Efficient detection of differentially methylated regions in the genome of patients with thoracic aortic dissection and association with MMP2 hypermethylation

Abstract

DNA methylation is known to regulate the expression of numerous genes but its role in the pathogenesis of thoracic aortic dissection (TAD) has remained largely elusive. In the present study, the DNA methylome of patients with TAD was analyzed using a methylation microarray and bisulfite pyrosequencing was used to determine whether the hypermethylation of matrix metalloproteinase 2 (MMP2) specifically is associated with TAD. Chip-based whole-DNA methylome analysis was performed on 4 male patients with TAD and 4 male healthy controls using an Illumina HumanMethylation EPIC 850K BeadChip. The resulting data were analyzed by clustering and principal component analysis, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the differentially methylated genes to interrogate their biological functions. Compared to the healthy controls, 3,362 loci were differentially methylated in the patients with TAD with a statistical significance of P<0.05, while 1,223 loci had a significance of P<0.01. Among these loci, 2,019 were hypermethylated and 1,343 were hypomethylated. From GO analysis within the biological process category, the MMP2, MMP14 and WNT2B genes were identified. enrichment was observed for loci involved in cellular component organization, enzyme-linked receptor protein signaling pathways (potentially having a key role in the development of cardiopulmonary function disorders) and vascular reconstruction. Bisulfite pyrosequencing of plasma samples indicated significantly increased methylation (P<0.01) of the CpG site at position 2 in the promoter of MMP2 in the TAD group relative to the healthy controls, and the mean methylation level of four CpG sites on the MMP2 gene in the TAD group was slightly higher than that in the control group, but not significantly. Hypermethylation of the MMP2 promoter may be a promising novel diagnostic and prognostic biomarker for TAD. Future studies on the epigenetics of biomarkers linked to vascular reconstruction and immune function may provide further insight into the pathogenesis and progression of TAD.

Cardiac ECM: Its Epigenetic Regulation and Role in Heart Development and Repair

“…In a zebrafish model, the tet2/3 mutant failed to demethylate genes associated with ECM organization in the endocardium and myocardium, leading to defects in the ECM for cardiogenesis [ 142 ]. Hypermethylated MMP2 was identified and demonstrated to be associated with an increased risk of aortic aneurysm [ 143 ]. More recently, in dilated cardiomyopathy, hypomethylations of MMP-2 and connective tissue growth factor (CTGF) were identified as contributing to heart failure [ 144 ].…”

DNA methylation alternation in Stanford- A acute aortic dissection

“…In our previous research, it was found that the protein expression level of DNMT1 and DNMT3B decreased significantly in AAD patients while DNMT3A and DNMTL had the decreased trends with no significance, which indicated the potential role of DNA methylation in AAD[ 17 ]. Several previous studies also paid attention to the DNA methylation changes in AAD[ 18 – 20 ]. Li N et al detected the DNA methylation in blood samples of TAD patients and found MMP2 promoter hypermethylated[ 18 ].…”

“…It was found in our previous study that the protein expression levels of DNMT1 and DNMT3B decreased significantly in AAD samples while the expression of DNMT3a and DNMTL had the decreased trends with no significance, which indicated the potential role of DNA methylation in AAD[ 17 ]. Most recently, several studies had paid attention to the DNA methylation in AAD[ 18 – 20 ]. However, the DNA methylation patterns in AAD remain not completely clear.…”

Identification of Molecular Regulatory Features and Markers for Acute Type A Aortic Dissection

“…The hub genes identified in this study were all modified by methylation. Alterations in gene methylation may mediate the involvement of vascular smooth muscle cells and inflammatory cells in the development of aortic dissection [ 24 ]. At present, there are relatively few studies on the regulation of methylation in ATAAD, and we believe that hub genes may be regulated by methylation and thus participate in the progress of ATAAD.…”

“…In many cardiovascular diseases, important epigenetic modifications, including methylation, have been shown to affect the development or progression of the disease [ 23 ]. Methylation modification of the gene may serve as a diagnostic and prognostic marker in patients with aortic dissection [ 24 ].…”