Ewing sarcoma is the second most common primary bone tumor in children, constituting 3% of all pediatric tumors. The 5 year survival rate is 59% to 76% for children younger than 15 years and from 20% to 49% for those aged 15 to 19 years. 85% of Ewing sarcoma are characterized by a chromosomal translocation between the Ewing sarcoma gene (EWS) breaking point and the ETS family of transcription factor FLI1, which creates a new type of fusion transcription factor with novel functions. While EWS-FLI1 is the predominating translocation event, other types of translocations between EWS and other ETS transcription factors have been reported. Mesenchymal stem cells (hMSC) are thought to be the cell of origin for Ewing sarcoma. The molecular mechanisms of transformation of hMSCs with ectopic EWS-FLI1 expression has been extensively studied, however, a complete transformation of hMSCs into Ewing sarcoma tumor cells is not yet achieved suggesting there are other elements required for the transformation of hMSCs.

RNAseq has proved to be a powerful new method for capturing multiple arrays of information simultaneously such as gene expression, nucleotide variation, alternative splicing patterns and fusion transcripts. RNAseq has been used only once in the literature in identification of a novel fusion transcript in Ewing sarcoma tumor cells. Here we obtained RNAseq data from Ewing sarcoma patients and cell lines to gather novel insight into the pathogenesis of Ewing sarcoma. We obtained sequencing data from two Ewing sarcoma cell lines (A673 and SK-PN-DW); human brain vascular pericytes (HBVP), 8 patient tumors and 3 matched normal control tissues. Initial data analysis was performed through an in-house developed pipeline that uses publicly available software and further data analysis was performed using R with various packages. We describe the gene expression changes in patients compared to normal tissues as well as HBVP. We also discovered a group of novel fusion transcripts that we subsequently confirmed with RT-PCR. Since EWS is also an RNA splicing protein, changes in alternative splicing are also described.

Citation Format: Ahmet Zehir, Srikanth R. Ambati, Malcolm AS Moore. Transcriptomic landscape of Ewing sarcoma based on RNAseq. [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 4021. doi:10.1158/1538-7445.AM2013-4021