Abstract Body: Background Despite extensive efforts to understand single-cell mechanisms driving plaque formation and stabilization in coronary artery disease (CAD), defining true cell–cell interactions remain challenging without critical information about cellular spatial organization. Here, we present a spatially resolved transcriptomic atlas of human atherosclerotic coronary plaques across disease stages, enabling the investigation of cellular states and interactions in their native tissue context.
Methods Spatial transcriptomics was performed using Visium HD on 38 coronary artery tissue sections from 32 individuals with varying disease stages. Image-based nuclei segmentation was applied at 4um to approximate single-cell resolution by aggregating transcripts at the cellular level. Level 1 and 2 cell type annotation was performed using the Metaplaq v2 integrated single-cell vascular atlas as a reference (n=279,155 cells). We then inferred spatial patterns of cell signaling activation and ligand-receptor co-expression.
Results By profiling an average of 13500 genes per sample, we identified 10 major vascular and immune cell populations, marked by both known and novel cell-specific markers. We identified 8 distinct smooth muscle cell (SMC) subtypes with defined anatomical localization and enriched biological processes. Contractile SMCs localized to the media, transitional SMCs to both media and fibrous cap, and fibrochondrocytes to the intima. Fibromyocytes were enriched in the intima and fibrous cap, while foam-like SMCs localized primarily to the intima and were largely absent from the fibrous cap. Across samples, TGFβ signaling was consistently active in medial contractile SMCs. In advanced plaques, JAK–STAT and TNFa signaling were enriched in the intima and plaque shoulder regions. Macrophages were observed adjacent to foam cells and surrounded by fibrochondrocytes in the shoulder regions, suggesting localized cellular niches that may contribute to plaque stability. Ligand–receptor analyses of these niches revealed APOE–TREM2, S100A9–CD68, and SPP1–CD44 co-expression, consistent with macrophage transition toward foam cell.
Conclusions: By resolving cell states, signaling pathways, and cell–cell interactions, this work provides a framework for linking plaque architecture to underlying molecular mechanisms in coronary artery disease and highlights the importance of spatial context in defining cell interactions within atherosclerotic plaques.