Abstract 115: An integrated framework of transcriptome analysis leads to mechanistic insights into the FTI/Taxol synergy
Authors: Gjyrezi Ada , Gümüş Zeynep H. , Van den Wyngaert Ilse , Talloen William , Göhlmann Hinrich W.H. , Weinstein Harel , Giannakakou Paraskevi 
Published: February 2011

Abstract
A novel class of anticancer agents, the farnesyltransferase inhibitors (FTIs), has exhibited modest activity in the clinic as single agents, but was found to have promising activity in combination with the microtubule-stabilizing drug Taxol (TX), both in vitro and in vivo models. Recent phase I and II oncology clinical trials with an FTI/TX combination have demonstrated a clinical benefit for a subset of patients refractory to previous taxane-treatment. However, the precise cellular machinery underlying the FTI/TX synergistic drug combination still needs to be better understood. To this end, we undertook an unbiased experimental/computational approach that combined (i) measurements of drug-mediated changes on tubulin biomarkers and overall survival; (ii) whole-genome transcriptome analysis; (iii) utilization of interaction and functional databases to identify functional and pathway connections, (iv) computational modeling and prediction based on an in silico model predictive of drug synergy.
Drug-induced transcriptome changes were examined using whole-genome Affymetrix HGU133 Plus 2 microarrays. The raw data were analyzed using two global statistical analysis methods (ANOVA and SAM). Gene changes that passed both tests, using a fold change criterion, were deemed significant and subjected to experimental validation by qPCR and siRNA. The transcriptome changes that were unique to the LNF/TX combination were evaluated in the context of detailed molecular interaction maps and groups of biological function. Our analyses identified several major network hubs that include: (i) repression of the mitotic spindle-checkpoint kinase, polo-like kinase 1 (Plk1) which is also implicated in carcinogenesis and was shown to directly bind and phosphorylate α- and β-tubulins. (ii) overexpression of CDKN1A and MDM2, both of which are shown to be inversely regulated by Plk1; (iii) overexpression of the class II beta tubulin isotype TUBB2A and of several heat shock protein such as HSPA1A and DNAJB9 and (iv) induction of the focal adhesion molecule paxillin (PXN). Interestingly, stable knockdown of protein farnesyltransferase mimicked the effects of FTI treatment and resulted in strong substratum attachment and migration defects suggesting that paxillin could be regulated by farnesyltransferase and its pharmacologic inhibitors. Functional studies to elucidate this mechanism are currently underway.
In summary, we demonstrate a combined experimental and computational approach that includes functional analysis, data-driven simulation and experimental validation, and its power to identify key cellular components, both known and novel, in the anticancer activity of drug combinations exhibiting therapeutic synergy.
(Supported by NCI P50 CA128613 & P01 CA116676)
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 115.