Comprehensive Analysis Identified and Validated CX3CR1 as Potential Biomarkers for Atherosclerosis

Abstract

Background: The etiology and disease development of atherosclerosis (AS) are still incompletely understood. In this research, we try to identify the gene biomarkers that play roles in the development and progression of AS and the relationship with immune cells.

Methods: By mining Gene Expression Omnibus (GEO) database, we acquired the dataset of AS for further research. After identifying the differentially expressed genes (DEGs) shared by AS and normal control samples, we performed functional enrichment analysis to them. Integrating the least absolute shrinkage and selection operator (LASSO) algorithm, support vector machine recursive feature elimination (SVM-RFE) algorithm, and random forest (RF) algorithm we ultimately selected genes candidates for the development of AS. Using CIBERSORT method, the difference of the immune infiltration of AS and normal control samples were analyzed. We also investigate the correlation of optimal gene biomarkers and specific several types of immune cells. 

Results: DEGs were involved in the Toll-like receptor signaling pathways and Leukocyte transendothelial migration. Results of Gene Ontology (GO) analysis showed significant enrichment of DEGs in regulation of inflammatory response, leukocyte migration, and immune receptor activity. While Disease Ontology (DO) analysis indicated that DEGs are significantly enriched in terms including lung disease, atherosclerosis, coronary artery disease, and arteriosclerosis. CX3CR1 and C3 were screened by the LASSO, SVM-REF, and RF algorithms. AS samples showed relatively low infiltration levels of naive B cells (P<0.001), plasma cells (P<0.001), resting memory CD4 T cells (P<0.001), activated memory CD4 T cells (P<0.001), monocytes (P<0.001), M1 macrophages (P<0.001), M2 macrophages (P<0.001), activated dendritic cells (P=0.009), resting mast cells (P<0.001), and neutrophils (P=0.049) than normal controls, While AS samples harbored higher infiltration levels of memory B cells (P<0.001), follicular helper T cells(P<0.001), gamma delta T cells (P<0.001), M0 macrophages (P<0.001), and activated mast cells (P<0.001) compared with normal control samples. We also identified non-negligible links between the expression levels of CX3CR1 and immune cells including M0 macrophages and M1 macrophages.

Conclusions: CX3CR1 played critical roles on the development of AS and had the potential as prognosis biomarkers for AS patients.