UC San Diego

Technological and scientific advances have allowed for a deeper understanding of human cancer and have led to rapid characterization and development of personalized treatments for many patients. Despite these advances, many tumors continue to develop resistance to their prescribed therapies. One mechanism of treatment resistance is through oncogene amplification on extrachromosomal DNA (ecDNA). ecDNA are acentric, circular fragments of genomic DNA, which are prevalent in many of the most aggressive cancers and are associated with poor patient prognosis. Unfettered by the constraints of linear chromosomes, ecDNA leads to novel genomic interactions, highly heterogeneous tumors, and rapid tumor evolution. Here, we report a series of studies investigating the unique cell biology of ecDNA. Due to the lack of centromeres, ecDNA does not follow the laws of Mendelian inheritance and can, therefore, be inherited asymmetrically. Using orthogonal sequencing-based and live-cell imaging technologies, we witness the rapid development of copy number heterogeneity and the dynamic nature of ecDNA copy number. Through live-cell imaging and four-dimensional image analysis, we witness a single cell giving rise to a highly diverse population of cells after only three cell divisions. Additionally, we report that many cancers have amplification of multiple oncogenes on distinct ecDNA species. We show that this co-occurrence is, in part, due to intermolecular interactions that allow for their coordinated inheritance during cell division. Taken together, the series of studies presented herein offer novel insight into ecDNA biology and begin to explain the functional implications of ecDNA copy number heterogeneity and the ability of ecDNA-containing cells to rapidly adapt to their microenvironment. These data indicate that the unique biology of ecDNA allows for the maintenance of important intermolecular interactions while driving rapid development of intratumoral heterogeneity.