Oncogene Silencing via ecDNA Micronucleation PMID: 40321211

ADC Targets in Oncology

2026-04-10

Oncogene Silencing via ecDNA Micronucleation

bioRxiv. 2025 Apr 18:2025.04.15.648906. doi: 10.1101/2025.04.15.648906.

Lotte Brückner ¹ ² ³ , Robin Xu ² ³ , Jun Tang ⁴ ⁵ , Alexander Herrmann ² , Ivy Tsz-Lo Wong ⁴ ⁵ , Shu Zhang ⁴ ⁵ , Fengyu Tu ⁶ , Madison Pilon ² , Alexander Kukalev ¹ ⁷ , Katharina Pardon ² ³ , Olga Sidorova ² ³ , Joshua Atta ² ³ , Qinghao Yu ² ³ , Davide Pradella ⁸ , Mila Ilić ⁹ , Marco-Novais-Cruz ⁹ , Sarah Kaltenbach ¹⁰ , Denise Treue ¹¹ , Madalina Giurgiu ² ³ , Sergej Herzog ¹ ⁷ , Ann-Sophie Hollinger ² ³ , Martina Fernandez ² ³ , Finnja Becker ² ³ , Varvara-Rigina Louma ² ³ , Rachel Schmargon ² ³ , Jan Dörr ² ³ , David Gamlin ² ³ , Annika Lehmann ¹¹ , Dennis Gürgen ¹² , Matthias Richter ¹³ , Frank Dubois ¹¹ , Fabrizio Simeoni ¹⁴ , Betheney R Pennycook ¹⁴ , Alastair Hamilton ¹⁴ , Ralph K Lindemann ¹⁴ , Matthias Fischer ¹⁵ ¹⁶ , Vineet Bafna ¹⁷ , Geoffrey Wahl ¹⁸ , Richard P Koche ¹⁹ , Howard Y Chang ²⁰ , Stamatis Papathanasiou ¹⁰ , René Medema ⁹ , Bastiaan Spanjaard ² ³ , Andrea Ventura ⁸ , Ana Pombo ¹ ⁷ ²¹ ²² , Weini Huang ²³ , Benjamin Werner ²⁴ , Paul S Mischel ⁴ ⁵ , Anton G Henssen ¹ ² ³ ²⁵

Affiliations

1. Max Delbrück Center for Molecular Medicine, Berlin, Germany.
2. Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Germany.
3. Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany.
4. Department of Pathology, Stanford University School of Medicine.
5. Sarafan ChEM-H, Stanford University.
6. Group of Theoretical Biology, The State Key Laboratory of Bio-control, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
7. Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany.
8. Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
9. Princess Maxima Center for Pediatric Oncology.
10. Institute of Molecular Biology, Mainz, Germany.
11. Institute of pathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Germany.
12. Experimental Pharmacology and Oncology (EPO), Berlin, Germany.
13. Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
14. Econic Biosciences, London, United Kingdom.
15. Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.
16. Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany.
17. University of San Diego, California, USA.
18. Salk Institute for Biological Studies, San Diego, USA.
19. Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
20. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
21. Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
22. Berlin Institute of Health, Berlin, Germany.
23. Queen Mary University of London, London, UK.
24. Evolutionary Dynamics Group, Centre for Cancer Evolution, Barts Cancer Institute, Queen Mary University London, UK.
25. German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.

Abstract

Extrachromosomal DNA (ecDNA) is a common source of oncogene amplification across many types of Cancer. The non-Mendelian inheritance of ecDNA contributes to heterogeneous tumour genomes that rapidly evolve to resist treatment. Here, using single-cell and live-cell imaging, single-micronucleus Sequencing, and computational modelling, we demonstrate that elevated levels of ecDNA predisposes cells to micronucleation. Damage on ecDNA, commonly arising from replication stress, detaches ecDNA from the chromosomes upon which they hitchhike during cell division, thereby causing micronucleus formation in daughter cells. Clusters of oncogene-containing, CIP2A-TOPBP1-associated ecDNA molecules form, and asymmetrically segregate into daughter cell micronuclei during cell division. ecDNA chromatin remains highly active during Mitosis, but upon micronucleation, it undergoes suppressive chromatin remodeling, largely ceasing oncogene transcription. These studies provide insight into the fate of damaged ecDNA during cell division.