Effects of nucleases on cell-free extrachromosomal circular DNA
Sarah T.K. Sin, … , Rossa W.K. Chiu, Y.M. Dennis Lo
Sarah T.K. Sin, … , Rossa W.K. Chiu, Y.M. Dennis Lo
Published April 22, 2022
Citation Information: JCI Insight. 2022;7(8):e156070. https://doi.org/10.1172/jci.insight.156070.
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Research Article Genetics

Effects of nucleases on cell-free extrachromosomal circular DNA

Abstract

Cell-free extrachromosomal circular DNA (eccDNA) as a distinct topological form from linear DNA has recently gained increasing research interest, with possible clinical applications as a class of biomarkers. In this study, we aimed to explore the relationship between nucleases and eccDNA characteristics in plasma. By using knockout mouse models with deficiencies in deoxyribonuclease 1 (DNASE1) or deoxyribonuclease 1 like 3 (DNASE1L3), we found that cell-free eccDNA in Dnase1l3−/− mice exhibited larger size distributions than that in wild-type mice. Such size alterations were not found in tissue eccDNA of either Dnase1−/− or Dnase1l3−/− mice, suggesting that DNASE1L3 could digest eccDNA extracellularly but did not seem to affect intracellular eccDNA. Using a mouse pregnancy model, we observed that in Dnase1l3−/− mice pregnant with Dnase1l3+/− fetuses, the eccDNA in the maternal plasma was shorter compared with that of Dnase1l3−/− mice carrying Dnase1l3−/− fetuses, highlighting the systemic effects of circulating fetal DNASE1L3 degrading the maternal eccDNA extracellularly. Furthermore, plasma eccDNA in patients with DNASE1L3 mutations also exhibited longer size distributions than that in healthy controls. Taken together, this study provided a hitherto missing link between nuclease activity and the biological manifestations of eccDNA in plasma, paving the way for future biomarker development of this special form of DNA molecules.

Authors

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

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Figure 1

Study design.

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Study design. Experimental approaches were designed to explore whether n...
Experimental approaches were designed to explore whether nucleases (DNASE1 and DNASE1L3) would have any effects on eccDNA characteristics. First, knockout mouse models with deficiencies in Dnase1 or Dnase1l3 were used to investigate whether eccDNA attributes such as abundance and size distribution were altered when compared with wild-type mice. Such comparisons were performed in both plasma and tissue (the liver and buffy coat) eccDNA among the 3 groups of mice to elucidate whether the nuclease effects on eccDNA, if any, were exerted extracellularly or intracellularly. Subsequently, a Dnase1l3−/− mouse pregnancy model was used to determine whether extracellular DNASE1L3 the fetuses released would act on the eccDNA molecules in maternal plasma, altering their size distributions. Furthermore, DNASE1L3’s effects on cell-free eccDNA were tested in human participants: size distributions of eccDNA from plasma samples were compared between healthy participants and patients with DNASE1L3 mutations.