2021
Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription
Zhu Y, Gujar A, Wong C, Tjong H, Ngan C, Gong L, Chen Y, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho A, Ruan Y, Verhaak R, Wei C. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell 2021, 39: 694-707.e7. PMID: 33836152, PMCID: PMC8119378, DOI: 10.1016/j.ccell.2021.03.006.Peer-Reviewed Original ResearchConceptsGenome-wide activationSingle-molecule resolutionMobile enhancerChromatin interactionsChromosomal interactionsChromatin contactsTranscription controlChromosomal transcriptionChromosomal targetsTranscriptional programsTranscriptional enhancersChromosomal genesChIA-PETGene transcriptionCancer genomesInteraction networksDNA functionH3K27ac signalProstate cancer cellsCircular DNAEcDNAsExpression levelsCancer cellsOncogenic alterationsTranscription
2018
Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma
deCarvalho A, Kim H, Poisson L, Winn M, Mueller C, Cherba D, Koeman J, Seth S, Protopopov A, Felicella M, Zheng S, Multani A, Jiang Y, Zhang J, Nam D, Petricoin E, Chin L, Mikkelsen T, Verhaak R. Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nature Genetics 2018, 50: 708-717. PMID: 29686388, PMCID: PMC5934307, DOI: 10.1038/s41588-018-0105-0.Peer-Reviewed Original ResearchConceptsExtrachromosomal DNA elementsDNA elementsChromosomal DNA alterationsDNA alterationsSomatic driver alterationsGenomic heterogeneitySingle nucleotide variantsOffspring cellsDiscordant inheritanceExtrachromosomal elementsEcDNAsGBM evolutionOncogenic potentialGBM samplesInheritance patternChromosomal alterationsSelection dynamicsModel systemCell culturesOrthotopic xenograft modelDriver alterationsXenograft modelOncogene amplificationCellsGlioblastoma