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 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, 15: 1225-1246. PMID: 40062518, PMCID: PMC12130809, DOI: 10.1158/2159-8290.cd-24-1532.Peer-Reviewed Original ResearchUrothelial carcinomaImmune microenvironmentWhole-genome sequencing dataExpression of major histocompatibility complex class I moleculesIncreased intratumoral heterogeneityTumor immune microenvironmentT cell immunityRecurrence of UCSamples of tumorHistocompatibility complex class I moleculesMajor histocompatibility complex class I moleculesSingle-cell RNA sequencing analysisMulti-region samplingRNA sequencing analysisClass I moleculesSequence dataUC tumorsExtrachromosomal DNAImmunosuppressive phenotypeSequence analysisT cellsClonal evolutionMalignant cellsPoor prognosisIntratumoral heterogeneity
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 identificationDNACCLESequenceOncogeneAbstract 4311: The interplay of SYNCRIP deficiency, APOBEC activity, and extrachromosomal DNA in castration-resistant prostate cancer drug resistance
Li X, Deng S, Wang C, Wang Y, Mu P. Abstract 4311: The interplay of SYNCRIP deficiency, APOBEC activity, and extrachromosomal DNA in castration-resistant prostate cancer drug resistance. Cancer Research 2024, 84: 4311-4311. DOI: 10.1158/1538-7445.am2024-4311.Peer-Reviewed Original ResearchProstate cancer drug resistanceCancer drug resistanceDrug resistanceProstate cancerTherapy resistanceAmerican Association for Cancer Research annual meetingsResistance to androgen receptor (AR)-targeted therapiesAndrogen receptor (AR)-targeted therapiesIncreased therapy resistanceTumor mutational burdenCRPC cell linesAPOBEC activityCastration-resistant formComplexity of drug resistanceWhole-exome sequencingContribution to drug resistanceDrivers of resistanceIn vivo modelsPatient-derived samplesExtrachromosomal DNAAPOBEC-mediated mutagenesisMutational burdenDNA damageFunctional CRISPR screensTumor behaviorDefining 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
2019
Extrachromosomal oncogene amplification in tumour pathogenesis and evolution
Verhaak R, Bafna V, Mischel P. Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nature Reviews Cancer 2019, 19: 283-288. PMID: 30872802, PMCID: PMC7168519, DOI: 10.1038/s41568-019-0128-6.Peer-Reviewed Original Research
2002
Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue
Kirby C, Waring A, Griffin T, Falkinham J, Grindley N, Derbyshire K. Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue. Molecular Microbiology 2002, 43: 173-186. PMID: 11849545, DOI: 10.1046/j.1365-2958.2002.02729.x.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBlotting, SouthernDNA Transposable ElementsDNA, BacterialDNA, CircularMolecular Sequence DataMutagenesis, InsertionalMycobacterium aviumMycobacterium bovisMycobacterium smegmatisPlasmidsReplication OriginRestriction MappingSequence Analysis, DNASequence Homology, Nucleic AcidConceptsEssential genetic toolsCryptic plasmidGenetic toolsOpportunistic pathogen Mycobacterium aviumGenetic exploitationTransposon insertionConjugative relaxaseTransposition systemSelectable markerExtrachromosomal DNAGenetic analysisHost rangePlasmid genesPlasmid originBacterial speciesPlasmid establishmentCircular DNAPlasmidMycobacterium smegmatisGenesMycobacterial plasmidsDNAReplicationMycobacterium aviumRescue
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