Abstract 1522: Gene expression profiling (GEP) reveals Epithelial Mesenchymal Transition (EMT) genes selectively differentiating eribulin sensitive breast cancer cell lines.
Authors: Dezso Zoltan , Oestreicher Judith , Weaver Amy , Kadowaki Tadashi , Yanagimachi Mamoru , Matsui Junji , Agoulnik Sergei I. , Funahashi Yasuhiro 
Published: August 2014

Abstract
Objectives: Eribulin mesylate (ERI) is a simplified synthetic macrocyclic ketone analog of the marine sponge natural product halichondrin B and an inhibitor of microtubule dynamics. In this study, we investigated whether selective signal pathways were associated with ERI activity compared to paclitaxel (PTX), which stabilize microtubules, based on GEP using 3 cancer cell line panels in vitro.
Methods: In vitro anti-proliferation activity (IC50) was determined in 27 breast, 19 endometrial and 21 ovarian cancer cell lines treated with ERI and PTX. We performed GEP for the same cancer panels treated for 24 hours at conc. of 10 x IC50 using Affimetrix Human Genome U133 Plus 2.0 arrays. We applied paired t-test (p&lt;0.01,FC&gt;1.5) to identify genes significantly altered between treatments. Pathway enrichment was performed using Metacore and Ingenuity Pathway Analysis software. Cell lines were clustered by hierarchical clustering based on Pearson correlation.
Results: We determined the sets of genes differentially altered between ERI and PTX treatments in 3 cancer panels. Regardless of cancer panels, several tubulins (TUBA1B, TUBA1C, TUBA3D, TUBA4A, TUBB2C, TUBBG1, TUBB3, TUBB2A, TUBB2C, TUBB and TUBB6) had significantly lower expression in cell lines treated with ERI, compared to PTX. Our analysis revealed that expression profiles of the gene sets correlated with drug sensitivity in cancer panels (p=0.004 for ERI in breast cancer, p=0.06 for PTX in endometrial cancer, p=0.05 for ERI in ovarian cancer). Pathway enrichment analysis of the gene revealed that the common pathways altered between 2 treatments in 3 cancer panels were related to cytoskeleton remodeling (p&lt;0.002) and role of NEK in cell cycle regulation (p&lt;0.0005). We also identified pathways specific to cancer types. EMT was enriched in genes with significantly altered expression between the two drugs for breast (p=3.4e-07) and endometrial cancer (p=0.001), but not for ovarian cancer. Expression of genes from EMT pathway correlated with breast cancer ERI sensitivity (p=0.1) and endometrial cancer PTX sensitivity (p=0.07). In breast cancer most genes from the EMT signature were up-regulated in ERI resistant cluster, allowing us differentiate cell line sensitivity based on expression. In addition, we found selective signaling pathways were associated to drug sensitivity in breast cancer panels among clustered 394 pathways based on GEP (13 and 4 pathways for ERI and PTX respectively, p&lt;0.01).
Conclusion: GEP analysis showed that gene sets altered with ERI and PTX were correlated to drug sensitivity in vitro anti-proliferative activity among 3 cancer panels. Breast cancer is the best target to differentiate ERI sensitivity based on GEP compared to PTX and EMT genes are selectively related to ERI sensitivity.
Citation Format: Zoltan Dezso, Judith Oestreicher, Amy Weaver, Tadashi Kadowaki, Mamoru Yanagimachi, Junji Matsui, Sergei I. Agoulnik, Yasuhiro Funahashi. Gene expression profiling (GEP) reveals Epithelial Mesenchymal Transition (EMT) genes selectively differentiating eribulin sensitive breast cancer cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1522. doi:10.1158/1538-7445.AM2013-1522