A Comparison of Genome-Wide DNA Methylation Patterns between Different Vascular Tissues from Patients with Coronary Heart Disease

<div><p>Epigenetic mechanisms of gene regulation in context of cardiovascular diseases are of considerable interest. So far, our current knowledge of the DNA methylation profiles for atherosclerosis affected and healthy human vascular tissues is still limited. Using the Illumina Infinium Human Methylation27 BeadChip, we performed a genome-wide analysis of DNA methylation in right coronary artery in the area of advanced atherosclerotic plaques, atherosclerotic-resistant internal mammary arteries, and great saphenous veins obtained from same patients with coronary heart disease. The resulting DNA methylation patterns were markedly different between all the vascular tissues. The genes hypomethylated in athero-prone arteries to compare with atherosclerotic-resistant arteries were predominately involved in regulation of inflammation and immune processes, as well as development. The great saphenous veins exhibited an increase of the DNA methylation age in comparison to the internal mammary arteries. Gene ontology analysis for genes harboring hypermethylated CpG-sites in veins revealed the enrichment for biological processes associated with the development. Four CpG-sites located within the <i>MIR10B</i> gene sequence and about 1 kb upstream of the <i>HOXD4</i> gene were also confirmed as hypomethylated in the independent dataset of the right coronary arteries in the area of advanced atherosclerotic plaques in comparison with the other vascular tissues. The DNA methylation differences observed in vascular tissues of patients with coronary heart disease can provide new insights into the mechanisms underlying the development of pathology and explanation for the difference in graft patency after coronary artery bypass grafting surgery.</p></div

Comparison of β-values (average ± s.d.) in paired vascular tissues from six patients with atherosclerosis.

<p>CAP indicates right coronary arteries in the area of advanced atherosclerotic plaques; IMA, internal mammary arteries; GSV, great saphenous veins.</p><p>Comparison of β-values (average ± s.d.) in paired vascular tissues from six patients with atherosclerosis.</p

Flow chart describing experiment and analysis.

<p>Flow chart describing experiment and analysis.</p

Multi-dimensional scaling for genome-wide methylation of right coronary artery in the area of advanced atherosclerotic plaques (CAP), internal mammary arteries (IMA), and great saphenous veins (GSV).

<p>Arabic numbers are sample IDs.</p

Volcano plot of - log10 (P-value) against delta beta value, representing the methylation difference between right coronary arteries in the area of advanced atherosclerotic plaques (CAP) and internal mammary arteries (IMA).

<p>A total of 194 CpG-sites hypermethylated in CAP with a delta beta ≥ 0.2 and FDR-adjusted p<0.05 are shown in red. A total of 164 CpG-sites hypomethylated in CAP with a delta beta ≤ -0.2 and FDR-adjusted p<0.05 are shown in blue. CpG-sites that exhibited a methylation level difference less 20% are shown in grey. Light red and light blue colors indicate highly differentially methylated CpG-sites (delta beta ≥ 0.40 or delta beta ≤ -0.40 with FDR-adjusted p<0.05). Dashed lines indicate cut-offs for significance.</p

Methylation level (mean ±SD) at the promoter of <i>HOXD4</i> gene in paired vascular tissues from twenty one patients with atherosclerosis.

<p>CAP indicates right coronary arteries in the area of advanced atherosclerotic plaques; IMA, internal mammary arteries; GSV, great saphenous veins.</p><p>Methylation level (mean ±SD) at the promoter of <i>HOXD4</i> gene in paired vascular tissues from twenty one patients with atherosclerosis.</p

Volcano plot of - log10 (P-value) against delta beta value, representing the methylation difference between great saphenous veins (GSV) and internal mammary arteries (IMA).

<p>A total of 200 CpG-sites hypermethylated in GSV with a delta beta ≥ 0.2 and FDR-adjusted p<0.05 are shown in red. A total of 135 CpG-sites hypomethylated in GSV with a delta beta ≤ -0.2 and FDR-adjusted p<0.05 are shown in blue. CpG-sites that exhibited a methylation level difference less 20% are shown in grey. Light red and light blue colors indicate highly differentially methylated CpG-sites (delta beta ≥ 0.40 or delta beta ≤ -0.40 with FDR-adjusted p<0.05). Dashed lines indicate cut-offs for significance.</p

Heatmap analysis of 22 highly differentially methylated CpG-sites (delta beta ≥ 0.40 or delta beta ≤ -0.40 with FDR-adjusted p<0.05) between right coronary arteries in the area of advanced atherosclerotic plaques (CAP) and internal mammary arteries (IMA).

<p>Regions shaded blue in the heat map represent hypomethylated regions, regions shaded red represent hypermethylated regions. The top black rectangles shows columns representing CpG-sites located inside CpG-island. Gene symbols and CpG-site IDs are shown on the bottom. Sample IDs are on the right.</p

Baseline characteristics of the study subjects.

<p>Hypertension was defined as a systolic blood pressure ≥140 or diastolic ≥90mm Hg or the current use of antihypertensive drugs. Patients were categorized as smokers if they were current smokers or had stopped smoking for less than 1 year. Obesity was appreciated by the Body Mass Index (BMI). Quantitative values are presented as mean±S.E. or median (min-max) and qualitative values as n (percentage).</p><p>Baseline characteristics of the study subjects.</p