Exploring epistatic relationships of NO biosynthesis pathway genes in susceptibility to CHD

Association of epistatic effects of MTHFR, ACE, APOB, and APOE gene polymorphisms with the risk of myocardial infarction and unstable angina in Egyptian patients

Despite remarkable discoveries in the genetic susceptibility of coronary artery disease (CAD), a large part of heritability awaits identification. Epistasis or gene-gene interaction has a profound influence on CAD and might contribute to its missed genetic variability; however, this impact was largely unexplored. Here, we appraised the associations of gene-gene interactions and haplotypes of five polymorphisms, namely methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C, angiotensin converting enzyme (ACE) insertion/deletion (I/D), apolipoprotein B (APOB) R3500Q, and apolipoprotein E (APOE) ε4 with the risk of myocardial infarction (MI) and unstable angina (UA). Gene-environment interactions with traditional risk factors and clinical data were also scrutinized. This study recruited 100 MI, 50 UA patients, and 100 apparently healthy controls. Logistic regression models were employed in association analyses. We remarked that the single locus effect of individual polymorphisms was relatively weak; however, a magnified effect of their combination via gene-gene interaction may predict MI risk after adjustment for multiple comparisons. Only MTHFR C677T, ACE I/D, and APOB R5300Q were associated with the risk of UA, and the ACE I/D-R3500Q interaction posed a decreased UA risk. APOB R3500Q was in strong linkage disequilibrium with MTHFR C677T, ACE I/D, and APE ε4 polymorphisms. The TCDGε3, CADGε4, and TADGε4-C677T-A1298C-ACE I/D-R3500Q-APOE haplotypes were associated with escalating MI risk, while the CDG or CIG-C677T-ACE I/D-R3500Q haplotype was highly protective against UA risk compared to controls. Interestingly, the CADGε4 and CAIGε3 haplotypes were strongly associated with the presence of diabetes and hypertension, respectively in MI patients; both haplotypes stratified patients according to the ECHO results. In UA, the CDG haplotype was negatively associated with the presence of diabetes or dilated heart. Conclusively, our results advocate that a stronger combined effect of polymorphisms in MTHFR, ACE, APOB, and APOE genes via gene-gene and gene-environment interactions might help in risk stratification of MI and UA patients.

Uncovering associations between mental illness diagnosis, nitric oxide synthase gene variation, and peripheral nitric oxide concentration

Nitric oxide (NO) signalling has been implicated in the pathogenesis of several mental illnesses; however, its specific contribution remains unclear. We investigated whether peripheral NO concentration is associated with specific diagnoses, and whether there is a correlation with genetic variation in NO synthase (NOS) genes. We included 185 participants in the study; 52 healthy controls, 43 major depressive disorder (MDD) patients, 41 bipolar disorder (BPD) patients, and 49 schizophrenia (SCZ) patients. Clinical, genetic, and biochemical data were collected at admission to a psychiatric hospital and at discharge. Serum was used to quantify concentration of the stable NO metabolites nitrite and nitrate. Individuals were genotyped for the NOS1 exon 1f variable number of tandem repeats 1 (VNTR1) polymorphism, and single nucleotide polymorphisms (SNPs) in the NOS1, NOS1AP and NOS3 genes. At admission, SCZ patients were found to have significantly higher peripheral NO metabolite (NO_x-) concentrations compared to healthy controls, MDD and BPD patients. NOS1 exon 1f VNTR1 short allele carriers were found to have significantly increased NO_x- concentration. Moreover, this result was still significant in patients even at discharge. The data also revealed that patients who did not remit in their depressive symptoms had significantly increased NO_x- concentration compared to remitters at discharge, supported by the finding of a significant positive correlation between depression symptom severity and NO_x- concentration. Taken together, it is possible that elevated peripheral NO_x- concentration is associated with increased severity of psychopathology, potentially due to NOS1 exon1f VNTR1 genotype. Our results further implicate NO signalling in mental illness pathogenesis, supporting its possible use as a peripheral biomarker, and imply that NOS genotype may play a significant role in regulating peripheral NO_x- concentration.

A roadmap to multifactor dimensionality reduction methods

Complex diseases are defined to be determined by multiple genetic and environmental factors alone as well as in interactions. To analyze interactions in genetic data, many statistical methods have been suggested, with most of them relying on statistical regression models. Given the known limitations of classical methods, approaches from the machine-learning community have also become attractive. From this latter family, a fast-growing collection of methods emerged that are based on the Multifactor Dimensionality Reduction (MDR) approach. Since its first introduction, MDR has enjoyed great popularity in applications and has been extended and modified multiple times. Based on a literature search, we here provide a systematic and comprehensive overview of these suggested methods. The methods are described in detail, and the availability of implementations is listed. Most recent approaches offer to deal with large-scale data sets and rare variants, which is why we expect these methods to even gain in popularity.

GTP cyclohydrolase I gene polymorphisms are associated with endothelial dysfunction and oxidative stress in patients with type 2 diabetes mellitus

BACKGROUND

The genetic background of atherosclerosis in type 2 diabetes mellitus (T2DM) is complex and poorly understood. Studying genetic components of intermediate phenotypes, such as endothelial dysfunction and oxidative stress, may aid in identifying novel genetic components for atherosclerosis in diabetic patients.

METHODS

Five polymorphisms forming two haplotype blocks within the GTP cyclohydrolase 1 gene, encoding a rate limiting enzyme in tetrahydrobiopterin synthesis, were studied in the context of flow and nitroglycerin mediated dilation (FMD and NMD), intima-media thickness (IMT), and plasma concentrations of von Willebrand factor (vWF) and malondialdehyde (MDA).

RESULTS

Rs841 was associated with FMD (p = 0.01), while polymorphisms Rs10483639, Rs841, Rs3783641 (which form a single haplotype) were associated with both MDA (p = 0.012, p = 0.0015 and p = 0.003, respectively) and vWF concentrations (p = 0.016, p = 0.03 and p = 0.045, respectively). In addition, polymorphism Rs8007267 was also associated with MDA (p = 0.006). Haplotype analysis confirmed the association of both haplotypes with studied variables.

CONCLUSIONS

Genetic variation of the GCH1 gene is associated with endothelial dysfunction and oxidative stress in T2DM patients.

The A640G polymorphism in the NAD(P)H oxidase p22phox gene (CYBA) is associated with risk reduction of coronary heart disease: a meta-analysis

BACKGROUND

Recently, studies have focused on the association between the p22phox gene A640G polymorphism and coronary heart disease (CHD). However, the results are inconsistent. In this study, we aimed to further evaluate this association by using meta-analysis.

METHODS

The PubMed, Embase, CBM, CNKI, WanFang and Chongqing VIP databases were searched for relevant articles. Hardy-Weinberg equilibrium (HWE) of the distribution of genotypes was tested using Pearson's chi-squared test. Odds ratios (ORs) with the corresponding 95% confidence intervals (CIs) were used to assess the strength of the association; Cochran's Q test and the I(2) statistic were used to evaluate heterogeneity. The random effects model and the fixed effects model were used according to heterogeneity; Begg's test and Egger's test were used to analyze publication bias. Sensitivity analysis was carried out to guarantee the stability of the results. Cumulative analysis was used to evaluate tendencies in the pooled OR.

RESULTS

A total of eight articles including 3904 CHD cases and 3498 controls were included. A significant association between the A640G polymorphism and CHD was observed in codominant model 2 (AG versus AA: OR=0.86, 95% CI: 0.77-0.96). In the subgroup analysis, a significant association was observed between the A640G polymorphism and CHD in Caucasians, and in PB (population-based), non-PB, HWE (studies followed HWE) and non-HWE studies.

CONCLUSIONS

Our results reveal that the A640G polymorphism may play a protective role in CHD.