Fig. 4

Identification and characterization of malignant cells in primary tumors and tumor thrombus. a, b Heatmaps showing large-scale CNVs for individual malignant cells (rows) from P02 (left) (a) and P06 (right) (b). Endothelial cells and myofibroblasts were treated as references (top), and malignant cells were observed in PTs and TTs (bottom). The color bar red indicates amplifications, and blue indicates deletions. c UMAP plot representing the subtypes of malignant cells from PT and TT samples. d UMAP plot showing malignant cells derived from PTs and TTs, colored by tissue origin. e UMAP plot illustrating color-coded tumor cells, according to each patient. f Differentially expressed pathways were scored per cell by GSVA among 4 malignant cell subtypes. g GSEA of the interferon-γ (IFN-γ) signaling pathway and antigen presentation and processing (Antigen Proc. and Pres.) enrichment scores in all malignant cells in PTs compared with in TTs; collagen containing extracellular matrix (Collagen conta. Extra. matrix) and response to metal ion enrichment scores in all tumor cells in TTs compared with in PTs. h Heatmap depicting the differential expression fold change of PTs compared with TTs for immune checkpoint and evasion-related genes. i Box plots showing the fraction of CD274⁺ and COL4A1⁺ tumor cells in PT and TT single-cell samples. p values were determined by a two-sided Wilcoxon test