Extended Data Fig. 10: Shared age-related DE genes found in aging mouse mammary cells and human breast tumors (related to Fig. 8).

(a) Age distribution of donors from which human TCGA normal breast tissues (n = 112) and tumor samples (luminal A n = 547; luminal B n = 207; basal n = 183; Her2 n = 77; normal-like n = 39) included in this analysis were obtained. (b) PCA analysis (gene expression) of human TCGA normal breast tissues (n = 112) and tumors (luminal A n = 547; luminal B n = 207; basal n = 183; Her2 n = 77; normal-like n = 39), colored by tissue type, tumor subtype, or age. (c,d) Overlap between DE genes from TCGA breast tumors samples (luminal A n = 547; luminal B n = 207; basal n = 183; Her2 n = 77; normal-like n = 39) vs. normal breast tissues (n = 112) (Wald test with BH correction; log₂FC > |0.5 | , p_adj < 0.05) and DE genes from 18 M vs. 3 M mouse luminal AV (c) or HS (d) cells (n = 6 per age). (e) Normalized expression of DE genes overlapping between aging mouse luminal AV, luminal HS, or myoepithelial cells (18 M vs. 13 M) and human TCGA breast tumors (tumor vs. normal) for each tumor subtypes (luminal A n = 547; luminal B n = 207; basal n = 183; Her2 n = 77; normal-like n = 39). Top 15 upregulated and downregulated gene names are listed. (f) Z-score distribution of observed (red lines) and 10,000 simulated random (blue lines) DEGs shared between aging mouse luminal AV, or luminal HS cells (18 M vs. 13 M) and human TCGA luminal A (n = 547) or luminal B (n = 207) breast tumors (tumor vs. normal) (left panel). Significance of the top 10 enriched pathways comparing the observed and 1,000 simulated DEG lists shared between aging mouse cells and human tumors (right panel) (permutation test to calculate empirical p-value; *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001). See also Supplementary Table 8.