Fig. 4. Aberrant differentiation of luminal progenitor cells is accompanied by an altered microenvironment with tumour-promoting characteristics.

a Net difference in the number of potential interactions between any immune and epithelial cell types between stage 4 and stage 1. The number of potential interactions was estimated in each stage using cellphoneDB at an FDR of 0.05. b Graphs representing potential interactions for Rankl:Rank and Igf2:Igf2r for Stage 4 of tumourigenesis (top row) and 9dG (bottom row). Nodes represent cell types and edges represent significant interactions with the width of the edge illustrating the mean expression of ligand and receptor. The arrow of the edges represents the direction from ligand expressing to receptor expressing. c Gene expression for the paracrine signalling factors Rankl and Igf2 in hormone-sensing cells and the alveolar markers Csn2 and Wap in luminal progenitors and alveolar cells. Expression is scaled across gestation and tumourigenesis to 0 and 1. In the tumourigenesis panel, the X-axis represents the values of PC1 that were scaled by (PC1 + min(PC1))/max(PC1−min(PC1)) × 100 d UMAP for all immune cell types captured in the gestation and tumourigenesis dataset. e Interaction plot as in b for Spp1:Cd44 during stage 1 of tumourigenesis. Right panel shows mean log expression of Spp1 across epithelial cell types in the mammary gland across various conditions. Grey represents conditions with no cells of that particular cell type. f Barplot of relative frequency of T-lymphocytes during tumourigenesis. g Differential expression analysis of Tregs from old wild-type animals and Tregs from stage 1. h Distribution of macrophage populations during gestation and tumourigenesis as in g. Data in barplots represent the mean per stage. For all pregnancy time points n = 3 independent animals were analysed; for the tumourigenesis stages the sample sizes are specified in Supplementary Fig. 1a. FC fold change, FDR false discovery rate.