Determining the cell of origin in Ewing sarcoma through genomic analysis

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Abstract Ewing sarcoma (ES) is a rare but deadly bone tumor which occurs mainly in adolescents and young adults. As survival for ES has not improved beyond ~60% in the last few decades, it is critical to understand its origins in order to improve therapy. Most attempts to determine the cell of origin of ES have relied on cells transformed by the EWS-FLI1 fusion protein, which exerts a strong transcriptional program, whereas we propose a method which uses untransformed candidate cell types. We will derive induced pluripotent stem cells (iPSC) or obtain primary cells for the following cell types: Undifferentiated iPSC, iPS-mesenchymal stem cells, bone marrow- derived mesenchymal stem cells, neural crest progenitors, and neural-crest/mesenchymal stem cells. An open chromatin profile of each cell type will be obtained via the ATAC-seq assay and cross referenced with a genomewide case-control dataset on ES to nominate a cell of origin. Lastly, variants in open chromatin in the nominated cell of origin will be comprehensively characterized. The experiments outlined below represent a novel method for determining the cell of origin for ES, which if successful would point the way to more precise animal models of the disease and potentially inform the development of therapy.