Fig. 1

Both our RNA-seq data and the bioinformation datasets analyses showed that TIM is associated with immunogenicity, especially with CD8⁺ T cells. a GSEA analysis of differential gene profiles between TIM siRNA transfected breast cancer MCF-7 cells and controls. There are immune-related pathways, lipid metabolism-related pathways, and other pathways. b Top 10 immune-related pathways in GSEA analysis with our RNA-seq data. c The detailed figure of top GSEA enrichments related to GO immune response to the tumor cell in MCF-7 siTIM group. d Comparison of lymphocyte infiltration signature score between TIM high and low expression groups with TCGA BRCA dataset. e GSEA analysis of differential gene profiles between the TIM high and low expression groups in the TCGA BRCA dataset. The GSEA enrichment circle plot showed the category of pathways, detailed pathway names, regulation tendency, and enrichment score. Three major types of pathways were enriched: DNA repair-, metabolism-, and immune-related pathways. f Immunophenogram for the visualization of terms determining antigen processing (MHC), immune stimulation (immunostimulators), and immune suppression (immunoinhibitors). g Volcano plot for the immune subsets in BRCA of TCGA dataset based on the MCPcounter immune score. h Boxplots of different T cell- or CD8⁺ T cell-associated functions based on the ssGESA immune algorithm of the TCGA dataset. i UMAP visualization of the total cells profiled in GSE161529, with each cell color-coded for the associated cell type. jTIM expression in each cell type in the UMAP visualization of GSE161529. k Villon plot of TIM expression in each cluster of cells of GSE161529 within the UMAP algorithm. Significance was tested as described in “Methods” section: *p-value < 0.05; **p-value < 0.01; ***p-value < 0.001; ****p-value < 0.0001. TIM TIMELESS, GSEA Gene Set Enrichment Analysis, BRCA breast cancer, MHC major histocompatibility complex, UMAP Uniform Manifold Approximation and Projection