Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach

Quantitative proteomic landscape of unstable atherosclerosis identifies molecular signatures and therapeutic targets for plaque stabilization

Atherosclerotic plaque rupture leading to myocardial infarction is a major global health burden. Applying the tandem stenosis (TS) mouse model, which distinctively exhibits the characteristics of human plaque instability/rupture, we use quantitative proteomics to understand and directly compare unstable and stable atherosclerosis. Our data highlight the disparate natures and define unique protein signatures of unstable and stable atherosclerosis. Key proteins and pathway networks are identified such as the innate immune system, and neutrophil degranulation. The latter includes calprotectin S100A8/A9, which we validate in mouse and human unstable plaques, and we demonstrate the plaque-stabilizing effects of its inhibition. Overall, we provide critical insights into the unique proteomic landscape of unstable atherosclerosis (as distinct from stable atherosclerosis and vascular tissue). We further establish the TS model as a reliable preclinical tool for the discovery and testing of plaque-stabilizing drugs. Finally, we provide a knowledge resource defining unstable atherosclerosis that will facilitate the identification and validation of long-sought-after therapeutic targets and drugs for plaque stabilization.

Correlation analysis between D-dimer-to-fibrinogen-ratio and carotid plaque in young patients aged 18-45 with acute cerebral infarction

BACKGROUND

D-Dimer and fibrinogen were commonly used to detect the coagulation and fibrinolytic function, but D-dimer to fibrinogen ratio (DFR) in carotid plaque in young patients aged 18-45 with acute cerebral infarction (ACI) has not been used clinically. In this work, we focused on the evaluation of the DFR value of this group of patients and analyzed its possible correlation.

METHODS

A total of 164 patients with ACI patients aged 18-45 were selected as research subjects after their first admission. They had undergone carotid plaque contrast-enhanced ultrasound (CEUS) and were divided into two groups with carotid plaque (n = 97) and with no carotid plaque (n = 67). According to NIHSS score and carotid plaque grade, the clinical symptoms of patients were judged. Univariate and multivariate analyses were conducted to compare the risk factors of carotid plaque in ACI patients.

RESULTS

The DFR value of patients in the carotid plaque group (103.41 ± 20.81) was significantly higher than that of the no carotid plaque control group (88.9 ± 26.51). We also identified DFR X10³ was the only independent risk factor (β = 0.53; 95% CI, 0.914-0.984; P = 0.05). DFR X10³ was increased with the severity of the disorder and with the CEUS grades. The area under the DFR curve was 0.673 (95% CI 0.584～0.762).

CONCLUSION

The value of the DFR is positively correlated with CEUS carotid plaque grading and NIHSS score, which can predict the severity of carotid plaque in ACI patients aged 18-45. Therefore it is worthy of clinical application.

Atorvastatin and blood flow regulate expression of distinctive sets of genes in mouse carotid artery endothelium

Hypercholesterolemia is a well-known pro-atherogenic risk factor and statin is the most effective anti-atherogenic drug that lowers blood cholesterol levels. However, despite systemic hypercholesterolemia, atherosclerosis preferentially occurs in arterial regions exposed to disturbed blood flow (d-flow), while the stable flow (s-flow) regions are spared. Given their predominant effects on endothelial function and atherosclerosis, we tested whether (1) statin and flow regulate the same or independent sets of genes and (2) statin can rescue d-flow-regulated genes in mouse artery endothelial cells in vivo. To test the hypotheses, C57BL/6 J mice (8-week-old male, n=5 per group) were pre-treated with atorvastatin (10mg/kg/day, Orally) or vehicle for 5 days. Thereafter, partial carotid ligation (PCL) surgery to induce d-flow in the left carotid artery (LCA) was performed, and statin or vehicle treatment was continued. The contralateral right carotid artery (RCA) remained exposed to s-flow to be used as the control. Two days or 2 weeks post-PCL surgery, endothelial-enriched RNAs from the LCAs and RCAs were collected and subjected to microarray gene expression analysis. Statin treatment in the s-flow condition (RCA+statin versus RCA+vehicle) altered the expression of 667 genes at 2-day and 187 genes at 2-week timepoint, respectively (P<0.05, fold change (FC)≥±1.5). Interestingly, statin treatment in the d-flow condition (LCA+statin versus LCA+vehicle) affected a limited number of genes: 113 and 75 differentially expressed genes at 2-day and 2-week timepoint, respectively (P<0.05, FC≥±1.5). In contrast, d-flow in the vehicle groups (LCA+vehicle versus RCA+vehicle) differentially regulated 4061 genes at 2-day and 3169 genes at 2-week timepoint, respectively (P<0.05, FC≥±1.5). Moreover, statin treatment did not reduce the number of flow-sensitive genes (LCA+statin versus RCA+statin) compared to the vehicle groups: 1825 genes at 2-day and 3788 genes at 2-week, respectively, were differentially regulated (P<0.05, FC≥±1.5). These results revealed that both statin and d-flow regulate expression of hundreds or thousands of arterial endothelial genes, respectively, in vivo. Further, statin and d-flow regulate independent sets of endothelial genes. Importantly, statin treatment did not reverse d-flow-regulated genes except for a small number of genes. These results suggest that both statin and flow play important independent roles in atherosclerosis development and highlight the need to consider their therapeutic implications for both.

The lipid paradox in neuroprogressive disorders: Causes and consequences

Chronic systemic inflammation is associated with an increased risk of cardiovascular disease in an environment of low low-density lipoprotein (LDL) and low total cholesterol and with the pathophysiology of neuroprogressive disorders. The causes and consequences of this lipid paradox are explored. Circulating activated neutrophils can release inflammatory molecules such as myeloperoxidase and the pro-inflammatory cytokines interleukin-1 beta, interleukin-6 and tumour necrosis factor-alpha. Since activated neutrophils are associated with atherosclerosis and cardiovascular disease and with major depressive disorder, bipolar disorder and schizophrenia, it seems reasonable to hypothesise that the inflammatory molecules released by them may act as mediators of the link between systemic inflammation and the development of atherosclerosis in neuroprogressive disorders. This hypothesis is tested by considering the association at a molecular level of systemic inflammation with increased LDL oxidation; increased small dense LDL levels; increased lipoprotein (a) concentration; secretory phospholipase A₂ activation; cytosolic phospholipase A₂ activation; increased platelet activation; decreased apolipoprotein A1 levels and function; decreased paroxonase-1 activity; hyperhomocysteinaemia; and metabolic endotoxaemia. These molecular mechanisms suggest potential therapeutic targets.

Resveratrol Treatment Is Associated with Lipid Regulation and Inhibition of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) in Rabbits Fed a High-Fat Diet

The effects of resveratrol on various conditions have been widely studied previously. This paper aimed to investigate the influence of resveratrol on atherosclerosis (AS). Twenty-four New Zealand male rabbits were randomly and equally assigned to the normal diet group (NDG), fat diet group (FDG), and fat diet with resveratrol group (80 mg/kg/d, RFG). Biochemical indicators from blood samples were analyzed at baseline and 3 months to investigate the effects of resveratrol on blood lipid, lipoprotein-associated phospholipase A2 (Lp-PLA2), liver, and renal function. The indicators including alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatinine (CREA), triglycerides (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and Lp-PLA2. At 3 months, arteries were stained with hematoxylin and eosin to study the influence of resveratrol on the aortic intima, smooth muscle layer, and the intima/media ratio. Comparisons of weight, ALT, AST, CREA, TG, TC, HDL-C, LDL-C, and Lp-PLA2 among the three groups showed no significant difference at baseline. However, at the end of 3 months, significant differences were observed in AST, CREA, TC, HDL-C, LDL-C, and Lp-PLA2 between the three groups (P < 0.05). In pairwise comparison, CREA, TC, LDL-C, and Lp-PLA2 had significant differences between any two groups (P < 0.05). In addition, there were significant differences in the AST and HDL-C levels between RFG and NDG groups (P < 0.05). Meanwhile, the HDL-C levels were also significantly different between the FDG and NDG groups (P < 0.01). The histologic analysis also showed that the thickness of the aortic intima and the ratio of the intima and aortic tunica media (P < 0.05) significantly decreased in RFG compared to FDG. Resveratrol may have an antiatherosclerosis effect on a rabbit model of AS.

Exploring disease comorbidity in a module-module interaction network

Understanding disease comorbidity contributes to improved quality of life in patients who are suffering from multiple diseases. Therefore, to better explore comorbid diseases, the clarification of associations between diseases based on biological functions is essential. In our study, we propose a method for identifying disease comorbidity in a module-based network, named the module-module interaction (MMI) network, which represents how biological functions influence each other. To construct the MMI network, we detected gene modules - sets of genes that have a higher probability of taking part in specific functions - and established a link between these modules. Subsequently, we constructed disease-related networks in the MMI network to understand inherent disease mechanisms and calculated comorbidity scores of disease pairs using Gene Ontology (GO) terms. Our results show that we can obtain further information on disease mechanisms by considering interactions between functional modules instead of between genes. In addition, we verified that predicted comorbid relationships of disease pairs based on the MMI network are more significant than those based on the protein-protein interaction (PPI) network. This study can be useful to elucidate the mechanisms underlying comorbidities for further study, which will provide a broader insight into the pathogenesis of diseases.

Conceptualization of Heterogeneity of Chronic Diseases and Atherosclerosis as a Pathway to Precision Medicine: Endophenotype, Endotype, and Residual Cardiovascular Risk

The article discusses modern approaches to the conceptualization of pathogenetic heterogeneity in various branches of medical science. The concepts of endophenotype, endotype, and residual cardiovascular risk and the scope of their application in internal medicine and cardiology are considered. Based on the latest results of studies of the genetic architecture of atherosclerosis, five endotypes of atherosclerosis have been proposed. Each of the presented endotypes represents one or another pathophysiological mechanism of atherogenesis, having an established genetic substrate, a characteristic panel of biomarkers, and a number of clinical features. Clinical implications and perspectives for the study of endotypes of atherosclerosis are briefly reviewed.

Atherosclerosis-associated differentially methylated regions can reflect the disease phenotype and are often at enhancers

BACKGROUND AND AIMS

Atherosclerosis is a widespread and complicated disease involving phenotypic modulation and transdifferentiation of vascular smooth muscle cells (SMCs), the predominant cells in aorta, as well as changes in endothelial cells and infiltrating monocytes. Alterations in DNA methylation are likely to play central roles in these phenotypic changes, just as they do in normal differentiation and cancer.

METHODS

We examined genome-wide DNA methylation changes in atherosclerotic aorta using more stringent criteria for differentially methylated regions (DMRs) than in previous studies and compared these DMRs to tissue-specific epigenetic features.

RESULTS

We found that disease-linked hypermethylated DMRs account for 85% of the total atherosclerosis-associated DMRs and often overlap aorta-associated enhancer chromatin. These hypermethylated DMRs were associated with functionally different sets of genes compared to atherosclerosis-linked hypomethylated DMRs. The extent and nature of the DMRs could not be explained as direct effects of monocyte/macrophage infiltration. Among the known atherosclerosis- and contractile SMC-related genes that exhibited hypermethylated DMRs at aorta enhancer chromatin were ACTA2 (aorta α2 smooth muscle actin), ELN (elastin), MYOCD (myocardin), C9orf3 (miR-23b and miR-27b host gene), and MYH11 (smooth muscle myosin). Our analyses also suggest a role in atherosclerosis for developmental transcription factor genes having little or no previous association with atherosclerosis, such as NR2F2 (COUP-TFII) and TBX18.

CONCLUSIONS

We provide evidence for atherosclerosis-linked DNA methylation changes in aorta SMCs that might help minimize or reverse the standard contractile character of many of these cells by down-modulating aorta SMC-related enhancers, thereby facilitating pro-atherosclerotic phenotypic changes in many SMCs.

Endothelial-Vascular Smooth Muscle Cells Interactions in Atherosclerosis

Atherosclerosis is a chronic progressive inflammatory process that can eventually lead to cardiovascular disease (CVD). Despite available treatment, the prevalence of atherosclerotic CVD, which has become the leading cause of death worldwide, persists. Identification of new mechanisms of atherogenesis are highly needed in order to develop an effective therapeutic treatment. The blood vessels contain two primary major cell types: endothelial cells (EC) and vascular smooth muscle cells (VSMC). Each of these performs an essential function in sustaining vascular homeostasis. EC-VSMC communication is essential not only to development, but also to the homeostasis of mature blood vessels. Aberrant EC-VSMC interaction could promote atherogenesis. Identification of the mode of EC-VSMC crosstalk that regulates vascular functionality and sustains homeostasis may offer strategic insights for prevention and treatment of atherosclerotic CVD. Here we will review the molecular mechanisms underlying the interplay between EC and VSMC that could contribute to atherosclerosis. We also highlight open questions for future research directions.

Recent advances and clinical insights into the use of proteomics in the study of atherosclerosis

INTRODUCTION

The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment. This review provides a comprehensive overview of the novel methods in proteomics, including state-of-the-art techniques, novel biological samples and applications for the study of atherosclerosis. Expert commentary: Collaboration between clinicians and researchers is crucial to further validate and introduce new molecular markers to manage atherosclerosis that are identified using the most up to date proteomic approaches.