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ObjectivesSystemic lupus erythematosus (SLE), an autoimmune disease with incompletely understood etiology, has a strong genetic component. Although genome-wide association studies (GWAS) have revealed multiple SLE susceptibility loci and associated single nucleotide polymorphisms (SNPs), the precise causal variants, target genes, cell types, tissues, and mechanisms of action remain largely unknown.MethodsHere, we report a comprehensive post-GWAS analysis using extensive annotation, molecular modeling, and integrative functional genomic and epigenomic analyses to optimize fine-mapping. We compile and cross-reference immune cell-specific expression quantitative trait loci (cis- andtrans-eQTLs) with promoter capture Hi-C, allele-specific chromatin accessibility, and massively parallel reporter assay data to define predisposing variants and target genes. To assess our predictions, we experimentally validate a locus using CRISPR/Cas9 genome editing, qPCR, and Western blot.ResultsAnchoring on 452 index SNPs, we selected 9,931 high-linkage disequilibrium (r2>0.8) SNPs and defined 182 independent non-HLA SLE loci. 3,746 SNPs from 143 loci were identified as regulating 564 unique genes. Target genes are enriched in lupus-related tissues and associated with other autoimmune diseases. Of these, 329 SNPs (106 loci) showed significant allele-specific chromatin accessibility or enhancer activity, indicating regulatory potential. Using CRISPR/Cas9, we validated rs57668933 as a functional variant regulating multiple targets, including SLE risk geneELF1, in B-cells.ConclusionWe demonstrate and validate post-GWAS strategies for utilizing multi-dimensional data to prioritize likely causal variants with cognate gene targets underlying SLE pathogenesis. Our results provide a catalog of significantly SLE-associated SNPs and loci, target genes, and likely biochemical mechanisms, to guide experimental characterization.

ObjectivePremature atherosclerosis is associated with systemic lupus erythematosus (SLE). We previously showed an association of anti-Ro60/La/Ro52 to anti-oxidized LDL in SLE. Here, we hypothesized that atherosclerotic plaque will be associated with anti-oxidized LDL (anti-oxLDL)/anti-lipoprotein lipase (ALPL) in a specific SLE autoantibody sub-set (anti-Ro60 positive, anti-RNP positive or extractable nuclear antigen antibody negative).MethodsWe carried out a case-control study (one time-point testing) of plaque, ALPL, anti-oxLDL, anti-low density lipoprotein (ALDL) or anti-LDL in 114 SLE and 117 age/sex matched controls. Total cholesterol, LDL, HDL, triglycerides, and HDL-Trig were also measured. Students t test was used for statistical analysisResultsInterestingly, plaque was highest in SLE subset with anti-Ro60 (23/114). Plaque and anti-oxLDL were statistically significantly elevated in the anti-Ro60 SLE subset (1.3 +/-1.66, pConclusionPlaque segregates in anti-Ro and ENA negative groups either with or without anti-oxLDL. It will be clinically important if cardiovascular events are augmented in SLE anti-Ro subset having elevated anti-oxidized LDL antibodies.Key pointsPlaque and anti-oxLDL significantly elevated in anti-Ro60 SLE subsetOnly plaque significantly elevated in SLE subset without antibodies against extractable nuclear antigensIt will be clinically important to see if augmented cardiovascular events occur in SLE anti-Ro subset having elevated anti-oxidized LDL antibodies.

Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component. We recently identified a novel SLE susceptibility locus near RASGRP1, which governs the ERK/MAPK kinase cascade and B-/T-cell differentiation and development. However, precise causal RASGRP1 functional variant(s) and their mechanisms of action in SLE pathogenesis remain undefined. Our goal was to fine-map this locus, prioritize genetic variants according to likely functionality, experimentally validate the contribution of three SNPs to SLE risk, and experimentally determine their biochemical mechanisms of action. We performed a meta-analysis across six Asian and European cohorts (9,529 cases; 22,462 controls), followed by in silico bioinformatic and epigenetic analyses to prioritize potentially functional SNPs. We experimentally validated the functional significance and mechanism of action of three SNPs in cultured T-cells. Meta-analysis identified 18 genome-wide significant (p−8) SNPs, mostly concentrated in two haplotype blocks, one intronic and the other intergenic. Epigenetic fine-mapping, allelic, eQTL and imbalance analyses predicted three transcriptional regulatory regions with four SNPs (rs7170151, rs11631591-rs7173565, and rs9920715) prioritized for functional validation. Luciferase reporter assays indicated significant allele-specific enhancer activity for intronic rs7170151 and rs11631591-rs7173565 in T-lymphoid (Jurkat) cells, but not in HEK293 cells. Following up with EMSA, mass spectrometry and ChIP-qPCR, we detected allele-dependent interactions between heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and rs11631591. Furthermore, inhibition of hnRNP-K in Jurkat and primary T-cells downregulated RASGRP1 and ERK/MAPK signaling. Comprehensive association, bioinformatics, and epigenetic analyses yielded putative functional variants of RASGRP1, which were experimentally validated. Notably, intronic variant (rs11631591) is located in a cell type-specific enhancer sequence, where its risk allele binds to the hnRNP-K protein and modulates RASGRP1 expression in Jurkat and primary T-cells. As risk allele dosage of rs11631591 correlates with increased RASGRP1 expression and ERK activity, we suggest that this SNP may underlie SLE risk at this locus.