Figure 3:
Impact of the Microenvironment on Breast Immune Cells
(A) Breast immune cell atlas constructed from combining all patient samples (BC1–8) and tissues using Biscuit, projected with t-SNE. Each dot represents a cell, colored by cluster; major cell types are marked according to Figure 2F, H and Table S2, 3.
(B) Subsets of immune atlas t-SNE in (A) showing cells from each tissue separately on the same coordinates as 3A to highlight the differences between tissue compartments.
(C) Proportions of cell types across tissue types.
(D) Distribution of variance of expression, computed for each gene across all immune cells (all patients), from tumor tissue compared to normal breast tissue.
(E) Most significant Hallmark GSEA enrichment results on genes with highest difference in variance in tumor T cells vs normal tissue T cells. See Figure S3B, C for enrichment in monocytic and NK cells. Full lists of enrichments are presented in Table S5.
(F) Phenotypic volume in log-scale (defined as pseudo-determinant of gene expression covariance matrix, detailed in STAR) of immune cell types in tumor compared to normal tissue, controlled for number of cells, showing siginificant (shown with asterisks) expansion of volume spanned by independent phenotypes in tumor compared to normal tissue.