Clinical Cancer Research: Surface and Global Proteome Analyses Identify ENPP1 and Other Surface Proteins as Actionable Immunotherapeutic Targets in Ewing Sarcoma (Kurmasheva)

Brian Mooney
Gian Luca Negri
Taras Shyp
Alberto Delaidelli
Hai-Feng Zhang
Sandra E. Spencer Miko
Amber K. Weiner
Alexander B. Radaoui
Rawan Shraim
Michael M. Lizardo
Christopher S. Hughes
Amy Li
Melanie Rouleau
Wei Li
Dimiter S. Dimitrov
Raushan T. Kurmasheva
Sharon J. Diskin
John M. Maris
Gregg B. Morin
Poul H. Sorensen

Purpose: Ewing sarcoma (EwS) is children’s second most common bone sarcoma, with 1 case per 1.5 million in the United States. While the survival rate of patients diagnosed with localized disease is ~70%, this decreases to ~30% for patients with metastatic disease and only ~10% for treatment-refractory disease, which has not changed for decades. Therefore, new therapeutic strategies are urgently needed for metastatic and refractory EwS. Experimental Design: Using proteomics to identify surface proteins for potential immunotherapeutic targeting, this study analyzed 19 unique EwS patient or cell line-derived xenografts (from 14 primary and five metastatic specimens). Plasma membranes were enriched using density gradient ultracentrifugation and compared to a reference standard of 12 immortalized non-EwS cell lines prepared similarly. In parallel, global proteome analysis was carried out on each model to complement the surfaceome data. All models were analyzed by Tandem Mass Tags (TMT)-based mass spectrometry to quantify identified proteins. Results: The surfaceome and global proteome analyses identified 1,131 and 1,030 annotated surface proteins, respectively. Among surface proteins identified, both approaches identified known EwS-associated proteins, including IL1RAP, CD99, STEAP1, and ADGRG2, and many new cell surface targets, including ENPP1 and CDH11. Robust staining of ENPP1 was demonstrated in EwS tumors compared to other childhood sarcomas and normal tissues. Conclusions: Our comprehensive proteomic characterization of the EwS surfaceome provides a rich resource of surface-expressed proteins in EwS. This dataset provides the preclinical justification for exploring targets such as ENPP1 for potential immunotherapeutic application in EwS.

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Article Categories: Research Paper