Fig. 3: T cell inhibitory states are differentially remodeled in GCPM progression. | Nature Communications

Fig. 3: T cell inhibitory states are differentially remodeled in GCPM progression.

From: Single-cell sequencing of ascites fluid illustrates heterogeneity and therapy-induced evolution during gastric cancer peritoneal metastasis

Fig. 3: T cell inhibitory states are differentially remodeled in GCPM progression.

a Uniform Manifold Approximation and Projection (UMAP) plot representing clusters of T/NK cells, colored by cluster. b The proportion of T/NK cells clusters in different groups from G0 (n = 4 samples), G1 (n = 4 samples), G2 (n = 10 samples) and G3 (n = 12 samples) Groups. Data are presented as mean values ± SEM (error bars); p-values are calculated by two-sided unpaired Student’s t-test. c Heatmap showing expression levels of selected genes of naïve, cytokines and effectors, inhibitory, co-stimulatory, Treg, NK cells, and proliferative markers in each T/NK cell cluster. d Dotplot showing the cytotoxic, inhibitory, naïve, proliferative, and Treg function scores of T/NK cells clusters in G0-G3 Groups. Dot size represents percent of expressing cells in each cluster and color represents z-score of normalized mean expression level of selected gene signatures. e Uniform Manifold Approximation and Projection (UMAP) plot of three clusters of cycling T cells, colored by cell cluster. f Histogram plot indicating the cell proportions of cycling T clusters in G0 (n = 4 samples), G1 (n = 4 samples), G2 (n = 10 samples), and G3 (n = 12 samples) Groups. Data are presented as mean values ± SEM (error bars); the p-values are calculated by two-sided unpaired Student’s t-test. g Developmental trajectory of cycling T cells inferred by Monocle 2 analysis, color-coded by cluster (left) and pseudotime (right). Each dot represents a single cell. h The distribution of cycling T cells is shown along pseudotime (upper panel), color-coded by T cell clusters. Heatmap showing dynamic expression changes of selected genes and related pathways along pseudotime (lower panel). i Curve plots showing dynamic changes of metabolism scores in cycling T cells along pseudotime. Point colors correspond to cell type colors in g. j Curve plots showing expression changes of function genes related to cytotoxic, naïve, and immune checkpoint genes in cycling T cells along pseudotime. Point colors correspond to cell type colors in g. Source data are provided as a Source Data file.

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