Fig 1: The origin of malignant T cells determines the tumor microenvironment.a UMAP plot shows non-T cells from the 10× Genomics dataset. Cells are colored by cell types (left) and molecular subtypes (right). b Summary of selected immune-associated ligand-receptor pairs between malignant T cells and the microenvironment in each subtgroup using CellPhoneDB. The size of each dot denotes the p value. The color gradient denotes the degree of interaction. Tu-TCyEM: malignant T cells in the TCyEM group. Tu-TCM: malignant T cells in the TCM group. Mac macrophages, B B cells, Epi epithelial cells, Endo endothelial cells, Myofib myofibroblasts. c 2D density plots show the M1 and M2 scores of macrophages in two groups from the 10× Genomics dataset. M1 and M2 score gene lists are provided in Supplementary Table 1. d Violin plots show the expression levels of selected genes of macrophages in the TCyEM and TCM groups (log2 fold-change >0.5, ***p < 0.001); Two-sided Mann–Whitney U-test. P = 9.98 × 10-30 (CD163), 9.24 × 10-27 (VEGFA), 4.01 × 10-10 (MAF), 4.17 × 10-6 (CCR5) and 3.52 × 10-18 (CCR1). e Violin plots show the expression levels of chemokine genes CCL5 and CCL4 of malignant T cells in the TCyEM and TCM groups (log2 fold-change >1, ***p < 0.001); Two-sided Mann–Whitney U-test. P = 0 (CCL5 and CCL4). f Immunofluorescence staining of CD40LG (green) and CD40 (red) on paraffin-embedded tissue. DAPI (blue) was used to visualize cell nuclei. Scale bar = 20 µm. Results are representative of three different samples. g Violin plots show the expression levels of Treg markers in the TCyEM and TCM groups (ns: not significant; ***p < 0.001; **p < 0.01); Two-sided Mann–Whitney U-test. P = 1 (FOXP3), 1.68 × 10-8 (LAG3) and 3.86 × 10-3 (TIGIT). h Multicolor IHC staining of tumor tissue samples to determine the expression levels of CD4 (green), granzyme A (magenta), CD163 (orange) and CD8 (yellow) in Panel 1 and the expression levels of TOX (green), CD20 (magenta), FOXP3 (white) and LAG3 (red) in Panel 2. DAPI (blue) was used to visualize cell nuclei. Scale bar = 100 µm. Results are representative of three different samples. See also Supplementary Fig. 4g. Source data relating genes in (a) and (c) are provided in the Source Data file.