Epigenomic functional characterization of genetic susceptibility variants in systemic vasculitis

Journal of Autoimmunity

Volumn 67, Issue , 2016, Pages 76-81

  Sawalha, Amr H ^a,b   Dozmorov, Mikhail G ^c  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

^c VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

DNAse hypersensitivity; Enhancer; Epigenetics; Genetics; Histone marks; Vasculitis

Indexed keywords

DEOXYRIBONUCLEASE; HISTONE; HISTONE 3 LYSINE 27 ACETYLATION; HISTONE 3 LYSINE 27 TRIMETHYLATION; HISTONE H3; HISTONE LYSINE 4 MONOMETHYLATION; UNCLASSIFIED DRUG;

ANCA ASSOCIATED VASCULITIS; AORTA ARCH SYNDROME; ARTICLE; B LYMPHOCYTE; BEHCET DISEASE; CELL SPECIFICITY; CELLS BY BODY ANATOMY; DISEASE PREDISPOSITION; ENHANCER REGION; EPIGENETICS; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HEMATOPOIETIC STEM CELL; HUMAN; HYPERSENSITIVITY; IMMUNOCOMPETENT CELL; MUCOCUTANEOUS LYMPH NODE SYNDROME; PRIORITY JOURNAL; RISK ASSESSMENT; RISK FACTOR; SYSTEMIC VASCULITIS; TH17 CELL; ANTIBODY SPECIFICITY; CLUSTER ANALYSIS; FEMALE; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETIC PREDISPOSITION; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MALE; METABOLISM; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM;

CLUSTER ANALYSIS; EPIGENESIS, GENETIC; EPIGENOMICS; FEMALE; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HISTONES; HUMANS; MALE; ORGAN SPECIFICITY; POLYMORPHISM, SINGLE NUCLEOTIDE; SYSTEMIC VASCULITIS;

EID: 84957426411     PISSN: 08968411     EISSN: 10959157     Source Type: Journal    
DOI: 10.1016/j.jaut.2015.10.002     Document Type: Article

References (43)

1. Jennette J.C., Falk R.J., Bacon P.A., Basu N., Cid M.C., Ferrario F., et al. 2012 revised international chapel hill consensus conference nomenclature of vasculitides. Arthritis Rheumat. 2013, 65:1-11.
2. Alberici F., Martorana D., Vaglio A. Genetic aspects of anti-neutrophil cytoplasmic antibody-associated vasculitis. Nephrol. Dialysis Transplant. Off. Publ. Eur. Dialysis Transpl. Assoc. Eur. Ren. Assoc. 2015, 30(Suppl. 1):i37-45.
3. Onouchi Y. Genetics of Kawasaki disease: what we know and don't know. Circulation J. Off. J. Jpn. Circulation Soc. 2012, 76:1581-1586.
4. Gul A. Genetics of Behcet's disease: lessons learned from genomewide association studies. Curr. Opin. Rheumatol. 2014, 26:56-63.
5. Saruhan-Direskeneli G., Hughes T., Aksu K., Keser G., Coit P., Aydin S.Z., et al. Identification of multiple genetic susceptibility loci in Takayasu arteritis. Am. J. Hum. Genet. 2013, 93:298-305.
6. Terao C., Yoshifuji H., Kimura A., Matsumura T., Ohmura K., Takahashi M., et al. Two susceptibility loci to Takayasu arteritis reveal a synergistic role of the IL12B and HLA-B regions in a Japanese population. Am. J. Hum. Genet. 2013, 93:289-297.
7. Renauer P.A., Saruhan-Direskeneli G., Coit P., Adler A., Aksu K., Keser G., et al. Identification of susceptibility loci in IL6, RPS9/LILRB3, and an intergenic locus on chromosome 21q22 in takayasu arteritis in a genome-wide association study. Arthritis Rheumatol. 2015, 67:1361-1368.
8. Renauer P., Coit P., Sawalha A.H. Epigenetics and vasculitis: a comprehensive review. Clin. Rev. Allergy Immunol. 2015 Jun 21, (Epub ahead of print). 10.1007/s12016-015-8495-6.
9. Hughes T., Ture-Ozdemir F., Alibaz-Oner F., Coit P., Direskeneli H., Sawalha A.H. Epigenome-wide scan identifies a treatment-responsive pattern of altered DNA methylation among cytoskeletal remodeling genes in monocytes and CD4+ T cells from patients with Behcet's disease. Arthritis Rheumatol. 2014, 66:1648-1658.
10. ENCODE Project Consortium The ENCODE (ENCyclopedia Of DNA Elements) project. Science 2004, 306:636-640.
11. Bernstein B.E., Stamatoyannopoulos J.A., Costello J.F., Ren B., Milosavljevic A., Meissner A., et al. The NIH roadmap epigenomics mapping consortium. Nat. Biotechnol. 2010, 28:1045-1048.
12. Shlyueva D., Stampfel G., Stark A. Transcriptional enhancers: from properties to genome-wide predictions. Nat. Rev. Genet. 2014, 15:272-286.
13. Dozmorov M.G., Cara L.R., Giles C.B., Wren J.D. GenomeRunner: automating genome exploration. Bioinformatics 2012, 28:419-420.
14. Dozmorov M.G. Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes. Epigenetics 2015, 10:484-495.
15. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
16. Team RDC R: a Language and Environment for Statistical Computing 2013.
17. Oliveros J.C., Venny An Interactive Tool for Comparing Lists with Venn Diagrams 2007.
18. Lyons P.A., Rayner T.F., Trivedi S., Holle J.U., Watts R.A., Jayne D.R., et al. Genetically distinct subsets within ANCA-associated vasculitis. N. Engl. J. Med. 2012, 367:214-223.
19. Xie G., Roshandel D., Sherva R., Monach P.A., Lu E.Y., Kung T., et al. Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis. Arthritis Rheum. 2013, 65:2457-2468.
20. Fei Y., Webb R., Cobb B.L., Direskeneli H., Saruhan-Direskeneli G., Sawalha A.H. Identification of novel genetic susceptibility loci for Behcet's disease using a genome-wide association study. Arthritis Res. Ther. 2009, 11:R66.
21. Kirino Y., Bertsias G., Ishigatsubo Y., Mizuki N., Tugal-Tutkun I., Seyahi E., et al. Genome-wide association analysis identifies new susceptibility loci for Behcet's disease and epistasis between HLA-B*51 and ERAP1. Nat. Genet. 2013, 45:202-207.
22. Hou S., Yang Z., Du L., Jiang Z., Shu Q., Chen Y., et al. Identification of a susceptibility locus in STAT4 for Behcet's disease in Han Chinese in a genome-wide association study. Arthritis Rheum. 2012, 64:4104-4113.
23. Mizuki N., Meguro A., Ota M., Ohno S., Shiota T., Kawagoe T., et al. Genome-wide association studies identify IL23R-IL12RB2 and IL10 as Behcet's disease susceptibility loci. Nat. Genet. 2010, 42:703-706.
24. Remmers E.F., Cosan F., Kirino Y., Ombrello M.J., Abaci N., Satorius C., et al. Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with Behcet's disease. Nat. Genet. 2010, 42:698-702.
25. Sawalha A.H., Hughes T., Nadig A., Yilmaz V., Aksu K., Keser G., et al. A putative functional variant within the UBAC2 gene is associated with increased risk of Behcet's disease. Arthritis Rheum. 2011, 63:3607-3612.
26. Lee Y.J., Horie Y., Wallace G.R., Choi Y.S., Park J.A., Choi J.Y., et al. Genome-wide association study identifies GIMAP as a novel susceptibility locus for Behcet's disease. Ann. Rheumat. Dis. 2013, 72:1510-1516.
27. Xavier J.M., Shahram F., Sousa I., Davatchi F., Matos M., Abdollahi B.S., et al. FUT2: filling the gap between genes and environment in Behcet's disease?. Ann. Rheumat. Dis. 2015, 74:618-624.
28. Hughes T., Coit P., Adler A., Yilmaz V., Aksu K., Duzgun N., et al. Identification of multiple independent susceptibility loci in the HLA region in Behcet's disease. Nat. Genet. 2013, 45:319-324.
29. Kim J.J., Park Y.M., Yoon D., Lee K.Y., Seob Song M., Doo Lee H., et al. Identification of KCNN2 as a susceptibility locus for coronary artery aneurysms in Kawasaki disease using genome-wide association analysis. J. Hum. Genet. 2013, 58:521-525.
30. Lin M.T., Hsu C.L., Taiwan Pediatric C.V.G., Chen P.L., Yang W.S., Wang J.K., et al. A genome-wide association analysis identifies novel susceptibility loci for coronary arterial lesions in patients with Kawasaki disease. Transl. Res. J. Lab. Clin. Med. 2013, 161:513-515.
31. Lee Y.C., Kuo H.C., Chang J.S., Chang L.Y., Huang L.M., Chen M.R., et al. Two new susceptibility loci for Kawasaki disease identified through genome-wide association analysis. Nat. Genet. 2012, 44:522-525.
32. Onouchi Y., Ozaki K., Burns J.C., Shimizu C., Terai M., Hamada H., et al. A genome-wide association study identifies three new risk loci for Kawasaki disease. Nat. Genet. 2012, 44:517-521.
33. Khor C.C., Davila S., Breunis W.B., Lee Y.C., Shimizu C., Wright V.J., et al. Genome-wide association study identifies FCGR2A as a susceptibility locus for Kawasaki disease. Nat. Genet. 2011, 43:1241-1246.
34. Tsai F.J., Lee Y.C., Chang J.S., Huang L.M., Huang F.Y., Chiu N.C., et al. Identification of novel susceptibility Loci for kawasaki disease in a Han chinese population by a genome-wide association study. PloS One 2011, 6:e16853.
35. Kim J.J., Hong Y.M., Sohn S., Jang G.Y., Ha K.S., Yun S.W., et al. A genome-wide association analysis reveals 1p31 and 2p13.3 as susceptibility loci for Kawasaki disease. Hum. Genet. 2011, 129:487-495.
36. Burgner D., Davila S., Breunis W.B., Ng S.B., Li Y., Bonnard C., et al. A genome-wide association study identifies novel and functionally related susceptibility loci for Kawasaki disease. PLoS Genet. 2009, 5:e1000319.
37. Xavier J.M., Davatchi F., Abade O., Shahram F., Francisco V., Abdollahi B.S., et al. Characterization of the major histocompatibility complex locus association with Behcet's disease in Iran. Arthritis Res. Ther. 2015, 17:81.
38. Carapito R., Shahram F., Michel S., Le Gentil M., Radosavljevic M., Meguro A., et al. On the genetics of the Silk Route: association analysis of HLA, IL10, and IL23R-IL12RB2 regions with Behcet's disease in an Iranian population. Immunogenetics 2015, 67:289-293.
39. Eriksson P., Andersson C., Cassel P., Nystrom S., Ernerudh J. Increase in Th17-associated CCL20 and decrease in Th2-associated CCL22 plasma chemokines in active ANCA-associated vasculitis. Scand. J. Rheumatol. 2015, 44:80-83.
40. Nogueira E., Hamour S., Sawant D., Henderson S., Mansfield N., Chavele K.M., et al. Serum IL-17 and IL-23 levels and autoantigen-specific Th17 cells are elevated in patients with ANCA-associated vasculitis. Nephrol. Dialysis Transplant. Off. Publ. Eur. Dialysis Transpl. Assoc. Eur. Ren. Assoc. 2010, 25:2209-2217.
41. van de Veerdonk F.L., Lauwerys B., Marijnissen R.J., Timmermans K., Di Padova F., Koenders M.I., et al. The anti-CD20 antibody rituximab reduces the Th17 cell response. Arthritis Rheum. 2011, 63:1507-1516.
42. Park S.J., Shin J.I. Another beneficial effect of rituximab on refractory ANCA-associated vasculitis: the role of interleukin-17 suppression?. Scand. J. Immunol. 2013, 77:221.
43. Kawamori J., Miyake T., Yoshida T. B-cell function in Kawasaki disease and the effect of high-dose gamma-globulin therapy. Acta Paediatr. Jpn. Overseas Ed. 1989, 31:537-543.