Publications

2026

Yi H, Zhang S, Swinderman J, Wang Y, Kanakaveti V, Hung KL, Wong IT, Srinivasan, Curtis EJ, Bhargava-Shah A, Li R, Jones MG et al. EcDNA-borne structural variants drive oncogenic fusion transcript amplification, Cell (2026). Read Full Article

Sankar V, Hung KL, Gnanasekar A, Wong IT, Shi Q, Kraft K, Jones MG, He BJ, Yan X, Belk JA, Liu KJ, Agarwal S, Wang SK, Henssen AG, Mischel PS, Chang HY. Genetic elements promote retention of extrachromosomal DNA in cancer cells. Nature. 2026 Jan;649(8095):152-160. Read Full Article

2025

Chowdhury B, Zhu K, Li C, Alsing J, Luebeck J, Stefanova ME, Chapman OS, Kraft K, Zhang S, Lim JYS, Xie Y, Kim YJ, Wu S, Chavez L, Nir G, Henssen AG, Mischel PS, Chang HY, Bafna V. Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D. Nat Commun. 2025 Dec 20. Read Full Article

Kraft K, Murphy SE, Jones MG, Shi Q, Bhargava-Shah A, Luong C, Hung KL, He BJ, Li R, Park SK, Montgomery MT, Weiser NE, Wang Y, Luebeck J, Bafna V, Boeke JD, Mischel PS, Boettiger AN, Chang HY. Enhancer activation from transposable elements in extrachromosomal DNA. Nat Cell Biol. 2025 Nov;27(11):1914-1924. Read Full Article

Montuori G, Tu F, Qin D, Schmargon R, Rodriguez-Fos E, Helmsauer K, Hui H, Mandal S, Purshouse K, Fankhänel L, Bosco B, Spanjaard B, Seyboldt H…Werner B, Huang W, Henssen AG, Dörr JR. Extrachromosomal DNA-Driven Oncogene Dosage Heterogeneity Promotes Rapid Adaptation to Therapy in MYCN-Amplified Cancers. Cancer Discov. 2025 Oct 6;15(10):2054-2077. Read Full Article

Noorani I, Haughey M, Luebeck J, Rowan A, Grönroos E, Terenzi F, Wong IT, Pradella D, Lisi M, Kittel J, Sharma N, Bailey C, Weeden CE, Bell DM, Joo E, Barbè V, Jones MG, Hung KL, Nye EL, Green M, Meader L, Norton EJ, Fabian M, Kanu N, Jamal-Hanjani M, Santarius T, Ventura A, Nicoll JAR, Boche D, Chang HY, Bafna V, Huang W, Mischel PS, Swanton C, Werner B. Extrachromosomal DNA-Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma. Cancer Discov. 2025 Oct 6;15(10):2078-2095. Read Full Article

Haughey M, Noorani I, Swanton C, Mischel PS, Werner B. Extrachromosomal DNA: shaping the evolutionary dynamics of cancer. Trends Cancer. 2025 Sep;11(9):901-916. Read Full Article

Drexler R, Drinnenberg A, Gavish A, Yalçin B, Shamardani K, Rogers AE, Mancusi R, Trivedi V, Taylor KR, Kim YS, Woo PJ, Soni N…Monje M. Cholinergic neuronal activity promotes diffuse midline glioma growth through muscarinic signaling. Cell. 2025 Aug 21;188(17):4640-4657.e30. Read Full Article

Yi E, Gujar AD, Zhao D, Suina K, Jin X, Pardon K, Yu Q, Kagermazova L, Korsah EE, Dusseau NA, Boeke JD, Henssen AG, Verhaak RGW. Selective Depletion of Cancer Cells with Extrachromosomal DNA via Lentiviral Infection. Cancer Res Commun. 2025 Aug 1;5(8):1458-1465. Read Full Article

Laplane L, Lamoureux A, Richker HI, Marquez Alcaraz G, Fortunato A, Shaffer Z, Aktipis A, Mischel PS, Plutynski A, Townsend JP, Maley CC. Applying multilevel selection to understand cancer evolution and progression. PLoS Biol. 2025 Jul 18;23(7):e3003290. Read Full Article

Weiser NE, Watkins TBK, Chang HY, Mischel PS. A Guide to Extrachromosomal DNA: Cancer’s Dynamic Circular Genome. Cancer Discov. 2025 Jun 3;15(6):1105-1114. Read Full Article

Yost, K.E., Zhao, Y., Hung, K.L. et al. Three-dimensional genome landscape of primary human cancers. Nat Genet 57, 1189–1200 (2025). Read Full Article

Huang YH, Belk JA, Zhang R, Weiser NE, Chiang Z, Jones MG, Mischel PS, Buenrostro JD, Chang HY. Unified molecular approach for spatial epigenome, transcriptome, and cell lineages. PNAS 2025 Apr 18;122(16):e2424070122. Read Full Article

Nakagawa, T., Luebeck, J., Zhu, K. et al. Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer. Nat Commun 16, 2964 (2025). Read Full Article

Koh, G.C.C., Nanda, A.S., Rinaldi, G. et al. A redefined InDel taxonomy provides insights into mutational signatures. Nat Genet 57, 1132–1141 (2025). Read Full Article

Lv W, Zeng Y, Li C, Liang Y, Tao H, Zhu Y, Sui X, Li Y, Jiang S, Gao Q, Rodriguez-Fos E, Prasad G, Wang Y, Zhou R, Xu Z, Pan X, Chen L, Xiang X, Teng H, Sun C, Qin T, Dong W, Li Y, Lan X, Li X, Lin L, Bolund L, Yang H, Verhaak RGW, Faltas BM, Hansen JB, Wu S, Mischel PS, Henssen AG, Bafna V, Luebeck J, Regenberg B, Luo Y, Lin C, Han P. Spatial-Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and Tumor-Immune Microenvironment. Cancer Discov. 2025 Mar 11. Read Full Article

Raeisi Dehkordi, S., Wong, I.TL., Ni, J. et al. Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity. Nat Commun 16, 1497 (2025). Read Full Article

Rose JC, Belk JA, Wong IT, Luebeck J, Horn HT, Daniel B, Jones MG, Yost KE, Hung KL, Kolahi KS, Curtis EJ, Kuo CJ, Bafna V, Mischel PS, Chang HY. Disparate Pathways for Extrachromosomal DNA Biogenesis and Genomic DNA Repair. Cancer Discov. 2025 Jan 13;15(1):69-82. Read Full Article

Yang, QL., Xie, Y., Qiao, K., Li, J.Y.S., Wu, S. Modern biology of extrachromosomal DNA: A decade-long voyage of discovery. Cell Res 35, 11–22 (2025). Read Full Article

2024

Bei Y, Brame L, Kirchner M, Fritsche-Guenther R, Kunz S, Bhattacharya A, … Henssen AG. (2024). Passenger gene co-amplifications create collateral therapeutic vulnerabilities in cancer. Cancer discovery. Read Full Article

Pradella D, Zhang M, Gao R, Yao MA, Gluchowska KM, Cendon-Florez Y, Mishra T, La Rocca G, Weigl M, Jiao Z, Nguyen HHM, Lisi M et al. Engineered extrachromosomal oncogene amplifications promote tumorigenesis. Nature. 2024 Dec 18. Read Full Article

Tang, J., Weiser, N.E., Wang, G. et al. Enhancing transcription–replication conflict targets ecDNA-positive cancers. Nature 635, 210–218 (2024). Read Full Article

Hung, K.L., Jones, M.G., Wong, I.TL. et al. Coordinated inheritance of extrachromosomal DNAs in cancer cells. Nature 635, 201–209 (2024). Read Full Article

Bailey, C., Pich, O., Thol, K. et al. Origins and impact of extrachromosomal DNA. Nature 635, 193–200 (2024). Read Full Article

Kim, H., Kim, S., Wade, T. et al. Mapping extrachromosomal DNA amplifications during cancer progression. Nat Genet 56, 2447–2454 (2024). Read Full Article

Giurgiu M, Wittstruck N, Rodriguez-Fos E, Chamorro González R, Brückner L, Krienelke-Szymansky A, Helmsauer K, Hartebrodt A, Euskirchen P, Koche RP, Haase K, Reinert K, et al. Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Genome Res. 2024 Oct11;34(9):1355-1364. Read Full Article

Zhu K, Jones MG, Luebeck J, Bu X, Yi H, Hung KL, Wong IT, Zhang S, Mischel PS, Chang HY, Bafna V. CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. Genome Res. 2024 Oct 11;34(9):1344-1354. Read Full Article

Njomen E, Hayward RE, DeMeester KE, Ogasawara D, Dix MM, Nguyen T, Ashby P, Simon GM, Schreiber SL, Melillo B, Cravatt BF. Multi-tiered chemical proteomic maps of tryptoline acrylamide-protein interactions in cancer cells. Nat Chem. 2024 Oct;16(10):1592-1604. Read Full Article

Stöber MC, Chamorro González R, Brückner L, Conrad T, Wittstruck N, Szymansky A, Eggert A, Schulte JH, Koche RP, Henssen AG, Schwarz RF, Haase K. Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity. Cell Rep. 2024 Sep 24;43(9):114711. Read Full Article

Lin MS, Jo SY, Luebeck J, Chang HY, Wu S, Mischel PS, Bafna V. Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors. Elife. 2024 Jun 19;12:RP88895. Read Full Article

Noorani I, Luebeck J, Rowan A, Grönroos E, Barbe V, Fabian M, Nicoll JAR, Boche D, Bafna V, Mischel PS, Swanton C. Oncogenic extrachromosomal DNA identification using whole-genome sequencing from formalin-fixed glioblastomas. Ann Oncol. 2024 Jun;35(6):570-573. Read Full Article

Curtis EJ, Rose JC, Mischel PM, Chang HY. 2024. Extrachromosomal DNA: Biogenesis and Functions in Cancer. Annu. Rev. Cancer Biol. 2024. 8:135–53 Read Full Article

Pal Choudhuri S, Girard L, Lim JYS, Wise JF, Freitas B, Yang D, Wong E, Hamilton S, Chien VD, Kim YJ, Gilbreath C, Zhong J et al. Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs. Cancer Discov. 2024 May 1;14(5):804-827. Read Full Article

Liu Z, Remsberg JR, Li H, Njomen E, DeMeester KE, Tao Y, Xia G, Hayward RE, Yoo M, Nguyen T, Simon GM, Schreiber SL et al. Proteomic Ligandability Maps of Spirocycle Acrylamide Stereoprobes Identify Covalent ERCC3 Degraders. J Am Chem Soc. 2024 Apr 17;146(15):10393-10406. Read Full Article

Yan, X., Mischel, P. & Chang, H. Extrachromosomal DNA in cancer. Nat Rev Cancer 24, 261–273 (2024). Read Full Article

2023

Chamorro González R, Conrad T, Stöber MC, Xu R, Giurgiu M, Rodriguez-Fos E, … Henssen AG. (2023). Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nature genetics, 55(5), pp. 880-890. Read Full Article

Chapman OS, Luebeck J, Sridhar S, Wong IT, Dixit D, Wang S, … Chavez L. (2023). Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nature genetics, 55(12), pp. 2189-2199. Read Full Article

Cravatt BF. (2023). Activity-based protein profiling – finding general solutions to specific problems. Israel journal of chemistry, 63(3-4). Read Full Article

Lazear MR, Remsberg JR, Jaeger MG, Rothamel K, Her HL, DeMeester KE, … Cravatt BF. (2023). Proteomic discovery of chemical probes that perturb protein complexes in human cells. Molecular cell, 83(10), pp. 1725-1742.e12. Read Full Article

Luebeck J, Ng AWT, Galipeau PC, Li X, Sanchez CA, Katz-Summercorn AC, … Mischel PS. (2023). Extrachromosomal DNA in the cancerous transformation of Barrett’s oesophagus. Nature, 616(7958), pp. 798-805. Read Full Article

Pusch FF, Dorado Garcia H, Xu R, Gürgen D, Bei Y, Brückner L, … Henssen AG. (2023). Elimusertib has anti-tumor activity in preclinical patient-derived pediatric solid tumor models. Molecular cancer therapeutics. Read Full Article

Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, … Chen C. (2023). Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proceedings of the National Academy of Sciences, (20). Read Full Article

Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, … Henssen AG. (2023). Mutational topography reflects clinical neuroblastoma heterogeneity. Cell genomics, 3(10), pp. 100402. Read Full Article

2022

Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong IT, … Chang HY. (2022). Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH. Nature genetics, 54(11), pp. 1746-1754. Read Full Article

Hung KL, Mischel PS, Chang HY. (2022). Gene regulation on extrachromosomal DNA. Nature structural & molecular biology, 29(8), pp. 736-744. Read Full Article

Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, … Mischel PS. (2022). The evolutionary dynamics of extrachromosomal DNA in human cancers. Nature genetics, 54(10), pp. 1527-1533. Read Full Article

Noorani I, Mischel PS, Swanton C. (2022). Leveraging extrachromosomal DNA to fine-tune trials of targeted therapy for glioblastoma: opportunities and challenges. Nature reviews. Clinical oncology, 19(11), pp. 733-743. Read Full Article

Pecorino LT, Verhaak RGW, Henssen A, Mischel PS. (2022). Extrachromosomal DNA (ecDNA): an origin of tumor heterogeneity, genomic remodeling, and drug resistance. Biochemical Society transactions, 50(6), pp. 1911-1920. Read Full Article

Weiser NE, Hung KL, Chang HY. (2022). Oncogene Convergence in Extrachromosomal DNA Hubs. Cancer discovery, 12(5), pp. 1195-1198. Read Full Article