Functional SNPs in CD244 increase the risk of rheumatoid arthritis in a Japanese population (original) (raw)

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GenBank/EMBL/DDBJ

Gene Expression Omnibus

References

  1. Cornelis, F. et al. New susceptibility locus for rheumatoid arthritis suggested by a genome-wide linkage study. Proc. Natl. Acad. Sci. USA 95, 10746–10750 (1998).
    Article CAS Google Scholar
  2. Shiozawa, S. et al. Identification of the gene loci that predispose to rheumatoid arthritis. Int. Immunol. 10, 1891–1895 (1998).
    Article CAS Google Scholar
  3. MacKay, K. et al. Whole-genome linkage analysis of rheumatoid arthritis susceptibility loci in 252 affected sibling pairs in the United Kingdom. Arthritis Rheum. 46, 632–639 (2002).
    Article CAS Google Scholar
  4. Jawaheer, D. et al. A genomewide screen in multiplex rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases. Am. J. Hum. Genet. 68, 927–936 (2001).
    Article CAS Google Scholar
  5. Seldin, M.F., Amos, C.I., Ward, R. & Gregersen, P.K. The genetics revolution and the assault on rheumatoid arthritis. Arthritis Rheum. 42, 1071–1079 (1999).
    Article CAS Google Scholar
  6. Begovich, A.B. et al. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am. J. Hum. Genet. 75, 330–337 (2004).
    Article CAS Google Scholar
  7. Suzuki, A. et al. Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat. Genet. 34, 395–402 (2003).
    Article CAS Google Scholar
  8. Remmers, E.F. et al. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N. Engl. J. Med. 357, 977–986 (2007).
    Article CAS Google Scholar
  9. Kochi, Y. et al. A functional variant in FCRL3, encoding Fc receptor-like 3, is associated with rheumatoid arthritis and several autoimmunities. Nat. Genet. 37, 478–485 (2005).
    Article CAS Google Scholar
  10. Tokuhiro, S. et al. An intronic SNP in a RUNX1 binding site of SLC22A4, encoding an organic cation transporter, is associated with rheumatoid arthritis. Nat. Genet. 35, 341–348 (2003).
    Article CAS Google Scholar
  11. Plenge, R.M. et al. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Am. J. Hum. Genet. 77, 1044–1060 (2005).
    Article CAS Google Scholar
  12. Iwamoto, T. et al. Association between PADI4 and rheumatoid arthritis: a meta-analysis. Rheumatology (Oxford) 45, 804–807 (2006).
    Article CAS Google Scholar
  13. Lee, Y.H. et al. The PTPN22 C1858T functional polymorphism and autoimmune diseases–a meta-analysis. Rheumatology (Oxford) 46, 49–56 (2007).
    Article CAS Google Scholar
  14. Yamada, R. & Yamamoto, K. Recent findings on genes associated with inflammatory disease. Mutat. Res. 573, 136–151 (2005).
    Article CAS Google Scholar
  15. Mori, M., Yamada, R., Kobayashi, K., Kawaida, R. & Yamamoto, K. Ethnic differences in allele frequency of autoimmune-disease-associated SNPs. J. Hum. Genet. 50, 264–266 (2005).
    Article Google Scholar
  16. Thomson, W. et al. Rheumatoid arthritis association at 6q23. Nat. Genet. 39, 1431–1433 (2007).
    Article CAS Google Scholar
  17. Scofield, R.H. et al. Thrombocytopenia identifies a severe familial phenotype of systemic lupus erythematosus and reveals genetic linkages at 1q22 and 11p13. Blood 101, 992–997 (2003).
    Article CAS Google Scholar
  18. de Bakker, P.I. et al. Efficiency and power in genetic association studies. Nat. Genet. 37, 1217–1223 (2005).
    Article CAS Google Scholar
  19. Graham, D.S. et al. Association of LY9 in UK and Canadian SLE families. Genes Immun. 9, 93–102 (2008).
    Article Google Scholar
  20. Balding, D.J. A tutorial on statistical methods for population association studies. Nat. Rev. Genet. 7, 781–791 (2006).
    Article CAS Google Scholar
  21. Devlin, B. & Roeder, K. Genomic control for association studies. Biometrics 55, 997–1004 (1999).
    Article CAS Google Scholar
  22. Stranger, B.E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848–853 (2007).
    Article CAS Google Scholar
  23. Tregouet, D.A. & Garelle, V. A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies. Bioinformatics 23, 1038–1039 (2007).
    Article CAS Google Scholar
  24. Cordell, H.J. & Clayton, D.G. A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes. Am. J. Hum. Genet. 70, 124–141 (2002).
    Article CAS Google Scholar
  25. Pajukanta, P. et al. Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). Nat. Genet. 36, 371–376 (2004).
    Article CAS Google Scholar
  26. Nakajima, H. & Colonna, M. 2B4: an NK cell activating receptor with unique specificity and signal transduction mechanism. Hum. Immunol. 61, 39–43 (2000).
    Article CAS Google Scholar
  27. Claus, M., Meinke, S., Bhat, R. & Watzl, C. Regulation of NK cell activity by 2B4, NTB-A and CRACC. Front. Biosci. 13, 956–965 (2008).
    Article CAS Google Scholar
  28. Yamamoto, K. & Yamada, R. Lessons from a genomewide association study of rheumatoid arthritis. N. Engl. J. Med. 357, 1250–1251 (2007).
    Article CAS Google Scholar
  29. The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–678 (2007).
  30. Hochberg, M.C. Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum. 40, 1725 (1997).
    Article CAS Google Scholar

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Acknowledgements

We thank K. Kobayashi, M. Ohtake-Yamanaka, E. Kanno and all members of the rheumatoid arthritis team for their advice and technical assistance; H. Kawakami and T. Kawaguchi for their expertise in computer programming; and members of the Center for Genomic Medicine of RIKEN and the Biomedical Research Laboratories of Sankyo Co. Ltd. for helpful discussions and assistance in various aspects of this study. We are also grateful to members of the Rotary Club of Osaka-Midosuji District 2660 Rotary International in Japan, the Pharma SNP Consortium in Japan and the BioBank Japan Project for supporting our study. This work was supported by grants from the Japanese Millennium Project and the Japanese Ministry of Health, Labor and Welfare.

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Authors and Affiliations

  1. Laboratory for Autoimmune Diseases, Center for Genomic Medicine, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan
    Akari Suzuki, Ryo Yamada, Yuta Kochi, Mikako Mori, Kenichi Shimane & Kazuhiko Yamamoto
  2. Laboratory of Functional Genomics, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan
    Ryo Yamada & Yukinori Okada
  3. Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
    Tetsuji Sawada, Mikako Mori, Kenichi Shimane & Kazuhiko Yamamoto
  4. Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan
    Koichi Matsuda, Yoichiro Kamatani & Yusuke Nakamura
  5. Department of Rheumatology and Hematology, Graduate School of Medicine, Tohoku University, 1-1 Seiryo-cho, Aoba-ku, Sendai, 980-8574, Miyagi, Japan
    Yasuhiko Hirabayashi
  6. Laboratory for Statistical Analysis and, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan
    Atsushi Takahashi & Naoyuki Kamatani
  7. Laboratory for Medical Informatics, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan
    Tatsuhiko Tsunoda
  8. Miyatake Asthma Clinic, 2-3-3 Nishi-Shinsaibashi, Chuo-ku, 542-0086, Osaka, Japan
    Akihiko Miyatake
  9. Laboratory for Genotyping, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan
    Michiaki Kubo
  10. Center for Genomic Medicine, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan
    Yusuke Nakamura

Authors

  1. Akari Suzuki
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  2. Ryo Yamada
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  3. Yuta Kochi
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  4. Tetsuji Sawada
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  5. Yukinori Okada
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  6. Koichi Matsuda
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  7. Yoichiro Kamatani
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  8. Mikako Mori
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  9. Kenichi Shimane
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  10. Yasuhiko Hirabayashi
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  11. Atsushi Takahashi
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  12. Tatsuhiko Tsunoda
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  13. Akihiko Miyatake
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  14. Michiaki Kubo
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  15. Naoyuki Kamatani
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  16. Yusuke Nakamura
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  17. Kazuhiko Yamamoto
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Contributions

A.S. performed most of the experiments and wrote the manuscript; R.Y. and Y.O. performed the data analysis and managed DNA samples and clinical information; Y. Kochi and M.M. summarized clinical data and performed SNP genotyping; T.S. and A.M. managed DNA samples and clinical information; K.S., K.M. and Y. Kamatani performed the SLE association study; Y.H. managed SLE samples; T.T., A.T. and N.K. performed the data analysis; M.K. contributed to SNP genotyping and managed DNA samples; Y.N. managed DNA samples and the project; and K.Y. planned and supervised the whole project.

Corresponding author

Correspondence toKazuhiko Yamamoto.

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Suzuki, A., Yamada, R., Kochi, Y. et al. Functional SNPs in CD244 increase the risk of rheumatoid arthritis in a Japanese population.Nat Genet 40, 1224–1229 (2008). https://doi.org/10.1038/ng.205

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