DNA methylation similarities in genes of Black South Africans with Systemic lupus erythematosus and Systemic sclerosis

Journal of Biomedical Science

Volumn 22, Issue 1, 2015, Pages

  Matatiele, Puleng ^a   Tikly, Mohamed ^b   Tarr, Gareth ^b   Gulumian, Mary ^a,c  

^a NATIONAL HEALTH LABORATORY SERVICE   (South Africa)

^b UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^c UNIVERSITY OF THE WITWATERSRAND   (South Africa)

Author keywords

Autoimmunity; Genomic DNA; Methyl qPCR arrays; Methylation; Peripheral blood; Systemic lupus erythematosus; Systemic sclerosis

Indexed keywords

ANTINUCLEAR ANTIBODY; AUTOANTIBODY; CENTROMERE ANTIBODY; DNA TOPOISOMERASE;

ADULT; AGED; ARTICLE; AUTOIMMUNITY; BLACK PERSON; CD70 GENE; CLINICAL ARTICLE; CONTROLLED STUDY; CTGF GENE; CXCR4 GENE; DISEASE COURSE; DNA METHYLATION; DNMT1 GENE; FEMALE; FIBROSIS; FLI1 GENE; FOXP3 GENE; GENE; GENE REPRESSION; GENE SILENCING; GENETIC SIMILARITY; HUMAN; IMMUNOPATHOGENESIS; INFLAMMATION; ITGAL GENE; MALE; MT1G GENE; OVERLAPPING GENE; P16INK4 GENE; POLYMERASE CHAIN REACTION; PRF1 GENE; RETROSPECTIVE STUDY; SOCS1 GENE; SOUTH AFRICAN; SYSTEMIC LUPUS ERYTHEMATOSUS; SYSTEMIC SCLEROSIS; SYSTEMIC VASCULITIS; THY1 GENE; UPREGULATION; GENETICS; LUPUS ERYTHEMATOSUS, SYSTEMIC; MIDDLE AGED; REAL TIME POLYMERASE CHAIN REACTION; SCLERODERMA, SYSTEMIC; SOUTH AFRICA; YOUNG ADULT;

ADULT; AFRICAN CONTINENTAL ANCESTRY GROUP; DNA METHYLATION; FEMALE; HUMANS; LUPUS ERYTHEMATOSUS, SYSTEMIC; MALE; MIDDLE AGED; REAL-TIME POLYMERASE CHAIN REACTION; SCLERODERMA, SYSTEMIC; SOUTH AFRICA; YOUNG ADULT;

EID: 84929430632     PISSN: 10217770     EISSN: 14230127     Source Type: Journal    
DOI: 10.1186/s12929-015-0142-2     Document Type: Article

References (66)

1. Ballestar E, Esteller M, Richardson BC. The epigenetic face of systemic lupus erythematosus. J Immunol. 2006;176(12):7143-7.
2. Abraham DJ, Varga J. Scleroderma: from cell and molecular mechanisms to disease models. Trends Immunol. 2005;26(11):587-95.
3. Fleming JN, Schwartz SM. The pathology of scleroderma vascular disease. Rheum Dis Clin North Am. 2008;34(1):41-55.
4. Zwijnenburg PJG, Meijers-Heijboer H, Boomsma DI. Identical but not the same: the value of discordant monozygotic twins in genetic research. Am J Med Genet B Neuropsychiatr Genet. 2010;153B(6):1134-49.
5. Agarwal SK. The genetics of systemic sclerosis. Discov Med. 2010;10(51):134-43.
6. Javierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, Rodriguez-Ubreva J, et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res. 2010;20:170-9.
7. Ballestar E. Epigenetics lessons from twins: prospects for autoimmune disease. Clin Rev Allergy Immunol. 2010;39(1):30-41.
8. Yasmin R, Siraj S, Hassan A, Khan AR, Abbasi R, Ahmad N. Epigenetic regulation of inflammatory cytokines and associated genes in human malignancies. Mediators Inflamm. 2015;2015:8.
9. Perl A. Oxidative stress in the pathology and treatment of systemic lupus erythematosus. Nat Rev Rheumatol. 2013;9(11):674-86.
10. Gaipl US, Franz S, Voll RE, Sheriff A, Kalden JR, Herrmann M. Defects in the disposal of dying cells lead to autoimmunity. Curr Rheumatol Rep. 2004;6(6):401-7.
11. Balada E, Ordi-Ros J, Serrano-Acedo S, Martinez-Lostao L, Rosa-Leyva M, Vilardell-Tarres M. Transcript levels of DNA methyltransferases DNMT1, DNMT3A and DNMT3B in CD4+ T cells from patients with systemic lupus erythematosus. Immunology. 2008;124(3):339-47.
12. Kikuchi R, Tsuda H, Kanai Y, Kasamatsu T, Sengoku K, Hirohashi S, et al. Promoter hypermethylation contributes to frequent inactivation of a putative conditional tumor suppressor gene connective tissue growth factor in ovarian cancer. Cancer Res. 2007;67(15):7095-105.
13. Velez G, Rodriguez FM, Rodriguez JM. Subexpression of SOCS1 and constitutive activation of IFNA receptor associated proteins in systemic lupus erythematosus. Int Immunol. 2010;22(Suppl 1 Pt 1):i110.i8.
14. Li A, Li YM, Yang AZ, Yao X, Chen ZQ. Phenomena and pathological significances of the methylated p16 promotor in DNA derived from plasma and blood cells of patients with systemic lupus erythematosus. Zhongguo Yi Xue Ke Xue Yuan Xue Bao. 2006;28(5):675-81.
15. Lei W, Luo Y, Lei W, Luo Y, Yan K, Zhao S, et al. Abnormal DNA methylation in CD4+ T cells from patients with systemic lupus erythematosus, systemic sclerosis, and dermatomyositis. Scand J Rheumatol. 2009;38(5):369-74.
16. Balada E, Ordi-Ros J, Vilardell-Tarres M. DNA methylation and systemic lupus erythematosus. Ann N Y Acad Sci. 2007;1108(1):127-136.
17. Higgs BW, Liu Z, White B, Zhu W, White WI, Morehouse C, et al. Patients with systemic lupus erythematosus, myositis, rheumatoid arthritis and scleroderma share activation of a common type I interferon pathway. Ann Rheum Dis. 2011;70(7):2029-36.
18. Assassi S, Mayes MD, Arnett FC, Gourh P, Agarwal SK, McNearney TA, et al. Systemic sclerosis and lupus: points in an interferon-mediated continuum. Arthritis Rheum. 2010;62(2):589-98.
19. Asano Y, Stawski L, Hant F, Highland K, Silver R, Szalai G, et al. Endothelial Fli1 deficiency impairs vascular homeostasis: a role in scleroderma vasculopathy. Am J Pathol. 2010;176(4):1983-98.
20. Asano Y, Bujor AM, Trojanowska M. The impact of Fli1 deficiency on the pathogenesis of systemic sclerosis. J Derm Sci. 2010;59(3):153-62.
21. Lo MS, Tsokos GC. T Cells in Systemic Lupus Erythematosus; progress toward targeted therapy. Rheumatologist, August 01, 2011. http://www.therheumatologist.org/details/print/1311659/August-2011.html. Accessed 11 May 2015.
22. Absher DM, Li X, Waite LL, Gibson A, Roberts K, Edberg J, et al. Genomewide DNA methylation analysis of systemic lupus erythematosus reveals persistent hypomethylation of interferon genes and compositional changes to CD4+ T-cell populations. PLoS Genet. 2013;9(8):e1003678.
23. Jeffries MA, Dozmorov M, Tang Y, Merrill JT, Wren JD, Sawalha AH. Genomewide DNA methylation patterns in CD4 (+) T cells from patients with systemic lupus erythematosus. Epigenetics. 2011;6(5):593-601.
24. Zouali M. The epigenetic landscape of B lymphocyte tolerance to self. FEBS Lett. 2013;587(13):2067-73.
25. Wang Y, Yang Y, Luo Y, Yin Y, Wang Q, Li Y, et al. Aberrant histone modification in peripheral blood B cells from patients with systemic sclerosis. Clin Immunol. 2013;149(1):46-54.
26. Lai AY, Mav D, Shah R, Grimm SA, Phadke D, Hatzi K, et al. DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation. Genome Res. 2013;23(12):2030-41.
27. Scheinberg MA, Cathcart ES. B cell and T cell lymphopenia in systemic lupus erythematosus. Cell Immunol. 1974;12(2):309-14.
28. Horwitz D, Juul-Nielsen K. Human blood L lymphocytes in patients with active systemic lupus erythematosus, rheumatoid arthritis and scleroderma: a comparison with T and B cells. Clin Exp Immunol. 1977;30(3):370.
29. Altorok N, Tsou P-S, Coit P, Khanna D, Sawalha AH. Genome-wide DNA methylation analysis in dermal fibroblasts from patients with diffuse and limited systemic sclerosis reveals common and subset-specific DNA methylation aberrancies. Ann Rheum Dis. 2014;8:2014.
30. Lim U, Song MA. Dietary and lifestyle factors of DNA methylation. Method Mol Biol. 2012;863:359-76.
31. Alegria-Torres JA, Baccarelli A, Bollati V. Epigenetics and lifestyle. Epigenomics. 2011;3(3):267-77.
32. Strickland FM, Hewagama A, Wu A, Sawalha AH, Delaney C, Hoeltzel MF, et al. Diet Influences Expression of Autoimmune-Associated Genes and Disease Severity by Epigenetic Mechanisms in a Transgenic Mouse Model of Lupus. Arthritis Rheum. 2013;65(7):1872-81.
33. Higgs BW, Zhu W, Richman L, Fiorentino DF, Greenberg SA, Jallal B, et al. Identification of activated cytokine pathways in the blood of systemic lupus erythematosus, myositis, rheumatoid arthritis, and scleroderma patients. Int J Rheum Dis. 2012;15(1):25-35.
34. Fernandis AZ, Cherla RP, Ganju RK. Differential regulation of CXCR4-mediated Tcell chemotaxis and mitogen-activated protein kinase activation by the membrane tyrosine phosphatase, CD45. J Biol Chem. 2003;278(11):9536-43.
35. Lal G, Zhang N, van der Touw W, Ding Y, Ju W, Bottinger EP, et al. Epigenetic regulation of Foxp3 expression in regulatory T cells by DNA methylation. J Immunol. 2009;182(1):259-73.
36. Thomas TJ, Meryhew NL, Messner RP. Enhanced binding of lupus sera to the polyamine-induced left-handed z-dna form of polynucleotides. Arthritis Rheum. 1990;33(3):356-65.
37. Adhami E. Calculating the etiology of systemic lupus erythematosus. Med Hypotheses. 2004;62(2):237-46.
38. Kano Y, Soda K, Konishi F. Suppression of LFA-1 Expression by Spermine Is Associated with Enhanced Methylation of ITGAL, the LFA-1 Promoter Area. PLoS One. 2013;8(2):e56056.
39. Dong R, Zhao R, Zheng S, Zheng Y, Xiong S, Chu Y. Abnormal DNA methylation of ITGAL (CD11a) in CD4+ T cells from infants with biliary atresia. Biochem Biophysic Res Comm. 2012;417(3):986-90.
40. Veraldi KL, Hsu E, Feghali-Bostwick CA. Pathogenesis of pulmonary fibrosis in systemic sclerosis: lessons from interstitial lung disease. Curr Rheumatol Rep. 2010;12(1):19-25.
41. Ke LY, Chang LL, Liu CC, Hung YH, Lin CH, Li RN, et al. Suppressor of cytokine signaling 1 gene expression and polymorphisms in systemic lupus erythematosus. Lupus. 2010;19(6):696-702.
42. Wang Y, Fan PS, Kahaleh B. Association between enhanced type I collagen expression and epigenetic repression of the FLI1 gene in scleroderma fibroblasts. Arthritis Rheum. 2006;54(7):2271-9.
43. Li Y, Luo H, Liu T, Zacksenhaus E, Ben-David Y. The ets transcription factor Fli-1 in development, cancer and disease. Oncogene. 2015;34(16):2022-203.
44. Svenson JL, Nowling TK. Altered Fli1 regulation and expression in lupus T cells and effects on T cell function. Arthritis Rheum. 2009;60(10):1093.
45. Chong MM, Chen Y, Darwiche R, Dudek NL, Irawaty W, Santamaria P, et al. Suppressor of cytokine signaling-1 overexpression protects pancreatic β cells from CD8+ T cell-mediated autoimmune destruction. J Immunol. 2004;172(9):5714-21.
46. Strickland FM, Richardson BC. Epigenetics in human autoimmunity: (Epigenetics in autoimmunity-DNA methylation in systemic lupus erythematosus and beyond). Autoimmunity. 2008;41(4), 278-286.
47. Kaneto H, Sasaki S, Yamamoto H, Itoh F, Toyota M, Suzuki H, et al. Detection of hypermethylation of the p16 (INK4A) gene promoter in chronic hepatitis and cirrhosis associated with hepatitis B or C virus. Gut. 2001;48(3):372-7.
48. Romagosa C, Simonetti S, Lopez-Vicente L, Mazo A, Lleonart ME, Castellvi J, et al. p16Ink4a overexpression in cancer: a tumor suppressor gene associated with senescence and high-grade tumors. Oncogene. 2011;30(18):2087-97.
49. Ivanova TA, Golovina DA, Zavalishina LE, Volgareva GM, Katargin AN, Andreeva YY, et al. Up-regulation of expression and lack of 5' CpG island hypermethylation of p16 INK4a in HPV-positive cervical carcinomas. BMC Cancer. 2007;7:47.
50. Gu Z, Cao X, Jiang J, Li L, Da Z, Liu H, et al. Upregulation of p16INK4A promotes cellular senescence of bone marrow-derived mesenchymal stem cells from systemic lupus erythematosus patients. Cell Signal. 2012;24(12):2307-14.
51. Liu CC, Ou TT, Wu CC, Li RN, Lin YC, Lin CH, et al. Global DNA methylation, DNMT1, and MBD2 in patients with systemic lupus erythematosus. Lupus. 2011;20(2):131-6.
52. Zhu X, Liang J, Li F, Yang Y, Xiang L, Xu J. Analysis of associations between the patterns of global DNA hypomethylation and expression of DNA methyltransferase in patients with systemic lupus erythematosus. Int J Dermatol. 2011;50(6):697-704.
53. Kanda M, Nomoto S, Okamura Y, Nishikawa Y, Sugimoto H, Kanazumi N, et al. Detection of metallothionein 1G as a methylated tumor suppressor gene in human hepatocellular carcinoma using a novel method of double combination array analysis. Int J Oncol. 2009;35(3):477-83.
54. Robert MF, Morin S, Beaulieu N, Gauthier F, Chute IC, Barsalou A, et al. DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells. Nat Genet. 2002;33:61-5.
55. Wiley KL, Treadwell E, Manigaba K, Word B, Lyn-Cook BD. Ethnic differences in DNA methyltransferases expression in patients with systemic lupus erythematosus. J Clin Immunol. 2013;33(2):342-8.
56. Kozłowska A, Hrycaj P, Łacki JK, Jagodziński PP. Perforin level in CD4+ T cells from patients with systemic lupus erythematosus. Rheumatol Int. 2010;30(12):1627-33.
57. Golder V, Connelly K, Staples M, Morand E, Hoi A. Association of Asian ethnicity with disease activity in SLE: an observational study from the Monash Lupus Clinic. Lupus. 2013;22(13):1425-30.
58. Hughes T, Sawalha A. The role of epigenetic variation in the pathogenesis of systemic lupus erythematosus. Arthritis Res Ther. 2011;13(5):245.
59. Kehrmann J, Tatura R, Zeschnigk M, Probst-Kepper M, Geffers R, Steinmann J, et al. Impact of 5-aza-2'-deoxycytidine and epigallocatechin-3-gallate for induction of human regulatory T cells. Immunology. 2014;142(3):384-95.
60. Hagemann S, Kuck D, Stresemann C, Prinz F, Brueckner B, Mund C, et al. Antiproliferative effects of DNA methyltransferase 3B depletion Are Not associated with DNA demethylation. PLoS One. 2012;7(5):e36125.
61. Nyce J, Liu L, Jones PA. Variable effects of DNA-synthesis inhibitors upon DNA methylation in mammalian cells. Nucleic Acids Res. 1986;14(10):4353-67.
62. Wan ES, Qiu W, Baccarelli A, Carey VJ, Bacherman H, Rennard SI, et al. Systemic steroid exposure is associated with differential methylation in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2012;186(12):1248-55.
63. Oaks Z, Perl A. Metabolic control of the epigenome in systemic lupus erythematosus. Autoimmunity. 2014;47(4):256-64.
64. Hoogen F, Khanna D, Fransen J, Johnson SR, Baron M, Tyndall A, et al. 2013 classification criteria for systemic sclerosis: an American college of rheumatology/European league against rheumatism collaborative initiative. Arthritis Rheum. 2013;65(11):2737-47.
65. Gladman D, Goldsmith C, Urowitz M, Bacon P, Fortin P, Ginzler E, et al. The systemic lupus international collaborating clinics/American college of rheumatology (SLICC/ACR) damage index for systemic lupus erythematosus international comparison. J Rheumatol. 2000;27(2):373-6.
66. Zielske SP, Epigenetic DNA. Methylation in radiation biology: on the field or on the sidelines? J Cell Biochem. 2015;116(2):212-7.