Gene expression profile analysis of the progression of carotid atherosclerotic plaques

Abstract

The present study aimed to examine the universal gene expression signature and the underlying molecular mechanisms involved in the progression of carotid atherosclerotic plaques. The gene expression dataset, GSE28829, containing 13 early and 16 advanced carotid atherosclerotic plaques was selected for analysis. The differentially expressed genes (DEGs) were identified and analyzed using bioinformatics analyses, including cluster analysis, Gene Ontology (GO) and pathway enrichment analyses. Finally, a protein-protein interaction (PPI) was constructed and analyzed. A total of 515 downregulated and 243 downregulated DEGs were identified. The cluster analysis revealed two separate two groups. In addition, the GO terms enriched by the upregulated DEGs were associated with immune response, and the downregulated DEGs were associated with cell adhesion. The upregulated DEGs were enriched in pathways associated with signaling in the immune system, and the downregulated DEGs were enriched in pathways associated with muscle contraction. In the PPI network analysis, ITGAM and ACTN2 had the highest decrees of connectivity in the upregulated and downregulated DEGs, respectively. These findings suggested that deregulation of the immune system and smooth muscle cell cytoskeleton accelerates the progression of carotid atherosclerotic plaques. The DEGs identified may offer potential in the prevention and treatment of atherosclerosis in the carotid artery.

Bioinformatics analysis of vascular RNA-seq data revealed hub genes and pathways in a novel Tibetan minipig atherosclerosis model induced by a high fat/cholesterol diet

“…GO biological process enrichment analysis showed that up-regulated DEGs are mainly related to immune-inflammatory responses, cell proliferation, differentiation and chemotaxis, response to lipids, reactive oxygen species metabolic process and cell death, which confirmed that cell proliferation and differentiation, cell adhesion, immune inflammation, and lipid metabolism are well associated with atherosclerosis [25]. Meanwhile, our analysis showed that the down-regulated DEGs are involved in muscle contraction, which is in agreement with the results in human carotid atherosclerotic plaque from Liu et al [26]. These results supported that lipid metabolism, oxidative stress and immune-inflammatory responses drive the development of atherosclerosis, which is consistent with the enrichment analysis results of hallmark gene sets in GSEA.…”

Comparative proteomic analysis uncovers potential biomarkers involved in the anticancer effect of Scutellarein in human gastric cancer cells

“…Further VINC was also found to stimulate tumor progression by increasing PI3K activation of phosphatidylinositol ( 3 , 4 , 5 )-triphosphate in cancer cells ( 34 ). VCL gene expression was found to be significantly elevated in GC tissues, indicating that VCL may contribute to GC progression by stimulation of tumor malignancy and its invasiveness ( 35 ). Targeting the depletion of VCL by anticancer agents may help to overcome cell metastasis and invasion.…”

Pathogenesis regarding development and structure of unstable atherosclerotic plaque in internal carotid artery in relation to high risk factors of an ischaemic stroke. Current status of knowledge

“…In most cases DEGs are related to immune response and maintain chronic inflammatory process, wich indicates a significant role of the immune response in the pathogenesis of atherosclerosis [9]. The analysis of DEGs profile in atherosclerotic carotid plaque revealed that upregulated genes were associated with inflammatory response and chemotaxis signal pathways within the immune system [10]. Downregulated genes were associated with contraction and cellular cytoskeleton structure of the vascular smooth muscle cells [10].…”

“…The analysis of DEGs profile in atherosclerotic carotid plaque revealed that upregulated genes were associated with inflammatory response and chemotaxis signal pathways within the immune system [10]. Downregulated genes were associated with contraction and cellular cytoskeleton structure of the vascular smooth muscle cells [10]. Furthermore, the analysis of DEGs showed that genes associated with antigen presentation are of key importance in development of atherosclerotic lesions [9].…”