Identification and characterization of extrachromosomal circular DNA in large-artery atherosclerotic stroke.

Kejie Chen, Yanqi Chi, Hang Cheng, Min Yang, Quandan Tan, Junli Hao, Yapeng Lin, Fengkai Mao, Song He, Jie Yang

Journal of cellular and molecular medicine 2024 Apr

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Extrachromosomal circular DNA (eccDNA) is a new biomarker and regulator of diseases. However, the role of eccDNAs in large-artery atherosclerotic (LAA) stroke remains unclear. Through high-throughput circle-sequencing technique, the length distribution, genomic characteristic and motifs feature of plasma eccDNA from healthy controls (CON) and patients with LAA stroke were analysed. Then, the potential functions of the annotated eccDNAs were investigated using GO and KEGG pathway analyses. EccDNAs mapped to the reference genome showed SHN3 and BCL6 were LAA stroke unique transcription factors. The genes of differentially expressed eccDNAs between LAA stroke patients and CON were mainly involved in axon/dendrite/neuron projection development and maintenance of cellular structure via Wnt, Rap1 and MAPK pathways. Moreover, LAA stroke unique eccDNA genes played a role in regulation of coagulation and fibrinolysis, and there were five LAA stroke unique eccDNAs (Chr2:12724406-12724784, Chr4:1867120-186272046, Chr4:186271494-186271696, Chr7:116560296-116560685 and Chr11:57611780-5761192). Additionally, POLR2C and AURKA carried by ecDNAs (eccDNA size >100 kb) of LAA stroke patients were significantly associated with development of LAA stroke. Our data firstly revealed the characteristics of eccDNA in LAA stroke and the functions of LAA stroke unique eccDNAs and eccDNA genes, suggesting eccDNA is a novel biomarker and mechanism of LAA stroke. © 2024 The Authors. Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.

Citation

Kejie Chen, Yanqi Chi, Hang Cheng, Min Yang, Quandan Tan, Junli Hao, Yapeng Lin, Fengkai Mao, Song He, Jie Yang. Identification and characterization of extrachromosomal circular DNA in large-artery atherosclerotic stroke. Journal of cellular and molecular medicine. 2024 Apr;28(7):e18210