Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma

Abstract

Background: Identifying novel epigenetic signatures associated with serum immunoglobulin E (IgE) may improve our understanding of molecular mechanisms underlying asthma and IgE-mediated diseases.

Methods: We performed an epigenome-wide association study using whole blood from Framingham Heart Study (FHS; n = 3,471, 46% females) participants and validated results using the Childhood Asthma Management Program (CAMP; n = 674, 39% females) and the Genetic Epidemiology of Asthma in Costa Rica Study (CRA; n = 787, 41% females). Using the closest gene to each IgE-associated CpG, we highlighted biologically plausible pathways underlying IgE regulation and analyzed the transcription patterns linked to IgE-associated CpGs (expression quantitative trait methylation loci; eQTMs). Using prior UK Biobank summary data from genome-wide association studies of asthma and allergy, we performed Mendelian randomization (MR) for causal inference testing using the IgE-associated CpGs from FHS with methylation quantitative trait loci (mQTLs) as instrumental variables.

Findings: We identified 490 statistically significant differentially methylated CpGs associated with IgE in FHS, of which 193 (39.3%) replicated in CAMP and CRA (FDR < 0.05). Gene ontology analysis revealed enrichment in pathways related to transcription factor binding, asthma, and other immunological processes. eQTM analysis identified 124 cis-eQTMs for 106 expressed genes (FDR < 0.05). MR in combination with drug-target analysis revealed CTSB and USP20 as putatively causal regulators of IgE levels (Bonferroni adjusted P < 7.94E-04) that can be explored as potential therapeutic targets.

Interpretation: By integrating eQTM and MR analyses in general and clinical asthma populations, our findings provide a deeper understanding of the multidimensional inter-relations of DNA methylation, gene expression, and IgE levels.

Funding: US NIH/NHLBI grants: P01HL132825, K99HL159234. N01-HC-25195 and HHSN268201500001I.

Keywords: Asthma; DNA methylation; Drug targets; EWAS; IgE; Lung; Mendelian randomization; RNA-Sequencing; eQTM.

Fig. 1

Flowchart of overall study design in discovery and replication cohorts. The study design shows the cohorts, the sample sizes and shared CpG loci. For these analyses, cohorts included the Framingham Heart Study (FHS), The Childhood Asthma Management Program (CAMP) and The Genetic Epidemiology of Asthma in Costa Rica Study (CRA) that were utilized for EWAS and meta-analysis. The overlapping CpGs between all three cohorts were subjected to pathway, eQTM, MR, Drug-target and eFORGE analyses for functional and clinical relevance. EWAS, epigenome-wide association study; eQTM, expression-methylation quantitative trait loci; MR, mendelian randomization; eFORGE, experimentally-derived Functional element Overlap analysis of ReGions from EWAS.

Fig. 2

Euler venn diagram showing the 193 shared DNA methylation CpG sites between FHS, CAMP, and CRA cohorts. These overlapping CpGs were significant in all three cohorts at an FDR threshold of 5%.

Fig. 3

Gene-disease associations for the overlapping set (n = 193 CpGs) between FHS, CRA and CAMP cohorts. The enriched terms are sorted based on the gene-overlap of the input set with the term set as represented by their size and the count key. The color key corresponds to the FDR adjusted P-value threshold of 5%.