Abstract
Abstract Ependymomas are tumors that present 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 profiled ependymomas for the expression of microRNAs (miRNAs) and other non-coding RNAs (ncRNAs). miRNAs are ncRNAs that can block mRNA translation and affect mRNA stability. Several lines of evidence have recently shown that up or down-regulation of miRNAs correlate with many human cancers indicating that they can function as classical tumor suppressors and/or oncogenes. In this study, we have evaluated with the use of TaqMan Low Density Arrays (TLDAs) and RNA-Seq the expression profiles of non-coding RNAs in ependymoma samples and normal brain tissue. We analyzed the miRNA expression profile of 34 ependymoma samples using paraffin tissue compared to 6 normal brain control samples enriched for ependymal cells. miRNA expression profiles were correlated with clinico-pathological parameters, morphological features and the location of the tumor in the brain. We have been able to classify the tumors based on the miRNA expression profile and to identify miRNAs that are differentilly expressed in ependymomas when compared to normal samples. For example, miR-135a, miR-594 and miR-34a were identified as over-expressed and miR-485-5p and miR-383 as down-regulated (p<0.01; FDR<0.05). We have also identified and are currently confirming some of the targets for these miRNAs. Finally, we have utilized high-throughput Whole Transcriptome (WT) analyses with the SOLiD system to identify other differentially expressed miRNAs and long ncRNAs in ependymomas. The transcriptome of 3 ependymomas and 2 controls were sequenced, thus generating approximately 5 Gb of data. In conclusion, using different strategies, we have been able to identify ncRNAs that are differentially expressed in ependymomas compared to normal ependymal tissue, some of which are of clinical importance. Financial Support: Children's Memorial Research Center, The Falk Brain Tumor Foundation and The Maeve McNicholas Memorial Foundation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 198. doi:1538-7445.AM2012-198
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