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Fig. 5 | Genome Biology

Fig. 5

From: Decoding the multicellular ecosystem of vena caval tumor thrombus in clear cell renal cell carcinoma by single-cell RNA sequencing

Fig. 5

Detailed characterizations of endothelial cells and myofibroblasts in ARTs, PTs and TTs. a UMAP plot showing the subtypes of endothelial cells derived from ART, PT and TT samples. Each cluster is color-coded according to cell type. b Bar plot illustrating the average proportion of each endothelial subtype among ARTs, PTs and TTs. c Heatmap showing the expression of marker genes in each subtype of endothelial cells. d Box plots illustrating the fraction of Endo2 subgroup in ARTs, PTs and TTs. p values were determined by a two-sided Wilcoxon test. e Box plots showing the percentage of Endo2 in paired PT and TT bulk RNA-seq samples, inferred by CIBERSORTx. p values were determined by a two-sided Wilcoxon test. f Kaplan-Meier plot showing that KIRC patients in the TCGA dataset with high expression of Endo2 signature had shorter progression free survival (PFS). g Heatmap of GSEA scores indicating the pathways significantly enriched in PTs or TTs. Extra. structure organization, extracellular structure organization. h UMAP plot showing the subtypes of myofibroblasts derived from the ART, PT and TT samples. Each cluster is color-coded according to cell type. i Bar plot illustrating the average proportion of each myofibroblast subtype among ARTs, PTs and TTs. j Heatmap showing the expression of marker genes in each subtype of myofibroblasts. k Box plot illustrating the average proportion of Myo2 subcluster among ARTs, PTs and TTs. p values were determined by a two-sided Wilcoxon test. l Box plot representing the proportions of subclusters of Myo2 in myofibroblasts between normal (N) and tumor (T) samples in the TCGA cohort. p values were determined by a two-sided Wilcoxon test. m Kaplan-Meier plot showing that KIRC patients in the TCGA dataset with high expression of CD248 had worse progression free survival (PFS). n Kaplan-Meier plot showing that patients from the sunitinib arm of the IMmotion150 cohort with a high Myo2 signature score had improved progression free survival. o Heatmap of GSEA enrichment scores for indicating gene sets significantly enriched in PTs or TTs. Collagen fibril organ, collagen fibril organization. Extra. structure organization, extracellular structure organization. EMT, epithelial- mesenchymal transition. p Violin and box plots demonstrating the expression levels of CD248, COL1A1, COL4A1, and FN1 between PTs and TTs. p values were determined by a two-sided Wilcoxon test. ***, p < 0.001

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