Abstract A30: Integrative genomic analysis of two Ewing's sarcoma cell lines that show differential drug sensitivity
Authors: MOHAMMAD TABREZ A. , Gorthi Aparna , Robles Andrew , Bernard Xavier , Hsiao Tzu-hung , Garcia Dawn , Lai Zhao , Mooberry Susan L. , Tomlinson Gail E. , Bishop Alexander JR , Chen Yidong 
Published: May 2015

Abstract
Background: Ewing's sarcoma is a rare form of highly aggressive bone tumor of children and young adults. Understanding the molecular mechanisms involved in the development of Ewing's sarcoma forms the key step in the design and development of new therapeutic interventions. Previous studies revealed that genomic alterations play an important role in oncogenesis, disease progression and response of tumors to different therapies. The recent advance of next generation sequencing-based methods provide unprecedented capabilities to scan Ewing's sarcoma genomes for changes such as mutations, insertions/deletions, copy number variations, differential gene expression and discovery of new gene fusions. In this study, we performed detailed investigation to identify the genetic basis of difference between two Ewing cell lines, RDES and SKES1, which show differential sensitivity to natural product extracts, by using RNA-seq, small RNA-seq and exome-capture-seq techniques.
Methods: Transcriptomes and genomic DNA of both the Ewing's cell lines, RDES and SKES1 were prepared for paired-end sequencing on the Illumina HiSeq2000 platform using the manufacturer's protocols, for RNA-seq and exome-capture-seq respectively. The reads were aligned to the human hg19 genome assembly and the abundance of mRNAs as well as small RNAs for all annotated genes from the UCSC annotation of human genome was calculated. The count data from abundance estimation was used to compute differentially expressed genes and small RNAs between these two cell lines. Furthermore, we used deFuse for the gene fusion identification and GATK pipeline for the DNA variant analysis.
Results: We studied the gene expression profiles from RNA-seq and small RNA-seq reads and identified approximately 270 and 114 differentially expressed genes and microRNAs, respectively between drug-sensitive and insensitive cell lines. Interestingly, we found that two of ABC transporters are significantly overexpressed in the resistant cell line. Moreover, many apoptotic genes show altered expression between these two cell lines. Gene fusion products were also identified from the RNA-seq analysis. Both the cell lines were found to harbor the well-known Ewing's sarcoma gene fusion EWS-FLI1. In addition to EWS-FLI1, we also discovered some new and unique gene fusion candidates in both cell lines. Furthermore, we used exome-capture sequence analysis to identify sequence variation and mutations in these two cell lines. Known mutations reported in COSMIC database and SNPs that are not included in normal populations from the 1000 genome project were carefully studied. Interestingly, some of the non-synonymous changes identified map to kinases and other known cancer-related genes.
Conclusions: Our studies suggest that the difference in drug sensitivity of two Ewing's sarcoma cell-lines is probably due to the expression of ATP-dependent efflux pumps as well as alterations in the apoptotic machinery. Further studies are warranted to understand the exact molecular mechanism of drug sensitivity.
Citation Format: TABREZ A. MOHAMMAD, Aparna Gorthi, Andrew Robles, Xavier Bernard, Tzu-hung Hsiao, Dawn Garcia, Zhao Lai, Susan L. Mooberry, Gail E. Tomlinson, Alexander JR Bishop, Yidong Chen. Integrative genomic analysis of two Ewing's sarcoma cell lines that show differential drug sensitivity. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A30.