Extended Data Fig. 4: Analysis of expanding T-cells trajectories. | Nature Medicine

Extended Data Fig. 4: Analysis of expanding T-cells trajectories.

From: A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

Extended Data Fig. 4

a, Barplots showing TCR richness for the indicated CD8+ T-cell phenotype. b, Clonotype sharing (thickness indicates proportion of sharing) between CD8+ T-cell phenotypes. c, Expression dynamics of transcription factors (TFs) along the CD8+ TEX-trajectory. d, Density plots reflecting the relative number of T-cells combined. e, Violin plots showing expression of T-cell effector, cytotoxicity and exhaustion markers in CD8+ TEX-cells on-treatment. ***P < 0.001 by two-sided Wilcoxon rank sum test per gene. f, LAMP1 expression by CITE-seq. ***P < 0.001 by two-sided Wilcoxon rank sum test and Bonferroni-corrected (Seurat). g, Cell cycle scores along the CD8+-trajectories pre- and on-treatment in E versus NE. h, Heatmap (left panel) and 2D density UMAP (right panel) showing that the major CD4+ T-cell phenotypes (CD4+ TN, TEM, TEX) can be split into subclusters with corresponding marker genes. i, Barplots showing TCR richness for the indicated CD4+ T-cell phenotype. j, Clonotype sharing (thickness indicates proportion of sharing) between the CD4+ T-cell phenotypes. k, Density plots reflecting the relative number of T-cells combined. l, Violin plots showing expression of T-cell effector, cytotoxicity and exhaustion markers in CD4+ TH1- and TFH-cells on-treatment. ***P < 0.001 by two-sided Wilcoxon rank sum test per gene. m, Cell cycle scores along the CD4+-trajectories. Gray shades in panel c, g and m represent the 95% confidence interval at any given pseudotime.

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