Mapping Genomic Heterogeneity in Pediatric and Adolescent-Young Adult Sarcomas: Insights from the Italian SAR-GEN2016 and SAR-GEN_ITA Prospective Multicenter Trials.

Sarcomas in pediatric and adolescent-young adult (AYA) populations represent rare and biologically heterogeneous tumors with complex genetic underpinnings. Genomic profiling reveals subtype-specific alterations and therapeutic targets. Such tumors still represent an unmet clinical need due to limited treatment options and poorer outcomes, especially in advanced stages. Here, we present the SAR-GEN2016 and SAR-GEN_ITA clinical trials, conducted across 12 Italian centers, which enrolled 201 patients, including 158 bone and soft-tissue sarcoma samples collected at diagnosis or relapse. Whole-exome sequencing was successfully performed on 120 tumor samples. The most representative histotypes were osteosarcoma (n = 53), Ewing sarcoma (n = 39), rhabdomyosarcoma (n = 13), and synovial sarcoma (n = 5), and the genomic analyses were mainly focused on these subtypes. Overall, our cohort showed genomic differences between subtypes, highlighting how genomic complex sarcomas and fusion-driven sarcomas are distinct entities. The genomic complex histotypes, such as osteosarcoma, were characterized by a lower tumor mutational burden (TMB) and higher copy-number variation burden with enrichment of the CN2 signature. Recurrent and metastatic Ewing sarcomas have a higher TMB compared with treatment-naïve primary tumors, along with increased intratumoral heterogeneity. Oncogenic pathway analyses revealed dysregulation of the RTK-RAS and NOTCH pathways across subtypes, particularly in metastatic and recurrent tumors. In 71 of 120 analyzed samples (59%), at least one potentially actionable genomic alteration was identified, and 16% of those patients with relapsed disease received a matched targeted therapy based on the molecular profiling results. All findings were classified as ESCAT tier II or III. Our findings support the value of integrating genomic and clinical data to accelerate translational research in rare tumors. SIGNIFICANCE: Pediatric and AYA sarcomas are rare with poor outcomes in advanced stages and limited treatment options. Through the SAR-GEN2016 and SAR-GEN_ITA multicenter trials, we performed whole-exome sequencing on 120 tumor samples with matched normal tissue from 158 patients with bone and soft-tissue sarcoma. Our integrative genomic analysis supports the genomic stratification and precision oncology in rare pediatric sarcomas.