
Gastroenterology, Journal Year: 2019, Volume and Issue: 156(8), P. 2174 - 2189
Published: March 14, 2019
The intestinal microbiota is a dynamic community of bacteria, fungi, and viruses that mediates mucosal homeostasis physiology. Imbalances in the microbiome aberrant immune responses to gut bacteria can disrupt are associated with inflammatory bowel diseases (IBDs) humans colitis mice. We review genetic variants IBD their effects on microbiome, response, disease pathogenesis. which includes microbial antigens, adjuvants, metabolic products, affects development function mucosa, influencing gut. Therefore, strategies manipulate might be used treatment IBD. microbe-based therapies for potential engineer patients' microbiota. discuss how studies patients mouse models have advanced our understanding interactions between factors challenges Inflammatory include Crohn (CD) ulcerative (UC), chronic develop through complex among genetic, immune, environmental, factors.1Abraham C. Medzhitov R. Interactions host innate system microbes disease.Gastroenterology. 2011; 140: 1729-1737Abstract Full Text PDF PubMed Scopus (314) Google Scholar, 2Belkaid Y. Hand T.W. Role immunity inflammation.Cell. 2014; 157: 121-141Abstract (1124) 3Sun M. He Cong et al.Regulatory cells regulation response microbiota.Mucosal Immunol. 2015; 8: 969-978Crossref (95) Scholar Dysregulation any components this network result inflammation Genetic identified regulators altered IBD—many these control microbes.4Hall A.B. Tolonen A.C. Xavier R.J. Human variation disease.Nat Rev Genet. 2017; 18: 690-699Crossref (108) 5Luca F. Kupfer S.S. Knights D. al.Functional genomics host–microbiome humans.Trends 2018; 34: 30-40Abstract (0) Variants risk been NOD2, ATG16L1, CARD9, CLEC7A.6Khor B. Gardet A. Genetics pathogenesis disease.Nature. 474: 307-317Crossref (1187) genes detection perturb promote inflammation. It important distinguish mediate pathogens from overall ecology, also affected by environmental (diet, medications, geography).7Rothschild Weissbrod O. Barkan E. al.Environment dominates over genetics shaping human microbiota.Nature. 555: 210-215Crossref (362) However, as we study mechanisms affect microbes, learn more about do so identify new targets diagnosis Studies model systems indicated modified increase or decrease severity introduction effectors, such lipids, small molecules, proteins, sugars. During past decade, interest has increased due number perceived safety therapies, correct one causes disease, rather than symptoms. Increased part insights antibiotics, probiotics, recently fecal transplantation (FMT) other disorders.8Hoffmann D.E. Palumbo F.B. Ravel J. al.A proposed definition regulatory purposes.Gut Microbes. 208-213Crossref (13) Strategies its functions UC CD produced inconsistent results, although antibiotics were found effective pouchitis, an excellent profile.9Lopez Grinspan Fecal disease.Gastroenterol Hepatol (N Y). 2016; 12: 374-379PubMed 10Khan K.J. Ullman T.A. Ford al.Antibiotic therapy disease: systematic meta-analysis.Am J Gastroenterol. 106: 661-673Crossref (324) 11Singh S. Stroud A.M. Holubar S.D. al.Treatment prevention pouchitis after ileal pouch-anal anastomosis colitis.Cochrane Database Syst Rev. 11: CD001176Google FMT was reported alleviate symptoms some UC, outcomes varied. Further required optimize selection donors, assess ability donated engraft, determine whether induction maintenance therapy. needed whose products microbe-sensing pathways (such NOD2) would therapies. IBD-associated gene therapeutically target specific functions.9Lopez 12Sartor R.B. Wu G.D. Roles viruses, fungi therapeutic approaches.Gastroenterology. 152: 327-339 e4Abstract (186) growth presents drug approval. Genes encode many proteins shape regulating availability nutrients, level microbes.13Benson A.K. Kelly S.A. Legge al.Individuality composition polygenic trait shaped multiple factors.Proc Natl Acad Sci U S 2010; 107: 18933-18938Crossref (640) 14Goodrich J.K. Waters J.L. Poole al.Human microbiome.Cell. 159: 789-799Abstract (953) 15Knights Silverberg M.S. Weersma R.K. al.Complex influence disease.Genome Med. 6: 107Crossref (157) 16Blekhman Goodrich Huang K. al.Host impacts across body sites.Genome Biol. 16: 191Crossref (232) Genome-wide association (Figure 1).6Khor 17Parkes Barrett J.C. Prescott N.J. al.Sequence autophagy IRGM replicating loci contribute Crohn's susceptibility.Nat 2007; 39: 830-832Crossref (856) 18Hampe Franke Rosenstiel P. genome-wide scan nonsynonymous SNPs identifies susceptibility variant ATG16L1.Nat 207-211Crossref (1343) 19Consortium W.T.C.C. 14,000 cases seven common 3,000 shared controls.Nature. 447: 661-678Crossref (6954) 20Franke McGovern D.P. al.Genome-wide meta-analysis increases 71 confirmed loci.Nat 42: 1118-1125Crossref (1677) 21Rivas M.A. Beaudoin al.Deep resequencing GWAS independent rare 43: 1066-1073Crossref (472) 22Anderson C.A. Boucher G. Lees C.W. al.Meta-analysis 29 additional loci, increasing associations 47.Nat 246-252Crossref (875) 23Jostins L. Ripke al.Host-microbe architecture 2012; 491: 119-124Crossref (2381) 24Liu J.Z. van Sommeren H. al.Association analyses 38 highlight populations.Nat 47: 979-986Crossref (661) 25Ellinghaus Jostins Spain S.L. al.Analysis five 27 highlights disease-specific patterns at 48: 510-518Crossref (189) NOD2 first CD. encodes intracellular pattern recognition receptor, interacts peptidoglycan motifs bacteria.26Hugot J.P. Chamaillard Zouali leucine-rich repeat 2001; 411: 599-603Crossref (4300) 27Ogura Bonen D.K. Inohara N. frameshift mutation 603-606Crossref (3839) 28Philpott D.J. Sorbara M.T. Robertson S.J. al.NOD proteins: health 14: 9-23Crossref (302) helps pathogenic hematopoietic non-hematopoietic cells. initially believed individuals could not efficiently clear bacterial pathogens, leading pathology.29Kobayashi K.S. Ogura al.Nod2-dependent adaptive tract.Science. 2005; 307: 731-734Crossref (1331) This hypothesis supported patient cohorts gastrointestinal onset.30Molodecky N.A. Kaplan G.G. Environmental 339-346PubMed it became apparent non-pathogenic commensal microbes. Patients microbiomes distinct without variants, characterized abundance Escherichia species decreased Faecalibacterium species, variants.15Knights 31Frank D.N. C.E. Hamm C.M. al.Disease phenotype genotype shifts intestinal-associated diseases.Inflamm Bowel Dis. 17: 179-184Crossref (360) 32Rehman Sina Gavrilova al.Nod2 essential temporal communities.Gut. 60: 1354-1362Crossref (204) 33Imhann Vich Vila Bonder M.J. al.Interplay underlying onset clinical presentation disease.Gut. 67: 108-119Crossref (139) Additionally, Nod2−/− mice dysbiosis, colitis, compared wild-type mice.32Rehman 34Petnicki-Ocwieja T. Hrncir Liu Y.J. intestine.Proc 2009; 15813-15818Crossref (380) 35Mondot Barreau Al Nabhani Z. al.Altered immune-impaired Nod2(−/−) mice.Gut. 61: 634-635Crossref 36Couturier-Maillard Secher Rehman al.NOD2-mediated dysbiosis predisposes transmissible colorectal cancer.J Clin Invest. 2013; 123: 700-711Crossref 37Ramanan Tang Bowcutt al.Bacterial sensor Nod2 prevents intestine restricting expansion Bacteroides vulgatus.Immunity. 41: 311-324Abstract (113) 38Alnabhani Hugot Montcuquet al.Respective roles nonhematopoietic homeostasis.Inflamm 22: 763-773Crossref 39Al Lepage Mauny deficiency leads mucosa-associated barrier defect.J Crohns Colitis. 10: 1428-1436Crossref Researchers (pathobionts) mice, vulgatus. Mucosal defects observed linked B vulgatus, including abnormalities goblet cells, expression genes, numbers intraepithelial lymphocytes express interferon γ.37Ramanan Depletion vulgatus reversed thus targeted depletion organisms exacerbate signaling restore Several regulate pathway IGRM, LRRK2). Autophagy functions, but lysosomal degradation clearance bacteria.18Hampe 40Rioux J.D. Taylor K.D. implicates pathogenesis.Nat 596-604Crossref (1307) demonstrated ATG16L1 CD-associated disrupts interaction impairing antigen presentation.41Cooney Baker Brain al.NOD2 stimulation induces dendritic handling presentation.Nat 90-97Crossref (719) 42Travassos L.H. Carneiro L.A. Ramjeet al.Nod1 direct recruiting plasma membrane site entry.Nat 55-62Crossref (854) encoding T300A substitution product caspase-3 cleavage decreases function.43Murthy Li Peng I. Atg16l1 enhances caspase 3.Nature. 506: 456-462Crossref Similar hypomorphic microbiota-dependent Toll-like receptor production antimicrobial peptides Paneth These cell who homozygous ATG16L1.44Saitoh Fujita Jang M.H. al.Loss protein Atg16L1 endotoxin-induced IL-1beta production.Nature. 2008; 456: 264-268Crossref (1269) 45Cadwell J.Y. Brown key role cells.Nature. 259-263Crossref (961) In disruption CD4+ T decreasing Foxp3+ T-regulatory (Treg) T-helper (Th) type 2 cell-mediated responses. impaired T-cell loss tolerance antigens immunoglobulin (Ig) G IgA against microbiota.46Kabat Harrison O.J. Riffelmacher al.The differentially regulates Treg TH2 inflammation.Elife. 5: e12444Crossref (72) Although carry autophagy, only proportion alterations epithelia likely deletion blocking immunomodulatory signals. For example, fragilis suppresses inducing produce interleukin (IL) 10.47Mazmanian S.K. Round Kasper D.L. A symbiosis factor 453: 620-625Crossref (1173) 48Round Mazmanian Inducible bacterium microbiota.Proc 12204-12209Crossref (1097) effect lost when defective signaling.49Chu Khosravi Kusumawardhani I.P. al.Gene-microbiota disease.Science. 352: 1116-1120Crossref (206) induce exposure fragilis. Bacteria most well-defined microbiota, fungal communities should surprising considering based antibodies Saccharomyces cerevisiae.50Mitsuyama Niwa Takedatsu al.Antibody markers disease.World 1304-1310Crossref (27) IBD, diversity certain atypical phyla dominate, Ascomycota Basidiomycota.51Sokol Leducq V. Aschard al.Fungal IBD.Gut. 66: 1039-1048Crossref (237) Fungal members interact receptors CLEC7A (also called DECTIN1), glycoprotein expressed recognizes β-1,3–linked β-1,6–linked glucans fungi. single-nucleotide polymorphism Mice lacking DECTIN1 community.52Iliev I.D. Funari V.A. al.Interactions C-type lectin Dectin-1 colitis.Science. 336: 1314-1317Crossref (492) Interestingly, medically refractory UC; no therapy.52Iliev signals adaptor recruitment domain containing 9 (CARD9).23Jostins Card9−/− structure, induced dextran sodium sulfate.53Sokol Conway K.L. Zhang al.Card9 epithelial restitution, 17 responses, infection mice.Gastroenterology. 145: 591-601 e3Abstract (81) results CARD9 Th17 consistent importance controlling infections. (rs10781499) severe mucocutaneous candiadiasis.53Sokol 54Gross Gewies Finger controls non-TLR signalling anti-fungal immunity.Nature. 2006; 442: 651-656Crossref (563) 55LeibundGut-Landmann Gross Robinson al.Syk- CARD9-dependent coupling helper 17.Nat 630-638Crossref (812) 56Glocker E.O. Hennigs Nabavi family infections.N Engl 361: 1727-1735Crossref (443) alter changes regulated nuclear κB, c-Jun N-terminal kinase, mitogen-activated kinase.54Gross NOD2.57Hsu Y.M. You pathogens.Nat 198-205Crossref (276) communities, dependent community. Variations phenotypes knockout show complexities functions; confounding variables interactions. tryptophan metabolites account variations phenotypes.58Lamas Richard M.L. al.CARD9 altering metabolism into aryl hydrocarbon ligands.Nat 598-605Crossref (311) Bacterial signal (AHRs), tolerance. Impaired susceptibility. Administration Lactobacillus strains metabolize AHR ligands sufficient samples polymorphisms lacked ligands. leukocyte (HLAs) encoded major histocompatibility (MHC), polymorphic humans. Proteins MHC locus coordination response. HLAs allows respond different inappropriate self-antigens.59Doherty P.C. Zinkernagel R.M. biological antigens.Lancet. 1975; 1: 1406-1409Abstract class II correlate location.60Cleynen al.Inherited determinants phenotypes: study.Lancet. 387: 156-167Abstract (510) heterozygosity lower UC.61Goyette Mallon al.High-density mapping HLA-DRB1*01:03 heterozygous advantage colitis.Nat 172-179Crossref (127) weaken microbes.61Goyette II-associated diseases, rheumatoid arthritis, celiac ankylosing spondylitis,62Bolnick D.I. Snowberg L.K. Caporaso J.G. al.Major Histocompatibility Complex IIb influences diversity.Mol Ecol. 23: 4831-4845Crossref (68) 63Lin Bach Asquith al.HLA-B27 beta2-microglobulin transgenic rats.PLoS One. 9: e105684Crossref 64Kubinak Stephens W.Z. Soto al.MHC sculpts individualized enteric infection.Nat Commun. 8642Crossref (49) 65Silverman Kua Tanca al.Protective allele 1 diabetes early ontogeny.Proc 114: 9671-9676Crossref 66De Palma Capilla Nadal colonization process newborn intestine.Curr Issues Mol 1-10PubMed 67Rosenbaum J.T. Davey M.P. Time check: evidence HLA-B27 spondylitis microbiome.Arthritis Rheum. 63: 3195-3198Crossref 68Olivares Neef Castillejo HLA-DQ2 selects infants high developing coeliac 64: 406-417Crossref (116) showed correlation HLA alleles permeability.69Scher J.U. Sczesnak Longman R.S. al.Expansion Prevotella copri correlates enhanced arthritis.Elife. 2: e01202Crossref Scho
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