Mendelian Randomization Integrating GWAS, eQTL, and mQTL Data Identified Genes Pleiotropically Associated With Atrial Fibrillation

Abstract

Background: Atrial fibrillation (AF) is the most common arrhythmia. Genome-wide association studies (GWAS) have identified more than 100 loci associated with AF, but the underlying biological interpretation remains largely unknown. The goal of this study is to identify gene expression and DNA methylation (DNAm) that are pleiotropically or potentially causally associated with AF, and to integrate results from transcriptome and methylome. Methods: We used the summary data-based Mendelian randomization (SMR) to integrate GWAS with expression quantitative trait loci (eQTL) studies and methylation quantitative trait loci (mQTL) studies. The HEIDI (heterogeneity in dependent instruments) test was introduced to test against the null hypothesis that there is a single causal variant underlying the association. Results: We prioritized 22 genes by eQTL analysis and 50 genes by mQTL analysis that passed the SMR & HEIDI test. Among them, 6 genes were overlapped. By incorporating consistent SMR associations between DNAm and AF, between gene expression and AF, and between DNAm and gene expression, we identified several mediation models at which a genetic variant exerted an effect on AF by altering the DNAm level, which regulated the expression level of a functional gene. One example was the genetic variant-cg18693985-CPEB4-AF axis. Conclusion: In conclusion, our integrative analysis identified multiple genes and DNAm sites that had potentially causal effects on AF. We also pinpointed plausible mechanisms in which the effect of a genetic variant on AF was mediated by genetic regulation of transcription through DNAm. Further experimental validation is necessary to translate the identified genes and possible mechanisms into clinical practice.

Keywords: GWAS; Mendelian randomization; atrial fibrillation; eQTL; mQTL; multi-omics.

Figure 1

A flowchat to identify mediation mechanism. The effects of DNAm on trait, DNAm on gene expression, and gene expression on trait are evaluated using the SMR & HEIDI method and integrated to identify potential mediation mechanisms in which an SNP exerts an effect on the trait by altering the DNAm level, which then regulates the expression levels of a functional gene.

Figure 2

Result of summary data-based Mendelian randomization (SMR). Shown are –log10 (P-values) from the SMR tests for AF against the physical positions of gene expression (left) or DNAm probes (right). Red dot lines represent the significance thresholds of the SMR tests.

Figure 3

Results of SNP and SMR associations across mQTL, eQTL, and GWAS at the CPEB4 locus. The top plot shows –log10 (P-values) of SNPs from the AF GWAS. The red diamond and blue circle represent –log10 (P-values) for probes from the SMR tests for associations of gene expression and DNAm probes, respectively. The second plot shows eQTL results for the probe ILMN_1722025 (tagging CPEB4). The third plot shows mQTL results for the DNAm probe cg18693985. The bottom plot shows 18 chromatin state annotations (indicated by colors) of 833 samples from EpiMap for different primary cells and tissue types (rows).