Representative Publications
EcDNA-borne structural variants drive oncogenic fusion transcript amplification
Hyerim Yi, Shu Zhang, Jason Swinderman, Yanbo Wang, Vishnupriya Kanakaveti, King L. Hung, Ivy Tsz-Lo Wong, Suhas Srinivasan, Ellis J. Curtis, Aarohi Bhargava-Shah, Rui Li, Matthew G. Jones, Jens Luebeck, Chris Bailey, Yanding Zhao, Julia A. Belk, Katerina Kraft, Quanming Shi, Xiaowei Yan, Simon K. Pritchard, Kabir S. Mahajan, Frances Liang, Mariam Jamal-Hanjani, Dean W. Felsher, Luke A. Gilbert, Vineet Bafna, Paul S. Mischel & Howard Y. Chang
Cell, 2026 January, doi: 10.1016/j.cell.2025.12.009
Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D
Biswanath Chowdhury, Kaiyuan Zhu, Chaohui Li, Jessica Alsing, Jens Luebeck, Maria E Stefanova, Owen S Chapman, Katerina Kraft, Shu Zhang, Jun Yi Stanley Lim, Yipeng Xie, Yoon Jung Kim, Sihan Wu, Lukas Chavez, Guy Nir, Anton G Henssen, Paul S Mischel, Howard Y Chang & Vineet Bafna
Nature Communications, 2025 December, doi: 10.1038/s41467-025-67614-7
Genetic elements promote retention of extrachromosomal DNA in cancer cells
Venkat Sankar, King L. Hung, Aditi Gnanasekar, Ivy Tsz-Lo Wong, Quanming Shi, Katerina Kraft, Matthew G. Jones, Britney Jiayu He, Xiaowei Yan, Julia A. Belk, Kevin J. Liu, Sangya Agarwal, Sean K. Wang, Anton G. Henssen, Paul S. Mischel & Howard Y. Chang
Nature, 2025 November, doi: 10.1038/s41586-025-09764-8
Enhancer activation from transposable elements in extrachromosomal DNA
Katerina Kraft, Sedona E Murphy, Matthew G Jones, Quanming Shi, Aarohi Bhargava-Shah, Christy Luong, King L Hung, Britney J He, Rui Li, Seung Kuk Park, Michael T Montgomery, Natasha E Weiser, Yanbo Wang, Jens Luebeck, Vineet Bafna, Jef D Boeke, Paul S Mischel, Alistair N Boettiger & Howard Y Chang
Nature Cell Biology, 2025 October, doi: 10.1038/s41556-025-01788-6
Extrachromosomal DNA-Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma
Imran Noorani, Magnus Haughey, Jens Luebeck, Andrew Rowan, Eva Grönroos, Francesco Terenzi, Ivy Tsz-Lo Wong, Davide Pradella, Marta Lisi, Jeanette Kittel, Natasha Sharma, Chris Bailey, Clare E Weeden, Donald M Bell, Eric Joo, Vittorio Barbè, Matthew G Jones, King L Hung, Emma L Nye, Mary Green, Lucy Meader, Emma J Norton, Mark Fabian, Nnennaya Kanu, Mariam Jamal-Hanjani, Thomas Santarius, Andrea Ventura, James A R Nicoll, Delphine Boche, Howard Y Chang, Vineet Bafna, Weini Huang, Paul S Mischel, Charles Swanton & Benjamin Werner
Cancer Discovery, 2025 October, doi: 10.1158/2159-8290.CD-24-1555
Extrachromosomal DNA: shaping the evolutionary dynamics of cancer
Magnus Haughey, Imran Noorani, Charles Swanton, Paul S Mischel, Benjamin Werner
Science Direct, 2025 September, doi: 10.1016/j.trecan.2025.06.004
A Guide to Extrachromosomal DNA: Cancer's Dynamic Circular Genome
Natasha E Weiser, Thomas B K Watkins, Howard Y Chang & Paul S Mischel
Cancer Discovery, 2025 June, doi: 10.1158/2159-8290.CD-25-0230
Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity
Siavash Raeisi Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, Jens Luebeck, Kaiyuan Zhu, Gino Prasad , Lena Krockenberger, Guanghui Xu, Biswanath Chowdhury, Utkrisht Rajkumar, Ann Caplin, Daniel Muliaditan, Aditi Gnanasekar, Ceyda Coruh, Qiushi Jin, Kristen Turner, Shu Xian Teo, Andy Wing Chun Pang, Ludmil B Alexandrov, Christelle En Lin Chua, Frank B Furnari, John Maciejowski, Thomas G Paulson, Julie A Law, Howard Y Chang, Feng Yue, Ramanuj DasGupta, Jean Zhao, Paul S Mischel & Vineet Bafna
Nature Communications, 2025 February, doi: 10.1038/s41467-025-56670-8
Disparate Pathways for Extrachromosomal DNA Biogenesis and Genomic DNA Repair
John C Rose, Julia A Belk, Ivy Tsz-Lo Wong, Jens Luebeck, Hudson T Horn, Bence Daniel, Matthew G Jones, Kathryn E Yost, King L Hung, Kevin S Kolahi, Ellis J Curtis, Calvin J Kuo, Vineet Bafna, Paul S Mischel & Howard Y Chang
Cancer Discovery, 2025 January, doi: 10.1158/2159-8290.CD-23-1117
Enhancing Transcription–replication Conflict Targets ecDNA-positive Cancers
Jun Tang, Natasha E. Weiser, Guiping Wang, Sudhir Chowdhry, Ellis J. Curtis, Yanding Zhao, Ivy Tsz-Lo Wong, Georgi K. Marinov, Rui Li, Philip Hanoian, Edison Tse, Salvador Garcia Mojica, Ryan Hansen, Joshua Plum, Auzon Steffy, Snezana Milutinovic, S. Todd Meyer, Jens Luebeck, Yanbo Wang, Shu Zhang, Nicolas Altemose, Christina Curtis, William J. Greenleaf, Vineet Bafna, Stephen J. Benkovic, Anthony B. Pinkerton, Shailaja Kasibhatla, Christian A. Hassig, Paul S. Mischel & Howard Y. Chang
Nature, 2024 November, doi: 10.1038/s41586-024-07802-5
Coordinated Inheritance of Extrachromosomal DNAs in Cancer Cells
King L. Hung, Matthew G. Jones, Ivy Tsz-Lo Wong, Ellis J. Curtis, Joshua T. Lange, Britney Jiayu He, Jens Luebeck, Rachel Schmargon, Elisa Scanu, Lotte Bruckner, Xiaowei Yan, Rui Li, Aditi Gnanasekar, Rocio Chamorro Gonzalez, Julia A. Belk, Zhonglin, Liu, Bruno Melillo, Vineet Bafna, Jan R. Dorr, Benjamin Werner, Weini Huang, Benjamin F. Cravatt, Anton G. Henssen, Paul S. Mischel & Howard Y. Chang
Nature, 2024 November, doi: 10.1038/s41586-024-07861-8
Origins and Impact of Extrachromosomal DNA
Chris Bailey, Oriol Pich, Kerstin Thol, Thomas B. K. Watkins, Jens Luebeck, Andrew Rowan, Georigia, Stavrou, Natasha E. Weiser, Bhargavi Dameracharla, Robert Bentham, Wei-Ting Lu, Jeanette Kittel, S. Y. Cindy Yang, Brooke E. Howitt, Natasha Sharma, Maria Litovchenko, Roverto Salgado, King L. Hung, Alex J. Cornish, David, A. Moore, Richard S. Houlston, Vineet Bafna, Howard Y. Chang, Serena Nik-Zainal, Nnennaya Kanu, Micholas McGranahan, Genomics England Consortium, Adrienne M. Flanagan, Paul S. Mischel, Mariam Jamal-Hanjani & Charles Swanton
Nature, 2024 November, doi: https://doi.org/10.1038/s41586-024-08107-3
Extrachromosomal DNA in the Cancerous Transformation of Barrett’s Oesophagus
Jens Luebeck, Alvin Wei Tian Ng, Patricia C. Galipeau, Xiaohong Li, Carissa A. Sanchez, Annalise C. Katz-Summercorn, Hoon Kim, Sriganesh Jammula, Yudou He, Scott M. Lippman, Roel G. W. Verhaak, Carlo C. Maley, Ludmil B. Alexandrov, Brian J. Reid, Rebecca C. Fitzgerald, Thomas, G. Paulson, Howard Y. Chang, Sihan Wu, Vineet Bafna & Paul Mischel
Nature, 2023 April, doi: 10.1038/s41586-023-05937-5
Targeted Profiling of Human Extrachromosomal DNA by CRISPR-CATCH
Hung KL, Luebeck J, Dehkordi SR, Colón CI, Li R, Wong IT, Coruh C, Dharanipragada P, Lomeli SH, Weiser NE, Moriceau G, Zhang X, Bailey C, Houlahan KE, Yang W, González RC, Swanton C, Curtis C, Jamal-Hanjani M, Henssen AG, Law JA, Greenleaf WJ, Lo RS, Mischel PS, Bafna V, Chang HY.
Nat Genet. 2022 Nov, doi: 10.1038/s41588-022-01190-0
Gene Regulation on Extrachromosomal DNA
Hung KL, Mischel PS, Chang HY.
Nat Struct Mol Biol. 2022 Aug, doi: 10.1038/s41594-022-00806-7
The evolutionary dynamics of extrachromosomal DNA in human cancers
Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, Liu Z, Huang W, Chang HY, Bafna V, Henssen AG, Werner B, Mischel PS.
Nature Genetics 2022 Sep 19, doi: 10.1038/s41588-022-01177-x
Form Follows Function in Cancer Genomes
Mischel PS, Bafna V.
Nature Cancer 2022 Aug, doi: 10.1038/s43018-022-00428-4
Extrachromosomal DNA in Cancer
Bafna V, Mischel PS
Annual Review of Genomics and Human Genetics 2022 May 24, doi: 10.1146/annurev-genom-120821-100535
Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA
Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB.
Nature 2022 Feb 9, doi: 10.1038/s41586-022-04398-6
Extrachromosomal DNA: An Emerging Hallmark in Human Cancer|
Sihan Wu, Vineet Bafna, Howard Y. Chang, and Paul S. Mischel
Annual Review of Pathology 2022 Jan 24, doi: 10.1146/annurev-pathmechdis-051821-114223
ecDNA Hubs Drive Cooperative Intermolecular Oncogene Expression
King L Hung, Kathryn E Yost , Liangqi Xie , Quanming Shi , Konstantin Helmsauer , Jens Luebeck , Robert Schöpflin , Joshua T Lange , Rocío Chamorro González , Natasha E Weiser , Celine Chen , Maria E Valieva , Ivy Tsz-Lo Wong , Sihan Wu , Siavash R Dehkordi , Connor V Duffy , Katerina Kraft , Jun Tang , Julia A Belk , John C Rose , M Ryan Corces , Jeffrey M Granja , Rui Li , Utkrisht Rajkumar , Jordan Friedlein , Anindya Bagchi , Ansuman T Satpathy , Robert Tjian , Stefan Mundlos , Vineet Bafna , Anton G Henssen , Paul S Mischel , Zhe Liu, Howard Y Chang
Nature 2021 Nov 24, doi: 10.1038/s41586-021-04116-8
Leveraging Extrachromosomal DNA to Fine-tune Trials of Targeted Therapy for Glioblastoma: Opportunities and Challenges
Imran Noorani, Paul S Mischel, Charles Swanton
Nature reviews clinical oncology 2022 Sep 21, doi: 10.1038/s41571-022-00679-1
Extrachromosomal DNA is Associated with Oncogene Amplification
and Poor Outcome Across Multiple Cancers
Kim, H., Nguyen, N., Turner, K., Wu, S., Gujar, A. D., Luebeck, J., Liu, J., Deshpande, V., Rajkumar, U., Namburi, S., Amin, S. B., Yi, E., Menghi, F., Schulte, J. H., Henssen, A. G., Chang, H. Y., Beck, C. R., Mischel, P. S., Bafna, V., & Verhaak R. G. W.
Nature Genetics 2020 August 17, doi: 10.1038/s41588-020-0678-2
Circular ecDNA Promotes Accessible Chromatin and High Oncogene Expression
Wu, S., K. M. Turner, N. Nguyen, R. Raviram, M. Erb, J. Santini, J. Luebeck, U. Rajkumar, Y. Diao, B. Li, W. Zhang, N. Jameson, M. R. Corces, J. M. Granja, X. Chen, C. Coruh, A. Abnousi, J. Houston, Z. Ye, R. Hu, M. Yu, H. Kim, J. A. Law, R. G. W. Verhaak, M. Hu, F. B. Furnari, H. Y. Chang, B. Ren, V. Bafna and P. S. Mischel.
Nature 2019 Nov 20, doi: 10.1038/s41586-019-1763-5
Oncogene Amplification in Growth Factor Signaling Pathways Renders Cancers Dependent on Membrane Lipid Remodeling
Bi, J., Ichu, TA., Zanca, C., Yang, H., Zhang, W., Gu, Y., Chowdhry, S., Reed, A., Ikegami, S., Turner, K.M., Zhang, W., Villa, G.R., Wu, S., Quehenberger, O., Yong, W.H., Kornblum, H.I., Rich, J.N., Cloughesy, T.F., Cavenee, W.K., Furnari, F.B., Cravatt, B.F., Mischel, P.S.
Cell Metabolism 2019 Jul 9, doi: 10.1016/j.cmet.2019.06.014
NAD Metabolic Dependency in Cancer is Shaped by Gene Amplification and Enhancer Remodelling
Chowdhry, S., Zanca, C., Rajkumar, U., Koga, T., Diao, Y., Raviram, R., Liu, F., Turner, K. M., Yang, H., Brunk, E., Bi, J., Furnari, F. B., Bafna, V., Ren, B., Mischel, P. S.
Nature 2019 Apr 24, doi: 10.1038/s41586-019-1150-2
Extrachromosomal Oncogene Amplification Drives Tumour Evolution and Genetic Heterogeneity
Turner, K. M., Deshpande, V., Beyter, D., Koga, T., Rusert, J., Lee, C., Li, B., Arden, K., Ren, B., Nathanson, D. A., Kornblum, H. I., Taylor, M. D., Kaushal, S., Cavenee, W. K., Wechsler-Reya, R., Furnari, F. B., Vandenberg, S. R., Rao, P. N., Wahl, G. M., Bafna, V. & Mischel, P. S.
Nature 2017 Mar 2, doi:10.1038/nature21356
mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation
of the Cystine-Glutamate Antiporter xCT
Gu, Y., Albuquerque, C. P., Braas, D., Zhang, W., Villa, G. R., Bi, J., Ikegami, S., Masui, K., Gini, B., Yang, H., Gahman, T. C., Shiau, A. K., Cloughesy, T. F., Christofk, H. R., Zhou, H., Guan, K. L. & Mischel, P. S.
Mol Cell 2017 Jul 6, doi:10.1016/j.molcel.2017.05.030
An LXR-Cholesterol Axis Creates a Metabolic Co-Dependency for Brain Cancers
Villa, G. R., Hulce, J. J., Zanca, C., Bi, J., Ikegami, S., Cahill, G. L., Gu, Y., Lum, K. M., Masui, K., Yang, H., Rong, X., Hong, C., Turner, K. M., Liu, F., Hon, G. C., Jenkins, D., Martini, M., Armando, A. M., Quehenberger, O., Cloughesy, T. F., Furnari, F. B., Cavenee, W. K., Tontonoz, P., Gahman, T. C., Shiau, A. K., Cravatt, B. F. & Mischel, P. S.
Cancer Cell 2016 Nov 14, doi: 10.1016/j.ccell.2016.09.008
Glucose-dependent Acetylation of Rictor Promotes Targeted Cancer Therapy Resistance
Masui, K., Tanaka, K., Ikegami, S., Villa, G. R., Yang, H., Yong, W. H., Cloughesy, T. F., Yamagata, K., Arai, N., Cavenee, W. K. & Mischel, P. S.
Proceedings of the National Academy of Science USA 2015 Jul 28, doi: 10.1073/pnas.1511759112
EGFR Mutation Promotes Glioblastoma through Epigenome
and Transcription Factor Network Remodeling
Liu, F., Hon, G. C., Villa, G. R., Turner, K. M., Ikegami, S., Yang, H., Ye, Z., Li, B., Kuan, S., Lee, A. Y., Zanca, C., Wei, B., Lucey, G., Jenkins, D., Zhang, W., Barr, C. L., Furnari, F. B., Cloughesy, T. F., Yong, W. H., Gahman, T. C., Shiau, A. K., Cavenee, W. K., Ren, B. & Mischel, P. S.
Mol Cell 2015 Oct 15, doi:10.1016/j.molcel.2015.09.002
Targeted Therapy Resistance Mediated by Dynamic Regulation
of Extrachromosomal Mutant EGFR DNA
Nathanson, D. A., Gini, B., Mottahedeh, J., Visnyei, K., Koga, T., Gomez, G., Eskin, A., Hwang, K., Wang, J., Masui, K., Paucar, A., Yang, H., Ohashi, M., Zhu, S., Wykosky, J., Reed, R., Nelson, S. F., Cloughesy, T. F., James, C. D., Rao, P. N., Kornblum, H. I., Heath, J. R., Cavenee, W. K., Furnari, F. B. & Mischel, P. S.
Science 2014 Jan 3, doi:10.1126/science.1241328
mTOR Complex 2 controls Glycolytic Metabolism in Glioblastoma Through FoxO Acetylation and Upregulation of c-Myc
Masui, K., Tanaka, K., Akhavan, D., Babic, I., Gini, B., Matsutani, T., Iwanami, A., Liu, F., Villa, G. R., Gu, Y., Campos, C., Zhu, S., Yang, H., Yong, W. H., Cloughesy, T. F., Mellinghoff, I. K., Cavenee, W. K., Shaw, R. J. & Mischel, P. S.
Cell Metabolism 2013 Nov 5, doi: 10.1016/j.cmet.2013.09.013
EGFR Mutation-induced Alternative Splicing of Max contributes
to Growth of Glycolytic Tumors in Brain Cancer
Babic, I., Anderson, E. S., Tanaka, K., Guo, D., Masui, K., Li, B., Zhu, S., Gu, Y., Villa, G. R., Akhavan, D., Nathanson, D., Gini, B., Mareninov, S., Li, R., Camacho, C. E., Kurdistani, S. K., Eskin, A., Nelson, S. F., Yong, W. H., Cavenee, W. K., Cloughesy, T. F., Christofk, H. R., Black, D. L. & Mischel, P. S.
Cell Metabolism 2013 Jun 4, doi: 10.1016/j.cmet.2013.04.013