Probing the epigenetic signatures in subjects with coronary artery disease

• Published in: Molecular biology reports Vol. 47; no. 9; pp. 6693 - 6703
• Main Authors: Indumathi, Bobbala, Oruganti, Sai Satish, Naushad, Shaik Mohammad, Kutala, Vijay Kumar
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.09.2020; Springer Nature B.V
• Subjects: Animal Anatomy; Animal Biochemistry; biomarkers; Biomedical and Life Sciences; Cardiovascular disease; Coronary artery; coronary artery disease; Diabetes; Diabetes mellitus; DNA methylation; Epigenetics; Fibroblast growth factor 2; Folic acid; Gene expression; Heart diseases; Histology; Homocysteine; Interleukin 6; Life Sciences; loci; Methionine; methylation; molecular biology; Morphology; Original Article; prediction; Prediction models; regression analysis; risk; risk reduction; Tumor necrosis factor-α; Epigenetics; Methylation; Gene expression; Coronary artery disease
• ISSN: 0301-4851; 1573-4978; 1573-4978
• DOI: 10.1007/s11033-020-05723-w

Depletion of S -adenosyl methionine and 5-methyltetrahydrofolate; and elevation of total plasma homocysteine were documented in CAD patients, which might modulate the gene-specific methylation status and alter their expression. In this study, we have aimed to delineate CAD-specific epigenetic signatures by investigating the methylation and expression of 11 candidate genes i.e. ABCG1, LIPC, PLTP, IL-6, TNF-α, CDKN2A, CDKN2B, F2RL3, FGF2, P66 and TGFBR3. The methylation-specific PCR and qRT-PCR were used to assess the methylation status and the expression of candidate genes, respectively. CAD patients showed the upregulation of IL-6, TNF-α, CDKN2A, CDKN2B, F2RL3, FGF2, P66, and TGFBR3. Hypomethylation of CDKN2A loci was shown to increase risk for CAD by 1.79-folds (95% CI 1.22–2.63). Classification and regression tree (CART) model of gene expression showed increased risk for CAD with F2RL3 > 3.4-fold, while demonstrating risk reduction with F2RL3 < 3.4-fold and IL-6 < 7.7-folds. This CAD prediction model showed the excellent sensitivity (0.98, 95% CI 0.88–1.00), specificity (0.91, 95% CI 0.86–0.92), positive predictive value (0.82, 95% CI 0.75–0.84), and negative predictive value (0.99, 95% CI 0.94–1.00) with an overall accuracy of 92.8% (95% CI 87.0–94.1%). Folate and B 12 deficiencies were observed in CAD cases, which were shown to contribute to hypomethylation and upregulation of the prime candidate genes i.e. CDKN2A and F2RL3. Early onset diabetes was associated with IL-6 and TNF-α hypomethylation and upregulation of CDKN2A. The expression of F2RL3 and IL-6 (or) hypomethylation status at CDKN2A locus are potential biomarkers in CAD risk prediction. Early epigenetic imprints of CAD were observed in early onset diabetes. Folate and B 12 deficiencies are the contributing factors to these changes in CAD-specific epigenetic signatures.