Differential gene expression patterns in HER2/neu-positive and -negative breast cancer cells

Overexpression of the oncogene HER2/neu (c-erbB-2) occurs in up to 30% of breast cancers and is correlated with reduced survival, especially in node positive disease. The aim of this study was to identify genes associated with the aggressive phenotype of HER2/neu-positive breast cancer cells using cDNA microarrays. Methods: RNA was extracted from three HER2/neu-positive and three HER2/neu-negative breast cancer cell lines. Pooled RNA was hybridized in duplicate to the breast specific microarrays from Research Genetics containing 5184 unique cDNAs. The phosphor images were compared in triplicate using Pathways™ software. Subsequently, a similar comparison was performed for pooled RNAs from 10 node positive, ER+ invasive ductal carcinomas, half of which were HER2/neu overexpressors. Results: In HER2/neu overexpressing breast cancer cell lines, 92 (1.8%) genes were upregulated and 46 (0.9%) downregulated, compared to cell lines with low HER2/neu protein levels. In contrast, in HER2/neu overexpressing primary breast cancers, more genes were downregulated (n=135,2.6%) than upregulated (n=19,0.4%). No genes were upregulated, and only a small number of genes were downregulated both in cell lines and in carcinomas overexpressing HER2/neu. These included transforming acidic coiled-coil containing protein 1, glycogen phosphoiylase BB, complement 1q and one EST. The differential expression of select genes was confirmed by Northern blotting (trefoil factor 3) or by immunocytochemistry (vimentin). Conclusion: This study demonstrates that cDNA microarrays can be used to identify a significant number of genes that are up- or downregulated in HER2/neu overexpressing breast cancer cells. Many of these genes have previously not been known to play a role in human neoplasia. Interestingly, the gene expression profiles in vitro and in vivo are not congruent.