Association of Promoter Methylation and Expression of Inflammatory Genes IL-6 and TNF-α with the Risk of Coronary Artery Disease in Diabetic and Obese Subjects among Asian Indians.

The inflammatory cytokines such as interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) are considered as the most important contributors to the endothelial dysfunction in subjects with type 2 diabetes mellitus (T2DM) and obesity. The hypomethylation of CpG sites in the promoter region of the IL-6 and TNF-α have shown to be associated with the increased expression of IL-6 and TNF-α. However, there are no studies on the methylation and expression of IL-6 and TNF-α with the risk of coronary artery disease (CAD) in subjects with T2DM and obesity in Asian Indians. Hence, the present study was aimed to investigate whether the IL-6, TNF-α promoter methylation and expression in blood leukocyte DNA is associated with the risk of CAD in diabetic and obese subjects in Asian Indians. For this study, we recruited 574 subjects which includes, 207 angiographically confirmed CAD patients, 100 T2DM patients, 82 obese subjects and 185 healthy controls. The methylation status of IL-6 and TNF-α gene loci was determined by methylation specific PCR (MPCR) and gene expression was determined by qPCR. We found significant hypomethylation of IL-6 in CAD and T2DM subjects (OR 1.98 95% CI: 1.32-2.97, p = 0.001, OR: 2.23 95% CI:1.34-3.76, p = 0.001, respectively). Further, a significant increase in the expression of IL-6 in CAD and T2DM subjects (fold change: 26.39 & 14.7, p = 0.0001) compared to the control subjects was observed. A significant increase in the hypomethylation of TNF-α in CAD, T2DM and obese subjects was observed as compared to the control (OR: 2.04 95% CI: 1.36-3.05, p = 0.0005, OR: 1.81 95% CI 1.10-2.96, p = 0.01, and OR: 2.1 95% CI 1.24-3.57, p = 0.007, respectively).We also found an increased expression of TNF-α in CAD, T2DM and obese subjects as compared to controls. In addition, presence of low folate, and hyperhomocysteinemia was observed in the present study, may be the contributing factors for the hypomethylation of IL-6 and TNF-α and oxidative stress. In conclusion, increased expression of IL-6 and TNF-α due to hypomethylation in T2DM and obese individuals may contribute to CAD risk in these subjects. The presence of hyperhomocysteinemia and increased oxidative risk may enhance the CAD risk further.

Probing the epigenetic signatures in subjects with coronary artery disease.

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 B12 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 B12 deficiencies are the contributing factors to these changes in CAD-specific epigenetic signatures.

Dual Effect of IL-6 -174 G/C Polymorphism and Promoter Methylation in the Risk of Coronary Artery Disease Among South Indians.

Inflammation plays an important role in the pathogenesis of atherosclerosis and coronary syndromes; moreover, various lines of evidence suggest that genetic factors do contribute to the risk of coronary artery disease (CAD). The proinflammatory cytokine IL-6 is a central mediator of inflammation associated with CAD. The present study is aimed to investigate the association of single nucleotide polymorphism in the promoter region of the IL-6 gene (-174 G > C) and methylation with the susceptibility of CAD. Genotyping of IL-6 -174 G/C polymorphism was performed by PCR-RFLP. Methylation-specific PCR method was used to study the IL-6 gene promoter methylation. Analysis of 470 subjects (265 CAD patients and 205 controls) showed association of the -174 G/C variant with the CAD risk in dominant model (OR 1.58, 95% CI, 1.024-2.23, P = 0.04). Further, the analysis of the distribution of genotypes and alleles of -174 G > C polymorphism according to clinical features of CAD, revealed significant association of genotype and allele (OR 1.86, 95% CI 1.18-2.84 P = 0.01, and OR 1.71, 95% CI 1.09-2.23 P = 0.02 respectively) with diabetes, and we found no association with hypertension (OR 0.95, 95% CI 0.57-1.59, P = 0.8). We also analyzed the methylation status of IL-6 promoter region between cases and controls showed significant hypo methylation in CAD subjects (OR 2.36, 95% CI 1.51-4.259, P = 0.006). Additionally, GC, CC genotypes and C allele carriers show hypomethylation in CAD cases compared to controls (54.58 vs. 76.85%, 29.83 vs. 40% respectively). In conclusion, the promoter polymorphism -174 G/C is associated with CAD risk and further carriers of 'C' allele at -174 locus showed significant hypo methylation which could contribute to increased risk of CAD. The present study highlights the association of allele and genotypes with differential DNA methylation of CpG islands in the IL-6 promoter region which may affect IL-6 gene regulation.

Machine learning algorithm-based risk prediction model of coronary artery disease.

In view of high mortality associated with coronary artery disease (CAD), development of an early predicting tool will be beneficial in reducing the burden of the disease. The database comprising demographic, conventional, folate/xenobiotic genetic risk factors of 648 subjects (364 cases of CAD and 284 healthy controls) was used as the basis to develop CAD risk and percentage stenosis prediction models using ensemble machine learning algorithms (EMLA), multifactor dimensionality reduction (MDR) and recursive partitioning (RP). The EMLA model showed better performance than other models in disease (89.3%) and stenosis prediction (82.5%). This model depicted hypertension and alcohol intake as the key predictors of CAD risk followed by cSHMT C1420T, GCPII C1561T, diabetes, GSTT1, CYP1A1 m2, TYMs 5'-UTR 28 bp tandem repeat and MTRR A66G. MDR and RP models are in agreement in projecting increasing age, hypertension and cSHMTC1420T as the key determinants interacting in modulating CAD risk. Receiver operating characteristic curves exhibited clinical utility of the developed models in the following order: EMLA (C = 0.96) > RP (C = 0.83) > MDR (C = 0.80). The stenosis prediction model showed that xenobiotic pathway genetic variants i.e. CYP1A1 m2 and GSTT1 are the key determinants of percentage of stenosis. Diabetes, diet, alcohol intake, hypertension and MTRR A66G are the other determinants of stenosis. These eleven variables contribute towards 82.5% stenosis. To conclude, the EMLA model exhibited higher predictability both in terms of disease prediction and stenosis prediction. This can be attributed to higher number of iterations in EMLA model that can increase the prediction accuracy.

Impact of eNOS 27-bp VNTR (4b/a) gene polymorphism with the risk of Systemic Lupus Erythematosus in south Indian subjects.

OBJECTIVE: Endothelial nitric oxide synthase (eNOS) is constitutively expressed by vascular endothelium including glomerular endothelium. Functional polymorphisms, -786T>C (rs2070744) promoter variant, 27 bp VNTR (4b/a) in intron 4 and 894G>T (rs1799983) exon variant of eNOS are known to alter the eNOS expression and activity leading to altered NO levels and contribute to the development of vascular and renal disease risk. Thus it might have a role in SLE risk and development of glomerulonephritis. Hence, the present study is aimed to investigate the role of eNOS polymorphisms in South Indian SLE patients. METHODS: Five hundred and four subjects (219 SLE cases and 285 controls) were included in the present case-control study. Genotyping was done using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for -786T>C and 894G>T SNPs. Another, 4a4b variable number of tandem repeat polymorphism was genotyped using direct PCR method using primer pairs flanking the 27 bp direct repeat region in intron 4 of eNOS gene. RESULTS: Our analysis revealed that intron 4 27 bp VNTR genotype frequency differ significantly between the SLE patients and controls (OR: 1.73, 95% CI %:1.18-2.54, P = 0.004). Further, "a allele" frequency was significantly higher in SLE patients as compared to the controls (20 vs. 13.8%) (OR: 1.56, 95%CI: 1.11-2.18, P = 0.01). However, promoter polymorphism -786T>C and missense variant 894G>T were not significantly different between the SLE cases and controls (OR: 0.92, 95%CI: 0.64-1.33, P = 0.7 and OR: 1.4, 95%CI: 0.95-2.06, P = 0.095 respectively). Furthermore, no association was found between any of the three polymorphisms with lupus nephritis phenotype. Increased plasma nitrate levels were observed in SLE patients (36.79 ±â€¯2.83 µM/L) as compared to healthy controls (28.53 ±â€¯1.94 µM/L) (P = 0.01). In addition, the genotype-based simulations have indicated that combined effect of eNOS polymorphisms contribute to 30.5% variability in NO production. CONCLUSION: Results of the present study indicate that 27-bp VNTR polymorphism in intron 4 of eNOS gene polymorphism may be the significant risk factor for SLE in south Indian subjects.

Impact of pharmacogenetics on statin-induced myopathy in South-Indian subjects.

OBJECTIVES: Statins are the most commonly prescribed medications for the treatment of atherosclerotic cardiovascular disease. Statin-associated adverse effects occur in ∼10% of patients and are associated with polymorphisms in several key genes coding for transporters and metabolizing enzymes that affect statin pharmacokinetics. In the present study, we examine the association between cytochrome P450 3A5*3 (CYP3A5*3) T>C (rs776746), COQ G>C (rs4693075), and SLCO1B1 T>C (rs4149056) genetic variants with the risk of myopathy in South Indian patients on statin therapy. METHODS: A total of 202 patients on atorvastatin or rosuvastatin therapy for 12 years were recruited in the study. Genotyping of drug metabolic CYP3A5*3 gene variant and drug transporter genes COQ G>C (rs4693075) and SLCO1B1 T>C (rs4149056) was analyzed by Sanger's sequencing. RESULTS: In our study subjects, the percentage of patients diagnosed to have statin-induced myopathy was 18%. The majority of the patients were on 10 mg/day dose of either atorvastatin or rosuvastatin. The homozygous nonexpressors genotype CYP3A5*3/3 frequency of the CYP3A5 polymorphism was higher in patients with myopathy. But we could not find association of CYP3A5, COQ, and SLCO1B1 gene polymorphisms with either rosuvastatin or atorvastatin. CONCLUSION: Our results clearly demonstrate that the frequency of CYP3A5*3 splicing variant is higher in myopathy group than in the tolerant group. We did not find significant association of genetic polymorphisms in CYP3A5, COQ, and SLCO1B1 with atorvastatin- or rosuvastatin-induced myopathy.