DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque

Abstract

Background Atherosclerotic plaque vulnerability is a key feature of atheroprogression and precipitating acute cardiovascular events. Although the pivotal role of epigenetic regulation in atherosclerotic plaque destabilization is being recognized, the DNA methylation profile and its potential role in driving the progression and destabilization of atherosclerotic cardiovascular disease remains largely unknown. We conducted a genome-wide analysis to identify differentially methylated genes in vulnerable and non-vulnerable atherosclerotic lesions to understand more about pathogenesis. Results We compared genome-wide DNA methylation profiling between carotid artery plaques of patients with clinically symptomatic (recent stroke or transient ischemic attack) and asymptomatic disease (no recent stroke) using Infinium Methylation BeadChip arrays, which revealed 90,368 differentially methylated sites (FDR < 0.05, |delta beta|> 0.03) corresponding to 14,657 annotated genes. Among these genomic sites, 30% were located at the promoter regions and 14% in the CpG islands, according to genomic loci and genomic proximity to the CpG islands, respectively. Moreover, 67% displayed hypomethylation in symptomatic plaques, and the differentially hypomethylated genes were found to be involved in various aspects of inflammation. Subsequently, we focus on CpG islands and revealed 14,596 differentially methylated sites (|delta beta|> 0.1) located at the promoter regions of 7048 genes. Integrated analysis of methylation and gene expression profiles identified that 107 genes were hypomethylated in symptomatic plaques and showed elevated expression levels in both advanced plaques and ruptured plaques. The imprinted gene PLA2G7, which encodes lipoprotein-associated phospholipase A2 (Lp-PLA2), was one of the top hypomethylated genes with an increased expression upon inflammation. Further, the hypomethylated CpG site at the promoter region of PLA2G7 was identified as cg11874627, demethylation of which led to increased binding of Sp3 and expression of Lp-PLA2 through bisulfate sequencing, chromatin immunoprecipitation assay and enzyme-linked immunosorbent assay. These effects were further enhanced by deacetylase. Conclusion Extensive DNA methylation modifications serve as a new and critical layer of biological regulation that contributes to atheroprogression and destabilization via inflammatory processes. Revelation of this hitherto unknown epigenetic regulatory mechanism could rejuvenate the prospects of Lp-PLA2 as a therapeutic target to stabilize the atherosclerotic plaque and reduce clinical sequelae.

Bioinformatic analysis and experimental validation identified DNA methylation–Related biomarkers and immune-cell infiltration of atherosclerosis

“…A bioinformatic study reported an imprinted gene PLA2G7, which encoded lipoprotein-associated phospholipase A2 (Lp-PLA2). The hypomethylation of PLA2G7 increased expression upon inflammation in AS, indicating the effects of DNA methylation modification on atheroprogression and destabilization via inflammatory processes ( Li et al, 2021 ). SMCs migrate from the media to the intima and form the AS plaques.…”

Effect of menopausal hormone therapy on methylation levels in early and late postmenopausal women

“…For example, a large EWAS analysis with > 6400 individuals also did not identify any genome-wide significant associations between CIMT and blood cell-derived methylation levels at any CpG site except for cg05575921 at the well-known smoking-associated AHRR locus [ 22 ]. By comparison, epigenetic analyses with tissue obtained from atherosclerotic and normal carotid, aortic, mammary, or femoral artery samples have identified thousands of associations with atherosclerosis [ 20 – 22 , 28 – 30 ]. Interestingly, several studies observed hypomethylation of CpG sites in atherosclerotic tissue compared to normal arteries and upregulation of multiple pathways that could potentially be causal drivers of plaque development [ 28 , 30 ].…”

“…By comparison, epigenetic analyses with tissue obtained from atherosclerotic and normal carotid, aortic, mammary, or femoral artery samples have identified thousands of associations with atherosclerosis [ 20 – 22 , 28 – 30 ]. Interestingly, several studies observed hypomethylation of CpG sites in atherosclerotic tissue compared to normal arteries and upregulation of multiple pathways that could potentially be causal drivers of plaque development [ 28 , 30 ]. These findings, taken together with our data, suggest that circulating leukocytes may not be an appropriate surrogate tissue in which to associate methylation modifications with vascular wall phenotypes, even in response to HT.…”

Theories and Molecular Basis of Vascular Aging: A Review of the Literature from VascAgeNet Group on Pathophysiological Mechanisms of Vascular Aging

“…Furthermore, promoter methylation changes occurring at AIRE1 and ALOX12 genes have been implicated as potential epigenetic alterations in the etiology of atherosclerotic plaques [ 122 ]. Importantly, large genome-wide analyses have revealed the predominance of extensive hypomethylation in atherosclerotic plaques which correlates with the expression of several genes implicated in atherogenesis such as RTL1, CDKN2B, and PLA2G7 [ 123 , 124 ]. Finally, from a clinical perspective, differentially methylated levels of BRCA1 and CRISP2 regions have been associated with subclinical atherosclerosis measures such as the coronary calcium score and carotid IMT in individuals with subclinical cardiovascular disease [ 125 ].…”