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Mitochondrial Dysfunction Is a Driver of SP-2509 Drug Resistance in Ewing Sarcoma
E John Tokarsky1, Jesse C Crow1, Lillian M Guenther2
1Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio.
Abstract:
Expression of the fusion oncoprotein EWS/FLI causes Ewing sarcoma, an aggressive pediatric tumor characterized by widespread epigenetic deregulation. These epigenetic changes are targeted by novel lysine-specific demethylase-1 (LSD1) inhibitors, which are currently in early-phase clinical trials. Single-agent-targeted therapy often induces resistance, and successful clinical development requires knowledge of resistance mechanisms, enabling the design of effective combination strategies. Here, we used a genome-scale CRISPR-Cas9 loss-of-function screen to identify genes whose knockout (KO) conferred resistance to the LSD1 inhibitor SP-2509 in Ewing sarcoma cell lines. Multiple genes required for mitochondrial electron transport chain (ETC) complexes III and IV function were hits in our screen. We validated this finding using genetic and chemical approaches, including CRISPR KO, ETC inhibitors, and mitochondrial depletion. Further global transcriptional profiling revealed that altered complex III/IV function disrupted the oncogenic program mediated by EWS/FLI and LSD1 and blunted the transcriptomic response to SP-2509.
Implications:
These findings demonstrate that mitochondrial dysfunction modulates SP-2509 efficacy and suggest that new therapeutic strategies combining LSD1 with agents that prevent mitochondrial dysfunction may benefit patients with this aggressive malignancy.
Insights
Mitochondrial dysfunction can cause resistance to lysine-specific demethylase-1 (LSD1) inhibitors in Ewing sarcoma. Combining LSD1 inhibitors with agents that prevent mitochondrial dysfunction may improve patient outcomes.
Area of Science:
- Oncology
- Epigenetics
- Mitochondrial Biology
Background:
- Ewing sarcoma is an aggressive pediatric cancer driven by the EWS/FLI oncoprotein and characterized by epigenetic alterations.
- Lysine-specific demethylase-1 (LSD1) inhibitors are a novel therapeutic strategy targeting these epigenetic changes and are in early clinical trials.
- Therapy resistance is a significant challenge, necessitating the understanding of resistance mechanisms for developing effective combination treatments.
Purpose of the Study:
- To identify genes conferring resistance to the LSD1 inhibitor SP-2509 in Ewing sarcoma using a genome-scale CRISPR-Cas9 screen.
- To investigate the role of mitochondrial function in mediating resistance to LSD1 inhibition.
- To explore potential combination therapies for Ewing sarcoma.
Main Methods:
- Genome-scale CRISPR-Cas9 loss-of-function screening in Ewing sarcoma cell lines.
- Validation of hits using genetic (CRISPR knockout) and chemical approaches (ETC inhibitors, mitochondrial depletion).
- Global transcriptional profiling to assess the impact of mitochondrial dysfunction on oncogenic pathways and drug response.
Main Results:
- Genes essential for mitochondrial electron transport chain (ETC) complexes III and IV function were identified as conferring resistance to SP-2509.
- Disruption of mitochondrial complex III/IV function was shown to impair the EWS/FLI oncogenic program and blunt the response to SP-2509.
- Mitochondrial dysfunction was demonstrated to modulate the efficacy of the LSD1 inhibitor SP-2509.
Conclusions:
- Mitochondrial dysfunction plays a critical role in resistance to LSD1 inhibitors in Ewing sarcoma.
- Combination strategies involving LSD1 inhibitors and agents targeting mitochondrial function may offer a promising therapeutic approach for Ewing sarcoma patients.
- Further research into the interplay between epigenetic regulation and mitochondrial metabolism in cancer is warranted.
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