APOE hypermethylation is significantly associated with coronary heart disease in males

Identification of an association between coronary heart disease and ITGB2 methylation in peripheral blood by a case-control study

BACKGROUND

Blood DNA methylation was associated with coronary heart disease (CHD) risk in Caucasians. We investigated the association between DNA methylation in peripheral blood at the reported loci and CHD in the Chinese population.

METHODS

The integrin subunit beta 2 (ITGB2) gene was identified in 196 CHD cases and 184 controls, and its methylation level was determined by mass spectrometry. Logistic regression was used to assess the association.

RESULTS

Hypomethylation of ITGB2 was significantly associated with heart failure CHD and NYHA Ⅰ&Ⅱ CHD patients with minor to medium cardiac function impairment (ITGB2_CpG_11/cg08422803, OR per -10 % methylation = 1.15 and 1.16; p = 0.012 and 0.018 by Bonferroni correction, respectively). Hypomethylation of ITGB2_CpG_11/cg08422803 was a risk factor for CHD in people < 65 years and males (p < 0.05 after Bonferroni correction). The combination of ITGB2 methylation and conventional CHD risk factors could efficiently discriminate CHD, heart failure CHD, NYHA I&II CHD, and myocardial infarction CHD patients from controls (AUC = 0.78, 0.81, 0.80, and 0.81, respectively).

CONCLUSION

Blood-based ITGB2 methylation has the potential as a biomarker for CHD. The combination of ITGB2 methylation and conventional CHD risk factors may improve the risk assessment and detection of CHD.

Sex differences in the genetic and molecular mechanisms of coronary artery disease

Sex differences in coronary artery disease (CAD) presentation, risk factors and prognosis have been widely studied. Similarly, studies on atherosclerosis have shown prominent sex differences in plaque biology. Our understanding of the underlying genetic and molecular mechanisms that drive these differences remains fragmented and largely understudied. Through reviewing genetic and epigenetic studies, we identified more than 40 sex-differential candidate genes (13 within known CAD loci) that may explain, at least in part, sex differences in vascular remodeling, lipid metabolism and endothelial dysfunction. Studies with transcriptomic and single-cell RNA sequencing data from atherosclerotic plaques highlight potential sex differences in smooth muscle cell and endothelial cell biology. Especially, phenotypic switching of smooth muscle cells seems to play a crucial role in female atherosclerosis. This matches the known sex differences in atherosclerotic phenotypes, with men being more prone to lipid-rich plaques, while women are more likely to develop fibrous plaques with endothelial dysfunction. To unravel the complex mechanisms that drive sex differences in CAD, increased statistical power and adjustments to study designs and analysis strategies are required. This entails increasing inclusion rates of women, performing well-defined sex-stratified analyses and the integration of multi-omics data.

Hypomethylation of ABCG1 in peripheral blood as a potential marker for the detection of coronary heart disease

BACKGROUND

Novel molecular biomarkers for the risk assessment and early detection of coronary heart disease (CHD) are urgently needed for disease prevention. Altered methylation of ATP-binding cassette subfamily G member 1 (ABCG1) has been implicated in CHD but was mostly studied in Caucasians. Exploring the potential relationship between ABCG1 methylation in blood and CHD among the Chinese population would yield valuable insights.

METHODS

Peripheral blood samples were obtained from a case-control study (287 CHD patients vs. 277 controls) and a prospective nested case-control study (171 CHD patients and 197 matched controls). DNA extraction and bisulfite-specific PCR amplification techniques were employed for sample processing. Quantitative assessment of methylation levels was conducted using mass spectrometry. Statistical analyses involved the utilization of logistic regression and nonparametric tests.

RESULTS

We found hypomethylation of ABCG1 in whole blood was associated with the risk of CHD in both studies, which was enhanced in heart failure (HF) patients, female and younger subjects. When combined with baseline characteristics, altered ABCG1 methylation showed improved predictive effect for differentiating CHD cases, ischemic cardiomyopathy (ICM) cases, younger than 60 years CHD cases, and female CHD cases from healthy controls (area under the curve (AUC) = 0.68, 0.71, 0.74, and 0.73, respectively).

CONCLUSIONS

We demonstrated a robust link between ABCG1 hypomethylation in whole blood and CHD risk in the Chinese population and provided novel evidence indicating that aberrant ABCG1 methylation in peripheral blood can serve as an early detection biomarker for CHD patients.

In silico identification of single nucleotide variations at CpG sites regulating CpG island existence and size

Genetic and epigenetic modifications of genes involved in the key regulatory pathways play a significant role in the pathophysiology and progression of multifactorial diseases. The present study is an attempt to identify single nucleotide variations (SNVs) at CpG sites of promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes influencing CpG island (CGI) existence and size associated with the pathophysiology of Diabetes mellitus, Coronary artery disease and Cancers. Promoter sequences located between -2000 to + 2000 bp were retrieved from the EPDnew database and predicted the CpG island using MethPrimer. Further, SNVs at CpG sites were accessed from NCBI, Ensembl while transcription factor (TF) binding sites were accessed using AliBaba2.1. CGI existence and size were determined for each SNV at CpG site with respect to wild type and variant allele by MethPrimer. A total of 200 SNVs at CpG sites were analyzed from the promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes. Of these, only 17 (8.5%) SNVs were found to influence the loss of CGI while 70 (35%) SNVs were found to reduce the size of CGI. It has also been found that 59% (10) of CGI abolishing SNVs are showing differences in binding of TFs. The findings of the study suggest that the candidate SNVs at CpG sites regulating CGI existence and size might influence the DNA methylation status and expression of genes involved in molecular pathways associated with several diseases. The insights of the present study may pave the way for new experimental studies to undertake challenges in DNA methylation, gene expression and protein assays.

DNA methylation in genes associated with the evolution of ageing and disease: A critical review

Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.

Epidemiology, Genetics and Epigenetics of Congenital Heart Diseases in Twins

Congenital heart defects (CHDs) refer to abnormalities in the heart function that arise at the fetal stages. It is the most common birth defect that affects 0.8% of all liveborn infants. There is an increase in the incidence of congenital heart disease in monochorionic twin gestation. A six-fold increase in CHDs exists among monochorionic twins especially in association with twin-twin transfusion syndrome (TTTS) compared to dichorionic twin pregnancy. In this review article, we discussed the epidemiology, the role of genetics like protein-coding genes, epigenetics, placenta, hemodynamics and environmental factors in the etiology of CHD in twins.

We conducted a literature search in PubMed indexed journals using the medical terms "twin pregnancy" and "congenital heart defect" to provide an overview of the uptrend in CHD in twin pregnancies, primarily due to assisted reproductive technologies (ARTs) and multiple other factors. Both the heart and placenta are vascular and share a common development window; therefore, CHD can develop secondary to placental pathologies. Among environmental factors, the strongest association of maternal smoking with CHD has been seen. We studied the causative factors to suggest improvement in echocardiographic skills in case of abnormal findings in twin gestations to decrease the CHD-associated morbidity and mortality, as early diagnosis allows doctors to precisely determine the risk of CHD. Systemic ultrasound scanning with five transverse views is very effective in diagnosing fetal CHD in twin pregnancy. In the case of genetics, prenatal counseling allows the expectant to understand the full ramifications of possible events after the pregnancy. The pathological basis of malformations specific to conjoined twinning and twin reversed arterial perfusion sequence is addressed. Also, there is evidence that folate supplementation may be protective against CHD but more research is needed to clarify the mechanisms.

We concluded from the literature that monochorionic twins are at high risk of CHD. Chorionicity seems to play a more vital role than zygosity. Even the type of heart defect in monochorial twin pregnancies was unique from single, dizygotic, or dichorionic twin pregnancies. We also emphasize improving echocardiographic skills of technicians in referring ART dichorionic twin fetuses with suspicious findings to fetal cardiologists and performing postnatal scans in the case of TTTS. To understand the role of the placenta, making use of newer technologies and examining the placenta both during pregnancy and beyond delivery will play a vital role in understanding the etiology. Even identifying early signals impacting the heart and placental vasculature and correcting them using advanced technology could downtrend the incidence in coming years. Increased maternal age as well as multiple pregnancies increasing the risk of CHD has also been implicated. For more clarity on the role of genetics, the cost of DNA sequencing needs to decrease. This will enable whole-genome sequencing in the future thus helping to discover the gene responsible for CHD ultimately proving beneficial for future generations. For environmental factors, we have to rely on observational studies to assess the risk to the unborn child. There is difficulty in studying natural factors due to the unreliability of exposure to contaminants like pesticides and air pollution.

Associations between Apolipoprotein E Gene Polymorphism, Diet and Dyslipidemia in a Yao Minority Area, China

OBJECTIVE

This study aimed to assess the effects of Apolipoprotein E (APOE) gene polymorphisms, dietary nutrient intake, and their interactions on the prevalence of dyslipidemia in a Yao minority area, China.

METHODS

rs429358, rs7412, rs7259620, and rs405509 of the APOE gene were genotyped in 1014 adults aged ≥30 years by using the MassArray system. Dietary nutrients intake data were ascertained from a 109-item food frequency questionnaire (FFQ).

RESULTS

Multifactorial logistics regression analysis showed that dyslipidemia was associated with rs7412-CT/TT genotype (OR: 0.540, Bonferroni correction confidence interval: 0.336-0.869), high fat intake (OR: 1.644, 95% CI: 1.128-2.395), high saturated fatty acid (SFA) intake (OR: 1.668, 95% CI: 1.146-2.428), medium carbohydrate intake (OR: 0.634, 95% CI: 0.461-0.873) and high carbohydrate intake (OR: 0.591, 95% CI: 0.406-0.858). The results of logistics regression multiplication model showed that medium carbohydrate intake in the carriers of the rs7412 minor alleles was associated with a low risk of dyslipidemia (OR: 0.433, Bonferroni correction confidence interval: 0.199-0.941).

CONCLUSIONS

Genetic variations at the rs7412, dietary fat, SFA, and carbohydrate intake and the interaction between APOE gene polymorphisms and carbohydrate intake are associated with dyslipidemia in Yao nationality people.

The association between serine hydroxymethyl transferase 1 gene hypermethylation and ischemic stroke

This study aimed to determine the correlation between serine hydroxymethyl transferase 1 (SHMT1) gene methylation and ischemic stroke. A total of 202 age- and sex-matched individuals were included. Quantitative methylation-specific polymerase chain reaction (qMSP-PCR) was used to analyze the DNA methylation level. The plasma homocysteine (Hcy) concentration was much higher in ischemic cases than in controls (p = 0.009), while the high-density lipoprotein (HDL) levels in stroke cases were considerably lower than in controls (p = 0.005). A significantly higher level of SHMT1 methylation was observed in the ischemic strokes (58.82 ± 17.83%) compared to that in the controls (42.59 ± 20.76%, p < 0.001). The SHMT1 methylation level was strongly correlated with HDL concentration in the healthy controls (r = 0.517, p < 0.001), while the high plasma level of Hcy showed strong association with SHMT1 methylation in ischemic strokes (r = 0.346, p < 0.001). Receiver operating characteristic (ROC) analysis of curve indicated that SHMT1 methylation has been an acceptable indicator for ischemic stroke in female patients [all sexes, area under the curve (AUC) = 0.71, p < 0.001; male patients AUC = 0.62, p = 0.032; and female patients AUC = 0.79, p < 0.001] and in all ages (AUC = 0.71, p < 0.001). In our samples, DNA methylation levels of the STHMI gene were significantly correlated with ischemic stroke in Han Chinese. STHMI hypermethylation was significantly associated with the high Hcy concentration in ischemic stroke and had value as a potential indicator for female ischemic stroke.

Membrane-type I matrix metalloproteinase (MT1-MMP), lipid metabolism and therapeutic implications

Lipids exert many essential physiological functions, such as serving as a structural component of biological membranes, storing energy, and regulating cell signal transduction. Dysregulation of lipid metabolism can lead to dyslipidemia related to various human diseases, such as obesity, diabetes, and cardiovascular disease. Therefore, lipid metabolism is strictly regulated through multiple mechanisms at different levels, including the extracellular matrix. Membrane-type I matrix metalloproteinase (MT1-MMP), a zinc-dependent endopeptidase, proteolytically cleaves extracellular matrix components, and non-matrix proteins, thereby regulating many physiological and pathophysiological processes. Emerging evidence supports the vital role of MT1-MMP in lipid metabolism. For example, MT1-MMP mediates ectodomain shedding of low-density lipoprotein receptor and increases plasma low-density lipoprotein cholesterol levels and the development of atherosclerosis. It also increases the vulnerability of atherosclerotic plaque by promoting collagen cleavage. Furthermore, it can cleave the extracellular matrix of adipocytes, affecting adipogenesis and the development of obesity. Therefore, the activity of MT1-MMP is strictly regulated by multiple mechanisms, such as autocatalytic cleavage, endocytosis and exocytosis, and post-translational modifications. Here, we summarize the latest advances in MT1-MMP, mainly focusing on its role in lipid metabolism, the molecular mechanisms regulating the function and expression of MT1-MMP, and their pharmacotherapeutic implications.

Epigenetic enzymes: A role in aging and prospects for pharmacological targeting

The development of interventions aimed at improving healthspan is one of the priority tasks for the academic and public health authorities. It is also the main objective of a novel branch in biogerontological research, geroscience. According to the geroscience concept, targeting aging is an effective way to combat age-related disorders. Since aging is an exceptionally complex process, system-oriented integrated approaches seem most appropriate for such an interventional strategy. Given the high plasticity and adaptability of the epigenome, epigenome-targeted interventions appear highly promising in geroscience research. Pharmaceuticals targeted at mechanisms involved in epigenetic control of gene activity are actively developed and implemented to prevent and treat various aging-related conditions such as cardiometabolic, neurodegenerative, inflammatory disorders, and cancer. In this review, we describe the roles of epigenetic mechanisms in aging; characterize enzymes contributing to the regulation of epigenetic processes; particularly focus on epigenetic drugs, such as inhibitors of DNA methyltransferases and histone deacetylases that may potentially affect aging-associated diseases and longevity; and discuss possible caveats associated with the use of epigenetic drugs.

Promoter polymorphisms in the lncRNA-MIAT gene associated with acute myocardial infarction in Chinese Han population: a case-control study

BACKGROUND

Coronary atherosclerotic disease (CAD) is one of the greatest causes of death and disability around the world, and has emerged as a major public health problem. Acute myocardial infarction (AMI) is the most serious type of CAD. Myocardial infarction (MI) association transcript (MIAT) has demonstrated that it plays an important role in AMI.

PURPOSE

To investigate the association between MIAT promoter polymorphisms and AMI in Chinese Han population.

METHODS

A total of 212 AMI patients and 218 healthy controls were recruited. The long non-coding RNA (lncRNA)-MIAT promoter polymorphisms (single nucleotide polymorphisms (SNPs)) were obtained using polymerase chain reaction (PCR) and sequencing techniques. Chi-square test was used to analyze the allele and genotype frequencies of each SNP in two groups. Logistic regression analysis was used to analyze the association of each SNP with AMI. Linkage disequilibrium (LD) and haplotype analysis were performed using SHEsis software. A JASPAR database search predicts transcription factors transition of linked polymorphism in MIAT promoter.

RESULTS

Ten SNPs were found, including rs56371714, rs55892869, rs151057042, rs2157598, rs150465374, rs5761664, rs8142890, rs5752375, rs9608515 and rs1055293700, whereas rs1055293700 was found only in the control group. Single and logistic regression analysis showed that there was a significant correlation between rs5752375 and rs9608515 polymorphisms and AMI, while other sites had no relationship with AMI. These MI association polymorphisms may change the binding sites with transcription factor.

CONCLUSIONS

The polymorphisms of lncRNA-MIAT promoter rs5752375 and rs9608515 were significantly associated with AMI in Chinese Han population. This result would be of clinical importance for the early diagnosis of AMI.

DNA methylation of AHCY may increase the risk of ischemic stroke

Genetic factors play an important role in the pathogenesis of ischemic stroke. Of these, epigenetic modifications provide a new direction for the study of ischemic stroke pathogenesis. This study aimed to determine the correlation between DNA methylation of the gene encoding S-adenosylhomocysteine hydrolase (AHCY) and the risk of ischemic stroke in 64 ischemic stroke patients and 138 patients with traumatic brain injury (control group). The methylation level of AHCY was analyzed using quantitative methylation-specific polymerase chain reaction. Statistically significant differences in AHCY methylation levels were observed between the case group [medians (interquartile range): 0.13% (0.09%, 0.27%)] and the control group [0.06% (0.00%, 0.17%), p < 0.0001], and these associations remained significant in both male (p = 0.003) and female (p = 0.0005) subjects. A subgroup analysis by age revealed a considerably higher percentage of methylated AHCY in the case group than the control group in all age groups (age < 60 years, p = 0.007; age ≥ 60 years, p < 0.0001). A receiver operating characteristic (ROC) curve analysis revealed a trend toward a role for AHCY methylation as an indicator of risk in all ischemic patients [area under the curve (AUC) = 0.70, p = 0.0001], male patients (AUC = 0.67, p = 0.004), and female patients (AUC = 0.75, p = 0.0002). Our study confirmed a significant association between the AHCY DNA methylation level and the risk of ischemic stroke, suggesting that this gene methylation pattern may be a potential diagnostic marker of ischemic stroke.

DNA methylation analysis in plants: review of computational tools and future perspectives

Genome-wide DNA methylation studies have quickly expanded due to advances in next-generation sequencing techniques along with a wealth of computational tools to analyze the data. Most of our knowledge about DNA methylation profiles, epigenetic heritability and the function of DNA methylation in plants derives from the model species Arabidopsis thaliana. There are increasingly many studies on DNA methylation in plants-uncovering methylation profiles and explaining variations in different plant tissues. Additionally, DNA methylation comparisons of different plant tissue types and dynamics during development processes are only slowly emerging but are crucial for understanding developmental and regulatory decisions. Translating this knowledge from plant model species to commercial crops could allow the establishment of new varieties with increased stress resilience and improved yield. In this review, we provide an overview of the most commonly applied bioinformatics tools for the analysis of DNA methylation data (particularly bisulfite sequencing data). The performances of a selection of the tools are analyzed for computational time and agreement in predicted methylated sites for A. thaliana, which has a smaller genome compared to the hexaploid bread wheat. The performance of the tools was benchmarked on five plant genomes. We give examples of applications of DNA methylation data analysis in crops (with a focus on cereals) and an outlook for future developments for DNA methylation status manipulations and data integration.

DNA methylation in APOE: The relationship with Alzheimer's and with cardiovascular health

INTRODUCTION

Genetic variation in the apolipoprotein E (APOE) gene is associated with Alzheimer's disease (AD) and risk factors for cardiovascular disease (CVD). DNA methylationat APOE has been associated with altered cognition and AD. It is unclear if epigenetic marks could be used for predicting future disease.

METHODS

We assessed blood-based DNA methylation at 13 CpGs in the APOE gene in 5828 participants from the Generation Scotland (GS) cohort. Using linear mixed models regression, we examined the relationships among APOE methylation, cognition, cholesterol, the family history of AD and the risk for CVD.

RESULTS

DNA methylation at two CpGs was associated with the ratio of total cholesterol and HDL cholesterol, but not with cognition, family history of AD, or the risk of CVD.

DISCUSSION

APOE methylation is associated with the levels of blood cholesterol, but there is no evidence for the utility of APOE methylation as a biomarker for predicting AD or CVD.

Overall and sex-specific associations between methylation of the ABCG1 and APOE genes and ischemic stroke or other atherosclerosis-related traits in a sibling study of Chinese population

Background

Identifying subjects with a high risk of ischemic stroke is fundamental for prevention of the disease. Both genetic and environmental risk factors contribute to ischemic stroke, but the underlying epigenetic mechanisms which mediate genetic and environmental risk effects are not fully understood. The aim of this study was to explore whether DNA methylation loci located in the ATP-binding cassette G1 (ABCG1) and apolipoprotein E (APOE) genes, both involved in the metabolism of lipids in the body, are related to ischemic stroke, using the Fangshan/Family-based Ischemic Stroke Study in China. We also tested if these CpG sites were associated with early signs of cardiovascular atherosclerosis (carotid intima–media thickness (cIMT), ankle–brachial index (ABI), and brachial–ankle pulse wave velocity (baPWV)).

Results

DNA methylation at the cg02494239 locus in ABCG1 was correlated with ischemic stroke after adjusting for gender, previous history of diabetes and hypertension, smoking, drinking, body mass index, and blood lipid levels (above vs below mean, OR = 2.416, 95% CI 1.024–5.700, P = 0.044; 75–100% percentile vs 0–25% percentile, OR = 4.461, 95% CI 1.226–16.225, P = 0.023). No statistically significant associations were observed for the cg06500161 site in ABCG1 and the cg14123992 site in APOE with ischemic stroke. The study detected that hypermethylation of the ABCG1 gene was significantly associated with cIMT, hypermethylation of the APOE gene was significantly related to ABI, and methylation of the APOE gene was statistically negatively correlated with baPWV. The above relationships demonstrated gender differences.

Conclusions

These findings suggest that epigenetic modification of ABCG1 and APOE may play a role in the pathway from disturbed blood lipid levels to the development of cardiovascular diseases. Future prospective validation of these findings is warranted.