This study investigates the single-cell gene expression patterns underlying the progression of atherosclerosis, focusing on the clinical and pathophysiological relevance of these changes. Single-cell RNA sequencing (scRNAseq) data from 16,588 single cells isolated from atherosclerosis progression in Ldlr-/-ApoB100/100 mice and human asymptomatic and symptomatic carotid plaques were analyzed. The data identified three smooth muscle cell (SMC) subtypes and three macrophage subtypes critical for advanced and symptomatic atherosclerosis. Integrative analysis with 135 tissue-specific gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients revealed significant enrichments of three arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage). GRN39, which was validated in five independent human datasets and experimentally in human vascular smooth muscle cells, was found to be critical for the transformation of contractile SMCs into an osteogenic phenotype, promoting advanced and symptomatic atherosclerosis. The study highlights the importance of GRN39 in understanding the molecular mechanisms underlying atherosclerosis progression and provides potential therapeutic targets.This study investigates the single-cell gene expression patterns underlying the progression of atherosclerosis, focusing on the clinical and pathophysiological relevance of these changes. Single-cell RNA sequencing (scRNAseq) data from 16,588 single cells isolated from atherosclerosis progression in Ldlr-/-ApoB100/100 mice and human asymptomatic and symptomatic carotid plaques were analyzed. The data identified three smooth muscle cell (SMC) subtypes and three macrophage subtypes critical for advanced and symptomatic atherosclerosis. Integrative analysis with 135 tissue-specific gene-regulatory networks (GRNs) inferred from 600 coronary artery disease patients revealed significant enrichments of three arterial wall GRNs: GRN33 (macrophage), GRN39 (SMC), and GRN122 (macrophage). GRN39, which was validated in five independent human datasets and experimentally in human vascular smooth muscle cells, was found to be critical for the transformation of contractile SMCs into an osteogenic phenotype, promoting advanced and symptomatic atherosclerosis. The study highlights the importance of GRN39 in understanding the molecular mechanisms underlying atherosclerosis progression and provides potential therapeutic targets.