Pharmacologic inhibition of epigenetic modification reveals targets of aberrant promoter methylation in ewing sarcoma

Background: Ewing sarcoma (ES), a highly aggressive tumor of children and young adults, is characterized most commonly by an 11;22 chromosomal translocation that fuses EWSR1 located at 22q12 with FLI1, coding for a member of the ETS family of transcription factors. Although genetic changes in ES have been extensively researched, our understanding of the role of epigenetic modifications in this neoplasm is limited. Procedure: In an effort to improve our knowledge in the role of epigenetic changes in ES we evaluated the in vitro antineoplastic effect of the DNA methyltransferase inhibitor 5-Aza-deoxycytidine (5-Aza-dC) and identified epigenetically silenced genes by pharmacologic unmasking of DNA methylation coupled with genome-wide expression profiling. Results: Comparisons between untreated and 5-Aza-dC treated ES cell lines (n=5) identified 208 probe sets with at least twofold difference in expression (P≤0.05). The 208 probe sets represented 145 upregulated and 31 down-regulated genes. Of the 145 genes upregulated after 5-Aza-dC treatment, four: were further characterized. ACRC, CLU, MEST, and NNAT were found to be hypermethylated and transcriptionally down-regulated in ES cell lines. Further studies revealed that ACRC, CLU, MEST, and NNAT were often hypermethylated in primary ES tumors. Transfection-mediated reexpression of ACRC, CLU, MEST, and NNAT in ES cell lines resulted in decreased growth in culture. Conclusions: This study demonstrated epigenetically modified genes in ES cell lines and primary tumors and suggested that epigenetic dysregulation may contribute to disease pathogenesis in ES.