Identification of potential crucial genes in monocytes for atherosclerosis using bioinformatics analysis

Novel insights into RNA polymerase II transcription regulation: transcription factors, phase separation, and their roles in cardiovascular diseases

Transcription factors (TFs) are specialized proteins that bind DNA in a sequence-specific manner and modulate RNA polymerase II (Pol II) in multiple steps of the transcription process. Phase separation is a spontaneous or driven process that can form membrane-less organelles called condensates. By creating different liquid phases at active transcription sites, the formation of transcription condensates can reduce the water content of the condensate and lower the dielectric constant in biological systems, which in turn alters the structure and function of proteins and nucleic acids in the condensate. In RNA Pol II transcription, phase separation formation shortens the time at which TFs bind to target DNA sites and promotes transcriptional bursting. RNA Pol II transcription is engaged in developing several diseases, such as cardiovascular disease, by regulating different TFs and mediating the occurrence of phase separation. This review aims to summarize the advances in the molecular mechanisms of RNA Pol II transcriptional regulation, in particular the effect of TFs and phase separation. The role of RNA Pol II transcriptional regulation in cardiovascular disease will be elucidated, providing potential therapeutic targets for the management and treatment of cardiovascular disease.

Integrative bioinformatics analysis of miRNA and mRNA expression profiles and identification of associated miRNA-mRNA network in intracranial aneurysms

Background

Intracranial aneurysms (IAs) represent protrusions in the vascular wall, with their growth and wall thinning influenced by various factors. These processes can culminate in the rupture of the aneurysm, leading to subarachnoid hemorrhage (SAH). Unfortunately, over half of the patients prove unable to withstand SAH, succumbing to adverse outcomes despite intensive therapeutic interventions, even in premier medical facilities. This study seeks to discern the pivotal microRNAs (miRNAs) and genes associated with the formation and progression of IAs.

Methods

The investigation gathered expression data of miRNAs (from GSE66240) and mRNAs (from GSE158558) within human aneurysm tissue and superficial temporal artery (STA) samples, categorizing them into IA and normal groups. This classification was based on the Gene Expression Omnibus (GEO) database.

Results

A total of 70 differentially expressed microRNAs (DEMs) and 815 differentially expressed mRNAs (DEGs) were pinpointed concerning IA. Subsequently, a miRNA-mRNA network was constructed, incorporating 9 significantly upregulated DEMs and 211 significantly downregulated DEGs. Simultaneously, functional enrichment and pathway analyses were conducted on both DEMs and DEGs. Through protein-protein interaction (PPI) network analysis and functional enrichment, 9 significantly upregulated DEMs (hsa-miR-188-5p, hsa-miR-590-5p, hsa-miR-320b, hsa-miR-423-5p, hsa-miR-140-5p, hsa-miR-486-5p, hsa-miR-320a, hsa-miR-342-3p, and hsa-miR-532-5p) and 50 key genes (such as ATP6V1G1, KBTBD6, VIM, PA2G4, DYNLL1, METTL21A, MDH2, etc.) were identified, suggesting their potential significant role in IA. Among these genes, ten were notably negatively regulated by at least two key miRNAs.

Conclusions

The findings of this study provide valuable insights into the potential pathogenic mechanisms underlying IA by elucidating a miRNA-mRNA network. This comprehensive approach sheds light on the intricate interplay between miRNAs and genes, offering a deeper understanding of the molecular dynamics involved in IA development and progression.

Artificial Intelligence in Cardiology and Atherosclerosis in the Context of Precision Medicine: A Scoping Review

Cardiovascular diseases remain the main cause of death worldwide which makes it essential to better understand, diagnose, and treat atherosclerosis. Artificial intelligence (AI) and novel technological solutions offer us new possibilities and enable the practice of individually tailored medicine. The study was performed using the PRISMA protocol. As of January 10, 2023, the analysis has been based on a review of 457 identified articles in PubMed and MEDLINE databases. The search covered reviews, original articles, meta-analyses, comments, and editorials published in the years 2009-2023. In total, 123 articles met inclusion criteria. The results were divided into the subsections presented in the review (genome-wide association studies, radiomics, and other studies). This paper presents actual knowledge concerning atherosclerosis, in silico, and big data analyses in cardiology that affect the way medicine is practiced in order to create an individual approach and adjust the therapy of atherosclerosis.

Methylation at CpG sites related to growth differentiation factor-15 was not prospectively associated with cardiovascular death in discordant monozygotic twins

Myocardial infarction patients had decreased methylation at four growth differentiating factor-15 (GDF-15) related CpG sites (cg13033858, cg16936953, cg17150809, and cg18608055). These sites had not been studied for their association with cardiovascular disease (CVD) deaths. Thus, we aimed to assess the associations independent of genes, shared environment, and traditional CVD risk factors. Nineteen white, male, monozygotic twin pairs discordant for CVD deaths were included from the National Heart, Lung and Blood Institute Twin Study (NHLBI) initiated in 1969. Data on vital status was collected through December 31, 2014. Methylation of buffy coat DNA at exam 3 (1986-87) was measured using the Illumina HumanMethylation450 BeadChip. Principal component analysis was used to generate a score representing blood leukocyte composition and baseline CVD risk factors and predominated with natural killer cells, CD4+ T cells, and Framingham risk score. Conditional logistic regression demonstrated that methylation at the four CpG sites was not associated with CVD deaths before (all p > 0.05, bootstrapped p > 0.05) and after adjustment for the score (all p > 0.05). Joint influences of cg16936953 and the score were statistically significant (p < 0.05). In conclusion, joint influences of methylation at the site cg16936953 and the score are prospectively associated with CVD deaths independent of germline and common environment.ClinicalTrials.gov Identifier for NHLBI Twin Study: NCT00005124.

Integrated Network and Gene Ontology Analysis Identifies Key Genes and Pathways for Coronary Artery Diseases

BACKGROUND

The prevalence of Coronary Artery Disease (CAD) in developing countries is on the rise, owing to rapidly changing lifestyle. Therefore, it is imperative that the underlying genetic and molecular mechanisms be understood to develop specific treatment strategies. Comprehensive disease network and Gene Ontology (GO) studies aid in prioritizing potential candidate genes for CAD and also give insights into gene function by establishing gene and disease pathway relationships.

METHODS

In the present study, CAD-associated genes were collated from different data sources and protein-protein interaction network was constructed using STRING. Highly interconnected network clusters were inferred and GO analysis was performed.

RESULTS

Interrelation between genes and pathways were analyzed on ClueGO and 38 candidates were identified from 1475 CAD-associated genes, which were significantly enriched in CAD-related pathways such as metabolism and regulation of lipid molecules, platelet activation, macrophage derived foam cell differentiation, and blood coagulation and fibrin clot formation.

DISCUSSION

Integrated network and ontology analysis enables biomarker prioritization for common complex diseases such as CAD. Experimental validation and future studies on the prioritized genes may reveal valuable insights into CAD development mechanism and targeted treatment strategies.

Diagnostic value of miR-637 in patients with atherosclerosis and its predictive significance for the future cardiovascular events

Objectives

Atherosclerosis is a common vascular disease. MiR-637 has been demonstrated to be low-expressed in hypertensive patients, and atherosclerosis is closely related to hypertension. Therefore, this study speculated that miR-637 may play an important role in the development of atherosclerosis. In brief, this study examined the expression level of miR-637 in patients with atherosclerosis and further analyzed its clinical value in patients with atherosclerosis.

Methods

The expression level of miR-637 was detected in serum from 86 patients with atherosclerosis and 75 healthy controls by using quantitative reverse transcription-polymerase chain reaction. The receiver operating characteristic curve was used to assess the diagnostic value of miR-637 in atherosclerosis. Pearson’s correlation analysis was performed to evaluate the relationship between serum miR-637 and different clinical parameters. The prognostic value of miR-637 in atherosclerosis was analyzed by the Kaplan–Meier survival curve and multivariate cox regression analysis.

Results

Compared with healthy individuals, miR-637 was downregulated in the serum of atherosclerosis patients. The receiver operating characteristic curve suggested the high diagnostic value of miR-637 for atherosclerosis, with the AUC of 0.853, specificity of 77.9%, and sensitivity of 80.0%. The expression level of miR-637 was negatively correlated with CIMT (r = –0.8101, P <  0.0001) and CRP (r = –0.6154, P <  0.0001), respectively. Survival analysis indicated that miR-637 was also found to be an independent prognostic factor for atherosclerosis.

Conclusions

MiR-637 is a potential noninvasive diagnostic marker of atherosclerosis and has important predictive value for the occurrence of future cardiovascular events.