Spatio-temporal dynamics of autophagy-associated genes in macrophage-driven atherosclerosis: an integrated omics and...

Atherosclerosis (AS) is a leading cardiovascular disease driven by lipid metabolism dysregulation and immune maladaptation. Although macrophage autophagy modulates plaque stability, the specific autophagy-related genes governing AS progression, particularly in spatial and immune contexts, remain poorly defined. This study aimed to systematically identify and characterize key macrophage autophagy-associated genes in AS using an integrated multi-omics approach.

Transcriptomic datasets (GSE270260, GSE100927) and single-cell RNA-seq data (GSE260657) were analyzed. Machine learning (LASSO and RF-SVM) screened for core autophagy-related genes. Their diagnostic value was evaluated using ROC and decision curve analysis. Immune infiltration, functional enrichment (GO/KEGG/GSEA), single-cell clustering, pseudotemporal trajectory analysis, and spatial transcriptomic mapping were performed. In vitro validation was conducted in ox-LDL-induced macrophages via qPCR, western blot, and immunofluorescence.

Three autophagy-related genes-SNX5, SMG1, and GSK3A-were identified as core regulators. They showed strong diagnostic potential for AS (combined AUC = 0.844) and correlated significantly with immune cell infiltration, particularly B cells and macrophages. Functional enrichment linked them to metabolic reprogramming and immune-inflammatory pathways, including NF-κB. Single-cell and spatial analysis revealed distinct expression patterns across plaque regions and cell types, with pseudotemporal trajectory indicating dynamic upregulation of GSK3A and SMG1 during macrophage-to-foam cell transition. In vitro experiments confirmed their upregulation at mRNA and protein levels upon ox-LDL induction.

SNX5, SMG1, and GSK3A are pivotal regulators of macrophage lipid handling and immune modulation in AS, exhibiting dynamic spatiotemporal expression within plaques. These genes represent promising diagnostic biomarkers and potential therapeutic targets for stabilizing atherosclerotic plaques.