Interaction of crohn's disease susceptibility genes in an australian paediatric cohort

PLoS ONE

Volumn 5, Issue 11, 2010, Pages

  Wagner, Josef ^a   Sim, Winnie H ^a   Ellis, Justine A ^a   Ong, Eng K ^a   Catto Smith, Anthony G ^b,c   Cameron, Donald J S ^c   Bishop, Ruth F ^a,b   Kirkwood, Carl D ^a,b  

^a MURDOCH CHILDREN'S RESEARCH INSTITUTE   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c ROYAL CHILDREN'S HOSPITAL   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 15; DECOY RECEPTOR 3; INTERLEUKIN 23 RECEPTOR; PROTEASOME; PROTEASOME ASSEMBLY CHAPERONE 1 PROTEIN; PROTEIN IBD5; PROTEIN IRGM; PROTEIN SLC22A4; PROTEIN SLC22A5; REGULATOR PROTEIN; TOLL LIKE RECEPTOR 4; UNCLASSIFIED DRUG; DSCR2 PROTEIN, HUMAN; GUANINE NUCLEOTIDE BINDING PROTEIN; IL23R PROTEIN, HUMAN; INTERLEUKIN RECEPTOR; IRGM PROTEIN, HUMAN; MEMBRANE PROTEIN; MUSCLE PROTEIN; NOD2 PROTEIN, HUMAN; ORGANIC CATION TRANSPORTER; SLC22A4 PROTEIN, HUMAN; SLC22A5 PROTEIN, HUMAN; TLR4 PROTEIN, HUMAN; TNFRSF6B PROTEIN, HUMAN;

ADOLESCENT; ARTICLE; AUSTRALIA; CHILD; CHROMOSOME 3P; CONTROLLED STUDY; CROHN DISEASE; FEMALE; GENE IDENTIFICATION; GENE INTERACTION; GENE LOCUS; GENE MUTATION; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HUMAN; MALE; PEDIATRICS; PRESCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM; CHI SQUARE DISTRIBUTION; COHORT ANALYSIS; GENE FREQUENCY; GENETIC EPISTASIS; GENETIC PREDISPOSITION; GENETICS; GENOTYPE; PATHOLOGY; PHENOTYPE; STATISTICAL MODEL;

AUSTRALIA; CHI-SQUARE DISTRIBUTION; CHILD; COHORT STUDIES; CROHN DISEASE; EPISTASIS, GENETIC; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; GTP-BINDING PROTEINS; HUMANS; LOGISTIC MODELS; MEMBRANE PROTEINS; MUSCLE PROTEINS; NOD2 SIGNALING ADAPTOR PROTEIN; ORGANIC CATION TRANSPORT PROTEINS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, INTERLEUKIN; RECEPTORS, TUMOR NECROSIS FACTOR, MEMBER 6B; TOLL-LIKE RECEPTOR 4;

EID: 78149482162     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015376     Document Type: Article

References (79)

1. Fiocchi C (1998) Inflammatory bowel disease: etiology and pathogenesis. Gastroenterology 115: 182-205.
2. Economou M, Pappas G (2008) New global map of Crohn's disease: Genetic, environmental, and socioeconomic correlations. Inflamm Bowel Dis 14: 709-720.
3. Phavichitr N, Cameron DJ, Catto-Smith AG (2003) Increasing incidence of Crohn's disease in Victorian children. J Gastroenterol Hepatol 18: 329-332.
4. Cosgrove M, Al-Atia RF, Jenkins HR (1996) The epidemiology of paediatric inflammatory bowel disease. Arch Dis Child 74: 460-461.
5. Vind I, Riis L, Jess T, Knudsen E, Pedersen N, et al. (2006) Increasing incidences of inflammatory bowel disease and decreasing surgery rates in Copenhagen City and County, 2003-2005: a population-based study from the Danish Crohn colitis database. Am J Gastroenterol 101: 1274-1282.
6. Shanahan F (2002) Crohn's disease. Lancet 359: 62-69.
7. Sartor RB (2006) Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol 3: 390-407.
8. Hugot JP, Chamaillard M, Zouali H, Lesage S, Cezard JP, et al. (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 411: 599-603.
9. Hugot JP, Laurent-Puig P, Gower-Rousseau C, Olson JM, Lee JC, et al. (1996) Mapping of a susceptibility locus for Crohn's disease on chromosome 16. Nature 379: 821-823.
10. Inohara N, Nunez G (2003) NODs: intracellular proteins involved in inflammation and apoptosis. Nat Rev Immunol 3: 371-382.
11. Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, et al. (2008) Genomewide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 40: 955-962.
12. de Ridder L, Weersma RK, Dijkstra G, van der Steege G, Benninga MA, et al. (2007) Genetic susceptibility has a more important role in pediatric-onset Crohn's disease than in adult-onset Crohn's disease. Inflamm Bowel Dis 13: 1083-1092.
13. Kugathasan S, Baldassano RN, Bradfield JP, Sleiman PM, Imielinski M, et al. (2008) Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. Nat Genet 40: 1211-1215.
14. Amre DK, Mack DR, Morgan K, Fujiwara M, Israel D, et al. (2009) Investigation of reported associations between the 20q13 and 21q22 loci and pediatric-onset Crohn's disease in Canadian children. Am J Gastroenterol 104: 2824-2828.
15. Deng HW, Chen WM, Recker RR (2000) QTL fine mapping by measuring and testing for Hardy-Weinberg and linkage disequilibrium at a series of linked marker loci in extreme samples of populations. American journal of human genetics 66: 1027-1045.
16. Lee WC (2003) Searching for disease-susceptibility loci by testing for Hardy- Weinberg disequilibrium in a gene bank of affected individuals. American journal of epidemiology 158: 397-400.
17. Ferraris A, Knafelz D, Torres B, Fortina P, Castro M, et al. (2005) Analysis of CARD15 gene variants in Italian pediatric patients with inflammatory bowel diseases. J Pediatr 147: 272-273.
18. Tomer G, Ceballos C, Concepcion E, Benkov KJ (2003) NOD2/CARD15 variants are associated with lower weight at diagnosis in children with Crohn's disease. Am J Gastroenterol 98: 2479-2484.
19. Yamazaki K, Takazoe M, Tanaka T, Kazumori T, Nakamura Y (2002) Absence of mutation in the NOD2/CARD15 gene among 483 Japanese patients with Crohn's disease. J Hum Genet 47: 469-472.
20. Libioulle C, Louis E, Hansoul S, Sandor C, Farnir F, et al. (2007) Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet 3: e58.
21. Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, et al. (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314: 1461-1463.
22. Amre DK, Mack D, Israel D, Morgan K, Lambrette P, et al. (2008) Association between genetic variants in the IL-23R gene and early-onset Crohn's disease: results from a case-control and family-based study among Canadian children. Am J Gastroenterol 103: 615-620.
23. Van Limbergen J, Russell RK, Nimmo ER, Drummond HE, Smith L, et al. (2007) IL23R Arg381Gln is associated with childhood onset inflammatory bowel disease in Scotland. Gut 56: 1173-1174.
24. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
25. Latiano A, Palmieri O, Corritore G, Valvano MR, Bossa F, et al. (2009) Variants at the 3p21 locus influence susceptibility and phenotype both in adults and early-onset patients with inflammatory bowel disease. Inflamm Bowel Dis.
26. Marquez A, Cenit MC, Nunez C, Mendoza JL, Taxonera C, et al. (2009) Effect of BSN-MST1 locus on inflammatory bowel disease and multiple sclerosis susceptibility. Genes Immun 10: 631-635.
27. Peterson N, Guthery S, Denson L, Lee J, Saeed S, et al. (2008) Genetic variants in the autophagy pathway contribute to paediatric Crohn's disease. Gut 57: 1336-1337; author reply 1337.
28. Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR, et al. (2003) Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 12: 205-216.
29. Bonen DK, Ogura Y, Nicolae DL, Inohara N, Saab L, et al. (2003) Crohn's disease-associated NOD2 variants share a signaling defect in response to lipopolysaccharide and peptidoglycan. Gastroenterology 124: 140-146.
30. Inohara N, Ogura Y, Fontalba A, Gutierrez O, Pons F, et al. (2003) Host recognition of bacterial muramyl dipeptide mediated through NOD2. Implications for Crohn's disease. J Biol Chem 278: 5509-5512.
31. Medzhitov R (2001) Toll-like receptors and innate immunity. Nat Rev Immunol 1: 135-145.
32. Hausmann M, Kiessling S, Mestermann S, Webb G, Spottl T, et al. (2002) Tolllike receptors 2 and 4 are up-regulated during intestinal inflammation. Gastroenterology 122: 1987-2000.
33. Rosenzweig R, Glickman MH (2008) Chaperone-driven proteasome assembly. Biochem Soc Trans 36: 807-812.
34. Visekruna A, Slavova N, Dullat S, Grone J, Kroesen AJ, et al. (2009) Expression of catalytic proteasome subunits in the gut of patients with Crohn's disease. Int J Colorectal Dis 24: 1133-1139.
35. Fitzpatrick LR, Small JS, Poritz LS, McKenna KJ, Koltun WA (2007) Enhanced intestinal expression of the proteasome subunit low molecular mass polypeptide 2 in patients with inflammatory bowel disease. Dis Colon Rectum 50: 337-348; discussion 348-350.
36. Stohwasser R, Giesebrecht J, Kraft R, Muller EC, Hausler KG, et al. (2000) Biochemical analysis of proteasomes from mouse microglia: induction of immunoproteasomes by interferon-gamma and lipopolysaccharide. Glia 29: 355-365.
37. Hayashi T, Faustman D (2000) Essential role of human leukocyte antigenencoded proteasome subunits in NF-kappaB activation and prevention of tumor necrosis factor-alpha-induced apoptosis. J Biol Chem 275: 5238-5247.
38. Hayden MS, Ghosh S (2004) Signaling to NF-kappaB. Genes Dev 18: 2195-2224.
39. McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, et al. (2008) Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet 40: 1107-1112.
40. Amre DK, Mack DR, Morgan K, Krupoves A, Costea I, et al. (2009) Autophagy gene ATG16L1 but not IRGM is associated with Crohn's disease in Canadian children. Inflamm Bowel Dis 15: 501-507.
41. Roberts RL, Hollis-Moffatt JE, Gearry RB, Kennedy MA, Barclay ML, et al. (2008) Confirmation of association of IRGM and NCF4 with ileal Crohn's disease in a population-based cohort. Genes Immun 9: 561-565.
42. Van Limbergen J, Russell RK, Nimmo ER, Drummond HE, G D, et al. (2009) Germline variants of IRGM in childhood-onset Crohn's disease. Gut 58: 610-611.
43. Latiano A, Palmieri O, Corritore G (2010) Variants at the 3p21 Locus influence susceptibility and phenotype both in adults and early-onset patients with inflammatory bowel disease. Inflamm Bowel Dis.
44. Waschke KA, Villani AC, Vermeire S, Dufresne L, Chen TC, et al. (2005) Tumor necrosis factor receptor gene polymorphisms in Crohn's disease: association with clinical phenotypes. Am J Gastroenterol 100: 1126-1133.
45. Silverberg MS, Satsangi J, Ahmad T, Arnott ID, Bernstein CN, et al. (2005) Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: Report of a Working Party of the 2005 Montreal World Congress of Gastroenterology. Can J Gastroenterol 19 Suppl A: 5-36.
46. Kirkwood CD, Wagner J, Boniface K, Vaughan J, Michalski WP, et al. (2009) Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn's disease. Inflamm Bowel Dis 15: 1643-1655.
47. Wagner J, Short K, Catto-Smith AG, Cameron DJ, Bishop RF, et al. (2008) Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease. PLoS One 3: e3578.
48. Jurinke C, van den Boom D, Cantor CR, Koster H (2002) Automated genotyping using the DNA MassArray technology. Methods Mol Biol 187: 179-192.
49. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. American journal of human genetics 81: 559-575.
50. Wacholder S, Chanock S, Garcia-Closas M, El Ghormli L, Rothman N (2004) Assessing the probability that a positive report is false: an approach for molecular epidemiology studies. J Natl Cancer Inst 96: 434-442.
51. Cucchiara S, Latiano A, Palmieri O, Staiano AM, D'Inca R, et al. (2007) Role of CARD15, DLG5 and OCTN genes polymorphisms in children with inflammatory bowel diseases. World J Gastroenterol 13: 1221-1229.
52. Lesage S, Zouali H, Cezard JP, Colombel JF, Belaiche J, et al. (2002) CARD15/ NOD2 mutational analysis and genotype-phenotype correlation in 612 patients with inflammatory bowel disease. Am J Hum Genet 70: 845-857.
53. Rigoli L, Romano C, Caruso RA, Lo Presti MA, Di Bella C, et al. (2008) Clinical significance of NOD2/CARD15 and Toll-like receptor 4 gene single nucleotide polymorphisms in inflammatory bowel disease. World J Gastroenterol 14: 4454-4461.
54. Franchimont D, Vermeire S, El Housni H, Pierik M, Van Steen K, et al. (2004) Deficient host-bacteria interactions in inflammatory bowel disease? The toll-like receptor (TLR)-4 Asp299gly polymorphism is associated with Crohn's disease and ulcerative colitis. Gut 53: 987-992.
55. Waller S, Tremelling M, Bredin F, Godfrey L, Howson J, et al. (2006) Evidence for association of OCTN genes and IBD5 with ulcerative colitis. Gut 55: 809-814.
56. Ogura Y, Bonen DK, Inohara N, Nicolae DL, Chen FF, et al. (2001) A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 411: 603-606.
57. McGovern DP, Hysi P, Ahmad T, van Heel DA, Moffatt MF, et al. (2005) Association between a complex insertion/deletion polymorphism in NOD1 (CARD4) and susceptibility to inflammatory bowel disease. Hum Mol Genet 14: 1245-1250.
58. Glas J, Seiderer J, Wetzke M, Konrad A, Torok HP, et al. (2007) rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants. PLoS One 2: e819.
59. Latiano A, Palmieri O, Valvano MR, D'Inca R, Cucchiara S, et al. (2008) Replication of interleukin 23 receptor and autophagy-related 16-like 1 association in adult- and pediatric-onset inflammatory bowel disease in Italy. World J Gastroenterol 14: 4643-4651.
60. Gasche C, Grundtner P, Zwirn P, Reinisch W, Shaw SH, et al. (2003) Novel variants of the IL-10 receptor 1 affect inhibition of monocyte TNF-alpha production. J Immunol 170: 5578-5582.
61. Stoll M, Corneliussen B, Costello CM, Waetzig GH, Mellgard B, et al. (2004) Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet 36: 476-480.
62. Newman WG, Gu X, Wintle RF, Liu X, van Oene M, et al. (2006) DLG5 variants contribute to Crohn disease risk in a Canadian population. Hum Mutat 27: 353-358.
63. Browning BL, Huebner C, Petermann I, Demmers P, McCulloch A, et al. (2007) Association of DLG5 variants with inflammatory bowel disease in the New Zealand Caucasian population and meta-analysis of the DLG5 R30Q variant. Inflamm Bowel Dis 13: 1069-1076.
64. Noble CL, Nimmo ER, Drummond H, Smith L, Arnott ID, et al. (2005) DLG5 variants do not influence susceptibility to inflammatory bowel disease in the Scottish population. Gut 54: 1416-1420.
65. Lakner L, Csongei V, Sarlos P, Jaromi L, Safrany E, et al. (2009) IGR2096a_1 T and IGR2198a_1 C alleles on IBD5 locus of chromosome 5q31 region confer risk for Crohn's disease in Hungarian patients. Int J Colorectal Dis 24: 503-507.
66. Rioux JD, Daly MJ, Silverberg MS, Lindblad K, Steinhart H, et al. (2001) Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat Genet 29: 223-228.
67. Noble CL, Nimmo ER, Drummond H, Ho GT, Tenesa A, et al. (2005) The contribution of OCTN1/2 variants within the IBD5 locus to disease susceptibility and severity in Crohn's disease. Gastroenterology 129: 1854-1864.
68. Russell RK, Drummond HE, Nimmo ER, Anderson NH, Noble CL, et al. (2006) Analysis of the influence of OCTN1/2 variants within the IBD5 locus on disease susceptibility and growth indices in early onset inflammatory bowel disease. Gut 55: 1114-1123.
69. Peltekova VD, Wintle RF, Rubin LA, Amos CI, Huang Q, et al. (2004) Functional variants of OCTN cation transporter genes are associated with Crohn disease. Nat Genet 36: 471-475.
70. Prescott NJ, Fisher SA, Franke A, Hampe J, Onnie CM, et al. (2007) A nonsynonymous SNP in ATG16L1 predisposes to ileal Crohn's disease and is independent of CARD15 and IBD5. Gastroenterology 132: 1665-1671.
71. Cummings JR, Cooney R, Pathan S, Anderson CA, Barrett JC, et al. (2007) Confirmation of the role of ATG16L1 as a Crohn's disease susceptibility gene. Inflamm Bowel Dis 13: 941-946.
72. Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, et al. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 39: 207-211.
73. Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, et al. (2007) Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet 39: 830-832.
74. Weersma RK, Stokkers PC, Cleynen I, Wolfkamp SC, Henckaerts L, et al. (2009) Confirmation of multiple Crohn's disease susceptibility loci in a large Dutch-Belgian cohort. Am J Gastroenterol 104: 630-638.
75. Yamazaki K, Takahashi A, Takazoe M, Kubo M, Onouchi Y, et al. (2009) Positive association of genetic variants in the upstream region of NKX2-3 with Crohn's disease in Japanese patients. Gut 58: 228-232.
76. Yu W, Lin Z, Kelly AA, Hegarty JP, Poritz LS, et al. (2009) Association of a Nkx2-3 polymorphism with Crohn's disease and expression of Nkx2-3 is upregulated in B cell lines and intestinal tissues with Crohn's disease. Journal of Crohn's and Colitis 3: 189.
77. Franke A, Hampe J, Rosenstiel P, Becker C, Wagner F, et al. (2007) Systematic association mapping identifies NELL1 as a novel IBD disease gene. PLoS One 2: e691.
78. Krupoves A, Seidman EG, Mack D, Israel D, Morgan K, et al. (2008) Associations between ABCB1/MDR1 gene polymorphisms and Crohn's disease: A gene-wide study in a pediatric population. Inflamm Bowel Dis.
79. Latiano A, Palmieri O, Valvano MR, D'Inca R, Caprilli R, et al. (2008) The association of MYO9B gene in Italian patients with inflammatory bowel diseases. Aliment Pharmacol Ther 27: 241-248.