Abstract Body (Do not enter title and authors here): BACKGROUND: Atherosclerosis (AS) progression involves complex interactions and phenotypic plasticity among vascular and immune cell lineages. Single-cell RNA-seq (scRNA-seq) studies have highlighted lineage-specific transcriptomic signatures, but human cell phenotypes and crucial pathogenic cell subsets remain controversial.

METHODS: We performed an integrated meta-analysis of single-cell sequencing data from our center along with four other scRNA-seq libraries (GSE247238, GSE235436, GSE155512, GSE159677) to generate a comprehensive map of human atherosclerotic plaques, including both coronary arteries with no discernible atherosclerotic lesions and diseased carotid plaques. To validate our conclusions, three independent datasets were used, including two bulk transcriptomics datasets and one proteomics dataset (GSE28829, GSE16315 and PXD031052). Besides, the Biobank of Karolinska Endarterectomy (BiKE) dataset was used for Kaplan–Meier (KM) analysis. Comparative analyses were performed between the groups, including cellular compositional analysis, cell type–resolved transcriptomic changes, and functional analysis.

RESULTS: The final integrated single-cell dataset, comprising 134,710 cells, consisted of 8 major cell types. The annotated cell subpopulations were generally present across the various studies, but their proportions varied between different studies. Pathway analysis identified that the most significantly impacted pathways were those associated with immune cell functions and cellular metabolism. Notably, SPP1 is highly expressed in macrophages. Survival analysis showed significantly lower ischemic event-free survival in the high SPP1 expression group compared to the low expression group. Besides, compared to atherosclerotic plaques with early stage (EA), non-intraplaque hemorrhage (IPH), and non-calcified conditions, SPP1 expression was highly up-regulated in all stages of plaque progression, including advanced plaques (AA), hemorrhagic plaques, and calcified plaques. Meanwhile, the differences in cellular composition and transcriptomic profiles between the lesion and non-lesion groups further highlighted the significance of lipid metabolism-related SPP1^hi foamy macrophages.

CONCLUSIONS: We created a unified atlas of human atherosclerosis informing cell state-specific mechanistic and translational studies of cardiovascular diseases. SPP1^hi foamy macrophages contributed importantly to AS progression.