Ewing sarcoma (EwS) is an aggressive pediatric
bone cancer in need of more effective
therapies than currently available. Most research into novel targeted therapeutic approaches is focused on the fusion oncogene EWSR1-FLI1, which is the genetic hallmark of this disease. In this study, a broad range of 3,325 experimental compounds, among them FDA approved drugs and natural products, were screened for their effect on EwS cell viability depending on
EWS-FLI1 expression. In a network-based approach we integrated the results from drug perturbation screens and
RNA sequencing, comparing EWS-FLI1-high (normal expression) with EWS-FLI1-low (knockdown) conditions, revealing novel interactions between compounds and
EWS-FLI1 associated biological processes. The top candidate list of druggable
EWS-FLI1 targets included genes involved in translation,
histone modification, microtubule structure, topoisomerase activity as well as apoptosis regulation. We confirmed our in silico results using viability and apoptosis assays, underlining the applicability of our integrative and systemic approach. We identified differential sensitivities of
Ewing sarcoma cells to BCL-2 family inhibitors dependent on the
EWS-FLI1 regulome including altered MCL-1 expression and subcellular localization. This study facilitates the selection of effective targeted approaches for future combinatorial
therapies of patients suffering from
Ewing sarcoma.