Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility

Genes and Immunity

Volumn 14, Issue 4, 2013, Pages 217-222

  Wang, C ^a   Ahlford, A ^a,h   Laxman, N ^a,b   Nordmark, G ^b   Eloranta, M L ^b   Gunnarsson, I ^c   Svenungsson, E ^c   Padyukov, L ^c   Sturfelt, G ^d   Joonsen A ^d   Bengtsson, A A ^d   Truedsson, L ^d   Rantapaa Dahlqvist S ^e   Sjoowall C ^f   Sandling, J K ^a,g   Ronnblom L ^b   Syvanen A C ^a  

^a SCIENCE FOR LIFE LABORATORY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^d LUND UNIVERSITY   (Sweden)

^e UMEÅ UNIVERSITY   (Sweden)

^f LINKÖPING UNIVERSITY   (Sweden)

^g WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^h STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

association study; IFIH1; IKBKE; resequencing; systemic lupus erythematosus

Indexed keywords

ARTICLE; CONTROLLED STUDY; DISEASE ASSOCIATION; GENE; GENE FREQUENCY; GENE SEQUENCE; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; IN VITRO STUDY; MAJOR CLINICAL STUDY; MISSENSE MUTATION; PRIORITY JOURNAL; RISK FACTOR; SWEDEN; SYSTEMIC LUPUS ERYTHEMATOSUS; TRANSCRIPTION REGULATION;

CASE-CONTROL STUDIES; DEAD-BOX RNA HELICASES; DNA-BINDING PROTEINS; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HAPLOTYPES; HUMANS; I-KAPPA B KINASE; LUPUS ERYTHEMATOSUS, SYSTEMIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN BINDING; TRANSCRIPTION FACTORS;

EID: 84878937710     PISSN: 14664879     EISSN: 14765470     Source Type: Journal    
DOI: 10.1038/gene.2013.9     Document Type: Article

References (49)

1. Hewagama A, Richardson B. The genetics and epigenetics of autoimmune diseases. J Autoimmun 2009; 33: 3-11.
2. Gateva V, Sandling JK, Hom G, Taylor KE, Chung SA, Sun X et al. A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Nat Genet 2009; 41: 1228-1233.
3. Ronnblom L, Alm GV, Eloranta ML. The type I interferon system in the development of lupus. Semin Immunol 2011; 23: 113-121.
4. Bronson PG, Chaivorapol C, Ortmann W, Behrens TW, Graham RR. The genetics of type I interferon in systemic lupus erythematosus. Curr Opin Immunol 2012; 24: 530-537.
5. Hom G, Graham RR, Modrek B, Taylor KE, Ortmann W, Garnier S et al. Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med 2008; 358: 900-909. (Pubitemid 351397089)
6. Harley JB, Alarcon-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, Moser KL et al. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet 2008; 40: 204-210. (Pubitemid 351171405)
7. Graham RR, Cotsapas C, Davies L, Hackett R, Lessard CJ, Leon JM et al. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet 2008; 40: 1059-1061.
8. Han JW, Zheng HF, Cui Y, Sun LD, Ye DQ, Hu Z et al. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet 2009; 41: 1234-1237.
9. Sandling JK, Garnier S, Sigurdsson S, Wang C, Nordmark G, Gunnarsson I et al. A candidate gene study of the type I interferon pathway implicates IKBKE and IL8 as risk loci for SLE. Eur J Hum Genet 2011; 19: 479-484.
10. Shimada T, Kawai T, Takeda K, Matsumoto M, Inoue J, Tatsumi Y et al. IKK-i, a novel lipopolysaccharide-inducible kinase that is related to IkappaB kinases. Int Immunol 1999; 11: 1357-1362. (Pubitemid 29355675)
11. Peters RT, Liao SM, Maniatis T. IKKepsilon is part of a novel PMA-inducible IkappaB kinase complex. Mol Cell 2000; 5: 513-522.
12. Sharma S, tenOever BR, Grandvaux N, Zhou GP, Lin R, Hiscott J. Triggering the interferon antiviral response through an IKK-related pathway. Science 2003; 300: 1148-1151. (Pubitemid 36583100)
13. Fitzgerald KA, McWhirter SM, Faia KL, Rowe DC, Latz E, Golenbock DT et al. IKKepsilon and TBK1 are essential components of the IRF3 signaling pathway. Nat Immunol 2003; 4: 491-496. (Pubitemid 36592443)
14. Mattioli I, Geng H, Sebald A, Hodel M, Bucher C, Kracht M et al. Inducible phosphorylation of NF-kappa B p65 at serine 468 by T cell costimulation is mediated by IKK epsilon. J Biol Chem 2006; 281: 6175-6183. (Pubitemid 43847547)
15. Dieguez-Gonzalez R, Akar S, Calaza M, Perez-Pampin E, Costas J, Torres M et al. Genetic variation in the nuclear factor kappaB pathway in relation to susceptibility to rheumatoid arthritis. Ann Rheum Dis 2009; 68: 579-583.
16. Nordmark G, Kristjansdottir G, Theander E, Appel S, Eriksson P, Vasaitis L et al. Association of EBF1, FAM167A(C8orf13)-BLK and TNFSF4 gene variants with primary Sjogren's syndrome. Genes Immun 2011; 12: 100-109.
17. Kang DC, Gopalkrishnan RV, Lin L, Randolph A, Valerie K, Pestka S et al. Expression analysis and genomic characterization of human melanoma differentiation associated gene-5, mda-5: a novel type I interferon-responsive apoptosis-inducing gene. Oncogene 2004; 23: 1789-1800. (Pubitemid 38445170)
18. Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M et al. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat Immunol 2004; 5: 730-737. (Pubitemid 39023305)
19. Barral PM, Sarkar D, Su ZZ, Barber GN, DeSalle R, Racaniello VR et al. Functions of the cytoplasmic RNA sensors RIG-I and MDA-5: key regulators of innate immunity. Pharmacol Ther 2009; 124: 219-234.
20. Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, Smink LJ et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet 2006; 38: 617-619. (Pubitemid 43927300)
21. Martinez A, Varade J, Lamas JR, Fernandez-Arquero M, Jover JA, de la Concha EG et al. Association of the IFIH1-GCA-KCNH7 chromosomal region with rheumatoid arthritis. Ann Rheum Dis 2008; 67: 137-138.
22. Enevold C, Oturai AB, Sorensen PS, Ryder LP, Koch-Henriksen N, Bendtzen K. Multiple sclerosis and polymorphisms of innate pattern recognition receptors TLR1-10, NOD1-2, DDX58, and IFIH1. J Neuroimmunol 2009; 212: 125-131.
23. Sutherland A, Davies J, Owen CJ, Vaikkakara S, Walker C, Cheetham TD et al. Genomic polymorphism at the interferon-induced helicase (IFIH1) locus contributes to Graves' disease susceptibility. J Clin Endocrinol Metab 2007; 92: 3338-3341. (Pubitemid 47236412)
24. Li Y, Liao W, Cargill M, Chang M, Matsunami N, Feng BJ et al. Carriers of rare missense variants in IFIH1 are protected from psoriasis. J Invest Dermatol 2010; 130: 2768-2772.
25. Cunninghame Graham DS, Morris DL, Bhangale TR, Criswell LA, Syvanen AC, Ronnblom L et al. Association of NCF2, IKZF1, IRF8, IFIH1, and TYK2 with systemic lupus erythematosus. PLoS Genet 2011; 7: e1002341.
26. Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 2011; 89: 82-93.
27. Zhang D, Paley AJ, Childs G. The transcriptional repressor ZFM1 interacts with and modulates the ability of EWS to activate transcription. J Biol Chem 1998; 273: 18086-18091. (Pubitemid 28334724)
28. Goldstrohm AC, Albrecht TR, Sune C, Bedford MT, Garcia-Blanco MA. The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1. Mol Cell Biol 2001; 21: 7617-7628. (Pubitemid 32988773)
29. Liu Z, Luyten I, Bottomley MJ, Messias AC, Houngninou-Molango S, Sprangers R et al. Structural basis for recognition of the intron branch site RNA by splicing factor 1. Science 2001; 294: 1098-1102. (Pubitemid 33041864)
30. Gupta A, Jenkins JL, Kielkopf CL. RNA induces conformational changes in the SF1/U2AF65 splicing factor complex. J Mol Biol 2011; 405: 1128-1138.
31. Robinson T, Kariuki SN, Franek BS, Kumabe M, Kumar AA, Badaracco M et al. Autoimmune disease risk variant of IFIH1 is associated with increased sensitivity to IFN-alpha and serologic autoimmunity in lupus patients. J Immunol 2011; 187: 1298-1303.
32. Aertgeerts K, Levin I, Shi L, Snell GP, Jennings A, Prasad GS et al. Structural and kinetic analysis of the substrate specificity of human fibroblast activation protein alpha. J Biol Chem 2005; 280: 19441-19444. (Pubitemid 41379462)
33. Brokopp CE, Schoenauer R, Richards P, Bauer S, Lohmann C, Emmert MY et al. Fibroblast activation protein is induced by inflammation and degrades type I collagen in thin-cap fibroatheromata. Eur Heart J 2011; 32: 2713-2722.
34. Bauer S, Jendro MC, Wadle A, Kleber S, Stenner F, Dinser R et al. Fibroblast activation protein is expressed by rheumatoid myofibroblast-like synoviocytes. Arthritis Res Ther 2006; 8: R171.
35. Rovedatti L, Di Sabatino A, Knowles CH, Sengupta N, Biancheri P, Corazza GR et al. Fibroblast activation protein expression in Crohn's disease strictures. Inflamm Bowel Dis 2011; 17: 1251-1253.
36. Boyhan A, Casimir CM, French JK, Teahan CG, Segal AW. Molecular cloning and characterization of grancalcin, a novel EF-hand calcium-binding protein abundant in neutrophils and monocytes. J Biol Chem 1992; 267: 2928-2933.
37. Liu F, Shinomiya H, Kirikae T, Hirata H, Asano Y. Characterization of murine grancalcin specifically expressed in leukocytes and its possible role in host defense against bacterial infection. Biosci Biotechnol Biochem 2004; 68: 894-902. (Pubitemid 39251461)
38. Prabhu S, Pe'er I. Overlapping pools for high-throughput targeted resequencing. Genome Res 2009; 19: 1254-1261.
39. Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR. Low-coverage sequencing: implications for design of complex trait association studies. Genome Res 2011; 21: 940-951.
40. Tan EM, Cohen AS, Fries JF, Masi AT, McShane DJ, Rothfield NF et al. The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1982; 25: 1271-1277. (Pubitemid 13221242)
41. Hochberg MC. Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1997; 40: 1725.
42. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008; 18: 1851-1858.
43. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009; 5: e1000529.
44. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575. (Pubitemid 47330214)
45. Stahl-Hallengren C, Jonsen A, Nived O, Sturfelt G. Incidence studies of systemic lupus erythematosus in Southern Sweden: increasing age, decreasing frequency of renal manifestations and good prognosis. J Rheumatol 2000; 27: 685-691. (Pubitemid 30151347)
46. Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E et al. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 2010; 38: D105-D110.
47. Wingender E, Dietze P, Karas H, Knuppel R. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 1996; 24: 238-241. (Pubitemid 26085775)
48. Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biol 2007; 8: R24.
49. Uzun A, Leslin CM, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res 2007; 35: W384-W392.