DNA Methylation Dynamics in Human Carotid Plaques After Cerebrovascular Events

Abstract

Recently, our high-coverage epigenomics study of the human aorta and carotid arteries has identified atherosclerosis-specific DNA methylation profiles that are lesion gradeindependent and are, therefore, established relatively early © 2015 American Heart Association, Inc. Objective-To understand whether cerebrovascular events, a major complication of atherosclerosis, are associated with any specific DNA methylation changes in the carotid plaque. Approach and Results-We profiled the DNA methylomes of human symptomatic carotid plaques obtained from patients who had cerebrovascular events (n=19) and asymptomatic counterparts (n=19) with a high-density microarray (≈485 000 CpG sites, Illumina), and crossed DNA methylation data with RNAseq-based expression data from an independent symptomatic carotid plaque set (n=8). Few (30) CpGs showed a significant (P<0.05; absolute Delta-Beta, >0.20) differential methylation between the 2 groups. Within symptomatic carotid plaques, DNA methylation correlated significantly with postcerebrovascular event time (range, 3-45 days; r-value range, −0.926 to 0.857; P<0.05) for ≈45 000 CpGs, the vast majority of which became hypomethylated with increasing postcerebrovascular event time. Hypomethylation was not due to erasure of the gene-body and CG-poor region hypermethylation that accompany the progression of stable lesions, but rather targeted promoters and CpG islands. Noticeably, promoter hypomethylation and increased expression of genes involved in the inhibition of the inflammatory response, defense against oxidative stress, and active DNA demethylation were observed with increasing postcerebrovascular event time. Concomitantly, histological changes consistent with phagocyte-driven plaque healing were observed. Conclusions-Weak changes in the DNA methylome distinguish symptomatic from asymptomatic plaques, but a widespread demethylation resulting in permissive transcriptional marks at atheroprotective gene promoters is established in plaques after a cerebrovascular event, thus mirroring previous observations that ruptured plaques tend to revert to a stable structure. The identified loci are candidate targets to accelerate the pace of carotid plaque stabilization. (Arterioscler Thromb Vasc

DNA methylation of MMPs and TIMPs in atherothrombosis process in carotid plaques and blood tissues

“…These findings were most evident at the body and TSS1500 regions of the genes. Our results are in line with those of others, who observed a broad trend of DNA hypermethylation in plaque progression [8][9][10]. Zaina et al, observed pattern of genome-wide hypermethylation in atherosclerotic plaques, suggesting that an atherosclerosis-specific DNA methylation profile is established in the early stages of plaque evolution [9].…”

“…A trend to hypermethylation is observed in unstable plaque-portion and non-stroke control samples, which falls into line with what has been postulated by others, i.e., that ruptured plaques tend to revert to a stable structure. Zaina et al, in their study, observed an initial hypermethylation in the transition from asymptomatic plaque to early post-cerebrovascular event time, followed by a reversion to initial methylation levels with increasing post-cerebrovascular event time, suggesting a process of plaque remodeling to a more stable phenotype [8]. Peeters W et al, proposed that ruptured plaques remodel to a relatively stable structure after stroke events [14].…”

“…Zaina et al, observed pattern of genome-wide hypermethylation in atherosclerotic plaques, suggesting that an atherosclerosis-specific DNA methylation profile is established in the early stages of plaque evolution [9]. In a separate study, Zaina et al, identified small DNAm changes between symptomatic and asymptomatic plaques and an association with increasing post-cerebrovascular event time [8]. They observed a general hypermethylation in the plaque in early postcerebrovascular event time compared to asymptomatic plaque.…”

“…Zaina et al, observed widespread hypermethylation in the atherosclerotic portion of 15 aorta samples compared to healthy counterparts [9]. In a different study, Zaina et al, detected small DNAm changes between 19 symptomatic and asymptomatic plaque pairs, and a drift toward hypomethylation, associated with increasing post-cerebrovascular event time [8], whereas others identified a set of CpGs that drift toward hypermethylation with lesion progression [10], in 15 sample-pairs.…”

“…Some studies have observed associations between protein plasma levels of MMPs, TIMPs, atheromatous plaque instability [5,6], stroke progression [7]. However, few studies have investigated the relationship between DNA methylation (DNAm) and atherosclerosis pathogenicity [8][9][10] and none have focused on the MMP and TIMP gene families. Zaina et al, observed widespread hypermethylation in the atherosclerotic portion of 15 aorta samples compared to healthy counterparts [9].…”