Abstract 3332: HER2-dependent RNA polymerase II binding in human breast tumors defines a regulon including a stem cell network
Authors: Rahmatpanah Farah , Chen Xin , Jia Zhenyu , Men Bozhao , McClelland Michael , Mercola Dan 
Published: May 2015

Abstract
HER2-positive breast cancer accounts for approximately 25% of all cases and has a poor overall prognosis in spite of gains in targeted therapy. Multiple modes of resistance have been identified. We identified genes regulated in HER2 positive disease as a means of understanding the mechanisms of aggression and resistance to therapy. Chip-on-chip with anti-RNA polymerase II (POL II) in breast cancer cell lines with little or no HER2 expression was compared to cells with very high HER2 expression. Compared to MCF-7 cells with little or no HER2 expression, cells engineered to express large amounts of HER2 exhibits new POL II binding to 606 identified genes. Many of these genes, 379 and 486, also exhibited POL II binding in two breast cancer cell lines with naturally occurring amplified HER2: MDA453 and BT474 respectively. These observations indicate that the expression of HER2 in MCF-7 cells causes a massive increase in the number of genes bound by POL II.
We performed whole genome expression analysis on the three HER2+/- cells and compared these to expression in 812 primary tumors stratified for HER2 +/- expression. Genes differentially expressed dependent on HER2 status were overwhelmingly regulated in the same direction in MCF7HER2, MDA453 and BT474 cell lines and in breast cancer tissues; 273/459 (60%), 335/502 (67%) and 349/502 (70%) respectively (Kappa ∼ 0.4, p &lt; 0.0001). The same comparisons were performed on randomly selected genes and kappa values were calculated for 1000 rounds. The random kappa values averaged ∼0.05 indicating minimal false discovery.
Second we identified genes that had HER2-dependent POLII binding in cell lines without significant expression. Of 737 such genes “poised” for expression, 113 were differentially expressed in breast tumors in a HER2 dependent manner, including a similar number of up and down-regulated genes in each class of tumors. We carried out pathway analysis of 113 “poised” genes identified having HER2-dependent POL II binding and exhibiting significant differential expression between high and low HER2-expressing breast cancer tissues. A pathway analysis tool (MetaCore) identified enrichment in GO terms for cell adhesion, regulation of translational initiation, inflammation, immune response especially for Interleukins -5 and 13, cytoskeleton remodeling, membrane domain ectodomain proteolysis (the proteolytic cleavage of trans membrane proteins and release of their extracellular domain), and development. The largest groups of genes are associated with stem cell and progenitor cell control as indicated by networks centered on NANOG and OCT3/4. Thus, the role of stem cells proliferation in HER2 regulated breast cancer is highly suggested. The massive gene regulation changes that are tissue context-dependent is a fundamental new insight for understanding HER2 mechanisms in breast cancer.
Citation Format: Farah Rahmatpanah, Xin Chen, Zhenyu Jia, Bozhao Men, Michael McClelland, Dan Mercola. HER2-dependent RNA polymerase II binding in human breast tumors defines a regulon including a stem cell network. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3332. doi:10.1158/1538-7445.AM2014-3332