Fig. 6

Distinct functions of stromal cells in liver tumors. A UMAP plot of scRNA-seq profiles from stroma cells separated into 4 cell clusters. Cells are colored according to different clusters. B UMAP plot showing 4 cell clusters in different types of tissues. C Dotplot showing the percentage of expressed cells and average expression levels of marker genes of 4 stroma cell clusters. D Tissue prevalence of major stroma cell clusters estimated by Ro/e scores. E Feature plots showing the expression levels of marker genes for vascular endothelial cells and lymphoid endothelial cells. F Differences in hallmark pathway activities scored by GSVA between endothelial cells in tumors (PTs + MTs) and non-tumor liver tissues (NTs). Shown are t values from a linear model, corrected for endothelial of origin. G Dotplot showing the percentage of expressed cells and average expression levels of angiogenesis- and immune activation-related genes in endothelial cells among three types of tissues. H Heatmap showing the activities of enriched transcription factors (TFs) in endothelial cells across three types of tissues. I Feature plot showing the activities (top) and the expression levels (bottom) of TFs HMGA1 and HEYL specifically activated in endothelial cells from MTs. J Metascape results of the significantly enriched signaling pathways by the genes highly expressed in MYH11+ fibroblasts. K Metascape results of the significantly enriched signaling pathways by the genes highly expressed in SERPINF1+ fibroblasts. L Heatmap of correlation analyses showing the similarity of signature genes between fibroblast cell clusters and epithelial cell clusters in fibroblasts and epithelial cells of scRNA-seq data. M Dotplot showing the percentage of expressed cells and average expression levels of epithelial-to-mesenchymal transition (EMT) effector genes in the two fibroblast clusters. N, O Scatter plot showing the correlation of signature scores between SERPINF1+ fibroblasts and EMT in PTs from the TCGA-LIHC cohort and MTs from the MT2020 cohort. P–R Semi-supervised pseudotime trajectory of fibroblasts and high-related epithelial clusters inferred by Monocle 2. P and Q Trajectory is colored by the pseudotime (P) or clusters (Q). R Ridgeline plot showing the order of appearance of cell clusters in time colored by clusters