The Breast Cancer Immune Landscape
(A) Frequencies of selected immune cell types in juxta-tumoral and tumor samples.
(B) t-SNE plots of the normalized marker expression of 40,000 T cells from all samples.
(C) t-SNE of T cells colored by PhenoGraph cluster.
(D) Heatmap of normalized T cell marker expression for 20 T cell clusters. CM, central memory; Eff/Mem, effector and memory; Reg, regulatory; PD-1, PD-1+.
(E) Boxplots showing the frequencies of the CD4+ (left) and CD8+ T cell clusters (right) in juxta-tumoral and tumor samples.
(F) PD-1+ T cell frequency (top) and mean PD-1 expression (bottom) among tumor-derived CD4+ and CD8+ T cells.
(G) Comparison of the PD-1+ T cell frequency and mean PD-1 expression for CD8+ (top) and CD4+ T cells (bottom).
(H and I) Frequencies of selected T cell clusters in (H) ER+ and ER− tumors and (I) luminal A and B tumors.
(J) t-SNE plots of normalized marker expression of 40,000 myeloid cells from all samples.
(K) t-SNE of myeloid cells colored by PhenoGraph cluster.
(L) Heatmap of normalized myeloid marker expression for 19 myeloid clusters. Mono, monocyte; T.-res, tissue-resident; E. im., early immigrant; TAM, tumor-associated macrophage; MDSC, myeloid-derived suppressor cell.
(M) Frequencies of the myeloid clusters in juxta-tumoral and tumor samples.
(N and O) Frequencies of the indicated myeloid clusters in (N) ER+ and ER− tumors and (O) luminal A and B tumors.
Wilcoxon rank-sum test was used for statistical analysis. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001. See also Figure S2.