GWAS loci associated with Chagas cardiomyopathy influences DNA methylation levels

Abstract

A recent genome-wide association study (GWAS) identified a locus in chromosome 11 associated with the chronic cardiac form of Chagas disease. Here we aimed to elucidate the potential functional mechanism underlying this genetic association by analyzing the correlation among single nucleotide polymorphisms (SNPs) and DNA methylation (DNAm) levels as cis methylation quantitative trait loci (cis-mQTL) within this region. A total of 2,611 SNPs were tested against 2,647 DNAm sites, in a subset of 37 chronic Chagas cardiomyopathy patients and 20 asymptomatic individuals from the GWAS. We identified 6,958 significant cis-mQTLs (False Discovery Rate [FDR]<0.05) at 1 Mb each side of the GWAS leading variant, where six of them potentially modulate the expression of the SAC3D1 gene, the reported gene in the previous GWAS. In addition, a total of 268 cis-mQTLs showed differential methylation between chronic Chagas cardiomyopathy patients and asymptomatic individuals. The most significant cis-mQTLs mapped in the gene bodies of POLA2 (FDR = 1.04x10-11), PLAAT3 (FDR = 7.22x10-03), and CCDC88B (FDR = 1.89x10-02) that have been associated with cardiovascular and hematological traits in previous studies. One of the most relevant interactions correlated with hypermethylation of CCDC88B. This gene is involved in the inflammatory response, and its methylation and expression levels have been previously reported in Chagas cardiomyopathy. Our findings support the functional relevance of the previously associated genomic region, highlighting the regulation of novel genes that could play a role in the chronic cardiac form of the disease.

Fig 1. Regional scatter plot of the cis-mQTL results for the selected genomic region under analysis (chr11:63814813–65814813).

Representation of the 6,958 cis-mQTLs identified in the genomic region previously associated to the disease. The x-axis corresponds to the genomic position of the SNP from each mQTL interaction; the y-axis refers to the transformed False Discovery Rate (FDR) of each signal.

Fig 2. Box plots of three of the most interesting genes comparing DNAm levels between chronic Chagas cardiomyopathy patients (CCC) and asymptomatic individuals (A).

Comparison of individuals’ SNP genotypes and CpGs Mvalues for the most interesting mQTL genes that also showed differences in methylation patterns in cases and controls. Significant differences between genotypes are marked with symbols according to their level of significance calculated with an ANOVA test (* p-value≤0.05; ** p-value≤0.01; *** p-value≤0.001).