Fig. 2: Single-cell RNA sequence characterization of SMC subcellular clusters in carotid plaques of female and male patients.
a, Subcellular clusters of human SMC carotid plaques visualized with UMAP. Ext_Fig1b, UMAP of major cell types. This shows that SMC cell types circled in black have been subclustered to get 9 subcellular clusters, SMC1–SMC9. b, Dot plot showing expression levels of functional gene markers within the SMC subclusters. SMC6 was excluded from further analysis because it emerged from only one patient. c, UMAP of SMC subcellular clusters highlighted for cells isolated from carotid plaques of female and male patients. d, Bar plots showing the relative sex specificity of SMC subcluster cells. The total number of cells in each category are shown in parentheses. P values were calculated using chi-square statistics assessing the statistical significance between observed and expected values. e, Volcano plot showing differentially expressed SMC3 genes (red, upregulated; blue, downregulated) using all other SMC subclusters as background. Cell-type-specific gene enrichment was calculated using the Wilcoxon rank-sum test (log2(fold) > 0.3, Bonferroni-adjusted P < 0.005). Dot plots show top-ranked biological processes according to GO. Gene ratios (x axis) are the relative number of subcluster genes in relation to the total gene count in each GO category. Dot size indicates the actual number of subcluster genes in each GO category. GO enrichment −log10(P values) were calculated with Fisher exact test. Cluster genes indicate the number of SMC3 subcluster genes overlapping with the GO category. ECM, extracellular matrix. f, Volcano plot showing differentially expressed SMC8 genes (red, upregulated; blue, downregulated) using all other SMC subclusters as background. Cell-type-specific gene enrichment was calculated using Wilcoxon rank–sum test (log2(fold) > 0.3, Bonferroni-adjusted P < 0.005). Dot plots show top-ranked biological processes according to GO. Gene ratios (x axis) are the relative number of subcluster genes in relation to the total gene count in each GO category. Dot size indicates the actual number of subcluster genes in each GO category. GO enrichment −log10(P values) were calculated with Fisher exact test. Cluster genes indicate the number of SMC8 subcluster genes overlapping with the GO category.
