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Biomolecules
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Recent Developments in the Biology of Extracellular or Cell-Free DNA
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Recent Developments in the Biology of Extracellular or Cell-Free DNA

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

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 12900

Special Issue Editor

Dr. Peter Celec

E-Mail Website
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
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Extracellular DNA (EcDNA) is often called cell-free DNA; in vivo, however, 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, althought 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 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 contribue 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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

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Related Special Issue

Published Papers (7 papers)

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Research

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14 pages, 16651 KiB  
Article
Accurate Early Detection and EGFR Mutation Status Prediction of Lung Cancer Using Plasma cfDNA Coverage Patterns: A Proof-of-Concept Study
by Zhixin Bie, Yi Ping, Xiaoguang Li, Xun Lan and Lihui Wang
Biomolecules 2024, 14(6), 716; https://doi.org/10.3390/biom14060716 - 17 Jun 2024
Viewed by 1862
Abstract
Lung cancer is a major global health concern with a low survival rate, often due to late-stage diagnosis. Liquid biopsy offers a non-invasive approach to cancer detection and monitoring, utilizing various features of circulating cell-free DNA (cfDNA). In this study, we established two [...] Read more.
Lung cancer is a major global health concern with a low survival rate, often due to late-stage diagnosis. Liquid biopsy offers a non-invasive approach to cancer detection and monitoring, utilizing various features of circulating cell-free DNA (cfDNA). In this study, we established two models based on cfDNA coverage patterns at the transcription start sites (TSSs) from 6X whole-genome sequencing: an Early Cancer Screening Model and an EGFR mutation status prediction model. The Early Cancer Screening Model showed encouraging prediction ability, especially for early-stage lung cancer. The EGFR mutation status prediction model exhibited high accuracy in distinguishing between EGFR-positive and wild-type cases. Additionally, cfDNA coverage patterns at TSSs also reflect gene expression patterns at the pathway level in lung cancer patients. These findings demonstrate the potential applications of cfDNA coverage patterns at TSSs in early cancer screening and in cancer subtyping. Full article
(This article belongs to the Special Issue Recent Developments in the Biology of Extracellular or Cell-Free DNA)
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18 pages, 3244 KiB  
Article
Extracellular Self-DNA Effects on Yeast Cell Cycle and Transcriptome during Batch Growth
by Emanuela Palomba, Maria Luisa Chiusano, Francesco Monticolo, Maria Chiara Langella, Massimo Sanchez, Valentina Tirelli, Elisabetta de Alteriis, Marco Iannaccone, Pasquale Termolino, Rosanna Capparelli, Fabrizio Carteni, Guido Incerti and Stefano Mazzoleni
Biomolecules 2024, 14(6), 663; https://doi.org/10.3390/biom14060663 - 6 Jun 2024
Viewed by 1333
Abstract
The cell cycle and the transcriptome dynamics of yeast exposed to extracellular self-DNA during an aerobic batch culture on glucose have been investigated using cytofluorimetric and RNA-seq analyses. In parallel, the same study was conducted on yeast cells growing in the presence of [...] Read more.
The cell cycle and the transcriptome dynamics of yeast exposed to extracellular self-DNA during an aerobic batch culture on glucose have been investigated using cytofluorimetric and RNA-seq analyses. In parallel, the same study was conducted on yeast cells growing in the presence of (heterologous) nonself-DNA. The self-DNA treatment determined a reduction in the growth rate and a major elongation of the diauxic lag phase, as well as a significant delay in the achievement of the stationary phase. This was associated with significant changes in the cell cycle dynamics, with slower exit from the G0 phase, followed by an increased level of cell percentage in the S phase, during the cultivation. Comparatively, the exposure to heterologous DNA did not affect the growth curve and the cell cycle dynamics. The transcriptomic analysis showed that self-DNA exposure produced a generalized downregulation of transmembrane transport and an upregulation of genes associated with sulfur compounds and the pentose phosphate pathway. Instead, in the case of the nonself treatment, a clear response to nutrient deprivation was detected. Overall, the presented findings represent further insights into the complex functional mechanisms of self-DNA inhibition. Full article
(This article belongs to the Special Issue Recent Developments in the Biology of Extracellular or Cell-Free DNA)
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9 pages, 1886 KiB  
Communication
Cell-Free Mitochondrial DNA: An Upcoming Non-Invasive Tool for Diagnosis of BK Polyomavirus-Associated Nephropathy
by Luying Guo, Sulin Luo, Xingxia Wang, Nengbo Zhang, Yamei Cheng, Jia Shen, Jianghua Chen and Rending Wang
Biomolecules 2024, 14(3), 348; https://doi.org/10.3390/biom14030348 - 14 Mar 2024
Viewed by 1301
Abstract
Mitochondria are essential organelles that possess their own DNA. Mitochondrial dysfunction has been revealed in many kidney diseases, including BK polyomavirus-associated nephropathy (BKPyVAN). In this study, we introduce an innovative approach for non-invasive monitoring of mitochondrial impairment through urinary donor-derived cell-free mitochondrial DNA [...] Read more.
Mitochondria are essential organelles that possess their own DNA. Mitochondrial dysfunction has been revealed in many kidney diseases, including BK polyomavirus-associated nephropathy (BKPyVAN). In this study, we introduce an innovative approach for non-invasive monitoring of mitochondrial impairment through urinary donor-derived cell-free mitochondrial DNA (ddcfmtDNA), addressing the crucial challenge of BKPyVAN diagnosis. Urinary samples were collected at the time of biopsy from a total of 60 kidney transplant recipients, comprising 12 with stable function, 22 with T cell-mediated rejection, and 21 with biopsy-proven BKPyVAN. Our findings reveal that the ddcfmtDNA-to-ddcfDNA ratio exhibits superior capability in distinguishing BKPyVAN from other conditions, with a cutoff value of 4.96% (area under curve = 0.933; sensitivity: 71.4%; and specificity: 97.1%). Notably, an elevation of ddcfmtDNA levels is associated with mitochondrial damage, as visualized through electron microscopy. These results underscore the promise of non-invasive monitoring for detecting subtle mitochondrial damage and its potential utility in BKPyVAN diagnosis. Further investigations are required to advance this field of research. Full article
(This article belongs to the Special Issue Recent Developments in the Biology of Extracellular or Cell-Free DNA)
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16 pages, 3412 KiB  
Article
SOS-Inducing Drugs Trigger Nucleic Acid Release and Biofilm Formation in Gram-Negative Bacteria
by Peter Demjanenko, Sam Zheng and John K. Crane
Biomolecules 2024, 14(3), 321; https://doi.org/10.3390/biom14030321 - 8 Mar 2024
Viewed by 1650
Abstract
Our laboratory recently reported that induction of the SOS response, triggered by SOS-inducing drugs, was accompanied by a large release of DNA from enteric bacteria. The SOS response release had not previously been reported to include release of extracellular DNA from bacterial cells. [...] Read more.
Our laboratory recently reported that induction of the SOS response, triggered by SOS-inducing drugs, was accompanied by a large release of DNA from enteric bacteria. The SOS response release had not previously been reported to include release of extracellular DNA from bacterial cells. We followed up on those observations in this current study and found that not just double-stranded DNA was being released, but also single-stranded DNA, RNA, and protein. SOS-inducing drugs also triggered formation of biofilm at the air–fluid interface on glass, and the biofilms contained DNA. We extended our study to test whether inhibitors of the SOS response would block DNA release and found that SOS inhibitors, including zinc salts, nitric oxide donors, and dequalinium, inhibited SOS-induced DNA release. The understanding that SOS-induced DNA release is associated with formation of biofilms increases our appreciation of the role of the SOS response in pathogenesis, as well as in emergence of new antibiotic resistance. Our findings with SOS inhibitors also suggest that regimens might be devised that could block the deleterious effects of the SOS response, at least temporarily, when this is desired. Full article
(This article belongs to the Special Issue Recent Developments in the Biology of Extracellular or Cell-Free DNA)
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14 pages, 1198 KiB  
Article
Mutated TP53 in Circulating Tumor DNA as a Risk Level Biomarker in Head and Neck Squamous Cell Carcinoma Patients
by Liyona Kampel, Sara Feldstein, Shlomo Tsuriel, Victoria Hannes, Narin N. Carmel Neiderman, Gilad Horowitz, Anton Warshavsky, Leonor Leider-Trejo, Dov Hershkovitz and Nidal Muhanna
Biomolecules 2023, 13(9), 1418; https://doi.org/10.3390/biom13091418 - 20 Sep 2023
Cited by 2 | Viewed by 1523
Abstract
Circulating tumor DNA (ctDNA) has been suggested as a surrogate biomarker for early detection of cancer recurrence. We aimed to explore the utility of ctDNA as a noninvasive prognostic biomarker in newly diagnosed head and neck squamous cell carcinoma (HNSCC) patients. Seventy HNSCC [...] Read more.
Circulating tumor DNA (ctDNA) has been suggested as a surrogate biomarker for early detection of cancer recurrence. We aimed to explore the utility of ctDNA as a noninvasive prognostic biomarker in newly diagnosed head and neck squamous cell carcinoma (HNSCC) patients. Seventy HNSCC specimens were analysed for the detection of TP53 genetic alterations utilizing next-generation sequencing (NGS). TP53 mutations were revealed in 55 (79%). Upon detection of a significant TP53 mutation, circulating cell-free DNA was scrutinized for the presence of the tumor-specific mutation. ctDNA was identified at a minimal allele frequency of 0.08% in 21 out of 30 processed plasma samples. Detectable ctDNA correlated with regional spread (N stage ≥ 1, p = 0.011) and poorer 5-year progression-free survival (20%, 95% CI 10.9 to 28.9, p = 0.034). The high-risk worst pattern of invasion (WPOI grade 4–5) and deep invasion were frequently found in patients whose ctDNA was detected (p = 0.087 and p = 0.072, respectively). Detecting mutated TP53 ctDNA was associated with poor progression-free survival and regional metastases, indicating its potential role as a prognostic biomarker. However, ctDNA detectability in early-stage disease and the mechanisms modulating its release into the bloodstream must be further elucidated. Full article
(This article belongs to the Special Issue Recent Developments in the Biology of Extracellular or Cell-Free DNA)
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Review

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13 pages, 972 KiB  
Review
Technical Advances in Circulating Cell-Free DNA Detection and Analysis for Personalized Medicine in Patients’ Care
by Monica Sorbini, Tullia Carradori, Gabriele Maria Togliatto, Tiziana Vaisitti and Silvia Deaglio
Biomolecules 2024, 14(4), 498; https://doi.org/10.3390/biom14040498 - 19 Apr 2024
Cited by 3 | Viewed by 2452
Abstract
Circulating cell-free DNA (cfDNA) refers to small fragments of DNA molecules released after programmed cell death and necrosis in several body fluids such as blood, saliva, urine, and cerebrospinal fluid. The discovery of cfDNA has revolutionized the field of non-invasive diagnostics in the [...] Read more.
Circulating cell-free DNA (cfDNA) refers to small fragments of DNA molecules released after programmed cell death and necrosis in several body fluids such as blood, saliva, urine, and cerebrospinal fluid. The discovery of cfDNA has revolutionized the field of non-invasive diagnostics in the oncologic field, in prenatal testing, and in organ transplantation. Despite the potential of cfDNA and the solid results published in the recent literature, several challenges remain, represented by a low abundance, a need for highly sensitive assays, and analytical issues. In this review, the main technical advances in cfDNA analysis are presented and discussed, with a comprehensive examination of the current available methodologies applied in each field. Considering the potential advantages of cfDNA, this biomarker is increasing its consensus among clinicians, as it allows us to monitor patients’ conditions in an easy and non-invasive way, offering a more personalized care. Nevertheless, cfDNA analysis is still considered a diagnostic marker to be further validated, and very few centers are implementing its analysis in routine diagnostics. As technical improvements are enhancing the performances of cfDNA analysis, its application will transversally improve patients’ quality of life. Full article
(This article belongs to the Special Issue Recent Developments in the Biology of Extracellular or Cell-Free DNA)
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14 pages, 1849 KiB  
Review
Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer
by Enze Deng and Xiaoying Fan
Biomolecules 2024, 14(4), 488; https://doi.org/10.3390/biom14040488 - 17 Apr 2024
Viewed by 1855
Abstract
Extrachromosomal circular DNA (eccDNA), a double-stranded circular DNA molecule found in multiple organisms, has garnered an increasing amount of attention in recent years due to its close association with the initiation, malignant progression, and heterogeneous evolution of cancer. The presence of eccDNA in [...] Read more.
Extrachromosomal circular DNA (eccDNA), a double-stranded circular DNA molecule found in multiple organisms, has garnered an increasing amount of attention in recent years due to its close association with the initiation, malignant progression, and heterogeneous evolution of cancer. The presence of eccDNA in serum assists in non-invasive tumor diagnosis as a biomarker that can be assessed via liquid biopsies. Furthermore, the specific expression patterns of eccDNA provide new insights into personalized cancer therapy. EccDNA plays a pivotal role in tumorigenesis, development, diagnosis, and treatment. In this review, we comprehensively outline the research trajectory of eccDNA, discuss its role as a diagnostic and prognostic biomarker, and elucidate its regulatory mechanisms in cancer. In particular, we emphasize the potential application value of eccDNA in cancer diagnosis and treatment and anticipate the development of novel tumor diagnosis strategies based on serum eccDNA in the future. Full article
(This article belongs to the Special Issue Recent Developments in the Biology of Extracellular or Cell-Free DNA)
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