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. 2022 Apr 21;10(6):680–697. doi: 10.1158/2326-6066.CIR-21-0804

Figure 1.

Figure 1. Histology and molecular features of NMU-induced mammary tumors. Virgin SD female mice were injected intraperitoneally with NMU and tumors harvested at various times after NMU administration herein referred as the characterization cohort. A–E, Paraffin-embedded tumor sections were analyzed by H&E (A), trichrome (B), IHC analysis of p63 (C), immunofluorescence for Ki67 and SMA (D), and immunofluorescence for PR and ER (E). Shown are representative images of well-differentiated adenocarcinomas, which were 55 of 59 tumors in the cohort. Scale bar, 100 μm. F–I, WGS of EpCAM+ tumor epithelial cells harvested from 31 NMU-induced tumors from 23 unique rats. Liver from tumor-free animal was used as control. F, Tumor mutational burden and types of mutations. G, Mutations found in breast cancer–driver genes. H, Frequency of mutations in selected breast cancer–driver genes. I, Population frequency of genetic aberrations in key breast cancer pathways. J–L, FACS sorted EpCAM+ tumor epithelial cells from NMU-induced tumors harvested from 10 tumors from 8 unique rats were analyzed by RNA-seq. Red and blue indicates HRlow and HRhigh tumors, respectively. Green and orange marks small and large tumors, respectively. J, Heatmap of gene expression Z-scores depicting the RNA expression of hormone receptors and selected luminal transcription factors. K, Heatmap of row-normalized Z-scores of genes differentially expressed between large (>7 mm) and small (≤7 mm) tumors. L, Pathways enriched in large and small tumors. Red lines indicate pathways highlighted in text. Node size indicates the number of genes within the pathway, line width indicates the number of shared genes between two gene sets. All tests for significance used Mann–Whitney–Wilcoxon test using a threshold of P = 0.05 unless otherwise specified; error bars representative of SD; box-whisker plots indicate 0th, 25th, 50th, 75th, and 100th percentiles.

Histology and molecular features of NMU-induced mammary tumors. Virgin SD female mice were injected intraperitoneally with NMU and tumors harvested at various times after NMU administration herein referred as the characterization cohort. A–E, Paraffin-embedded tumor sections were analyzed by H&E (A), trichrome (B), IHC analysis of p63 (C), immunofluorescence for Ki67 and SMA (D), and immunofluorescence for PR and ER (E). Shown are representative images of well-differentiated adenocarcinomas, which were 55 of 59 tumors in the cohort. Scale bar, 100 μm. F–I, WGS of EpCAM+ tumor epithelial cells harvested from 31 NMU-induced tumors from 23 unique rats. Liver from tumor-free animal was used as control. F, Tumor mutational burden and types of mutations. G, Mutations found in breast cancer–driver genes. H, Frequency of mutations in selected breast cancer–driver genes. I, Population frequency of genetic aberrations in key breast cancer pathways. J–L, FACS sorted EpCAM+ tumor epithelial cells from NMU-induced tumors harvested from 10 tumors from 8 unique rats were analyzed by RNA-seq. Red and blue indicates HRlow and HRhigh tumors, respectively. Green and orange marks small and large tumors, respectively. J, Heatmap of gene expression Z-scores depicting the RNA expression of hormone receptors and selected luminal transcription factors. K, Heatmap of row-normalized Z-scores of genes differentially expressed between large (>7 mm) and small (≤7 mm) tumors. L, Pathways enriched in large and small tumors. Red lines indicate pathways highlighted in text. Node size indicates the number of genes within the pathway, line width indicates the number of shared genes between two gene sets. All tests for significance used Mann–Whitney–Wilcoxon test using a threshold of P = 0.05 unless otherwise specified; error bars representative of SD; box-whisker plots indicate 0th, 25th, 50th, 75th, and 100th percentiles.