Fig. 4: Characterization of the immune landscape.

Decomposition of immune cell density scores by non-negative matrix factorization (NMF) into a W-matrix which shows the composition of the Meta-Markers (columns MM1-4) according to the densities scores (red scale) of each cell type (BC: B-cells, TC: T-cells, TREG: regulatory T-cells), proliferative state (p: Ki67+, np: KI67−, t: total) and regional location (Epi: Epithelium, Str: Stroma) and b H-matrix which classifies normal and DCIS regions into three immune states according to Meta-Markers. c Fraction of stromal and epithelial regions from samples in each immune state with high, low or no T-cells (T), B-cells (B) and regulatory T-cells (Treg) densities. d Immune-state comparison in 20 samples (rows) with matching normal (left column) and DCIS (right column) regions. e Expression of immune checkpoint receptors genes, PDCD1 and CTLA4 in each immune state. f GSEA normalized enrichment score (NES) for a Reactome gene set across immune states. g Distribution of the expression of the MHC-I complex scored by immunohistochemical staining in DCIS and normal adjacent regions. The median scores of the adjacent and DCIS region in each immune state are connected with a dotted line. Error bars in the box and whiskers plot represent 1.5 fold the interquartile range above (resp. below) the first (resp third) quartile of the distribution.