Comprehensive analysis of immunocyte infiltration and the key genes associated with intraplaque hemorrhage in carotid atherosclerotic plaques

Flow chart of analysis in this study. [Display omitted] •Comprehensive bioinformatics methods are widely used in mining hub genes in atherosclerosis plaque.•The mechanisms of intraplaque hemorrhage still are elusive and rarely studied.•Immune genes and cells are involved in transforming stable plaque to prone-rupture one.•Eight genes were found to be involved in IPH, and four genes (ITGB2, VAV1, ITGAM, TYROBP) may be an important biomarkers for IPH. To identify key biomarkers associated with intraplaque hemorrhage (IPH). We conducted a comprehensive analysis combined with DEGs, xCell, WGCNA, GSEA, and GSVA methods to identify immune infiltration cells and key genes involved in IPH by using GSE163154 from the gene expression omnibus (GEO). E-MTAB-1470 and E-MTAB-2055 from the ArrayExpress database were utilized as the verification datasets. Finally, the candidate hub genes were further validated by RT-qPCR in clinical samples. A total of 280 genes were upregulated and 234 genes were downregulated in GSE163154. Among the upregulated pathways, the lysosome and chemokine signaling pathway were enriched, while the vascular smooth muscle (VSMC) contraction and focal adhesion were downregulated. In addition, ten coexpression modules were obtained by using the WGCNA method and two IPH and immunity-related modules were identified. In total, 454 genes overlapped by DEGs and WGCNA results were imported into Cytoscape to construct a protein–protein network. Eight genes (FCER1G, ITGB2, VAV1, CSF1R, ITGAM, TYROBP, PTK2, and PTPN11) were identified as the IPH-related gene set with area under curves (AUC) of 0.961, 0.905, and 0.857 in GSE163154, E-MTAB-2055, and E-MTAB-1470, respectively. The expression of four genes (ITGB2, VAV1, ITGAM, TYROBP) from our analysis were consistent with RT-qPCR results. Eight genes were found to be involved in IPH, and four genes (ITGB2, VAV1, ITGAM, TYROBP) may be an important biomarkers for IPH.