2025
Tethered to survive: Mitotic transcription secures faithful inheritance of extrachromosomal DNA
Jin X, Verhaak R. Tethered to survive: Mitotic transcription secures faithful inheritance of extrachromosomal DNA. Molecular Cell 2025, 85: 2813-2815. PMID: 40780177, DOI: 10.1016/j.molcel.2025.07.010.Peer-Reviewed Original ResearchSelective Depletion of Cancer Cells with Extrachromosomal DNA via Lentiviral Infection
Yi E, Gujar A, Zhao D, Suina K, Jin X, Pardon K, Yu Q, Kagermazova L, Korsah E, Dusseau N, Boeke J, Henssen A, Verhaak R. Selective Depletion of Cancer Cells with Extrachromosomal DNA via Lentiviral Infection. Cancer Research Communications 2025, 5: 1458-1465. PMID: 40787829, PMCID: PMC12392265, DOI: 10.1158/2767-9764.crc-25-0144.Peer-Reviewed Original ResearchSpatial-Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment.
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 R, Faltas B, Hansen J, Wu S, Mischel P, Henssen A, Bafna V, Luebeck J, Regenberg B, Luo Y, Lin C, Han P. Spatial-Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and the Tumor Immune Microenvironment. Cancer Discovery 2025, of1-of22. PMID: 40331621, DOI: 10.1158/2159-8290.cd-24-1532.Peer-Reviewed Original Research
2024
Mapping extrachromosomal DNA amplifications during cancer progression
Kim H, Kim S, Wade T, Yeo E, Lipsa A, Golebiewska A, Johnson K, An S, Ko J, Nam Y, Lee H, Kang S, Chung H, Niclou S, Moon H, Paek S, Bafna V, Luebeck J, Verhaak R. Mapping extrachromosomal DNA amplifications during cancer progression. Nature Genetics 2024, 56: 2447-2454. PMID: 39402156, PMCID: PMC11549044, DOI: 10.1038/s41588-024-01949-7.Peer-Reviewed Original ResearchConceptsPretreatment tumorsCancer progressionChemotherapy-pretreated patientsNewly diagnosed tumorsVariant allele fractionUntreated metastasesPrimary cancerUntreated cancerTreatment responseFocal amplificationTumor samplesChromosomal amplificationsDiagnosed cancerTumorExtrachromosomal DNA amplificationsAdvanced cancerCancerEcDNATime pointsMetastasisNewlyDNA amplificationProgressionExtrachromosomal DNAPatients13. AmpliconSuite: Analyzing focal amplifications in cancer genomes
Luebeck J, Huang E, Dameracharla B, Kim F, Liefeld T, Ahuja R, Prasad D, Prasad G, Kim S, Kim H, Bailey P, Verhaak R, Deshpande V, Reich M, Mischel P, Mesirov J, Bafna V. 13. AmpliconSuite: Analyzing focal amplifications in cancer genomes. Cancer Genetics 2024, 286: s5. DOI: 10.1016/j.cancergen.2024.08.015.Peer-Reviewed Original ResearchWhole-genome sequencingWhole-genome sequencing dataFocal amplificationCancer genomesStructural variationsAmplification of oncogenesExtrachromosomal DNACopy numberEcDNAGenomeOncogene amplificationAmpliconArchitectCancer progressionAmplificationAmplification typeTumor samplesBiocondaNextflowPCAWGGenePatternRobust identificationDNACCLESequenceOncogeneDefining the Role of Extrachromosomal DNA Amplifications in Medulloblastoma.
Zhao D, Verhaak R. Defining the Role of Extrachromosomal DNA Amplifications in Medulloblastoma. Cancer Research 2024, 84: 515-516. PMID: 38175761, DOI: 10.1158/0008-5472.can-23-4025.Peer-Reviewed Original ResearchConceptsCell-to-cell variabilityWhole-genome sequencingCircular extrachromosomal DNACRISPRi experimentsRewiring eventsExtrachromosomal DNAMultiomics sequencingExtrachromosomal DNA amplificationsCopy numberEcDNADNA amplificationAssociated with worse survivalOncogene amplificationSequenceAmplificationWorse survivalPatient cohortTumor heterogeneityIntratumoral heterogeneityCRISPRiMedulloblastomaPatient outcomesDNA
2022
Extrachromosomal DNA amplifications in cancer
Yi E, Chamorro González R, Henssen A, Verhaak R. Extrachromosomal DNA amplifications in cancer. Nature Reviews Genetics 2022, 23: 760-771. PMID: 35953594, PMCID: PMC9671848, DOI: 10.1038/s41576-022-00521-5.Peer-Reviewed Original ResearchConceptsExtrachromosomal DNA amplificationsNew therapeutic vulnerabilitiesCopy number heterogeneityEpigenetic architectureDNA amplificationCell divisionNuclear bodiesMost cancer typesNumber heterogeneityRegulatory landscapeTherapeutic vulnerabilitiesFunctional impactCancer typesDriver alterationsCircular structureEcDNAsChromatinizationChromosomesGenesAmplificationEcDNARecent investigationsEnhancerDeregulationCancer
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