Figure 2.

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.