Insight from genome-wide association studies in rheumatoid arthritis and multiple sclerosis

FEBS Letters

Volumn 585, Issue 23, 2011, Pages 3627-3632

  Suzuki, Akari ^a   Kochi, Yuta ^a   Okada, Yukinari ^a,b   Yamamoto, Kazuhiko ^a,b  

^a INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Genetic risk factor; GWAS; HLA; Multiple sclerosis; Non HLA gene; Rheumatoid arthritis

Indexed keywords

C TYPE LECTIN DOMAIN FAMILY 16 MEMBER A; CD40 ANTIGEN; CHEMOKINE RECEPTOR CCR6; HLA DR ANTIGEN; INTERLEUKIN 2 RECEPTOR; LECTIN; MAJOR HISTOCOMPATIBILITY ANTIGEN; METHYLTRANSFERASE; METHYLTRANSFERASE LIKE PROTEIN 1; NON RECEPTOR PROTEIN TYROSINE PHOSPHATASE 22; PROTEIN ARGININE DEIMINASE; PROTEIN ARGININE DEIMINASE 4; TUMOR NECROSIS FACTOR ALPHA INDUCED PROTEIN 3; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR; UNCLASSIFIED DRUG;

AUTOIMMUNE DISEASE; CCR6 GENE; CD40 GENE; CLEC16A GENE; GENE; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HEREDITY; HERITABILITY; HLA GENE; HUMAN; IL2RA GENE; MAJOR HISTOCOMPATIBILITY COMPLEX GENE; METTL1 GENE; MULTIPLE SCLEROSIS; PADI4 GENE; PRIORITY JOURNAL; PTPN22 GENE; REVIEW; RHEUMATOID ARTHRITIS; RISK ASSESSMENT; SINGLE NUCLEOTIDE POLYMORPHISM; TNFAIP3 GENE;

ARTHRITIS, RHEUMATOID; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INHERITANCE PATTERNS; MULTIPLE SCLEROSIS;

EID: 81755179420     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2011.05.025     Document Type: Review

References (94)

1. A.J. MacGregor, H. Snieder, A.S. Rigby, M. Koskenvuo, J. Kaprio, K. Aho, and A.J. Silman Characterizing the quantitative genetic contribution to rheumatoid arthritis using data from twins Arthritis Rheum. 43 2000 30 37 (Pubitemid 30368210)
2. G. Lettre, and J.D. Rioux Autoimmune diseases: insights from genome-wide association studies Hum. Mol. Genet. 17 2008 R116 R121
3. Y. Kochi, A. Suzuki, R. Yamada, and K. Yamamoto Ethnogenetic heterogeneity of rheumatoid arthritis-implications for pathogenesis Nat. Rev. Rheumatol. 6 2010 290 295
4. M. Mori, R. Yamada, K. Kobayashi, R. Kawaida, and K. Yamamoto Ethnic differences in allele frequency of autoimmune-disease-associated SNPs J. Hum. Genet. 50 2005 264 266 (Pubitemid 40922327)
5. M. Ban A non-synonymous SNP within membrane metalloendopeptidase-like 1 (MMEL1) is associated with multiple sclerosis Genes Immun 11 2010 660 664
6. P.R. Burton Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants Nat. Genet. 39 2007 1329 1337 (Pubitemid 350041542)
7. P.K. Gregersen, J. Silver, and R.J. Winchester The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis Arthritis Rheum. 30 1987 1205 1213 (Pubitemid 18005792)
8. A. Baccar Are HLA DQB1 alleles correlated with breast cancer histopronostic parameters in Tunisia? Tunis. Med. 87 2009 372 374
9. S. Nejentsev Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A Nature 450 2007 887 892 (Pubitemid 350231332)
10. S.T. du Montcel New classification of HLA-DRB1 alleles supports the shared epitope hypothesis of rheumatoid arthritis susceptibility Arthritis Rheum. 52 2005 1063 1068
11. T. Furuya, M. Hakoda, N. Ichikawa, K. Higami, Y. Nanke, T. Yago, N. Kamatani, and S. Kotake Associations between HLA-DRB1, RANK, RANKL, OPG, and IL-17 genotypes and disease severity phenotypes in Japanese patients with early rheumatoid arthritis Clin. Rheumatol. 26 2007 2137 2141 (Pubitemid 350120354)
12. L.F. Barcellos Heterogeneity at the HLA-DRB1 locus and risk for multiple sclerosis Hum. Mol. Genet. 15 2006 2813 2824 (Pubitemid 44400408)
13. D.S. Goodin The causal cascade to multiple sclerosis: A model for MS pathogenesis PLoS ONE 4 2009 e4565
14. D. Jawaheer A genomewide screen in multiplex rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases Am. J. Hum. Genet. 68 2001 927 936 (Pubitemid 32289739)
15. F. Cornelis New susceptibility locus for rheumatoid arthritis suggested by a genome-wide linkage study Proc. Natl. Acad. Sci. USA 95 1998 10746 10750
16. S. Shiozawa Identification of the gene loci that predispose to rheumatoid arthritis Int. Immunol. 10 1998 1891 1895 (Pubitemid 28566051)
17. S.E. Baranzini Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis Hum. Mol. Genet. 18 2009 767 778
18. D.A. Hafler Risk alleles for multiple sclerosis identified by a genomewide study N. Engl. J. Med. 357 2007 851 862 (Pubitemid 47347319)
19. R.J. Xavier, and J.D. Rioux Genome-wide association studies: A new window into immune-mediated diseases Nat. Rev. Immunol. 8 2008 631 643
20. Y. Kochi A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility Nat. Genet. 42 2010 515 519
21. R.M. Plenge TRAF1-C5 as a risk locus for rheumatoid arthritis - a genomewide study N. Engl. J. Med. 357 2007 1199 1209 (Pubitemid 47443179)
22. M. Sirota, M.A. Schaub, S. Batzoglou, W.H. Robinson, and A.J. Butte Autoimmune disease classification by inverse association with SNP alleles PLoS Genet. 5 2009 e1000792
23. W. Bodmer, and C. Bonilla Common and rare variants in multifactorial susceptibility to common diseases Nat. Genet. 40 2008 695 701 (Pubitemid 351748875)
24. J. Bowes Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis Hum. Genet. 128 2010 627 633
25. M.F. Seldin, C.I. Amos, R. Ward, and P.K. Gregersen The genetics revolution and the assault on rheumatoid arthritis Arthritis Rheum. 42 1999 1071 1079 (Pubitemid 29268942)
26. C.M. Weyand, and J.J. Goronzy Association of MHC and rheumatoid arthritis. HLA polymorphisms in phenotypic variants of rheumatoid arthritis Arthritis Res. 2 2000 212 216 (Pubitemid 32223730)
27. P.K. Gregersen Susceptibility genes for rheumatoid arthritis - a rapidly expanding harvest Bull. Hosp. Jt. Dis. (N.Y.) 68 2010 179 182
28. A. Suzuki Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis Nat. Genet. 34 2003 395 402 (Pubitemid 36935332)
29. A.B. Begovich A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis Am. J. Hum. Genet. 75 2004 330 337 (Pubitemid 38943877)
30. P. Stastny Association of the B-cell alloantigen DRw4 with rheumatoid arthritis N. Engl. J. Med. 298 1978 869 871 (Pubitemid 8330170)
31. H.S. Lee, K.W. Lee, G.G. Song, H.A. Kim, S.Y. Kim, and S.C. Bae Increased susceptibility to rheumatoid arthritis in Koreans heterozygous for HLA-DRB1*0405 and 0901 Arthritis Rheum. 50 2004 3468 3475 (Pubitemid 39488671)
32. F.A. Van Gaalen Association between HLA class II genes and autoantibodies to cyclic citrullinated peptides (CCPs) influences the severity of rheumatoid arthritis Arthritis Rheum. 50 2004 2113 2121 (Pubitemid 38924388)
33. B. Ding Different patterns of associations with anti-citrullinated protein antibody-positive and anti-citrullinated protein antibody-negative rheumatoid arthritis in the extended major histocompatibility complex region Arthritis Rheum. 60 2009 30 38
34. A. Kastbom, G. Strandberg, A. Lindroos, and T. Skogh Anti-CCP antibody test predicts the disease course during 3 years in early rheumatoid arthritis (the Swedish TIRA project) Ann. Rheum. Dis. 63 2004 1085 1089 (Pubitemid 39120359)
35. A.H. n Mil, K.N. Verpoort, F.C. Breedveld, R.E. Toes, and T.W. Huizinga Antibodies to citrullinated proteins and differences in clinical progression of rheumatoid arthritis Arthritis Res. Ther. 7 2005 R949 R958
36. T. Furuya Differential association of HLA-DRB1 alleles in Japanese patients with early rheumatoid arthritis in relationship to autoantibodies to cyclic citrullinated peptide Clin. Exp. Rheumatol. 25 2007 219 224 (Pubitemid 46851425)
37. P. Irigoyen Regulation of anti-cyclic citrullinated peptide antibodies in rheumatoid arthritis: contrasting effects of HLA-DR3 and the shared epitope alleles Arthritis Rheum. 52 2005 3813 3818 (Pubitemid 41798219)
38. S.Y. Bang, K.H. Lee, S.K. Cho, H.S. Lee, K.W. Lee, and S.C. Bae Smoking increases rheumatoid arthritis susceptibility in individuals carrying the HLA-DRB1 shared epitope, regardless of rheumatoid factor or anti-cyclic citrullinated peptide antibody status Arthritis Rheum. 62 2010 369 377
39. S. Raychaudhuri Common variants at CD40 and other loci confer risk of rheumatoid arthritis Nat. Genet. 40 2008 1216 1223
40. N. Bottini A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes Nat. Genet. 36 2004 337 338 (Pubitemid 38437254)
41. Y.H. Lee, Y.H. Rho, S.J. Choi, J.D. Ji, G.G. Song, S.K. Nath, and J.B. Harley The PTPN22 C1858T functional polymorphism and autoimmune diseases - a meta-analysis Rheumatology (Oxford) 46 2007 49 56 (Pubitemid 44932783)
42. G. Orozco Association of a functional single-nucleotide polymorphism of PTPN22, encoding lymphoid protein phosphatase, with rheumatoid arthritis and systemic lupus erythematosus Arthritis Rheum. 52 2005 219 224 (Pubitemid 40129251)
43. A. Hinks Association between the PTPN22 gene and rheumatoid arthritis and juvenile idiopathic arthritis in a UK population: further support that PTPN22 is an autoimmunity gene Arthritis Rheum. 52 2005 1694 1699 (Pubitemid 40852877)
44. L.A. Criswell 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)
45. P. Dieude The PTPN22 620W allele confers susceptibility to systemic sclerosis: findings of a large case-control study of European Caucasians and a meta-analysis Arthritis Rheum. 58 2008 2183 2188 (Pubitemid 351988112)
46. H. Asaga, K. Nakashima, T. Senshu, A. Ishigami, and M. Yamada Immunocytochemical localization of peptidylarginine deiminase in human eosinophils and neutrophils J. Leukoc. Biol. 70 2001 46 51 (Pubitemid 32613661)
47. X. Chang, R. Yamada, A. Suzuki, T. Sawada, S. Yoshino, S. Tokuhiro, and K. Yamamoto Localization of peptidylarginine deiminase 4 (PADI4) and citrullinated protein in synovial tissue of rheumatoid arthritis Rheumatology (Oxford) 44 2005 40 50 (Pubitemid 40124330)
48. H. Asaga, M. Yamada, and T. Senshu Selective deimination of vimentin in calcium ionophore-induced apoptosis of mouse peritoneal macrophages Biochem. Biophys. Res. Commun. 243 1998 641 646 (Pubitemid 28414131)
49. J. Worthington, and S. John Association of PADI4 and rheumatoid arthritis: A successful multidisciplinary approach Trends Mol. Med. 9 2003 405 407 (Pubitemid 37309638)
50. T. Iwamoto, K. Ikari, T. Nakamura, M. Kuwahara, Y. Toyama, T. Tomatsu, S. Momohara, and N. Kamatani Association between PADI4 and rheumatoid arthritis: A meta-analysis Rheumatology (Oxford) 45 2006 804 807 (Pubitemid 43985366)
51. K. Ikari, M. Kuwahara, T. Nakamura, S. Momohara, M. Hara, H. Yamanaka, T. Tomatsu, and N. Kamatani Association between PADI4 and rheumatoid arthritis: A replication study Arthritis Rheum. 52 2005 3054 3057 (Pubitemid 41447085)
52. C.P. Kang, H.S. Lee, H. Ju, H. Cho, C. Kang, and S.C. Bae A functional haplotype of the PADI4 gene associated with increased rheumatoid arthritis susceptibility in Koreans Arthritis Rheum. 54 2006 90 96 (Pubitemid 43122191)
53. A. Barton, J. Bowes, S. Eyre, K. Spreckley, A. Hinks, S. John, and J. Worthington A functional haplotype of the PADI4 gene associated with rheumatoid arthritis in a Japanese population is not associated in a United Kingdom population Arthritis Rheum. 50 2004 1117 1121 (Pubitemid 38480821)
54. L. Caponi A family based study shows no association between rheumatoid arthritis and the PADI4 gene in a white French population Ann. Rheum. Dis. 64 2005 587 593 (Pubitemid 40469089)
55. A. Barton, J. Bowes, S. Eyre, D. Symmons, J. Worthington, and A. Silman Investigation of polymorphisms in the PADI4 gene in determining severity of inflammatory polyarthritis Ann. Rheum. Dis. 64 2005 1311 1315 (Pubitemid 41206248)
56. S.M. Harney, C. Meisel, A.M. Sims, P.Y. Woon, B.P. Wordsworth, and M.A. Brown Genetic and genomic studies of PADI4 in rheumatoid arthritis Rheumatology (Oxford) 44 2005 869 872 (Pubitemid 41511180)
57. B. Hoppe, T. Haupl, R. Gruber, H. Kiesewetter, G.R. Burmester, A. Salama, and T. Dorner Detailed analysis of the variability of peptidylarginine deiminase type 4 in German patients with rheumatoid arthritis: A case-control study Arthritis Res. Ther. 8 2006 R34
58. L. Klareskog A new model for an etiology of rheumatoid arthritis: smoking may trigger HLA-DR (shared epitope)-restricted immune reactions to autoantigens modified by citrullination Arthritis Rheum. 54 2006 38 46 (Pubitemid 43122184)
59. L. Klareskog, L. Padyukov, J. Ronnelid, and L. Alfredsson Genes, environment and immunity in the development of rheumatoid arthritis Curr. Opin. Immunol. 18 2006 650 655 (Pubitemid 44635174)
60. H. Kallberg Gene-gene and gene-environment interactions involving HLA-DRB1, PTPN22, and smoking in two subsets of rheumatoid arthritis Am. J. Hum. Genet. 80 2007 867 875 (Pubitemid 46668455)
61. D. Makrygiannakis Smoking increases peptidylarginine deiminase 2 enzyme expression in human lungs and increases citrullination in BAL cells Ann. Rheum. Dis. 67 2008 1488 1492
62. L. Mei, X. Li, K. Yang, J. Cui, B. Fang, X. Guo, and J.I. Rotter Evaluating gene x gene and gene x smoking interaction in rheumatoid arthritis using candidate genes in GAW15 BMC Proc. 1 Suppl. 1 2007 S17
63. Y. Kochi PADI4 polymorphism predisposes male smokers to rheumatoid arthritis Ann. Rheum. Dis. 70 2011 512 515
64. G. Orozco Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study Ann. Rheum. Dis. 69 2009 813 816
65. R.M. Plenge Two independent alleles at 6q23 associated with risk of rheumatoid arthritis Nat. Genet. 39 2007 1477 1482 (Pubitemid 350191346)
66. G. Orozco Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23 Hum. Mol. Genet. 18 2009 2693 2699
67. H.S. Lee, B.D. Korman, J.M. Le, D.L. Kastner, E.F. Remmers, P.K. Gregersen, and S.C. Bae Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations Arthritis Rheum. 60 2009 364 371
68. ANZgene Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20 Nat. Genet. 41 2009 824 828
69. E.A. Stahl Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci Nat. Genet. 42 2010 508 514
70. K. Hirota Preferential recruitment of CCR6-expressing Th17 cells to inflamed joints via CCL20 in rheumatoid arthritis and its animal model J. Exp. Med. 204 2007 2803 2812 (Pubitemid 350179551)
71. T. Matsui Selective recruitment of CCR6-expressing cells by increased production of MIP-3 alpha in rheumatoid arthritis Clin. Exp. Immunol. 125 2001 155 161 (Pubitemid 32703379)
72. J.M. Frischer The relation between inflammation and neurodegeneration in multiple sclerosis brains Brain 132 2009 1175 1189
73. N.R. Wray, and M.E. Goddard Multi-locus models of genetic risk of disease Genome Med. 2 2010 10
74. P.I. Terasaki, M.S. Park, G. Opelz, and A. Ting Multiple sclerosis and high incidence of a B lymphocyte antigen Science 193 1976 1245 1247
75. T.W. Yeo A second major histocompatibility complex susceptibility locus for multiple sclerosis Ann. Neurol. 61 2007 228 236 (Pubitemid 46557347)
76. S. Sawcer The genetic aspects of multiple sclerosis Ann. Indian Acad. Neurol. 12 2009 206 214
77. R. Zivadinov Smoking is associated with increased lesion volumes and brain atrophy in multiple sclerosis Neurology 73 2009 504 510
78. A. Ligers, D.A. Dyment, C.J. Willer, A.D. Sadovnick, G. Ebers, N. Risch, and J. Hillert Evidence of linkage with HLA-DR in DRB1*15-negative families with multiple sclerosis Am. J. Hum. Genet. 69 2001 900 903 (Pubitemid 32868536)
79. P.L. De Jager Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci Nat. Genet. 41 2009 776 782
80. S.A. Bahreini, M.R. Jabalameli, M. Saadatnia, and H. Zahednasab The role of non-HLA single nucleotide polymorphisms in multiple sclerosis susceptibility J. Neuroimmunol. 229 2010 5 15
81. TMSGC Refining genetic associations in multiple sclerosis Lancet Neurol. 7 2008 567 569
82. C.E. Lowe Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes Nat. Genet. 39 2007 1074 1082 (Pubitemid 47340651)
83. L.M. Maier IL2RA genetic heterogeneity in multiple sclerosis and type 1 diabetes susceptibility and soluble interleukin-2 receptor production PLoS Genet. 5 2009 e1000322
84. WTCCC Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls Nature 447 2007 661 678
85. J.A. Todd Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes Nat. Genet. 39 2007 857 864 (Pubitemid 47018195)
86. J.P. Rubio Replication of KIAA0350, IL2RA, RPL5 and CD58 as multiple sclerosis susceptibility genes in Australians Genes Immun. 9 2008 624 630
87. A.E. Handel, L. Handunnetthi, A.J. Berlanga, C.T. Watson, J.M. Morahan, and S.V. Ramagopalan The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression PLoS ONE 5 2010 e10142
88. S.E. Baranzini The genetics of autoimmune diseases: A networked perspective Curr. Opin. Immunol. 21 2009 596 605
89. S.E. Baranzini Pathway and network-based analysis of genome-wide association studies in multiple sclerosis Hum. Mol. Genet. 18 2009 2078 2090
90. J.P. Lin, J.M. Cash, S.Z. Doyle, S. Peden, K. Kanik, C.I. Amos, S.J. Bale, and R.L. WilDer Familial clustering of rheumatoid arthritis with other autoimmune diseases Hum. Genet. 103 1998 475 482 (Pubitemid 28542960)
91. IMSGC The expanding genetic overlap between multiple sclerosis and type I diabetes Genes Immun. 10 2009 11 14
92. G. Orozco, and A. Barton Update on the genetic risk factors for rheumatoid arthritis Expert Rev. Clin. Immunol. 6 2010 61 75
93. W.S. Bush, S.J. Sawcer, P.L. De Jager, J.R. Oksenberg, J.L. McCauley, M.A. Pericak-Vance, and J.L. Haines Evidence for polygenic susceptibility to multiple sclerosis - the shape of things to come Am. J. Hum. Genet. 86 2010 621 625
94. J. Yang Common SNPs explain a large proportion of the heritability for human height Nat. Genet. 42 2010 565 569