Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation

Ewing sarcoma is an aggressive, genomic rather simple, but clinically heterogeneous cancer mainly affecting adolescents and young adults. Research in the field of Ewing sarcoma based on two or three cell line models is not sufficient to model the clinically observed heterogeneity. Furthermore complex interaction of the pathognomonic fusion oncogenes with genetic variants influencing epigenome and transcriptome demand a multi-dimensional view on the mechanisms of Ewing sarcoma tumorigenesis and progression. To this end, we created the Ewing Sarcom CellLine Atlas (ESCLA), comprising 18 Ewing sarcoma cell lines characterized by whole genome sequencing (150bp, paired-end, PCR-free protocol, Illumina HiSeqXTen), chromatin immunoprecipitation and sequencing, DNA microarrays, methylation arrays and mass spectrometry.