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Volume 2012, Article ID 498472, 11 pages
Research Article

DNA Methylation and Gene Expression Profiling of Ewing Sarcoma Primary Tumors Reveal Genes That Are Potential Targets of Epigenetic Inactivation

1Department of Quality Control, XBiotech, Inc., Austin, TX 78744, USA
2Department of Pathology, Vanderbilt University, Nashville, TN 37232, USA
3Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA
4Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
5Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
6Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
7Department of Pediatrics and Pathology, University of Michigan, Ann Arbor, MI 48109, USA
8Division of Pediatric Hematology-Oncology, Department of Pediatrics, Vanderbilt University, Nashville, TN 37232-6510, USA

Received 23 April 2012; Accepted 14 July 2012

Academic Editor: Maria Tsokos

Copyright © 2012 Nikul Patel et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The role of aberrant DNA methylation in Ewing sarcoma is not completely understood. The methylation status of 503 genes in 52 formalin-fixed paraffin-embedded EWS tumors and 3 EWS cell lines was compared to human mesenchymal stem cell primary cultures (hMSCs) using bead chip methylation analysis. Relative expression of methylated genes was assessed in 5-Aza-2-deoxycytidine-(5-AZA)-treated EWS cell lines and in a cohort of primary EWS samples and hMSCs by gene expression and quantitative RT-PCR. 129 genes demonstrated statistically significant hypermethylation in EWS tumors compared to hMSCs. Thirty-six genes were profoundly methylated in EWS and unmethylated in hMSCs. 5-AZA treatment of EWS cell lines resulted in upregulation of expression of hundreds of genes including 162 that were increased by at least 2-fold. The expression of 19 of 36 candidate hypermethylated genes was increased following 5-AZA. Analysis of gene expression from an independent cohort of tumors confirmed decreased expression of six of nineteen hypermethylated genes (AXL, COL1A1, CYP1B1, LYN, SERPINE1,) and VCAN. Comparing gene expression and DNA methylation analyses proved to be an effective way to identify genes epigenetically regulated in EWS. Further investigation is ongoing to elucidate the role of these epigenetic alterations in EWS pathogenesis.