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Morisi N, Virzì GM, Ferrarini M, Alfano G, Zanella M, Ronco C, Donati G. Exploring the Role of Cell-Free Nucleic Acids and Peritoneal Dialysis: A Narrative Review. Genes (Basel) 2024; 15:553. [PMID: 38790182 PMCID: PMC11121405 DOI: 10.3390/genes15050553] [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: 03/30/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
INTRODUCTION Cell-free nucleic acids (cf-NAs) represent a promising biomarker of various pathological and physiological conditions. Since its discovery in 1948, cf-NAs gained prognostic value in oncology, immunology, and other relevant fields. In peritoneal dialysis (PD), blood purification is performed by exposing the peritoneal membrane. Relevant sections: Complications of PD such as acute peritonitis and peritoneal membrane aging are often critical in PD patient management. In this review, we focused on bacterial DNA, cell-free DNA, mitochondrial DNA (mtDNA), microRNA (miRNA), and their potential uses as biomarkers for monitoring PD and its complications. For instance, the isolation of bacterial DNA in early acute peritonitis allows bacterial identification and subsequent therapy implementation. Cell-free DNA in peritoneal dialysis effluent (PDE) represents a marker of stress of the peritoneal membrane in both acute and chronic PD complications. Moreover, miRNA are promising hallmarks of peritoneal membrane remodeling and aging, even before its manifestation. In this scenario, with multiple cytokines involved, mtDNA could be considered equally meaningful to determine tissue inflammation. CONCLUSIONS This review explores the relevance of cf-NAs in PD, demonstrating its promising role for both diagnosis and treatment. Further studies are necessary to implement the use of cf-NAs in PD clinical practice.
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Affiliation(s)
- Niccolò Morisi
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
| | - Grazia Maria Virzì
- Department of Nephrology, Dialysis and Transplant, St. Bortolo Hospital, 36100 Vicenza, Italy
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Marco Ferrarini
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
| | - Gaetano Alfano
- Nephrology Dialysis and Transplant Unit, University Hospital of Modena, 41124 Modena, Italy
| | - Monica Zanella
- Department of Nephrology, Dialysis and Transplant, St. Bortolo Hospital, 36100 Vicenza, Italy
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Claudio Ronco
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Gabriele Donati
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
- Nephrology Dialysis and Transplant Unit, University Hospital of Modena, 41124 Modena, Italy
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Petito V, Di Vincenzo F, Putignani L, Abreu MT, Regenberg B, Gasbarrini A, Scaldaferri F. Extrachromosomal Circular DNA: An Emerging Potential Biomarker for Inflammatory Bowel Diseases? Genes (Basel) 2024; 15:414. [PMID: 38674347 PMCID: PMC11049804 DOI: 10.3390/genes15040414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Inflammatory bowel disease (IBD) comprising ulcerative colitis and Crohn's disease is a chronic immune-mediated disease which affects the gastrointestinal tract with a relapsing and remitting course, causing lifelong morbidity. IBD pathogenesis is determined by multiple factors including genetics, immune and microbial factors, and environmental factors. Although therapy options are expanding, remission rates are unsatisfiable, and together with the disease course, response to therapy remains unpredictable. Therefore, the identification of biomarkers that are predictive for the disease course and response to therapy is a significant challenge. Extrachromosomal circular DNA (eccDNA) fragments exist in all tissue tested so far. These fragments, ranging in length from a few hundreds of base pairs to mega base pairs, have recently gained more interest due to technological advances. Until now, eccDNA has mainly been studied in relation to cancer due to its ability to act as an amplification site for oncogenes and drug resistance genes. However, eccDNA could also play an important role in inflammation, expressed both locally in the- involved tissue and at distant sites. Here, we review the current evidence on the molecular mechanisms of eccDNA and its role in inflammation and IBD. Additionally, the potential of eccDNA as a tissue or plasma marker for disease severity and/or response to therapy is evaluated.
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Affiliation(s)
- Valentina Petito
- Digestive Disease Center-CEMAD, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Federica Di Vincenzo
- Digestive Disease Center-CEMAD, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Lorenza Putignani
- UOS Microbiomica, UOC Microbiologia e Diagnostica di Immunologia, Dipartimento di Medicina Diagnostica e di Laboratorio, Ospedale Pediatrico “Bambino Gesù” IRCCS, 00146 Rome, Italy
| | - Maria T. Abreu
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Birgitte Regenberg
- Department of Biology, Section for Ecology and Evolution, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Antonio Gasbarrini
- Digestive Disease Center-CEMAD, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Franco Scaldaferri
- Digestive Disease Center-CEMAD, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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Xiang Z, Xie Q, Yu Z. Exosomal DNA: Role in Reflecting Tumor Genetic Heterogeneity, Diagnosis, and Disease Monitoring. Cancers (Basel) 2023; 16:57. [PMID: 38201485 PMCID: PMC10778000 DOI: 10.3390/cancers16010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Extracellular vesicles (EVs), with exosomes at the forefront, are key in transferring cellular information and assorted biological materials, including nucleic acids. While exosomal RNA has been thoroughly examined, exploration into exosomal DNA (exoDNA)-which is stable and promising for cancer diagnostics-lags behind. This hybrid genetic material, combining contributions from both nuclear and mitochondrial DNA (mtDNA), is rooted in the cytoplasm. The enigmatic process concerning its cytoplasmic encapsulation continues to captivate researchers. Covering the entire genetic landscape, exoDNA encases significant oncogenic alterations in genes like TP53, ALK, and IDH1, which is vital for clinical assessment. This review delves into exosomal origins, the ins and outs of DNA encapsulation, and exoDNA's link to tumor biology, underscoring its superiority to circulating tumor DNA in the biomarker arena for both detection and therapy. Amidst scientific progress, there are complexities in the comprehension and practical application of the exoDNA surface. Reflecting on these nuances, we chart the prospective research terrain and potential pitfalls, forging a path for future inquiry. By illuminating both the known and unknown facets of exoDNA, the objective of this review is to provide guidance to the field of liquid biopsy (LB) while minimizing the occurrence of avoidable blind spots and detours.
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Affiliation(s)
- Ziyi Xiang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China;
| | - Qihui Xie
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China;
| | - Zili Yu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China;
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, China
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Lou C, Ma X, Chen Z, Zhao Y, Yao Q, Zhou C, Zhao X, Meng X. The mtDNA fragments within exosomes might be novel diagnostic biomarkers of non-small cell lung cancer. Pathol Res Pract 2023; 249:154718. [PMID: 37544132 DOI: 10.1016/j.prp.2023.154718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/14/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND A portion of circulating mtDNAs is encapsulated in exosomes, but their contribution to cancers is rarely studied. We aim to investigate the diagnostic potential of exosomal mtDNA content for non-small cell lung cancer (NSCLC). METHODS Exosomes were isolated from plasma and identified by western blot, scanning electron microscopy, and particle size analysis. The plasma and plasma exosomal mtDNA fragment levels (mtDNA79, mtDNA230, and MTATP8) in healthy, pneumonia, benign lung tumors, and NSCLC were quantified by qPCR. Statistical analyses were performed to compare the levels of mtDNA fragments in different subgroups. ROC analyses were used to evaluate mtDNA fragments' diagnostic sensitivity and specificity. RESULTS We found that plasma mtDNAs were partially present in exosomes. Both plasma and exosomal mtDNA fragments (mtDNA79, mtDNA230, and MTATP8) were increased in NSCLC, particularly more malignant NSCLC. Compared to plasma mtDNAs and traditional tumor markers, exosomal mtDNAs are more closely associated with aggressive features of NSCLC, like bigger tumor sizes, advanced stages, lymph node metastasis, and distant metastasis, showing higher sensitivity and specificity to diagnose NSCLC. CONCLUSIONS Changed contents of plasma and plasma exosomal mtDNAs show great potential to diagnose NSCLC, and exosomal mtDNAs might be promising biomarkers for more aggressive NSCLC.
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Affiliation(s)
- Chengtao Lou
- Department of Biochemistry and Molecular Biology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xinyi Ma
- Department of Biochemistry and Molecular Biology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhenhua Chen
- Department of Biochemistry and Molecular Biology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yikai Zhao
- Department of Biochemistry and Molecular Biology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Qunsheng Yao
- Department of Biochemistry and Molecular Biology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chengwei Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, China
| | - Xiaodong Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, China
| | - Xiaodan Meng
- Department of Biochemistry and Molecular Biology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China.
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Demirel O, Berezin AE, Mirna M, Boxhammer E, Gharibeh SX, Hoppe UC, Lichtenauer M. Biomarkers of Atrial Fibrillation Recurrence in Patients with Paroxysmal or Persistent Atrial Fibrillation Following External Direct Current Electrical Cardioversion. Biomedicines 2023; 11:1452. [PMID: 37239123 PMCID: PMC10216298 DOI: 10.3390/biomedicines11051452] [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: 03/31/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Atrial fibrillation (AF) is associated with atrial remodeling, cardiac dysfunction, and poor clinical outcomes. External direct current electrical cardioversion is a well-developed urgent treatment strategy for patients presenting with recent-onset AF. However, there is a lack of accurate predictive serum biomarkers to identify the risks of AF relapse after electrical cardioversion. We reviewed the currently available data and interpreted the findings of several studies revealing biomarkers for crucial elements in the pathogenesis of AF and affecting cardiac remodeling, fibrosis, inflammation, endothelial dysfunction, oxidative stress, adipose tissue dysfunction, myopathy, and mitochondrial dysfunction. Although there is ample strong evidence that elevated levels of numerous biomarkers (such as natriuretic peptides, C-reactive protein, galectin-3, soluble suppressor tumorigenicity-2, fibroblast growth factor-23, turn-over collagen biomarkers, growth differential factor-15) are associated with AF occurrence, the data obtained in clinical studies seem to be controversial in terms of their predictive ability for post-cardioversion outcomes. Novel circulating biomarkers are needed to elucidate the modality of this approach compared with conventional predictive tools. Conclusions: Biomarker-based strategies for predicting events after AF treatment require extensive investigation in the future, especially in the presence of different gender and variable comorbidity profiles. Perhaps, a multiple biomarker approach exerts more utilization for patients with different forms of AF than single biomarker use.
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Affiliation(s)
- Ozan Demirel
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (O.D.); (M.M.); (E.B.); (S.X.G.); (U.C.H.); (M.L.)
| | - Alexander E. Berezin
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (O.D.); (M.M.); (E.B.); (S.X.G.); (U.C.H.); (M.L.)
- Internal Medicine Department, Zaporozhye State Medical University, 69035 Zaporozhye, Ukraine
| | - Moritz Mirna
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (O.D.); (M.M.); (E.B.); (S.X.G.); (U.C.H.); (M.L.)
| | - Elke Boxhammer
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (O.D.); (M.M.); (E.B.); (S.X.G.); (U.C.H.); (M.L.)
| | - Sarah X. Gharibeh
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (O.D.); (M.M.); (E.B.); (S.X.G.); (U.C.H.); (M.L.)
| | - Uta C. Hoppe
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (O.D.); (M.M.); (E.B.); (S.X.G.); (U.C.H.); (M.L.)
| | - Michael Lichtenauer
- Department of Internal Medicine II, Division of Cardiology, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (O.D.); (M.M.); (E.B.); (S.X.G.); (U.C.H.); (M.L.)
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Ryan KM, Doody E, McLoughlin DM. Whole blood mitochondrial DNA copy number in depression and response to electroconvulsive therapy. Prog Neuropsychopharmacol Biol Psychiatry 2023; 121:110656. [PMID: 36216200 DOI: 10.1016/j.pnpbp.2022.110656] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
Mitochondrial dysfunction may play a role in various psychiatric conditions. Mitochondrial DNA copy number (mtDNAcn), the ratio of mitochondrial DNA to nuclear DNA, represents an attractive marker of mitochondrial health that is easily measured from stored DNA samples, and has been shown to be altered in depression. In this study, we measured mtDNAcn in whole blood samples from medicated patients with depression (n = 100) compared to healthy controls (n = 89) and determined the relationship between mtDNAcn and depression severity and the therapeutic response to electroconvulsive therapy (ECT). We also explored the relationship between mtDNAcn and telomere length and inflammatory markers. Our results show that mtDNAcn was significantly elevated in blood from patients with depression when compared to control samples, and this result survived statistical adjustment for potential confounders (p = 0.002). mtDNAcn was significantly elevated in blood from subgroups of patients with non-psychotic or unipolar depression. There was no difference in mtDNAcn noted in subgroups of ECT remitters/non-remitters or responders/non-responders. Moreover, mtDNAcn was not associated with depression severity, telomere length, or circulating inflammatory marker concentrations. Overall, our results show that mtDNAcn is elevated in blood from patients with depression, though whether this translates to mitochondrial function is unknown. Further work is required to clarify the contribution of mitochondria and mtDNA to the pathophysiology of depression and the therapeutic response to antidepressant treatments.
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Affiliation(s)
- Karen M Ryan
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, St. Patrick's University Hospital, Trinity College Dublin, James Street, Dublin 8, Ireland
| | - Eimear Doody
- Department of Psychiatry, St. Patrick's University Hospital, Trinity College Dublin, James Street, Dublin 8, Ireland
| | - Declan M McLoughlin
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, St. Patrick's University Hospital, Trinity College Dublin, James Street, Dublin 8, Ireland.
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7
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Bitenc M, Grebstad Tune B, Melheim M, Atneosen-Åsegg M, Lai X, Rajar P, Solberg R, Baumbusch LO. Assessing nuclear versus mitochondrial cell-free DNA (cfDNA) by qRT-PCR and droplet digital PCR using a piglet model of perinatal asphyxia. Mol Biol Rep 2023; 50:1533-1544. [PMID: 36512170 PMCID: PMC9889441 DOI: 10.1007/s11033-022-08135-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Since the discovery more than half a century ago, cell-free DNA (cfDNA) has become an attractive objective in multiple diagnostic, prognostic, and monitoring settings. However, despite the increasing number of cfDNA applications in liquid biopsies, we still lack a comprehensive understanding of the nature of cfDNA including optimal assessment. In the presented study, we continued testing and validation of common techniques for cfDNA extraction and quantification (qRT-PCR or droplet digital PCR) of nuclear- and mitochondrial cfDNA (ncfDNA and mtcfDNA) in blood, using a piglet model of perinatal asphyxia to determine potential temporal and quantitative changes at the levels of cfDNA. METHODS AND RESULTS Newborn piglets (n = 19) were either exposed to hypoxia (n = 11) or were part of the sham-operated control group (n = 8). Blood samples were collected at baseline (= start) and at the end of hypoxia or at 40-45 min for the sham-operated control group. Applying the qRT-PCR method, ncfDNA concentrations in piglets exposed to hypoxia revealed an increasing trend from 7.1 ng/ml to 9.5 ng/ml for HK2 (hexokinase 2) and from 4.6 ng/ml to 7.9 ng/ml for β-globulin, respectively, whereas the control animals showed a more balanced profile. Furthermore, median levels of mtcfDNA were much higher in comparison to ncfDNA, but without significant differences between intervention versus the control group. CONCLUSIONS Both, qRT-PCR and the droplet digital PCR technique identified overall similar patterns for the concentration changes of cfDNA; but, the more sensitive digital PCR methodology might be required to identify minimal responses.
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Affiliation(s)
- Marie Bitenc
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway
| | - Benedicte Grebstad Tune
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maria Melheim
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway
| | | | - Xiaoran Lai
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Polona Rajar
- Department of Neonatal Intensive Care, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Ullevål, Oslo, Norway
- Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Rønnaug Solberg
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway
- Department of Pediatrics, Vestfold Hospital Trust, Tønsberg, Norway
| | - Lars Oliver Baumbusch
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, Postbox 4950, 0424, Nydalen, Oslo, Norway.
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Procyk G, Bilicki D, Balsam P, Lodziński P, Grabowski M, Gąsecka A. Extracellular Vesicles in Atrial Fibrillation—State of the Art. Int J Mol Sci 2022; 23:ijms23147591. [PMID: 35886937 PMCID: PMC9325220 DOI: 10.3390/ijms23147591] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/20/2022] Open
Abstract
Extracellular vesicles are particles released from cells and delimited by a lipid bilayer. They have been widely studied, including extensive investigation in cardiovascular diseases. Many scientists have explored their role in atrial fibrillation. Patients suffering from atrial fibrillation have been evidenced to present altered levels of these particles as well as changed amounts of their contents such as micro-ribonucleic acids (miRs). Although many observations have been made so far, a large randomized clinical trial is needed to assess the previous findings. This review aims to thoroughly summarize current research regarding extracellular vesicles in atrial fibrillation.
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Affiliation(s)
- Grzegorz Procyk
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland; (P.B.); (P.L.); (M.G.); (A.G.)
- Correspondence: ; Tel.: +48-723-488-305
| | - Dominik Bilicki
- Faculty of Medicine, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland;
| | - Paweł Balsam
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland; (P.B.); (P.L.); (M.G.); (A.G.)
| | - Piotr Lodziński
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland; (P.B.); (P.L.); (M.G.); (A.G.)
| | - Marcin Grabowski
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland; (P.B.); (P.L.); (M.G.); (A.G.)
| | - Aleksandra Gąsecka
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland; (P.B.); (P.L.); (M.G.); (A.G.)
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9
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Chetty VK, Ghanam J, Anchan S, Reinhardt K, Brenzel A, Gelléri M, Cremer C, Grueso-Navarro E, Schneider M, von Neuhoff N, Reinhardt D, Jablonska J, Nazarenko I, Thakur BK. Efficient Small Extracellular Vesicles (EV) Isolation Method and Evaluation of EV-Associated DNA Role in Cell-Cell Communication in Cancer. Cancers (Basel) 2022; 14:cancers14092068. [PMID: 35565197 PMCID: PMC9099953 DOI: 10.3390/cancers14092068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Small extracellular vesicles (sEVs) released by all cell types function as a mediator in intercellular communication that can promote cell division and survival to remodel the tumor microenvironment to develop tumor invasion and metastasis. Even though dsDNA baggage is associated with all small EV populations, the functional role of EV-DNA in cancer remains poorly understood. This is due to a lack of methods allowing the efficient separation of small EVs (sEVs) from other non-sEV components. The main aim of our study was to develop an efficient sEV isolation method along with EV-associated DNA (EV-DNA) monitoring tool to evaluate the role of EV-DNA as a mediator of cell–cell communication in cancer. Our detailed small EV-DNA characterization confirmed that isolated sEVs using the TSU method (Tangential flow filtration + Size exclusion chromatography + Ultrafiltration) are free from contaminants such as cell-free and apoptotic bodies DNA, making TSU ideal for performing EV-DNA functional studies. Next, we revealed the exact EV-DNA distribution in the recipient cells using 3D image analysis and the association of EV-DNA with key cellular proteins, which may have an essential role in cancer. In the leukemia model, EV-DNA isolated from leukemia cell lines associated with mesenchymal stromal cells (MSCs), a crucial factor in the bone marrow (BM) microenvironment. Abstract Small extracellular vesicles (sEVs) play essential roles in intercellular signaling both in normal and pathophysiological conditions. Comprehensive studies of dsDNA associated with sEVs are hampered by a lack of methods, allowing efficient separation of sEVs from free-circulating DNA and apoptotic bodies. In this work, using controlled culture conditions, we enriched the reproducible separation of sEVs from free-circulated components by combining tangential flow filtration, size-exclusion chromatography, and ultrafiltration (TSU). EV-enriched fractions (F2 and F3) obtained using TSU also contained more dsDNA derived from the host genome and mitochondria, predominantly localized inside the vesicles. Three-dimensional reconstruction of high-resolution imaging showed that the recipient cell membrane barrier restricts a portion of EV-DNA. Simultaneously, the remaining EV-DNA overcomes it and enters the cytoplasm and nucleus. In the cytoplasm, EV-DNA associates with dsDNA-inflammatory sensors (cGAS/STING) and endosomal proteins (Rab5/Rab7). Relevant to cancer, we found that EV-DNA isolated from leukemia cell lines communicates with mesenchymal stromal cells (MSCs), a critical component in the BM microenvironment. Furthermore, we illustrated the arrangement of sEVs and EV-DNA at a single vesicle level using super-resolution microscopy. Altogether, employing TSU isolation, we demonstrated EV-DNA distribution and a tool to evaluate the exact EV-DNA role of cell–cell communication in cancer.
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Affiliation(s)
- Venkatesh Kumar Chetty
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Srishti Anchan
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Katarina Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Alexandra Brenzel
- Imaging Center Essen (IMCES), University Hospital Essen, 45147 Essen, Germany;
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; (M.G.); (C.C.)
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; (M.G.); (C.C.)
- Max Planck Institutes for Polymer Research and for Chemistry, 55128 Mainz, Germany
| | - Elena Grueso-Navarro
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany; (E.G.-N.); (I.N.)
| | - Markus Schneider
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Nils von Neuhoff
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Jadwiga Jablonska
- Department of Otorhinolaryngology, University Hospital Essen, 45147 Essen, Germany;
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany; (E.G.-N.); (I.N.)
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
- Correspondence: ; Tel.: +49-201-723-2504
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10
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Liquid Biopsy as a Source of Nucleic Acid Biomarkers in the Diagnosis and Management of Lynch Syndrome. Int J Mol Sci 2022; 23:ijms23084284. [PMID: 35457101 PMCID: PMC9029375 DOI: 10.3390/ijms23084284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Lynch syndrome (LS) is an autosomal dominant inherited cancer predisposition disorder, which may manifest as colorectal cancer (CRC), endometrial cancer (EC) or other malignancies of the gastrointestinal and genitourinary tract as well as the skin and brain. Its genetic cause is a defect in one of the four key DNA mismatch repair (MMR) loci. Testing of patients at risk is currently based on the absence of MMR protein staining and detection of mutations in cancer tissue and the germline, microsatellite instability (MSI) and the hypermethylated state of the MLH1 promoter. If LS is shown to have caused CRC, lifetime follow-up with regular screening (most importantly, colonoscopy) is required. In recent years, DNA and RNA markers extracted from liquid biopsies have found some use in the clinical diagnosis of LS. They have the potential to greatly enhance the efficiency of the follow-up process by making it minimally invasive, reproducible, and time effective. Here, we review markers reported in the literature and their current clinical applications, and we comment on possible future directions.
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11
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Ghanam J, Chetty VK, Barthel L, Reinhardt D, Hoyer PF, Thakur BK. DNA in extracellular vesicles: from evolution to its current application in health and disease. Cell Biosci 2022; 12:37. [PMID: 35346363 PMCID: PMC8961894 DOI: 10.1186/s13578-022-00771-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/07/2022] [Indexed: 02/08/2023] Open
Abstract
Extracellular vesicle (EV) secretion is a highly conserved evolutionary trait in all organisms in the three domains of life. The packaging and release of EVs appears to be a bulk-flow process which takes place mainly under extreme conditions. EVs participate in horizontal gene transfer, which supports the survival of prokaryotic and eukaryotic microbes. In higher eukaryotes, almost all cells secrete a heterogeneous population of EVs loaded with various biomolecules. EV secretion is typically higher in cancer microenvironments, promoting tumor progression and metastasis. EVs are now recognized as additional mediators of autocrine and paracrine communication in health and disease. In this context, proteins and RNAs have been studied the most, but extracellular vesicle DNA (EV-DNA) has started to gain in importance in the last few years. In this review, we summarize new findings related to the loading mechanism(s), localization, and post-shedding function of EV-DNA. We also discuss the feasibility of using EV-DNA as a biomarker when performing a liquid biopsy, at the same time emphasizing the lack of data from clinical trials in this regard. Finally, we outline the potential of EV-DNA uptake and its interaction with the host genome as a promising tool for understanding the mechanisms of cancer evolution. Protecting DNA in membrane vesicles seems to be a conserved phenomenon for the horizontal genetic flux between prokaryotes and lower eukaryotes. Capturing and analyzing this vesicular DNA enables quick and non-invasive monitoring of natural ecosystems. Cancer-derived extracellular vesicles containing DNA open up novel directions in cell-to-cell communication and therefore disease monitoring. Complex and fluctuating conditions of the tumor microenvironment, mimicking natural ecosystems, could favor EV-DNA release, mediating tumor multi-clonal evolution and providing survival benefits.
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Affiliation(s)
- Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Venkatesh Kumar Chetty
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Lennart Barthel
- Department of Neurosurgery and Spine Surgery, Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany.,Institute of Medical Psychology and Behavioral Immunobiology, Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Peter-Friedrich Hoyer
- Department of Pediatrics II, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany.
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12
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Yang J, Zou X, Jose PA, Zeng C. Extracellular vesicles: Potential impact on cardiovascular diseases. Adv Clin Chem 2021; 105:49-100. [PMID: 34809830 DOI: 10.1016/bs.acc.2021.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Extracellular vesicles (EVs) have received considerable attention in biological and clinical research due to their ability to mediate cell-to-cell communication. Based on their size and secretory origin, EVs are categorized as exosomes, microvesicles, and apoptotic bodies. Increasing number of studies highlight the contribution of EVs in the regulation of a wide range of normal cellular physiological processes, including waste scavenging, cellular stress reduction, intercellular communication, immune regulation, and cellular homeostasis modulation. Altered circulating EV level, expression pattern, or content in plasma of patients with cardiovascular disease (CVD) may serve as diagnostic and prognostic biomarkers in diverse cardiovascular pathologies. Due to their inherent characteristics and physiological functions, EVs, in turn, have become potential candidates as therapeutic agents. In this review, we discuss the evolving understanding of the role of EVs in CVD, summarize the current knowledge of EV-mediated regulatory mechanisms, and highlight potential strategies for the diagnosis and therapy of CVD. We also attempt to look into the future that may advance our understanding of the role of EVs in the pathogenesis of CVD and provide novel insights into the field of translational medicine.
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Affiliation(s)
- Jian Yang
- Department of Clinical Nutrition, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, PR China.
| | - Xue Zou
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, PR China; Chongqing Institute of Cardiology and Chongqing Key Laboratory for Hypertension Research, Chongqing, PR China
| | - Pedro A Jose
- Division of Renal Disease & Hypertension, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Chunyu Zeng
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, PR China; Chongqing Institute of Cardiology and Chongqing Key Laboratory for Hypertension Research, Chongqing, PR China; State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, The Third Military Medical University, Chongqing, PR China; Heart Center of Fujian Province, Union Hospital, Fujian Medical University, Fuzhou, PR China.
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13
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Huang S, Deng Y, Xu J, Liu J, Liu L, Fan C. The Role of Exosomes and Their Cargos in the Mechanism, Diagnosis, and Treatment of Atrial Fibrillation. Front Cardiovasc Med 2021; 8:712828. [PMID: 34395566 PMCID: PMC8355361 DOI: 10.3389/fcvm.2021.712828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
Atrial fibrillation (AF) is the most common persistent arrhythmia, but the mechanism of AF has not been fully elucidated, and existing approaches to diagnosis and treatment face limitations. Recently, exosomes have attracted considerable interest in AF research due to their high stability, specificity and cell-targeting ability. The aim of this review is to summarize recent literature, analyze the advantages and limitations of exosomes, and to provide new ideas for their use in understanding the mechanism and improving the diagnosis and treatment of AF.
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Affiliation(s)
- Shengyuan Huang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yating Deng
- Xiangya Medical College of Central South University, Changsha, China
| | - Jiaqi Xu
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Jiachen Liu
- Xiangya Medical College of Central South University, Changsha, China
| | - Liming Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chengming Fan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
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14
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Yamazoe M, Sasano T, Ihara K, Takahashi K, Nakamura W, Takahashi N, Komuro H, Hamada S, Furukawa T. Sparsely methylated mitochondrial cell free DNA released from cardiomyocytes contributes to systemic inflammatory response accompanied by atrial fibrillation. Sci Rep 2021; 11:5837. [PMID: 33737532 PMCID: PMC7973420 DOI: 10.1038/s41598-021-85204-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/22/2021] [Indexed: 01/05/2023] Open
Abstract
Systemic inflammation is assumed to be the consequence and the cause of atrial fibrillation (AF); however, the underlying mechanism remains unclear. We aimed to evaluate the level of cell-free DNA (cfDNA) in patients with AF and AF mimicking models, and to illuminate its impact on inflammation. Peripheral blood was obtained from 54 patients with AF and 104 non-AF controls, and cfDNA was extracted. We extracted total cfDNA from conditioned medium after rapid pacing to HL-1 cells. Nuclear and mitochondrial DNA were separately extracted and fragmented to simulate nuclear-cfDNA (n-cfDNA) and mitochondrial-cfDNA (mt-cfDNA). The AF group showed higher cfDNA concentration than the non-AF group (12.6 [9.0–17.1] vs. 8.1 [5.3–10.8] [ng/mL], p < 0.001). The copy numbers of n-cfDNA and mt-cfDNA were higher in AF groups than in non-AF groups; the difference of mt-cfDNA was particularly apparent (p = 0.011 and p < 0.001, respectively). Administration of total cfDNA and mt-cfDNA to macrophages significantly promoted IL-1β and IL-6 expression through TLR9, whereas n-cfDNA did not. Induction of cytokine expression by methylated mt-cfDNA was lower than that by unmethylated mt-cfDNA. Collectively, AF was associated with an increased cfDNA level, especially mt-cfDNA. Sparsely methylated mt-cfDNA released from cardiomyocytes may be involved in sterile systemic inflammation accompanied by AF.
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Affiliation(s)
- Masahiro Yamazoe
- Department of Bio-Informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Cardiovascular Physiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tetsuo Sasano
- Department of Cardiovascular Physiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan. .,Department of Cardiovascular Medicine, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| | - Kensuke Ihara
- Department of Bio-Informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kentaro Takahashi
- Department of Bio-Informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Wakana Nakamura
- Department of Cardiovascular Physiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Naomi Takahashi
- Department of Cardiovascular Physiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroaki Komuro
- Department of Cardiovascular Physiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Satomi Hamada
- Department of Cardiovascular Physiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tetsushi Furukawa
- Department of Bio-Informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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15
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Wang M, Chen X, Yu F, Ding H, Zhang Y, Wang K. Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer. Int J Biol Sci 2021; 17:1010-1025. [PMID: 33867825 PMCID: PMC8040306 DOI: 10.7150/ijbs.54614] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of cellular DNAs in eukaryotes are organized into linear chromosomes. In addition to chromosome DNAs, genes also reside on extrachromosomal elements. The extrachromosomal DNAs are commonly found to be circular, and they are referred to as extrachromosomal circular DNAs (eccDNAs). Recent technological advances have enriched our knowledge of eccDNA biology. There is currently increasing concern about the connection between eccDNA and cancer. Gene amplification on eccDNAs is prevalent in cancer. Moreover, eccDNAs commonly harbor oncogenes or drug resistance genes, hence providing a growth or survival advantage to cancer cells. eccDNAs play an important role in tumor heterogeneity and evolution, facilitating tumor adaptation to challenging circumstances. In addition, eccDNAs have recently been identified as cell-free DNAs in circulating system. The altered level of eccDNAs is observed in cancer patients relative to healthy controls. Particularly, eccDNAs are associated with cancer progression and poor outcomes. Thus, eccDNAs could be useful as novel biomarkers for the diagnosis and prognosis of cancer. In this review, we summarize current knowledge regarding the formation, characteristics and biological importance of eccDNAs, with a focus on the molecular mechanisms associated with their roles in cancer progression. We also discuss their potential applications in the detection and treatment of cancer. A better understanding of the functional role of eccDNAs in cancer would facilitate the comprehensive analysis of molecular mechanisms involved in cancer pathogenesis.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xinzhe Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Fei Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Han Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
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16
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Abstract
The liquid biopsy preserves a noninvasive technique to analyze promising biomarkers in cell-free bodyfluids, mainly in cell-free plasma. The most cells secrete extracellular vesicles into the extracellular place which can be isolated, analyzed easily due to the wide range of different protocols and commercial kits. The mitochondrial DNA isolated from biofluids can serve as new view in early diagnosis of various diseases (e.g. cancers, cardiovascular diseases). In this chapter, possible protocols of mitochondrial DNA copy number quantification are discussed presenting some ways to determine the mtDNA level of extracellular vesicles in different diseases.
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17
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Pös Z, Pös O, Styk J, Mocova A, Strieskova L, Budis J, Kadasi L, Radvanszky J, Szemes T. Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes. Int J Mol Sci 2020; 21:ijms21228634. [PMID: 33207777 PMCID: PMC7697251 DOI: 10.3390/ijms21228634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Affiliation(s)
- Zuzana Pös
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jakub Styk
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Faculty of Medicine, Institute of Medical Biology, Genetics and Clinical Genetics, 811 08 Bratislava, Slovakia
| | - Angelika Mocova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | | | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jan Radvanszky
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
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18
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Wang X, Weidling I, Koppel S, Menta B, Perez Ortiz J, Kalani A, Wilkins HM, Swerdlow RH. Detection of mitochondria-pertinent components in exosomes. Mitochondrion 2020; 55:100-110. [PMID: 32980480 PMCID: PMC7669644 DOI: 10.1016/j.mito.2020.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/27/2020] [Accepted: 09/18/2020] [Indexed: 01/01/2023]
Abstract
We screened cell line and plasma-derived exosomes for molecules that localize to mitochondria or that reflect mitochondrial integrity. SH-SY5Y cell-derived exosomes contained humanin, citrate synthase, and fibroblast growth factor 21 protein, and plasma-derived exosomes contained humanin, voltage-dependent anion-selective channel 1, and transcription factor A protein. Nuclear mitochondrial (NUMT) DNA complicated analyses of mitochondrial DNA (mtDNA), which otherwise suggested exosomes contain at most very low amounts of extended mtDNA sequences but likely contain degraded pieces of mtDNA. Cell and plasma-derived exosomes contained several mtDNA-derived mRNA sequences, including those for ND2, CO2, and humanin. These results can guide exosome-focused, mitochondria-pertinent biomarker development.
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Affiliation(s)
- Xiaowan Wang
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Ian Weidling
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Scott Koppel
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Blaise Menta
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Judit Perez Ortiz
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Anuradha Kalani
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Heather M Wilkins
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Russell H Swerdlow
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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19
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Circulating Cell-Free Nucleic Acids: Main Characteristics and Clinical Application. Int J Mol Sci 2020; 21:ijms21186827. [PMID: 32957662 PMCID: PMC7555669 DOI: 10.3390/ijms21186827] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy recently became a very promising diagnostic method that has several advantages over conventional invasive methods. Liquid biopsy may serve as a source of several important biomarkers including cell-free nucleic acids (cf-NAs). Cf-DNA is widely used in prenatal testing in order to characterize fetal genetic disorders. Analysis of cf-DNA may provide information about the mutation profile of tumor cells, while cell-free non-coding RNAs are promising biomarker candidates in the diagnosis and prognosis of cancer. Many of these markers have the potential to help clinicians in therapy selection and in the follow-up of patients. Thus, cf-NA-based diagnostics represent a new path in personalized medicine. Although several reviews are available in the field, most of them focus on a limited number of cf-NA types. In this review, we give an overview about all known cf-NAs including cf-DNA, cf-mtDNA and cell-free non-coding RNA (miRNA, lncRNA, circRNA, piRNA, YRNA, and vtRNA) by discussing their biogenesis, biological function and potential as biomarker candidates in liquid biopsy. We also outline possible future directions in the field.
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20
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Abstract
The discovery of cell-free DNA (cfDNA) dates back to 1948, when Mandel and Metais found it in the sera of cancer patients [...].
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