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.