Abstract B29: Alternative splicing studies for the identification of novel cancer targets and markers.
Authors: Laurent Desire , Casagrande Anne-Sophie , Kotraiah Vin , Mahe Florence , Pando Matt 
Published: June 2012

Abnormal alternative splicing occurs in cancer, resulting in the production of novel transcript variants. Understanding the diverse mechanisms by which splicing dysregulation contributes to human disease will generate new perspectives for drug development and biomarkers identification.

The overall aim of this work is the generation of libraries of alternative splicing events that are deregulated in cancer and during anti-cancer treatments. The goal of these libraries is to be interrogated for the identification of novel biomarkers, allowing to monitor disease status, progression/relapse, and specificity/selectivity of drug response. The platform used is Exonhit's Genome Wide SpliceArray, a new generation of microarray that extends transcriptomic profiling to the monitoring of alternative splicing, thereby increasing the discriminatory power of the analyses. Here, we profiled different cancers to identify novel targets and markers that are either commonly regulated across multiple cancers or specific of a given cancer type. Alternatively spliced transcripts were isolated from breast, colon, and lung tumors and their corresponding adjacent normal tissues (20 each). Different splicing patterns were evidenced in tumoral versus normal tissues and from specificity analysis performed across a pool of 20 normal organs. Events of interest, focused on splicing events that generate potential novel amino acid sequences, were selected based on combination of statistical analysis of probe sets deregulations, protein knowledge and pathway analyses. The events were subsequently validated by QPCR analysis in these 3 cancers. These validated events will be used to identify novel cell surface epitopes for antibody development with therapeutic or diagnostic usefulness.

Following this same approach, we also performed a comparative analysis of the transcriptomic response of endothelial cells to tubulin polymerization inhibitors, in order to test the feasibility of identifying differential drug response markers. To do so, we profiled various tubulin inhibitors in an in vitro angiogenesis inhibition assay. HUVEC cells were induced to form neovessels in vitro in the presence or absence of the tested tubulin inhibitors. Then, microarray profiling was performed, followed by a detailed analysis with Ingenuity, focusing on up-regulated genes with biomarker potential.

Our results demonstrate that alternative RNA splicing offers a currently underexploited source of biological information for cancer research. Platforms dedicated to alternative splicing such as the SpliceArray can be integrated into discovery processes to allow identification of novel targets for drug discovery and biomarkers identification. Further, such platforms may also provide guidance in the selection and follow-up of patients in clinical trials.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr B29.