Fig. 3: The cellular state and function of CD4⁺ T cells, CD8⁺ T cells, and myeloid cells.

a UMAP plot showing the distribution of CD4⁺ T cell subsets. b Bar graphs showing the percentages of TCR expanded clonotypes in the CD4⁺ T cell subsets. c Bar graphs showing the percentage of Tregs (CD4-Treg) among the total CD4⁺ T cells in different sample types (n = 50 samples from 22 patients). d UMAP plot showing the distribution of CD8⁺ T cell subsets. e Dot plot showing the highly expressed marker genes in each CD8⁺ T cell subset. The dot size represents the percentage of cells expressing the marker genes in each cell type, and the dot color represents the average expression level of the marker genes in each cell type. f Bar graphs showing the percentages of TCR expanded clonotypes in the CD8⁺ T cell subsets. g Bar graphs showing the percentages of cytotoxic CD8⁺ T cells (CD8-CTL), precursor exhausted CD8⁺ T cells (CD8-PEX), and transitory exhausted CD8⁺ T cells (CD8-TEX) among the total CD8⁺ T cells in different sample types (n = 50 samples from 22 patients). h Box plots showing the cytotoxic score and exhausted score in CD8⁺ T cells from different sample types (n = 22,813 cells). i UMAP plot showing the distribution of myeloid cell subsets. j Box plots showing the M1 scores (left) and M2 scores (right) in myeloid cell subsets (n = 42,618 cells). k Bar graphs showing the percentage of Macro_CCL4 among the total myeloid cells in different sample types (n = 50 samples from 22 patients). In h and j, the center line of the box represents the median value, the upper and lower limits of the box represent the 25th and 75th percentile points. In c, g, h and k, Wilcoxon rank sum test followed by Bonferroni’s multiple-comparison test. In c, g, and k, filtering out non-significant values when displaying significance levels. Source data are provided as a Source Data file. In c, h and k, AD adjacent normal gastric tissues, PT primary gastric tumors, OM ovarian metastases, PM peritoneal metastases, AS ascites samples.