Fig. 4.

HER2 overexpression promotes the transcriptional upregulation of hypoxia metagenes and HIF target genes in hypoxia. a Three hypoxic gene signatures (top: Winter et al. (2007), middle: Buffa et al. (2010), bottom: Toustrup et al. (2011)) reported to show genes commonly altered by hypoxia were assessed in microarray gene expression data of MCF7 and MCF7-HER2 cultured in normoxia, acute hypoxia or chronic hypoxia. In general, MCF7-HER2 showed a stronger induction of a large proportion of genes upregulated in acute and chronic hypoxia (red clusters), with no equivalent seen for MCF7 cells. In addition, the larger signatures contained clusters which appeared to be downregulated by hypoxia in MCF7. These were constitutively lower in MCF7-HER2 (blue clusters), suggesting an increased hypoxic response in terms of both upregulated and downregulated genes. Finally, a small cluster in the largest signature (green) showed no hypoxic response, but these genes were still constitutively higher in MCF7-HER2. b Hierarchical clustering of HIF target genes (as determined from combined gene lists of two references Mole et al. 2009 and Schӧdel et al. 2011 who used ChIP in MCF7 to identify HIF-1 and HIF-2 target genes) was used to assess the hypoxic upregulation of HIF target genes in MCF7 and MCF7-HER2 in acute hypoxia. A large proportion of HIF targets were either constitutively higher in MCF7-HER2 (green), more strongly induced in hypoxia in MCF7-HER2 (red), or downregulated in hypoxia whilst being constitutively low in MCF7-HER2 (blue). Beside this, a small proportion behaved similarly between cell lines (pink) or were more strongly induced in MCF7 (black)