Abstract Extrachromosomal DNA (ecDNA) amplification represents one of the critical mechanisms driving cancer evolution and progression. In medulloblastoma, ecDNA is present in approximately 18% of cases and correlates with poor patient survival, yet its role in tumor progression and treatment resistance remains poorly characterized. This study investigates how ecDNA dynamics influence therapy resistance in medulloblastoma, with a particular focus on tumors harboring MYC amplifications. Using patient-derived xenografts established from tumors biopsies collected at Rady Children’s Hospital-San Diego and cell line models, we track tumor response and ecDNA copy number alterations during standard-of-care treatment, which includes radio- and chemotherapy. Multiome single-cell sequencing analysis is employed to identify therapy-induced emergence of novel ecDNA variants. Furthermore, we integrate RNA sequencing with CRISPR(i)-based functional genomics to investigate medulloblastoma tumors containing ecDNA-amplified genes of unknown significance but lacking canonical oncogenes. This comprehensive approach aims to elucidate the mechanistic role of ecDNA in medulloblastoma evolution and therapeutic resistance, with potential at identifying novel therapeutic vulnerabilities.
Wang et al. (2025) studied this question.