Preservation and clonal behavior of extrachromosomal DNA in patient-derived xenograft models of childhood cancers.

backgroundExtrachromosomal DNA (ecDNA) is a structural variant linked to poor prognosis in pediatric cancers. Patient-derived xenograft (PDX) models are crucial tools for cancer research, as they are believed to recapitulate the molecular features and intratumoral heterogeneity in patient tumors. However, ecDNA demonstrates unique evolutionary dynamics under selective pressure, and its behavior during PDX development remains largely uncharacterized. This study investigates the fidelity of PDX models in representing ecDNA from primary tumors. By analyzing ecDNA sequence composition and copy number conservation across pediatric solid cancers, we assess how well PDX models recapitulate the ecDNA landscape observed in human tumors.

methodsAmpliconArchitect was used to analyze whole-genome sequencing (WGS) of 338 PDX models and 127 corresponding primary tumors. ecDNA status, sequence, copy number, and associated genes were compared between PDX models and their matched human tumors. Additionally, multiome RNA and ATAC single-cell sequencing of a PDX tumor enabled comparison of ecDNA intratumoral heterogeneity relative to similar data from the primary tumor.

resultsecDNA in PDX models largely recapitulated oncogene amplifications observed in human tumors, with MYCN being the most frequently amplified. ecDNA status remained unchanged for a majority of the PDX models (105/127, 83%) compared to primary tumors, with 20% of previously ecDNA-negative cases acquiring ecDNA during PDX development. Consequently, ecDNA was more prevalent in the PDX models than in their corresponding human tumors (McNemar's test, p = 0.00086). Detailed examination of ecDNA sequences in tumor-PDX pairs showed substantial conservation (67% with > 90% sequence overlap) but variable breakpoint concordance. Single-cell analysis demonstrated that rare ecDNA-positive cells from the primary tumor preferentially drive PDX tumor development.

conclusionThis study highlights the prevalence, oncogenic content, and conservation of ecDNA in PDX models relative to pediatric patient tumors. We observed that ecDNA frequently recapitulates oncogene amplifications found in human cancers, is generally preserved during PDX establishment, and reflects subtype-specific patterns across tumor types. These findings support the utility of PDX models in studying ecDNA biology in pediatric cancer progression and therapy. Longitudinal sampling during PDX tumor growth and under therapeutic pressure could provide insights into molecular evolution, clonal selection, and ecDNA-driven therapy resistance.