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EWS::FLI1-DHX9 interaction promotes Ewing sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop
Joaquin Olmedo-Pelayo1,2,3, Esperanza Granado-Calle1,4, Daniel Delgado-Bellido1,2
1Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.
Abstract:
Drug resistance is an ill-defined cause of dismal outcomes in cancer. Ewing sarcoma (EwS), a pediatric cancer characterized by high therapy failure rates, is driven by a single oncogenic event generating EWSR1::ETS gene fusions (primarily EWSR1::FLI1) in a silent genomic background. This provides a straightforward model to study the impact of gene fusions on drug responses. Here, we describe a novel mechanism of sensitivity to DNA topoisomerase 1 poisons in EwS. We discovered that EWS::FLI1 prevents the resolution of R-loops induced by these drugs via sequestering DHX9 helicase, ultimately resulting in R-loop accumulation, replication stress, and genome instability. In turn, excessive DHX9 or reduced EWS::FLI1 levels render EwS cells resistant to the active metabolite of irinotecan (SN-38) independent of proliferation and global transcription rates. This resistance helps explain how elevated DHX9 levels predict worse clinical outcomes. Overall, our research demonstrates the impact of a dominant mutation on cancer drug sensitivity, highlighting its significant clinical implications.
Insights
Ewing sarcoma (EwS) cells resist irinotecan by EWS::FLI1 sequestering DHX9, preventing R-loop resolution. This mechanism explains drug resistance and poor outcomes in pediatric cancer.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Drug resistance significantly impacts cancer treatment outcomes.
- Ewing sarcoma (EwS) is a pediatric cancer with high treatment failure rates, driven by EWSR1::ETS gene fusions.
- Understanding gene fusion roles in drug response is crucial for EwS therapy.
Purpose of the Study:
- To elucidate a novel mechanism of sensitivity to DNA topoisomerase 1 poisons in EwS.
- To investigate the role of EWS::FLI1 and DHX9 helicase in drug resistance.
- To explore the clinical implications of DHX9 levels in EwS patient outcomes.
Main Methods:
- Investigated R-loop resolution dynamics in EwS cells treated with topoisomerase 1 inhibitors.
- Analyzed the interaction between EWS::FLI1 and DHX9 helicase.
- Assessed the impact of altered DHX9 or EWS::FLI1 levels on drug sensitivity and cellular phenotypes.
Main Results:
- EWS::FLI1 sequesters DHX9, inhibiting R-loop resolution and causing accumulation of replication stress and genome instability.
- Elevated DHX9 or reduced EWS::FLI1 confers resistance to SN-38 (irinotecan metabolite) independent of proliferation and transcription.
- High DHX9 levels correlate with worse clinical outcomes in EwS patients.
Conclusions:
- A novel mechanism of drug sensitivity involving EWS::FLI1-mediated DHX9 sequestration and R-loop accumulation in EwS is described.
- This mechanism explains SN-38 resistance and highlights DHX9 as a potential predictive biomarker for EwS.
- Targeting this pathway may offer new therapeutic strategies for pediatric cancer.
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