Abstract
Ewing sarcoma (EWS), a rare pediatric bone tumor, poses unique therapeutic challenges due to its distinct microenvironment and limited molecular understanding. To gain a comprehensive molecular and functional view of the tumors in their microenvironment, we perform a deep mass spectrometry-based proteomic analysis of 170 tumor samples from 74 patients from primary, relapsed, and metastatic tumors. Analysis of more than 10,000 proteins across patients reveals insights into cancer prognosis, chemo-resistance, and progression. Our analyses suggest that ferroptosis pathways may be associated with chemotherapy response in EWS, and we delineate molecular subclasses that correlate the tumor immune landscape with DNA damage repair, ubiquitin-related proteins, and patient outcomes. Multiplexed immunofluorescence imaging indicates possible associations between neutrophils and poorer prognosis, and between macrophages/T cells and a more favorable prognosis. Altogether, this investigation provides valuable insights into the intricate biology of EWS, paving the way for developing therapeutic strategies.
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Data availability
The raw mass spectrometry data generated in this study have been deposited in the PRIDE ProteomExchange database under accession code PXD050234. The processed proteomics data generated in this study are provided in the Supplementary data. The Image data used in this study are available in the BioImage Archive database under accession code S-BIAD1597. Source data are provided with this paper.
Code availability
The code for image processing and the Github MIT license document are available via the following GitHub79: [https://github.com/WIS-MICC-CellObservatory/Ewing-Sarcoma-Proteomics-and-Immune-Landscape].
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Acknowledgements
We thank the members of the Geiger lab for fruitful discussions and technical assistance. Opal slide imaging was made possible thanks to the support of the de Picciotto Cancer Cell Observatory in Memory of Wolfgang and Ruth Lesser, a research grant from the Quinquin Foundation, and a research grant from the Morris Kahn Institute for Human Immunology and the Fabrikant-Morse Families Research Fund for Humanity. This work was funded by the Israel Science Foundation grant #3106/21 and the European Council ERC-consolidator grant #101044574. This research was also generously supported by the Applebaum Foundation and the Vera and John Schwartz Family Center for Metabolic Biology.
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S.G. performed the experiments, analyzed the data and drafted the manuscript; R.S., S.G., R.E., and T.G. conceptualized, designed the research and interpreted the results; S.G., R.S., O.S., and M.M. assembled samples and clinical information; V.M., S.G., R.O., and L.F.A. performed the multiplexed imaging; V.M., O.G., and Y.A. acquired the multiplexed imaging data, developed the analytical pipelines and performed the image analyses; V.M., S.G., and S.M. performed the spheroid and ferroptosis analysis; L.B. established the proteomic sample preparation methods; V.M. contributed to figure preparation and the writing of the manuscript; B.D. initialized the research; T.G. supervised the research, analyzed the data and wrote the manuscript.
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Gordon, S., Mohan, V., Shukrun, R. et al. Proteomic landscape of Ewing sarcoma primary tumors and metastases. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70449-5
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DOI: https://doi.org/10.1038/s41467-026-70449-5
