biostudies-literatureUnknown55(5)Chamorro Gonzalez RExtrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. InterNature genetics880-890https://www.ebi.ac.uk/biostudies/studies/S-EPMC10181933biostudies-literatureParallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.PMC10181933Schwarz RFvan Leen EDeubzer HERodriguez-Fos ESchmelz KSchulte JHChamorro Gonzalez RConrad TBei YBruckner LHenssen AGEggert AStober MCKasack KStefanova MEKoche RPXu RLodrini MChang HYSauer SMundlos SGiurgiu MDorado Garcia HHaase KHelmsauer KHung KLfalseParallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Inter2023-01-01T00:00:00Z2023 May2025-04-18T13:56:05.191Z2025-04-06T23:45:33.331ZS-EPMC101819333714284910.1038/s41588-023-01386-y