Colocalization of Gene Expression and DNA Methylation with Genetic Risk Variants Supports Functional Roles of <i>MUC5B</i> and <i>DSP</i> in Idiopathic Pulmonary Fibrosis.

Abstract

<b>Rationale:</b> Common genetic variants have been associated with idiopathic pulmonary fibrosis (IPF). <b>Objectives:</b> To determine functional relevance of the 10 IPF-associated common genetic variants we previously identified. <b>Methods:</b> We performed expression quantitative trait loci (eQTL) and methylation quantitative trait loci (mQTL) mapping, followed by co-localization of eQTL and mQTL with genetic association signals and functional validation by luciferase reporter assays. Illumina multi-ethnic genotyping arrays, mRNA sequencing, and Illumina 850k methylation arrays were performed on lung tissue of participants with IPF (234 RNA and 345 DNA samples) and non-diseased controls (188 RNA and 202 DNA samples). <b>Measurements and Main Results:</b> Focusing on genetic variants within 10 IPF-associated genetic loci, we identified 27 eQTLs in controls and 24 eQTLs in cases (false-discovery-rate-adjusted <i>P</i> < 0.05). Among these signals, we identified associations of lead variants rs35705950 with expression of <i>MUC5B</i> and rs2076295 with expression of <i>DSP</i> in both cases and controls. mQTL analysis identified CpGs in gene bodies of <i>MUC5B</i> (cg17589883) and <i>DSP</i> (cg08964675) associated with the lead variants in these two loci. We also demonstrated strong co-localization of eQTL/mQTL and genetic signal in <i>MUC5B</i> (rs35705950) and <i>DSP</i> (rs2076295). Functional validation of the mQTL in <i>MUC5B</i> using luciferase reporter assays demonstrates that the CpG resides within a putative internal repressor element. <b>Conclusions:</b> We have established a relationship of the common IPF genetic risk variants rs35705950 and rs2076295 with respective changes in <i>MUC5B</i> and <i>DSP</i> expression and methylation. These results provide additional evidence that both <i>MUC5B</i> and <i>DSP</i> are involved in the etiology of IPF.