Multi-omics analysis revealed clonal evolution of sarcoma patient-derived xenografts

Patient-derived xenografts (PDXs) are used in translational research and are particularly valuable for studying rare cancers such as sarcomas. Although it is critical to understand how accurately they reflect the genetic and phenotypic features of the original tumor, comprehensive analyses that access changes in both single-nucleotide variants (SNVs) and copy number variants (CNVs) during the establishment and passaging of PDXs remain scarce. In addition, as previous studies have focused on those derived from early-stage tumors or major cancer types, it remains unclear how genomic features are preserved in PDXs derived from advanced, treatment-resistant sarcomas. Here we performed whole-exome sequencing, RNA-seq and DNA methylation analysis of 144 sarcoma PDXs established from 39 patients, along with their matched primary tumors when available. The cohort was enriched for highly recurrent cases (n = 29) and included not only major sarcoma types, such as osteosarcoma (n = 11), but also ultra-rare sarcomas, including alveolar rhabdomyosarcoma (n = 4) and CIC -rearranged sarcoma (n = 2). PDXs were successfully established from a wide range of molecular subtypes, including fusion-driven tumors, TP53 -mutated cases, and hypermutated types associated with microsatellite instability. Targetable genomic alterations, including amplifications of CCNE1 or MDM2 and deletions of MTAP , were identified in 55% of cases. Several PDXs harbored mutations associated with resistance to molecular targeted agents and immunotherapies. The vast majority of somatic alterations detected in the primary tumors were retained in the PDXs (97% for SNVs, 99% for CNVs). Moreover, mutational signature analysis suggested that mutations detected exclusively in PDXs likely represent low-frequency mutations already present in the original tumors. Extrachromosomal DNAs involving oncogenes such as MYC , CDK4 , and MDM2 were also identified in 28% of PDXs and were retained in 83% of cases during serial PDX passaging. Despite overall genomic stability, clonal architecture changed during establishment and passaging, with highly diverse patterns, and clonal shifts were observed in 53%, 65%,71% of cases based on SNVs, CNVs, and both combined, respectively. Interestingly, clonal shifts were observed in all models derived from diagnostic samples (n = 9) and primary tumors (n = 8), which was much more frequent than in models derived from relapsed or metastatic tumors (62%). In addition, gene expression and methylation clustering revealed distinct clusters within each cancer type and individual cases, suggesting that key tumor characteristics were preserved during PDX establishment and passaging. Our data reveal the genetic and phenotypic stability of sarcoma-derived PDX models during their establishment and passaging, and provide new insights into their clonal evolution, which we believe will contribute to the clinical utility of PDX models.