Fig. 3

scRNA-seq analysis of macrophage subclusters. a UMAP plot showing the four subclusters of macrophages. b Fraction of macrophages in each subcluster in each treatment group. The subclusters are annotated with the same color scheme as a. c Representative marker genes in the macrophage subclusters. The size of the dots indicates percent cells expressing the gene, while the color of the dots indicates average gene expression level. d Functional enrichment analysis of genes upregulated in the Mac_0 subcluster, for each of the treatment group when compared to the PBS group. The size and color of the circles indicate the number of upregulated genes and the −log₁₀ adjusted p value, respectively, for the enriched terms indicated on the y-axis. e Gene concept network showing representative enriched terms for the genes upregulated in Mac_0 in the aPD-L1 plus aTGF-β group. The upregulated genes associated with the pathway are shown, with the color of the nodes representing log₂ fold change in gene expression relative to the PBS group. f Heatmap showing relative (z-scored per row) gene expression levels for differentially expressed chemokine genes in Mac_0