Over the full duration of CancerCirculome, we made substantial progress in understanding the structure, function, and clinical relevance of extrachromosomal circular DNA.
First, we developed a suite of new technologies to study ecDNA, including computational methods for reconstructing complex circular DNA structures from sequencing data (DeCoil), and a single-cell sequencing method (scEC&Tseq) that allows simultaneous analysis of ecDNA and gene expression. These tools enabled us to map ecDNA architecture and heterogeneity at unprecedented resolution.
Using these approaches, we demonstrated that ecDNA is highly heterogeneous across cancer cells and is inherited in a non-Mendelian manner, generating rapid variability in oncogene copy number. We further showed that ecDNA can form spatial clusters (“ecDNA hubs”) within the nucleus, enabling cooperative regulation of oncogenes.
Importantly, we established that ecDNA is a dynamic driver of therapy resistance. Cancer cells can increase or decrease ecDNA copy number under treatment pressure, allowing rapid adaptation without requiring genetic mutations. This reveals a new mechanism of tumor evolution.
In the final phase of the project, we uncovered mechanisms that explain how ecDNA is maintained in dividing cells, identified its three-dimensional organization using new computational approaches (ec3D), and demonstrated that circular DNA can also contribute to tumor-promoting processes such as inflammation.
Finally, we translated these findings into clinical applications by developing liquid biopsy approaches that detect tumor-specific circular DNA features in patient blood, enabling improved disease monitoring.
