Fig. 2

scRNA-seq of EMT6 tumors from mice treated with anti-PD-L1 ± anti-TGF-β. a Single-cell transcriptomes for all cells visualized on a Uniform Manifold Approximation and Projection (UMAP) plot. Cells are colored based on cell type annotations, as indicated in the legend. b UMAP plots for cells from individual treatment groups. Cell types are annotated with the same color scheme as a. c Number of up- (top panel) and down- (bottom panel) regulated genes in various cell types, when comparing each treatment sample to the PBS sample. d UMAP plot showing the two subclusters of fibroblasts. e Fraction of fibroblasts in Fib_0 (green) and Fib_1 (purple) in each treatment group. f Representative marker genes in the fibroblast subclusters. The size of the dots indicates percent cells expressing the gene, while the color of the dots indicates average gene expression level. g Functional enrichment analysis of genes downregulated in the Fib_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 downregulated genes and the −log₁₀ adjusted p value, respectively, for the enriched terms indicated on the y-axis. h Gene concept network showing representative enriched terms for the genes downregulated in Fib_0 in the aPD-L1 plus aTGF-β group. The downregulated 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. i Heatmap showing relative (z-scored per row) gene expression levels for representative differentially expressed genes in Fib_0