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A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma

Abstract

Many sarcomas and leukemias carry nonrandom chromosomal translocations encoding tumor-specific mutant fusion transcription factors that are essential to their molecular pathogenesis. Ewing's sarcoma family tumors (ESFTs) contain a characteristic t(11;22) translocation leading to expression of the oncogenic fusion protein EWS-FLI1. EWS-FLI1 is a disordered protein that precludes standard structure-based small-molecule inhibitor design. EWS-FLI1 binding to RNA helicase A (RHA) is important for its oncogenic function. We therefore used surface plasmon resonance screening to identify compounds that bind EWS-FLI1 and might block its interaction with RHA. YK-4-279, a derivative of the lead compound from the screen, blocks RHA binding to EWS-FLI1, induces apoptosis in ESFT cells and reduces the growth of ESFT orthotopic xenografts. These findings provide proof of principle that inhibiting the interaction of mutant cancer-specific transcription factors with the normal cellular binding partners required for their oncogenic activity provides a promising strategy for the development of uniquely effective, tumor-specific anticancer agents.

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Figure 1: RHA is necessary for optimal transformation by EWS-FLI1.
Figure 2: E9R peptide prevents EWS-FLI1 binding to RHA with specific detrimental effects upon ESFT growth and transformation.
Figure 3: Small molecule binds EWS-FLI1 and displaces E9R from EWS-FLI1.
Figure 4: YK-4-279 reduces EWS-FLI1 functional activity.
Figure 5: YK-4-279 is a potent and specific inhibitor of ESFTs.
Figure 6: YK-4-279 inhibits the growth of ESFT xenograft tumors.

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Acknowledgements

This work was generously supported by the Children's Cancer Foundation of Baltimore (J.T. and A.Ü.), Go4theGoal Foundation (J.T.), Dani's Foundation of Denver (J.T.), the Liddy Shriver Sarcoma Initiative (J.T.), the Amschwand Sarcoma Cancer Foundation (J.T.), the Burroughs-Wellcome Clinical Scientist Award in Translational Research (J.T.), US National Institutes of Health grants R01CA138212 (J.T.) and R01CA133662 (J.T.), and the Georgetown University Medical Center Drug Discovery Program. US National Institutes of Health support is through the Cancer Center Support Grant P30 CA051008 for use of Flow Cytometry and Cell Sorting, Biacore Molecular Interaction, Tissue Culture and microscopy core facilities and grant P01 CA47179 (M.M.). We would like to thank S. Metallo for training in fluorescence polarization. Also, T. Cripe and L. Whitesell provided critical review of our manuscript. We also thank S. Lessnick from Hunstamn Cancer Institute, for providing NROB1 reporter plasmid, J.V. Frangioni from Beth Israel Deaconess Medical Center for providing pG, pGN and pGC vectors, O. Delattre from INSERM France for providing the A673 shEWS-FLI1 cell line, and R. Schlegel, Lombardi Comprehensive Cancer Center, for providing HFK and HEC cell lines. We thank the Developmental Therapeutics Program of the US National Cancer Institute for providing the Diversity set of compounds for screening. This article is dedicated to our patients who have fought but succumbed to ESFT.

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H.V.E., J.S.B.-R., M.M., L.Y., O.D.A., S.S., T.-h.C., A.Ü. and J.A.T. designed and carried out experiments. Y.K., S.D. and M.L.B. designed and synthesized chemical compounds. H.V.E. and J.A.T. wrote the manuscript. All authors reviewed, critiqued and offered comments to the text.

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Correspondence to Jeffrey A Toretsky.

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J.A.T., M.L.B., A.Ü. and Y.K. are inventors on a patent application to the US Patent Office that has been filed by Georgetown University related to the small molecule technology described in this paper.

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Supplementary Figs. 1–5, Supplementary Table 1 and Supplementary Methods (PDF 877 kb)

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Erkizan, H., Kong, Y., Merchant, M. et al. A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma. Nat Med 15, 750–756 (2009). https://doi.org/10.1038/nm.1983

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