Researchers have discovered a vulnerability in extrachromosomal DNA (ecDNA) — circular fragments of genetic material found in approximately 17% of cancer cases that can provide tumor cells with additional copies of genes that promote their growth. Experiments have shown that blocking one of the DNA repair mechanisms makes these rings unstable and leads to their gradual loss by cancer cells. In the future, this mechanism could become a way to increase the sensitivity of certain tumors to therapy.

Normally, most human DNA is packaged into chromosomes. However, some cancer cells contain extrachromosomal DNA, or ecDNA. It consists of large circular DNA fragments, up to millions of base pairs in size, that exist separately from normal chromosomes. These rings often contain additional copies of oncogenes — genes whose activity contributes to tumor development. Unlike chromosomes, ecDNA is distributed between daughter cells more randomly during cell division. As a result, cells with different numbers of copies of important genes can rapidly emerge within the same tumor. This variability helps tumors adapt to changing conditions and pressure from drugs. The presence of ecDNA has been associated with aggressive progression of certain cancers, resistance to therapy, and poorer clinical outcomes.

However, the circular form of DNA also creates vulnerabilities. Researchers discovered regions in ecDNA that are particularly prone to damage. These regions contain a high number of repetitive TA sequences, in which the bases thymine and adenine alternate with each other. When genes located on ecDNA are actively expressed, the DNA molecule experiences mechanical stress and can become twisted. TA-rich regions can then form unusual cruciform structures. Double-strand DNA breaks occur particularly frequently at these sites. To preserve circular DNA, cancer cells must constantly prevent such damage or repair it when it occurs.

The scientists identified a two-step protective system. The FANCM protein helps eliminate potentially dangerous structures before the DNA breaks. If a break nevertheless occurs, another mechanism — microhomology-mediated end joining (MMEJ) — participates in repairing the damage. One of its key components is DNA polymerase theta, known as Polθ. Polθ appears to be a potentially vulnerable link in this system. When researchers inhibited its activity, damage accumulated in the circular DNA. The ecDNA became unstable, some damaged rings ended up in micronuclei — small structures separate from the main cell nucleus — and the amount of ecDNA gradually decreased.

The effect was selective. Inhibiting other major DNA repair mechanisms did not lead to the same pronounced loss of ecDNA. Single-cell whole-genome sequencing also showed that disruption of Polθ or FANCM activity is accompanied by rearrangements of circular DNA, with breakpoints occurring particularly often in regions containing TA repeats.