Admixture Mapping in Lupus Identifies Multiple Functional Variants within IFIH1 Associated with Apoptosis, Inflammation, and Autoantibody Production

Abstract

Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease with a strong genetic component. African-Americans (AA) are at increased risk of SLE, but the genetic basis of this risk is largely unknown. To identify causal variants in SLE loci in AA, we performed admixture mapping followed by fine mapping in AA and European-Americans (EA). Through genome-wide admixture mapping in AA, we identified a strong SLE susceptibility locus at 2q22–24 (LOD = 6.28), and the admixture signal is associated with the European ancestry (ancestry risk ratio ∼1.5). Large-scale genotypic analysis on 19,726 individuals of African and European ancestry revealed three independently associated variants in the IFIH1 gene: an intronic variant, rs13023380 [Pmeta = 5.20×10−14; odds ratio, 95% confidence interval = 0.82 (0.78–0.87)], and two missense variants, rs1990760 (Ala946Thr) [Pmeta = 3.08×10−7; 0.88 (0.84–0.93)] and rs10930046 (Arg460His) [Pdom = 1.16×10−8; 0.70 (0.62–0.79)]. Both missense variants produced dramatic phenotypic changes in apoptosis and inflammation-related gene expression. We experimentally validated function of the intronic SNP by DNA electrophoresis, protein identification, and in vitro protein binding assays. DNA carrying the intronic risk allele rs13023380 showed reduced binding efficiency to a cellular protein complex including nucleolin and lupus autoantigen Ku70/80, and showed reduced transcriptional activity in vivo. Thus, in SLE patients, genetic susceptibility could create a biochemical imbalance that dysregulates nucleolin, Ku70/80, or other nucleic acid regulatory proteins. This could promote antibody hypermutation and auto-antibody generation, further destabilizing the cellular network. Together with molecular modeling, our results establish a distinct role for IFIH1 in apoptosis, inflammation, and autoantibody production, and explain the molecular basis of these three risk alleles for SLE pathogenesis.

Association of interferon-induced helicase C domain (IFIH1) gene polymorphisms with systemic lupus erythematosus and a relevant updated meta-analysis

“…rs6432714 has never been investigated in patients with SLE; however, it has been associated with type 1 diabetes, an autoimmune disease, in the population of northeast Brazil (Moura et al, 2013). Recently, a whole-genome admixture mapping study identified IFIH1 rs10930046 to be related to apoptosis, inflammation, and autoantibody production in patients with SLE (Molineros et al, 2013). In this study, we did not find any association between rs10930046 and SLE or its clinical features, confirming an earlier finding by Wang et al (2013).…”

“…Our results reinforced a previous GWAS, which reported a trend for association between rs1990760 and SLE susceptibility (SLEGEN et al, 2008). rs1990760 is located within the RIG-1 regulatory domain encoded by exons 14-16 and was linked to increased IFN-a levels in patients with SLE positive for anti-dsDNA autoantibodies (Robinson et al, 2011;Molineros et al 2013). rs1990760 is also the most studied IFIH1 SNP associated with SLE, and has been demonstrated to increase IFIH1 expression.…”

Effects of Type 1 Diabetes-Associated IFIH1 Polymorphisms on MDA5 Function and Expression

“…Franek et al showed that the SLE/T1D risk allele, Thr 946 , was associated with lower IFNα serum levels but higher IFN-induced expression of MX1 [57]. In line with this observation, ectopic expression of the Thr 946 allele in K562 cells resulted in a relative decrease in IFNα, TNFα, and Casp8 expression and concomitant increase in MX1, MAVS, and MAPK8 [52]. As IFNβ is essential for expression of MX1, these results suggest an IFNβ-mediated IFN response [58,59].…”

“…Significant advances have been made to our understanding of the role of this SNP in the context of T1D pathogenesis. The A946T (rs1990760) SNP resides within the CTD domain, and it was observed that the Ala 946 genotype is highly conserved across a variety of mammalian species suggesting its importance to IFIH1/MDA5 function [52]. Horvath et al has previously shown that mutations that inhibit MDA5 ATPase activity are capable of enhancing the IFN-I (IFNβ) response [53].…”

Confirmation of five novel susceptibility loci for Systemic Lupus Erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci

“…As we have done before (47), testing of promoter/enhancer fragments (differing only at the predicted risk/protective SNP) in reporter assays can reveal profound differences in activity. Such results can be explored further with electrophoretic mobility shift assays (EMSAs) (47), bound proteins in shifted bands can be identified by mass spectrometry, and finally bands can be 'super-shifted' with antibodies to bound proteins.…”