Single-cell transcriptomics reveals zinc and copper ions homeostasis in epicardial adipose tissue of heart failure

Figures

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  Figure 1. ScRNA-seq analyses of EAT cells from neonates, infants, children, and adults with and without HF reveal their cellular subpopulations. (A) Cell sorting and single-cell data analysis workflow. (B) The cellular subpopulations within human EAT are visualized through UMAP plots, highlighting both cell identity and different groups. Each dot in the UMAP plots represents a cell, with distinct colors indicating specific cell types. (C) A heatmap is presented to display the differentially expressed marker genes across various cell types. The color gradient from blue to red signifies the expression levels, ranging from low to high. (D) Histograms of the proportions of each cell type in different groups. (E) Feature plots are provided to demonstrate the expression distribution of representative genes for the eight major cell types in EAT, with color-coded expression levels overlaid onto the UMAP plot.

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  Figure 2. Diverse subsets were identified in T-NK cells and functional changes suggested metabolic disorders of zinc and copper ions in CD4+ T cells in EAT of HF patients. (A) UMAP plots visualizing T-NK cell sub-clusters in human EAT based on cell identity (left) and different groups (right). (B) Marker genes for T-NK cell subtypes as displayed in a bubble chart. The expression of a gene is marked by the presence of a cercle, the size of which indicates the proportion of cells that expressing this gene. Color gradient from blue to red indicates a low-high level of expression. (C) A heatmap shows comparison of pathway activities across different CD4+ cell subtypes in Adults-Non HF and Adults-HF groups by GSVA. Pathway scores are normalized. (D-E) Pseudo-time trajectories of the CD4+ T cells inferred by Monocle analysis. Cells are colored based on cell type (D) and group (E). (F) Heatmap displaying expression patterns of top DEGs that cataloged into three major modules in a Pseudo-time manner. (G) The expression dynamics of genes in modules 1 and 3 under cell fate1 and cell fate 2 states (left), and their enriched biological progresses (right). (H) Bubble chart shows selected…

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  Figure 3. Functional changes in CD8+ T cells in EAT of HF patients. (A) Volcano plots illustrating the DEGs of CD8+ Tem1 (left), CD8+ Tem2 (middle), and CD8+ Tem3 (left) cell subsets between the Adults-Non HF and Adults-HF groups. Each dot represents a DEG, with green and red representing down- and up-regulated respectively. (B) Bar plots displaying the comparisons of pathway activities of CD8+ Tem1 (left), CD8+ Tem2 (middle), and CD8+ Tem3 (left) cell subsets between the Adults-Non HF and Adults-HF groups. (C-D) Pseudo-time trajectories of the CD8+ T cells inferred by Monocle analysis. Cells are colored according to cell type (C) and group (D). (E) A heatmap shows the expression patterns of top DEGs that assigned into three major modules in a pseudo-time manner. (F) The expression dynamics of genes in modules 1 and 3 under cell fate1 and cell fate 2 states (left), and their enriched biological progresses (right). (G) Bubble chart shows selected ligand-receptor interactions between CD8+ T cells and fibroblasts or SMCs.

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  Figure 4. Diverse subsets were identified in myeloid cells of EAT and functional changes in monocytes of HF patients. (A) Visualizing subclusters of myeloid cells in human EAT using UMAP plots by cell identity (left) and different groups (right). Each dot represents a cell, colored according to cell type. (B) Bubble chart of marker genes for each identified cell subtype in myeloid cells. The expression of a gene is marked by the presence of a cercle, the size of which indicates the proportion of cells that expressing this gene. Color gradient from blue to red indicates a low-high level of expression. (C) A heatmap shows comparison of pathway activities across different myeloid cell subtypes in Adults-Non HF and Adults-HF groups by GSVA. The scores of pathways are normalized. (D) Pseudo-time trajectory of the monocytes inferred by Monocle analysis. Cells are colored according to cell type. (E) The trajectories of CD14+ Mono, CD14+CD16+ Mono, and CD16+Mono in the Adults-Non HF and Adults-HF groups respectively. (F) A heatmap shows the expression patterns of top DEGs that assigned into three major modules in a Pseudo-time manner. (G) The top biological progresses enriched in each module. (H)…

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  Figure 5. Endothelial cells clustered into five subsets and their functional changes along the Pseudo-time trajectory in EAT of HF patients. (A) The visualization of these sub-clusters is depicted through UMAP plots, with each dot representing a cell and its color indicating the cell type. The UMAP plots display the different groups of endothelial cells. (B) Bubble chart of marker genes for each identified cell subtype in endothelial cells. The expression of a gene is marked by the presence of a cercle, the size of which indicates the proportion of cells that expressing this gene. Color gradient from blue to red indicates a low-high level of expression. (C) Bar plots shows the proportions of lymphatic endothelial cell in different groups. (D-E) Pseudo-time trajectory of the endothelial cells inferred by Monocle analysis. Cells are colored based on the predicted Pseudo-time (D) and groups (E). (F) A heatmap shows the expression patterns of top DEGs that assigned into three major modules in a Pseudo-time manner. (G) The top biological progresses enriched in each module.

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  Figure 6. Fibroblasts clustered into distinct cell subtypes and their functional changes along the Pseudo-time trajectory in EAT of different development stages. (A) The utilization of UMAP plots to visually represent fibroblast sub-clusters in human EAT, based on cell identity (left) and different groups (right), is demonstrated in this study. Each dot on the plot represents a cell, with color indicating the specific cell type. (B) A bubble chart is employed to display the marker genes associated with each identified cell subtype within the fibroblast population. The expression of a gene is marked by the presence of a cercle, the size of which indicates the proportion of cells that expressing this gene. Color gradient from blue to red indicates a low-high level of expression. (C) Bar plots shows the proportions of DLK1+ Fib in different groups. (D) GO enrichment analysis of marker genes of DLK1+ Fibs. (E) UMAP diagram of the RNA velocity of fibroblasts. (F) Pseudo-time trajectory of the fibroblasts inferred by Monocle analysis. Cells are colored based on different groups. (G) A heatmap shows the expression patterns of top DEGs that assigned into two major modules in a Pseudo-time manner.…

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  Figure 7. SMCs clustered into distinct cell subtypes and their functional changes along the Pseudo-time trajectory in EAT of HF patients. (A) The utilization of UMAP plots to visually represent SMC sub-clusters in human EAT, based on cell identity (left) and different groups (right), is demonstrated in this study. Each dot on the plot represents a cell, with color indicating the specific cell type. (B) A bubble chart is employed to display the marker genes associated with each identified cell subtype within the SMCs population. The expression of a gene is marked by the presence of a cercle, the size of which indicates the proportion of cells that expressing this gene. Color gradient from blue to red indicates a low-high level of expression. (C) Bar plots shows the proportions of CFD+ SMC in different groups. (D) GO enrichment analysis of marker genes of CFD+ SMCs. (E) Comparison of pathway activities between the Adults-Non HF and Adults-HF groups of CFD+ SMCs. (F) Pseudo-time trajectory of the SMCs inferred by Monocle analysis. Cells are colored based on different groups. (G) A heatmap is presented to depict the expression patterns of top DEGs assigned to two major modules, in a…