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Thorsen SU, Moseholm KF, Clausen FB. Circulating cell-free DNA and its association with cardiovascular disease: what we know and future perspectives. Curr Opin Lipidol 2024; 35:14-19. [PMID: 37800671 DOI: 10.1097/mol.0000000000000907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
PURPOSE OF REVIEW The aim of this review is to explore a possible link between cell-free DNA (cfDNA) and cardiovascular disease (CVD), which may hold valuable potential for future diagnostics. RECENT FINDINGS cfDNA has become topic of high interest across several medical fields. cfDNA is used as a diagnostic biomarker in cancer, prenatal care, and transplantation. In addition, cfDNA may play an unrecognized role in biological processes that are involved in or underlying various disease states, for example, inflammation. Elevated levels of cfDNA are associated with various elements of CVD, cardio-metabolic risk factors, and autoimmune diseases. Mitochondrial cfDNA and neutrophil extracellular traps may play distinct roles. Total circulating cfDNA may reflect the unspecific accumulation of stressors and the organism's susceptibility and resilience to such stressors. As such, cfDNA, in a stressful situation, may provide predictive value for future development of CVD. We suggest exploring such possibility through a large-scale prospective cohort study of pregnant women. SUMMARY There is no doubt that cfDNA is a valuable biomarker. For CVD, its potential is indicated but less explored. New studies may identify cfDNA as a valuable circulating cardiovascular risk marker to help improve risk stratification.
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Affiliation(s)
| | - Kristine Frøsig Moseholm
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
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2
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Aucamp J, van der Zwan H, Geldenhuys Z, Abera A, Louw R, van der Sluis R. Diagnostic applications and limitations for the use of cell-free fetal DNA (cffDNA) in animal husbandry and wildlife management. Res Vet Sci 2023; 158:106-116. [PMID: 36989830 DOI: 10.1016/j.rvsc.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/02/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
In animal breeding, a species sex can influence the value of the animal. For example, in the horse breeding industry, mares are preferred as polo horses, while in wildlife breeding males with larger horns are more valuable. Therefore, the economic advantages of knowing the unborn fetus' sex are important to successful animal management. Ultrasonography is used to determine the sex of unborn fetuses, but this method places additional stress on the animal and require specialized equipment and expertise. Conversely, molecular-based sexing techniques require less invasive sampling and can determine sex more reliably. Although in humans, various studies have evaluated the use of cell-free fetal DNA (cffDNA) for prenatal sexing, very few animal studies have been published in this field. Several factors can affect the sensitivity of cffDNA-based sex determination, for example the gestational age. These factors are often not optimized and validated when establishing a protocol for prenatal sexing. In this review, we summarize the current literature on cffDNA in animals. We discuss the diagnostic applications and limitations in the use thereof in animal husbandry and wildlife management. Lastly, the feasibility of implementing diagnostic tests is evaluated and solutions are given to the current drawbacks of the technology.
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New Therapeutics for Extracellular Vesicles: Delivering CRISPR for Cancer Treatment. Int J Mol Sci 2022; 23:ijms232415758. [PMID: 36555398 PMCID: PMC9779094 DOI: 10.3390/ijms232415758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Cancers are defined by genetic defects, which underlines the prospect of using gene therapy in patient care. During the past decade, CRISPR technology has rapidly evolved into a powerful gene editing tool with high fidelity and precision. However, one of the impediments slowing down the clinical translation of CRISPR-based gene therapy concerns the lack of ideal delivery vectors. Extracellular vesicles (EVs) are nano-sized membrane sacs naturally released from nearly all types of cells. Although EVs are secreted for bio-information conveyance among cells or tissues, they have been recognized as superior vectors for drug or gene delivery. Recently, emerging evidence has spotlighted EVs in CRISPR delivery towards cancer treatment. In this review, we briefly introduce the biology and function of the CRISPR system and follow this with a summary of current delivery methods for CRISPR applications. We emphasize the recent progress in EV-mediated CRISPR editing for various cancer types and target genes. The reported strategies for constructing EV-CRISPR vectors, as well as their limitations, are discussed in detail. The review aims to throw light on the clinical potential of engineered EVs and encourage the expansion of our available toolkit to defeat cancer.
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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Ershova ES, Shmarina GV, Porokhovnik LN, Zakharova NV, Kostyuk GP, Umriukhin PE, Kutsev SI, Sergeeva VA, Veiko NN, Kostyuk SV. In Vitro Analysis of Biological Activity of Circulating Cell-Free DNA Isolated from Blood Plasma of Schizophrenic Patients and Healthy Controls. Genes (Basel) 2022; 13:genes13030551. [PMID: 35328103 PMCID: PMC8955124 DOI: 10.3390/genes13030551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/09/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia is associated with low-grade systemic inflammation. Circulating cell-free DNA (c-cfDNA) belongs to the DAMP class. The major research question was: can the c-cfDNA of schizophrenic patients (sz-cfDNA) stimulate the DNA sensor genes, which control the innate immunity? We investigated the in vitro response of ten human skin fibroblast (HSF) lines to five DNA probes containing different amounts of a GC-rich marker (the ribosomal repeat) and a DNA oxidation marker (8-oxodG) including sz-cfDNA and healthy control c-cfDNA (hc-cfDNA) probes. After 1 h, 3 h, and 24 h of incubation, the expression of 6 protein genes responsible for cfDNA transport into the cell (EEA1 and HMGB1) and the recognition of cytosolic DNA (TLR9, AIM2, STING and RIG-I) was analyzed at the transcriptional (RT-qPCR) and protein level (flow cytometry and fluorescence microscopy). Additionally, we analyzed changes in the RNA amount of 32 genes (RT-qPCR), which had been previously associated with different cellular responses to cell-free DNA with different characteristics. Adding sz-cfDNA and hc-cfDNA to the HSF medium in equal amounts (50 ng/mL) blocked endocytosis and stimulated TLR9 and STING gene expression while blocking RIG-I and AIM2 expression. Sz-cfDNA and hc-cfDNA, compared to gDNA, demonstrated much stronger stimulated transcription of genes that control cell proliferation, cytokine synthesis, apoptosis, autophagy, and mitochondrial biogenesis. No significant difference was observed in the response of the cells to sz-cfDNA and hc-cfDNA. Sz-cfDNA and hc-cfDNA showed similarly high biological activity towards HSFs, stimulating the gene activity of TLR9 and STING DNA sensor proteins and blocking the activity of the AIM2 protein gene. Since the sz-cfDNA content in the patients’ blood is several times higher than the hc-cfDNA content, sz-cfDNA may upregulate pro-inflammatory cytokines in schizophrenia.
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Affiliation(s)
- Elizaveta S. Ershova
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Galina V. Shmarina
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Lev N. Porokhovnik
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
- Correspondence:
| | - Natalia V. Zakharova
- N.A. Alekseev Clinical Psychiatric Hospital No. 1, 117152 Moscow, Russia; (N.V.Z.); (G.P.K.)
| | - George P. Kostyuk
- N.A. Alekseev Clinical Psychiatric Hospital No. 1, 117152 Moscow, Russia; (N.V.Z.); (G.P.K.)
| | - Pavel E. Umriukhin
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
- Department of Physiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Sergey I. Kutsev
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Vasilina A. Sergeeva
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Natalia N. Veiko
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Svetlana V. Kostyuk
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
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Naito Y, Kato H, Zhou L, Sugita S, He H, Zheng J, Hao Q, Sawa T, Lee JW. Therapeutic Effects of Hyaluronic Acid Against Cytotoxic Extracellular Vesicles Released During Pseudomonas Aeruginosa Pneumonia. Shock 2022; 57:408-416. [PMID: 34387224 PMCID: PMC8840981 DOI: 10.1097/shk.0000000000001846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT Extracellular vesicles (EVs) have now been recognized as important mediators of cellular communication during injury and repair. We previously found that plasma EVs isolated from ex vivo perfused human lungs injured with Escherichia coli bacterial pneumonia were inflammatory, and exogenous administration of high molecular weight (HMW) hyaluronic acid (HA) as therapy bound to these EVs, decreasing inflammation and injury. In the current study, we studied the role of EVs released during severe Pseudomonas aeruginosa (PA) pneumonia in mice and determined whether intravenous administration of exogenous HMW HA would have therapeutic effects against the bacterial pneumonia. EVs were collected from the bronchoalveolar lavage fluid (BALF) of mice infected with PA103 by ultracentrifugation and analyzed by NanoSight and flow cytometry. In a cytotoxicity assay, administration of EVs released from infected mice (I-EVs) decreased the viability of A549 cells compared to EV isolated from sham control mice (C-EVs). Either exogenous HMW HA or an anti-CD44 antibody, when co-incubated with I-EVs, significantly improved the viability of the A549 cells. In mice with PA103 pneumonia, administration of HMW HA improved pulmonary edema and bacterial count in the lungs and decreased TNF-α and caspase-3 levels in the supernatant of lung homogenates. In conclusion, EVs isolated from BALF of mice with P. aeruginosa pneumonia were cytotoxic and inflammatory, and intravenous HMW HA administration was protective against P. aeruginosa pneumonia.
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Affiliation(s)
- Yoshifumi Naito
- Department of Anesthesiology, Kyoto Prefectural University of Medicine, Japan
| | - Hideya Kato
- Department of Anesthesiology, Kyoto Prefectural University of Medicine, Japan
| | - Li Zhou
- Department of Anesthesiology, University of California San Francisco, San Francisco, California
| | - Shinji Sugita
- Department of Anesthesiology, University of California San Francisco, San Francisco, California
| | - Hongli He
- Department of Anesthesiology, University of California San Francisco, San Francisco, California
| | - Justin Zheng
- Department of Anesthesiology, University of California San Francisco, San Francisco, California
| | - Qi Hao
- Department of Anesthesiology, University of California San Francisco, San Francisco, California
| | - Teiji Sawa
- Department of Anesthesiology, Kyoto Prefectural University of Medicine, Japan
| | - Jae-Woo Lee
- Department of Anesthesiology, University of California San Francisco, San Francisco, California
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Krasic J, Abramovic I, Vrtaric A, Nikolac Gabaj N, Kralik-Oguic S, Katusic Bojanac A, Jezek D, Sincic N. Impact of Preanalytical and Analytical Methods on Cell-Free DNA Diagnostics. Front Cell Dev Biol 2021; 9:686149. [PMID: 34552921 PMCID: PMC8451956 DOI: 10.3389/fcell.2021.686149] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/13/2021] [Indexed: 01/18/2023] Open
Abstract
While tissue biopsy has for the longest time been the gold-standard in biomedicine, precision/personalized medicine is making the shift toward liquid biopsies. Cell-free DNA (cfDNA) based genetic and epigenetic biomarkers reflect the molecular status of its tissue-of-origin allowing for early and non-invasive diagnostics of different pathologies. However, selection of preanalytical procedures (including cfDNA isolation) as well as analytical methods are known to impact the downstream results. Calls for greater standardization are made continuously, yet comprehensive assessments of the impact on diagnostic parameters are lacking. This study aims to evaluate the preanalytic and analytic factors that influence cfDNA diagnostic parameters in blood and semen. Text mining analysis has been performed to assess cfDNA research trends, and identify studies on isolation methods, preanalytical and analytical impact. Seminal and blood plasma were tested as liquid biopsy sources. Traditional methods of cfDNA isolation, commercial kits (CKs), and an in-house developed protocol were tested, as well as the impact of dithiothreitol (DTT) on cfDNA isolation performance. Fluorimetry, qPCR, digital droplet PCR (ddPCR), and bioanalyzer were compared as cfDNA quantification methods. Fragment analysis was performed by qPCR and bioanalyzer while the downstream application (cfDNA methylation) was analyzed by pyrosequencing. In contrast to blood, semen as a liquid biopsy source has only recently begun to be reported as a liquid biopsy source, with almost half of all publications on it being review articles. Experimental data revealed that cfDNA isolation protocols give a wide range of cfDNA yields, both from blood and seminal plasma. The addition of DTT to CKs has improved yields in seminal plasma and had a neutral/negative impact in blood plasma. Capillary electrophoresis and fluorometry reported much higher yields than PCR methods. While cfDNA yield and integrity were highly impacted, cfDNA methylation was not affected by isolation methodology or DTT. In conclusion, NucleoSnap was recognized as the kit with the best overall performance. DTT improved CK yields in seminal plasma. The in-house developed protocol has shown near-kit isolation performance. ddPCR LINE-1 assay for absolute detection of minute amounts of cfDNA was established and allowed for quantification of samples inhibited in qPCR. cfDNA methylation was recognized as a stable biomarker unimpacted by cfDNA isolation method. Finally, semen was found to be an abundant source of cfDNA offering potential research opportunities and benefits for cfDNA based biomarkers development related to male reproductive health.
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Affiliation(s)
- Jure Krasic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Irena Abramovic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Alen Vrtaric
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Nora Nikolac Gabaj
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Sasa Kralik-Oguic
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Clinical Institute of Laboratory Diagnostics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Davor Jezek
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
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8
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Bazzan E, Tinè M, Casara A, Biondini D, Semenzato U, Cocconcelli E, Balestro E, Damin M, Radu CM, Turato G, Baraldo S, Simioni P, Spagnolo P, Saetta M, Cosio MG. Critical Review of the Evolution of Extracellular Vesicles' Knowledge: From 1946 to Today. Int J Mol Sci 2021; 22:ijms22126417. [PMID: 34203956 PMCID: PMC8232679 DOI: 10.3390/ijms22126417] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are a family of particles/vesicles present in blood and body fluids, composed of phospholipid bilayers that carry a variety of molecules that can mediate cell communication, modulating crucial cell processes such as homeostasis, induction/dampening of inflammation, and promotion of repair. Their existence, initially suspected in 1946 and confirmed in 1967, spurred a sharp increase in the number of scientific publications. Paradoxically, the increasing interest for EV content and function progressively reduced the relevance for a precise nomenclature in classifying EVs, therefore leading to a confusing scientific production. The aim of this review was to analyze the evolution of the progress in the knowledge and definition of EVs over the years, with an overview of the methodologies used for the identification of the vesicles, their cell of origin, and the detection of their cargo. The MISEV 2018 guidelines for the proper recognition nomenclature and ways to study EVs are summarized. The review finishes with a “more questions than answers” chapter, in which some of the problems we still face to fully understand the EV function and potential as a diagnostic and therapeutic tool are analyzed.
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Affiliation(s)
- Erica Bazzan
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
- Correspondence: ; Tel.: +39-0498213449
| | - Mariaenrica Tinè
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Alvise Casara
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Davide Biondini
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Umberto Semenzato
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Elisabetta Cocconcelli
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Elisabetta Balestro
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Marco Damin
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Claudia Maria Radu
- Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy;
- Department of Medicine, University of Padova, 35128 Padova, Italy;
| | - Graziella Turato
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Simonetta Baraldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Paolo Simioni
- Department of Medicine, University of Padova, 35128 Padova, Italy;
| | - Paolo Spagnolo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Marina Saetta
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
| | - Manuel G. Cosio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy; (M.T.); (A.C.); (D.B.); (U.S.); (E.C.); (E.B.); (M.D.); (G.T.); (S.B.); (P.S.); (M.S.); (M.G.C.)
- Meakins-Christie Laboratories, Respiratory Division, McGill University, Montreal, QC H3A 0G4, Canada
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9
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Fernández-Domínguez IJ, Manzo-Merino J, Taja-Chayeb L, Dueñas-González A, Pérez-Cárdenas E, Trejo-Becerril C. The role of extracellular DNA (exDNA) in cellular processes. Cancer Biol Ther 2021; 22:267-278. [PMID: 33858306 DOI: 10.1080/15384047.2021.1890319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nowadays, extracellular DNA or circulating cell-free DNA is considered to be a molecule with clinical applications (diagnosis, prognosis, monitoring of treatment responses, or patient follow-up) in diverse pathologies, especially in cancer. Nevertheless, because of its molecular characteristics, it can have many other functions. This review focuses on the participation of extracellular DNA (exDNA) in fundamental processes such as cell signaling, coagulation, immunity, evolution through horizontal transfer of genetic information, and adaptive response to inflammatory processes. A deeper understanding of its role in each of these processes will allow development of better tools to monitor and control pathologies, as well as helping to generate new therapeutic options, beyond the applicability of DNA in liquid biopsy.
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Affiliation(s)
| | | | - Lucia Taja-Chayeb
- Division of Basic Research, Instituto Nacional de Cancerología, México City
| | - Alfonso Dueñas-González
- Division of Basic Research, Instituto Nacional de Cancerología, México City.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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10
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Nejabati HR, Shahnazi V, Faridvand Y, Fathi-Maroufi N, Bahrami-Asl Z, Nikanfar S, Nouri M. Epididymosomes: the black box of Darwin’s pangenesis? Mol Hum Reprod 2021; 27:6031918. [DOI: 10.1093/molehr/gaaa079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/14/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
Darwin, in the pangenesis theory, imagined particles, named as ‘gemmules’, which are released from all (‘pan’) cells of the body. By cell–cell communication and also circulation through the body, they finally reach the germ cells to participate in the generation (‘genesis’) of the new individual. It has been shown that circulatory exosomes are affected by environmental stressors and they can reach the parental germ cells. Therefore, in the mirror of his theory, circulatory exosomes could interact with epididymosomes: epididymis-derived exosomes which have a wide spectrum of variation in content and size, are very sensitive to environmental stressors, and may be involved in translating external information to the germ cells. The protein and RNA cargo would be transferred by epididymosomes to sperm during sperm maturation, which would be then delivered to the embryo at fertilization and inherited by offspring. Therefore, in this study, we will briefly discuss Darwin’s pangenesis theory and its possible relation with epididymosomes. We believed that epididymosomes could be considered as an attractive candidate for the storage of RNA contents, changing the epigenome of the next generations, and allowing the reappearance acquired characteristics of ancestors. Therefore, epididymosomes, as a black box of Darwin’s pangenesis, may unravel parental life history and also disclose the historical events that affect the life of offspring.
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Affiliation(s)
- Hamid Reza Nejabati
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Medical Philosophy and History Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahideh Shahnazi
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Faridvand
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazila Fathi-Maroufi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Bahrami-Asl
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saba Nikanfar
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Nouri
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
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11
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Bryzgunova OE, Konoshenko MY, Laktionov PP. Concentration of cell-free DNA in different tumor types. Expert Rev Mol Diagn 2020; 21:63-75. [PMID: 33270495 DOI: 10.1080/14737159.2020.1860021] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Cell-free DNA (cfDNA) circulates in the blood for a long time. The levels of cfDNA in the blood are assayed in cancer diagnostics because they are closely related to the tumor burden of patients.Areas covered: cfDNA escapes the action of DNA-hydrolyzing enzymes, being a part of supramolecular complexes or interacting with the plasma membrane of blood cells. cfDNA has heterogeneous size and composition, which impose various restrictions on both isolation methods and subsequent analysis. cfDNA concentration and structural changes with the development of diseases highlight the high potential of cfDNA as a diagnostic and prognostic marker. The concentration of cfDNA released in the blood by tumor cells determines the specificity of such diagnostics and the required blood volume. The present review aimed to synthesize the available data on cfDNA concentration in the cancer patient's blood as well as pre-analytical, analytical, and biological factors, which interfere with cfDNA concentration.Expert opinion: The concentration of cfDNA and tumor cell DNA (ctDNA), and the over-presentation of DNA loci in cfDNA must be considered when looking for tumor markers. Some inconsistent data on cfDNA concentrations (like those obtained by different methods) suggest that the study of cfDNA should be continued.
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Affiliation(s)
- O E Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
| | - M Yu Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
| | - P P Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, Novosibirsk, Russia
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12
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Bline AP, Le Goff A, Allard P. What Is Lost in the Weismann Barrier? J Dev Biol 2020; 8:E35. [PMID: 33339122 PMCID: PMC7768413 DOI: 10.3390/jdb8040035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/01/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
The Weismann barrier has long been regarded as a basic tenet of biology. However, upon close examination of its historical origins and August Weismann's own writings, questions arise as to whether such a status is warranted. As scientific research has advanced, the persistence of the concept of the barrier has left us with the same dichotomies Weismann contended with over 100 years ago: germ or soma, gene or environment, hard or soft inheritance. These dichotomies distract from the more important questions we need to address going forward. In this review, we will examine the theories that have shaped Weismann's thinking, how the concept of the Weismann barrier emerged, and the limitations that it carries. We will contrast the principles underlying the barrier with recent and less recent findings in developmental biology and transgenerational epigenetic inheritance that have profoundly eroded the oppositional view of germline vs. soma. Discarding the barrier allows us to examine the interactive processes and their response to environmental context that generate germ cells in the first place, determine the entirety of what is inherited through them, and set the trajectory for the health status of the progeny they bear.
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Affiliation(s)
- Abigail P. Bline
- Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA;
| | - Anne Le Goff
- UCLA EpiCenter on Epigenetics, Reproduction & Society, University of California Los Angeles, Los Angeles, CA 90095, USA;
- Institute for Society & Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Patrick Allard
- Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA;
- UCLA EpiCenter on Epigenetics, Reproduction & Society, University of California Los Angeles, Los Angeles, CA 90095, USA;
- Institute for Society & Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
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13
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Korabecna M, Zinkova A, Brynychova I, Chylikova B, Prikryl P, Sedova L, Neuzil P, Seda O. Cell-free DNA in plasma as an essential immune system regulator. Sci Rep 2020; 10:17478. [PMID: 33060738 PMCID: PMC7566599 DOI: 10.1038/s41598-020-74288-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/04/2020] [Indexed: 02/08/2023] Open
Abstract
The cell-free DNA (cfDNA) is always present in plasma, and it is biomarker of growing interest in prenatal diagnostics as well as in oncology and transplantology for therapy efficiency monitoring. But does this cfDNA have a physiological role? Here we show that cfDNA presence and clearance in plasma of healthy individuals plays an indispensable role in immune system regulation. We exposed THP1 cells to healthy individuals' plasma with (NP) and without (TP) cfDNA. In cells treated with NP, we found elevated expression of genes whose products maintain immune system homeostasis. Exposure of cells to TP triggered an innate immune response (IIR), documented particularly by elevated expression of pro-inflammatory interleukin 8. The results of mass spectrometry showed a higher abundance of proteins associated with IIR activation due to the regulation of complement cascade in cells cultivated with TP. These expression profiles provide evidence that the presence of cfDNA and its clearance in plasma of healthy individuals regulate fundamental mechanisms of the inflammation process and tissue homeostasis. The detailed understanding how neutrophil extracellular traps and their naturally occurring degradation products affect the performance of immune system is of crucial interest for future medical applications.
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Affiliation(s)
- M Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
| | - A Zinkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - I Brynychova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - B Chylikova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - P Prikryl
- First Faculty of Medicine, Institute of Pathological Physiology, Charles University, Prague, Czech Republic
| | - L Sedova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - P Neuzil
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, People's Republic of China
- CEITEC, Brno University of Technology, Brno, Czech Republic
| | - O Seda
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
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Pessoa LS, Heringer M, Ferrer VP. ctDNA as a cancer biomarker: A broad overview. Crit Rev Oncol Hematol 2020; 155:103109. [PMID: 33049662 DOI: 10.1016/j.critrevonc.2020.103109] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/17/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in fluids has gained attention because ctDNA seems to identify tumor-specific abnormalities, which could be used for diagnosis, follow-up of treatment, and prognosis: the so-called liquid biopsy. Liquid biopsy is a minimally invasive approach and presents the sum of ctDNA from primary and secondary tumor sites. It has been possible not only to quantify the amount of ctDNA but also to identify (epi)genetic changes. Specific mutations in genes have been identified in the plasma of patients with several types of cancer, which highlights ctDNA as a possible cancer biomarker. However, achieving detectable concentrations of ctDNA in body fluids is not an easy task. ctDNA fragments present a short half-life, and there are no cut-off values to discriminate high and low ctDNA concentrations. Here, we discuss the use of ctDNA as a cancer biomarker, the main methodologies, the inherent difficulties, and the clinical predictive value of ctDNA.
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Affiliation(s)
- Luciana Santos Pessoa
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil; Center for Experimental Surgery, Graduate Program in Surgical Sciences, Department of Surgery, Faculty of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manoela Heringer
- Brain's Biomedicine Laboratory, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Department of Cellular and Molecular Biology, Institute of Biology, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil.
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15
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Manoharan A, Sambandam R, Bhat V. Recent technologies enhancing the clinical utility of circulating tumor DNA. Clin Chim Acta 2020; 510:498-506. [PMID: 32795543 DOI: 10.1016/j.cca.2020.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
Circulating tumor DNA (ctDNA) is a promising blood based biomarker that is set to revolutionize cancer management. Non-invasive biopsy takes precedence over tissue biopsy for enabling longitudinal monitoring, providing a comprehensive profile of tumor heterogeneity and the ease of repeated sampling. Advanced genomic technologies enable real-time disease monitoring, detect minimal residual disease and recurrence at the earliest stages, the potential time points when treatment significantly reduces morbidity and mortality and enable tailored and personalized therapy. The review highlights evidence from literature that make ctDNA a potential liquid biopsy marker and the clinical utility of the recent techniques that leverage up on ctDNA.
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Affiliation(s)
- Aarthi Manoharan
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India
| | - Ravikumar Sambandam
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India.
| | - Vishnu Bhat
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India
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16
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Chang X, Fang L, Bai J, Wang Z. Characteristics and Changes of DNA in Extracellular Vesicles. DNA Cell Biol 2020; 39:1486-1493. [PMID: 32551866 DOI: 10.1089/dna.2019.5005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) have been known to carry multiple bioactive molecules, including lipids, mRNA/miRNA, and proteins. However, recent studies show that specific DNAs are also packed into EVs secreted by various cells, which are considered as powerful markers for diagnosis and prognosis of disease. DNAs in EVs are derived from parental cells, representing the mutation and even spanning of the whole genomic DNA of parental cells. Interestingly, increasing numbers of studies have found that the genetic materials in different EVs are not only universal but also random and different, which may be related to the size of EVs. In this review, we discuss the different characteristics of DNAs in EVs and the rules of their variation. We hope our review will trigger the continuing exploration of the origins, characteristics, and variations of DNAs in EVs.
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Affiliation(s)
- Xiulin Chang
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founded by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Liaoqiong Fang
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founded by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Jin Bai
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founded by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Zhibiao Wang
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founded by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
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17
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations. Crit Rev Clin Lab Sci 2019:1-17. [PMID: 31865831 DOI: 10.1080/10408363.2019.1700902] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early diagnosis of cancer improves the efficacy of curative therapies. However, due to the difficulties involved in distinguishing between small early-stage tumors and normal biological variation, early detection of cancer is an extremely challenging task and there are currently no clinically validated biomarkers for a pan-cancer screening test. It is thus of particular significance that increasing evidence indicates the potential of circulating tumor DNA (ctDNA) molecules, which are fragmented segments of DNA shed from tumor cells into adjacent body fluids and the circulatory system, to serve as molecular markers for early cancer detection and thereby allow early intervention and improvement of therapeutic and survival outcomes. This is possible because ctDNA molecules bear cancer-specific fragmentation patterns, nucleosome depletion motifs, and genetic and epigenetic alterations, as distinct from plasma DNA originating from non-cancerous tissues/cells. Compared to traditional biomarkers, ctDNA analysis therefore presents the distinctive advantage of detecting tumor-specific alterations. However, based on a thorough survey of the literature, theoretical and empirical evidence suggests that current ctDNA analysis strategies, which are mainly based on DNA mutation detection, do not demonstrate the necessary diagnostic sensitivity and specificity that is required for broad clinical implementation in a screening context. Therefore, in this review we explain the biological, physiological, and analytical challenges toward the development of clinically meaningful ctDNA tests. In addition, we explore some approaches that can be implemented in order to increase the sensitivity and specificity of ctDNA assays.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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18
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Extracellular DNA Containing (dG)n Motifs Penetrates into MCF7 Breast Cancer Cells, Induces the Adaptive Response, and Can Be Expressed. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:7853492. [PMID: 31781350 PMCID: PMC6874983 DOI: 10.1155/2019/7853492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/03/2019] [Indexed: 11/29/2022]
Abstract
Background Oxidized human DNA or plasmid DNAs containing human ribosomal genes can easily penetrate into the breast cancer cells MCF7 and stimulate the adaptive response induction. Plasmid DNA containing a CMV promoter, gene EGFP, and the insertion of the human ribosomal genes can be expressed. A hypothesis is proposed: these features of the ribosomal DNA are due to the presence of dGn motifs that are prone to oxidize. Methods Cells of MCF7 line were cultured with plasmids which contained a CMV promoter and gene of fluorescent protein EGFP. Genetic construction pEGFP-Gn contains pEGFP vector and a small insertion with dG11 and dG13 motifs that are inclined to oxidation. The accumulation of pEGFP and pEGFP-Gn in MCF7 (qPCR), the levels of ROS in the cells, the content of 8-oxodG in plasmids and cellular DNA (flow cytometry, immunoassay, and fluorescent microscopy), the expression of NOX4 and EGFP, the localization of NOX4 and EGFP in MCF7 (qPCR, flow cytometry, and fluorescent microscopy), and the levels of the cell DNA damage (comet assay) were analyzed. Results (dG)n insertions in the plasmid pEGFP increase the levels of ROS, the cell DNA oxidation and DNA damage, and the level of transfection of plasmid into the MCF7 cells. NOX4 participates in the oxidation of pEGFP-Gn and pEGFP. The expression of EGFP gene in MCF7 is significantly increased in case of pEGFP-Gn. Stimulation of ROS synthesis (H2O2 40 μM or 10 cGy IR) increases the level of expression of EGFP. Conclusions GC-rich DNA fragments containing dGn motifs that are inclined to oxidation penetrate into MCF7 cancer cells, stimulate the adaptive response, and can be expressed. This property of GC-rich cell-free DNA should be considered and/or could potentially be used in therapy of tumors.
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19
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Li J, Wang L, Yang G, Wang Y, Guo C, Liu S, Gao Q, Zhang H. Changes in circulating cell-free nuclear DNA and mitochondrial DNA of patients with adolescent idiopathic scoliosis. BMC Musculoskelet Disord 2019; 20:479. [PMID: 31653238 PMCID: PMC6815015 DOI: 10.1186/s12891-019-2869-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/09/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Adolescent idiopathic scoliosis (AIS) which characterized by complex three-dimensional deformity of spine has been difficult to cure because of the unknown etiopathology and uncertainty of progression. Nowadays, circulating cell-free (ccf) DNA was found to be a potential biomarker for several benign and malignant diseases. However, whether ccf DNA can be a biomarker for AIS has not been reported yet. In this study, we investigate the circulating cell-free nuclear DNA (ccf n-DNA) and mitochondrial DNA (ccf mt-DNA) concentrations in the plasma of patients with AIS and controls (CT), and the changed plasma ccf n-DNA and ccf mt-DNA levels and their association with clinical parameters were assessed. METHODS The plasma of peripheral blood from 69 AIS patients and 21 age-matched CT was collected for ccf DNA analysis. Quantitative PCR was used to detect ccf n-DNA and ccf mt-DNA levels, and correlation analyses between the ccf n-DNA and ccf mt-DNA levels and clinical characteristics were conducted. Receiver operator curves (ROC) were used to analyze the sensitivity and specificity of ccf n-DNA and ccf mt-DNA levels to different characteristics. RESULTS The plasma ccf n-DNA levels of both GAPDH and ACTB were significantly decreased in AIS patients compared with those in controls, while the plasma ccf mt-DNA levels did not changed. According to sex-related analyses, the ccf n-DNA levels in male CT-M was higher than that in female CT and male AIS, but the ccf n-DNA levels in female AIS was not significantly changed when compared with male AIS or female CT. However, the concentration of ccf mt-DNA in female AIS increased significantly when compared with male AIS. Surprisingly, Lenke type-related analyses suggested that Lenke type 1 patients had lower ccf n-DNA levels, whereas Lenke type 5 patients had higher ccf mt-DNA levels compared with those of controls. However, a lower sensitivity and specificity of AIS predicted by ccf n-DNA or ccf mt-DNA levels was observed, whether in total, by sex, or by Lenke type. CONCLUSION Although with no/little predictive accuracy of AIS/progressed AIS by ccf DNA levels, significantly changed plasma ccf DNA levels were observed in AIS patients compared with those in controls.
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Affiliation(s)
- Jiong Li
- Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008 China
| | - Longjie Wang
- Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008 China
| | - Guanteng Yang
- Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008 China
| | - Yunjia Wang
- Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008 China
| | - Chaofeng Guo
- Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008 China
| | - Shaohua Liu
- Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008 China
| | - Qile Gao
- Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008 China
| | - Hongqi Zhang
- Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008 China
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Tuaeva NO, Falzone L, Porozov YB, Nosyrev AE, Trukhan VM, Kovatsi L, Spandidos DA, Drakoulis N, Kalogeraki A, Mamoulakis C, Tzanakakis G, Libra M, Tsatsakis A. Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. Cells 2019; 8:E1251. [PMID: 31615102 PMCID: PMC6829588 DOI: 10.3390/cells8101251] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/30/2019] [Accepted: 10/12/2019] [Indexed: 02/06/2023] Open
Abstract
In recent years, the introduction of new molecular techniques in experimental and clinical settings has allowed researchers and clinicians to propose circulating-tumor DNA (ctDNA) analysis and liquid biopsy as novel promising strategies for the early diagnosis of cancer and for the definition of patients' prognosis. It was widely demonstrated that through the non-invasive analysis of ctDNA, it is possible to identify and characterize the mutational status of tumors while avoiding invasive diagnostic strategies. Although a number of studies on ctDNA in patients' samples significantly contributed to the improvement of oncology practice, some investigations generated conflicting data about the diagnostic and prognostic significance of ctDNA. Hence, to highlight the relevant achievements obtained so far in this field, a clearer description of the current methodologies used, as well as the obtained results, are strongly needed. On these bases, this review discusses the most relevant studies on ctDNA analysis in cancer, as well as the future directions and applications of liquid biopsy. In particular, special attention was paid to the early diagnosis of primary cancer, to the diagnosis of tumors with an unknown primary location, and finally to the prognosis of cancer patients. Furthermore, the current limitations of ctDNA-based approaches and possible strategies to overcome these limitations are presented.
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Affiliation(s)
- Natalia O Tuaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Luca Falzone
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131 Naples, Italy.
| | - Yuri B Porozov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- ITMO University, Saint Petersburg 197101, Russia.
| | - Alexander E Nosyrev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Vladimir M Trukhan
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54248 Thessaloniki, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Zografou, Greece.
| | - Alexandra Kalogeraki
- Department of Pathology-Cytopathology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, Medical School, Heraklion, 70013 Crete, Greece.
| | - George Tzanakakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Massimo Libra
- Department of Biomedical and Biotechnlogical Sciences, University of Catania, 95123 Catania, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123 Catania, Italy.
| | - Aristides Tsatsakis
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119048 Moscow, Russia.
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, Heraklion, 71003 Crete, Greece.
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Meddeb R, Pisareva E, Thierry AR. Guidelines for the Preanalytical Conditions for Analyzing Circulating Cell-Free DNA. Clin Chem 2019; 65:623-633. [DOI: 10.1373/clinchem.2018.298323] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/05/2019] [Indexed: 12/13/2022]
Abstract
Abstract
Circulating cell-free DNA (cfDNA) isolated from blood has been identified as a potential biomarker in numerous fields, and has been the object of intensive research over the past decade, although its original discovery dates back 60 years. While it is already used routinely in commercial and clinical practice in oncology and prenatal testing, other potential applications have emerged, including for diabetes, cardiovascular diseases, organ transplantation, autoimmune diseases, sepsis, trauma, and sport management. As with the discovery and development of any biomarker, preanalytical requirements and documentation are as important as analytical requirements. Except for the case of noninvasive prenatal testing and prenatal diagnosis, the implementation of cfDNA in a clinical setting remains limited because of the lack of standardization of cfDNA analysis. In particular, only a few attempts have been made to collect and pool scientific data on the relevant preanalytical factors, and no standard operating procedure has yet been set. For this report, we have performed a thorough and systematic search via MEDLINE® for relevant preanalytical variables and patient factors. These form the basis of the guidelines we propose for analyzing nuclear cfDNA.
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Affiliation(s)
- Romain Meddeb
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- University of Montpellier, Montpellier, France
- Regional Institute of Cancer of Montpellier, Montpellier, France
| | - Ekaterina Pisareva
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- University of Montpellier, Montpellier, France
- Regional Institute of Cancer of Montpellier, Montpellier, France
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- University of Montpellier, Montpellier, France
- Regional Institute of Cancer of Montpellier, Montpellier, France
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22
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Abstract
To our knowledge, this is the first comprehensive study on the influence of several pre-analytical and demographic parameters that could be a source of variability in the quantification of nuclear and mitochondrial circulating DNA (NcirDNA and McirDNA). We report data from a total of 222 subjects, 104 healthy individuals and 118 metastatic colorectal cancer (mCRC) patients. Approximately 50,000 and 3,000-fold more mitochondrial than nuclear genome copies were found in the plasma of healthy individuals and mCRC patients, respectively. In healthy individuals, NcirDNA concentration was statistically influenced by age (p = 0.009) and gender (p = 0.048). Multivariate analysis with logistic regression specified that age over 47 years-old was predictive to have higher NcirDNA concentration (OR = 2.41; p = 0.033). McirDNA concentration was independent of age and gender in healthy individuals. In mCRC patients, NcirDNA and McirDNA levels were independent of age, gender, delay between food intake and blood collection, and plasma aspect, either with univariate or multivariate analysis. Nonetheless, ad hoc study suggested that menopause and blood collection time might have tendency to influence cirDNA quantification. In addition, high significant statistical differences were found between mCRC patients and healthy individuals for NcirDNA (p < 0.0001), McirDNA (p < 0.0001) and McirDNA/NcirDNA ratio (p < 0.0001). NcirDNA and McirDNA levels do not vary in the same way with regards to cancer vs healthy status, pre-analytical and demographic factors.
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23
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Increased Transfection of the Easily Oxidizable GC-Rich DNA Fragments into the MCF7 Breast Cancer Cell. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:2348165. [PMID: 30867888 PMCID: PMC6379852 DOI: 10.1155/2019/2348165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/16/2018] [Accepted: 11/14/2018] [Indexed: 01/15/2023]
Abstract
Objective Easily oxidizable GC-rich DNA (GC-DNA) fragments accumulate in the cell-free DNA (cfDNA) of patients with various diseases. The human oxidized DNA penetrates the MCF7 breast cancer cells and significantly changes their physiology. It can be assumed that readily oxidizable GC-DNA fragments can penetrate the cancer cells and be expressed. Methods MCF7 cells were cultured in the presence of two types of GC-DNA probes: (1) vectors pBR322 and pEGFP and (2) plasmids carrying inserted human rDNA (pBR322-rDNA and pEGFP-rDNA). pEGFP and pEGFP-rDNA contained a CMV promoter and a fluorescent protein gene EGFP. ROS generation rate, accumulation of the DNA probes in MCF7, 8-oxodG content, expression of EGFP and NOX4, and localization of EGFP, NOX4, and 8-oxodG in MCF7 were explored. The applied methods were qPCR, fluorescent microscopy (FM), immunoassay, and flow cytometry (FCA). Results When GC-DNA is added to the cell culture medium, it interacts with the cell surface. At the site of GC-DNA contact with the cell, NOX4 is expressed, and ROS level increases. The ROS oxidize the GC-DNA. When using the plasmids pEGFP and pEGFP-rDNA, an increase in the amount of the DNA EGFP, RNA EGFP, and EGFP proteins was detected in the cells. These facts suggest that GC-DNA penetrates the cells and the EGFP gene is expressed. Insertions of the rDNA significantly increase the GC-DNA oxidation degree as well as the rate of plasmid transfection into the cells and the EGFP expression level. In the nucleus, the oxidized GC-rDNA fragments, but not the vectors, are localized within the nucleolus. Conclusions GC-rich cfDNA fragments that are prone to oxidation can easily penetrate the cancer cells and be expressed. The cfDNA should become a target for the antitumor therapy.
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24
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New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis. NPJ Genom Med 2018; 3:31. [PMID: 30479833 PMCID: PMC6251887 DOI: 10.1038/s41525-018-0069-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/19/2018] [Indexed: 02/06/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has received increasing interest as an apparent breakthrough approach in diagnostics, personalized medicine, and tumor biology. However, the structural features of cfDNA are poorly characterized. Specifically, the literature has discrepancies with regards to cfDNA size profile. We performed a blinded study of the distribution of cfDNA fragment sizes in cancer patient plasma (n = 11), by various ultra-deep-sequencing approaches and quantitative PCR (Q-PCR). Whole-genome sequencing of single-stranded DNA library preparation (SSP-S) revealed that nearly half of the total cfDNA fragment number are below 120 nucleotides, which are not readily detectable by standard double-stranded DNA library preparation (DSP) protocols. Fractional size distribution of cancer patient circulating DNA was very similar using both SSP-S-based or Q-PCR-based methods also revealing that high molecular weight (over 350 bp) cfDNA is a minor component (~2%). These extra small detected cfDNA fragments may mostly result from nicks occurring in blood circulation in one or both DNA strands, which are subsequently revealed through the denaturation step of the SSP and Q-PCR procedures. Detailed analysis of the data suggested that most of the detectable cfDNA in blood has a nucleosome footprint (∼10-bp periodicity repeats). The nucleosome is thus the most stabilizing structure of DNA in the circulation. cfDNA molecules, which are initially packed in chromatin, are released from cells and are then dynamically degraded in blood both within and between nucleosomes or transcription factor-associated subcomplexes. While this study provides new insights into cfDNA size profiles harmonizing sequencing and Q-PCR findings, our data validate the use of a specific Q-PCR method and SSP-S for obtaining an optimal qualitative and quantitative analytical signal.
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Nagler M, Insam H, Pietramellara G, Ascher-Jenull J. Extracellular DNA in natural environments: features, relevance and applications. Appl Microbiol Biotechnol 2018; 102:6343-6356. [PMID: 29858957 PMCID: PMC6061472 DOI: 10.1007/s00253-018-9120-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/15/2018] [Accepted: 05/19/2018] [Indexed: 01/13/2023]
Abstract
Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.
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Affiliation(s)
- Magdalena Nagler
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria.
| | - Heribert Insam
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
| | - Giacomo Pietramellara
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
| | - Judith Ascher-Jenull
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
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26
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Abstract
Darwin's gemmules were supposed to be "thrown off" by cells and were "inconceivably minute and numerous as the stars in heaven." They were capable of self-propagation and diffusion from cell to cell, and circulation through the system. The word "gene" coined by Wilhelm Johannsen, was derived from de Vries's term "pangen," itself a substitute for "gemmule" in Darwin's Pangenesis. Johannsen resisted the "morphological" conception of genes as particles with a certain structure. Morgan's genes were considered to be stable entities arranged in an orderly linear pattern on chromosomes, like beads on a string. In the late 1940s, McClintock challenged the concept of the stability of the gene when she discovered that some genes could move within a chromosome and between chromosomes. In 1948, Mandel and Metais reported the presence of cell-free nucleic acids in human blood for the first time. Over the past several decades, it has been universally accepted that almost all types of cells not only shed molecules such as cell-free DNA (including genomic DNA, tumor DNA and fetal DNA), RNAs (including mRNA and small RNAs) and prions, but also release into the extracellular environment diverse types of membrane vesicles (known as extracellular vesicles) containing DNA, RNA and proteins. Thus Darwin's speculative gemmules of the 19th century have become the experimentally demonstrated circulating cell-free DNA, mobile RNAs, prions and extracellular vesicles.
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Affiliation(s)
- Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China; Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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27
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. The diverse origins of circulating cell-free DNA in the human body: a critical re-evaluation of the literature. Biol Rev Camb Philos Soc 2018; 93:1649-1683. [PMID: 29654714 DOI: 10.1111/brv.12413] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 12/13/2022]
Abstract
Since the detection of cell-free DNA (cfDNA) in human plasma in 1948, it has been investigated as a non-invasive screening tool for many diseases, especially solid tumours and foetal genetic abnormalities. However, to date our lack of knowledge regarding the origin and purpose of cfDNA in a physiological environment has limited its use to more obvious diagnostics, neglecting, for example, its potential utility in the identification of predisposition to disease, earlier detection of cancers, and lifestyle-induced epigenetic changes. Moreover, the concept or mechanism of cfDNA could also have potential therapeutic uses such as in immuno- or gene therapy. This review presents an extensive compilation of the putative origins of cfDNA and then contrasts the contributions of cellular breakdown processes with active mechanisms for the release of cfDNA into the extracellular environment. The involvement of cfDNA derived from both cellular breakdown and active release in lateral information transfer is also discussed. We hope to encourage researchers to adopt a more holistic view of cfDNA research, taking into account all the biological pathways in which cfDNA is involved, and to give serious consideration to the integration of in vitro and in vivo research. We also wish to encourage researchers not to limit their focus to the apoptotic or necrotic fraction of cfDNA, but to investigate the intercellular messaging capabilities of the actively released fraction of cfDNA and to study the role of cfDNA in pathogenesis.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
| | - Abel J Bronkhorst
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Human Metabolomics, Biochemistry Division, Hoffman Street, North-West University, Private bag X6001 Potchefstroom, 2520, South Africa
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28
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Nana-Sinkam SP, Acunzo M, Croce CM, Wang K. Extracellular Vesicle Biology in the Pathogenesis of Lung Disease. Am J Respir Crit Care Med 2017; 196:1510-1518. [PMID: 28678586 PMCID: PMC5754438 DOI: 10.1164/rccm.201612-2457pp] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 06/29/2017] [Indexed: 12/22/2022] Open
Affiliation(s)
- Serge P. Nana-Sinkam
- Division of Pulmonary Disease and Critical Care Medicine, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Mario Acunzo
- Division of Pulmonary Disease and Critical Care Medicine, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, James Comprehensive Cancer Center, Ohio State University, Columbus, Ohio; and
| | - Kai Wang
- Institutes for Systems Biology, Seattle, Washington
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29
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Macías M, Alegre E, Díaz-Lagares A, Patiño A, Pérez-Gracia JL, Sanmamed M, López-López R, Varo N, González A. Liquid Biopsy: From Basic Research to Clinical Practice. Adv Clin Chem 2017; 83:73-119. [PMID: 29304904 DOI: 10.1016/bs.acc.2017.10.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the molecular analysis in biological fluids of nucleic acids, subcellular structures, especially exosomes, and, in the context of cancer, circulating tumor cells. In the last 10 years, there has been an intensive research in liquid biopsy to achieve a less invasive and more precise personalized medicine. Molecular assessment of these circulating biomarkers can complement or even surrogate tissue biopsy. Because of this research, liquid biopsy has been introduced in clinical practice, especially in oncology, prenatal screening, and transplantation. Here we review the biology, methodological approaches, and clinical applications of the main biomarkers involved in liquid biopsy.
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Affiliation(s)
| | - Estibaliz Alegre
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Angel Díaz-Lagares
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Ana Patiño
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Jose L Pérez-Gracia
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Miguel Sanmamed
- Yale University School of Medicine, New Haven, CT, United States
| | - Rafael López-López
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain; Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Nerea Varo
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain
| | - Alvaro González
- Clínica Universidad de Navarra, Pamplona, Spain; The Health Research Institute of Navarra (IDISNA), Pamplona, Spain.
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30
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Aucamp J, Calitz C, Bronkhorst AJ, Wrzesinski K, Hamman S, Gouws C, Pretorius PJ. Cell-free DNA in a three-dimensional spheroid cell culture model: A preliminary study. Int J Biochem Cell Biol 2017; 89:182-192. [DOI: 10.1016/j.biocel.2017.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/07/2017] [Accepted: 06/22/2017] [Indexed: 02/07/2023]
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31
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Aucamp J, Bronkhorst AJ, Peters DL, Van Dyk HC, Van der Westhuizen FH, Pretorius PJ. Kinetic analysis, size profiling, and bioenergetic association of DNA released by selected cell lines in vitro. Cell Mol Life Sci 2017; 74:2689-2707. [PMID: 28315952 PMCID: PMC11107759 DOI: 10.1007/s00018-017-2495-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/19/2017] [Accepted: 02/22/2017] [Indexed: 01/09/2023]
Abstract
Although circulating DNA (cirDNA) analysis shows great promise as a screening tool for a wide range of pathologies, numerous stumbling blocks hinder the rapid translation of research to clinical practice. This is related directly to the inherent complexity of the in vivo setting, wherein the influence of complex systems of interconnected cellular responses and putative DNA sources creates a seemingly arbitrary representation of the quantitative and qualitative properties of the cirDNA in the blood of any individual. Therefore, to evaluate the potential of in vitro cell cultures to circumvent the difficulties encountered in in vivo investigations, the purpose of this work was to elucidate the characteristics of the DNA released [cell-free DNA (cfDNA)] by eight different cell lines. This revealed three different forms of cfDNA release patterns and the presence of nucleosomal fragments as well as actively released forms of DNA, which are not only consistently observed in every tested cell line, but also in plasma samples. Correlations between cfDNA release and cellular origin, growth rate, and cancer status were also investigated by screening and comparing bioenergetics flux parameters. These results show statistically significant correlations between cfDNA levels and glycolysis, while no correlations between cfDNA levels and oxidative phosphorylation were observed. Furthermore, several correlations between growth rate, cancer status, and dependency on aerobic glycolysis were observed. Cell cultures can, therefore, successfully serve as closed-circuit models to either replace or be used in conjunction with biofluid samples, which will enable sharper focus on specific cell types or DNA origins.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Dimetrie L Peters
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Hayley C Van Dyk
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
| | | | - Piet J Pretorius
- Human Metabolomics, North-West University, Hoffman Street, Potchefstroom, 2520, South Africa
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32
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Aucamp J, Van Dyk HC, Bronkhorst AJ, Pretorius PJ. Valproic acid alters the content and function of the cell-free DNA released by hepatocellular carcinoma (HepG2) cells in vitro. Biochimie 2017; 140:93-105. [PMID: 28668269 DOI: 10.1016/j.biochi.2017.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 06/27/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND It has long been believed that cell-free DNA (cfDNA) actively released into circulation can serve as intercellular messengers, and their involvement in processes such as the bystander effect strongly support this. However, this intercellular messaging function of cfDNA may have clinical implications that have not yet been considered. METHODS CfDNA was isolated from the growth medium of HepG2 cells treated with valproic acid (VPA). This cfDNA was then administered to untreated cells and cellular metabolic activity was measured. RESULTS VPA altered the characteristics of cfDNA released by treated HepG2 cells in vitro. When administered to untreated cells, the cfDNA from cells treated with VPA resulted in the dose-dependent induction of glycolytic activity within 36 min of administration, but little to no alterations in oxidative phosphorylation. The glycolytic activity lasted for 4-6 h, whereas changes in subsequent cfDNA release and characteristics were found to remain persistent after two 24 h treatments. Fragmented genomic DNA from VPA-treated cells did not induce the effects observed for cfDNA obtained VPA-treated cells. CONCLUSIONS It is possible for cfDNA to, under in vitro conditions, transfer pharmaceutically-induced effects to untreated recipient cells. Further investigation regarding this occurrence under in vivo conditions is, therefore, strongly encouraged. GENERAL SIGNIFICANCE The intercellular messaging functions of cfDNA present in donated biological fluids has potential clinical implications that require urgent attention. These implications may, however, also have potential as new forms of treatment that can circumvent pharmacological barriers.
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Affiliation(s)
- Janine Aucamp
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa.
| | - Hayley C Van Dyk
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Abel J Bronkhorst
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
| | - Piet J Pretorius
- Human Metabolomics, North-West University, Private Bag X6001, Hoffman Street, Potchefstroom, 2520, South Africa
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33
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Sharma A. Transgenerational epigenetics: Integrating soma to germline communication with gametic inheritance. Mech Ageing Dev 2017; 163:15-22. [PMID: 28093237 DOI: 10.1016/j.mad.2016.12.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/07/2016] [Accepted: 12/13/2016] [Indexed: 12/28/2022]
Abstract
Evidence supporting germline mediated epigenetic inheritance of environmentally induced traits has increasingly emerged over the past several years. Although the mechanisms underlying this inheritance remain unclear, recent findings suggest that parental gamete-borne epigenetic factors, particularly RNAs, affect post-fertilization and developmental gene regulation, ultimately leading to phenotypic appearance in the offspring. Complex processes involving gene expression and epigenetic regulation are considered to perpetuate across generations. In addition to transfer of germline factors, epigenetic inheritance via gametes also requires a mechanism whereby the information pertaining to the induced traits is communicated from soma to germline. Despite violating a century-old view in biology, this communication seems to play a role in transmission of environmental effects across generations. Circulating RNAs, especially those associated with extracellular vesicles like exosomes, are emerging as promising candidates that can transmit gene regulatory information in this direction. Cumulatively, these new observations provide a basis to integrate epigenetic inheritance. With significant implications in health, disease and ageing, the latter appears poised to revolutionize biology.
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Affiliation(s)
- Abhay Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.
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