Systematic identification of trans eQTLs as putative drivers of known disease associations

Abstract

Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE), altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE. DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3' UTR levels of IKZF1 in cis, and chromatin immunoprecipitation and sequencing analysis of the trans-regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.

Figure 1. Trans-eQTL SNPs are enriched for functional elements

We investigated whether the trans-eQTL SNPs are enriched for certain functional elements. We used the online tools SNPInfo, SNPNexus, and HaploReg that rely upon data from, amongst others, the ENCODE project. (a) We observed that trans-eQTL SNPs are enriched for mapping within miRNA binding sites (b) trans-eQTL SNPs show strong enrichment (as annotated using HaploReg) for enhancer regions that are present in K562 (myeloid) and GM12878 (lymphoid) cell-lines (error bars represent one standard deviation).

Figure 2. Independent trans-eQTL effects emanating from the IKZF1 locus

Systemic lupus erythematosus SNP rs4917014 and unlinked mean corpuscular volume SNP rs4917014 both affect expression of IKZF1 in cis. rs12718597 affects 50 trans-genes (mostly involved in hemoglobin metabolism) while rs4917014 affects eight different genes in trans: the rs4917014*T risk allele increases expression of genes involved in type I interferon response. At a somewhat lower significance threshold of FDR 0.28 rs4917014*T decreases complement C1QB expression. Both processes are hallmark features of SLE.

Figure 3. Cholesterol SNP rs174546 affects LDLR in trans

The rs174546*T allele is known to be associated with a decrease in serum LDL cholesterol and triglycerides levels. It increases the expression levels of three genes in cis, but also increases gene expression levels of LDLR that encodes the LDL receptor.

Figure 4. For 21 complex traits, pairs of unlinked trait-associated SNPs affect the same downstream genes

We observed that for 21 different traits, there were pairs of unlinked SNPs that have previously been reported to be associated with these traits and which also affect exactly the same downstream genes in trans, whereas this is rarely observed when using an equally sized, but permuted list of trans-eQTLs.

Figure 5. Two unlinked type-1 diabetes risk alleles both increase STAT1 and GBP4 expression

rs3184504*T, a risk allele for type 1 diabetes (chromosome 12), affects the expression of SH2B3 in cis, but also affects the expression levels of fourteen unique genes in trans, including two interferon-γ response genes GBP4 and STAT1. Another unlinked type-1 diabetes risk allele (rs4788084*C on chromosome 16) also increases expression levels of these two interferon-γ response genes, indicating that an elevated interferon-γ response is important in type 1 diabetes.