SNPs identified by GWAS affect asthma risk through DNA methylation and expression of cis-genes in airway epithelium

Abstract

The Trans-National Asthma Genetic Consortium (TAGC) identified 878 SNPs associated with asthma. We hypothesized that those SNPs affect asthma risk by regulating gene expression in airway epithelium, and conducted expression quantitative trait loci (eQTL) and mediation analyses to identify direct associations between the SNPs and expression levels of cis-genes (within 1 Mb) in nasal (airway) epithelium from Puerto Rican children with (n=228) and without (n=241) asthma. We then tested whether genes whose expression is associated with TAGC SNPs are differentially expressed (DE) in atopic asthma. We identified 1,150 direct associations between 418 TAGC SNPs and the expression of 55 cis-genes. Most SNPs regulate distant cis-genes (average distance ~200 kb). Our mediation analysis showed that 4,571 (89.2%) of 5,119 (direct and indirect) SNP-gene expression associations are mediated by methylation. Of 114 genes whose expression is associated with TAGC SNPs, 54 are DE in atopic asthma, including novel and previously reported genes. In an independent cohort of 72 African American children, 50 of the 54 DE genes were available, and 21 (42%) were also DE in atopic asthma. Thus, we show that many TAGC SNPs are associated with expression of distant cis-genes in airway epithelium, and that this is predominantly mediated by DNA methylation. Moreover, nearly half of the genes whose expression in airway epithelium is associated with TAGC SNPs are also DE in atopic asthma. Our findings support a key role of regulation of airway epithelial gene expression on atopic asthma in children.

Figure 1.. eQTL and mediation analysis of 869 TAGC SNPs

(A) Percentage of eQTL SNPs that are located outside (blue) or inside (orange) of their paired gene region (Promoter – 5’UTR). When SNPs were associated with expression of multiple genes, they were counted multiple times. (B) Histogram of distance between eQTL SNPs and transcription start site of their associated genes (in Kb). (C) Venn diagram of the number of SNPs associated with gene expression (eQTL) (pink) and the number of SNPs associated with gene expression through mediation by methylation (blue). To test mediation effects of methylation between SNPs and gene expression, the Sobel test was conducted (at FDR-P < 0.05). (D) Composition of TAGC GWAS SNPs according to whether they are associated with cis-gene expression (left) and composition of the SNPs that regulate cis-gene expression, according to whether they are directly associated with gene expression (eQTL only) or indirectly associated with gene expression through mediation effects of methylation. (E) An example of a SNP that is indirectly associated with HLA-DQA2 gene expression through DNA methylation, and the gene is differentially expressed in atopic asthma. 1. Violin plots of the relationship between the eQTL SNP and an associated methylation probe (red, homozygous major allele; green, heterozygous; blue, homozygous minor allele) 2. Scatter plots of the relationship between DNA methylation and expression of the gene. 3. Violin plots of data from atopic asthmatic vs. those from non-atopic non-asthmatic controls against differential gene expression.