A major focus of the group is understanding the links between replication and mutagenesis. Extrachromosomal DNA (ecDNA) circles are present in a substantial proportion of cancers and frequently harbour oncogenes that drive tumour proliferation. The mechanisms governing their replication, and the extent to which this mirrors replication of the corresponding chromosomal loci, remain poorly understood. In addition to self-maintenance, ecDNAs can reintegrate into the host genome, often forming tandem arrays known as homogenously staining regions (HSRs). Such reintegration events have the potential to disrupt chromosome architecture, yet the molecular processes underlying this transition remain unclear.
Our recent work shows that ecDNA replication is disorganised both in the location of DNA synthesis initiation and in its timing during S phase. Replication on ecDNA also appears more fragile, with increased fork stalling. How these stalled forks are rescued, and whether the underlying mechanisms are linked to ecDNA reintegration, is unknown.
This project will employ established ecDNA-containing cancer cell line models alongside synthetic ecDNA constructs. Using CRISPR-based genetic perturbations combined with high-resolution replication mapping, we will dissect the molecular mechanisms that sustain ecDNA replication and examine how these processes interface with pathways leading to reintegration. These questions have relevance beyond cancer biology: the Synthetic Human Genome (SynHG) project proposes to build synthetic chromosomes in part via episomal intermediates that must ultimately integrate into the host genome. Insights into how natural ecDNA circles achieve stable reintegration will help define the mechanisms and sequence features governing efficient, high-fidelity integration of engineered episomes, informing next-generation genome-writing strategies. Our ultimate aim is to clarify the balance between ecDNA maintenance and reintegration, understand how this balance shapes genome architecture and tumour evolution and apply this knowledge to harnessing episomal integration for synthetic genomics.