Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy

Abstract

The aim of this study was to determine, through a genome-wide association study (GWAS), the genetic components contributing to different clinical sub-phenotypes of systemic sclerosis (SSc). We considered limited (lcSSc) and diffuse (dcSSc) cutaneous involvement, and the relationships with presence of the SSc-specific auto-antibodies, anti-centromere (ACA), and anti-topoisomerase I (ATA). Four GWAS cohorts, comprising 2,296 SSc patients and 5,171 healthy controls, were meta-analyzed looking for associations in the selected subgroups. Eighteen polymorphisms were further tested in nine independent cohorts comprising an additional 3,175 SSc patients and 4,971 controls. Conditional analysis for associated SNPs in the HLA region was performed to explore their independent association in antibody subgroups. Overall analysis showed that non-HLA polymorphism rs11642873 in IRF8 gene to be associated at GWAS level with lcSSc (P = 2.32×10(-12), OR = 0.75). Also, rs12540874 in GRB10 gene (P = 1.27 × 10(-6), OR = 1.15) and rs11047102 in SOX5 gene (P = 1.39×10(-7), OR = 1.36) showed a suggestive association with lcSSc and ACA subgroups respectively. In the HLA region, we observed highly associated allelic combinations in the HLA-DQB1 locus with ACA (P = 1.79×10(-61), OR = 2.48), in the HLA-DPA1/B1 loci with ATA (P = 4.57×10(-76), OR = 8.84), and in NOTCH4 with ACA P = 8.84×10(-21), OR = 0.55) and ATA (P = 1.14×10(-8), OR = 0.54). We have identified three new non-HLA genes (IRF8, GRB10, and SOX5) associated with SSc clinical and auto-antibody subgroups. Within the HLA region, HLA-DQB1, HLA-DPA1/B1, and NOTCH4 associations with SSc are likely confined to specific auto-antibodies. These data emphasize the differential genetic components of subphenotypes of SSc.

Figure 1. New loci associated with subphenotypes of SSc.

The lower part shows the Manhattan Plot with corrected P values of the GWAS cohorts. The upper part shows the ORs and the 95% CI interval of the novel associated regions in the GWAS cohorts (HLA region, left panel) and all cohorts (non-HLA loci, right panel) for the overall analysis and each subphenotype considered in the study. (Note: the ORs and CIs on the forest plot do not exactly correspond to the numbers in Table 1 and Table 2. Table 1 and Table 2 shows marginal effects of these SNPs while this figure presents ORs and CIs after the adjustment for the other SNPs claimed as independent for that phenotype).

Figure 2. Manhattan plot showing the -log10 of the Mantel-Haenszel P value of all 1,112 SNPs in HLA region for the GWAS cohorts comprising 2,296 cases and 5,171 controls.

Associations for the whole SSc set are in black, while associations in ACA (760 cases) and ATA (447 cases) positive subgroups are in orange and red, respectively. Loci which were independently associated according to conditional logistic regression analysis are highlighted in grey.