Genomic landscape of Ewing sarcoma: a pooled analysis of 538 cases and clinicopathological correlation

Background: Ewing sarcoma (EwS) is a highly aggressive bone and soft tissue cancer mainly affecting children, adolescents, and young adults. The rarity of the disease, relatively small cohort sizes of prior studies, and overall low mutational burden of EwS have limited the ability to establish robust correlations of genomic findings and clinicopathological factors. Methods: To overcome these limitations, we integrated genomic and clinical data from the seven major sequencing studies encompassing 538 EwS patients. Mutational profiles (SNV, indels and CNVs), and their correlation with clinicopathological features in the aggregated cohort were systematically analyzed to provide an integrated view of the EwS genomic landscape. Results: This study compiles the largest EwS genomic dataset reported to date. In the aggregated cohort (n=538) bone tumors were more common (65.4%) than soft-tissue tumors (34.6%), the latter being more frequent in older male patients and associated with poorer outcomes. EWSR1::FLI1 was the most prevalent fusion (87.2%). No major clinicopathological differences were identified between fusion types. The mutational landscape was dominated by STAG2 (15.6%) and TP53 (7.1%) alterations, associated with younger or with older age at diagnosis and poor survival, respectively. Strikingly, the coexistence of STAG2 and TP53 mutations, although rare (n=12), was associated with lethal outcome in all cases. CDKN2A loss (9.1%) was associated with older age, poor survival, and linked to a higher frequency of TP53-mutations in soft tissue EwS. Among frequent CNVs, gain of chr1q (25.2%) and loss of chr16q (21.9%) were per se frequently associated with fatal outcome and their co-occurrence further increased the risk of lethality. Conclusions: We delineate recurrent genomic alterations with important clinicopathological associations, including a uniformly lethal STAG2/TP53 co-mutation and CNV signatures marking aggressive disease. This comprehensive pooled analysis of EwS genomic studies provides a foundation for refined biological risk-stratification.