Effects of nucleases on cell-free extrachromosomal circular DNA

Sin, Sarah T K; Deng, Jiaen; Lu, Junyan; Yukawa, Masashi; Chan, Rebecca Wing-Yan; Volpi, Stefano; Vaglio, Augusto; Fenaroli, Paride; Bocca, Paola; Cheng, Suk Hang; Wong, Danny K L; Lui, Kathy O.; Jiang, Peiyong; Chan, K. C. Allen; Chiu, Rossa W.K.; Lo, Y.M. Dennis

doi:10.1172/jci.insight.156070

Cited by 16 publications

(33 citation statements)

References 37 publications

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“…eccDNAs in the maternal plasma were shorter in Dnase1l3 −/− mice pregnant with Dnase1l3 +/− fetuses than in the maternal plasma of Dnase1l3 −/− mice carrying Dnase1l3 −/− fetuses. This study demonstrates the biological association between plasma eccDNA and nuclease ( Sin et al, 2022 ).…”

Section: Eccdna In Human Diseasessupporting

confidence: 52%

Extrachromosomal circular DNA: Current status and future prospects

Zhao

Zhang

et al. 2022

eLife

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Extrachromosomal circular DNA (eccDNA) is a double-stranded DNA molecule found in various organisms, including humans. In the past few decades, the research on eccDNA has mainly focused on cancers and their associated diseases. Advancements in modern omics technologies have reinvigorated research on eccDNA and shed light on the role of these molecules in a range of diseases and normal cell phenotypes. In this review, we first summarize the formation of eccDNA and its modes of action in eukaryotic cells. We then outline eccDNA as a disease biomarker and reveal its regulatory mechanism. We finally discuss the future prospects of eccDNA, including basic research and clinical application. Thus, with the deepening of understanding and exploration of eccDNAs, they hold great promise in future biomedical research and clinical translational application.

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Section: Eccdna In Human Diseasessupporting

confidence: 52%

Extrachromosomal circular DNA: Current status and future prospects

Zhao

Zhang

et al. 2022

eLife

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“…As biomarkers, there are several differences between eccDNA and linear circulating cfDNA, and eccDNA is more advantageous in some respects (Table 5 ). 289 , 290 First, eccDNAs are resistant to exonuclease digestion due to their closed circular structure. Therefore, they are more stable than their linear counterparts.…”

Section: Potential Applications Of Eccdnamentioning

confidence: 99%

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

Yang

Jia

et al. 2022

Sig Transduct Target Ther

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Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.

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“…Reminiscent of nuclear cfDNA patterns, fetal cf-eccDNA shows relatively lower methylation levels than those of the maternal cf-eccDNA and clears rapidly after delivery with a half-life of 30 min. Longer cf-eccDNA fragments appears to carry higher methylation densities in plasma of both pregnant and non-pregnant subjects [176] . Furthermore, nuclease activity on cf-eccDNA was reported, showing that DNASE1L3 affected eccDNA characteristics [177] .…”

Section: "New" Components Of Cfdnamentioning

confidence: 93%

Expanded knowledge of cell-free DNA biology: potential to broaden the clinical utility

Che¹,

Stanley²,

Jatsenko³

et al. 2022

Extracell Vesicles Circ Nucleic Acids

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Noninvasive sampling of an individual’s body fluids is an easy means to capture circulating cell-free DNA (cfDNA). These small fragments of DNA carry information on the contributing cell’s genome, epigenome, and nuclease content. Analysis of cfDNA for the assessment of genetic risk has already revolutionized clinical practice, and a compendium of increasingly higher-resolution approaches based on epigenetic and fragmentomic cfDNA signatures continues to expand. Profiling cfDNA has unlocked a wealth of molecular information that can be translated to the clinic. This review covers the biological characteristics of cfDNA, recent advances in liquid biopsy and the clinical utility of cfDNA.

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Effects of nucleases on cell-free extrachromosomal circular DNA

Cited by 16 publications

References 37 publications

Extrachromosomal circular DNA: Current status and future prospects

Extrachromosomal circular DNA: Current status and future prospects

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

Expanded knowledge of cell-free DNA biology: potential to broaden the clinical utility

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