Gene expression analysis of doxorubicin-treated tumors and cell lines reveals enrichment of phagocytosis signatures. (A–E) GSEA was performed with RNA-seq data from MMTV-Wnt1 mammary tumors (p53 wild type, red line; p53-null, black line) for NT (Ctl) versus doxorubicin-treated cells harvested 24 h after the final treatment (left panels); from control MCF-7 cells and MCF-7 cells 8 d after doxorubicin (0.5 µM) treatment (middle panels); and from NT 4226 cells versus cells 24 h (green line) and 8 d (blue line) after doxorubicin (0.75 µM) or treated for 24 h (red line) and 8 d (yellow line) with nutlin (15 µM every other day), as indicated. RNA-seq was performed on MCF-7 and 4226 using samples from three independent experiments each. RNA was extracted from six doxorubicin-treated and six NT MMTV-Wnt1 tumor samples and sent for sequencing. GSEA was performed for “HALLMARK_E2F_TARGETS” (A); KEGG_LYSOSOME (B); GO_PHAGOCYTOSIS_ENGULFMENT (C); GO_PHAGOCYTOSIS (D); and genes involved in macrophage sensing their environment as listed in Ley et al. (2016) (E). Enrichment scores (ES) were plotted. Statistical analysis using GSEA software is provided as false discovery rate q values (significance at false discovery rate q < 0.25) in Table S2. GO, gene ontology.