Figure 4

Sorted ATG5^−/− macrophages display a typical transcription program. (A) Heat map of the genes differentially expressed (using a threshold of twofold change and p value < 0.05) between WT and ATG5^−/− hepatic macrophages isolated from mice after control or DEN treatment. (B) Venn diagram for upregulated (left) and downregulated (right) genes in DEN vs Control WT or ATG5^−/− macrophages. (C) Volcano plot of the differentially expressed genes of WT macrophages sorted from DEN-treated mice as compared to WT macrophages sorted from control mice. (D) Volcano plot of the differentially expressed genes of ATG5^−/− macrophages sorted from DEN-treated mice as compared to WT macrophages sorted from DEN-treated mice. (E) RT-PCR analysis of JunB mRNA expression in peritoneal macrophages isolated from WT or ATG5^Mye−/− mice (upper panel) and in peritoneal macrophages exposed to the conditioned medium of Hepa1-6 cells (CMH) in the presence or absence of 100 nM bafilomycin A or 100 nM rapamycin. Data are shown as mean ± SEM of 6 samples per condition. ^&p < 0.05 for WT vs ATG5^−/−, ^∇p < 0.05 for CMH vs CMH + bafilomycin A or CMH + rapamycin. (F) Gene ontology enrichment analysis show the top 10 modulated pathways by p-value enriched (false discovery rate, FDR) for genes significantly upregulated in ATG5^−/− macrophages isolated from DEN-treated mice. n = 3 for WT DEN, n = 4 for ATG5^−/− PBS, n = 3 for WT DEN; n = 4 for ATG5^−/− DEN.