Figure S2.

Immune Cell Phenotyping in Breast Tumor and Non-Tumor Tissue, Related to Figure 2

(A) Gate for immune cells. (B) t-SNE plots of normalized expression of markers used to identify the main immune cell types among 40,000 representative immune cells of all samples. (C) t-SNE plot of immune cells colored by cluster. (D) Heatmap of normalized marker expression for 27 clusters. NK cells, natural killer cells; pDCs, plasmacytoid dendritic cells. (E) Diffusion maps showing the CD4⁺ and CD8⁺ T cell clusters as a phenotypic continuum. T-regs were omitted. (F-I) PD-1⁺ T cell frequencies in F) juxta-tumoral and tumor samples, G) ER⁺ and ER^- tumors, H) juxta-tumoral tissue and tumors by subtype, and I) tumors by grade. (J) T cell cluster frequencies in tumors by grade. (K-N) PD-L1⁺ TAM frequencies in K) juxta-tumoral and tumor samples, L) ER⁺ and ER^- tumors, M) juxta-tumoral tissue and tumors by subtype, and N) tumors by grade. (O) Myeloid cluster frequencies in tumors by grade. Wilcoxon rank-sum test was used for statistical analysis. ^∗ p < 0.05, ^∗∗ p < 0.01, ^∗∗∗ p < 0.001.