Extrachromosomal DNA in cancer: Molecular mechanisms underlying oncogene amplification and tumor heterogeneity

Extrachromosomal DNA (ecDNA) is a large (typically >5 kb), functional, circular double-stranded DNA molecule that exists independently of chromosomes within the cell nucleus. Its widespread presence in human tumors and crucial role in tumorigenesis have garnered notable attention. Critically, in cancer, they often carry full-length oncogenes along with their regulatory elements. They are distinguished by their ability to rapidly amplify copy number, display a non-Mendelian pattern of segregation, and maintain a highly accessible chromatin structure. Altogether, these features provide a molecular basis underlying ecDNA-mediated promotion of tumorigenesis and tumor heterogeneity. Various technological advances, such as high-throughput sequencing, single-cell analysis, and real-time imaging, have significantly contributed to the study of ecDNA. This review aims to systematically summarize the mechanisms underlying ecDNA formation, its genetic properties, and ecDNA-associated molecular mechanisms that promote tumorigenesis and tumor heterogeneity. This review attaches importance to oncogene amplification, enhancer hijacking, ecDNA hub formation, and the synergistic regulation of multiple molecules. Notably, ecDNA hubs are transcriptionally active structures formed by the spatial aggregation of multiple oncogene-bearing ecDNA molecules. This co-localization enables robust intermolecular transcriptional regulation, amplifying oncogene expression and accelerating tumor progression. Furthermore, the random distribution of ecDNA enhances tumor heterogeneity, providing a molecular foundation for selective pressure-induced rapid adaptation and development of drug resistance. Overall, the widespread presence and significant role of ecDNA in cancer make it a promising therapeutic target with potential for clinical applications as a diagnostic biomarker and prognostic predictor.