Single-cell gene-regulatory networks of advanced symptomatic atherosclerosis were analyzed using single-cell RNA sequencing data from 16,588 cells isolated from atherosclerosis progression in Ldlr-/-Apob100/100 mice and from humans with asymptomatic and symptomatic carotid plaques. The data were clustered into multiple subtypes, and advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET study. The results showed that advanced stages of atherosclerosis and symptomatic carotid plaques were characterized by three smooth muscle cell (SMC) subtypes and three macrophage subtypes with extracellular matrix organization/osteogenic and M1-type proinflammatory/Trem2-high lipid-associated phenotypes. Integrative analysis of these six clusters with STARNET revealed significant enrichments of three arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage), which contributed to coronary artery disease heritability and were strongly associated with clinical scores of coronary atherosclerosis severity. GRN39 was validated in five independent RNAseq datasets and experimentally in human vascular smooth muscle cells. The study concluded that GRN39 is critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced, symptomatic atherosclerosis. The study provides a comprehensive understanding of the pathophysiological and clinical relevance of the identified cell subtypes and gene-regulatory networks in atherosclerosis.Single-cell gene-regulatory networks of advanced symptomatic atherosclerosis were analyzed using single-cell RNA sequencing data from 16,588 cells isolated from atherosclerosis progression in Ldlr-/-Apob100/100 mice and from humans with asymptomatic and symptomatic carotid plaques. The data were clustered into multiple subtypes, and advanced-stage and symptomatic subtype clusters were integrated with 135 tissue-specific gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients in the STARNET study. The results showed that advanced stages of atherosclerosis and symptomatic carotid plaques were characterized by three smooth muscle cell (SMC) subtypes and three macrophage subtypes with extracellular matrix organization/osteogenic and M1-type proinflammatory/Trem2-high lipid-associated phenotypes. Integrative analysis of these six clusters with STARNET revealed significant enrichments of three arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage), which contributed to coronary artery disease heritability and were strongly associated with clinical scores of coronary atherosclerosis severity. GRN39 was validated in five independent RNAseq datasets and experimentally in human vascular smooth muscle cells. The study concluded that GRN39 is critical for the transformation of contractile SMCs into an osteogenic phenotype promoting advanced, symptomatic atherosclerosis. The study provides a comprehensive understanding of the pathophysiological and clinical relevance of the identified cell subtypes and gene-regulatory networks in atherosclerosis.