Identification Of Susceptibility Genes On X Chromosome In Systemic Lupus Erythematosus

Introduction: Systemic lupus erythematosus is a female-dominated incidence of autoimmune connective tissue disease. Its clinical manifestations have varied, and often involving multiple organ systems. SLE can be life-threatening of severe cases, which often accompanied by cancer, and other autoimmune diseases, etc. Women of childbearing age are most affected, and with significant gender differneces between male to female ratio is about 1:9. The prevalence of SLE is relatively high in different races. SLE global average of prevalence is about 12 to 39/100,000, and 30.13 to 70.41/ 100,000 in China. SLE is also a complex disease with multiple genes involved, its etiology and pathogenesis has not yet clear, most scholars believe that interactions of genetic factors, immune abnormalities, hormone and environmental factors lead person sensitive to SLE, and interactions between genetic and environmental may play an important role in the this process. Genetic model for SLE is multiple major gene inheritance patterns(including dominant, recessive, cumulative and major genes), the heritability of Chinese Han population is about 43.6%. There are some differences in clinical manifestations of SLE in different races, Chinese people suffering from lupus nephritis is higher than European, suggesting significant association between clinical phenotypic and genetic heterogeneity. Over the past few decades, global geneticists had identified more than 70 SLE autosomal susceptibility loci/genes in different populations by a variety of genetic methods(such as linkage analysis, genome-wide association study, etc.). These including 9 SLE susceptibility loci were indentified using genome-wide association studies in Chinese Han population in 2009 by our team. There are a few susceptibility loci/genes on X chromosome had been indentified, and only one is associated with Chinese population. Early studies suggest that susceptibility mutation on the X chromosome associated with the pathogenesis of SLE. However, most of these associations on X chromosome are found in European populations. Genetic heterogeneity exists among different populations. So, we think it is important to identify genetic variations on X chromosome of SLE in Chinese Han population.Objective: We aim to identify genetic variations on X chromosome of SLE in Chinese Han population by GWAS.Methods: We collected blood samples of matched SLE cases and healthy controls using the same uniform standards from nationwide hospuitals. The samples are divided into four separate groups: initial stage(samples are from central China: 1023 cases and 547 healthy controls); validation stage 1(samples are from central China: 1156 cases and 2330 healthy controls); validation stage 2(samples are from southern China: 1012 cases and 335 healthy controls); validation stage 3(samples are from northern China: 274 cases and 133 healthy controls). We genotyped initial stage samples using Illumina 610-Quad Human Beadchip chips. Imputation of the X chromosome SNPs was performed on the discovery dataset for female individuals using X chromosome nonpseudoautosomal region data from the 1000 Genomes project(phase 1 integrated version 3) as reference. We selected suscepbitility SNPs though strict quality control and genome-wide association analysis, and then performed a validation study using Sequenom Mass Array i Plex Gold platform in three populations(samples are from central, southern, northern China). Association analysis was performed in PLINK v1.07 using sample area as a covariate. We did Meta-analysis for initial stage data and validation stages data using Metasoft version 2.0.0. Genotype and phenotype association analysis was performed using PLINK v1.07. GEO database was used for gene expression analysis.Results: 189 SNPs showed P value less than 0.01 by statistical analysis of initial data, including rs1059702(IRAK1) 、 rs2239464(MECP2) 、 rs5914778(LINC01420) 、rs2266888(TMEM187) and so on. We selected 15 unreported susceptibility loci for further independent validation studies. Sequenom genotyping validation results show that there are two susceptibility loci are significant in the first validation study of central population(P <0.05). Rs5914778 reached genome-wide significance level after combined initial data and first validation study data(Pcombined = 1.00×10–8,odds ratio(OR) = 1.32). We also confirmed rs5914778 in the southern Chinese sample cohort(P = 5.31× 10-05; OR = 1.51), and meta-analysis of the samples from the discovery, central and southern validations regions provided robust evidence for the association of rs5914778(P = 5.26 × 10-12; OR = 1.35). However, this SNP did not show association with SLE in the northern sample(P = 0.33). Further analysis represent the association of northern was significantly heterogeneous compared to central and southern respectively(Phet = 0.034, I2 = 65.3). No positive association results were found in genotype and phenotype analysis and gene expression analysis.Conclusions: We performed a X chromosome GWAS study of SLE in the Chinese Han population and discovered a novel susceptibility locus rs5914778 on Xp11.21. The discovery of this novel locus has further expanded the role of the X chromosome in the development of SLE in the Chinese Han population. Genetic heterogeneity may play a role in susceptibility to SLE. This study not only advanced our understanding of the genetic basis of SLE susceptibility, but also provided enlightenment for reveal the pathogenesis of SLE, and provided theoretical basis for the prevention, diagnosis and treatment of SLE.