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. 2024 Apr 5;12:RP91729. doi: 10.7554/eLife.91729

Figure 5. Endothelial cells (ECs) from ex vivo human atherosclerotic plaques show two major populations.

(A) scRNA-seq UMAP of different cell subtypes across 17 samples of ex vivo human atherosclerotic plaques. (B) Dot plot of top markers for each cell type. (C) Heatmap of pathway enrichment analysis (PEA) results generated from submitting 200 differentially expressed genes (DEGs) between endothelial cells 1 (Endo1) and endothelial cells 2 (Endo2). Rows (pathways) and columns (cell subtypes) are clustered based on -Log10(P). (E) Heatmap displaying expression of genes belonging to ribosome cytoplasmic pathway for Endo1 and Endo2.

Figure 5.

Figure 5—figure supplement 1. Characterization of RNA-seq profiles from ex vivo arterial samples.

Figure 5—figure supplement 1.

(A) UMAP displaying original clusters formed from scRNA-seq data taken from 17 samples across four studies of human ex vivo atherosclerotic plaques. Colors denote different clusters. (B) UMAP from (A). Colors denote anatomical location from which cells derived. (C) Stacked bar graph showing the distribution of anatomic location (red denoting carotid, blue denoting coronary arteries) from which cells derived. (D) Heatmap of pathway enrichment analysis (PEA) results from submitting top 100 differentially expressed genes (DEGs) (by ascending p-value) between ex vivo cell types. Rows (pathways) and columns (cell subtypes) are clustered based on -Log10(P). (E) PEA of the top 100 DEGs (by ascending p-value) for plasmacytoid dendritic cells (PDCs). (F) PEA of the top 100 DEGs (by ascending p-value) for neurons. (G) PEA of the top 100 DEGs (by ascending p-value) for basophils. Adjusted p-value<0.05 for DEGs submitted in (D–G).
Figure 5—figure supplement 2. Violin plots displaying upregulation of several EndMT markers in Endo2, compared to Endo1, including FN1, BGN, COL8A1, ELN, CCN1, FBLN5.

Figure 5—figure supplement 2.

Figure 5—figure supplement 3. Cross comparisons between in vitro and ex vivo RNA-based module scores.

Figure 5—figure supplement 3.

(A) Feature plots for each ex vivo module score across in vitro cells. Briefly, ex vivo module scores are generated using top marker genes for each ex vivo cell subtype. The Seurat function AddModuleScore is used to score each cell for visualization. (B) Violin plots displaying endothelial cells 1 (Endo1), endothelial cells 2 (Endo2), and vascular smooth muscle cell 5 (VSMC5) module scores for each perturbation across in vitro EC1–4. (C) Feature plots displaying distribution of Endo1 (red) versus Endo2 (green) module scores across in vitro cells. (D) Feature plots displaying distribution of Endo1 (red) versus VSMC5 (green) module scores across in vitro cells. (E) Feature plots displaying distribution of Endo2 (red) versus VSMC5 (green) modules scores across in vitro cells.
Figure 5—figure supplement 4. Heatmap and pathway analysis for marker genes of the VSMC5 ex vivo cluster.

Figure 5—figure supplement 4.

(A) Heatmap displaying average expression of VSMC5 maker genes (black arrow) across in vitro and ex vivo datasets. Rows (genes) and columns (cell subtypes) are clustered based on average expression for each given gene. (B) Pathway enrichment analysis (PEA) of the top 200 genes for VSMC5 (adjusted p-value<0.05).
Figure 5—figure supplement 5. Breakdown of ex vivo module scores across in vitro clusters and sample identity.

Figure 5—figure supplement 5.

(A) Violin plots of ex vivo Endo1 module scores across EC1–4. (B), Violin plots of ex vivo Endo2 module scores across EC1–4. (C) Violin plots of ex vivo VSMC5 module scores across EC1–4. Adjusted p-value for (A–C) generated using Wilcoxon rank sum test with continuity correction by setting the alternative hypothesis to ‘two.sided’.