Alpha-defensin DEFA1A3 gene copy number variation in Asians and its genetic association study in Chinese systemic lupus erythematosus patients |
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| Authors: | Fa-juan Cheng Xu-jie ZhouYan-feng Zhao Ming-hui ZhaoHong Zhang |
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| Affiliation: | Renal Division, Department of Medicine, Peking University First Hospital, Peking University Institute of Nephrology, China; Key Laboratory of Renal Disease, Ministry of Health of China, China; Key Laboratory of Chronic Kidney Disease Prevention, Treatment, Peking University, Ministry of Education, Beijing, China |
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| Abstract: | Neutrophil extracellular traps (NETs) were closely associated with activation of type I interferon (IFN) pathway in systemic lupus erythematosus (SLE). We aimed to study the genetic basis of NETs-DEFA1A3 copy number variations (CNV) in SLE and HapMap CHB + JPT populations by quantitative real-time PCR and whole genome sequences data. DEFA1A3 CNs did not differ significantly between SLE patients and controls. DEFA1A3 CNs ranged from 3 to 11 in CHB and 4 to 16 in JPT. The median of DEFA1A3 CNV of CHB (6 copies) was significantly lower than that of JPT (9 copies). Associations of genotype of tag SNP rs2738113 with DEFA1A3 CNs and mRNA expression of IFNα were observed in CHB and JPT populations. Our data provided a genetic reference of DEFA1A3 CNV for further studies and suggested that the genetic pathogenesis of NETs, as well as DEFA1A3 in SLE should be further evaluated, specially in different populations. |
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| Keywords: | DEFA1A3, α-defensin 1&ndash 3 gene NET, neutrophil extracellular traps IFN, interferon SLE, systemic lupus erythematosus CNV, copy number variant CHB, Han Chinese in Beijing JPT, Japanese in Tokyo SNP, single nucleotide polymorphism GWAS, genome-wide association study FCGR3A, Fc gamma receptor III-A gene FCGR3B, Fc-gamma receptor IIIb gene CCL3L1, chemokine (C-C motif) ligand 3-like 1 gene DEFB4, β-defensin 4 gene GBM, glomerular basement membrane ANCA, anti-neutrophil cytoplasmic antibody HNP, human neutrophil peptide SLEDAI, Systemic Lupus Erythematosus Disease Activity Index TE, Tris-EDTA OD, optical density TBP, TATA box-binding protein PCR, polymerase chain reaction Ct, threshold cycle MPO, myeloperoxidase MAF, minor allele frequency EBV, Epstein&ndash Barr virus GENEVAR, Gene Expression Variation dsDNA, double strand DNA ANA, anti-nuclear antibody eQTL, expression quantitative trait loci |
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