An efficient analytic approach in genome-wide identification of methylation quantitative trait loci response to fenofibrate treatment

Abstract

Background: The study of DNA methylation quantitative trait loci (meQTLs) helps dissect regulatory mechanisms underlying genetic associations of human diseases. In this study, we conducted the first genome-wide examination of genetic drivers of methylation variation in response to a triglyceride-lowering treatment with fenofibrate (response-meQTL) by using an efficient analytic approach.

Methods: Subjects (n = 429) from the GAW20 real data set with genotype and both pre- (visit 2) and post- (visit 4) fenofibrate treatment methylation measurements were included. Following the quality control steps of removing certain cytosine-phosphate-guanine (CpG) probes, the post-/premethylation changes (post/pre) were log transformed and the association was performed on 208,449 CpG sites. An additive linear mixed-effects model was used to test the association between each CpG probe and single nucleotide polymorphisms (SNPs) around ±1 Mb region, with age, sex, smoke, batch effect, and principal components included as covariates. Bonferroni correction was applied to define the significance threshold (p < 5.6 × 10^{- 10}, given a total of 89,217,303 tests). Finally, we integrated our response-meQTL (re-meQTL) findings with the published genome-wide association study (GWAS) catalog of human diseases/traits.

Results: We identified 1087 SNPs as cis re-meQTLs associated with 610 CpG probes/sites located in 351 unique gene loci. Among these 1087 cis re-meQTL SNPs, 229 were unique and 6 were co-localized at 8 unique disease/trait loci reported in the GWAS catalog (enrichment p = 1.51 × 10^{- 23}). Specifically, a lipid SNP, rs10903129, located in intron regions of gene TMEM57, was a re-meQTL (p = 3.12 × 10^{- 36}) associated with the CpG probe cg09222892, which is in the upstream region of the gene RHCE, indicating a new target gene for rs10903129. In addition, we found that SNP rs12710728 has a suggestive association with cg17097782 (p = 1.77 × 10^{- 4}), and that this SNP is in high linkage disequilibrium (LD) (R² > 0.8) with rs7443270, which was previously reported to be associated with fenofibrate response (p = 5.00 × 10^{- 6}).

Conclusions: By using a novel analytic approach, we efficiently identified thousands of cis re-meQTLs that provide a unique resource for further characterizing functional roles and gene targets of the SNPs that are most responsive to fenofibrate treatment. Our efficient analytic approach can be extended to large response quantitative trait locus studies with large sample sizes and multiple time points data.

Fig. 1

Q-Q plot of cis re-mQTLs, Expected p value of a null distribution was plotted on a negative log scale (black line) and the p values of the re-mQTLs was plotted on a negative log scale (black dots).The 95% confidence interval of the observed p value is shown in gray. The genomic inflation lambda is 1.097

Fig. 2

The Manhattan plot of cis re-mQTLs (p < 5.6 × 10^− 10) identified in this study with GWAS SNPs reported in the National Human Genome Research Institute (NHGRI) Catalog (highlighted in red)

Fig. 3

Regional plot of SNP rs10903129. a Associated with cg09222892 probe (chr1: 25861512–25,861,513). b Associated with total cholesterol GWAS results in which the SNP is mapped to TMEM57

Fig. 4

Regional plot of SNP rs12710728–associated cg17097782 probe (annotation: OSR1)