Abstract 794: RNA-Seq and whole transcriptome analyses in ependymomas.

Abstract

Abstract Ependymoma is a common pediatric central nervous system (CNS) tumor that is believed to originate from ependymal cells located in the lining of ventricular surfaces in the brain. This type of pediatric tumor presents great challenges in treatment despite the advances in neurosurgical techniques and adjuvant therapy. In order to identify possible molecular markers that could improve clinical management and better treatment, we have used RNA-Seq to profile the transcriptome of ependymoma samples with different outcomes. In this study, the ABI SOLiD WT (Whole Transcriptome) technology was utilized to sequence three different ependymoma tumor samples and one normal control brain tissue (enriched for ependymal cells). Whole Transcriptome sequencing produced approximately 10-30 million reads per sample and an average of 30-40% were mapped to the human reference sequence (NCBI Build 36.1) using Novoalign software. After obtaining these mapped locations, Perl scripts were written to overlap these intervals with other annotations and Genespring was used to visualize the reads. Different protein-coding, non-coding and microRNA gene databases were searched for known genes and to calculate the RPKM (Reads Per Kilobase of transcript per Million mapped reads) for each clustered gene. Multiple gene lists were generated corresponding to different RPKM-based comparisons between tumor and control tissues, ultimately enabling the identification of protein-coding genes, non-coding RNAs and microRNAs that are differentially expressed in ependymomas. Protein interaction networks were then built with these genes using the software GeneGo (Thomson Reuters). Thirty genes that are present in these networks are being selected for validation of differential expression in a larger cohort by Real-Time PCR TaqMan customized arrays. In conclusion, we have been able to identify genes differentially expressed in ependymomas, some of which of potential clinical importance. Financial Support: Ann & Robert H Lurie Children's Hospital of Chicago, The Falk Brain Tumor Foundation and The Maeve McNicholas Memorial Foundation. [FF Costa, JM Bischof, and C Hamm contributed equally to this work.] Citation Format: Fabricio F. Costa, Jared M. Bischof, Chris Hamm, Elio F. Vanin, Maria F. Bonaldo, Stephen Iannaccone, Veena Rajaram, Tadanori Tomita, Stewart Goldman, Marcelo B. Soares. RNA-Seq and whole transcriptome analyses in ependymomas. [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 794. doi:10.1158/1538-7445.AM2013-794