Extrachromosomal DNA: A New Therapeutic Frontier for Overcoming Cancer Drug Resistance

Extrachromosomal DNAs (ecDNAs) are acentric circular DNA molecules that frequently harbor amplified oncogenes and their regulatory elements. Although ecDNAs occur at low levels in normal cells, oncogenic ecDNAs are enriched in cancer, where they promote tumor evolution, intratumoral heterogeneity, and therapeutic resistance. Advances in long-read sequencing, single-cell multi-omics, and high-resolution imaging have provided new insights into their biogenesis, structure, inheritance, and function. EcDNAs can arise through chromothripsis, breakage–fusion–bridge cycles, replication stress, and aberrant DNA repair, all of which lead to the excision, circularization, and amplification of genomic fragments. Because they lack centromeres and telomeres, ecDNAs undergo dynamic copy-number variation, enhanced chromatin accessibility, enhancer rewiring, and non-Mendelian segregation, thereby facilitating rapid adaptation to selective pressures. EcDNAs contribute to resistance to chemotherapy, targeted therapy, and radiotherapy, and they may also promote immune evasion and immunotherapy resistance through oncogene amplification, enhancer-driven transcription, ecDNA hub formation, and remodeling of the tumor microenvironment. Here, we review recent advances in ecDNA biogenesis, inheritance, and function, with an emphasis on therapeutic resistance, and we discuss emerging strategies that target ecDNA formation, maintenance, and segregation, as well as ecDNA hubs, DNA damage response (DDR) pathways, and replication stress. Collectively, these advances highlight the potential of ecDNA-based biomarkers and ecDNA-directed therapies in precision oncology.