DNA methylation and gene expression profiling of ewing sarcoma primary tumors reveal genes that are potential targets of epigenetic inactivation

Nikul Patel, Jennifer Black, Xi Chen, A. Mario Marcondes, William M. Grady, Elizabeth R. Lawlor, Scott C. Borinstein

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number498472
JournalSarcoma
Volume2012
DOIs
StatePublished - Oct 16 2012
Externally publishedYes

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Ewing's Sarcoma
Gene Expression Profiling
DNA Methylation
Epigenomics
Mesenchymal Stromal Cells
Gene Expression
Cell Culture Techniques
Genes
Neoplasms
decitabine
Cell Line
Methylation
Paraffin
Formaldehyde
Up-Regulation
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Oncology
  • Radiology Nuclear Medicine and imaging

Cite this

DNA methylation and gene expression profiling of ewing sarcoma primary tumors reveal genes that are potential targets of epigenetic inactivation. / Patel, Nikul; Black, Jennifer; Chen, Xi; Marcondes, A. Mario; Grady, William M.; Lawlor, Elizabeth R.; Borinstein, Scott C.

In: Sarcoma, Vol. 2012, 498472, 16.10.2012.

Research output: Contribution to journalArticle

Patel, Nikul ; Black, Jennifer ; Chen, Xi ; Marcondes, A. Mario ; Grady, William M. ; Lawlor, Elizabeth R. ; Borinstein, Scott C. / DNA methylation and gene expression profiling of ewing sarcoma primary tumors reveal genes that are potential targets of epigenetic inactivation. In: Sarcoma. 2012 ; Vol. 2012.
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