Endothelial-to-mesenchymal transition gene signature derived from single-cell transcriptomics of human atherosclerotic tissue associates with stable plaque histological characteristics

Background: Endothelial cells within atherosclerotic plaques can differentiate into a mesenchymal-like phenotype through endothelial-to-mesenchymal transition (EndoMT). Our understanding of the molecular mechanisms underlying EndoMT in human atherosclerosis remains limited. Current gene expression signatures are often derived from in vitro experiments or animal studies and typically reflect genes upregulated in fully differentiated mesenchymal cell states, while genes upregulated during the process are omitted. To address this knowledge gap, we utilized in silico lineage tracing in single-cell transcriptomic (scRNA-seq) data from human plaque tissues to identify the EndoMT gene expression signature. Methods and results: We constructed three candidate EndoMT lineages across subpopulations of ECs and SMCs in human carotid scRNA-seq data (n = 46). We examined gene expression over the course of these lineages and identified a core signature of 73 genes upregulated in EndoMT. Upregulation of those genes was confirmed in EndoMT trajectories of other human datasets derived from plaque tissue and in Cdh5-CreERT2 Rosa-eYFP apoE−/− lineage-traced mice. Analysis of human carotid plaque bulk RNA-seq data (632 patients) found the association of core gene signature with fibrous and more stable histological phenotypes. Conclusion: This study defines the core gene signature of EndoMT in human atherosclerotic plaques, which can serve as a reference for future studies and gene set enrichment analysis.