Identification and characterization of extrachromosomal circular DNA in patients with high myopia and cataract

Wen, Ke; Zhang, Lujie; Cai, Yuyan; Teng, Hui; Liang, Jingli; Yue, Yi; Li, Yaoling; Huang, Yudong; Liu, Ming; Zhang, Yufeng; Wei, Ruihua; Sun, Jing

doi:10.1080/15592294.2023.2192324

Cited by 10 publications

(7 citation statements)

References 42 publications

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“…Compared with the healthy controls (CON), the size distribution and genomic characteristics of plasma eccDNA were not significantly altered in the LAA stroke patients. Similar with previous researches on plasma and cells/tissues from patients and healthy controls, 17 , 18 , 19 the formation of eccDNAs was positively related to the distribution of genes on the chromosomes both in the CON and LAA stroke patients. The size of more than 90% eccDNAs was <1 kb, and two peaks were observed within 1 kb in the CON and LAA stroke patients.…”

Section: Discussionsupporting

confidence: 88%

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

Chen,

Chi,

Cheng

et al. 2024

J Cellular Molecular Medi

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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.

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Section: Discussionsupporting

confidence: 88%

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

Chen,

Chi,

Cheng

et al. 2024

J Cellular Molecular Medi

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“…Moreover, the average length of eccDNAs in young ASCs was larger than those in aged ASCs, suggesting loss of large-size eccDNAs during aging. The basic features of eccDNAs, e.g., distribution pattern and GC contents, were similar among ASC samples, which were also similar to those characterized in the plasma [ 36 ], anterior capsule [ 37 ], femoral head [ 38 ] and ovarian cancer [ 16 ]. Interestingly, unlike the typical predominant peak clusters of eccDNA size at ~ 200 bp and 350 bp [ 15 , 28 , 39 ], eccDNA distribution in our analysis presented only one large peak around 200 bp, reflecting a specific characteristic of eccDNAs in ASCs.…”

Section: Discussionsupporting

confidence: 61%

Deciphering the role of extrachromosomal circular DNA in adipose stem cells from old and young donors

Ren,

Wu,

Shen

et al. 2023

Stem Cell Res Ther

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Background The functional impairment of adipose stem cells (ASCs) during aging limits their clinical transformation. Studies have shown that extrachromosomal circular DNAs (eccDNAs) are associated with tumor progression and cell aging, but the roles of eccDNAs in ASCs remain unknown. Method We conducted Circle sequencing (Circle-seq) to identify eccDNAs in ASCs isolated from young and old donors. The differentially expressed eccDNAs were calculated, annotated and validated via polymerase chain reaction. Results Thousands of eccDNAs were identified and comprehensively characterized. Most of them were GC-rich, < 1000 base pairs in size, and were enriched on chromosome 19 and 17 with a high density of Alu elements and genes, 2 kb upstream/downstream of genes and satellites. In total, 3025 eccDNAs were differentially expressed among the two ASC groups. Conjoint analysis of the Circle-seq results and previous RNA-seq results revealed that 73 eccDNAs and 55 genes exhibited the same differential expression between the two groups. KEGG and GO analyses revealed that genes encoding differentially expressed eccDNAs were enriched for cell adhesion, cellular senescence and TGF-β receptor signaling pathway. We also found that aged ASCs exhibited loss of eccDNAs, including CAMK2G (chr10: 75577899-75578176), TRABD2B (chr1: 48305638-48307008) and TRABD2B (chr1: 48305425-48307091). Conclusion In this study, we elucidated the first eccDNA profile relating to ASCs and demonstrated that three eccDNAs are lost in aged ASCs, which may be potential biomarkers of stem cell aging and valuable targets for stem cell rejuvenation.

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“…This atypical motif signature is consistent with findings from tissue research involving the RCA step. 36 Indeed, a typical model was previously proposed in plasma cell-free eccDNA using the tagmentation method without the RCA step. 25 Furthermore, the characteristics of the motif signature appeared to vary with the size of eccDNAs in our non-RCA group.…”

Section: Resultsmentioning

confidence: 99%

A comprehensive analysis of library preparation methods shows high heterogeneity of extrachromosomal circular DNA but distinct chromosomal amount levels reflecting different cell states

Lu,

Li,

Ouyang

et al. 2024

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Identification and characterization of extrachromosomal circular DNA in patients with high myopia and cataract

Cited by 10 publications

References 42 publications

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

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

Deciphering the role of extrachromosomal circular DNA in adipose stem cells from old and young donors

A comprehensive analysis of library preparation methods shows high heterogeneity of extrachromosomal circular DNA but distinct chromosomal amount levels reflecting different cell states

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