Cardiovascular diseases and genome-wide association studies

Investigating the genetic characteristics of CAD: Is there a role for myocardial perfusion imaging techniques?

Several environmental and genetic factors have been found to influence the development and progression of coronary artery disease (CAD). Although the effects of the environmental hazards on CAD pathophysiology are well documented, the genetic architecture of the disease remains quite unclear. A number of single-nucleotide polymorphisms have been identified based on the results of the genome-wide association studies. However, there is a lack of strong evidence regarding molecular causality. The minority of the reported predisposing variants can be related to the conventional risk factors of CAD, while most of the polymorphisms occur in non-protein-coding regions of the DNA. However, independently of the specific underlying mechanisms, genetic information could lead to the identification of a population at higher genetic risk for the long-term development of CAD. Myocardial single-photon emission computed tomography (SPECT) and positron emission tomography (PET) are functional imaging techniques that can evaluate directly myocardial perfusion, and detect vascular and/or endothelial dysfunction. Therefore, these techniques could have a role in the investigation of the underlying mechanisms associated with the identified predisposing variants, advancing our understanding regarding molecular causality. In the population at higher genetic risk, myocardial SPECT or PET could provide important evidence through the early depiction of sub-clinical dysfunctions, well before any atherosclerosis marker could be identified. Notably, SPECT and PET techniques have been already used for the investigation of the functional consequences of several CAD-related polymorphisms, as well as the response to certain treatments (statins). Furthermore, therefore, in the clinical setting, the combination of genetic evidence with the findings of myocardial SPECT, or PET, functional imaging techniques could lead to more efficient screening methods and may improve decision making with regard to the diagnostic investigation and patients' management.

Potential regulatory role of epigenetic RNA methylation in cardiovascular diseases

Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide, especially in developing countries. To date, several approaches have been proposed for the prevention and treatment of CVDs. However, the increased risk of developing cardiovascular events that result in hospitalization has become a growing public health concern. The pathogenesis of CVDs has been analyzed from various perspectives. Recent data suggest that regulatory RNAs play a multidimensional role in the development of CVDs. Studies have identified several mRNA modifications that have contributed to the functional characterization of various cardiac diseases. RNA methylation, such as N6-methyladenosine, N1-methyladenosine, 5-methylcytosine, N7-methylguanosine, N4-acetylcytidine, and 2'-O-methylation are novel epigenetic modifications that affect the regulation of cell growth, immunity, DNA damage, calcium signaling, apoptosis, and aging in cardiomyocytes. In this review, we summarize the role of RNA methylation in the pathophysiology of CVDs and the potential of using epigenetics to treat such disorders.

Circulating microRNAs: Biomarkers of disease

MicroRNAs are a class of endogenous noncoding single-stranded RNA molecules with approximately 20-24 nucleotides and are associated with a broad range of biological processes. Researchers found that microRNAs are abundant in tissues, and more importantly, there are also trace circulating microRNAs that exist in biological fluids. In recent years, circulating microRNAs had emerged as promising diagnostic and prognostic biomarkers for the noninvasive detection of diseases with high specificity and sensitivity. More importantly, specific microRNA expression signatures reflect not only the existence of early-stage diseases but also the dynamic development of advanced-stage diseases, disease prognosis prediction, and drug resistance. To date, an increasing number of potential miRNA biomarkers have been reported, but their practical application prospects are still unclear. Therefore, microRNAs, as potential diagnostic and prognostic biomarkers in a variety of diseases, need to be updated, as they are of great importance in the diagnosis, prognosis and prediction of therapeutic responses. In this review, we summary our current understanding of microRNAs as potential biomarkers in the major diseases (e.g., cancers and cardio-cerebrovascular diseases), which provide the basis for the design of diagnosis and treatment plan and the improvement of the cure rate.

Obesity status modifies the association between rs7556897T>C in the intergenic region SLC19A3-CCL20 and blood pressure in French children

Background Growing evidence reports an association between inflammatory markers, obesity and blood pressure (BP). Specifically, the intergenic single nucleotide polymorphism (SNP) rs7556897T > C (MAF = 0.34) located between SLC19A3 and the CCL20 was shown to be associated with chronic inflammatory diseases. In addition, CCL20 expression was found increased in pancreatic islets of obese rodents and human pancreatic β cells under the influence of inflammation. In this study, we hypothesized that SNP rs7556897 could affect BP levels, thus providing a link between inflammation, BP and obesity. Methods BP was measured under supine position with a manual sphygmomanometer; values reported were the means of three readings. We analyzed rs7556897 in 577 normal weight and 689 obese French children. Using real-time polymerase chain reaction (PCR), we quantified CCL20 and SLC19A3 expression in adipose tissue and peripheral blood mononuclear cells (PBMCs) of normal weight and overweight children. Results The rs7556897C allele was negatively associated with diastolic BP in normal weight children (β = -0.012 ± 0.004, p = 0.006) but positively associated in obese children (β = 2.178 ± 0.71, p = 0.002). A significant interaction between rs7556897T > C and the obesity status (obese or normal weight) was detected (β = 3.49, p = 9.79 × 10-5) for BP in a combined population analysis. CCL20 mRNA was only expressed in the adipose tissue of overweight children, and its expression levels were 10.7×  higher in PBMCs of overweight children than normal weight children. Finally, CCL20 mRNA levels were positively associated with rs7556897T > C in PBMCs of 58 normal weight children (β = 0.43, p = 0.002). SLC19A3 was not expressed in PBMCs, and in adipose tissue, it showed same levels of expression in normal weight and overweight children. The gene expression results may highlight a specific involvement of CCL20 via communicating obesity/inflammation pathways that regulate BP. Conclusions Childhood obesity reverses the effect of rs7556897T > C on diastolic BP, possibly via the modulation of CCL20 expression levels.

Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease

BACKGROUND

Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis.

METHODS

LC-MS/MS was employed to analyze plasma from 32 subjects (19 cases of various CVD phenotypes and 13 controls) in two steps: discovery (13 cases and 8 controls) and test (6 cases and 5 controls) set analysis. Following label-free quantification, the detected proteins were correlated to existing plasma proteomics datasets (plasma proteome database; PPD) and functionally annotated (Cytoscape, Ingenuity Pathway Analysis). Differential expression was defined based on identification confidence (≥ 2 peptides per protein), statistical significance (Mann-Whitney p value ≤ 0.05) and a minimum of twofold change.

RESULTS

Peptides detected in at least 50% of samples per group were considered, resulting in a total of 3796 identified proteins (838 proteins based on ≥ 2 peptides). Pathway annotation confirmed the functional relevance of the findings (representation of complement cascade, fibrin clot formation, platelet degranulation, etc.). Correlation of the relative abundance of the proteins identified in the discovery set with their reported concentrations in the PPD was significant, confirming the validity of the quantification method. The discovery set analysis revealed 100 differentially expressed proteins between cases and controls, 39 of which were verified (≥ twofold change) in the test set. These included proteins already studied in the context of CVD (such as apolipoprotein B, alpha-2-macroglobulin), as well as novel findings (such as low density lipoprotein receptor related protein 2 [LRP2], protein SZT2) for which a mechanism of action is suggested.

CONCLUSIONS

This proteomic study provides a comprehensive dataset to be used for integrative and functional studies in the field. The observed protein changes reflect known CVD-related processes (e.g. lipid uptake, inflammation) but also novel hypotheses for further investigation including a potential pleiotropic role of LPR2 but also links of SZT2 to CVD.

A Matter of the Heart: The African Clawed Frog Xenopus as a Model for Studying Vertebrate Cardiogenesis and Congenital Heart Defects

The African clawed frog, Xenopus, is a valuable non-mammalian model organism to investigate vertebrate heart development and to explore the underlying molecular mechanisms of human congenital heart defects (CHDs). In this review, we outline the similarities between Xenopus and mammalian cardiogenesis, and provide an overview of well-studied cardiac genes in Xenopus, which have been associated with congenital heart conditions. Additionally, we highlight advantages of modeling candidate genes derived from genome wide association studies (GWAS) in Xenopus and discuss commonly used techniques.

Integromic analysis of genetic variation and gene expression identifies networks for cardiovascular disease phenotypes

BACKGROUND

Cardiovascular disease (CVD) reflects a highly coordinated complex of traits. Although genome-wide association studies have reported numerous single nucleotide polymorphisms (SNPs) to be associated with CVD, the role of most of these variants in disease processes remains unknown.

METHODS AND RESULTS

We built a CVD network using 1512 SNPs associated with 21 CVD traits in genome-wide association studies (at P≤5×10(-8)) and cross-linked different traits by virtue of their shared SNP associations. We then explored whole blood gene expression in relation to these SNPs in 5257 participants in the Framingham Heart Study. At a false discovery rate <0.05, we identified 370 cis-expression quantitative trait loci (eQTLs; SNPs associated with altered expression of nearby genes) and 44 trans-eQTLs (SNPs associated with altered expression of remote genes). The eQTL network revealed 13 CVD-related modules. Searching for association of eQTL genes with CVD risk factors (lipids, blood pressure, fasting blood glucose, and body mass index) in the same individuals, we found examples in which the expression of eQTL genes was significantly associated with these CVD phenotypes. In addition, mediation tests suggested that a subset of SNPs previously associated with CVD phenotypes in genome-wide association studies may exert their function by altering expression of eQTL genes (eg, LDLR and PCSK7), which in turn may promote interindividual variation in phenotypes.

CONCLUSIONS

Using a network approach to analyze CVD traits, we identified complex networks of SNP-phenotype and SNP-transcript connections. Integrating the CVD network with phenotypic data, we identified biological pathways that may provide insights into potential drug targets for treatment or prevention of CVD.

HDL-cholesterol in coronary artery disease risk: function or structure?

High-density lipoproteins (HDL) are inversely related with coronary artery disease (CAD) and HDL-cholesterol is the only standardized and reproducible parameter available to estimate plasma concentration of these lipoproteins. However, pharmacological interventions intended to increase HDL-cholesterol have not been consistently associated to an effective CAD risk reduction. Among patients with a myocardial infarction, 43 and 44% of men and women, respectively, had normal plasma levels of HDL-cholesterol, whereas genetic studies have failed to show a causal association between HDL-cholesterol and CAD risk. Instead, HDL functionality seems to be the target to be evaluated, but the existing methods are still poorly reproducible and far to be adapted to the clinical laboratory. HDL subclasses rise as a potential alternative for the evaluation of CAD risk; HDL subclasses are a surrogate of intravascular metabolism of these lipoproteins and probably of their functionality. Low levels of large HDL and increased proportions of small particles are the most remarkable features associated to an increased risk of type 2 diabetes mellitus (T2DM) or CAD. However, inflammation and other environmental factors are related with abnormal HDL structure, and, as a consequence, more prospective studies are needed to better support the clinical usefulness of HDL subclasses. New insights from proteome and lipidome profiles of HDL will provide potential HDL-related biomarkers in the coming years.

A common variant highly associated with plasma VEGFA levels also contributes to the variation of both LDL-C and HDL-C

Vascular endothelial growth factor A (VEGFA) is among the most-significant stimulators of angiogenesis. Its effect on cardiovascular diseases and on the variation of related risk factors such as lipid parameters is considered important, although as yet unclear. Recently, we identified four common variants (rs6921438, rs4416670, rs6993770, and rs10738760) that explain up to 50% of the heritability of plasma VEGFA levels. In the present study, we aimed at assessing the contribution of these variants to the variation of blood lipid levels (including apoE, triglycerides, total cholesterol, low- and high-density lipoprotein cholesterol levels (LDL-C and HDL-C)] in healthy subjects. The effect of these single-nucleotide polymorphisms (SNPs) on lipid levels was assessed using linear regression in discovery and replication samples (n = 1,006 and n = 1,145; respectively), followed by a meta-analysis. Their gene×gene and gene×environment interactions were also assessed. SNP rs6921438 was associated with HDL-C (β = -0.08 mmol/l, P(overall) = 1.2 × 10(-7)) and LDL-C (β = 0.13 mmol/l, P(overall) = 1.5 × 10(-4)). We also identified a significant association between the interaction rs4416670×hypertension and apoE variation (P(overall) = 1.7 × 10(-5)). Therefore, our present study shows a common genetic regulation between VEGFA and cholesterol homeostasis molecules. The SNP rs6921438 is in linkage disequilibrium with variants located in an enhancer- and promoter-associated histone mark region and could have a regulatory effect in the expression of surrounding genes, including VEGFA.

Genetic biomarkers of hypertension and future challenges integrating epigenomics

Essential hypertension is a multifactorial disease, considered to be one of the world's greatest public health problems. Despite recent, major, technical advances aiming to elucidate its genetic component, the discovered biomarkers up to now were reported to have only small effects, explaining consequently a tiny fraction of its phenotypic variance and resulting in a large proportion of missing heritability. Likewise, little evidence is available with regard to the epigenetic regulation of essential hypertension, since no robust biomarkers have yet been reported. In the current review, we discuss the main approaches used exclusively to study the genetics and epigenetics of essential hypertension, the biomarkers identified, their clinical utility and the difficulties to be overcome. Furthermore, we propose a new category of functional genetic-epigenetic biomarkers, eMethSNPs, and we provide their hypothetical gene expression profiles for a genetic functional regulation of hypertension via DNA methylation. Though believed to be infrequent, eMethSNPs could constitute a new category of mechanistically-based genetic biomarkers predisposing to essential hypertension.

Functional epistatic interaction between rs6046G>A in F7 and rs5355C>T in SELE modifies systolic blood pressure levels

Background

Although numerous genetic studies have been performed, only 0.9% of blood pressure phenotypic variance has been elucidated. This phenomenon could be partially due to epistatic interactions. Our aim was to identify epistatic interaction(s) associated with blood pressure levels in a pre-planned two-phase approach.

Methods and Results

In a discovery cohort composed of 3,600 French individuals, we found rs6046A allele in F7 associated with decreased blood pressure levels (P≤3.7×10⁻³) and rs5355T allele in SELE associated with decreased diastolic blood pressure levels (P = 5×10⁻³). Both variants interacted in order to influence blood pressure levels (P≤0.048). This interaction was replicated with systolic blood pressure in 4,620 additional European individuals (P = 0.03). Similarly, in this replication cohort, rs6046A was associated with decreased blood pressure levels (P≤8.5×10⁻⁴). Furthermore, in peripheral blood mononuclear cells of a subsample of 90 supposed healthy individuals, we found rs6046A positively associated with NAMPT mRNA levels (P≤9.1×10⁻⁵), suggesting an eventual involvement of NAMPT expression in blood pressure regulation. Confirming this hypothesis, further transcriptomic analyses showed that increased NAMPT mRNA levels were positively correlated with ICAM1, SELL, FPR1, DEFA1-3, and LL-37 genes expression (P≤5×10⁻³). The last two mRNA levels were positively associated with systolic blood pressure levels (P≤0.01) and explained 4% of its phenotypic variation.

Conclusion

These findings reveal the importance of epistatic interactions in blood pressure genetics and give new insights for the role of inflammation in its complex regulation.

The matrix metalloproteinase 2-1575 gene polymorphism is associated with the risk of developing myocardial infarction in Mexican patients

AIM

Was to evaluate the role of seven matrix metalloproteinase (MMP) polymorphisms in the genetic susceptibility to develop myocardial infarction in Mexican individuals.

METHODS

Seven polymorphisms in the MMP genes were genotyped by 5' exonuclease TaqMan genotyping assays in 300 patients with myocardial infarction and 300 healthy unrelated controls.

RESULTS

A similar distribution of MMP2-1306 (rs243865), MMP2-790 (rs243864), MMP2-735 (rs22850553), MMP7-153(rs11568819), MMP7-181(rs11568818), and MMP12-82(rs2276109) polymorphisms was observed in both studied groups. On the other hand, patients showed increased frequencies of MMP2-1575 A allele and AA genotype when compared to controls (pC= 0.001; OR= 1.58 and pC= 0.036; OR= 2.37, respectively). According to the dominant model, individuals with AG+AA genotypes had a 1.65-fold increased risk of developing the disease (p= 0.002). After adjusting for known risk factors, we found a significant contribution of gender, BMI, smoking habit, diabetes mellitus, and hypertension to the inheritance model. In this analysis, individuals with the-1575 AA genotype had a 4.23-fold increased risk of developing MI (p= 0.003). On the other hand, an association of the MMP12-82 polymorphism with the extent of coronary artery disease (CAD) was observed. In our study, it was possible to distinguish two risk haplotypes and one protective haplotype for this disease in the MMP2 gene.

CONCLUSIONS

The results suggest that the MMP2-1575 (rs243866) gene polymorphism could be involved in the risk of developing myocardial infarction in Mexican individuals.