Abstract 4860: Identification of novel epitopes, drug resistance markers and drug resistance mechanism using alternative splicing studies
Authors: Casagrande Anne-Sophie , Mahe Florence , Kotraiah Vin , Pando Matt , Desire Laurent 
Published: June 2012

Alternative RNA splicing is a key molecular mechanism for the generation of functional protein diversity. Abnormal alternative splicing can occur in cancer, resulting in the production of novel transcript variants. Therefore, development of platform technologies aimed at studying alternative splicing will help to understand the diverse mechanisms by which splicing dysregulation contribute to human disease. The impact of alternative splicing in disease and its regulation by drug actions have opened up new perspectives for target discovery, drug development and drug response monitoring. ExonHit has generated this type of discovery platform, the Genome Wide SpliceArrayTM, and is currently building libraries of alternative splicing events that are deregulated in cancer and in cases of therapy resistance. These libraries can be interrogated to answer questions such as drug response monitoring, specificity and selectivity of drug response, diagnostics for monitoring disease status, progression or relapse.

Using ExonHit's SpliceArrayTM, we previously reported a significant contribution of splicing to cancer development and drug response (1). Here, we demonstrated the capability of ExonHit's platforms 1/ to identify novel cell surface epitopes for antibody development and 2/ to study drug resistance.

Based on SpliceArray™ microarray analysis, transcripts alternatively spliced were isolated from breast tumor tissues for the epitope study. Different splicing patterns were evidenced in tumoral versus normal tissues and specificity analysis was performed too. Based on combination of statistical analysis and protein knowledge, most relevant events were selected as alternatively spliced transcripts encoding novel amino acid sequence that can be used to target monoclonal antibodies. Finally, QPCR expression analysis validate the specificity of the selected events identified by the probe sets that emerged from the genome-wide splicing analysis.

For the drug resistance study, two types of Imatinib-resistant leukemia cell lines were established. Distinct splicing patterns were evidenced using principal component analysis, through statistical analysis of differential splicing and pathway analyses. We also implemented selectivity filters allowing to identify a drug resistance signature and a set of pathways/genes involved in drug resistance. These signatures will need to be confirmed in subsequent studies.

Our results demonstrate that alternative RNA splicing offers a currently underexploited source of novel disease targets. Platforms dedicated to studying alternative splicing can be integrated into discovery processes to allow identification of novel targets for drug discovery and we have began to identify genomic expression profiles related to drug treatment that will ultimately help monitoring drug response and clinical trial design.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4860. doi:10.1158/1538-7445.AM2011-4860