Identification of PGF+ endothelial cells associated with plaque instability in carotid atherosclerosis by scRNA-seq and RNA-seq analysis

Vascular endothelial dysfunction plays a critical role in the development of atherosclerosis; however, the mechanisms by which endothelial cells contribute to plaque instability remain incompletely understood. In this study, we performed an integrated analysis of single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data to characterize endothelial cell heterogeneity associated with carotid plaque instability. Clustering analysis, gene set variation analysis (GSVA), differential gene expression analysis, and KEGG pathway enrichment were conducted to identify key endothelial cell subsets and their functional characteristics. We identified three endothelial cell subsets (subsets 9, 10, and 11) that were significantly enriched in unstable plaques and exhibited upregulation of multiple pro-inflammatory cytokines. Pathway analysis revealed that these subsets were associated with activation of the PI3K – Akt signaling pathway and other inflammation-related pathways. Furthermore, findings were validated in an apolipoprotein E-deficient (ApoE−/−) mouse model, where increased expression of placental growth factor (PGF) and a higher proportion of PGF-positive endothelial cells were observed in atherosclerotic lesions. In conclusion, this study reveals the heterogeneity of endothelial cells in atherosclerotic plaques and identifies pro-inflammatory endothelial subsets potentially associated with plaque instability, providing new insights into the pathogenesis of atherosclerosis.Trial registration: This study was approved by the Experimental Animal Ethics Committee of Guizhou University of Chinese Medicine (approval number: 2,024,010).