Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway

Wang, Y.; Cope, O.; Chen, J.; Mehta, A.; Fleifel, D.; Ford, C.; Benhamie, P.; Haase, S.; Gulec, S.; Elston, T.; Spanheimer, P. M.; Tomblin, C. A.; Rojas, A.; Tate, T.; Purvis, J.; Wang, J. R.; Dahl, J. M.; Wolff, S. C.; Cook, J.; Brunk, E. C.

doi:10.1101/2025.04.26.650733

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bioRxiv · 10.1101/2025.04.26.650733

Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway

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Abstract

During tumor progression, it has been assumed that individual cells that have acquired advantageous mutations overtake the population. Cancers driven by extrachromosomal DNA (ecDNA) do not follow this paradigm. Instead, these tumors have a spectrum of oncogene copy numbers across cells, and graded ecDNA variation may function as a form of bet-hedging that equips tumors with a broad range of phenotypes. Using imaging, single-cell multiomics, and multiplexed proteomics, we systematically characterized ecDNA levels across thousands of single cells. Higher ecDNA dosage produces proportional changes in transcript abundance, chromatin accessibility, protein levels, cell-cycle progression, and proliferation. Genes amplified on ecDNA exhibit distinct transcriptional scaling regimes that shift when the same genes are reintegrated into chromosomal homogeneous staining regions. When we experimentally disrupted the continuum of ecDNA dosage by sorting cells into low- and high-copy number states, the population rapidly recovered its original, continuous distribution. Our time-course data, live-cell imaging, and stochastic models collectively show that restoring this spectrum is an active, deterministic process rather than the passive outcome of random segregation. Together, these findings position ecDNA-mediated expression as a distinct evolutionary mechanism that endows tumors with rapid, population-level adaptability. These findings offer insight into why ecDNA-driven cancers are among the most aggressive and treatment-resistant.

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Wang, Y., Cope, O., Chen, J., Mehta, A., Fleifel, D., Ford, C., Benhamie, P., Haase, S., Gulec, S., Elston, T., Spanheimer, P. M., Tomblin, C. A., Rojas, A., Tate, T., Purvis, J., Wang, J. R., Dahl, J. M., Wolff, S. C., Cook, J., Brunk, E. C.. 2025-04-29. Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway. https://doi.org/10.1101/2025.04.26.650733

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