Recent Developments in the Biology of Extracellular or Cell-Free DNA, 2nd Edition

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 1034

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Guest Editor
Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
Interests: extracellular mitochondrial DNA; endogenous and exogenous deoxyribonuclease; trauma-induced immunomodulation; neutrophil extracellular traps; the role of neutrophil activation in rheumatoid arthritis
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Special Issue Information

Dear Colleagues,

Following a very successful first edition, we are pleased to announce the launch of the second edition of this Special Issue entitled “Recent Developments in the Biology of Extracellular or Cell-Free DNA, 2nd Edition”.

Extracellular DNA (EcDNA) is often called cell-free DNA; however, in vivo, it is everything but cell-free. It interacts with various immunocompetent cells and eventually induces inflammation. Inflammation, especially the activation of neutrophils, leads to the release of ecDNA and more inflammation. While the diagnostic applications for non-invasive prenatal screening and for cancer screening are moving towards use in clinical routine, the biology of ecDNA is still understudied. In plasma, DNA from both nuclei and mitochondria contributes to the whole ecDNA pool, although they differ in their stability, fragment length, and also immunogenicity. Recent advances in epigenetic analyses have enabled the possibility of revealing the tissues or cell types that contribute to plasma ecDNA. However, many questions remain unsolved. What is the fate and what are the effects of ecDNA protected by histones, antimicrobial peptides, or other positively charged molecules? Is mitochondrial DNA quickly cleared by deoxyribonucleases or does it contribute to the effects of extracellular mitochondria as a damage-associated molecular pattern? Does the fragmentation of ecDNA affect its immunogenicity? What are the effects of degradation products of ecDNA cleavage?

We invite contributions in the form of reviews, research articles, communications, and concept papers.

Dr. Peter Celec
Guest Editor

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Keywords

  • neutrophil extracellular traps
  • DNase
  • toll-like receptor 9
  • exosomes
  • autoimmunity

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Research

19 pages, 5081 KiB  
Article
Pulmozyme Ameliorates LPS-Induced Lung Fibrosis but Provokes Residual Inflammation by Modulating Cell-Free DNA Composition and Controlling Neutrophil Phenotype
by Ludmila A. Alekseeva, Aleksandra V. Sen’kova, Khetam Sounbuli, Innokenty A. Savin, Marina A. Zenkova and Nadezhda L. Mironova
Biomolecules 2025, 15(2), 298; https://doi.org/10.3390/biom15020298 - 17 Feb 2025
Viewed by 616
Abstract
Pulmonary fibrosis, a chronic progressive lung disorder, can be the result of previous acute inflammation-associated lung injury and involves a wide variety of inflammatory cells, causing the deposition of extracellular matrix (ECM) components in the lungs. Such lung injury is often associated with [...] Read more.
Pulmonary fibrosis, a chronic progressive lung disorder, can be the result of previous acute inflammation-associated lung injury and involves a wide variety of inflammatory cells, causing the deposition of extracellular matrix (ECM) components in the lungs. Such lung injury is often associated with excessive neutrophil function and the formation of DNA networks in the lungs, which are also some of the most important factors for fibrosis development. Acute lung injury with subsequent fibrosis was initiated in C57Bl/6 mice by a single intranasal (i.n.) administration of LPS. Starting from day 14, human recombinant DNase I in the form of Pulmozyme for topical administration was instilled i.n. twice a week at a dose of 50 U/mouse. Cell-free DNA (cfDNA), DNase activity, and cell content were analyzed in blood serum and bronchoalveolar lavage fluid (BALF). Inflammatory and fibrotic changes in lung tissue were evaluated by histological analysis. The gene expression profile in spleen-derived neutrophils was analyzed by RT-qPCR. We demonstrated that Pulmozyme significantly reduced connective tissue expansion in the lungs. However, despite the reliable antifibrotic effect, complete resolution of inflammation in the respiratory system of mice treated with Pulmozyme was not achieved, possibly due to enhanced granulocyte recruitment and changes in the nuclear/mitochondrial cfDNA balance in the BALF. Moreover, Pulmozyme introduction caused the enrichment of the spleen-derived neutrophil population by those with an unusual phenotype, combining pro-inflammatory and anti-inflammatory features, which can also maintain lung inflammation. Pulmozyme can be considered a promising drug for lung fibrosis management; however, the therapy may be accompanied by residual inflammation. Full article
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