan, China.
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14
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Mussard E, Lencina C, Gallo L, Barilly C, Poli M, Feve K, Albin M, Cauquil L, Knudsen C, Achard C, Devailly G, Soler L, Combes S, Beaumont M. The phenotype of the gut region is more stably retained than developmental stage in piglet intestinal organoids. Front Cell Dev Biol 2022; 10:983031. [PMID: 36105361 PMCID: PMC9465596 DOI: 10.3389/fcell.2022.983031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Intestinal organoids are innovative in vitro tools to study the digestive epithelium. The objective of this study was to generate jejunum and colon organoids from suckling and weaned piglets in order to determine the extent to which organoids retain a location-specific and a developmental stage-specific phenotype. Organoids were studied at three time points by gene expression profiling for comparison with the transcriptomic patterns observed in crypts in vivo. In addition, the gut microbiota and the metabolome were analyzed to characterize the luminal environment of epithelial cells at the origin of organoids. The location-specific expression of 60 genes differentially expressed between jejunum and colon crypts from suckling piglets was partially retained (48%) in the derived organoids at all time point. The regional expression of these genes was independent of luminal signals since the major differences in microbiota and metabolome observed in vivo between the jejunum and the colon were not reproduced in vitro. In contrast, the regional expression of other genes was erased in organoids. Moreover, the developmental stage-specific expression of 30 genes differentially expressed between the jejunum crypts of suckling and weaned piglets was not stably retained in the derived organoids. Differentiation of organoids was necessary to observe the regional expression of certain genes while it was not sufficient to reproduce developmental stage-specific expression patterns. In conclusion, piglet intestinal organoids retained a location-specific phenotype while the characteristics of developmental stage were erased in vitro. Reproducing more closely the luminal environment might help to increase the physiological relevance of intestinal organoids.
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Affiliation(s)
- Eloïse Mussard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
- Lallemand Animal Nutrition, Blagnac Cedex, France
| | - Corinne Lencina
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Lise Gallo
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Céline Barilly
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Maryse Poli
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Katia Feve
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Mikael Albin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Laurent Cauquil
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | | | | | - Laura Soler
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sylvie Combes
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
- *Correspondence: Martin Beaumont,
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15
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Transcriptional Integration of Distinct Microbial and Nutritional Signals by the Small Intestinal Epithelium. Cell Mol Gastroenterol Hepatol 2022; 14:465-493. [PMID: 35533983 PMCID: PMC9305020 DOI: 10.1016/j.jcmgh.2022.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS The intestine constantly interprets and adapts to complex combinations of dietary and microbial stimuli. However, the transcriptional strategies by which the intestinal epithelium integrates these coincident sources of information remain unresolved. We recently found that microbiota colonization suppresses epithelial activity of hepatocyte nuclear factor 4 nuclear receptor transcription factors, but their integrative regulation was unknown. METHODS We compared adult mice reared germ-free or conventionalized with a microbiota either fed normally or after a single high-fat meal. Preparations of unsorted jejunal intestinal epithelial cells were queried using lipidomics and genome-wide assays for RNA sequencing and ChIP sequencing for the activating histone mark H3K27ac and hepatocyte nuclear factor 4 alpha. RESULTS Analysis of lipid classes, genes, and regulatory regions identified distinct nutritional and microbial responses but also simultaneous influence of both stimuli. H3K27ac sites preferentially increased by high-fat meal in the presence of microbes neighbor lipid anabolism and proliferation genes, were previously identified intestinal stem cell regulatory regions, and were not hepatocyte nuclear factor 4 alpha targets. In contrast, H3K27ac sites preferentially increased by high-fat meal in the absence of microbes neighbor targets of the energy homeostasis regulator peroxisome proliferator activated receptor alpha, neighbored fatty acid oxidation genes, were previously identified enterocyte regulatory regions, and were hepatocyte factor 4 alpha bound. CONCLUSIONS Hepatocyte factor 4 alpha supports a differentiated enterocyte and fatty acid oxidation program in germ-free mice, and that suppression of hepatocyte factor 4 alpha by the combination of microbes and high-fat meal may result in preferential activation of intestinal epithelial cell proliferation programs. This identifies potential transcriptional mechanisms for intestinal adaptation to multiple signals and how microbiota may modulate intestinal lipid absorption, epithelial cell renewal, and systemic energy balance.
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16
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A cell atlas of microbe-responsive processes in the zebrafish intestine. Cell Rep 2022; 38:110311. [PMID: 35108531 DOI: 10.1016/j.celrep.2022.110311] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 10/28/2021] [Accepted: 01/07/2022] [Indexed: 02/08/2023] Open
Abstract
Gut microbial products direct growth, differentiation, and development in animal hosts. However, we lack system-wide understanding of cell-specific responses to the microbiome. We profiled cell transcriptomes from the intestine, and associated tissue, of zebrafish larvae raised in the presence or absence of a microbiome. We uncovered extensive cellular heterogeneity in the conventional zebrafish intestinal epithelium, including previously undescribed cell types with known mammalian homologs. By comparing conventional to germ-free profiles, we mapped microbial impacts on transcriptional activity in each cell population. We revealed intricate degrees of cellular specificity in host responses to the microbiome that included regulatory effects on patterning and on metabolic and immune activity. For example, we showed that the absence of microbes hindered pro-angiogenic signals in the developing vasculature, causing impaired intestinal vascularization. Our work provides a high-resolution atlas of intestinal cellular composition in the developing fish gut and details the effects of the microbiome on each cell type.
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17
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Epithelial NELF guards intestinal barrier function to ameliorate colitis by maintaining junctional integrity. Mucosal Immunol 2022; 15:279-288. [PMID: 34697434 PMCID: PMC8881342 DOI: 10.1038/s41385-021-00465-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 09/27/2021] [Accepted: 10/09/2021] [Indexed: 02/04/2023]
Abstract
Well-orchestrated transcriptional programs in intestinal epithelial cells (IECs) are essential for maintenance of optimal mucosal barrier functions, whereas the contribution of elongation-related mechanisms to barrier function remains unknown. Here, a combination of genetic and genomic approaches defined a critical role of IEC-intrinsic negative elongation factor (NELF) complex in maintenance of epithelial homeostasis. By direct occupancy at endogenous gene loci, NELF sustained expression of a subset of genes related to junctional integrity. As a result, epithelial NELF deficiency results in subdued levels of these junction-related genes and excessive IEC necroptosis in vivo secondary to commensal microbial invasion. In a colitis model, NELF-deficient mice exhibited severely impaired barrier integrity characterized by increased intestinal permeability and significantly exacerbated intestinal inflammation with lethal consequences. Our findings reveal the protective function of the NELF complex against intestinal damage and inflammation and suggest that elongation represents a biologically important step in defining IEC transcriptome.
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18
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Microenvironmental Metabolites in the Intestine: Messengers between Health and Disease. Metabolites 2022; 12:metabo12010046. [PMID: 35050167 PMCID: PMC8778376 DOI: 10.3390/metabo12010046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 02/01/2023] Open
Abstract
The intestinal mucosa is a highly absorptive organ and simultaneously constitutes the physical barrier between the host and a complex outer ecosystem. Intestinal epithelial cells (IECs) represent a special node that receives signals from the host and the environment and translates them into corresponding responses. Specific molecular communication systems such as metabolites are known to transmit information across the intestinal boundary. The gut microbiota or food-derived metabolites are extrinsic factors that influence the homeostasis of the intestinal epithelium, while mitochondrial and host-derived cellular metabolites determine the identity, fitness, and regenerative capacity of IECs. Little is known, however, about the role of intrinsic and extrinsic metabolites of IECs in the initiation and progression of pathological processes such as inflammatory bowel disease and colorectal cancer as well as about their impact on intestinal immunity. In this review, we will highlight the most recent contributions on the modulatory effects of intestinal metabolites in gut pathophysiology, with a particular focus on metabolites in promoting intestinal inflammation or colorectal tumorigenesis. In addition, we will provide a perspective on the role of newly identified oncometabolites from the commensal and opportunistic microbiota in shaping response and resistance to antitumor therapy.
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IκBζ controls IL-17-triggered gene expression program in intestinal epithelial cells that restricts colonization of SFB and prevents Th17-associated pathologies. Mucosal Immunol 2022; 15:1321-1337. [PMID: 35999460 PMCID: PMC9705257 DOI: 10.1038/s41385-022-00554-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 02/04/2023]
Abstract
Control of gut microbes is crucial for not only local defense in the intestine but also proper systemic immune responses. Although intestinal epithelial cells (IECs) play important roles in cytokine-mediated control of enterobacteria, the underlying mechanisms are not fully understood. Here we show that deletion of IκBζ in IECs in mice leads to dysbiosis with marked expansion of segmented filamentous bacteria (SFB), thereby enhancing Th17 cell development and exacerbating inflammatory diseases. Mechanistically, the IκBζ deficiency results in decrease in the number of Paneth cells and impairment in expression of IL-17-inducible genes involved in IgA production. The decrease in Paneth cells is caused by aberrant activation of IFN-γ signaling and a failure of IL-17-dependent recovery from IFN-γ-induced damage. Thus, the IL-17R-IκBζ axis in IECs contributes to the maintenance of intestinal homeostasis by serving as a key component in a regulatory loop between the gut microbiota and immune cells.
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Greco L, Rubbino F, Morelli A, Gaiani F, Grizzi F, de’Angelis GL, Malesci A, Laghi L. Epithelial to Mesenchymal Transition: A Challenging Playground for Translational Research. Current Models and Focus on TWIST1 Relevance and Gastrointestinal Cancers. Int J Mol Sci 2021; 22:ijms222111469. [PMID: 34768901 PMCID: PMC8584071 DOI: 10.3390/ijms222111469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022] Open
Abstract
Resembling the development of cancer by multistep carcinogenesis, the evolution towards metastasis involves several passages, from local invasion and intravasation, encompassing surviving anoikis into the circulation, landing at distant sites and therein establishing colonization, possibly followed by the outgrowth of macroscopic lesions. Within this cascade, epithelial to mesenchymal transition (EMT) works as a pleiotropic program enabling cancer cells to overcome local, systemic, and distant barriers against diffusion by replacing traits and functions of the epithelial signature with mesenchymal-like ones. Along the transition, a full-blown mesenchymal phenotype may not be accomplished. Rather, the plasticity of the program and its dependency on heterotopic signals implies a pendulum with oscillations towards its reversal, that is mesenchymal to epithelial transition. Cells in intermixed E⇔M states can also display stemness, enabling their replication together with the epithelial reversion next to successful distant colonization. If we aim to include the EMT among the hallmarks of cancer that could modify clinical practice, the gap between the results pursued in basic research by animal models and those achieved in translational research by surrogate biomarkers needs to be filled. We review the knowledge on EMT, derived from models and mechanistic studies as well as from translational studies, with an emphasis on gastrointestinal cancers (GI).
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Affiliation(s)
- Luana Greco
- Laboratory of Molecular Gastroenterology, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (L.G.); (F.R.); (A.M.)
| | - Federica Rubbino
- Laboratory of Molecular Gastroenterology, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (L.G.); (F.R.); (A.M.)
| | - Alessandra Morelli
- Laboratory of Molecular Gastroenterology, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (L.G.); (F.R.); (A.M.)
| | - Federica Gaiani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (F.G.); (G.L.d.)
- Gastroenterology and Endoscopy Unit, University-Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Fabio Grizzi
- Department of Immunology and Inflammation, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy;
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy;
| | - Gian Luigi de’Angelis
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (F.G.); (G.L.d.)
- Gastroenterology and Endoscopy Unit, University-Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Alberto Malesci
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy;
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
| | - Luigi Laghi
- Laboratory of Molecular Gastroenterology, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (L.G.); (F.R.); (A.M.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (F.G.); (G.L.d.)
- Correspondence:
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Ojeda J, Ávila A, Vidal PM. Gut Microbiota Interaction with the Central Nervous System throughout Life. J Clin Med 2021; 10:1299. [PMID: 33801153 PMCID: PMC8004117 DOI: 10.3390/jcm10061299] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 02/08/2023] Open
Abstract
During the last years, accumulating evidence has suggested that the gut microbiota plays a key role in the pathogenesis of neurodevelopmental and neurodegenerative diseases via the gut-brain axis. Moreover, current research has helped to elucidate different communication pathways between the gut microbiota and neural tissues (e.g., the vagus nerve, tryptophan production, extrinsic enteric-associated neurons, and short chain fatty acids). On the other hand, altering the composition of gut microbiota promotes a state known as dysbiosis, where the balance between helpful and pathogenic bacteria is disrupted, usually stimulating the last ones. Herein, we summarize selected findings of the recent literature concerning the gut microbiome on the onset and progression of neurodevelopmental and degenerative disorders, and the strategies to modulate its composition in the search for therapeutical approaches, focusing mainly on animal models studies. Readers are advised that this is a young field, based on early studies, that is rapidly growing and being updated as the field advances.
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Affiliation(s)
- Jorge Ojeda
- Neuroimmunology and Regeneration of the Central Nervous System Unit, Biomedical Science Research Laboratory, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile;
| | - Ariel Ávila
- Developmental Neurobiology Unit, Biomedical Science Research Laboratory, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile;
| | - Pía M. Vidal
- Neuroimmunology and Regeneration of the Central Nervous System Unit, Biomedical Science Research Laboratory, Basic Sciences Department, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile;
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