Advances in inflammatory bowel disease pathogenesis: Linking host genetics and the microbiome

Gut

Volumn 62, Issue 10, 2013, Pages 1505-1510

  Knights, Dan ^a,b,c   Lassen, Kara G ^a,b   Xavier, Ramnik J ^a,b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC HYDROCARBON RECEPTOR; CASPASE RECRUITMENT DOMAIN PROTEIN 15; INTERLEUKIN 23; OXYGENASE;

ANTIGEN PRESENTATION; ARTICLE; BACTERIAL COLONIZATION; CD4+ T LYMPHOCYTE; CLOSTRIDIUM DIFFICILE INFECTION; COHORT ANALYSIS; ENTERITIS; EPIGENETICS; GENE INTERACTION; GENE MUTATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HOMEOSTASIS; HOST; HUMAN; IMMUNE RESPONSE; LYMPHOCYTE ACTIVATION; LYMPHOCYTOPOIESIS; MICROBIOME; MYCOBACTERIOSIS; NONHUMAN; PATHOGENESIS; PHENOTYPE; PRIORITY JOURNAL; REGULATORY T LYMPHOCYTE; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; TAXONOMY; TH17 CELL;

CROHN'S DISEASE; GENETICS; INFLAMMATORY BOWEL DISEASE; INTESTINAL BACTERIA; ULCERATIVE COLITIS;

BACTERIA; GENETIC PREDISPOSITION TO DISEASE; HOST-PATHOGEN INTERACTIONS; HUMANS; INFLAMMATORY BOWEL DISEASES; INTESTINES; MICROBIOTA; PHENOTYPE; SIGNAL TRANSDUCTION;

EID: 84884273778     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2012-303954     Document Type: Article

References (52)

1. Ogura Y, Bonen DK, Inohara N, et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 2001;411:603-6. (Pubitemid 32531409)
2. Hugot JP, Chamaillard M, Zouali H, et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 2001;411:599-603. (Pubitemid 32531408)
3. Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012;491:119-24.
4. Abecasis GR, Auton A, Brooks LD, et al. Genomes Project C. An integrated map of genetic variation from 1, 092 human genomes. Nature 2012;491:56-65.
5. MacArthur DG, Balasubramanian S, Frankish A, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012;335:823-8.
6. Coccia M, Harrison OJ, Schiering C, et al. IL-1beta mediates chronic intestinal inflammation by promoting the accumulation of IL-17A secreting innate lymphoid cells and CD4 (+) Th17 cells. J Exp Med 2012;209:1595-609.
7. Griseri T, McKenzie BS, Schiering C, et al. Dysregulated hematopoietic stem and progenitor cell activity promotes interleukin-23-driven chronic intestinal inflammation. Immunity 2012;37:1116-29.
8. Consortium EP, Dunham I, Kundaje A, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74.
9. Graur D, Zheng Y, Price N, et al. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 2013;5:578-90.
10. Maurano MT, Humbert R, Rynes E, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012;337:1190-5.
11. Hardison RC. Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. J Biol Chem 2012;287:30932-40.
12. Nicolae DL, Gamazon E, Zhang W, et al. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 2010;6:e1000888.
13. Yang ML, Gee AJ, Gee RJ, et al. Lupus autoimmunity altered by cellular methylation metabolism. Autoimmunity 2013;46:21-31.
14. Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature 2012;482:339-46.
15. Hasler R, Jacobs G, Till A, et al. Microbial pattern recognition causes distinct functional micro-RNA signatures in primary human monocytes. PLoS One 2012;7:e31151.
16. Pekow JR, Kwon JH. MicroRNAs in inflammatory bowel disease. Inflamm Bowel Dis 2012;18:187-93.
17. Morgan XC, Tickle TL, Sokol H, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 2012;13:R79.
18. Sokol H, Seksik P. The intestinal microbiota in inflammatory bowel diseases: time to connect with the host. Curr Opin Gastroenterol 2010;26:327-31.
19. Willing BP, Dicksved J, Halfvarson J, et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 2010;139:1844-54 e1.
20. Lupp C, Robertson ML, Wickham ME, et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2007;2:119-29. (Pubitemid 47209521)
21. Duncan SH, Hold GL, Barcenilla A, et al. Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. Int J Syst Evol Microbiol 2002;52:1615-20.
22. Watanabe Y, Nagai F, Morotomi M. Characterization of Phascolarctobacterium succinatutens sp. nov., an asaccharolytic, succinate-utilizing bacterium isolated from human feces. Appl Environ Microbiol 2012;78:511-18.
23. Nagano Y, Itoh K, Honda K. The induction of Treg cells by gut-indigenous Clostridium. Curr Opin Immunol 2012;24:392-7.
24. Kamada N, Kim YG, Sham HP, et al. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 2012;336:1325-9.
25. Van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent clostridium difficile. N Engl J Med 2013;368:407-15.
26. Issa M, Ananthakrishnan AN, Binion DG. Clostridium difficile and inflammatory bowel disease. Inflamm Bowel Dis 2008;14:1432-42.
27. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-14.
28. Caporaso JG, Lauber CL, Costello EK, et al. Moving pictures of the human microbiome. Genome Biol 2011;12:R50.
29. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174-80.
30. Koren O, Knights D, Gonzalez A, et al. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol 2013;9:e1002863.
31. Steck N, Mueller K, Schemann M, et al. Bacterial proteases in IBD and IBS. Gut 2012;61:1610-18.
32. Rivas MA, Beaudoin M, Gardet A, et al. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet 2011;43:1066-73.
33. Deshmukh HS, Hamburger JB, Ahn SH, et al. Critical role of NOD2 in regulating the immune response to Staphylococcus aureus. Infect Immun 2009;77:1376-82.
34. Riol-Blanco L, Lazarevic V, Awasthi A, et al. IL-23 receptor regulates unconventional IL-17-producing T cells that control bacterial infections. J Immunol 2010;184:1710-20.
35. Fujiya M, Inaba Y, Musch MW, et al. Cytokine regulation of OCTN2 expression and activity in small and large intestine. Inflamm Bowel Dis 2011;17:907-16.
36. Iwasaki A, Medzhitov R. Toll-like receptor control of the adaptive immune responses. Nat Immunol 2004;5:987-95. (Pubitemid 41057715)
37. Nguyen NT, Kimura A, Nakahama T, et al. Aryl hydrocarbon receptor negatively regulates dendritic cell immunogenicity via a kynurenine-dependent mechanism. Proc Natl Acad Sci USA 2010;107:19961-6.
38. Nowak EC, De Vries VC, Wasiuk A, et al. Tryptophan hydroxylase-1 regulates immune tolerance and inflammation. J Exp Med 2012;209:2127-35.
39. Hashimoto T, Perlot T, Rehman A, et al. ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation. Nature 2012;487:477-81.
40. Diegelmann J, Olszak T, Goke B, et al. A novel role for interleukin-27 (IL-27) as mediator of intestinal epithelial barrier protection mediated via differential signal transducer and activator of transcription (STAT) protein signaling and induction of antibacterial and anti-inflammatory proteins. J Biol Chem 2012;287:286-98.
41. Wu GD, Chen J, Hoffmann C, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011;334:105-8.
42. Devkota S, Wang Y, Musch MW, et al. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/-mice. Nature 2012;487:104-8.
43. Divaris K, Monda KL, North KE, et al. Genome-wide association study of periodontal pathogen colonization. J Dent Res 2012;91:21S-8S.
44. Timmann C, Thye T, Vens M, et al. Genome-wide association study indicates two novel resistance loci for severe malaria. Nature 2012;489:443-6.
45. Cooney R, Baker J, Brain O, et al. NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation. Nat Med 2010;16:90-7.
46. Abraham C, Cho JH. Inflammatory bowel disease. N Engl J Med 2009;361:2066-78.
47. Derrien M, Van Passel MW, Van De Bovenkamp JH, et al. Mucin-bacterial interactions in the human oral cavity and digestive tract. Gut Microbes 2010;1:254-68.
48. Elinav E, Strowig T, Kau AL, et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 2011;145:745-57.
49. Couturier-Maillard A, Secher T, Rehman A, et al. NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer. J Clin Invest 2013;123:700-11.
50. Hand TW, Dos Santos LM, Bouladoux N, et al. Acute gastrointestinal infection induces long-lived microbiota-specific T cell responses. Science 2012;337:1553-6.
51. Franke A, McGovern DP, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 2010;42:1118-25.
52. Kaser A, Zeissig S, Blumberg RS. Inflammatory bowel disease. Annu Rev Immunol 2010;28:573-621.