Disulfidptosis-related genes define a prognostic signature and novel therapeutic targets in Ewing’s sarcoma through transcriptomic analysis and experimental validation

Background Ewing’s sarcoma (ES) is a malignant osseous neoplasm characterized by a dismal prognosis, particularly in its metastatic variant. The significance of disulfidptosis—a newly identified cell death mechanism induced by cystine metabolic imbalance and mitochondrial dysfunction—has yet to be investigated in ES. Thus, the aim of this study was to assess the prognostic significance of disulfidptosis-related genes (DRGs) in this disease. Methods We analyzed four GEO datasets to examine nine DRGs through differential expression, co-expression networks, and functional enrichment analyses. A predictive risk signature was developed using unsupervised clustering, Cox regression, and LASSO. Drug sensitivity was predicted using the GDSC database, and immune infiltration was quantified by ssGSEA. Single-cell RNA sequencing data was analyzed to explore DRGs distribution and functional heterogeneity. Molecular docking simulations were performed to evaluate interactions between DRGs and chemotherapeutic agents. Experimental validation of key DRGs was conducted in RD-ES cells using PCR and Western blotting, followed by functional studies of NDUFA11 via siRNA knockdown, assessing proliferation, migration, and invasion. Results Eight of nine DRGs were dysregulated in ES tissues. A five-gene risk model ( NDUFS1 , LRPPRC , NDUFA11 , OXSM , NUBPL ) stratified patients into high- and low-risk groups with significantly different survival outcomes. The risk score was an independent prognostic indicator. Drug sensitivity analysis revealed enhanced response to microtubule inhibitors in the low-risk group. Single-cell analysis demonstrated predominant enrichment of these five DRGs in malignant ES cells. NDUFA11 -high malignant cells exhibited distinct metabolic and signaling pathway enrichment and stronger intercellular communication with the tumor microenvironment. Molecular docking confirmed stable binding between DRGs proteins and chemotherapeutic compounds. Experimental validation confirmed dysregulation of all five DRGs at both RNA and protein levels in RD-ES cells. Functional studies revealed that NDUFA11 knockdown significantly suppressed ES cell proliferation, migration, and invasion. Conclusion This study provides the first prognostic signature connected to disulfidptosis for ES. Functional validation of NDUFA11 highlights its oncogenic role and potential as a therapeutic target. Single-cell analysis further elucidates the metabolic heterogeneity and microenvironmental interactions underlying ES progression.