Common variants near IKZF1 are associated with primary Sjögren's syndrome in Han Chinese

PLoS ONE

Volumn 12, Issue 5, 2017, Pages

  Qu, Susu ^a,b   Du, Yang ^a,b   Chang, Suhua ^a,b   Guo, Liyuan ^a,b   Fang, Kechi ^a,b   Li, Yongzhe ^c   Zhang, Fengchun ^c   Zhang, Kunlin ^a,b   Wang, Jing ^a,b  

^a INSTITUTE OF PSYCHOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c PEKING UNION MEDICAL COLLEGE HOSPITAL   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; ENHANCER REGION; FEMALE; GENE; GENE LOCUS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; GTF2I GENE; HAN CHINESE; HUMAN; IKZF1 GENE; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; PRIMARY SJOEGREN SYNDROME; PROTEIN PROTEIN INTERACTION; SINGLE NUCLEOTIDE POLYMORPHISM; SJOEGREN SYNDROME; ADOLESCENT; AGED; CHINA; ETHNIC GROUP; GENETIC PREDISPOSITION; GENETICS; YOUNG ADULT;

IKAROS TRANSCRIPTION FACTOR; IKZF1 PROTEIN, HUMAN;

ADOLESCENT; ADULT; AGED; CHINA; ETHNIC GROUPS; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; IKAROS TRANSCRIPTION FACTOR; MALE; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; SJOGREN'S SYNDROME; YOUNG ADULT;

EID: 85019738660     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0177320     Document Type: Article

References (36)

1. Fox RI. Sjogren's syndrome. Lancet. 2005; 366(9482):321-31. https://doi.org/10.1016/S0140-6736(05)66990-5 PMID: 16039337
2. Helmick CG, Felson DT, Lawrence RC, Gabriel S, Hirsch R, Kwoh CK, et al. Estimates of the prevalence of arthritis and other rheumatic conditions in the United States. Part I. Arthritis and rheumatism. 2008; 58(1):15-25. https://doi.org/10.1002/art.23177 PMID: 18163481
3. Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nature reviews Genetics. 2009; 10(4):241-51. https://doi.org/10.1038/nrg2554 PMID: 19293820
4. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature reviews Genetics. 2008; 9(5):356-69. https://doi.org/10.1038/nrg2344 PMID: 18398418
5. Li Y, Zhang K, Chen H, Sun F, Xu J, Wu Z, et al. A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjogren's syndrome at 7q11.23. Nature genetics. 2013; 45 (11):1361-5. https://doi.org/10.1038/ng.2779 PMID: 24097066
6. Lessard CJ, Li H, Adrianto I, Ice JA, Rasmussen A, Grundahl KM, et al. Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjogren's syndrome. Nature genetics. 2013; 45(11):1284-92. https://doi.org/10.1038/ng.2792 PMID: 24097067
7. Yap WH, Yeoh E, Tay A, Brenner S, Venkatesh B. STAT4 is a target of the hematopoietic zinc-finger transcription factor Ikaros in T cells. FEBS letters. 2005; 579(20):4470-8. https://doi.org/10.1016/j.febslet.2005.07.018 PMID: 16081070
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. Nature genetics. 2009; 41(11):1234-7. https://doi.org/10.1038/ng.472 PMID: 19838193
9. Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, Ahmad T, et al. Genome-wide metaanalysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nature genetics. 2010; 42(12):1118-25. https://doi.org/10.1038/ng.717 PMID: 21102463
10. Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012; 491(7422):119-24. https://doi.org/10.1038/nature11582 PMID: 23128233
11. Vitali C, Bombardieri S, Jonsson R, Moutsopoulos HM, Alexander EL, Carsons SE, et al. Classification criteria for Sjogren's syndrome: a revised version of the European criteria proposed by the American- European Consensus Group. Annals of the rheumatic diseases. 2002; 61(6):554-8. https://doi.org/10.1136/ard.61.6.554 PMID: 12006334
12. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genetic epidemiology. 2010; 34(8):816-34. https://doi.org/10.1002/gepi.20533 PMID: 21058334
13. Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics. 2010; 26(18):2336-7. https://doi.org/10.1093/bioinformatics/btq419 PMID: 20634204
14. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for wholegenome association and population-based linkage analyses. American journal of human genetics. 2007; 81(3):559-75. https://doi.org/10.1086/519795 PMID: 17701901
15. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005; 21(2):263-5. https://doi.org/10.1093/bioinformatics/bth457 PMID: 15297300
16. Guo L, Du Y, Qu S, Wang J. rVarBase: an updated database for regulatory features of human variants. Nucleic acids research. 2016; 44(D1):D888-93. https://doi.org/10.1093/nar/gkv1107 PMID: 26503253
17. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome research. 2012; 22(9):1790-7. https://doi.org/10.1101/gr.137323.112 PMID: 22955989
18. Oti M, Snel B, Huynen MA, Brunner HG. Predicting disease genes using protein-protein interactions. J Med Genet. 2006; 43(8):691-8. https://doi.org/10.1136/jmg.2006.041376 PMID: 16611749
19. Oti M, Brunner HG. The modular nature of genetic diseases. Clinical genetics. 2007; 71(1):1-11. https://doi.org/10.1111/j.1399-0004.2006.00708.x PMID: 17204041
20. Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, et al. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proceedings of the National Academy of Sciences of the United States of America. 2008; 105(52):20870-5. https:/doi.org/10.1073/pnas.0810772105 PMID: 19104045
21. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nature biotechnology. 2007; 25 (3):309-16. https://doi.org/10.1038/nbt1295 PMID: 17344885
22. Roadmap Epigenomics C, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518(7539):317-30. https://doi.org/10.1038/nature14248 PMID: 25693563
23. Roy AL. Biochemistry and biology of the inducible multifunctional transcription factor TFII-I: 10 years later. Gene. 2012; 492(1):32-41. https://doi.org/10.1016/j.gene.2011.10.030 PMID: 22037610
24. Falkenberg KJ, Johnstone RW. Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders. Nature reviews Drug discovery. 2014; 13(9):673-91. https://doi.org/10.1038/nrd4360 PMID: 25131830
25. Guo J, Zhou W. Histone Deacetylase 1 But Not 2 Is Highly Expressed In The Lymphocyte Foci In The Labial Glands Of Patients With Sjogren's Syndrome. Abstracts of the 2013 American College of Rheumatology/Association of Rheumatology Health Professionals Annual Meeting. San Diego, CA. October 25-30,2013. ABSTRACT NUMBER: 1492. http://acrabstracts.org/abstract/histone-deacetylase-1-butnot-2-is-highly-expressed-in-the-lymphocyte-foci-in-the-labial-glands-of-patients-with-sjogrenssyndrome/.
26. Kim J, Sif S, Jones B, Jackson A, Koipally J, Heller E, et al. Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes. Immunity. 1999; 10(3):345-55. PMID: 10204490
27. Georgopoulos K, Winandy S, Avitahl N. The role of the Ikaros gene in lymphocyte development and homeostasis. Annual review of immunology. 1997; 15:155-76. https://doi.org/10.1146/annurev.immunol.15.1.155 PMID: 9143685
28. Georgopoulos K, Bigby M, Wang JH, Molnar A, Wu P, Winandy S, et al. The Ikaros gene is required for the development of all lymphoid lineages. Cell. 1994; 79(1):143-56. PMID: 7923373
29. Ganesh SK, Zakai NA, van Rooij FJ, Soranzo N, Smith AV, Nalls MA, et al. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. Nature genetics. 2009; 41(11):1191-8. https://doi.org/10.1038/ng.466 PMID: 19862010
30. Papaemmanuil E, Hosking FJ, Vijayakrishnan J, Price A, Olver B, Sheridan E, et al. Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia. Nature genetics. 2009; 41(9):1006-10. https://doi.org/10.1038/ng.430 PMID: 19684604
31. Trevino LR, Yang W, French D, Hunger SP, Carroll WL, Devidas M, et al. Germline genomic variants associated with childhood acute lymphoblastic leukemia. Nature genetics. 2009; 41(9):1001-5. https://doi.org/10.1038/ng.432 PMID: 19684603
32. Merkenschlager M. Ikaros in immune receptor signaling, lymphocyte differentiation, and function. FEBS letters. 2010; 584(24):4910-4. https://doi.org/10.1016/j.febslet.2010.09.042 PMID: 20888815
33. Fang CM, Roy S, Nielsen E, Paul M, Maul R, Paun A, et al. Unique contribution of IRF-5-Ikaros axis to the B-cell IgG2a response. Genes and immunity. 2012; 13(5):421-30. https://doi.org/10.1038/gene.2012.10 PMID: 22535200
34. Hu SJ, Wen LL, Hu X, Yin XY, Cui Y, Yang S, et al. IKZF1: a critical role in the pathogenesis of systemic lupus erythematosus? Modern rheumatology. 2013; 23(2):205-9. https://doi.org/10.1007/s10165-012-0706-x PMID: 22782532
35. Ueta M, Sawai H, Sotozono C, Hitomi Y, Kaniwa N, Kim MK, et al. IKZF1, a new susceptibility gene for cold medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis with severe mucosal involvement. The Journal of allergy and clinical immunology. 2015; 135(6):1538-45 e17. https://doi.org/10.1016/j.jaci.2014.12.1916 PMID: 25672763
36. Burbelo PD, Ambatipudi K, Alevizos I. Genome-wide association studies in Sjogren's syndrome: What do the genes tell us about disease pathogenesis? Autoimmunity reviews. 2014; 13(7):756-61. https://doi.org/10.1016/j.autrev.2014.02.002 PMID: 24657515