scRNA-seq reveals transcriptionally distinct monocyte or macrophage populations in the liver of A/A and S/S mice. (A) Dot plot showing the expression of monocyte or macrophage makers in different cell clusters identified using liver single cells from 4 groups of mice (2-month-old): A/A and S/S mice at baseline (n = 2 mice per genotype), and A/A and S/S mice after TNF challenge (n = 2 mice per genotype). (B) Uniform Manifold Approximation and Projection (UMAP) showing the monocyte and macrophage populations from panel A. (C) Comparison of the monocyte or macrophage numbers between baseline A/A and S/S mice (top), and between baseline S/S and TNF-challenged S/S mice (bottom). (D) UMAP showing a total of 19 cell clusters (0-18) derived from the livers of TNF-challenged 2-month-old A/A (n = 2) and S/S mice (n = 2). (E) Heat map showing the differentially expressed genes across subsets of macrophages in the liver. Seven groups of transcriptionally distinct macrophages were identified in the liver of TNF-challenged A/A and S/S mice. The color key to the right of the heat map indicates the gene expression levels (high-to-low expression corresponding to yellow to cyan). (F) Trajectory analysis of the different macrophage subsets. The differences in cell distribution between TNF-challenged A/A (blue) and S/S (orange) mice are shown in the t-distributed stochastic neighbor embedding (t-SNE) map, and the cell cluster exhibiting the most different transcriptomic profile is circled in red, which corresponds to Kupffer cells (cluster 2). (G) Bubble plots showing functional annotations of the upregulated biological processes (top) and KEGG pathways (bottom) in Kupffer cells from the livers of TNF-challenged S/S mice when compared with those from the livers of TNF-challenged A/A mice. In the bubble plots, the bubble size represents the number of enriched genes whereas the bubble color represents the P-value. Mono/mac, monocytes/macrophages; pMac, peritoneal macrophages.