Extended Data Fig. 5: Expression signatures and phenotypes predictive of T-cell expansion. | Nature Medicine

Extended Data Fig. 5: Expression signatures and phenotypes predictive of T-cell expansion.

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

Extended Data Fig. 5

a,b, Volcano plot showing DEGs between CD8+ (a) and CD4+ (b) T-cells that expand versus those that not expand pre-treatment. Black dots: P=ns; gray: P < 0.05; red: P < 0.05 and absolute log2FC≥0.5. P values by MAST test and Bonferroni-corrected (Seurat). Genes in bold are discussed in the manuscript. c-d, GSEA (hypeR) on genes up- or down-regulated in pre-treatment T-cells that expand (c) versus T-cells that do not expand upon treatment (d) on REACTOME (upper panel) and GO (lower panel) pathways. e, Scatterplots showing Spearman correlations between the number of expanded clonotypes versus the abundance of phenotypes, or average expression of marker genes and signature module scores per patient. Signature module scores were calculated using the Seurat function AddModuleScore per cell and then averaged per patient. P values by two-sided Spearman’s rank correlation test. R values are Spearman’s rank correlation coefficients (rho). f, ROC curve based on the average module expression of our 50-gene signature in CD4+ T-cells (excluding TREG) pre-treatment to predict T-cell expansion. AUC-value and 95% confidence interval are shown. g, Heatmap showing protein expression of 7 immune stimulation-induced immune-checkpoints in all T-cells, CD8+ and CD4+ T-cells.

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