Abstract 4147: An alternative splicing study approach to discriminate between NSCLC subtypes.
Authors: Désiré Laurent , Casagrande Anne-Sophie , Mahé Florence , Throo Emeline , Pando Matthew P. 
Published: August 2014

Alternative splicing of pre-mRNA, a key post-transcriptional mechanism allowing for the production of distinct proteins from a single gene, affects over 90% of human genes. Splicing plays a major role in gene regulation in normal tissues as well as in disease. In cancer, alternative splicing permits the generation of protein isoforms having different biological activities. Thus, splicing alterations participate in the diversity and phenotypic plasticity of tumor cells. The identification of such molecular changes represent promising avenues for cancer diagnosis and therapy.Lung cancer is the leading cause of cancer mortality. Over 80% of lung cancers are non-small cell lung carcinomas (NSCLC). Adenocarcinoamas (AC) and Squamous Cell Carcinomas (SCC) are the two most common subtypes of NSCLC and account for more than 60% of lung cancer cases. Despite being categorized together in NSCLC due to similar microscopic appearance of their tumour cells and similar treatment options in the clinic, AC and SCC are heterogeneous in many clinical aspects, these include distinct oncogenic mutations and divergent therapeutic responses, thus heightening the emphasis on accurate NSCLC subtyping.Here, we describe two approaches to seek transcriptome changes that discriminate between SCC and AC subtypes. To do so, we profiled SCC and AC biopsies together with their adjacent normal tissues on 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. Through this discovery platform, disease status, progression, and drug response can be monitored.

First, we developed transcriptomic signatures using combinations of exon body, exon-intron junction, evidenced and discovery probes and performed principal component analyses at various q values and fold change thresholds. Using a t-test on the first principal component, we compared their respective efficacy to discriminate between SCC and AC subtypes. The data that will be discussed highlight the importance of discovery and junction probes in the signatures.

Second, an epitope identification approach was conducted. We focused on splicing events that generate potential novel amino acid sequences. Events up-regulated were selected based on combination of statistical analysis of probe sets deregulations, protein knowledge and pathway analyses. The events were used to identify novel cell surface epitopes which may be suitable for antibody development.

These findings should be validated with larger sample numbers but indicate that alternative RNA splicing offers a currently underexploited source of biological information for cancer research. Platforms dedicated to splicing can be useful to allow identification of biomarkers and novel targets, as well as guidance in the selection and follow-up of patients for therapy.

Citation Format: Laurent Désiré, Anne-Sophie Casagrande, Florence Mahé, Emeline Throo, Matthew P. Pando. An alternative splicing study approach to discriminate between NSCLC subtypes. [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 4147. doi:10.1158/1538-7445.AM2013-4147