Fig. 3

Detailed characterization of myeloid cells in primary tumors and tumor thrombus. a UMAP plot showing the subtypes of myeloid-derived 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 myeloid subtype among ARTs, PTs and TTs. c Heatmap showing the expression of marker genes in each subtype of myeloid-derived cells. d Box plots illustrating the fraction of the subclusters of Macro1–3 and neutrophils in ARTs, PTs and TTs. p values were determined by a two-sided Wilcoxon test. e Dot plot showing the percentage of cells and expression level in each cell type expressing immune checkpoint and evasion-related genes. f Violin plots representing the expression levels of M1, M2 and TAM marker genes in macrophage subtypes. p values were determined by a two-sided Wilcoxon test. g Heatmap of GSEA scores indicating the pathways significantly enriched in PTs or TTs. INF-γ, interferon- γ. INF-α, interferon- α. Antigen Proc. and Pres., antigen presentation and processing. Extra. structure organization, extracellular structure organization. EMT, epithelial-mesenchymal transition. h Violin and box plots comparing the expression distributions of immune checkpoint and evasion-related genes and ECM remodeling and angiogenesis-related genes between PTs and TTs. p values were determined by a two-sided Wilcoxon test. ***, p < 0.001