Abstract 114: Identification of HER2 oncogene-regulated genes and pathways from dynamic gene expression data
Authors: Bollig-Fischer Aliccia B. , Ethier Stephen P. 
Published: February 2011

Abstract
A fundamental tenet of cancer biology is that cell transformation is driven by oncogenes, activated forms of proto-oncogenes. Yet, we have poor understanding of how oncogenes transform cells and induce phenotypes not expressed by normal cells. To examine signaling by the HER2 proto-oncogene and activated oncogene, we studied how HER2 signaling affects gene expression in a panel of well characterized isogenic breast cell lines: non-transformed MCF10A cells, HER2 over expressing and partially transformed MCF10HER2 cells, and fully transformed MCF10HER2/E7 cells. Cells were treated with small molecule kinase inhibitors to block HER2 signaling and RNA was collected every 3 hours for 45 hours (16 time points). Whole genome expression profiling was performed using Illumina microarrays. Analysis of time series expression data in the three cell lines identified genes specifically down and up-regulated by the proto-oncogene compared to the activated oncogene. Among the genes that were most highly up-regulated specifically by activated HER2 were chaperone proteins such as SCG5, and the heat shock proteins HSP6 and HSPA1A. Genes that were the most down regulated specifically by the activated oncogene included CITED2, the gene for a transcription factor that suppresses HIF1a expression, and DKK1, the gene for a repressor of Wnt signaling. Ingenuity Pathway Analysis identified several canonical pathways that were enriched for HER2 regulated genes in the most transformed cells compared to the nontransformed cells. For example, HER2 signaling in transformed cells upregulated more genes in pathways associated with cell motility and invasion than in MCF10A cells. Further, HER2 signaling in MCF10A cells did not influence the expression of any genes in the glucocorticoid, NRF2, Wnt, HIF1a, or aryl hydrocarbon signaling pathways. By contrast, signaling by the activated HER2 oncogene in MCF10HER2 cells up-regulated several genes in these pathways, including NFKBIB, PCK2, BAX, HSP40. HER2 oncogene signaling in fully transformed MCF10HER2/E7 cells stimulated upregulatation of still more genes associated with these pathways, including SOX4, RARA, HSP70, HSP90, MAPK6, SHC1, LDHA, MMP3, SLC2A1, HRAS. Similar experiments were performed with SUM-225 cells, a human breast cancer cell line with HER2 gene amplification. Activated HER2 regulated similar pathways in the SUM-225 cells as in the HER2 transformed MCF10 cells. In addition, we observed a significant enrichment of pathways unique to the HER2-upregulated genes in the SUM225 cells, such as the Nanog signaling pathway that has a role in stem cell pluripotency. This study identified many genes specifically regulated by the HER2 oncogene in HER2-transformed cells. Associating these oncogene-regulated genes with signaling pathways and biological networks helps to shed light on the mechanisms by which the HER2 oncogene regulates the expression of transformed phenotypes.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 114.