Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers

Abstract

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.

High-content drug screening in zebrafish xenografts reveals high efficacy of dual MCL-1/BCL-XL inhibition against Ewing sarcoma

“…In good agreement with our results, MCL-1 has been identified as a Ewing sarcoma dependency protein and specific sensitivity to combined MCL-1 and BCL-X L inhibition was recently also reported for a larger panel of solid pediatric tumor cell lines in vitro, including two Ewing sarcoma cell lines, SK-ES-1 and A4573 [45][46][47][48]. However, we did not observe enhanced effects for dual MCL-1/BCL-X L inhibition in osteosarcoma xenografts, suggesting that Ewing sarcoma cells might be exquisitely sensitive to combined MCL-1/BCL-X L targeting.…”

Mitochondrial Dysfunction Is a Driver of SP-2509 Drug Resistance in Ewing Sarcoma

“…Potential combination approaches may be achieved by using mitochondrial modulators such as BH3 mimetics (obatoclax and navitoclax) or the oxidative stress inducing compound, Elesclomol. The BH3 mimetics, obatoclax and navitoclax, are compounds that drive the intrinsic apoptosis pathway and have been shown to be effective at targeting Ewing sarcoma ( 45 ). Elesclomol has been shown to promote apoptosis in Ewing sarcoma cells by leading to elevated ROS, particularly in mitochondrial ROS ( 46 ).…”

Ewing sarcoma from molecular biology to the clinic

“…For example, EWS-FLI1 stimulates the expression of c-Myc ( Dauphinot et al, 2001 ), Gli1 (Glioma-associated Oncogene Homolog 1) ( Merchant et al, 2009 ; Mullard et al, 2020 ) or NR0B1 (Nuclear Receptor subfamily 0 group B member 1) ( Kinsey et al, 2006 ; Gangwal et al, 2008 ), genes involved in tumor progression and metastatic development. Conversely, EWS-FLI1 reduces the expression of genes involved in tumor suppressor mechanism (ex: apoptosis), such as FOXO1 (Forkhead Box O1) ( Yang et al, 2010 ), or IER3 (Immediate Early Response 3) ( Tsafou et al, 2018 ), tumor suppressor genes regulating mechanisms such as DNA repair, cell cycle arrest and apoptosis.…”