Genetic variants modify the effect of age on APOE methylation in the Genetics of Lipid Lowering Drugs and Diet Network study

Abstract

Although apolipoprotein E (APOE) variants are associated with age-related diseases, the underlying mechanism is unknown and DNA methylation may be a potential one. With methylation data, measured by the Infinium Human Methylation 450 array, from 993 participants (age ranging from 18 to 87 years) in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study, and from Encyclopedia of DNA Elements (ENCODE) consortium, combined with published methylation datasets, we described the methylation pattern of 13 CpG sites within APOE locus, their correlations with gene expression across cell types, and their relationships with age, plasma lipids, and sequence variants. Based on methylation levels and the genetic regions, we categorized the 13 APOE CpG sites into three groups: Group 1 showed hypermethylation (> 50%) and were located in the promoter region, Group 2 exhibited hypomethylation (< 50%) and were located in the first two exons and introns, and Group 3 showed hypermethylation (> 50%) and were located in the exon 4. APOE methylation was negatively correlated with gene expression (minimum r = −0.66, P = 0.004). APOE methylation was significantly associated with age (minimum P = 2.06E-08) and plasma total cholesterol (minimum P = 3.53E-03). Finally, APOE methylation patterns differed across APOE ε variants (minimum P = 3.51E-05) and the promoter variant rs405509 (minimum P = 0.01), which further showed a significant interaction with age (P = 0.03). These findings suggest that methylation may be a potential mechanistic explanation for APOE functions related to aging and call for further molecular mechanistic studies.

Living long and ageing well: is epigenomics the missing link between nature and nurture?

“…Lindahl as early as 1981 had shown higher methylation levels for carriers of ApoE rs405509 A allele promoter and E4 allele carriers which are consistent with those recently described (Ma et al 2015). Differential methylation may provide a potential mechanistic explanation for research which links the A allele of Rs405509 to greater risk of myocardial infarction (Lambert et al 2000), premature coronary heart disease (Viitanen et al 2001) and Alzheimer's disease (Lambert et al 1998), but with lower plasma concentration of ApoE (Lambert et al 2000) and for differential ageing-related functions of the ApoE gene allelic variants in healthy ageing cohorts of nonagenarians/centenarians.…”

“…Recent work by Ma et al (2015) may begin to provide a partial explanation in that their qualitative and quantitative evidence appears to support connections between ApoE methylation, age and plasma lipids. Methylation patterns at 13 CpG sites within the ApoE locus were shown to separate into 3 groups-Group 1 associated with the ApoE promoter region (rs405509) which showed hypermethylation ([50 %), Group 2 within the first 2 exons and introns exhibited hypomethylation (\50 %) and Group 3 in exon 4 (rs429458 and rs7412 which defines the E2/E3/E4 isoforms of ApoE) showed hypermethylation ([50 %), with each Group showing consistent patterns of methylation across different cell types.…”

DNA methylation in the APOE gene: its link with Alzheimer’s and cardiovascular health

“…The predictor-specific covariates used in the fully-adjusted model varied according to the predictor variable of the model and, whenever possible, corresponded with previous studies [15,22]. Both the basic-and the fully-adjusted model included as covariates the batch in which the samples of a given participant were processed on the array (fitted as a random effect on the intercept) and the estimated proportions of CD8+-and CD4+-T-cells, natural killer cells, B cells, monocytes, and granulocytes.…”

“…Twelve CpGs exhibited similar methylation levels to those previously described (Supp . Table 1; [15,16,22]), whereas one of them (cg20051876, which is unique to the Illumine EPIC array) had not been reported before. Based on the Illumina-annotated locations of the CpGs on the chromosome, their relative distances to each other, and their methylation levels, the CpGs were classified into three groups: hypermethylated (each site > 50% mean methylation) and lying in the promoter region (region 1: cg20051876, cg14123992, cg04406254), hypomethylated (each site < 50% mean methylation) and lying in the region encompassing the first two exons and introns (region 2: cg26190885, cg12049787, cg08955609, cg18768621, cg19514613, cg06750524), and hypermethylated and lying in the 4 th exon (region 3: cg16471933, cg05501958, cg18799241, cg21879725).…”

“…Associations have been suggested between epigenetic mechanisms and risk factors for cardiovascular disease [20,21,22,23]. Whereas a recent systematic review identified 34 candidate-gene studies on methylation in CVD [4], few have explored modifications in APOE, and there have been some conflicting results: while Karlsson et al [15] found no evidence for differences in APOE methylation in blood between patients with CVD and healthy controls, Ji et al [24] reported APOE hypermethylation in the blood of patients with coronary heart disease compared to controls.…”