Fig. 4: Communication of malignant cells and non-malignant cells.

a Ligand–receptor interactions of malignant cells and non-malignant cells in six cases with viable malignant cells. Each column indicates a ligand–receptor pair, with the first and the second gene representing a ligand and a receptor, respectively. Each row represents a non-malignant cell type that interacts with malignant cells. The direction of an interaction is indicated by colored dot. Purple, malignant cells provide ligands and interact with receptors from non-malignant cells in the TME; green, non-malignant cells in the TME provide ligands and interact with receptors from malignant cells. The size of each dot represents the proportion of tumor regions within each case in identifying a specific interaction pair, with 1 indicating occurrence in all tumor regions and 0 indicating occurrence in none of the tumor regions. b Illustration of ligand–receptor interactions of tumor and the TME. Purple dots, ligands from tumor; green dots, ligands from TME. c Stacked bar plot of the percentage of ligand–receptor pairs in each individual case found in certain proportion of tumor regions. One means that a pair was found in all tumor regions within a case while zero means that a pair was found in none of the tumor regions. d Similarity of ligand–receptor interactions among multiple regions of different cases. Zero indicates no overlap of ligand–receptor interactions while 1 means a full overlap of ligand–receptor interactions between samples. e Illustration of switching TME and switching tumor. Switching TME indicates that tumor cells from one case are combined with TMEs from other cases to form distinct tumor ecosystems. Switching tumor indicates that TME from one case are combined with tumors from other cases to form distinct tumor ecosystems. f The proportion of matched ligand–receptor interactions from switching tumor or TME with the original search of using paired tumor and TME from the same case. Student’s t-test (two-sided) was applied with p value provided. b and e were generated using BioRender.