Abstract Extrachromosomal DNA (ecDNA) drives tumor heterogeneity and is associated with poor prognosis in cancer, including pediatric brain tumors. Patient-derived mouse xenograft (PDX) models provide in vivo platforms for preclinical drug testing and molecular tumor profiling, enabling detailed investigations of intratumoral heterogeneity and drug resistance mechanisms. However, it remains unclear to what extent ecDNA amplifications are preserved in PDX models, thereby accurately reflecting the characteristics of ecDNA in human tumors. This study examines the abundance, sequence conservation, and distribution of ecDNA in PDX models relative to their originating tumors across a range of pediatric cancers, especially pediatric brain tumors. We analyzed whole-genome sequencing (WGS) data from 311 samples spanning 261 patients across 32 pediatric cancer types, including 117 PDX models for which WGS of the primary tumor was also available. This allows for a direct comparison of ecDNA amplifications in the human tumor and the derived PDX model. Our findings reveal that among ecDNA-positive primary tumors, 88% generated ecDNA-positive PDX models, underscoring the preservation of ecDNA during the process of PDX model establishment. Furthermore, multiome single-cell RNA and ATAC-sequencing enabled the comparison of intratumoral ecDNA heterogeneity between a primary medulloblastoma tumor and corresponding PDX model. While approximately 9% of cells in the primary tumor contained ecDNA amplifications, we observed ecDNA in nearly all PDX tumor cells, suggesting clonal selection of ecDNA-positive tumor cells during PDX establishment. In summary, tumor cells with ecDNA are ubiquitously represented in PDX models and contain conserved ecDNA sequence and oncogenes found in the original tumor.
Kenkre et al. (2025) studied this question.