Novel histo-proteomic subtyping of coronary atherosclerosis identifies CAPG as a key inflammatory driver in plaque destabilisation

Background The molecular heterogeneity underlying human coronary atherosclerosis progression remains poorly characterized. Integrating proteomic subtypes with histopathological stages may uncover novel drivers of plaque destabilization and therapeutic targets. Methods We applied proteomics to 317 human coronary artery samples across all modified AHA-defined histopathological stages, quantifying over 10,000 proteins. Unsupervised clustering identified five distinct molecular subtypes (C1–C5). Machine learning models were constructed to predict pathological stages based on these subtypes. These subtypes were integrated with single-cell RNA sequencing (381,592 cells) and spatial transcriptomics via deconvolution to identify cell-type-specific and spatially resolved targets. Functional validation of a candidate target was performed in vitro and in ApoE⁻/⁻ mice via knockdown and overexpression. Results Five proteomic subtypes strongly correlated with pathological stages. Notably, subtype C3 corresponded to fibroatheromas (FA) with fibrosis-related protein signatures, while subtype C4 corresponded to thin-cap fibroatheromas (TCFA) and exhibited strong inflammatory features, representing the transition to unstable plaques. Machine learning models based on these subtypes accurately predicted pathological stages. Through integrative analysis of single-cell data, spatial transcriptomics, and deconvolution of C3 and C4 proteomic profiles, we identified APOE+ foamy macrophages as the key cellular drivers of this transition, with these cells predominantly localized in lipid-rich core regions. Within this population, CAPG emerged as a plaque stage-specific pro-inflammatory regulator, showing progressive upregulation from early atherogenesis to rupture. Population-based evidence confirmed elevated plasma CAPG in CAD and MI patients, with genetic analyses supporting a causal role. In vivo, macrophage-specific CAPG knockdown attenuated lesion formation, necrotic core expansion, and macrophage infiltration, while overexpression exacerbated these phenotypes. Conclusion This study establishes a proteomic classification linking molecular subtypes to coronary plaque progression and identifies CAPG as a functionally critical inflammatory mediator in APOE+ foamy macrophages. CAPG represents a promising target for precision diagnostics and therapy in atherosclerotic disease.Figure 1Figure 2