We introduce scEC&T-seq, a new single-cell sequencing method that enables parallel profiling of extrachromosomal circular DNA and mRNAs in single cells. Using scEC&T-seq, we characterized all types of circular DNA elements in single human cancer cells and profiled the intercellular heterogeneity and structural dynamics of cancer-specific extrachromosomal DNA.
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Yi, E., Chamorro González, R., Henssen, A. G. & Verhaak, R. G. W. Extrachromosomal DNA amplifications in cancer. Nat. Rev. Genet. 23, 760–771 (2022). This review article summarizes the genetic and epigenetic features of ecDNA and how they influence oncogene deregulation.
Noer, J. B., Hørsdal, O. K., Xiang, X., Luo, Y. & Regenberg, B. Extrachromosomal circular DNA in cancer: history, current knowledge, and methods. Trends Genet. 38, 766–781 (2022). This review summarizes the nomenclature of extrachromosomal circular DNAs.
Lange, J. T. et al. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nat. Genet. 54, 1527–1533 (2022). This article describes how ecDNA is segregated to daughter cells and how this segregation affects inter-cellular ecDNA copy number heterogeneity as well as treatment response.
Kim, H. et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. Genet. 52, 891–897 (2020). This paper presents the first pan-cancer analysis of ecDNA amplification across cancer types and reveals that ecDNA is common in cancer and associated with poor outcome.
Møller, H. D., Parsons, L., Jørgensen, T. S., Botstein, D. & Regenberg, B. Extrachromosomal circular DNA is common in yeast. Proc. Natl Acad. Sci. USA 112, E3114–E3122 (2015). This paper describes the Circle-seq method.
Koche, R. P. et al. Extrachromosomal circular DNA drives oncogenic genome remodelling in neuroblastoma. Nat. Genet. 52, 29–34 (2020). This work is the first to use circular DNA sequencing to describe ecDNA in neuroblastoma samples and reveals how ecDNA affects genome organization.
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This is a summary of: González, R. C. et al. Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nat. Genet. https://doi.org/10.1038/s41588-023-01386-y (2023).
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Disentangling extrachromosomal circular DNA heterogeneity in single cells with scEC&T-seq. Nat Genet 55, 740–741 (2023). https://doi.org/10.1038/s41588-023-01385-z