Lung eQTLs to Help Reveal the Molecular Underpinnings of Asthma

Genome-wide association studies (GWAS) have identified loci reproducibly associated with pulmonary diseases; however, the molecular mechanism underlying these associations are largely unknown. The objectives of this study were to discover genetic variants affecting gene expression in human lung tissue, to refine susceptibility loci for asthma identified in GWAS studies, and to use the genetics of gene expression and network analyses to find key molecular drivers of asthma. We performed a genome-wide search for expression quantitative trait loci (eQTL) in 1,111 human lung samples. The lung eQTL dataset was then used to inform asthma genetic studies reported in the literature. The top ranked lung eQTLs were integrated with the GWAS on asthma reported by the GABRIEL consortium to generate a Bayesian gene expression network for discovery of novel molecular pathways underpinning asthma. We detected 17,178 cis- and 593 trans- lung eQTLs, which can be used to explore the functional consequences of loci associated with lung diseases and traits. Some strong eQTLs are also asthma susceptibility loci. For example, rs3859192 on chr17q21 is robustly associated with the mRNA levels of GSDMA (P = 3.55 × 10(-151)). The genetic-gene expression network identified the SOCS3 pathway as one of the key drivers of asthma. The eQTLs and gene networks identified in this study are powerful tools for elucidating the causal mechanisms underlying pulmonary disease. This data resource offers much-needed support to pinpoint the causal genes and characterize the molecular function of gene variants associated with lung diseases

Lung eQTLs found on chromosome 17q21.

<p>(a) The upper panel is a region of chromosome 17q21 from the UCSC browser showing the genes located in this region. The next panel shows the results from the GABRIEL consortium <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003029#pgen.1003029-Moffatt1" target="_blank">[9]</a> (each bar represents a SNP and the y-axis shows −log₁₀<i>P</i> values for association with asthma). The following three panels show the lung eQTL results for expression levels of <i>ORMDL3</i> (blue bars), <i>GSDMB</i> (green bars), and <i>GSDMA</i> (red bars), respectively. The y-axis represents −log₁₀<i>P</i> values derived from the meta-analysis of gene expression. The black horizontal lines are drawn at <i>P</i> = 0.05. (b) Boxplots of lung gene expression levels for GSDMA according to genotype groups for SNPs rs3859192 and rs7216389 in 1,111 subjects.</p

Relative expression of <i>GSDMA</i> and <i>GSDMB</i>.

<p>Primary human airway epithelial cells in monolayer culture were analyzed for; (a) the relative abundance of mRNA for <i>GSDMA</i> and <i>GSDMB</i> (n = 7) and (b) Protein expression of <i>GSDMA</i> and <i>GSDMB</i> by Western blot normalized to expression of β-tubulin (n = 10). (c) Representative image of <i>GSDMA</i> expression in human conducting airway by immunohistochemistry, which shows expression of <i>GSDMA</i> in both basal and apical cells within the airway epithelium.</p

Demographic and clinical characteristics of study cohort.

<p>PreBD, before bronchodilator use; FEV₁, forced expiratory volume in one second; FVC, forced vital capacity.</p>*<p>significantly different among groups at p<0.01 level (Kruskal Wallis and χ² tests were applied to quantitative and categorical traits, respectively).</p

Expression eQTL underlying Asthma GWAS hits.

*<p>Beneath the SNP ID in column 1, the reference allele and risk allele are shown (e.g. for rs7216389, C is the reference allele and T the risk allele).</p>**<p>Moffatt et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003029#pgen.1003029-Moffatt1" target="_blank">[9]</a> reported that rs3859192 in the 17q region was associated with asthma (<i>P</i> = 1.12×10⁻¹²). SNP rs3859192 was the most significant eSNP at this locus – strongly associated with GSDMA levels (<i>P</i> = 3.55×10⁻¹⁵¹) but weakly associated with GSDMB levels (<i>P</i> = 3.86×10⁻⁵).</p>***<p>Moffatt et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003029#pgen.1003029-Moffatt1" target="_blank">[9]</a> reported that SNPs at the IL1RL1 locus were associated with asthma and the GWAS peak was located at rs3771166. The latter SNP was not a strong lung eSNP (failed to pass 10% FDR). Another SNP at the IL1RL1 locus, rs13431828, was strongly associated with asthma (Moffatt et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003029#pgen.1003029-Moffatt1" target="_blank">[9]</a>, <i>P</i> = 1×10⁻¹⁰) and IL1RL1 expression level (<i>P</i> = 7.48×10⁻⁸).</p

Q–Q plot for the GABRIEL meta-analysis among eSNPs found in the lung eQTL study.

<p>Among all SNPs surveyed by the GABRIEL meta-analysis, 60,530 were eSNPs in the Lung eQTL study and considered in this Q-Q plot. As is apparent eQTLs were enriched for lower <i>P</i> values (enrichment <i>P</i> value<2.2E−16). Panel (a) is GABRIEL eSNPs plotted against GABRIEL SNPs, panel (b) is eSNPs of canonical asthma genes plotted against GABRIEL SNPs and panel (c) is eSNPs of canonical asthma genes plotted against GABRIEL eSNPs.</p

Overall study design and analysis workflow.

<p>Overall study design and analysis workflow.</p