Recent insights into the genetics of inflammatory bowel disease

Gastroenterology

Volumn 140, Issue 6, 2011, Pages 1704-1712.e2

  Cho, Judy H ^a   Brant, Steven R ^b  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Autophagy; Crohn's Disease; Genetics; Genome Wide Association Studies; Interleukin 23; Ulcerative Colitis

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 15; HLA ANTIGEN CLASS 2; INTERLEUKIN 23; PROTEIN ZMIZ1; SMAD3 PROTEIN; STAT3 PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NKX2 3; TRANSCRIPTION FACTOR REL; UNCLASSIFIED DRUG;

ARTICLE; AUTOPHAGY; CELL GROWTH; CELL SURVIVAL; CHROMOSOME 6P; CROHN DISEASE; ENTERITIS; GENE CONTROL; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; HUMAN; INNATE IMMUNITY; LYMPHOCYTE ACTIVATION; PATHOGENESIS; PRIORITY JOURNAL; ULCERATIVE COLITIS;

EID: 79955566359     PISSN: 00165085     EISSN: None     Source Type: Journal    
DOI: 10.1053/j.gastro.2011.02.046     Document Type: Article

References (100)

1. M. Orholm, P. Munkholm, and E. Langholz Familial occurrence of inflammatory bowel disease N Engl J Med 324 1991 84 88
2. A.M. Lowe, P.O. Roy, and M. B-Poulin Epidemiology of Crohn's disease in Quebec, Canada Inflamm Bowel Dis 15 2009 429 435
3. S.R. Brant Update on the heritability of inflammatory bowel disease: the importance of twin studies Inflamm Bowel Dis 17 2011 1 5
4. E.O. Glocker, D. Kotlarz, and K. Boztug Inflammatory bowel disease and mutations affecting the interleukin-10 receptor N Engl J Med 361 2009 2033 2045
5. Glocker EO, Frede N, Perro M, et al. Infant colitisit's in the genes. Lancet;376:1272.
6. B.E. Marciano, S.D. Rosenzweig, and D.E. Kleiner Gastrointestinal involvement in chronic granulomatous disease Pediatrics 114 2004 462 468 (Pubitemid 39006676)
7. B.K. Dieckgraefe, J.R. Korzenik, and A. Husain Association of glycogen storage disease 1b and Crohn disease: results of a North American survey Eur J Pediatr 161 Suppl 1 2002 S88 S92
8. A. Franke, T. Balschun, and T.H. Karlsen Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility Nat Genet 40 2008 1319 1323
9. C.A. Anderson, G. Boucher, and C.W. Lees Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47 Nat Genet 43 2011 246 252
10. S.R. Brant, M.H. Wang, and P. Rawsthorne A population-based case-control study of CARD15 and other risk factors in Crohn's disease and ulcerative colitis Am J Gastroenterol 102 2007 313 323 (Pubitemid 46160545)
11. P.C. Stokkers, P.H. Reitsma, and G.N. Tytgat HLA-DR and -DQ phenotypes in inflammatory bowel disease: a meta- analysis Gut 45 1999 395 401 (Pubitemid 29400716)
12. K. Yamazaki, D. McGovern, and J. Ragoussis Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease Hum Mol Genet 14 2005 3499 3506 (Pubitemid 41672132)
13. Y. Kakuta, N. Ueki, and Y. Kinouchi TNFSF15 transcripts from risk haplotype for Crohn's disease are overexpressed in stimulated T cells Hum Mol Genet 18 2009 1089 1098
14. K.S. Michelsen, L.S. Thomas, and K.D. Taylor IBD-associated TL1A gene (TNFSF15) haplotypes determine increased expression of TL1A protein PLoS One 4 2009 e4719
15. A. Franke, D.P. McGovern, and J.C. Barrett Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci Nat Genet 42 2010 1118 1125
16. J.P. Hugot, M. Chamaillard, and H. Zouali Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease Nature 411 2001 599 603 (Pubitemid 32531408)
17. Y. Ogura, D.K. Bonen, and N. Inohara A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease Nature 411 2001 603 606 (Pubitemid 32531409)
18. C. Abraham, and J.H. Cho Functional consequences of NOD2 (CARD15) mutations Inflamm Bowel Dis 12 2006 641 650 (Pubitemid 43977746)
19. M. Economou, T.A. Trikalinos, and K.T. Loizou Differential effects of NOD2 variants on Crohn's disease risk and phenotype in diverse populations: a metaanalysis Am J Gastroenterol 99 2004 2393 2404 (Pubitemid 40039371)
20. S. Lesage, H. Zouali, and J.P. Cezard CARD15/NOD2 mutational analysis and genotype-phenotype correlation in 612 patients with inflammatory bowel disease Am J Hum Genet 70 2002 845 857 (Pubitemid 34259301)
21. S. Kugathasan, A. Loizides, and U. Babusukumar Comparative phenotypic and CARD15 mutational analysis among African American, Hispanic, and White children with Crohn's disease Inflamm Bowel Dis 11 2005 631 638 (Pubitemid 40961076)
22. T. Dassopoulos, G.C. Nguyen, and M.V. Talor NOD2 mutations and anti-Saccharomyces cerevisiae antibodies are risk factors for Crohn's disease in African Americans Am J Gastroenterol 105 2010 378 386
23. N. Inoue, K. Tamura, and Y. Kinouchi Lack of common NOD2 variants in Japanese patients with Crohn's disease Gastroenterology 123 2002 86 91 (Pubitemid 34747528)
24. K. Yamazaki, M. Takazoe, and T. Tanaka Absence of mutation in the NOD2/CARD15 gene among 483 Japanese patients with Crohn's disease J Hum Genet 47 2002 469 472 (Pubitemid 34988282)
25. F. Coulombe, M. Divangahi, and F. Veyrier Increased NOD2-mediated recognition of N-glycolyl muramyl dipeptide J Exp Med 206 2009 1709 1716
26. F.R. Zhang, W. Huang, and S.M. Chen Genomewide association study of leprosy N Engl J Med 361 2009 2609 2618
27. B. Levine, and V. Deretic Unveiling the roles of autophagy in innate and adaptive immunity Nat Rev Immunol 7 2007 767 777 (Pubitemid 47480305)
28. K. Cadwell, J.Y. Liu, and S.L. Brown A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells Nature 456 2008 259 263
29. P. Kuballa, A. Huett, and J.D. Rioux Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant PLoS One 3 2008 e3391
30. K. Cadwell, K.K. Patel, and N.S. Maloney Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine Cell 141 2010 1135 1145
31. R. Cooney, J. Baker, and O. Brain NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation Nat Med 16 2010 90 97
32. L.H. Travassos, L.A. Carneiro, and M. Ramjeet Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry Nat Immunol 11 2010 55 62
33. J.C. Barrett, S. Hansoul, and D.L. Nicolae Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease Nat Genet 40 2008 955 962
34. M. Parkes, J.C. Barrett, and N.J. Prescott Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility Nat Genet 39 2007 830 832 (Pubitemid 47014496)
35. S.A. McCarroll, A. Huett, and P. Kuballa Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease Nat Genet 40 2008 1107 1112
36. N.J. Prescott, K.M. Dominy, and M. Kubo Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease Hum Mol Genet 19 2010 1828 1839
37. L. Skipper, Y. Li, and C. Bonnard Comprehensive evaluation of common genetic variation within LRRK2 reveals evidence for association with sporadic Parkinson's disease Hum Mol Genet 14 2005 3549 3556 (Pubitemid 41754656)
38. Y. Tong, H. Yamaguchi, and E. Giaime Loss of leucine-rich repeat kinase 2 causes impairment of protein degradation pathways, accumulation of alpha-synuclein, and apoptotic cell death in aged mice Proc Natl Acad Sci U S A 107 2010 9879 9884
39. M.M. Fernando, C.R. Stevens, and E.C. Walsh Defining the role of the MHC in autoimmunity: a review and pooled analysis PLoS Genet 4 2008 e1000024
40. N. Bottini, L. Musumeci, and A. Alonso A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes Nat Genet 36 2004 337 338 (Pubitemid 38437254)
41. L.A. Criswell, K.A. Pfeiffer, and R.F. Lum Analysis of Families in the Multiple Autoimmune Disease Genetics Consortium (MADGC) Collection: the PTPN22 620W Allele Associates with Multiple Autoimmune Phenotypes Am J Hum Genet 76 2005 561 571 (Pubitemid 40432164)
42. D.A. Hafler, A. Compston, and S. Sawcer Risk alleles for multiple sclerosis identified by a genomewide study N Engl J Med 357 2007 851 862 (Pubitemid 47347319)
43. D.J. Cua, J. Sherlock, and Y. Chen Interleukin-23 rather than interleukin-12 is the critical cytokine for autoimmune inflammation of the brain Nature 421 2003 744 748 (Pubitemid 36227625)
44. Y. Momozawa, M. Mni, and K. Nakamura Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease Nat Genet 43 2010 43 47
45. M. Cargill, S.J. Schrodi, and M. Chang A large-scale genetic association study confirms IL12B and leads to the identification of IL23R as psoriasis-risk genes Am J Hum Genet 80 2007 273 290 (Pubitemid 46175676)
46. R.P. Nair, K.C. Duffin, and C. Helms Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways Nat Genet 41 2009 199 204
47. P.R. Burton, D.G. Clayton, and L.R. Cardon Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants Nat Genet 39 2007 1329 1337 (Pubitemid 350041542)
48. P.J. Mannon, I.J. Fuss, and L. Mayer Anti-interleukin-12 antibody for active Crohn's disease N Engl J Med 351 2004 2069 2079 (Pubitemid 39482500)
49. G.G. Krueger, R.G. Langley, and C. Leonardi A human interleukin-12/23 monoclonal antibody for the treatment of psoriasis N Engl J Med 356 2007 580 592 (Pubitemid 46220818)
50. K. Wang, H. Zhang, and S. Kugathasan Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn Disease Am J Hum Genet 84 2009 399 405
51. J.H. Cho The genetics and immunopathogenesis of inflammatory bowel disease Nat Rev Immunol 8 2008 458 466 (Pubitemid 351733422)
52. D.P. McGovern, M.R. Jones, and K.D. Taylor Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease Hum Mol Genet 19 2010 3468 3476
53. A. Kaser, A.H. Lee, and A. Franke XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease Cell 134 2008 743 756
54. B. Carlsson, E. Kindberg, and J. Buesa The G428A nonsense mutation in FUT2 provides strong but not absolute protection against symptomatic GII.4 Norovirus infection PLoS One 4 2009 e5593
55. S.A. Fisher, M. Tremelling, and C.A. Anderson Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease Nat Genet 40 2008 710 712 (Pubitemid 351748865)
56. A. Franke, T. Balschun, and T.H. Karlsen Replication of signals from recent studies of Crohn's disease identifies previously unknown disease loci for ulcerative colitis Nat Genet 40 2008 713 715 (Pubitemid 351748866)
57. R. Derynck, and Y.E. Zhang Smad-dependent and Smad-independent pathways in TGF-beta family signalling Nature 425 2003 577 584 (Pubitemid 37280136)
58. X. Li, G. Thyssen, and J. Beliakoff The novel PIAS-like protein hZimp10 enhances Smad transcriptional activity J Biol Chem 281 2006 23748 23756 (Pubitemid 44274150)
59. E.A. Stahl, S. Raychaudhuri, and E.F. Remmers Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci Nat Genet 42 2010 508 514
60. V. Gateva, J.K. Sandling, and G. Hom A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus Nat Genet 41 2009 1228 1233
61. O. Pabst, R. Zweigerdt, and H.H. Arnold Targeted disruption of the homeobox transcription factor Nkx2-3 in mice results in postnatal lethality and abnormal development of small intestine and spleen Development 126 1999 2215 2225 (Pubitemid 29271706)
62. M. Nishimura, Y. Kuboi, and K. Muramoto Chemokines as novel therapeutic targets for inflammatory bowel disease Ann N Y Acad Sci 1173 2009 350 356
63. L. Liu, D.C. Cara, and J. Kaur LSP1 is an endothelial gatekeeper of leukocyte transendothelial migration J Exp Med 201 2005 409 418 (Pubitemid 40229415)
64. M.S. Silverberg, J.H. Cho, and J.D. Rioux Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study Nat Genet 41 2009 216 220
65. F.R.J. Nimmerjahn Fcgamma receptors: old friends and new family members Immunity 24 2006 19 28
66. C.N. Bernstein, J.F. Blanchard, and P. Rawsthorne The prevalence of extraintestinal diseases in inflammatory bowel disease: a population-based study Am J Gastroenterol 96 2001 1116 1122 (Pubitemid 32319146)
67. T.H. Karlsen, A. Franke, and E. Melum Genome-wide association analysis in primary sclerosing cholangitis Gastroenterology 138 2010 1102 1111
68. E. Melum, A. Franke, and C. Schramm Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci Nat Genet 43 2011 17 19
69. G.M. Hirschfield, X. Liu, and C. Xu Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants N Engl J Med 360 2009 2544 2555
70. E.F. Remmers, F. Cosan, and Y. Kirino Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with Behcet's disease Nat Genet 42 2010 698 702
71. N. Mizuki, A. Meguro, and M. Ota Genome-wide association studies identify IL23R-IL12RB2 and IL10 as Behcet's disease susceptibility loci Nat Genet 42 2010 703 706
72. C. Miceli-Richard, S. Lesage, and M. Rybojad CARD15 mutations in Blau syndrome Nat Genet 29 2001 19 20 (Pubitemid 32801800)
73. J.D. Reveille, A.M. Sims, and P. Danoy Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci Nat Genet 42 2010 123 127
74. A. Strange, F. Capon, and C.C. Spencer A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1 Nat Genet 42 2010 985 990
75. C. Chen, X. Zhang, and Y. Wang Analysis of JAK2 and STAT3 polymorphisms in patients with ankylosing spondylitis in Chinese Han population Clin Immunol 136 2010 442 446
76. A. Zhernakova, E.M. Festen, and L. Franke Genetic analysis of innate immunity in Crohn's disease and ulcerative colitis identifies two susceptibility loci harboring CARD9 and IL18RAP Am J Hum Genet 82 2008 1202 1210
77. J.J. Pointon, D. Harvey, and T. Karaderi Elucidating the chromosome 9 association with AS; CARD9 is a candidate gene Genes Immun 11 2010 490 496
78. S. Kugathasan, R.N. Baldassano, and J.P. Bradfield Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease Nat Genet 40 2008 1211 1215
79. G.P. Thomas, and M.A. Brown Genetics and genomics of ankylosing spondylitis Immunol Rev 233 2010 162 180
80. K.A. Hunt, A. Zhernakova, and G. Turner Newly identified genetic risk variants for celiac disease related to the immune response Nat Genet 40 2008 395 402 (Pubitemid 351450876)
81. D.A. van Heel, L. Franke, and K.A. Hunt A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21 Nat Genet 39 2007 827 829 (Pubitemid 47014494)
82. N. Craddock, M.E. Hurles, and N. Cardin Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls Nature 464 2010 713 720
83. E. Holler, G. Rogler, and H. Herfarth Both donor and recipient NOD2/CARD15 mutations associate with transplant-related mortality and GvHD following allogeneic stem cell transplantation Blood 104 2004 889 894 (Pubitemid 38970589)
84. K. Yamazaki, M. Takazoe, and T. Tanaka Association analysis of SLC22A4, SLC22A5 and DLG5 in Japanese patients with Crohn disease J Hum Genet 49 2004 664 668
85. M. Tosa, K. Negoro, and Y. Kinouchi Lack of association between IBD5 and Crohn's disease in Japanese patients demonstrates population-specific differences in inflammatory bowel disease Scand J Gastroenterol 41 2006 48 53 (Pubitemid 43030891)
86. J.C. Barrett, D.G. Clayton, and P. Concannon Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes Nat Genet 41 2009 703 707
87. T.G. Dubois PC, L. Franke, and K.A. Hunt Multiple common variants for celiac disease influencing immune gene expression Nat Genet 42 2010 295 302
88. S.K. Yang, M. Park, and J. Lim Contribution of IL23R but not ATG16L1 to Crohn's disease susceptibility in Koreans Inflamm Bowel Dis 15 2009 1385 1390
89. K. Yamazaki, Y. Onouchi, and M. Takazoe Association analysis of genetic variants in IL23R, ATG16L1 and 5p13.1 loci with Crohn's disease in Japanese patients J Hum Genet 52 2007 575 583 (Pubitemid 47012531)
90. C.D. Intemann, T. Thye, and S. Niemann Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains PLoS Pathog 5 9 2009 e1000577
91. W. Satake, Y. Nakabayashi, and I. Mizuta Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease Nat Genet 41 2009 1303 1307
92. K. Asano, T. Matsushita, and J. Umeno A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population Nat Genet 41 2009 1325 1329
93. J.B. Harley, M.E. Alarcon-Riquelme, and L.A. Criswell Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci Nat Genet 40 2008 204 210 (Pubitemid 351171405)
94. J.E. Salmon, S. Millard, and L.A. Schachter Fc gamma RIIA alleles are heritable risk factors for lupus nephritis in African Americans J Clin Invest 97 1996 1348 1354 (Pubitemid 26085492)
95. B.Z. Alizadeh, G. Valdigem, and M.J. Coenen Association analysis of functional variants of the FcgRIIa and FcgRIIIa genes with type 1 diabetes, celiac disease and rheumatoid arthritis Hum Mol Genet 16 2007 2552 2559 (Pubitemid 47617722)
96. P.L. De Jager, X. Jia, and J. Wang Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci Nat Genet 41 2009 776 782
97. S.K. Yang, J. Lim, and H.S. Chang Association of TNFSF15 with Crohn's disease in Koreans Am J Gastroenterol 103 2008 1437 1442 (Pubitemid 351813898)
98. C. Quan, Y.Q. Ren, and L.H. Xiang Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC Nat Genet 42 2010 614 618
99. K. Yamazaki, A. Takahashi, and M. Takazoe Positive association of genetic variants in the upstream region of NKX2-3 with Crohn's disease in Japanese patients Gut 58 2009 228 232
100. M.F. Moffatt, I.G. Gut, and F. Demenais A large-scale, consortium-based genomewide association study of asthma N Engl J Med 363 2010 1211 1221