DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

Developmental tumors in children and young adults carry few genetic alterations, yet they have diverse clinical presentation. Focusing on Ewing sarcoma, we sought to establish the prevalence and characteristics of epigenetic heterogeneity in genetically homogeneous cancers. We performed genome-scale DNA methylation sequencing for a large cohort of Ewing sarcoma tumors and analyzed epigenetic heterogeneity on three levels: between cancers, between tumors, and within tumors. We observed consistent DNA hypomethylation at enhancers regulated by the disease-defining EWS-FLI1 fusion protein, thus establishing epigenomic enhancer reprogramming as a ubiquitous and characteristic feature of Ewing sarcoma. DNA methylation differences between tumors identified a continuous disease spectrum underlying Ewing sarcoma, which reflected the strength of an EWS-FLI1 regulatory signature and a continuum between mesenchymal and stem cell signatures. There was substantial epigenetic heterogeneity within tumors, particularly in patients with metastatic disease. In summary, our study provides a comprehensive assessment of epigenetic heterogeneity in Ewing sarcoma and thereby highlights the importance of considering nongenetic aspects of tumor heterogeneity in the context of cancer biology and personalized medicine.The following associations supported this work: Courir pour Mathieu, Dans les pas du Géant, Olivier Chape, Les Bagouzamanon, Enfants et Santé, and les Amis de Claire. The study was performed in the context of the following European Union consortia: Euro Ewing (grant agreement no. 602856), BLUEPRINT (grant agreement no. 282510), PROVABES (grant agreement no. 01KT1310), ASSET (grant agreement no. 259348), and TECHNOBEAT (grant agreement no. 668724). N.C.S. was supported by a long-term fellowship of the Human Frontier Science Program (LT000211/2014). J.K. was supported by a DOC Fellowship of the Austrian Academy of Sciences. D. Surdez was supported by the Institut Curie-SIRIC (Site de Recherche Intégrée en Cancérologie) program. E.d.A. was supported by Ministry of Economy and Competitiveness of Spain-FEDER grants (CIBERONC, RD12/0036/0017, PI14/01466), María García-Estrada, CRIS contra el Cáncer Foundations, and Pablo Ugarte Association. C.B. was supported by a New Frontiers Group award of the Austrian Academy of Sciences and by a European Research Council (ERC) Starting Grant (European Union's Horizon 2020 research and innovation program; grant 679146). E.M.T. was supported by fellowships of the Austrian Science Fund (FWF, Lise Meitner Fellowship M1448-B13; and Elise Richter Fellowship V506-B28)