Extended Data Fig. 6: T-cell expansion according to BC subtype and in patients receiving neoadjuvant chemotherapy followed by anti-PD1.
From: A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer
a, UMAP pre- and on-treatment color-coded for expanded clonotypes in TNBC (n = 5; upper panel) and ER+/HER2± (n = 3; lower panel) Es. b, Relative contribution of T-cells pre-treatment in Es, comparing TNBC (n = 5) and ER+/HER2± (n = 3). c, Volcano plots showing DEGs for CD8+ expanding T-cells in TNBC versus ER+/HER2± Es pre-treatment (left panel) and on-treatment (right panel). d, Volcano plots showing DEGs for CD4+ expanding T-cells in TNBC versus ER+/HER2± Es pre-treatment (left panel) and on-treatment (right panel). e, UMAP of 50,693 cells from n = 11 BC patients with neoadjuvant chemotherapy followed by anti-PD1 (replication cohort or cohort 2) by scRNA-seq color-coded for the indicated cell type. f, Relative contribution of each cell type (in %) pre-treatment in the replication cohort, comparing Es (n = 3) versus NEs (n = 8). g, Normalized PD1 expression in T-cells (cohort 2). h, Relative contribution of each T-cell phenotype (in %) on-treatment in the replication cohort, comparing Es (n = 3) versus NEs (n = 8). i, Volcano plot showing DEGs between pre-treatment T-cells that expand (n = 347 cells) versus those that do not expand (n = 3159 cells) in the replication cohort. j, ROC curve based on the average module expression of TH1-activity and our 50-gene signature in CD4+ T-cells (excluding TREG) pre-treatment to predict T-cell expansion. AUC values and 95% confidence intervals are shown. Black dots in Volcano plots (panels c, d and i): P=ns; gray: P < 0.05; red: P < 0.05 and absolute log2FC≥0.5. P values Volcano plots by MAST test and Bonferroni-corrected (Seurat). Genes in bold are discussed in the manuscript. Panels b, f and h: exact P values by two-sided (b) or one-sided (f,h) Mann-Whitney test; *P < 0.05, *P < 0.01, ***P < 0.001. Panels b, f and h: box, median ± interquartile range; whiskers, minimum and maximum. Panel g: **P < 0.01, ***P < 0.001 by MAST test (Seurat).
