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Open Access Highly Accessed Research article

Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer

Wolfram Langer12*, Florian Sohler1, Gabriele Leder1, Georg Beckmann1, Henrik Seidel1, Jörn Gröne3, Michael Hummel4 and Anette Sommer1*

Author Affiliations

1 Bayer Schering Pharma AG, Global Drug Discovery (GDD) - Target Discovery, Müllerstrasse 178, 13342 Berlin, Germany

2 Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany

3 Dept. of General, Vascular and Thoracic Surgery, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany

4 Institute of Pathology, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany

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BMC Genomics 2010, 11:676  doi:10.1186/1471-2164-11-676

Published: 30 November 2010

Abstract

Background

Treatment of non-small cell lung cancer with novel targeted therapies is a major unmet clinical need. Alternative splicing is a mechanism which generates diverse protein products and is of functional relevance in cancer.

Results

In this study, a genome-wide analysis of the alteration of splicing patterns between lung cancer and normal lung tissue was performed. We generated an exon array data set derived from matched pairs of lung cancer and normal lung tissue including both the adenocarcinoma and the squamous cell carcinoma subtypes. An enhanced workflow was developed to reliably detect differential splicing in an exon array data set. In total, 330 genes were found to be differentially spliced in non-small cell lung cancer compared to normal lung tissue. Microarray findings were validated with independent laboratory methods for CLSTN1, FN1, KIAA1217, MYO18A, NCOR2, NUMB, SLK, SYNE2, TPM1, (in total, 10 events) and ADD3, which was analysed in depth. We achieved a high validation rate of 69%. Evidence was found that the activity of FOX2, the splicing factor shown to cause cancer-specific splicing patterns in breast and ovarian cancer, is not altered at the transcript level in several cancer types including lung cancer.

Conclusions

This study demonstrates how alternatively spliced genes can reliably be identified in a cancer data set. Our findings underline that key processes of cancer progression in NSCLC are affected by alternative splicing, which can be exploited in the search for novel targeted therapies.