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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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Picca A, Guerra F, Calvani R, Romano R, Coelho-Junior HJ, Damiano FP, Bucci C, Marzetti E. Circulating Mitochondrial DNA and Inter-Organelle Contact Sites in Aging and Associated Conditions. Cells 2022; 11:cells11040675. [PMID: 35203322 PMCID: PMC8870554 DOI: 10.3390/cells11040675] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are primarily involved in cell bioenergetics, regulation of redox homeostasis, and cell death/survival signaling. An immunostimulatory property of mitochondria has also been recognized which is deployed through the extracellular release of entire or portioned organelle and/or mitochondrial DNA (mtDNA) unloading. Dynamic homo- and heterotypic interactions involving mitochondria have been described. Each type of connection has functional implications that eventually optimize mitochondrial activity according to the bioenergetic demands of a specific cell/tissue. Inter-organelle communications may also serve as molecular platforms for the extracellular release of mitochondrial components and subsequent ignition of systemic inflammation. Age-related chronic inflammation (inflamm-aging) has been associated with mitochondrial dysfunction and increased extracellular release of mitochondrial components—in particular, cell-free mtDNA. The close relationship between mitochondrial dysfunction and cellular senescence further supports the central role of mitochondria in the aging process and its related conditions. Here, we provide an overview of (1) the mitochondrial genetic system and the potential routes for generating and releasing mtDNA intermediates; (2) the pro-inflammatory pathways elicited by circulating mtDNA; (3) the participation of inter-organelle contacts to mtDNA homeostasis; and (4) the link of these processes with senescence and age-associated conditions.
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Affiliation(s)
- Anna Picca
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.P.D.); (E.M.)
| | - Flora Guerra
- Department of Biological and Environmental Sciences and Technologies, Università del Salento, 73100 Lecce, Italy; (F.G.); (R.R.); (C.B.)
| | - Riccardo Calvani
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.P.D.); (E.M.)
- Correspondence: ; Tel.: +39-06-3015-5559; Fax: +39-06-3051-911
| | - Roberta Romano
- Department of Biological and Environmental Sciences and Technologies, Università del Salento, 73100 Lecce, Italy; (F.G.); (R.R.); (C.B.)
| | - Hélio José Coelho-Junior
- Department of Geriatrics and Orthopedics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Francesco P. Damiano
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.P.D.); (E.M.)
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies, Università del Salento, 73100 Lecce, Italy; (F.G.); (R.R.); (C.B.)
| | - Emanuele Marzetti
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (F.P.D.); (E.M.)
- Department of Geriatrics and Orthopedics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
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Barbagallo C, Platania CBM, Drago F, Barbagallo D, Di Pietro C, Purrello M, Bucolo C, Ragusa M. Do Extracellular RNAs Provide Insight into Uveal Melanoma Biology? Cancers (Basel) 2021; 13:5919. [PMID: 34885029 PMCID: PMC8657116 DOI: 10.3390/cancers13235919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignant tumor in adults, showing a high mortality due to metastasis. Although it is considered a rare disease, a growing number of papers have reported altered levels of RNAs (i.e., coding and non-coding RNAs) in cancerous tissues and biological fluids from UM patients. The presence of circulating RNAs, whose dysregulation is associated with UM, paved the way to the possibility of exploiting it for diagnostic and prognostic purposes. However, the biological meaning and the origin of such RNAs in blood and ocular fluids of UM patients remain unexplored. In this review, we report the state of the art of circulating RNAs in UM and debate whether the amount and types of RNAs measured in bodily fluids mirror the RNA alterations from source cancer cells. Based on literature data, extracellular RNAs in UM patients do not represent, with rare exceptions, a snapshot of RNA dysregulations occurring in cancerous tissues, but rather the complex and heterogeneous outcome of a systemic dysfunction, including immune system activity, that modifies the mechanisms of RNA delivery from several cell types.
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Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Chiara Bianca Maria Platania
- Department of Biomedical and Biotechnological Sciences—Section of Pharmacology, University of Catania, 95123 Catania, Italy; (C.B.M.P.); (F.D.)
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences—Section of Pharmacology, University of Catania, 95123 Catania, Italy; (C.B.M.P.); (F.D.)
- Center of Research in Ocular Pharmacology—CERFO, University of Catania, 95123 Catania, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
| | - Claudio Bucolo
- Department of Biomedical and Biotechnological Sciences—Section of Pharmacology, University of Catania, 95123 Catania, Italy; (C.B.M.P.); (F.D.)
- Center of Research in Ocular Pharmacology—CERFO, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy; (C.B.); (D.B.); (C.D.P.); (M.P.); (M.R.)
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Yuan Z, Wang X, Geng X, Li Y, Tan F, Xue Q, Gao S, He J. Multi-region sequencing reveals genetic correlation between esophageal squamous cell carcinoma and matched cell-free DNA. Cancer Genet 2021; 258-259:93-100. [PMID: 34688997 DOI: 10.1016/j.cancergen.2021.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/23/2021] [Accepted: 08/28/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE This study aimed to determine if both ubiquitous and heterogeneous somatic mutations could be detected in circulating cell-free DNA (cfDNA) in patients with esophageal squamous cell carcinoma (ESCC). METHODS Paired multi-regional tumor tissues, cfDNA, and white blood cells (WBCs) were collected from five ESCC patients before treatment, as part of an ongoing prospective study (NCT02395705). Samples from Cohort 1 were sequenced by whole-exome sequencing and samples from Cohort 2 were sequenced by targeted capture sequencing. Somatic single-nucleotide variations (SNVs) were detected by comparing solid tumor or cfDNA with matched WBCs, with a minimum variant allele frequency (VAF) of 0.1% and P value <0.05. RESULTS Genomic DNA (gDNA) and plasma-derived cfDNA from 26 samples were sequenced successfully. In Cohort 1, a significant linear relationship between the tumor and cfDNA VAFs (R2= 0.78, P < 0.0001) was found. In Cohort 2, cfDNA could recover an average of 60.7% (31/51; range, 35.7-76.2%) of somatic mutations present in matched solid tumors. There was a significant positive correlation in VAFs between cfDNA and matched solid tumor tissues (R2= 0.92, P < 0.0001). CONCLUSIONS Both sequencing approaches revealed high intratumoral heterogeneity in ESCC, and enabled the detection of both ubiquitous and heterogeneous mutations in cfDNA.
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Affiliation(s)
- Zuyang Yuan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xiao Geng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Yin Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China.
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Stawski R, Stec-Martyna E, Chmielecki A, Nowak D, Perdas E. Current Trends in Cell-Free DNA Applications. Scoping Review of Clinical Trials. BIOLOGY 2021; 10:biology10090906. [PMID: 34571783 PMCID: PMC8468988 DOI: 10.3390/biology10090906] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023]
Abstract
We aimed to summarize the current knowledge about the trends in cfDNA application based on the analysis of clinical trials registered until April 2021. International Clinical Trials Registry Platform (ICTRP) and Clinicaltrials.gov were searched with the keywords: "cf-DNA"; "Circulating DNA"; "Deoxyribonucleic Acid"; and "Cell-Free Deoxyribonucleic Acid". Of 605 clinical trials, we excluded 237 trials, and 368 remaining ones were subject to further analysis. The subject, number of participants, and study design were analyzed. Our scoping review revealed three main trends: oncology (n = 255), non-invasive prenatal diagnostic (n = 48), and organ transplantation (n = 41), and many (n = 22) less common such as sepsis, sport, or autoimmune diseases in 368 clinical trials. Clinical trials are translating theory into clinical care. However, the diagnostic value of cfDNA remains controversial, and diagnostic accuracy still needs to be evaluated. Thus, further studies are necessary until cfDNA turns into a standard in clinical practice.
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Affiliation(s)
- Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
- Correspondence: (R.S.); (E.P.)
| | - Emilia Stec-Martyna
- Central Scientific Laboratory, Medical University of Lodz, 6/8 Mazowiecka St., 92-215 Lodz, Poland;
| | - Adam Chmielecki
- Sport Centre of the Medical University of Lodz, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Ewelina Perdas
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
- Correspondence: (R.S.); (E.P.)
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Chiusano ML, Incerti G, Colantuono C, Termolino P, Palomba E, Monticolo F, Benvenuto G, Foscari A, Esposito A, Marti L, de Lorenzo G, Vega-Muñoz I, Heil M, Carteni F, Bonanomi G, Mazzoleni S. Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081744. [PMID: 34451789 PMCID: PMC8400022 DOI: 10.3390/plants10081744] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 01/14/2023]
Abstract
The inhibitory effect of extracellular DNA (exDNA) on the growth of conspecific individuals was demonstrated in different kingdoms. In plants, the inhibition has been observed on root growth and seed germination, demonstrating its role in plant-soil negative feedback. Several hypotheses have been proposed to explain the early response to exDNA and the inhibitory effect of conspecific exDNA. We here contribute with a whole-plant transcriptome profiling in the model species Arabidopsis thaliana exposed to extracellular self- (conspecific) and nonself- (heterologous) DNA. The results highlight that cells distinguish self- from nonself-DNA. Moreover, confocal microscopy analyses reveal that nonself-DNA enters root tissues and cells, while self-DNA remains outside. Specifically, exposure to self-DNA limits cell permeability, affecting chloroplast functioning and reactive oxygen species (ROS) production, eventually causing cell cycle arrest, consistently with macroscopic observations of root apex necrosis, increased root hair density and leaf chlorosis. In contrast, nonself-DNA enters the cells triggering the activation of a hypersensitive response and evolving into systemic acquired resistance. Complex and different cascades of events emerge from exposure to extracellular self- or nonself-DNA and are discussed in the context of Damage- and Pathogen-Associated Molecular Patterns (DAMP and PAMP, respectively) responses.
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Affiliation(s)
- Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
- Correspondence: (M.L.C.); (S.M.)
| | - Guido Incerti
- Department of Agri-Food, Animal and Environmental Sciences, University of Udine, 33100 Udine, Italy;
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine, via campi Flegrei, 34 Pozzuoli, 80078 Napoli, Italy;
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), 80055 Portici, Italy;
| | - Emanuela Palomba
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
| | - Francesco Monticolo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Giovanna Benvenuto
- Biology and Evolution of Marine Organisms Department (BEOM), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
| | - Alessandro Foscari
- Dipartimento di Scienze della Vita, University of Trieste, 34127 Trieste, Italy;
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Trento, Italy;
| | - Lucia Marti
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (L.M.); (G.d.L.)
| | - Giulia de Lorenzo
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (L.M.); (G.d.L.)
| | - Isaac Vega-Muñoz
- Departemento de Ingeniería Genética, CINVESTAV-Irapuato, Guanajuato 36821, Mexico; (I.V.-M.); (M.H.)
| | - Martin Heil
- Departemento de Ingeniería Genética, CINVESTAV-Irapuato, Guanajuato 36821, Mexico; (I.V.-M.); (M.H.)
| | - Fabrizio Carteni
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
- Correspondence: (M.L.C.); (S.M.)
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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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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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9
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Yuan Z, Wang X, Geng X, Li Y, Mu J, Tan F, Xue Q, Gao S, He J. Liquid biopsy for esophageal cancer: Is detection of circulating cell-free DNA as a biomarker feasible? Cancer Commun (Lond) 2020; 41:3-15. [PMID: 33264481 PMCID: PMC7819547 DOI: 10.1002/cac2.12118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/19/2020] [Accepted: 11/19/2020] [Indexed: 12/25/2022] Open
Abstract
Esophageal cancer (EC) is a common cancer and is histopathologically classified into esophageal squamous cell carcinoma and esophageal adenocarcinoma. EC is a worldwide public health issue because of late diagnosis and lack of effective therapy. In contrast to standard tumor biopsies, liquid biopsies are emerging as a tool which is minimally invasive that can complement or even substitute more classical approaches. Specifically, cell-free DNA (cfDNA) has shown promise in cancer-related clinical applications. Indeed, cfDNA has been shown to be an effective circulating biomarker for non-invasive cancer diagnosis and monitoring of cancer patients. Although the clinical application of cfDNA has been reported on other cancers, few studies have evaluated its use in EC. Here, we review this relevant literature and discuss limitations and advantages of its application in the diagnosis and monitoring of EC.
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Affiliation(s)
- Zuyang Yuan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xinfeng Wang
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xiao Geng
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Yin Li
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Juwei Mu
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Fengwei Tan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Qi Xue
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Shugeng Gao
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Jie He
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
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10
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McClure T, Goh SK, Cox D, Muralidharan V, Dobrovic A, Testro AG. Donor-specific cell-free DNA as a biomarker in liver transplantation: A review. World J Transplant 2020; 10:307-319. [PMID: 33312892 PMCID: PMC7708879 DOI: 10.5500/wjt.v10.i11.307] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/09/2020] [Accepted: 10/30/2020] [Indexed: 02/05/2023] Open
Abstract
Due to advances in modern medicine, liver transplantation has revolutionised the prognosis of many previously incurable liver diseases. This progress has largely been due to advances in immunosuppressant therapy. However, despite the judicious use of immunosuppression, many liver transplant recipients still experience complications such as rejection, which necessitates diagnosis via invasive liver biopsy. There is a clear need for novel, minimally-invasive tests to optimise immunosuppression and improve patient outcomes. An emerging biomarker in this ''precision medicine'' liver transplantation field is that of donor-specific cell free DNA. In this review, we detail the background and methods of detecting this biomarker, examine its utility in liver transplantation and discuss future research directions that may be most impactful.
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Affiliation(s)
- Tess McClure
- Liver Transplant Unit, Austin Health, Heidelberg 3084, VIC, Australia
| | - Su Kah Goh
- Department of Surgery, Austin Health, Heidelberg 3084, VIC, Australia
| | - Daniel Cox
- Department of Surgery, Austin Health, Heidelberg 3084, VIC, Australia
| | | | - Alexander Dobrovic
- Department of Surgery, The University of Melbourne, Heidelberg 3084, VIC, Australia
| | - Adam G Testro
- Liver Transplant Unit, Austin Health, Heidelberg 3084, VIC, Australia
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11
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Di Pizio P, Celton N, Menoud PA, Belloc S, Cohen Bacrie M, Belhadri-Mansouri N, Rives N, Cabry R, Benkhalifa M. Seminal cell-free DNA and sperm characteristic's: An added biomarker for male infertility investigation. Andrologia 2020; 53:e13822. [PMID: 33040391 DOI: 10.1111/and.13822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/08/2020] [Accepted: 07/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cell-free DNA (Cf-DNA) fragments may constitute an easy-to-measure molecular tool for guiding the choice of care provided to infertile couples who benefit assisted reproductive technology (ART) programmes. Data on Cf-DNA levels in the seminal plasma of men with sperm alterations are scarce. The objective of the present study was to quantify the presence of Cf-DNA in semen by using a quantitative real-time PCR. We compared men with abnormal sperm characteristics (n = 21) with normospermic controls (n = 21). The PCR assay evidenced significantly higher mean Cf-DNA levels in patients with sperm abnormalities than in controls (2.09 versus 1.18 µg/ml, respectively; p = .0003). The Cf-DNA levels were notably higher in men with azoospermia (3.65 µg/ml, versus 1.34 µg/ml in matched controls; p = .03) and men with teratozoospermia (1.80 µg/ml, versus 1.29 µg/ml in matched controls; p = .008). Our data report a significant association between elevated Cf-DNA levels and sperm abnormalities. These results may open up new diagnostic and prognostic perspectives in male infertility.
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Affiliation(s)
- Pierre Di Pizio
- Reproductive Medicine & Biology, Amiens University, Amiens, France.,Reproductive Biology Laboratory, University Hospital Centre Rouen, Rouen, France
| | - Noemie Celton
- Reproductive Medicine & Biology, Amiens University, Amiens, France
| | - Pierre Alain Menoud
- Molecular Diagnostic Laboratory, Unilabs Laboratoire d'Analyses Medicales SA, Genève, Switzerland
| | - Stéphanie Belloc
- Laboratoire CERBA, Laboratoire Lavergne, Saint Ouen l'Aumone, France
| | | | | | - Nathalie Rives
- Reproductive Biology Laboratory, University Hospital Centre Rouen, Rouen, France
| | - Rosalie Cabry
- Reproductive Medicine & Biology, Amiens University, Amiens, France
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12
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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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13
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Shmarina GV, Ershova ES, Simashkova NV, Nikitina SG, Chudakova JM, Veiko NN, Porokhovnik LN, Basova AY, Shaposhnikova AF, Pukhalskaya DA, Pisarev VM, Korovina NJ, Gorbachevskaya NL, Dolgikh OA, Bogush M, Kutsev SI, Kostyuk SV. Oxidized cell-free DNA as a stress-signaling factor activating the chronic inflammatory process in patients with autism spectrum disorders. J Neuroinflammation 2020; 17:212. [PMID: 32677958 PMCID: PMC7364812 DOI: 10.1186/s12974-020-01881-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/25/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Autism spectrum disorders (ASD) are known to be associated with an inflammatory process related to immune system dysfunction. This study's aim was to investigate the role of cell-free DNA in chronic inflammatory process in ASD patients. METHODS The study included 133 ASD patients and 27 healthy controls. Sixty-two ASD patients were demonstrated to have mild-to-moderate disease severity (group I) and 71 individuals to have severe ASD (group II). Plasma cell-free (cf) DNA characteristics, plasma cytokine concentrations, expression of the genes for NFкB1 transcription factor and pro-inflammatory cytokines TNFα, IL-1β and IL-8 in peripheral blood lymphocytes (PBL) of ASD patients, and unaffected controls were investigated. Additionally, in vitro experiments with oxidized DNA supplementation to PBL cultures derived from ASD patients and healthy controls were performed. RESULTS The data indicates that ASD patients have demonstrated increased cfDNA concentration in their circulation. cfDNA of patients with severe ASD has been characterized by a high abundance of oxidative modification. Furthermore, ASD patients of both groups have shown elevated plasma cytokine (IL-1β, IL-8, IL-17A) levels and heightened expression of genes for NFкB1 nuclear factor and pro-inflammatory cytokines TNFα, IL-1β, and IL-8 in PBL. In vitro experiments have shown that NF-κB/cytokine mRNA expression profiles of ASD patient PBL treated with oxidized DNA fragments were significantly different from those of healthy controls. CONCLUSIONS It may be proposed that oxidized cfDNA plays a role of stress-signaling factor activating the chronic inflammatory process in patients with ASD.
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Affiliation(s)
- Galina V Shmarina
- Research Centre for Medical Genetics, Moscow, Russia.
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.
- G.N. Gabrichevsky Institute of Epidemiology and Microbiology, Moscow, Russia.
| | - Elizaveta S Ershova
- Research Centre for Medical Genetics, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | | | | | | | | | - Anna Y Basova
- G.E. Sukhareva Scientific-Practical Centre for Mental Health of Children and Adolescents, Moscow, Russia
| | - Antonina F Shaposhnikova
- G.E. Sukhareva Scientific-Practical Centre for Mental Health of Children and Adolescents, Moscow, Russia
| | | | - Vladimir M Pisarev
- V. A. Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Natalia J Korovina
- G.E. Sukhareva Scientific-Practical Centre for Mental Health of Children and Adolescents, Moscow, Russia
| | - Natalia L Gorbachevskaya
- G.E. Sukhareva Scientific-Practical Centre for Mental Health of Children and Adolescents, Moscow, Russia
| | | | - Marina Bogush
- Rowan University Biological Sciences Department, Science Hall, Glassboro, NJ, USA
| | | | - Svetlana V Kostyuk
- Research Centre for Medical Genetics, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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Current applications and challenges of circulating tumor DNA (ctDNA) in squamous cell carcinoma of the head and neck (SCCHN). Cancer Treat Rev 2020; 85:101992. [PMID: 32092618 DOI: 10.1016/j.ctrv.2020.101992] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 12/21/2022]
Abstract
Liquid biopsies (LB) are emerging in the oncology field, with promising data as new diagnostic, prognostic and treatment-monitoring tools. Squamous cell carcinoma of the head and neck (SCCHN) is a heterogenous disease and many challenges remain to improve patient outcomes. Liquid biopsy could be of interest at different stages of SCCHN disease, including better screening to diagnose more patients at an early stage, early detection of relapse after curative treatment, and the implementation of precision medicine. As LB is very attractive by the ease of sampling, this field is moving fast. Therefore, it is important to be aware of the potential applications but also the limitations of these new tools in regards to technical aspects and interpretation of the data. In this review, we will first give an overview of potential clinical applications and technical challenges of circulating tumor DNA (ctDNA) and then focus on current available data of ctDNA in SCCHN. Although the literature on ctDNA analysis for SCCHN is scarce compared to other tumors, preliminary results seem to hold promise for the future, including the detection of minimal residual disease or the detection of potentially targetable events through liquid biopsy. Prospective liquid-biopsy driven clinical trials are needed to validate its clinical relevance.
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15
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Perdas E, Stawski R, Kaczka K, Nowak D, Zubrzycka M. Altered levels of circulating nuclear and mitochondrial DNA in patients with Papillary Thyroid Cancer. Sci Rep 2019; 9:14438. [PMID: 31594998 PMCID: PMC6783406 DOI: 10.1038/s41598-019-51000-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/20/2019] [Indexed: 12/28/2022] Open
Abstract
Papillary thyroid cancer is the most common thyroid cancer type. However, diagnostics based on fine needle biopsy cannot make a definitive diagnosis in 25% of thyroid nodules. Additionally, approximately 70% to 80% of thyroid lobectomies performed just for diagnostic purposes are benign. Despite this, biopsy still remains the main method of evaluation of thyroid nodules. Cell-free DNA (cf-DNA) measurement could give a new diagnostic opportunities which may reduce the number of unnecessary thyroid procedures. In this study, using a qPCR, we have examined the nuclear cf-DNA and mitochondrial cf-DNA in the plasma of 32 patients. We have found that the level of nuclear cf-DNA is almost 2-fold increased (median 3 089 vs. 1 872, p = 0.022), whereas mitochondrial cf-DNA content was significantly decreased in respect to healthy controls (median 44 992 vs. 92 220, p = 0.010). The ROC curve analysis showed high specificity for nuclear cf-DNA and mitochondrial cf-DNA, which may serve as a useful tool to decrease the number of unneeded surgeries. Our study reports the first epidemiological evidence for lower mitochondrial cf-DNA content in the patient group, what suggests that apart from nuclear cf-DNA also mitochondrial cf-DNA is affected by disease development.
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Affiliation(s)
- Ewelina Perdas
- Department of Cardiovascular Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland.
| | - Robert Stawski
- Department of Clinical Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Krzysztof Kaczka
- Department of General and Oncological Surgery, Medical University of Lodz, Lodz, Poland
| | - Dariusz Nowak
- Department of Clinical Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Maria Zubrzycka
- Department of Cardiovascular Physiology, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
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16
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Liu Y, Shen Q, Zhao X, Zou M, Shao S, Li J, Ren X, Zhang L. Cell-free mitochondrial DNA in human follicular fluid: a promising bio-marker of blastocyst developmental potential in women undergoing assisted reproductive technology. Reprod Biol Endocrinol 2019; 17:54. [PMID: 31291946 PMCID: PMC6621940 DOI: 10.1186/s12958-019-0495-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cell-free mitochondrial DNA (cf-mtDNA) in body fluids has attracted much attention for the purpose of monitoring disease because of the clinical advantages. This study investigated whether the cf-mtDNA content in human follicular fluid samples was associated with oocyte and embryo developmental competence. METHODS We collected 225 individual follicular fluid samples from 92 patients undergoing conventional in vitro fertilization (n = 53) or intracytoplasmic sperm injection (n = 39). cf-mtDNA and cell-free nuclear DNA (cf-nDNA) were measured using real-time quantitative PCR for the ND1 and β-globin genes. Multivariate logistic regression and linear regression were used to analyze data. RESULTS The relative cf-mtDNA content (cf-ND1/cf-β-globin ratio) in follicular fluid was significantly lower in the group showing blastocyst development than in the non-blastocyst group (P = 0.030). Additionally, the relative cf-mtDNA content was significantly and positively correlated with the age of the female patient (P = 0.009), while the relative cf-mtDNA content for older women (≥38 years old) with anti-Müllerian hormone (AMH) ≤1.1 ng/ml was significantly higher than in those with AMH > 1.1 ng/ml (P <0.05). The cf-nDNA content was significantly positively correlated with the antral follicle count (P = 0.012), and significantly negatively correlated with both the number of days of stimulation and the total dose of gonadotropin administration (P = 0.039 and P = 0.015, respectively). Neither cf-mtDNA nor cf-nDNA levels in follicular fluid were associated with oocyte maturation, fertilization, or Day 3 embryo morphological scoring. CONCLUSIONS The relative cf-mtDNA content in human follicular fluid was negatively correlated with blastulation and positively correlated with the patient age, indicating that it is a promising bio-marker to evaluate oocyte developmental competence.
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Affiliation(s)
- Yu Liu
- Family Planning Research Institute and Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,, 430030, People's Republic of China
| | - Qiuzi Shen
- Family Planning Research Institute and Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,, 430030, People's Republic of China
| | - Xue Zhao
- Family Planning Research Institute and Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,, 430030, People's Republic of China
| | - Min Zou
- Family Planning Research Institute and Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,, 430030, People's Republic of China
| | - Shumin Shao
- Family Planning Research Institute and Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,, 430030, People's Republic of China
| | - Jiao Li
- Family Planning Research Institute and Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,, 430030, People's Republic of China
| | - Xinling Ren
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Ling Zhang
- Family Planning Research Institute and Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan,, 430030, People's Republic of China.
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17
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Accuracy of Raman spectroscopy in discrimination of nasopharyngeal carcinoma from normal samples: a systematic review and meta-analysis. J Cancer Res Clin Oncol 2019; 145:1811-1821. [DOI: 10.1007/s00432-019-02934-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/10/2019] [Indexed: 12/30/2022]
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18
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Prisco M, Casalino J, Cefaliello C, Giuditta A. Brain Metabolic DNA Is Reverse Transcribed in Cytoplasm: Evidence by Immunofluorescence Analysis. Mol Neurobiol 2019; 56:6770-6776. [PMID: 30919215 DOI: 10.1007/s12035-019-1569-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/18/2019] [Indexed: 10/27/2022]
Abstract
In a previous study (Mol Neurobiol 55:7476-7486, 2017), newly synthesized brain metabolic DNA (BMD) from rat subcellular fractions has been shown to behave as a DNA-RNA hybrid when analyzed in cesium gradients at early [3H] thymidine incorporation times but to assume the double-stranded configuration at later times. Conversely, BMD from purified nuclei displayed the dsDNA configuration even at early incorporation times. The results were interpreted to support the BMD origin by reverse transcription in the cytoplasm and its later acquisition of the double-stranded configuration before the partial transfer to the nuclei. This interpretation has now been confirmed by immunofluorescence analyses of newly synthesized BrdU-labeled BMD from the mouse brain that demonstrates its cytoplasmic localization and colocalization with DNA-RNA hybrids. In addition, BrdU-labeled BMD has been shown to colocalize with astroglial anti-GFAP antibodies and with presynaptic anti-synaptophysin antibodies.
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Affiliation(s)
- Marina Prisco
- Biology Department, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Naples, Italy
| | - Joyce Casalino
- Biology Department, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Naples, Italy
| | - Carolina Cefaliello
- Department of Neurology, University of Massachusetts Medical School, Albert Sherman Center 6-1008, 368 Plantation St., Worcester, MA, 01605, USA
| | - Antonio Giuditta
- Accademia di Scienze Fisiche e Matematiche, Via Mezzocannone 8, 80134, Naples, Italy.
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20
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Ho JR, Arrach N, Rhodes-Long K, Ahmady A, Ingles S, Chung K, Bendikson KA, Paulson RJ, McGinnis LK. Pushing the limits of detection: investigation of cell-free DNA for aneuploidy screening in embryos. Fertil Steril 2018; 110:467-475.e2. [PMID: 29960707 DOI: 10.1016/j.fertnstert.2018.03.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/20/2018] [Accepted: 03/23/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To determine the accuracy of cell-free DNA (cfDNA) in spent embryo medium (SEM) for ploidy and sex detection at the cleavage and blastocyst stages. To determine if assisted hatching (AH) and morphologic grade influence cfDNA concentration and accuracy. DESIGN Prospective cohort. SETTING Academic fertility center. PATIENT(S) Nine patients undergoing IVF; 41 donated two-pronuclei embryos and 20 embryos from patients undergoing preimplantation genetic testing for aneuploidy (PGT-A). INTERVENTIONS(S) In a donated embryo arm, SEM was collected on days 3 and 5, with one-half of the embryos undergoing AH before and one-half after. In a clinical arm, SEM was collected on day 5 before trophectoderm (TE) biopsy. Samples underwent PGT-A with the use of next-generation sequencing. cfDNA results were compared with corresponding whole embryos and TE biopsies. MAIN OUTCOME MEASURE(S) Concordance rates, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for ploidy and sex detection with the use of cfDNA. RESULT(S) Of 141 samples, cfDNA was amplified in 39% and 80.4% of days 3 and 5 SEM, respectively. Concordances for ploidy and sex, respectively, were 56.3% and 81.3% between day 3 cfDNA and whole embryos, and 65% and 70% between day 5 cfDNA and TE biopsies. Day 5 cfDNA sensitivity and specificity for aneuploidy were 0.8 and 0.61, respectively. PPV and NPV were 0.47 and 0.88, respectively. Timing of AH and morphology did not influence cfDNA concentration or accuracy. CONCLUSION(S) cfDNA is detectable on days 3 and 5, but more accurate on day 5. Although our data suggest moderate concordance rates, PGT-A with the use of cfDNA must be further optimized before clinical implementation.
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Affiliation(s)
- Jacqueline R Ho
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California.
| | - Nabil Arrach
- Department of Microbiology and Molecular Genetics, University of California, Irvine, California; Progenesis, La Jolla, California
| | - Katherine Rhodes-Long
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Ali Ahmady
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Sue Ingles
- Department of Preventative Medicine, University of Southern California, Los Angeles, California
| | - Karine Chung
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Kristin A Bendikson
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Richard J Paulson
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Lynda K McGinnis
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
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21
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Cefaliello C, Prisco M, Crispino M, Giuditta A. DNA in Squid Synaptosomes. Mol Neurobiol 2018; 56:56-60. [PMID: 29675577 DOI: 10.1007/s12035-018-1071-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 11/26/2022]
Abstract
The synthesis of brain metabolic DNA (BMD) is modulated by learning and circadian oscillations and is not involved in cell division or DNA repair. Data from rats have highlighted its prevalent association with the mitochondrial fraction and its lack of identity with mtDNA. These features suggested that BMD could be localized in synaptosomes that are the major contaminants of brain mitochondrial fractions. The hypothesis has been examined by immunochemical analyses of the large synaptosomes of squid optic lobes that are readily prepared and identified. Optic lobe slices were incubated with 5-bromo-2-deoxyuridine (BrdU) and the isolated synaptosomal fraction was exposed to the green fluorescent anti-BrdU antibody. This procedure revealed that newly synthesized BrdU-labeled BMD is present in a significant percent of the large synaptosomes derived from the nerve terminals of retinal photoreceptor neurons and in synaptosomal bodies of smaller size. Synaptosomal BMD synthesis was strongly inhibited by actinomycin D. In addition, treatment of the synaptosomal fraction with Hoechst 33258, a blue fluorescent dye specific for dsDNA, indicated that native DNA was present in all synaptosomes. The possible role of synaptic BMD is briefly discussed.
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Affiliation(s)
- Carolina Cefaliello
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126, Naples, Italy
- Department of Neurology, University of Massachusetts Medical School, Albert Sherman Center 6-1008, 368 Plantation St., Worcester, MA, 01605, USA
| | - Marina Prisco
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126, Naples, Italy
| | - Marianna Crispino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126, Naples, Italy
| | - Antonio Giuditta
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126, Naples, Italy.
- Accademia di Scienze Fisiche e Matematiche, Via Mezzocannone 8, 80134, Naples, Italy.
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22
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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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23
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Abstract
Brain metabolic DNA (BMD) is not involved in cell division or DNA repair but is modulated by memory acquisition, sleep processing, and circadian oscillations. Using routine methods of subcellular fractionation, newly synthesized BMD from male rats is shown to be localized in crude nuclear, mitochondrial, and microsomal fractions and in two fractions of purified nuclei. Sub-fractionation of the mitochondrial fraction indicates the prevalent localization of BMD in free mitochondria and to a lesser degree in synaptosomes and myelin. Cesium density profiles of homogenate, subcellular fractions, and purified nuclei obtained after incorporation periods from 30 min to 4 h indicate that BMD synthesis takes place by reverse transcription in cytoplasmic organelles. Following the acquisition of the double-stranded structure, BMD is transferred to nuclei. Kinetic analyses lasting several weeks highlight the massive BMD turnover in subcellular fractions and purified nuclei and its dependence on age. Data are in agreement with the role of BMD as a temporary information store of cell responses of potential use in comparable forthcoming experiences.
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Glebova KV, Veiko NN, Nikonov AA, Porokhovnik LN, Kostuyk SV. Cell-free DNA as a biomarker in stroke: Current status, problems and perspectives. Crit Rev Clin Lab Sci 2018; 55:55-70. [PMID: 29303618 DOI: 10.1080/10408363.2017.1420032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
There is currently no proposed stroke biomarker with consistent application in clinical practice. A number of studies have examined cell-free DNA (cfDNA), which circulates in biological fluids during stroke, as a potential biomarker of this disease. The data available suggest that dynamically-determined levels of blood cfDNA may provide new prognostic information for assessment of stroke severity and outcome. However, such an approach has its own difficulties and limitations. This review covers the potential role of cfDNA as a biomarker in stroke, and includes evidence from both animal models and clinical studies, protocols used to analyze cfDNA, and hypotheses on the origin of cfDNA.
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Affiliation(s)
- Kristina V Glebova
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Natalya N Veiko
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Aleksey A Nikonov
- b Department of Neurology, Neurosurgery and Medical Genetics , Pirogov Russian National Research Medical University , Moscow , Russia
| | - Lev N Porokhovnik
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Svetlana V Kostuyk
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
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Volckmar AL, Sültmann H, Riediger A, Fioretos T, Schirmacher P, Endris V, Stenzinger A, Dietz S. A field guide for cancer diagnostics using cell-free DNA: From principles to practice and clinical applications. Genes Chromosomes Cancer 2017; 57:123-139. [DOI: 10.1002/gcc.22517] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Holger Sültmann
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
| | - Anja Riediger
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
| | - Thoas Fioretos
- Department of Clinical Genetics; Lund University; Lund Sweden
- Department of Clinical Genetics; University and Regional Laboratories; Region Skåne Lund Sweden
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg; Heidelberg Germany
- German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ); Heidelberg Germany
| | - Steffen Dietz
- Division of Cancer Genome Research; German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK); Heidelberg Germany
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Affiliation(s)
- Thaiz Rivera Vargas
- Centre de Recherche; INSERM U1231; Facultés de Médecine et de Pharmacie; Dijon France
- Faculté de Médecine; Université de Bourgogne Franche comté; Dijon France
| | - Lionel Apetoh
- Centre de Recherche; INSERM U1231; Facultés de Médecine et de Pharmacie; Dijon France
- Faculté de Médecine; Université de Bourgogne Franche comté; Dijon France
- Centre Georges François Leclerc; Dijon France
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Ershova E, Sergeeva V, Klimenko M, Avetisova K, Klimenko P, Kostyuk E, Veiko N, Veiko R, Izevskaya V, Kutsev S, Kostyuk S. Circulating cell-free DNA concentration and DNase I activity of peripheral blood plasma change in case of pregnancy with intrauterine growth restriction compared to normal pregnancy. Biomed Rep 2017; 7:319-324. [PMID: 29085628 DOI: 10.3892/br.2017.968] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/30/2017] [Indexed: 12/31/2022] Open
Abstract
The level of apoptosis is increased during pregnancy. Dying cells emit DNA that remains in blood circulation and is known as cell-free DNA (cfDNA). The concentration of cfDNA can reflect the level of cell death. The present article is the result of studying cfDNA concentration and DNase I activity in the blood plasma of 40 non-pregnant women (control), 40 healthy pregnant women (over 37 weeks) and 40 pregnant women with a diagnosis of intrauterine growth restriction (IUGR). In order to explain the obtained results, a program modeling the change of cfDNA concentration under the influence of different internal and external factors was written. It was reported that, despite the fact that the level of cell death is increased, cfDNA concentration in blood can be decreased due to activation of cfDNA elimination system. A significant increase of DNase I activity has been reported in cases of IUGR. Increase in DNase I activity over a certain threshold indicates presence of pathological processes in the organism. CfDNA circulating in blood cannot be a reliable marker of increased cell death during pregnancy. Thus, assessment of the level of cell death during pregnancy should be done by simultaneous analysis of cfDNA level and DNase I activity.
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Affiliation(s)
- Elizaveta Ershova
- Federal State Budgetary Institution 'Research Centre For Medical Genetics', Moscow 115478, Russia.,Federal State Budgetary Institution 'V.A. Negovsky Research Institute of General Reanimatology', Moscow 107031, Russia
| | - Vasilina Sergeeva
- Federal State Budgetary Institution 'Research Centre For Medical Genetics', Moscow 115478, Russia
| | - Maria Klimenko
- Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Kristina Avetisova
- Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Peter Klimenko
- Pediatric Faculty, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Edmund Kostyuk
- Center of Family Planning and Reproduction, Moscow 117209, Russia
| | - Natalia Veiko
- Federal State Budgetary Institution 'Research Centre For Medical Genetics', Moscow 115478, Russia.,Federal State Budgetary Institution 'V.A. Negovsky Research Institute of General Reanimatology', Moscow 107031, Russia
| | - Roman Veiko
- Federal State Budgetary Institution 'Research Centre For Medical Genetics', Moscow 115478, Russia
| | - Vera Izevskaya
- Federal State Budgetary Institution 'Research Centre For Medical Genetics', Moscow 115478, Russia
| | - Sergey Kutsev
- Federal State Budgetary Institution 'Research Centre For Medical Genetics', Moscow 115478, Russia
| | - Svetlana Kostyuk
- Federal State Budgetary Institution 'Research Centre For Medical Genetics', Moscow 115478, Russia.,Federal State Budgetary Institution 'V.A. Negovsky Research Institute of General Reanimatology', Moscow 107031, Russia
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Kubaczkova V, Vrabel D, Sedlarikova L, Besse L, Sevcikova S. Cell-free DNA - Minimally invasive marker of hematological malignancies. Eur J Haematol 2017; 99:291-299. [PMID: 28692178 DOI: 10.1111/ejh.12925] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2017] [Indexed: 12/13/2022]
Abstract
Although tumor cells are the most reliable source of tumor DNA, biopsy of the tumor is an invasive procedure that should be avoided in some cases. The main limitation of any biopsy is sampling of one tumor site, which may not represent all malignant clones due to the heterogeneity of the tumor. These clones respond to treatment differently and thus directly influence survival of the patient. Circulating cell-free DNA (cfDNA) is released from multiple tumor sites, reflects overall heterogeneity of the tumor, and correlates with its progression. Detection of tumor-specific genetic and epigenetic aberrations in cfDNA could have a direct impact on molecular diagnosis, prognosis, follow-up of disease, monitoring of minimal residual disease, and response to treatment. While most cfDNA data are still experimental, they are very promising. This review focuses on cfDNA in hematological malignancies.
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Affiliation(s)
- Veronika Kubaczkova
- Faculty of Medicine, Babak Myeloma Group, Department of Pathological Physiology, Masaryk University, Brno, Czech Republic
| | - David Vrabel
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Lenka Sedlarikova
- Faculty of Medicine, Babak Myeloma Group, Department of Pathological Physiology, Masaryk University, Brno, Czech Republic
| | - Lenka Besse
- Experimental Oncology and Hematology, Department of Oncology and Hematology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Sabina Sevcikova
- Faculty of Medicine, Babak Myeloma Group, Department of Pathological Physiology, Masaryk University, Brno, Czech Republic
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29
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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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30
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Krapfenbauer K. Identification of beta cell dysfunction at the pre-symptomatic stage of diabetes mellitus by novel analytical system: liquid biopsy measurements in femtograms. EPMA J 2017; 8:35-41. [PMID: 28228865 PMCID: PMC5306424 DOI: 10.1007/s13167-017-0079-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 11/22/2022]
Abstract
Background Diabetes mellitus is produced and progresses as a consequence of complex and gradual processes, in which a variety of alterations of the endocrine pancreas, are involved and which mainly result in beta cell failure. Those molecular alterations can be found in the bloodstream, which suggests that we could quantify specific biomarkers in plasma or serum by very sensitive methods before the onset diabetes mellitus is diagnosed. However, classical methods of protein analysis such as electrophoresis, Western blot, ELISA, and liquid chromatography are generally time-consuming, lab-intensive, and not sensitive enough to detect such alteration in a pre-symptomatic state of the disease. Method A very sensitive and novel analytical detection conjugate system by using the combination of polyfluorophor technology with protein microchip method was developed. Results This innovative system facilitates the use of a very sensitive microchip assays that measure selected biomarkers in a small sample volume (10 μL) with a much higher sensitivity (92%) compare to common immune assay systems. Further advances of the application of this technology combine the power of miniaturization and faster quantification (around 10 min). Conclusion The power of this technology offers great promise for point-of-care clinical testing and monitoring of specific biomarkers for diabetes in femtogram level in serum or plasma. In conclusion, the results indicate that the technical performance of this new technology is valid and that the assay is able to quantified PPY-specific antigens in plasma at femtogram levels which can be used for identification of beta cell dysfunction at the pre-symptomatic stage of diabetes mellitus.
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Affiliation(s)
- Kurt Krapfenbauer
- 0000 0000 9259 8492grid.22937.3dDepartment of Cranio-Maxillofacial and Oral Surgery, Medical University of Vienna, Waehringerguertel 18-20, A-1090 Vienna, Austria
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31
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Thierry AR, El Messaoudi S, Gahan PB, Anker P, Stroun M. Origins, structures, and functions of circulating DNA in oncology. Cancer Metastasis Rev 2017; 35:347-76. [PMID: 27392603 PMCID: PMC5035665 DOI: 10.1007/s10555-016-9629-x] [Citation(s) in RCA: 532] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While various clinical applications especially in oncology are now in progress such as diagnosis, prognosis, therapy monitoring, or patient follow-up, the determination of structural characteristics of cell-free circulating DNA (cirDNA) are still being researched. Nevertheless, some specific structures have been identified and cirDNA has been shown to be composed of many “kinds.” This structural description goes hand-in-hand with the mechanisms of its origins such as apoptosis, necrosis, active release, phagocytosis, and exocytose. There are multiple structural forms of cirDNA depending upon the mechanism of release: particulate structures (exosomes, microparticles, apoptotic bodies) or macromolecular structures (nucleosomes, virtosomes/proteolipidonucleic acid complexes, DNA traps, links with serum proteins or to the cell-free membrane parts). In addition, cirDNA concerns both nuclear and/or mitochondrial DNA with both species exhibiting different structural characteristics that potentially reveal different forms of biological stability or diagnostic significance. This review focuses on the origins, structures and functional aspects that are paradoxically less well described in the literature while numerous reviews are directed to the clinical application of cirDNA. Differentiation of the various structures and better knowledge of the fate of cirDNA would considerably expand the diagnostic power of cirDNA analysis especially with regard to the patient follow-up enlarging the scope of personalized medicine. A better understanding of the subsequent fate of cirDNA would also help in deciphering its functional aspects such as their capacity for either genometastasis or their pro-inflammatory and immunological effects.
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Affiliation(s)
- A R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France.
| | - S El Messaoudi
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France
| | - P B Gahan
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France
| | - P Anker
- , 135 route des fruitières, 74160, Beaumont, France
| | - M Stroun
- , 6 Pedro-meylan, 1208, Geneva, Switzerland
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Goh SK, Muralidharan V, Christophi C, Do H, Dobrovic A. Probe-Free Digital PCR Quantitative Methodology to Measure Donor-Specific Cell-Free DNA after Solid-Organ Transplantation. Clin Chem 2017; 63:742-750. [PMID: 28100495 DOI: 10.1373/clinchem.2016.264838] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/21/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND Donor-specific cell-free DNA (dscfDNA) is increasingly being considered as a noninvasive biomarker to monitor graft health and diagnose graft rejection after solid-organ transplantation. However, current approaches used to measure dscfDNA can be costly and/or laborious. A probe-free droplet digital PCR (ddPCR) methodology using small deletion/insertion polymorphisms (DIPs) was developed to circumvent these limitations without compromising the quantification of dscfDNA. This method was called PHABRE-PCR (Primer to Hybridize across an Allelic BREakpoint-PCR). The strategic placement of one primer to hybridize across an allelic breakpoint ensured highly specific PCR amplification, which then enabled the absolute quantification of donor-specific alleles by probe-free ddPCR. METHODS dscfDNA was serially measured in 3 liver transplant recipients. Donor and recipient genomic DNA was first genotyped against a panel of DIPs to identify donor-specific alleles. Alleles that differentiated donor-specific from recipient-specific DNA were then selected to quantify dscfDNA in the recipient plasma. RESULTS Lack of amplification of nontargeted alleles confirmed that PHABRE-PCR was highly specific. In recipients who underwent transplantation, dscfDNA was increased at day 3, but decreased and plateaued at a low concentration by 2 weeks in the 2 recipients who did not develop any complications. In the third transplant recipient, a marked increase of dscfDNA coincided with an episode of graft rejection. CONCLUSIONS PHABRE-PCR was able to quantify dscfDNA with high analytical specificity and sensitivity. The implementation of a DIP-based approach permits surveillance of dscfDNA as a potential measure of graft health after solid-organ transplantation.
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Affiliation(s)
- Su Kah Goh
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | | | - Christopher Christophi
- Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.,Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia; .,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.,Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
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33
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Giuditta A, Grassi-Zucconi G, Sadile AG. Brain metabolic DNA in memory processing and genome turnover. Rev Neurosci 2017; 28:21-30. [DOI: 10.1515/revneuro-2016-0027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/15/2016] [Indexed: 11/15/2022]
Abstract
AbstractSophisticated methods are currently used to investigate the properties of brain DNA and clarify its role under physiological conditions and in neurological and psychiatric disorders. Attention is now called on a DNA fraction present in the adult rat brain that is characterized by an elevated turnover and is not involved in cell division or DNA repair. The fraction, known as brain metabolic DNA (BMD), is modulated by strain, stress, circadian oscillations, exposure to enriched or impoverished environment, and notably by several training protocols and post-trial sleep. BMD is frequently localized in glial cells but is also present in neurons, often in the perinucleolar region. Its distribution in repetitive and non-repetitive DNA fractions shows that BMD differs from native DNA and that in learning rats its profile differs from that of control rats. More detailed knowledge of the molecular, cellular, and time-dependent BMD features will be necessary to define its role in memory acquisition and processing and in the pathogenesis of neurologic disorders.
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Affiliation(s)
- Antonio Giuditta
- 1Department of Biology, Federico II University, Via Mezzocannone 8, I-80134 Napoli, Italy
| | - Gigliola Grassi-Zucconi
- 2Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, I-37129 Verona, Italy
| | - Adolfo G. Sadile
- 3Department of Experimental Medicine, Second University of Naples, Via S. Andrea delle dame 7, I-80138 Naples, Italy
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles. Cell Mol Life Sci 2016; 73:4355-4381. [PMID: 27652382 PMCID: PMC11108302 DOI: 10.1007/s00018-016-2370-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/20/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.
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Affiliation(s)
- Janine Aucamp
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
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35
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A Historical and Evolutionary Perspective on Circulating Nucleic Acids and Extracellular Vesicles: Circulating Nucleic Acids as Homeostatic Genetic Entities. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 924:91-95. [PMID: 27753025 DOI: 10.1007/978-3-319-42044-8_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The quantitative and qualitative differences of circulating nucleic acids (cirNAs) between healthy and diseased individuals have motivated researchers to utilize these differences in the diagnosis and prognosis of various pathologies. The position maintained here is that reviewing the rather neglected early work associated with cirNAs and extracellular vesicles (EVs) is required to fully describe the nature of cirNAs. This review consists of an empirically up-to-date schematic summary of the major events that developed and integrated the concepts of heredity, genetic information and cirNAs. This reveals a clear pattern implicating cirNA as a homeostatic entity or messenger of genetic information. The schematic summary paints a picture of how cirNAs may serve as homeostatic genetic entities that promote synchrony of both adaptation and damage in tissues and organs depending on the source of the message.
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36
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Siravegna G, Bardelli A. Blood circulating tumor DNA for non-invasive genotyping of colon cancer patients. Mol Oncol 2015; 10:475-80. [PMID: 26774880 DOI: 10.1016/j.molonc.2015.12.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/30/2015] [Accepted: 12/03/2015] [Indexed: 12/13/2022] Open
Abstract
Most solid tumors, including colorectal cancers, shed cell-free DNA (ctDNA) in the blood. ctDNA can be analyzed to generate molecular profiles which capture the heterogeneity of the disease more comprehensively then tumor tissue biopsies. This approach commonly called 'liquid biopsy' can be applied to monitor response to therapy, to assess minimal residual disease and to uncover the emergence of drug resistance. This review will discuss current and future developments of ctDNA analysis in the clinical management of colorectal cancer patients.
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Affiliation(s)
- Giulia Siravegna
- University of Torino, Department of Oncology, SP 142, KM 3.95, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy; FIRC Institute of Molecular Oncology (IFOM), Milano, Italy
| | - Alberto Bardelli
- University of Torino, Department of Oncology, SP 142, KM 3.95, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy.
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37
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Qiu S, Xu Y, Huang L, Zheng W, Huang C, Huang S, Lin J, Lin D, Feng S, Chen R, Pan J. Non-invasive detection of nasopharyngeal carcinoma using saliva surface-enhanced Raman spectroscopy. Oncol Lett 2015; 11:884-890. [PMID: 26870300 DOI: 10.3892/ol.2015.3969] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 09/28/2015] [Indexed: 11/05/2022] Open
Abstract
The present study evaluated the use of saliva surface-enhanced Raman spectroscopy (SERS) for the detection of non-invasive nasopharyngeal carcinoma (NPC). SERS measurements were taken from 62 saliva samples, of which 32 were from NPC patients and 30 from healthy volunteers. Notable biochemical Raman bands in the SERS spectra were tentatively assigned to various saliva components. The saliva SERS spectra obtained from the NPC patients and the healthy volunteers were also analyzed by multivariate statistical techniques based on principal component analysis and linear discriminant analysis (PCA-LDA). Significant differences were observed between the saliva SERS spectral intensities for NPC patients and healthy volunteers, particularly at 447, 496, 635, 729, 1134, 1270 and 1448 cm-1, which primarily contained signals associated with proteins, nucleic acids, fatty acids, glycogen and collagen. The classification results based on the PCA-LDA method provided a relatively high diagnostic sensitivity of 86.7%, specificity of 81.3% and diagnostic accuracy of 83.9% for NPC identification. The results from the present study demonstrate that saliva SERS analysis used in conjunction with PCA-LDA diagnostic algorithms possesses a promising clinical application for the non-invasive detection of NPC.
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Affiliation(s)
- Sufang Qiu
- The Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Yuanji Xu
- The Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Lingling Huang
- The Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Wei Zheng
- Department of Radiation Oncology, Fujian Provincial Cancer Hospital, Fuzhou, Fujian 350014, P.R. China
| | - Chaobin Huang
- Department of Radiation Oncology, Fujian Provincial Cancer Hospital, Fuzhou, Fujian 350014, P.R. China
| | - Shaohua Huang
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Normal University, Fuzhou, Fujian 350007, P.R. China
| | - Jinyong Lin
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Normal University, Fuzhou, Fujian 350007, P.R. China
| | - Duo Lin
- College of Integrated Traditional Chinese and Western Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Shangyuan Feng
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Normal University, Fuzhou, Fujian 350007, P.R. China
| | - Rong Chen
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Normal University, Fuzhou, Fujian 350007, P.R. China
| | - Jianji Pan
- The Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China; Department of Radiation Oncology, Fujian Provincial Cancer Hospital, Fuzhou, Fujian 350014, P.R. China
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38
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Gielis EM, Ledeganck KJ, De Winter BY, Del Favero J, Bosmans JL, Claas FHJ, Abramowicz D, Eikmans M. Cell-Free DNA: An Upcoming Biomarker in Transplantation. Am J Transplant 2015; 15:2541-51. [PMID: 26184824 DOI: 10.1111/ajt.13387] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/01/2015] [Accepted: 05/13/2015] [Indexed: 01/25/2023]
Abstract
After organ transplantation, donor-derived cell-free DNA (ddcfDNA) can be detected in the recipient's blood and urine. Different ddcfDNA quantification techniques have been investigated but a major breakthrough was made with the introduction of digital droplet PCR and massive parallel sequencing creating the opportunity to increase the understanding of ddcfDNA kinetics after transplantation. The observations of increased levels of ddcfDNA during acute rejection and even weeks to months before histologic features of graft rejection point to a possible role of ddcfDNA as an early, noninvasive rejection marker. In this review, we summarize published research on ddcfDNA in the transplantation field thereby elaborating on its clinical utility.
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Affiliation(s)
- E M Gielis
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, Antwerp, Belgium.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - K J Ledeganck
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, Antwerp, Belgium
| | - B Y De Winter
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, Antwerp, Belgium
| | | | - J-L Bosmans
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, Antwerp, Belgium.,Department of Nephrology and Hypertension, Antwerp University Hospital, Antwerp, Belgium
| | - F H J Claas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - D Abramowicz
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, Antwerp, Belgium.,Department of Nephrology and Hypertension, Antwerp University Hospital, Antwerp, Belgium
| | - M Eikmans
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
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Chandrananda D, Thorne NP, Bahlo M. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA. BMC Med Genomics 2015; 8:29. [PMID: 26081108 PMCID: PMC4469119 DOI: 10.1186/s12920-015-0107-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/04/2015] [Indexed: 12/13/2022] Open
Abstract
Background High-throughput sequencing of cell-free DNA fragments found in human plasma has been used to non-invasively detect fetal aneuploidy, monitor organ transplants and investigate tumor DNA. However, many biological properties of this extracellular genetic material remain unknown. Research that further characterizes circulating DNA could substantially increase its diagnostic value by allowing the application of more sophisticated bioinformatics tools that lead to an improved signal to noise ratio in the sequencing data. Methods In this study, we investigate various features of cell-free DNA in plasma using deep-sequencing data from two pregnant women (>70X, >50X) and compare them with matched cellular DNA. We utilize a descriptive approach to examine how the biological cleavage of cell-free DNA affects different sequence signatures such as fragment lengths, sequence motifs at fragment ends and the distribution of cleavage sites along the genome. Results We show that the size distributions of these cell-free DNA molecules are dependent on their autosomal and mitochondrial origin as well as the genomic location within chromosomes. DNA mapping to particular microsatellites and alpha repeat elements display unique size signatures. We show how cell-free fragments occur in clusters along the genome, localizing to nucleosomal arrays and are preferentially cleaved at linker regions by correlating the mapping locations of these fragments with ENCODE annotation of chromatin organization. Our work further demonstrates that cell-free autosomal DNA cleavage is sequence dependent. The region spanning up to 10 positions on either side of the DNA cleavage site show a consistent pattern of preference for specific nucleotides. This sequence motif is present in cleavage sites localized to nucleosomal cores and linker regions but is absent in nucleosome-free mitochondrial DNA. Conclusions These background signals in cell-free DNA sequencing data stem from the non-random biological cleavage of these fragments. This sequence structure can be harnessed to improve bioinformatics algorithms, in particular for CNV and structural variant detection. Descriptive measures for cell-free DNA features developed here could also be used in biomarker analysis to monitor the changes that occur during different pathological conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0107-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dineika Chandrananda
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Natalie P Thorne
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Melanie Bahlo
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia.
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Scalici E, Traver S, Mullet T, Ferrières A, Monforte M, Vintejoux E, Hamamah S. Acides nucléiques circulants et fécondation in vitro. ACTA ACUST UNITED AC 2014; 42:696-701. [DOI: 10.1016/j.gyobfe.2014.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 07/07/2014] [Indexed: 12/22/2022]
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41
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Scalici E, Traver S, Molinari N, Mullet T, Monforte M, Vintejoux E, Hamamah S. Cell-free DNA in human follicular fluid as a biomarker of embryo quality. Hum Reprod 2014; 29:2661-9. [DOI: 10.1093/humrep/deu238] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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42
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Rodrigues Filho EM, Simon D, Ikuta N, Klovan C, Dannebrock FA, Oliveira de Oliveira C, Regner A. Elevated cell-free plasma DNA level as an independent predictor of mortality in patients with severe traumatic brain injury. J Neurotrauma 2014; 31:1639-46. [PMID: 24827371 DOI: 10.1089/neu.2013.3178] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Trauma is the leading cause of death in individuals less than 45 years old worldwide, and up to 50% of trauma fatalities are because of brain injury. Prediction of outcome is one of the major problems associated with severe traumatic brain injury (TBI), and research efforts have focused on the investigation of biomarkers with prognostic value after TBI. Therefore, our aim was to investigate whether cell-free DNA concentrations correlated to short-term primary outcome (survival or death) and Glasgow Coma Scale (GCS) scores after severe TBI. A total of 188 patients with severe TBI were enrolled in this prospective study; outcome variables comprised survival and neurological assessment using the GCS at intensive care unit (ICU) discharge. Control blood samples were obtained from 25 healthy volunteers. Peripheral venous blood was collected at admission to the ICU. Plasma DNA was measured using a real-time quantitative polymerase chain reaction (PCR) assay for the β-globin gene. There was correlation between higher DNA levels and both fatal outcome and lower hospital admission GCS scores. Plasma DNA concentrations at the chosen cutoff point (≥171,381 kilogenomes-equivalents/L) predicted mortality with a specificity of 90% and a sensitivity of 43%. Logistic regression analysis showed that elevated plasma DNA levels were independently associated with death (p<0.001). In conclusion, high cell-free DNA concentration was a predictor of short-term mortality after severe TBI.
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Traver S, Assou S, Scalici E, Haouzi D, Al-Edani T, Belloc S, Hamamah S. Cell-free nucleic acids as non-invasive biomarkers of gynecological cancers, ovarian, endometrial and obstetric disorders and fetal aneuploidy. Hum Reprod Update 2014; 20:905-23. [PMID: 24973359 DOI: 10.1093/humupd/dmu031] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Proper folliculogenesis is fundamental to obtain a competent oocyte that, once fertilized, can support the acquisition of embryo developmental competence and pregnancy. MicroRNAs (miRNAs) are crucial regulators of folliculogenesis, which are expressed in the cumulus-oocyte complex and in granulosa cells and some can also be found in the bloodstream. These circulating miRNAs are intensively studied and used as diagnostic/prognostic markers of many diseases, including gynecological and pregnancy disorders. In addition, serum contains small amounts of cell-free DNA (cfDNA), presumably resulting from the release of genetic material from apoptotic/necrotic cells. The quantification of nucleic acids in serum samples could be used as a diagnostic tool for female infertility. METHODS An overview of the published literature on miRNAs, and particularly on the use of circulating miRNAs and cfDNA as non-invasive biomarkers of gynecological diseases, was performed (up to January 2014). RESULTS In the past decade, cell-free nucleic acids have been studied for potential use as biomarkers in many diseases, particularly in gynecological cancers, ovarian and endometrial disorders, as well as in pregnancy-related pathologies and fetal aneuploidy. The data strongly suggest that the concentration of cell-free nucleic acids in serum from IVF patients or in embryo culture medium could be related to the ovarian hormone status and embryo quality, respectively, and be used as a non-invasive biomarker of IVF outcome. CONCLUSIONS The profiling of circulating nucleic acids, such as miRNAs and cfDNA, opens new perspectives for the diagnosis/prognosis of ovarian disorders and for the prediction of IVF outcomes, namely (embryo quality and pregnancy).
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Affiliation(s)
- S Traver
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France
| | - S Assou
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France Université Montpellier 1, UFR de Médecine, Montpellier, France
| | - E Scalici
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France Université Montpellier 1, UFR de Médecine, Montpellier, France
| | - D Haouzi
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France
| | - T Al-Edani
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France Université Montpellier 1, UFR de Médecine, Montpellier, France
| | - S Belloc
- Eylau-Unilabs Laboratory, Paris, France
| | - S Hamamah
- CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, INSERM U1040, Montpellier, France Université Montpellier 1, UFR de Médecine, Montpellier, France ART-PGD Department, Hôpital Arnaud de Villeneuve, CHU Montpellier, Montpellier, France
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Ralla B, Stephan C, Meller S, Dietrich D, Kristiansen G, Jung K. Nucleic acid-based biomarkers in body fluids of patients with urologic malignancies. Crit Rev Clin Lab Sci 2014; 51:200-31. [PMID: 24878357 DOI: 10.3109/10408363.2014.914888] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review focuses on the promising potential of nucleic acids in body fluids such as blood and urine as diagnostic, prognostic, predictive and monitoring biomarkers in urologic malignancies. The tremendous progress in the basic knowledge of molecular processes in cancer, as shown in the companion review on nucleic acid-based biomarkers in tissue of urologic tumors, provides a strong rationale for using these molecular changes as non-invasive markers in body fluids. The changes observed in body fluids are an integrative result, reflecting both tissue changes and processes occurring in the body fluids. The availability of sensitive methods has only recently made possible detailed studies of DNA- and RNA-based markers in body fluids. In addition to these biological aspects, methodological aspects of the determination of nucleic acids in body fluids, i.e. pre-analytical, analytical and post-analytical issues, are particularly emphasized. The characteristic changes of RNA (differential mRNA and miRNA expression) and DNA (concentrations, integrity index, mutations, microsatellite and methylation alterations) in serum/plasma and urine samples of patients suffering from the essential urologic cancers of the prostate, bladder, kidney and testis are summarized and critically discussed below. To translate the promising results into clinical practice, laboratory scientists and clinicians have to collaborate to resolve the challenges of harmonized and feasible pre-analytical and analytical conditions for the selected markers and to validate these markers in well-designed and sufficiently powered multi-center studies.
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Affiliation(s)
- Bernhard Ralla
- Department of Urology, Charité - Universitätsmedizin Berlin , Berlin , Germany
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Abstract
This papers deals with the preanalytical and analytical phase of cell-free DNA analysis, highlighting some criticism on sample collection and extraction. We describe a method to accurately quantify total cfDNA in plasma and our particular approach to the measurement of tumor deriving cfDNA.
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Affiliation(s)
- Pamela Pinzani
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Viale Pieraccini 6, Florence 50139, Italy,
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The concentration of cell-free DNA in focal epilepsy. Epilepsy Res 2013; 105:292-8. [DOI: 10.1016/j.eplepsyres.2013.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/21/2013] [Accepted: 03/17/2013] [Indexed: 12/21/2022]
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González-Masiá JA, García-Olmo D, García-Olmo DC. Circulating nucleic acids in plasma and serum (CNAPS): applications in oncology. Onco Targets Ther 2013; 6:819-32. [PMID: 23874104 PMCID: PMC3711950 DOI: 10.2147/ott.s44668] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The presence of small amounts of circulating nucleic acids in plasma and serum (CNAPS) is not a new finding. The verification that such amounts are significantly increased in cancer patients, and that CNAPS might carry a variety of genetic and epigenetic alterations related to cancer development and progression, has aroused great interest in the scientific community in the last decades. Such alterations potentially reflect changes that occur during carcinogenesis, and include DNA mutations, loss of heterozygosity, viral genomic integration, disruption of microRNA, hypermethylation of tumor suppressor genes, and changes in the mitochondrial DNA. These findings have led to many efforts toward the implementation of new clinical biomarkers based on CNAPS analysis. In the present article, we review the main findings related to the utility of CNAPS analysis for early diagnosis, prognosis, and monitoring of cancer, most of which appear promising. However, due to the lack of harmonization of laboratory techniques, the heterogeneity of disease progression, and the small number of recruited patients in most of those studies, there has been a poor translation of basic research into clinical practice. In addition, many aspects remain unknown, such as the release mechanisms of cell-free nucleic acids, their biological function, and the way by which they circulate in the bloodstream. It is therefore expected that in the coming years, an improved understanding of the relationship between CNAPS and the molecular biology of cancer will lead to better diagnosis, management, and treatment.
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Affiliation(s)
| | - Damián García-Olmo
- Department of Surgery, Universidad Autónoma de Madrid and La Paz University Hospital, IdiPaz, Madrid, Spain
| | - Dolores C García-Olmo
- Experimental Research Unit, General University Hospital of Albacete, Albacete, Spain
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Abstract
It has been estimated that 10(11) -10(12) cells, primarily of haematogenous origin, die in the adult human body daily, and a similar number is regenerated to maintain homeostasis. Despite the presence of an efficient scavenging system for dead cells, considerable amounts of fragmented genetic material enter the circulation in healthy individuals. Elevated blood levels of extracellular nucleic acids have been reported in various disease conditions; such as ageing and age-related degenerative disorders, cancer; acute and chronic inflammatory conditions, severe trauma and autoimmune disorders. In addition to genomic DNA and nucleosomes, mitochondrial DNA is also found in circulation, as are RNA and microRNA. There is extensive literature that suggests that extraneously added nucleic acids have biological actions. They can enter into cells in vitro and in vivo and induce genetic transformation and cellular and chromosomal damage; and experimentally added nucleic acids are capable of activating both innate and adaptive immune systems and inducing a sterile inflammatory response. The possibility as to whether circulating nucleic acids may, likewise, have biological activities has not been explored. In this review we raise the question as to whether circulating nucleic acids may have damaging effects on the host and be implicated in ageing and diverse acute and chronic human pathologies.
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50
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Liu Y, Li X. Does Darwin's Pangenesis have fatal flaws? Int J Epidemiol 2012; 41:1492-3; author reply 1493-4. [DOI: 10.1093/ije/dys132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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