Round DNA Teaches Tumors to Play Hide and Seek: How ecDNA Makes Cancer Cells Invulnerable

Cancer Discovery showed why some tumors adapt to treatment so quickly. When the key oncogene is located not on the chromosome, but on the extrachromosomal DNA (ecDNA - small DNA rings), the number of its copies in cells constantly "jumps" due to the uneven distribution of these rings during division. As a result, in the same tumor, cells with very high and low "dosage" of the oncogene coexist - and they respond differently to therapy. In a model of high-risk neuroblastoma (childhood cancer), the authors showed that it is this "dose diversity" that accelerates tumor evolution and breaks the clinical effectiveness of standard approaches. Moreover, cells with a small number of ecDNA rings go into senescence ("hibernation") and survive chemotherapy, and then can "wake up" - this is how a relapse occurs. Scientists have proposed a strategy for the targeted "finishing off" of such dormant cells.

Background

What is ecDNA and why is it important?
Extrachromosomal DNA (ecDNA) is a small, centromere-less DNA ring that often carries oncogenes and enhancers. Its presence is associated with aggressive disease progression and poorer prognosis in a number of cancers; large genome panels have shown that ecDNA is present in approximately one-sixth of patients and is associated with lower survival compared with linear (chromosomal) amplifications.

Key feature: "breaks" inheritance
Since ecDNA do not have centromeres, they are distributed unevenly between daughter cells during mitosis. As a result, a "motley" landscape of oncogene copy number (dosage) quickly arises in one tumor - fertile ground for rapid adaptation to therapy. Live visualizations also showed clustering in so-called ecDNA hubs, where the transcription of "cargo" oncogenes is concentrated.

Regulatory tricks of ecDNA
The rings pull along not only genes, but also rebuilt regulatory landscapes (enhancer-hacking, hubs), which further increases oncogene expression and enhances the phenotype. These features distinguish ecDNA amplifications from classical chromosomal copies and partially explain their connection with tumor aggressiveness.

Neuroblastoma and MYCN on ecDNA
In neuroblastoma, MYCN amplification is a key high-risk driver; often, extra copies of MYCN are found on ecDNA. Recent papers and clinical abstracts suggest that ecDNA-MYCN creates specific vulnerabilities (e.g., dependence on DNA damage response pathways, CHK1) and facilitates rapid “switching” of cellular states under therapy pressure.

Why ecDNA interferes with treatment
Due to the rapid intercellular variability of oncogene doses (sometimes too much, sometimes too little), the tumor population always contains subclones that survive the drug hit and “replace” the tumor composition. Review and experimental works from 2022-2025 describe how ecDNA accelerates evolution, increases heterogeneity and resistance to treatment.

New mechanistic clues (context to the article)
Recent studies reveal additional elements of the picture: ecDNA has disorganized replication and is vulnerable to transcription/replication conflicts; mechanisms of “tethering” and clustering in mitosis are observed, helping the rings to avoid degradation. This suggests therapeutic ideas - from enhancing transcription↔replication conflicts to targeting checkpoints (e.g. CHK1).

Practical implications
In the clinic, two directions are increasingly discussed: (1) ecDNA biomarkers for early risk stratification and monitoring; (2) combinations that hit not only fast-growing subclones with a high dose of oncogene, but also “survival reservoirs” - cells with low copy numbers that go into dormancy/senescence and are capable of triggering a relapse.

This context explains why the new work in Cancer Discovery focuses specifically on ecDNA-related oncogene dose heterogeneity and on combination therapy windows in MYCN-positive tumors.

What did they do?

• We combined mathematical models of tumor cell "fitness" depending on the number of oncogene copies with single-cell measurements of ecDNA and phenotyping. We worked on cell lines, patient xerotransplants in mice, and primary neuroblastoma samples where the MYCN oncogene is amplified on ecDNA.
• We traced how asymmetric distribution of ecDNA during mitosis creates intercellular copy number diversity and how this switches cell fates (sensitivity to therapy vs. “hibernation”).

Main results

• ecDNA → "oncogene dose on the wheel" regulates phenotype. The more copies of MYCN on ecDNA, the more aggressive the growth - but the higher the short-term sensitivity to chemotherapy. Cells with fewer rings go into senescence (are metabolically active but do not divide), survive treatment, and can reactivate later.
• Such oncogenic "dose" variegation is a property of ecDNA, not classical chromosomal amplifications: the rings do not obey Mendelian inheritance, they divide "as they have to", quickly changing the composition of clones. This gives the tumor an evolutionary advantage under the pressure of therapy.
• The team outlined a therapeutic loophole: targeting senescent cells with low ecDNA counts in addition to standard treatment to close the door to relapse. (The approach is described as a proof of concept; further preclinical testing is needed.)

Why is this important?

• ecDNA is a marker of "evil" tumors. ecDNA is detected in ~17% of tumors in patients; they are associated with resistance and poor prognosis. New work shows the mechanism of how ecDNA destroys the effectiveness of therapy: through the dynamics of oncogene doses and the emergence of dormant "zombie" cells. This explains late relapses, in particular in neuroblastoma.
• Pinpoint vulnerabilities. Since ecDNA creates special cell states, they can be targeted. The “anti-ecDNA” direction is already developing (for example, exploiting vulnerabilities in the response to DNA damage, CHK1, etc.), and a new study suggests another scenario - a blow to senescent reservoirs after the main therapy.

How does this fit into the ecDNA field?

In recent years, ecDNA has transformed from a “cytogenetic curiosity” into a central topic in oncology: it has been found that ring elements carry oncogenes, enhancers, and immunoregulatory genes, increase the expression of “cargo,” and accelerate intratumor heterogeneity. The work by Montuori et al. adds a direct link between ecDNA copy number → phenotype → treatment response and indicates a specific target for preventing relapses.

Restrictions

This is preclinical work (cells, xenomodels, sample analyses). The proposed strategy of "finishing off" senescent cells requires selection of drugs, doses and timing, and separate safety testing. Generalization to tumors without ecDNA amplifications is questionable.

What's next?

• To identify drug combinations that effectively clear senescent reservoirs after first-line therapy.
• Develop ecDNA biomarkers (including liquid ones) for early detection of patients at risk of relapse and monitoring the dynamics of oncogene copy number during treatment.
• To test approaches against ecDNA-positive tumors in expanded preclinical models and early clinical studies.

Source: Montuori G. et al. Cancer Discovery (online 7 August 2025); MDC Berlin and EurekAlert press materials; review articles on the role of ecDNA in resistance and prognosis. https://doi.org/10.1158/2159-8290.CD-24-1738