2023
Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells
Chamorro González R, Conrad T, Stöber M, Xu R, Giurgiu M, Rodriguez-Fos E, Kasack K, Brückner L, van Leen E, Helmsauer K, Dorado Garcia H, Stefanova M, Hung K, Bei Y, Schmelz K, Lodrini M, Mundlos S, Chang H, Deubzer H, Sauer S, Eggert A, Schulte J, Schwarz R, Haase K, Koche R, Henssen A. Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nature Genetics 2023, 55: 880-890. PMID: 37142849, PMCID: PMC10181933, DOI: 10.1038/s41588-023-01386-y.Peer-Reviewed Original ResearchConceptsExtrachromosomal circular DNACircular DNAParallel sequencingCancer cellsIntercellular differencesFull-length mRNADNA elementsExtrachromosomal DNATranscriptome sequencingTranscriptional impactSingle cancer cellsEcDNAExpression differencesDNATranscriptomeCellsIntratumoral heterogeneityStructural heterogeneitySequenceStructural dynamicsMRNACancerRecombination
2020
Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma
Helmsauer K, Valieva M, Ali S, Chamorro González R, Schöpflin R, Röefzaad C, Bei Y, Dorado Garcia H, Rodriguez-Fos E, Puiggròs M, Kasack K, Haase K, Keskeny C, Chen C, Kuschel L, Euskirchen P, Heinrich V, Robson M, Rosswog C, Toedling J, Szymansky A, Hertwig F, Fischer M, Torrents D, Eggert A, Schulte J, Mundlos S, Henssen A, Koche R. Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma. Nature Communications 2020, 11: 5823. PMID: 33199677, PMCID: PMC7669906, DOI: 10.1038/s41467-020-19452-y.Peer-Reviewed Original ResearchConceptsExtrachromosomal circular DNACore regulatory circuitEnhancer hijackingAmplicon structureDistal chromosomal fragmentsGene regulatory elementsMYCN amplificationChIP-seqShort readsHi-C.ATAC-seqChromatin landscapeNanopore sequencingRegulatory elementsRegulatory circuitsChromosome fragmentsMYCN ampliconGene copiesProximal enhancerCo-amplifiedCircular DNAAmpliconsMYCN overexpressionFunctional relevanceMYCNPublisher Correction: Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma
Koche R, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur I, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz R, Eggert A, Torrents D, Schulte J, Henssen A. Publisher Correction: Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nature Genetics 2020, 52: 464-464. PMID: 32107479, DOI: 10.1038/s41588-020-0598-1.Peer-Reviewed Original Research
2019
Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma
Koche R, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur I, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz R, Eggert A, Torrents D, Schulte J, Henssen A. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nature Genetics 2019, 52: 29-34. PMID: 31844324, PMCID: PMC7008131, DOI: 10.1038/s41588-019-0547-z.Peer-Reviewed Original Research
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