The Ewing Sarcoma Cell Line Atlas (ESCLA) - expression profiling of 18 Ewing sarcoma cell lines in EWSR1-ETS-high versus -low condition. The Ewing Sarcoma Cell Line Atlas (ESCLA) - expression profiling of 18 Ewing sarcoma cell lines in EWSR1-ETS-high versus -low condition

Cell lines have been essential for major discoveries in cancer including Ewing sarcoma (EwS). EwS is a highly aggressive pediatric bone or soft-tissue cancer characterized by oncogenic EWSR1-ETS fusion transcription factors converting polymorphic GGAA-microsatellites (mSats) into neo-enhancers. However, further detailed mechanistic evaluation of gene regulation in EwS have been hindered by the limited number of well-characterized cell line models. Here, we present the Ewing Sarcoma Cell Line Atlas (ESCLA) comprising 18 EwS cell lines with inducible EWSR1-ETS knockdown that were profiled by whole-genome-sequencing, DNA methylation arrays, gene expression and splicing arrays, mass spectrometry, and ChIP-seq for EWSR1-ETS and histone marks. Systematic analysis of these multi-dimensional data illuminated hundreds of new potential EWSR1-ETS target genes, the nature of EWSR1-ETS-preferred GGAA-mSats, and potential indirect modes of EWSR1-ETS-mediated gene regulation. Moreover, we identified putative co-regulatory transcription factors and heterogeneously regulated EWSR1-ETS target genes that may have implications for the clinical heterogeneity of EwS. Collectively, our freely available ESCLA constitutes an extremely rich resource for EwS research and highlights the power of leveraging multidimensional and comprehensive datasets to unravel principles of heterogeneous gene regulation by dominant fusion oncogenes. Overall design: 18 established Ewing sarcoma cell lines were stably transduced with an inducible shRNA expressing construct targeting the EWSR1-ETS fusion of the respective cell line. EWSR1-ETS knockdown was induced by the addition of 1 µg doxycycline to growth medium for 96 h. Total RNA was isolated from three replicates treated with doxycycline and three controls. The transcriptome was profiled on Affymetrix Clariom D Human microarrays. Raw data were processed using the Transcriptome Analysis Console (version 4.0) by ThermoFisher, the SST-RMA analysis algorithm and the manufacturer's array description file (version 2). Please note that the sample data tables (containing normalized data) and GSM5359685 CEL file have been updated on June 9th, 2022.