Abstract A60: An epigenetic map of Ewing sarcoma revealed by comprehensive epigenome sequencing
Authors: Tomazou Eleni Marina , Sheffield Nathan , Schuster Michael , Schönegger Andreas , Kauer Maximilian , Bock Christoph , Kovar Heinrich 
Published: May 2015

Epigenetic marks, including DNA methylation, histone modifications and long non-coding RNAs, are frequently deregulated in pediatric cancers. Even in pediatric cancers that are driven by well-defined genetic events, changes in the epigenome are prevalent, suggesting that epigenetic defects constitute an emerging hallmark of pediatric cancers and a promising new target for drug development.

To define the epigenetic basis of Ewing sarcoma, we performed comprehensive epigenome sequencing in a cellular model that provides precise temporal control of the EWS/FLI1 fusion gene, which is the main cause and driving event in Ewing sarcoma. Specifically, we established reference epigenome maps in the A673 cell line in the presence and absence of the EWS/FLI1 oncogene. All mapping experiments were performed in accordance with the standards of the International Human Epigenome Consortium, thus adhering to stringent requirements for quality control, sequencing depth, and reproducibility in biological replicates.

The epigenome maps we established include comprehensive DNA methylation maps obtained by whole genome bisulfite sequencing (WGBS), genome-wide maps of eight histone modifications (H3K4me3, H3K4me1, H3K27me3, H3K9me3, H3K27ac, H3K36me, H3K56ac, H4K16ac) obtained by ChIP-seq and deep transcript annotations, and expression maps obtained by RNA-seq. The epigenome datasets were further complemented by ChIP-seq maps of EWS/FLI1-binding throughout the genome.

Integrative bioinformatic analysis of our dataset enables testing of the following hypothesis:

i. EWS/FLI1 induces changes in the global distribution of specific epigenetic marks

ii. EWS/FLI1 introduces de novo enhancers that rewire the transcriptional network in Ewing sarcoma

iii. EWS/FLI1 binding of super-enhancers provides a mechanism for oncogene addiction

iv. EWS/FLI1 regulates a novel class of long non-coding RNAs that are expected to play a role in EWS/FLI1-induced tumorgenesis

In summary, the comprehensive nature of our dataset (10 different epigenetic marks, including DNA methylation, histone modifications, and long non-coding RNAs, mapped genome-wide in 4 different cell populations) constitutes a unique resource for the Ewing sarcoma community, and it provides a foundation that allowed us to conduct a systematic bioinformatic dissection of the interplay between EWS/FLI1 and the epigenome. These results shed light on the functional relevance of the epigenetic deregulation in Ewing sarcoma cells, and have the potential to provide a rational basis for testing the therapeutic utility of epigenetic drugs in preclinical models.

This study is supported by the 7th framework program of the European commission, grant 259348 (“ASSET”) and a generous donation by the Kapsch group for next generation sequencing. EMT is a recipient of a Lise Meitner Fellowship of the Austrian Science Fund (FWF, M1448-B13).

Citation Format: Eleni Marina Tomazou, Nathan Sheffield, Michael Schuster, Andreas Schönegger, Maximilian Kauer, Christoph Bock, Heinrich Kovar. An epigenetic map of Ewing sarcoma revealed by comprehensive epigenome sequencing. [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 A60.