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Hu X, Zhang H, Wang Y, Lin Y, Li Q, Li L, Zeng G, Ou R, Cheng X, Zhang Y, Jin X. Effects of blood-processing protocols on cell-free DNA fragmentomics in plasma: Comparisons of one- and two-step centrifugations. Clin Chim Acta 2024; 560:119729. [PMID: 38754575 DOI: 10.1016/j.cca.2024.119729] [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: 03/29/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Cell-free DNA (cfDNA) fragmentomic characteristics are promising analytes with abundant physiological signals for non-invasive disease diagnosis and monitoring. Previous studies on plasma cfDNA fragmentomics commonly employed a two-step centrifugation process for removing cell debris, involving a low-speed centrifugation followed by a high-speed centrifugation. However, the effects of centrifugation conditions on the analysis of cfDNA fragmentome remain uncertain. METHODS We collected blood samples from 10 healthy individuals and divided each sample into two aliquots for plasma preparation with one- and two-step centrifugation processes. We performed whole genome sequencing (WGS) of the plasma cfDNA in the two groups and comprehensively compared the cfDNA fragmentomic features. Additionally, we reanalyzed the fragmentomic features of cfDNA from 16 healthy individuals and 16 COVID-19 patients, processed through one- and two-step centrifugation in our previous study, to investigate the impact of centrifugation on disease signals. RESULTS Our results showed that there were no significant differences observed in the characteristics of nuclear cfDNA, including size, motif diversity score (MDS) of end motifs, and genome distribution, between plasma samples treated with one- and two-step centrifugation. The cfDNA size shortening in COVID-19 patients was observed in plasma samples with one- and two-step centrifugation methods. However, we observed a significantly higher relative abundance and longer size of cell-free mitochondrial DNA (mtDNA) in the one-step samples compared to the two-step samples. This difference in mtDNA caused by the one- and two-step centrifugation methods surpasses the pathological difference between COVID-19 patients and healthy individuals. CONCLUSIONS Our findings indicate that one-step low-speed centrifugation is a simple and potentially suitable method for analyzing nuclear cfDNA fragmentation characteristics. These results offer valuable guidance for cfDNA research in various clinical scenarios.
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Affiliation(s)
- Xintao Hu
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China; BGI Research, Shenzhen 518083, China
| | | | | | - Yu Lin
- BGI Research, Shenzhen 518083, China
| | - Qiuyan Li
- BGI Research, Shenzhen 518083, China
| | | | | | - Rijing Ou
- BGI Research, Shenzhen 518083, China
| | - Xinyu Cheng
- Engineering Research Center of Text Computing & Cognitive Intelligence, Ministry of Education, Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province, State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang 550025, China
| | - Yan Zhang
- BGI Research, Shenzhen 518083, China.
| | - Xin Jin
- BGI Research, Shenzhen 518083, China; School of Medicine, South China University of Technology, Guangzhou 510006, China.
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2
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Dasgupta SK, Gollamudi J, Rivera S, Poche RA, Rumbaut RE, Thiagarajan P. β2-glycoprotein I promotes the clearance of circulating mitochondria. PLoS One 2024; 19:e0293304. [PMID: 38271349 PMCID: PMC10810532 DOI: 10.1371/journal.pone.0293304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/10/2023] [Indexed: 01/27/2024] Open
Abstract
β2-glycoprotein I (β2-Gp1) is a cardiolipin-binding plasma glycoprotein. It is evolutionarily conserved from invertebrates, and cardiolipin-bound β2-Gp1 is a major target of antiphospholipid antibodies seen in autoimmune disorders. Cardiolipin is almost exclusively present in mitochondria, and mitochondria are present in circulating blood. We show that β2-Gp1 binds to cell-free mitochondria (CFM) in the circulation and promotes its phagocytosis by macrophages at physiological plasma concentrations. Exogenous CFM had a short circulation time of less than 10 minutes in mice. Following infusion of CFM, β2-Gp1-deficient mice had significantly higher levels of transfused mitochondria at 5 minutes (9.9 ± 6.4 pg/ml versus 4.0 ± 2.3 pg/ml in wildtype, p = 0.01) and at 10 minutes (3.0 ± 3.6 pg/ml versus 1.0 ± 0.06 pg/ml in wild-type, p = 0.033, n = 10). In addition, the splenic macrophages had less phagocytosed CFM in β2-Gp1-deficient mice (24.4 ± 2.72% versus 35.6 ± 3.5 in wild-type, p = 0.001, n = 5). A patient with abnormal β2-Gp1, unable to bind cardiolipin, has increased CFM in blood (5.09 pg/ml versus 1.26 ± 1.35 in normal) and his plasma induced less phagocytosis of CFM by macrophages (47.3 ± 1.6% versus 54.3 ± 1.3, p = 0.01) compared to normal plasma. These results show the evolutionarily conserved β2-Gp1 is one of the mediators of the clearance of CFM in circulation.
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Affiliation(s)
- Swapan Kumar Dasgupta
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center and Departments of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jahnavi Gollamudi
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Stefanie Rivera
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center and Departments of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ross A. Poche
- Department of Medicine Integrative Physiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rolando E. Rumbaut
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Perumal Thiagarajan
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey Veterans Affairs Medical Center and Departments of Pathology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
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3
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Roch B, Pisareva E, Mirandola A, Sanchez C, Pastor B, Tanos R, Frayssinoux F, Diab-Assaf M, Anker P, Al Amir Dache Z, Thierry AR. Impact of platelet activation on the release of cell-free mitochondria and circulating mitochondrial DNA. Clin Chim Acta 2024; 553:117711. [PMID: 38101467 DOI: 10.1016/j.cca.2023.117711] [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: 05/09/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Research on circulating mitochondrial DNA (cir-mtDNA) based diagnostic is insufficient, as to its function, origin, structural features, and particularly its standardization of isolation. To date, plasma preparation performed in previous studies do not take into consideration the potential bias resulting from the release of mitochondria by activated platelets. METHODS To tackle this, we compared the mtDNA amount determined by a standard plasma preparation method or a method optimally avoiding platelet activation. MtDNA extracted from the plasma of seven healthy individuals was quantified by Q-PCR in the course of the process of both methods submitted to filtration, freezing or differential centrifugation. RESULTS 98.7 to 99.4% of plasma mtDNA corresponded to extracellular mitochondria, either free or into large extracellular vesicles. Without platelet activation, the proportion of both types of entities remained preponderant (76-80%), but the amount of detected mtDNA decreased 67-fold. CONCLUSION We show the high capacity of platelets to release free mitochondria in "in vitro" conditions. This represents a potent confounding factor when extracting mtDNA for cir-mtDNA investigation. Platelet activation during pre-analytical conditions should therefore be avoided when studying cir-mtDNA. Our findings lead to a profound revision of the assumptions previously made by most works in this field. Overall, our data suggest the need to characterize or isolate mtDNA associated various structural forms, as well as to standardize plasma preparation, to better circumscribe cir-mtDNA's diagnostic capacity.
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Affiliation(s)
- Benoit Roch
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France; Thoracic Oncology Unit, Arnaud de Villeneuve Hospital, University Hospital of Montpellier, Montpellier F-34295, France
| | - Ekaterina Pisareva
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Alexia Mirandola
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Cynthia Sanchez
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Brice Pastor
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Rita Tanos
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Florence Frayssinoux
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Mona Diab-Assaf
- Faculty of Sciences II, Lebanese University Fanar, Beirut, Lebanon
| | - Philippe Anker
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Zahra Al Amir Dache
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Alain R Thierry
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France; ICM, Institut Régional du Cancer de Montpellier, Montpellier F-34298, France.
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4
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Ogata H, Higasa K, Kageyama Y, Tahara H, Shimamoto A, Takekita Y, Koshikawa Y, Nonen S, Kato T, Kinoshita T, Kato M. Relationship between circulating mitochondrial DNA and microRNA in patients with major depression. J Affect Disord 2023; 339:538-546. [PMID: 37467797 DOI: 10.1016/j.jad.2023.07.073] [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: 02/28/2023] [Revised: 06/22/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) and circulating cell-free mitochondrial DNA (ccf-mtDNA) have attracted interest as biological markers of affective disorders. In response to stress, it is known that miRNAs in mitochondria diffuse out of the cytoplasm alongside mtDNA; however, this process has not yet been identified. We hypothesized that miRNAs derived from specific cell nuclei cause mitochondrial damage and mtDNA fragmentation under MDD-associated stress conditions. METHODS A comprehensive analysis of the plasma miRNA levels and quantification of the plasma ccf-mtDNA copy number were performed in 69 patients with depression to determine correlations and identify genes and pathways interacting with miRNAs. The patients were randomly assigned to receive either selective serotonin reuptake inhibitors (SSRI) or mirtazapine. Their therapeutic efficacy over four weeks was evaluated in relation to miRNAs correlated with ccf-mtDNA copy number. RESULTS The expression levels of the five miRNAs showed a significant positive correlation with the ccf-mtDNA copy number after correcting for multiple testing. These miRNAs are involved in gene expression related to thyroid hormone synthesis, the Hippo signaling pathway, vasopressin-regulated water reabsorption, and lysine degradation. Of these five miRNAs, miR-6068 and miR-4708-3p were significantly associated with the SSRI and mirtazapine treatment outcomes, respectively. LIMITATIONS This study did not show comparison with a healthy group. CONCLUSIONS The expression levels of specific miRNAs were associated with ccf-mtDNA copy number in untreated depressed patients; moreover, these miRNAs were linked to antidepressant treatment outcomes. These findings are expected to lead to the elucidation of new pathological mechanism of depression.
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Affiliation(s)
- Haruhiko Ogata
- Department of Neuropsychiatry, Kansai Medical University, Osaka, Japan
| | - Koichiro Higasa
- Institute of Biomedical Science, Department of Genome Analysis, Kansai Medical University, Osaka, Japan
| | - Yuki Kageyama
- Department of Neuropsychiatry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Hidetoshi Tahara
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akira Shimamoto
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo Onoda, Yamaguchi, Japan
| | | | - Yosuke Koshikawa
- Department of Neuropsychiatry, Kansai Medical University, Osaka, Japan
| | - Shinpei Nonen
- Department of Pharmacy, Hyogo University of Health Sciences, Hyogo, Japan
| | - Tadafumi Kato
- Department of Psychiatry & Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | | | - Masaki Kato
- Department of Neuropsychiatry, Kansai Medical University, Osaka, Japan.
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5
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van der Pol Y, Moldovan N, Ramaker J, Bootsma S, Lenos KJ, Vermeulen L, Sandhu S, Bahce I, Pegtel DM, Wong SQ, Dawson SJ, Chandrananda D, Mouliere F. The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection. Genome Biol 2023; 24:229. [PMID: 37828498 PMCID: PMC10571306 DOI: 10.1186/s13059-023-03074-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Existing methods to detect tumor signal in liquid biopsy have focused on the analysis of nuclear cell-free DNA (cfDNA). However, non-nuclear cfDNA and in particular mitochondrial DNA (mtDNA) has been understudied. We hypothesize that an increase in mtDNA in plasma could reflect the presence of cancer, and that leveraging cell-free mtDNA could enhance cancer detection. RESULTS We survey 203 healthy and 664 cancer plasma samples from three collection centers covering 12 cancer types with whole genome sequencing to catalogue the plasma mtDNA fraction. The mtDNA fraction is increased in individuals with cholangiocarcinoma, colorectal, liver, pancreatic, or prostate cancer, in comparison to that in healthy individuals. We detect almost no increase of mtDNA fraction in individuals with other cancer types. The mtDNA fraction in plasma correlates with the cfDNA tumor fraction as determined by somatic mutations and/or copy number aberrations. However, the mtDNA fraction is also elevated in a fraction of patients without an apparent increase in tumor-derived cfDNA. A predictive model integrating mtDNA and copy number analysis increases the area under the curve (AUC) from 0.73 when using copy number alterations alone to an AUC of 0.81. CONCLUSIONS The mtDNA signal retrieved by whole genome sequencing has the potential to boost the detection of cancer when combined with other tumor-derived signals in liquid biopsies.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Norbert Moldovan
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Jip Ramaker
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Sanne Bootsma
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Idris Bahce
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pulmonology, Amsterdam, the Netherlands
| | - D Michiel Pegtel
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Australia.
- Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia.
| | - Dineika Chandrananda
- Peter MacCallum Cancer Centre, Melbourne, Australia.
- Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, Australia.
| | - Florent Mouliere
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands.
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands.
- Cancer Research UK Cancer Biomarker Centre, Manchester, UK.
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6
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Czarny P, Ziółkowska S, Kołodziej Ł, Watała C, Wigner-Jeziorska P, Bliźniewska-Kowalska K, Wachowska K, Gałecka M, Synowiec E, Gałecki P, Bijak M, Szemraj J, Śliwiński T. Single-Nucleotide Polymorphisms in Genes Maintaining the Stability of Mitochondrial DNA Affect the Occurrence, Onset, Severity and Treatment of Major Depressive Disorder. Int J Mol Sci 2023; 24:14752. [PMID: 37834200 PMCID: PMC10573273 DOI: 10.3390/ijms241914752] [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: 09/02/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
One of the key features of major depressive disorder (MDD, depression) is increased oxidative stress manifested by elevated levels of mtROS, a hallmark of mitochondrial dysfunction, which can arise from mitochondrial DNA (mtDNA) damage. Thus, the current study explores possibility that the single-nucleotide polymorphisms (SNPs) of genes encoding the three enzymes that are thought to be implicated in the replication, repair or degradation of mtDNA, i.e., POLG, ENDOG and EXOG, have an impact on the occurrence, onset, severity and treatment of MDD. Five SNPs were selected: EXOG c.-188T > G (rs9838614), EXOG c.*627G > A (rs1065800), POLG c.-1370T > A (rs1054875), ENDOG c.-394T > C (rs2977998) and ENDOG c.-220C > T (rs2997922), while genotyping was performed on 538 DNA samples (277 cases and 261 controls) using TaqMan probes. All SNPs of EXOG and ENDOG modulated the risk of depression, but the strongest effect was observed for rs1065800, while rs9838614 and rs2977998 indicate that they might influence the severity of symptoms, and, to a lesser extent, treatment effectiveness. Although the SNP located in POLG did not affect occurrence of the disease, the result suggests that it may influence the onset and treatment outcome. These findings further support the hypothesis that mtDNA damage and impairment in its metabolism play a crucial role not only in the development, but also in the treatment of depression.
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Affiliation(s)
- Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (S.Z.); (J.S.)
| | - Sylwia Ziółkowska
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (S.Z.); (J.S.)
| | - Łukasz Kołodziej
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 92-215 Lodz, Poland; (Ł.K.)
| | - Cezary Watała
- Department of Haemostatic Disorders, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Paulina Wigner-Jeziorska
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, 90-136 Lodz, Poland;
| | | | - Katarzyna Wachowska
- Department of Adult Psychiatry, Medical University of Lodz, 91-229 Lodz, Poland; (K.B.-K.); (K.W.); (P.G.)
| | - Małgorzata Gałecka
- Department of Psychotherapy, Medical University of Lodz, 91-229 Lodz, Poland;
| | - Ewelina Synowiec
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 92-215 Lodz, Poland; (Ł.K.)
| | - Piotr Gałecki
- Department of Adult Psychiatry, Medical University of Lodz, 91-229 Lodz, Poland; (K.B.-K.); (K.W.); (P.G.)
| | - Michał Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, 90-136 Lodz, Poland;
| | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (S.Z.); (J.S.)
| | - Tomasz Śliwiński
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 92-215 Lodz, Poland; (Ł.K.)
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7
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Horner E, Lord JM, Hazeldine J. The immune suppressive properties of damage associated molecular patterns in the setting of sterile traumatic injury. Front Immunol 2023; 14:1239683. [PMID: 37662933 PMCID: PMC10469493 DOI: 10.3389/fimmu.2023.1239683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Associated with the development of hospital-acquired infections, major traumatic injury results in an immediate and persistent state of systemic immunosuppression, yet the underlying mechanisms are poorly understood. Detected in the circulation in the minutes, days and weeks following injury, damage associated molecular patterns (DAMPs) are a heterogeneous collection of proteins, lipids and DNA renowned for initiating the systemic inflammatory response syndrome. Suggesting additional immunomodulatory roles in the post-trauma immune response, data are emerging implicating DAMPs as potential mediators of post-trauma immune suppression. Discussing the results of in vitro, in vivo and ex vivo studies, the purpose of this review is to summarise the emerging immune tolerising properties of cytosolic, nuclear and mitochondrial-derived DAMPs. Direct inhibition of neutrophil antimicrobial activities, the induction of endotoxin tolerance in monocytes and macrophages, and the recruitment, activation and expansion of myeloid derived suppressor cells and regulatory T cells are examples of some of the immune suppressive properties assigned to DAMPs so far. Crucially, with studies identifying the molecular mechanisms by which DAMPs promote immune suppression, therapeutic strategies that prevent and/or reverse DAMP-induced immunosuppression have been proposed. Approaches currently under consideration include the use of synthetic polymers, or the delivery of plasma proteins, to scavenge circulating DAMPs, or to treat critically-injured patients with antagonists of DAMP receptors. However, as DAMPs share signalling pathways with pathogen associated molecular patterns, and pro-inflammatory responses are essential for tissue regeneration, these approaches need to be carefully considered in order to ensure that modulating DAMP levels and/or their interaction with immune cells does not negatively impact upon anti-microbial defence and the physiological responses of tissue repair and wound healing.
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Affiliation(s)
- Emily Horner
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Janet M. Lord
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Jon Hazeldine
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
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8
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Al Amir Dache Z, Thierry AR. Mitochondria-derived cell-to-cell communication. Cell Rep 2023; 42:112728. [PMID: 37440408 DOI: 10.1016/j.celrep.2023.112728] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 02/21/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
In addition to their intracellular mobility, mitochondria and their components can exist outside the cells from which they originate. As a result, they are capable of acting on non-parental distant cells and mediate intercellular communication in physiological conditions and in a variety of pathologies. It has recently been demonstrated that this horizontal transfer governs a wide range of biological processes, such as tissue homeostasis, the rescue of injured recipient cells, and tumorigenesis. In addition, due to mitochondria's bacterial ancestry, they and their components can be recognized as damage-associated molecular patterns (DAMPs) by the immune cells, leading to inflammation. Here, we provide an overview of the most current and significant findings concerning the different structures of extracellular mitochondria and their by-products and their functions in the physiological and pathological context. This account illustrates the ongoing expansion of our understanding of mitochondria's biological role and functions in mammalian organisms.
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Affiliation(s)
- Zahra Al Amir Dache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France; INSERM U1316, CNRS UMR7057, Université Paris Cité, Paris, France
| | - Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France; ICM, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France.
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9
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Borah S, Mishra R, Dey S, Suchanti S, Bhowmick NA, Giri B, Haldar S. Prognostic Value of Circulating Mitochondrial DNA in Prostate Cancer and Underlying Mechanism. Mitochondrion 2023; 71:40-49. [PMID: 37211294 DOI: 10.1016/j.mito.2023.05.005] [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: 01/09/2023] [Revised: 04/03/2023] [Accepted: 05/14/2023] [Indexed: 05/23/2023]
Abstract
Circulating DNAs are considered as degraded DNA fragments of approximately 50-200 bp, found in blood plasma, consisting of cell-free mitochondrial and nuclear DNA. Such cell-free DNAs in the blood are found to be altered in different pathological conditions including lupus, heart disease, and malignancies. While nuclear DNAs are being used and being developed as a powerful clinical biomarker in liquid biopsies, mitochondrial DNAs (mtDNAs) are associated with inflammatory conditions including cancer progression. Patients with cancer including prostate cancer are found to have measurable concentrations of mitochondrial DNA in circulation in comparison with healthy controls. The plasma content of mitochondrial DNA is dramatically elevated in both prostate cancer patients and mouse models treated with the chemotherapeutic drug. Cell-free mtDNA, in its oxidized form, induced a pro-inflammatory condition and activates NLRP3-mediated inflammasome formation which causes IL-1β-mediated activation of growth factors. On the other hand, interacting with TLR9, mtDNAs trigger NF-κB-mediated complement C3a positive feedback paracrine loop and activate pro-proliferating signaling through upregulating AKT, ERK, and Bcl2 in the prostate tumor microenvironment. In this review, we discuss the growing evidence supporting cell-free mitochondrial DNA copy number, size, and mutations in mtDNA genes as potential prognostic biomarkers in different cancers and targetable prostate cancer therapeutic candidates impacting stromal-epithelial interactions essential for chemotherapy response.
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Affiliation(s)
- Supriya Borah
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles 90048, CA, USA
| | - Rajeev Mishra
- Department of Life Sciences, CSJM University, Kanpur, Uttar Pradesh 208012, India
| | - Sananda Dey
- Department of Research, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Surabhi Suchanti
- Department of Biosciences, Manipal University Jaipur, Rajasthan 303007, India
| | - Neil A Bhowmick
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles 90048, CA, USA; Department of Research, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Biplab Giri
- Department of Physiology, University of Gour Banga, Malda 732103, India.
| | - Subhash Haldar
- Department of Biochemistry, Bose Institute, Kolkata 700091, India.
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10
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Zhao Y, Gao C, Pan X, Lei K. Emerging roles of mitochondria in animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:14. [PMID: 37142814 PMCID: PMC10160293 DOI: 10.1186/s13619-023-00158-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/19/2023] [Indexed: 05/06/2023]
Abstract
The regeneration capacity after an injury is critical to the survival of living organisms. In animals, regeneration ability can be classified into five primary types: cellular, tissue, organ, structure, and whole-body regeneration. Multiple organelles and signaling pathways are involved in the processes of initiation, progression, and completion of regeneration. Mitochondria, as intracellular signaling platforms of pleiotropic functions in animals, have recently gained attention in animal regeneration. However, most studies to date have focused on cellular and tissue regeneration. A mechanistic understanding of the mitochondrial role in large-scale regeneration is unclear. Here, we reviewed findings related to mitochondrial involvement in animal regeneration. We outlined the evidence of mitochondrial dynamics across different animal models. Moreover, we emphasized the impact of defects and perturbation in mitochondria resulting in regeneration failure. Ultimately, we discussed the regulation of aging by mitochondria in animal regeneration and recommended this for future study. We hope this review will serve as a means to advocate for more mechanistic studies of mitochondria related to animal regeneration on different scales.
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Affiliation(s)
- Yun Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
- Fudan University, Shanghai, China
| | - Chong Gao
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Xue Pan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kai Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, 310024, China.
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11
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Fan Z, Feng Y, Zang L, Guo Y, Zhong XY. Association of circulating MtDNA with CVD in hemodialysis patients and in vitro effect of exogenous MtDNA on cardiac microvascular inflammation. BMC Cardiovasc Disord 2023; 23:74. [PMID: 36755219 PMCID: PMC9906832 DOI: 10.1186/s12872-023-03104-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) patients sustain a fairly high prevalence of cardiovascular disease (CVD). Microvascular inflammation is an early manifestation of CVD, and the released mitochondrial DNA (MtDNA) has been proposed to be a crucial integrator of inflammatory signals. Herein, the aim of this study was to determine the relationship between CVD, microvessel, and circulating MtDNA in the settings of uremia. METHODS Forty-two maintenance hemodialysis (MHD) patients and 36 health controls were enrolled in this study. Plasma cell-free MtDNA was detected by TaqMan-based qPCR assay. CVD risk markers including high-sensitive C-reactive protein (Hs-CRP), monocyte chemoattractant protein-1 (MCP-1), fibrinogen, and erythrocyte sedimentation rate (ESR) were measured by standard assays. Ten-year CVD risk was calculated from the Framingham risk score (FRS) model. In vitro study, human cardiac microvascular endothelial cells (HCMECs) were incubated with normal or uremic serum, with or without exogenous MtDNA. Intracellular toll-like receptor 9 (TLR9), adhesion molecule 1 (ICAM-1), MCP-1 and tumor necrosis factor-α (TNF-α) and cytosolic MtDNA were detected by qPCR. RESULTS Plasma MtDNA in MHD patients was significantly higher than healthy controls (4.74 vs. 2.41 × 105 copies/mL; p = 0.000). Subsequently, the MHD patients were classified into two groups based on the MtDNA median (4.34 × 105 copies/mL). In stratified analyses, the levels of Hs-CRP (5.02 vs. 3.73 mg/L; p = 0.042) and MCP-l (99.97 vs. 64.72 pg/mL; p = 0.008) and FRS (21.80 vs. 16.52; p = 0.016) in the high plasma MtDNA group were higher than those in the low plasma MtDNA group. In vitro study, we found that exogenous MtDNA aggravated uremic serum-induced microvascular inflammation (ICAM-1 and TNF-α) in HCMECs (all p < 0.05). Besides, the addition of MtDNA to the medium resulted in a further increase in cytosolic MtDNA and TLR9 levels in uremic serum-treated cells (all p < 0.05). In patients with MHD, MtDNA levels in plasma were significantly reduced after a single routine hemodialysis (pre 4.47 vs. post 3.45 × 105 copies/mL; p = 0.001) or hemodiafiltration (pre 4.85 vs. post 4.09 × 105 copies/mL; p = 0.001). These two approaches seem similar in terms of MtDNA clearance rate (21.26% vs. 11.94%; p = 0.172). CONCLUSIONS Overall, the present study suggests that MtDNA released into the circulation under the uremic toxin environment may adversely affect the cardiovascular system by exacerbating microvascular inflammation, and that reducing circulating MtDNA might be a future therapeutic strategy for the prevention of MHD-related CVD.
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Affiliation(s)
- Zhen Fan
- Department of Geriatrics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan China
| | - Ya Feng
- grid.414880.1Department of Nephrology, Clinical Medical College, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan China
| | - Li Zang
- grid.414880.1Department of Nephrology, Clinical Medical College, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan China
| | - Yi Guo
- Department of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32, West Section 2, Yihuan Road, Qingyang District, Chengdu, 610072, Sichuan, China.
| | - Xiao-yi Zhong
- grid.417298.10000 0004 1762 4928Department of Nephrology, Xinqiao Hospital, Army Medical University (Third Military Medical University), No. 83 Xinqiao Zhengjie, Shapingba District, Chongqing, 400037 China
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12
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Robles MC, Heard TC, Chao T, Alcover K, Wagner A, Akers KS, Burmeister DM. DIAGNOSTIC VALUE OF MITOCHONDRIAL DNA AND PERIPHERAL BLOOD MONONUCLEAR CELL RESPIROMETRY FOR BURN-RELATED SEPSIS. Shock 2023; 59:294-299. [PMID: 36730861 DOI: 10.1097/shk.0000000000002025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
ABSTRACT Background: Sepsis is the leading cause of mortality among burn patients that survive acute resuscitation. Clinical criteria have poor diagnostic value for burn-induced sepsis, making it difficult to diagnose. Protein biomarkers (e.g., procalcitonin) have been examined with limited success. We aimed to explore other biomarkers related to mitochondria (mitochondrial DNA [mtDNA]) and mitochondrial function of peripheral blood mononuclear cells (PBMCs) for sepsis diagnosis in burn patients. Methods: We conducted a follow-up analysis of a single center, prospective observational study of subjects (n = 10 healthy volunteers, n = 24 burn patients) to examine the diagnostic value of mtDNA and PBMC respirometry. Patients were enrolled regardless of sepsis status and followed longitudinally. Patient samples were classified as septic or not based on empiric clinical criteria. Isolated PBMCs were loaded into a high-resolution respirometer, and circulating mtDNA was measured with a PCR-based assay. Sequential Organ Failure Assessment (SOFA) criteria were also compared. Results: The SOFA criteria comparing septic versus before/nonseptic patients revealed significantly higher heart rate ( P = 0.012) and lower mean arterial pressure ( P = 0.039) in burn sepsis. MtDNA was significantly elevated in septic burn patients compared with healthy volunteers ( P < 0.0001) and nonseptic patients ( P < 0.0001), with no significant difference between healthy volunteers and nonseptic burn patients ( P = 0.187). The area under the ROC curve (AUC) for mtDNA was 0.685 (95% confidence interval = 0.50-0.86). For PBMC respirometry, burn patients exhibited increased routine and maximal respiration potential compared with healthy volunteers. However, no difference was found between nonseptic and septic patient samples. A subanalysis revealed a significant mortality difference in PBMC respirometry after sepsis diagnosis, wherein survivors had higher routine respiration ( P = 0.003) and maximal respiration ( P = 0.011) compared with nonsurvivors. Conclusion: Our findings reveal that mtDNA may have diagnostic value for burn sepsis, whereas PBMC respirometry is nonspecifically elevated in burns, but may have value in mortality prognosis. A larger, multisite study is warranted for further validity of the diagnostic value of mtDNA and PBMC respirometry as biomarkers for prognosis of sepsis and outcomes in burn patients.
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Affiliation(s)
| | - Tiffany C Heard
- United States Army Institute of Surgical Research, JBSA Fort Sam Houston, TX
| | - Tony Chao
- United States Army Institute of Surgical Research, JBSA Fort Sam Houston, TX
| | | | - Amanda Wagner
- United States Army Institute of Surgical Research, JBSA Fort Sam Houston, TX
| | - Kevin S Akers
- United States Army Institute of Surgical Research, JBSA Fort Sam Houston, TX
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13
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Pisareva E, Roch B, Sanchez C, Pastor B, Mirandola A, Diab-Assaf M, Mazard T, Prévostel C, Al Amir Dache Z, Thierry AR. Comparison of the structures and topologies of plasma extracted circulating nuclear and mitochondrial cell-free DNA. Front Genet 2023; 14:1104732. [PMID: 37152979 PMCID: PMC10158822 DOI: 10.3389/fgene.2023.1104732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/27/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction: The function, origin and structural features of circulating nuclear DNA (cir-nDNA) and mitochondrial DNA (cir-mtDNA) are poorly known, even though they have been investigated in numerous clinical studies, and are involved in a number of routine clinical applications. Based on our previous report disproving the conventional plasma isolation used for cirDNA analysis, this work enables a direct topological comparison of the circulating structures associated with nuclear DNA and mitochondrial cell-free DNA. Materials and methods: We used a Q-PCR and low-pass whole genome sequencing (LP-WGS) combination approach of cir-nDNA and cir-mtDNA, extracted using a procedure that eliminates platelet activation during the plasma isolation process to prevent mitochondria release in the extracellular milieu. Various physical procedures, such as filtration and differential centrifugation, were employed to infer their circulating structures. Results: DSP-S cir-mtDNA mean size profiles distributed on a slightly shorter range than SSP-S. SSP-S detected 40-fold more low-sized cir-mtDNA fragments (<90 bp/nt) and three-fold less long-sized fragments (>200 bp/nt) than DSP-S. The ratio of the fragment number below 90 bp over the fragment number above 200 bp was very homogenous among both DSP-S and SSP-S profiles, being 134-fold lower with DSP-S than with SSP-S. Cir-mtDNA and cir-nDNA DSP-S and SSP-S mean size profiles of healthy individuals ranged in different intervals with periodic sub-peaks only detectable with cir-nDNA. The very low amount of cir-mtDNA fragments of short size observed suggested that most of the cir-mtDNA is poorly fragmented and appearing longer than ∼1,000 bp, the readout limit of this LP-WGS method. Data suggested that cir-nDNA is, among DNA extracted in plasma, associated with ∼8.6% of large structures (apoptotic bodies, large extracellular vesicles (EVs), cell debris…), ∼27.7% in chromatin and small EVs and ∼63.7% mainly in oligo- and mono-nucleosomes. By contrast, cir-mtDNA appeared to be preponderantly (75.7%) associated with extracellular mitochondria, either in its free form or with large EVs; to a lesser extent, it was also associated with other structures: small EVs (∼18.4%), and exosomes or protein complexes (∼5.9%). Conclusion: This is the first study to directly compare the structural features of cir-nDNA and cir-mtDNA. The significant differences revealed between both are due to the DNA topological structure contained in the nucleus (chromatin) and in the mitochondria (plasmid) that determine their biological stability in blood. Although cir-nDNA and cir-mtDNA are principally associated with mono-nucleosomes and cell-free mitochondria, our study highlights the diversity of the circulating structures associated with cell-free DNA. They consequently have different pharmacokinetics as well as physiological functions. Thus, any accurate evaluation of their biological or diagnostic individual properties must relies on appropriate pre-analytics, and optimally on the isolation or enrichment of one category of their cirDNA associated structures.
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Affiliation(s)
- Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Benoit Roch
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
- Thoracic Oncology Unit, Arnaud De Villeneuve Hospital, University Hospital of Montpellier, Montpellier, France
| | - Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Alexia Mirandola
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Mona Diab-Assaf
- Faculty of Sciences II, Lebanese University Fanar, Beirut, Lebanon
| | - Thibault Mazard
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Corinne Prévostel
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Zahra Al Amir Dache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
| | - Alain R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Montpellier University, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, Montpellier, France
- *Correspondence: Alain R. Thierry,
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14
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Telekes A, Horváth A. The Role of Cell-Free DNA in Cancer Treatment Decision Making. Cancers (Basel) 2022; 14:6115. [PMID: 36551600 PMCID: PMC9776613 DOI: 10.3390/cancers14246115] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
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Affiliation(s)
- András Telekes
- Omnimed-Etosz, Ltd., 81 Széher Rd., 1021 Budapest, Hungary
- Semmelweis University, 26. Üllői Rd., 1085 Budapest, Hungary
| | - Anna Horváth
- Department of Internal Medicine and Haematology, Semmelweis University, 46. Szentkirályi Rd., 1088 Budapest, Hungary
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15
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Peak Plasma Levels of mtDNA Serve as a Predictive Biomarker for COVID-19 in-Hospital Mortality. J Clin Med 2022; 11:jcm11237161. [PMID: 36498735 PMCID: PMC9740249 DOI: 10.3390/jcm11237161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Several predictive biomarkers for coronavirus disease (COVID-19)-associated mortality in critically ill patients have been described. Although mitochondrial DNA (mtDNA) is elevated in patients with COVID-19, the association with coagulation function and its predictive power for mortality is unclear. Accordingly, this study investigates the predictive power of mtDNA for in-hospital mortality in critically ill patients with COVID-19, and whether combining it with thromboelastographic parameters can increase its predictive performance. This prospective explorative study included 29 patients with COVID-19 and 29 healthy matched controls. mtDNA encoding for NADH dehydrogenase 1 (ND1) was quantified using a quantitative polymerase chain reaction analysis, while coagulation function was evaluated using thromboelastometry and impedance aggregometry. Receiver operating characteristic (ROC) curves were used for the prediction of in-hospital mortality. Within the first 24 h, the plasma levels of mtDNA peaked significantly (controls: 65 (28-119) copies/µL; patients: 281 (110-805) at t0, 403 (168-1937) at t24, and 467 (188-952) copies/µL at t72; controls vs. patients: p = 0.02 at t0, p = 0.03 at t24, and p = 0.44 at t72). The mtDNA levels at t24 showed an excellent predictive performance for in-hospital mortality (area under the ROC curve: 0.90 (0.75-0.90)), which could not be improved by the combination with thromboelastometric or aggregometric parameters. Critically ill patients with COVID-19 present an early increase in the plasma levels of ND1 mtDNA, lasting over 24 h. They also show impairments in platelet function and fibrinolysis, as well as hypercoagulability, but these do not correlate with the plasma levels of fibrinogen. The peak plasma levels of mtDNA can be used as a predictive biomarker for in-hospital mortality; however, the combination with coagulation parameters does not improve the predictive validity.
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16
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Abstract
Liquid biopsy provides a noninvasive window to the cancer genome and physiology. In particular, cell-free DNA (cfDNA) is a versatile analyte for guiding treatment, monitoring treatment response and resistance, tracking minimal residual disease, and detecting cancer earlier. Despite certain successes, brain cancer diagnosis is amongst those applications that has so far resisted clinical implementation. Recent approaches have highlighted the clinical gain achievable by exploiting cfDNA biological signatures to boost liquid biopsy or unlock new applications. However, the biology of cfDNA is complex, still partially understood, and affected by a range of intrinsic and extrinsic factors. This guide will provide the keys to read, decode, and harness cfDNA biology: the diverse sources of cfDNA in the bloodstream, the mechanism of cfDNA release from cells, the cfDNA structure, topology, and why accounting for cfDNA biology matters for clinical applications of liquid biopsy.
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Affiliation(s)
- Florent Mouliere
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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17
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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18
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Briggs GD, Gelzinnis S, Meakes S, King KL, Balogh ZJ. NOT ALL CELL-FREE MITOCHONDRIAL DNA IS EQUAL IN TRAUMA PATIENTS. Shock 2022; 58:231-235. [PMID: 36125357 PMCID: PMC9512242 DOI: 10.1097/shk.0000000000001969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/20/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
ABSTRACT Mitochondrial DNA (mtDNA) acts as a proinflammatory damage-associated molecular pattern that stimulates innate immune activation via Toll-like receptor 9, similarly to bacterial DNA. A number of clinical studies have measured elevated cell-free mtDNA in the plasma of trauma patients, thought to originate from tissue injury and inflammatory processes; however, the magnitude of this increase, the absolute concentration, and the association with poor outcomes varies considerably across studies. Measurements of cell-free mtDNA in healthy individuals have shown that the majority of "cell-free" mtDNA (>95%) can be centrifuged/filtered from plasma in the size range of 0.45 to 5 μm, suggesting that there are larger forms of mtDNA-containing complexes in the plasma that could be considered cell-free. Whether this is true for trauma patients (and other relevant disease states) and the clinical relevance of the larger forms of mtDNA is unknown. These findings from healthy individuals also suggest that the centrifugation speeds used to generate cell-free plasma (which are rarely consistent among studies) could result in mixed populations of cell-free mtDNA that could confound associations with outcomes. We demonstrate in this study of 25 major trauma patients that the majority of the cell-free mtDNA in trauma patient plasma (>95%) is removed after centrifugation at 16,000g. Despite the larger forms of mtDNA being predominant, they do not correlate with outcomes or expected parameters such as injury/shock severity, multiple organ failure, and markers of inflammation, whereas low-molecular-weight cell-free mtDNA correlates strongly with these variables.
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Affiliation(s)
- Gabrielle D. Briggs
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Scott Gelzinnis
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Simone Meakes
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Kate L. King
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Zsolt J. Balogh
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
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19
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Streng LWJM, de Wijs CJ, Raat NJH, Specht PAC, Sneiders D, van der Kaaij M, Endeman H, Mik EG, Harms FA. In Vivo and Ex Vivo Mitochondrial Function in COVID-19 Patients on the Intensive Care Unit. Biomedicines 2022; 10:biomedicines10071746. [PMID: 35885051 PMCID: PMC9313105 DOI: 10.3390/biomedicines10071746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial dysfunction has been linked to disease progression in COVID-19 patients. This observational pilot study aimed to assess mitochondrial function in COVID-19 patients at intensive care unit (ICU) admission (T1), seven days thereafter (T2), and in healthy controls and a general anesthesia group. Measurements consisted of in vivo mitochondrial oxygenation and oxygen consumption, in vitro assessment of mitochondrial respiration in platelet-rich plasma (PRP) and peripheral blood mononuclear cells (PBMCs), and the ex vivo quantity of circulating cell-free mitochondrial DNA (mtDNA). The median mitoVO2 of COVID-19 patients on T1 and T2 was similar and tended to be lower than the mitoVO2 in the healthy controls, whilst the mitoVO2 in the general anesthesia group was significantly lower than that of all other groups. Basal platelet (PLT) respiration did not differ substantially between the measurements. PBMC basal respiration was increased by approximately 80% in the T1 group when contrasted to T2 and the healthy controls. Cell-free mtDNA was eight times higher in the COVID-T1 samples when compared to the healthy controls samples. In the COVID-T2 samples, mtDNA was twofold lower when compared to the COVID-T1 samples. mtDNA levels were increased in COVID-19 patients but were not associated with decreased mitochondrial O2 consumption in vivo in the skin, and ex vivo in PLT or PBMC. This suggests the presence of increased metabolism and mitochondrial damage.
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Affiliation(s)
- Lucia W. J. M. Streng
- Laboratory of Experimental Anesthesiology, Department of Anesthesiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (C.J.d.W.); (N.J.H.R.); (P.A.C.S.); (D.S.); (M.v.d.K.); (E.G.M.); (F.A.H.)
- Correspondence:
| | - Calvin J. de Wijs
- Laboratory of Experimental Anesthesiology, Department of Anesthesiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (C.J.d.W.); (N.J.H.R.); (P.A.C.S.); (D.S.); (M.v.d.K.); (E.G.M.); (F.A.H.)
| | - Nicolaas J. H. Raat
- Laboratory of Experimental Anesthesiology, Department of Anesthesiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (C.J.d.W.); (N.J.H.R.); (P.A.C.S.); (D.S.); (M.v.d.K.); (E.G.M.); (F.A.H.)
| | - Patricia A. C. Specht
- Laboratory of Experimental Anesthesiology, Department of Anesthesiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (C.J.d.W.); (N.J.H.R.); (P.A.C.S.); (D.S.); (M.v.d.K.); (E.G.M.); (F.A.H.)
| | - Dimitri Sneiders
- Laboratory of Experimental Anesthesiology, Department of Anesthesiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (C.J.d.W.); (N.J.H.R.); (P.A.C.S.); (D.S.); (M.v.d.K.); (E.G.M.); (F.A.H.)
| | - Mariëlle van der Kaaij
- Laboratory of Experimental Anesthesiology, Department of Anesthesiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (C.J.d.W.); (N.J.H.R.); (P.A.C.S.); (D.S.); (M.v.d.K.); (E.G.M.); (F.A.H.)
| | - Henrik Endeman
- Department of Intensive Care, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Egbert G. Mik
- Laboratory of Experimental Anesthesiology, Department of Anesthesiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (C.J.d.W.); (N.J.H.R.); (P.A.C.S.); (D.S.); (M.v.d.K.); (E.G.M.); (F.A.H.)
| | - Floor A. Harms
- Laboratory of Experimental Anesthesiology, Department of Anesthesiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (C.J.d.W.); (N.J.H.R.); (P.A.C.S.); (D.S.); (M.v.d.K.); (E.G.M.); (F.A.H.)
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20
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Chronic Lung Allograft Dysfunction Is Associated with Increased Levels of Cell-Free Mitochondrial DNA in Bronchoalveolar Lavage Fluid of Lung Transplant Recipients. J Clin Med 2022; 11:jcm11144142. [PMID: 35887906 PMCID: PMC9322792 DOI: 10.3390/jcm11144142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 12/04/2022] Open
Abstract
Chronic Lung Allograft Dysfunction (CLAD) is a life-threatening complication that limits the long-term survival of lung transplantation patients. Early diagnosis remains the basis of efficient management of CLAD, making the need for distinctive biomarkers critical. This explorative study aimed to investigate the predictive power of mitochondrial DNA (mtDNA) derived from bronchoalveolar lavages (BAL) to detect CLAD. The study included 106 lung transplant recipients and analyzed 286 BAL samples for cell count, cell differentiation, and inflammatory and mitochondrial biomarkers, including mtDNA. A receiver operating curve analysis of mtDNA levels was used to assess its ability to detect CLAD. The results revealed a discriminatory pro-inflammatory cytokine profile in the BAL fluid of CLAD patients. The concentration of mtDNA increased in step with each CLAD stage, reaching its highest concentration in stage 4, and correlated significantly with decreasing FEV1. The receiver operating curve analysis of mtDNA in BAL revealed a moderate prediction of CLAD when all stages were grouped together (AUROC 0.75, p-value < 0.0001). This study has found the concentration mtDNA in BAL to be a potential predictor for the early detection of CLAD and the differentiation of different CLAD stages, independent of the underlying pathology.
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21
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Ullah H, Arbab S, Li K, Khan MIU, Qadeer A, Muhammad N. Schistosomiasis related circulating cell-free DNA: A useful biomarker in diagnostics. Mol Biochem Parasitol 2022; 251:111495. [PMID: 35835258 DOI: 10.1016/j.molbiopara.2022.111495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 12/26/2022]
Abstract
Schistosoma is a genus of trematodes causing schistosomiasis, a major neglected tropical disease infecting more than 240 million people and with 700 million people at the risk of infection in the tropical and subtropical regions of the world, especially low-income countries. For the elimination of the disease, accurate diagnostic tools are needed. Besides allowing early treatment, early detection prevents environmental contamination and in turn ensures safe water sources in the endemic areas. Cell-free DNA (cfDNA) biomarker detection is a relatively new tool, used for the diagnosis of schistosomiasis in the early stages of infection from non-invasive clinical or experimental samples. cfDNA can be detected in Schistosoma infected host body fluids such as urine, serum, saliva and tissues, mainly in blood offering significant benefits for accurate diagnosis. In the current review, we described different characteristics of cfDNA, evidencing and supporting its potential uses in Schistosoma diagnosis and the improvement of treatment effectiveness.
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Affiliation(s)
- Hanif Ullah
- West China School of Nursing, Sichuan University, Chengdu, China.
| | - Safia Arbab
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China; Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ka Li
- West China School of Nursing, Sichuan University, Chengdu, China.
| | - Muhammad Inayat Ullah Khan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Abdul Qadeer
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai 200241, China
| | - Nehaz Muhammad
- Department of Zoology, University of Swabi, Swabi 23561, Khyber Pakhtunkhwa, Pakistan
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22
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Zhong XY, Guo Y, Fan Z. Increased level of free-circulating MtDNA in maintenance hemodialysis patients: Possible role in systemic inflammation. J Clin Lab Anal 2022; 36:e24558. [PMID: 35708020 PMCID: PMC9279998 DOI: 10.1002/jcla.24558] [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: 12/29/2021] [Revised: 03/17/2022] [Accepted: 06/02/2022] [Indexed: 12/15/2022] Open
Abstract
Background Mitochondrial DNA (MtDNA) exposed to the extracellular space due to cell death and stress has immunostimulatory properties. However, the clinical significance of circulating MtDNA in maintenance hemodialysis (MHD) patients and the precise mechanism of its emergence have yet to be investigated. Methods This cross‐sectional study consisted of 52 MHD patients and 32 age‐ and sex‐matched healthy controls. MHD patients were further categorized into high and low circulating cell‐free MtDNA (ccf‐MtDNA) groups based on the median value. Copy number of MtDNA was quantified using TaqMan‐based qPCR. Plasma cytokines were measured using ELISA kits. Reactive oxygen species (ROS) and mitochondrial membrane potential (Δψm) in peripheral blood mononuclear cells (PBMCs) were detected using DCFH‐DA or JC‐1 staining. Results The copy numbers of ccf‐MtDNA in patients with MHD were higher than those in healthy controls, and these alterations were correlated with changes of cytokines TNF‐α and IL‐6. Adjusted model in multivariate analysis showed that the presence of anuria and longer dialysis vintage were independently associated with higher levels of ccf‐MtDNA. Meanwhile, although not statistically significant, an inverse correlative trend between urinary MtDNA and ccf‐MtDNA was observed in patients with residual urine. Afterward, using PBMCs as surrogates for mitochondria‐rich cells, we found that patients in the high ccf‐MtDNA group exhibited a significantly higher ROS production and lower Δψm in cells. Conclusions Our data suggested that changes in ccf‐MtDNA correlate with the degree of inflammatory status in MHD patients, and that the excessive MtDNA may be caused by mitochondrial dysfunction and reduced urinary MtDNA excretion.
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Affiliation(s)
- Xiao-Yi Zhong
- Department of Nephrology, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yi Guo
- Department of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhen Fan
- Department of Geriatrics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
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23
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Fan Z, Yang JY, Guo Y, Liu YX, Zhong XY. Altered levels of circulating mitochondrial DNA in elderly people with sarcopenia: Association with mitochondrial impairment. Exp Gerontol 2022; 163:111802. [DOI: 10.1016/j.exger.2022.111802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/25/2022] [Accepted: 04/04/2022] [Indexed: 01/07/2023]
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24
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Minimized Extracorporeal Circulation Is Associated with Reduced Plasma Levels of Free-Circulating Mitochondrial DNA Compared to Conventional Cardiopulmonary Bypass: A Secondary Analysis of an Exploratory, Prospective, Interventional Study. J Clin Med 2022; 11:jcm11112994. [PMID: 35683383 PMCID: PMC9181034 DOI: 10.3390/jcm11112994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/10/2022] [Accepted: 05/23/2022] [Indexed: 01/25/2023] Open
Abstract
The use of minimized extracorporeal circulation (MiECC) during cardiac surgery is associated with a reduced inflammatory reaction compared to conventional cardiopulmonary bypass (cCPB). Since it is unknown if MiECC also reduces the amount of free-circulating mitochondrial DNA (mtDNA), this study aims to compare MiECC-induced mtDNA release to that of cCPB as well as to identify potential relations between the plasma levels of mtDNA and an adverse outcome. Overall, 45 patients undergoing cardiac surgery with either cCPB or MiECC were included in the study. MtDNA encoding for NADH dehydrogenase 1 was quantified with quantitative polymerase chain reaction. The plasma amount of mtDNA was significantly lower in patients undergoing cardiac surgery with MiECC compared to cCPB (MiECC: 161.8 (65.5−501.9); cCPB 190.8 (82−705.7); p < 0.001). Plasma levels of mtDNA showed comparable kinetics independently of the study group and peaked during CPB (MiECC preoperative: 68.2 (26.5−104.9); MiECC 60 min after start of CPB: 536.5 (215.7−919.6); cCPB preoperative: 152.5 (80.9−207.6); cCPB 60 min after start of CPB: 1818.0 (844.2−3932.2); all p < 0.001). Patients offering an mtDNA blood concentration of >650 copies/µL after the commencement of CPB had a 5-fold higher risk for postoperative atrial fibrillation independently of the type of cardiopulmonary bypass. An amount of mtDNA being higher than 650 copies/µL showed moderate predictive power (AUROC 0.71 (0.53−071)) for the identification of postoperative atrial fibrillation. In conclusion, plasma levels of mtDNA were lower in patients undergoing cardiac surgery with MiECC compared to cCPB. The amount of mtDNA at the beginning of the CPB was associated with postoperative atrial fibrillation independent of the type of cardiopulmonary bypass.
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25
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Anguita E, Chaparro A, Candel FJ, Ramos-Acosta C, Martínez-Micaelo N, Amigó N, Torrejón MJ, Llopis-García G, del Mar Suárez-Cadenas M, Matesanz M, del Castillo JG, Martín-Sánchez FJ. Biomarkers of stable and decompensated phases of heart failure with preserved ejection fraction. Int J Cardiol 2022; 361:91-100. [DOI: 10.1016/j.ijcard.2022.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/03/2022] [Accepted: 05/02/2022] [Indexed: 12/14/2022]
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26
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Park J, Kang E, Kang S, Kim D, Kim D, Park SJ, Jhang WK. Mitochondrial gene mutations in pediatric septic shock. Pediatr Res 2021; 90:1016-1022. [PMID: 33504965 DOI: 10.1038/s41390-020-01358-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND There has been a growing interest in the association between mitochondrial dysfunction and sepsis. However, most studies have focused on mitochondrial structural damage, functional aspects, or the clinical phenotypes in sepsis. The purpose of this study was to evaluate mitochondrial DNA (mtDNA) gene mutations in critically ill pediatric patients with septic shock. METHOD Thirteen patients with severe sepsis or septic shock admitted to the pediatric intensive care unit (PICU) of a tertiary children's hospital were enrolled in this prospective observational study. Clinical data from electronic medical records were obtained. Whole-blood samples were collected within 24 h of PICU admission to perform PBMC isolation, mtDNA extraction, and mtDNA sequencing using next-generation sequencing. RESULTS mtDNA sequencing revealed mutations in 9 of the 13 patients, presenting 27 point mutations overall, with 15 (55.6%) located in the locus related to adenosine triphosphate production and superoxide metabolism, including electron transport. CONCLUSION In this pilot study, significant numbers of mtDNA point mutations were detected in critically ill pediatric patients with septic shock. These mutations could provide promising evidence for mitochondrial dysfunction in sepsis and a basis for further large-scale studies. IMPACT This study is the first to examine mitochondrial DNA mutations in pediatric patients with septic shock using next-generation sequencing. A high frequency of mitochondrial DNA mutations was detected in these patients indicating an association with septic shock. This pilot study may provide a potential explanation for the association between mitochondrial dysfunction and septic shock on a genetic basis.
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Affiliation(s)
- Junsung Park
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eunju Kang
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seoon Kang
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Deokhoon Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dahyun Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seong Jong Park
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Won Kyoung Jhang
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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27
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Haupts A, Vogel A, Foersch S, Hartmann M, Maderer A, Wachter N, Huber T, Kneist W, Roth W, Lang H, Moehler M, Hartmann N. Comparative analysis of nuclear and mitochondrial DNA from tissue and liquid biopsies of colorectal cancer patients. Sci Rep 2021; 11:16745. [PMID: 34408162 PMCID: PMC8373949 DOI: 10.1038/s41598-021-95006-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/20/2021] [Indexed: 01/05/2023] Open
Abstract
The current standard for molecular profiling of colorectal cancer (CRC) is using resected or biopsied tissue specimens. However, they are limited regarding sampling frequency, representation of tumor heterogeneity, and sampling can expose patients to adverse side effects. The analysis of cell-free DNA (cfDNA) from blood plasma, which is part of a liquid biopsy, is minimally invasive and in principle enables detection of all tumor-specific mutations. Here, we analyzed cfDNA originating from nucleus and mitochondria and investigated their characteristics and mutation status in a cohort of 18 CRC patients and 10 healthy controls using targeted next-generation sequencing (NGS) and digital PCR. Longitudinal analyses of nuclear cfDNA level and size during chemotherapy revealed a decreasing cfDNA content and a shift from short to long fragments, indicating an appropriate therapy response, while shortened cfDNAs and increased cfDNA content corresponded with tumor recurrence. Comparative NGS analysis of nuclear tissue and plasma DNA demonstrated a good patient-level concordance and cfDNA revealed additional variants in three of the cases. Analysis of mitochondrial cfDNA surprisingly revealed a higher plasma copy number in healthy subjects than in CRC patients. These results highlight the potential clinical utility of liquid biopsies in routine diagnostics and surveillance of CRC patients as complementation to tissue biopsies or as an attractive alternative in cases where tissue biopsies are risky or the quantity/quality does not allow testing.
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Affiliation(s)
- Anna Haupts
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.
| | - Anne Vogel
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Sebastian Foersch
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Monika Hartmann
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Annett Maderer
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Nicolas Wachter
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Tobias Huber
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Werner Kneist
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.,Department of General and Visceral Surgery, St. Georg Hospital Eisenach gGmbH, Mühlhäuser Straße 94, 99817, Eisenach, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplantation Surgery, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Markus Moehler
- Department of Internal Medicine I, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center JGU Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.
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28
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Lin W, Chen S, Wang Y, Wang M, Lee WYW, Jiang X, Li G. Dynamic regulation of mitochondrial-endoplasmic reticulum crosstalk during stem cell homeostasis and aging. Cell Death Dis 2021; 12:794. [PMID: 34400615 PMCID: PMC8368094 DOI: 10.1038/s41419-021-03912-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/07/2023]
Abstract
Cellular therapy exerts profound therapeutic potential for curing a broad spectrum of diseases. Adult stem cells reside within a specified dynamic niche in vivo, which is essential for continuous tissue homeostatic maintenance through balancing self-renewal with lineage selection. Meanwhile, adult stem cells may be multipotent or unipotent, and are present in both quiescent and actively dividing states in vivo of the mammalians, which may switch to each other state in response to biophysical cues through mitochondria-mediated mechanisms, such as alterations in mitochondrial respiration and metabolism. In general, stem cells facilitate tissue repair after tissue-specific homing through various mechanisms, including immunomodulation of local microenvironment, differentiation into functional cells, cell "empowerment" via paracrine secretion, immunoregulation, and intercellular mitochondrial transfer. Interestingly, cell-source-specific features have been reported between different tissue-derived adult stem cells with distinct functional properties due to the different microenvironments in vivo, as well as differential functional properties in different tissue-derived stem cell-derived extracellular vehicles, mitochondrial metabolism, and mitochondrial transfer capacity. Here, we summarized the current understanding on roles of mitochondrial dynamics during stem cell homeostasis and aging, and lineage-specific differentiation. Also, we proposed potential unique mitochondrial molecular signature features between different source-derived stem cells and potential associations between stem cell aging and mitochondria-endoplasmic reticulum (ER) communication, as well as potential novel strategies for anti-aging intervention and healthy aging.
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Affiliation(s)
- Weiping Lin
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
- Stem Cells and Regenerative Medicine Laboratory, Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Shuxun Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, China
| | - Yan Wang
- Stem Cells and Regenerative Medicine Laboratory, Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ming Wang
- Stem Cells and Regenerative Medicine Laboratory, Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wayne Yuk-Wai Lee
- Stem Cells and Regenerative Medicine Laboratory, Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
- SH Ho Scoliosis Research Laboratory, Joint Scoliosis Research Center of the Chinese University of Hong Kong and Nanjing University, Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaohua Jiang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Faculty of Medicine, MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Gang Li
- Stem Cells and Regenerative Medicine Laboratory, Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
- Faculty of Medicine, MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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29
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Rosa H, Malik AN. Accurate Measurement of Cellular and Cell-Free Circulating Mitochondrial DNA Content from Human Blood Samples Using Real-Time Quantitative PCR. Methods Mol Biol 2021; 2277:247-268. [PMID: 34080155 DOI: 10.1007/978-1-0716-1270-5_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Changes in circulating mitochondrial DNA (mtDNA) are widely used to indicate mitochondrial dysfunction in common non-genetic diseases where mitochondrial dysfunction may play a role. However, the methodology being used is not always specific and reproducible, and most studies use whole blood rather than evaluating cellular and cell-free mtDNA separately. Cellular mtDNA is contained within the mitochondrion and encodes vital subunits of the OXPHOS machinery. Conversely, cell-free mtDNA can have harmful effects, triggering inflammatory responses and potentially contributing to pathogenic processes. In this chapter, we describe a protocol to accurately measure the amount of cellular and cell-free human mtDNA in peripheral blood. Absolute quantification is carried out using real-time quantitative PCR (qPCR) to quantify cellular mtDNA, measured as the mitochondrial genome to nuclear genome ratio (designated the Mt/N ratio) in whole blood and peripheral blood mononuclear cells (PBMCs) and the number of mtDNA copies per μL in plasma and serum. We describe how to (1) separate whole blood into PBMCs, plasma, and serum fractions, (2) prepare DNA from each of these fractions, (3) prepare dilution standards for absolute quantification, (4) carry out qPCR for either relative or absolute quantification from test samples, (5) analyze qPCR data, and (6) calculate the sample size to adequately power studies. The protocol presented here is suitable for high-throughput use and can be modified to quantify mtDNA from other body fluids, human cells, and tissues.
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Affiliation(s)
- Hannah Rosa
- Department of Diabetes, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King's College London, London, UK
| | - Afshan N Malik
- Department of Diabetes, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King's College London, London, UK.
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30
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Trumpff C, Michelson J, Lagranha CJ, Taleon V, Karan KR, Sturm G, Lindqvist D, Fernström J, Moser D, Kaufman BA, Picard M. Stress and circulating cell-free mitochondrial DNA: A systematic review of human studies, physiological considerations, and technical recommendations. Mitochondrion 2021; 59:225-245. [PMID: 33839318 PMCID: PMC8418815 DOI: 10.1016/j.mito.2021.04.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/23/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
Cell-free mitochondrial DNA (cf-mtDNA) is a marker of inflammatory disease and a predictor of mortality, but little is known about cf-mtDNA in relation to psychobiology. A systematic review of the literature reveals that blood cf-mtDNA varies in response to common real-world stressors including psychopathology, acute psychological stress, and exercise. Moreover, cf-mtDNA is inducible within minutes and exhibits high intra-individual day-to-day variation, highlighting the dynamic regulation of cf-mtDNA levels. We discuss current knowledge on the mechanisms of cf-mtDNA release, its forms of transport ("cell-free" does not mean "membrane-free"), potential physiological functions, putative cellular and neuroendocrine triggers, and factors that may contribute to cf-mtDNA removal from the circulation. A review of in vitro, pre-clinical, and clinical studies shows conflicting results around the dogma that physiological forms of cf-mtDNA are pro-inflammatory, opening the possibility of other physiological functions, including the cell-to-cell transfer of whole mitochondria. Finally, to enhance the reproducibility and biological interpretation of human cf-mtDNA research, we propose guidelines for blood collection, cf-mtDNA isolation, quantification, and reporting standards, which can promote concerted advances by the community. Defining the mechanistic basis for cf-mtDNA signaling is an opportunity to elucidate the role of mitochondria in brain-body interactions and psychopathology.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Jeremy Michelson
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Claudia J Lagranha
- University of Pittsburgh, School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, United States
| | - Veronica Taleon
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Kalpita R Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Daniel Lindqvist
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden; Office of Psychiatry and Habilitation, Region Skåne, Sweden
| | - Johan Fernström
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden
| | - Dirk Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - Brett A Kaufman
- University of Pittsburgh, School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, United States
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, USA; New York State Psychiatric Institute, NY, USA.
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31
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Cox DRA, Wong BKL, Yang L, Yoshino O, Testro A, Muralidharan V, Dobrovic A. High Speed Centrifugation Before Frozen Storage of Plasma Is Critical for Quantitative Analysis of Mitochondrial-Derived Cell-Free DNA. Clin Chem 2021; 66:1111-1114. [PMID: 32671378 DOI: 10.1093/clinchem/hvaa127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Daniel R A Cox
- Department of Surgery, The University of Melbourne, Heidelberg, Melbourne, Victoria, Australia.,HPB & Transplant Unit, Department of Surgery, Austin Hospital, Heidelberg, Melbourne, Victoria, Australia.,Translational Genomics and Epigenomics Laboratory, Departmentof Surgery, University of Melbourne, Austin Hospital, Heidelberg, Melbourne, Victoria, Australia
| | - Boris K L Wong
- Translational Genomics and Epigenomics Laboratory, Departmentof Surgery, University of Melbourne, Austin Hospital, Heidelberg, Melbourne, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Victoria, Australia
| | - Luija Yang
- Translational Genomics and Epigenomics Laboratory, Departmentof Surgery, University of Melbourne, Austin Hospital, Heidelberg, Melbourne, Victoria, Australia
| | - Osamu Yoshino
- Department of Surgery, The University of Melbourne, Heidelberg, Melbourne, Victoria, Australia.,HPB & Transplant Unit, Department of Surgery, Austin Hospital, Heidelberg, Melbourne, Victoria, Australia
| | - Adam Testro
- Liver Transplant Unit, Department of Gastroenterology & Hepatology, Austin Hospital, Heidelberg, Melbourne, Victoria, Australia
| | - Vijayaragavan Muralidharan
- Department of Surgery, The University of Melbourne, Heidelberg, Melbourne, Victoria, Australia.,HPB & Transplant Unit, Department of Surgery, Austin Hospital, Heidelberg, Melbourne, Victoria, Australia
| | - Alexander Dobrovic
- Department of Surgery, The University of Melbourne, Heidelberg, Melbourne, Victoria, Australia.,Translational Genomics and Epigenomics Laboratory, Departmentof Surgery, University of Melbourne, Austin Hospital, Heidelberg, Melbourne, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Victoria, Australia
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Cheng ML, Pectasides E, Hanna GJ, Parsons HA, Choudhury AD, Oxnard GR. Circulating tumor DNA in advanced solid tumors: Clinical relevance and future directions. CA Cancer J Clin 2021; 71:176-190. [PMID: 33165928 DOI: 10.3322/caac.21650] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/21/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
The application of genomic profiling assays using plasma circulating tumor DNA (ctDNA) is rapidly evolving in the management of patients with advanced solid tumors. Diverse plasma ctDNA technologies in both commercial and academic laboratories are in routine or emerging use. The increasing integration of such testing to inform treatment decision making by oncology clinicians has complexities and challenges but holds significant potential to substantially improve patient outcomes. In this review, the authors discuss the current role of plasma ctDNA assays in oncology care and provide an overview of ongoing research that may inform real-world clinical applications in the near future.
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Affiliation(s)
- Michael L Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Eirini Pectasides
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Glenn J Hanna
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey R Oxnard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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Santa P, Garreau A, Serpas L, Ferriere A, Blanco P, Soni C, Sisirak V. The Role of Nucleases and Nucleic Acid Editing Enzymes in the Regulation of Self-Nucleic Acid Sensing. Front Immunol 2021; 12:629922. [PMID: 33717156 PMCID: PMC7952454 DOI: 10.3389/fimmu.2021.629922] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of microbial nucleic acids by the innate immune system is mediated by numerous intracellular nucleic acids sensors. Upon the detection of nucleic acids these sensors induce the production of inflammatory cytokines, and thus play a crucial role in the activation of anti-microbial immunity. In addition to microbial genetic material, nucleic acid sensors can also recognize self-nucleic acids exposed extracellularly during turn-over of cells, inefficient efferocytosis, or intracellularly upon mislocalization. Safeguard mechanisms have evolved to dispose of such self-nucleic acids to impede the development of autoinflammatory and autoimmune responses. These safeguard mechanisms involve nucleases that are either specific to DNA (DNases) or RNA (RNases) as well as nucleic acid editing enzymes, whose biochemical properties, expression profiles, functions and mechanisms of action will be detailed in this review. Fully elucidating the role of these enzymes in degrading and/or processing of self-nucleic acids to thwart their immunostimulatory potential is of utmost importance to develop novel therapeutic strategies for patients affected by inflammatory and autoimmune diseases.
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Affiliation(s)
- Pauline Santa
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Anne Garreau
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | | | - Patrick Blanco
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
- Immunology and Immunogenetic Department, Bordeaux University Hospital, Bordeaux, France
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
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Kim HJ, Hamer GL, Hamer SA, Lopez JE, Teel PD. Identification of Host Bloodmeal Source in Ornithodoros turicata Dugès (Ixodida: Argasidae) Using DNA-Based and Stable Isotope-Based Techniques. Front Vet Sci 2021; 8:620441. [PMID: 33681326 PMCID: PMC7925843 DOI: 10.3389/fvets.2021.620441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/11/2021] [Indexed: 11/28/2022] Open
Abstract
The ecology and host feeding patterns of many soft ticks (Ixodida: Argasidae) remain poorly understood. To address soft tick-host feeding associations, we fed Ornithodoros turicata Dugès on multiple host species and evaluated quantitative PCR (qPCR) and stable isotope analyses to identify the vertebrate species used for the bloodmeal. The results showed that a qPCR with host-specific probes for the cytochrome b gene successfully identified bloodmeals from chicken (Gallus gallus L.), goat (Capra aegagrus hircus L), and swine (Sus scrofa domesticus) beyond 330 days post-feeding and through multiple molting. Also, qPCR-based bloodmeal analyses could detect multiple host species within individual ticks that fed upon more than one species. The stable isotope bloodmeal analyses were based on variation in the natural abundance of carbon (13C/12C) and nitrogen (15N/14N) isotopes in ticks fed on different hosts. When compared to reference isotope signatures, this method discerned unique δ13C and δ15N signatures in the ticks fed on each host taxa yet could not discern multiple host species from O. turicata that fed on more than one host species. Given the significance of soft tick-borne zoonoses and animal diseases, elucidating host feeding patterns from field-collected ticks using these methods may provide insight for an ecological basis to disease management.
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Affiliation(s)
- Hee J. Kim
- Department of Entomology, Texas A&M AgriLife Research, College Station, TX, United States
| | - Gabriel L. Hamer
- Department of Entomology, Texas A&M AgriLife Research, College Station, TX, United States
| | - Sarah A. Hamer
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Job E. Lopez
- Department of Pediatrics, Center for Tropical Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Pete D. Teel
- Department of Entomology, Texas A&M AgriLife Research, College Station, TX, United States
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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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Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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Brestoff JR, Wilen CB, Moley JR, Li Y, Zou W, Malvin NP, Rowen MN, Saunders BT, Ma H, Mack MR, Hykes BL, Balce DR, Orvedahl A, Williams JW, Rohatgi N, Wang X, McAllaster MR, Handley SA, Kim BS, Doench JG, Zinselmeyer BH, Diamond MS, Virgin HW, Gelman AE, Teitelbaum SL. Intercellular Mitochondria Transfer to Macrophages Regulates White Adipose Tissue Homeostasis and Is Impaired in Obesity. Cell Metab 2021; 33:270-282.e8. [PMID: 33278339 PMCID: PMC7858234 DOI: 10.1016/j.cmet.2020.11.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/03/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Recent studies suggest that mitochondria can be transferred between cells to support the survival of metabolically compromised cells. However, whether intercellular mitochondria transfer occurs in white adipose tissue (WAT) or regulates metabolic homeostasis in vivo remains unknown. We found that macrophages acquire mitochondria from neighboring adipocytes in vivo and that this process defines a transcriptionally distinct macrophage subpopulation. A genome-wide CRISPR-Cas9 knockout screen revealed that mitochondria uptake depends on heparan sulfates (HS). High-fat diet (HFD)-induced obese mice exhibit lower HS levels on WAT macrophages and decreased intercellular mitochondria transfer from adipocytes to macrophages. Deletion of the HS biosynthetic gene Ext1 in myeloid cells decreases mitochondria uptake by WAT macrophages, increases WAT mass, lowers energy expenditure, and exacerbates HFD-induced obesity in vivo. Collectively, this study suggests that adipocytes and macrophages employ intercellular mitochondria transfer as a mechanism of immunometabolic crosstalk that regulates metabolic homeostasis and is impaired in obesity.
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Affiliation(s)
- Jonathan R Brestoff
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Craig B Wilen
- Department of Laboratory Medicine and Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - John R Moley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yongjia Li
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wei Zou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole P Malvin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marina N Rowen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian T Saunders
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongming Ma
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Madison R Mack
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barry L Hykes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dale R Balce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Vir Biotechnology, San Francisco, CA 94158, USA
| | - Anthony Orvedahl
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jesse W Williams
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nidhi Rohatgi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyan Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R McAllaster
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian S Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bernd H Zinselmeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Vir Biotechnology, San Francisco, CA 94158, USA; Department of Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew E Gelman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven L Teitelbaum
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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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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Bronkhorst AJ, Ungerer V, Diehl F, Anker P, Dor Y, Fleischhacker M, Gahan PB, Hui L, Holdenrieder S, Thierry AR. Towards systematic nomenclature for cell-free DNA. Hum Genet 2020; 140:565-578. [PMID: 33123832 PMCID: PMC7981329 DOI: 10.1007/s00439-020-02227-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023]
Abstract
Cell-free DNA (cfDNA) has become widely recognized as a promising candidate biomarker for minimally invasive characterization of various genomic disorders and other clinical scenarios. However, among the obstacles that currently challenge the general progression of the research field, there remains an unmet need for unambiguous universal cfDNA nomenclature. To address this shortcoming, we classify in this report the different types of cfDNA molecules that occur in the human body based on its origin, genetic traits, and locality. We proceed by assigning existing terms to each of these cfDNA subtypes, while proposing new terms and abbreviations where clarity is lacking and more precise stratification would be beneficial. We then suggest the proper usage of these terms within different contexts and scenarios, focusing mainly on the nomenclature as it relates to the domains of oncology, prenatal testing, and post-transplant surgery surveillance. We hope that these recommendations will serve as useful considerations towards the establishment of universal cfDNA nomenclature in the future. In addition, it is conceivable that many of these recommendations can be transposed to cell-free RNA nomenclature by simply exchanging “DNA” with “RNA” in each acronym/abbreviation. Similarly, when describing DNA and RNA collectively, the suffix can be replaced with “NAs” to indicate nucleic acids.
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Affiliation(s)
- Abel J Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Frank Diehl
- Thrive Earlier Detection Corp., Cambridge, MA, USA
| | - Philippe Anker
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- University of Montpellier, Montpellier, France
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Michael Fleischhacker
- DRK Kliniken Berlin Mitte, Klinik für Innere Medizin, Pneumologie und Schlafmedizin, Drontheimer Str. 39-40, 13359, Berlin, Germany
| | - Peter B Gahan
- Fondazione "Enrico Puccinelli" Onlus, 06126, Perugia, Italy
| | - Lisa Hui
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, VIC, Australia
- Department of Obstetrics and Gynaecology, The Northern Hospital, Epping, VIC, Australia
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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Rappeneau V, Wilmes L, Touma C. Molecular correlates of mitochondrial dysfunctions in major depression: Evidence from clinical and rodent studies. Mol Cell Neurosci 2020; 109:103555. [PMID: 32979495 DOI: 10.1016/j.mcn.2020.103555] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/24/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
Major depressive disorder (MDD) is one of the most prevalent stress-related mental disorders worldwide. Several biological mechanisms underlying the pathophysiology of MDD have been proposed, including endocrine disturbances, neurotransmitter deficits, impaired neuronal plasticity, and more recently, mitochondrial dysfunctions. In this review, we provide an overview of relevant molecular correlates of mitochondrial dysfunction in MDD, based on findings from clinical studies and stress-induced rodent models. We also compare differences and similarities between the phenotypes of MDD patients and animal models. Our analysis of the literature reveals that both MDD and stress are associated, in humans and animals, with changes in mitochondrial biogenesis, redox imbalance, increased oxidative damages of cellular macromolecules, and apoptosis. Yet, a considerable amount of conflicting data exist and therefore, the translation of findings from clinical and preclinical research to novel therapies for MDD remains complex. Further studies are needed to advance our understanding of the molecular networks and biological mechanisms involving mitochondria in the pathophysiology of MDD.
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Affiliation(s)
- Virginie Rappeneau
- Department of Behavioural Biology, University of Osnabrück, Osnabrück, Germany.
| | - Lars Wilmes
- Department of Behavioural Biology, University of Osnabrück, Osnabrück, Germany
| | - Chadi Touma
- Department of Behavioural Biology, University of Osnabrück, Osnabrück, Germany
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Ware SA, Desai N, Lopez M, Leach D, Zhang Y, Giordano L, Nouraie M, Picard M, Kaufman BA. An automated, high-throughput methodology optimized for quantitative cell-free mitochondrial and nuclear DNA isolation from plasma. J Biol Chem 2020; 295:15677-15691. [PMID: 32900851 DOI: 10.1074/jbc.ra120.015237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/03/2020] [Indexed: 02/06/2023] Open
Abstract
Progress in the study of circulating, cell-free nuclear DNA (ccf-nDNA) in cancer detection has led to the development of noninvasive clinical diagnostic tests and has accelerated the evaluation of ccf-nDNA abundance as a disease biomarker. Likewise, circulating, cell-free mitochondrial DNA (ccf-mtDNA) is under similar investigation. However, optimal ccf-mtDNA isolation parameters have not been established, and inconsistent protocols for ccf-nDNA collection, storage, and analysis have hindered its clinical utility. Until now, no studies have established a method for high-throughput isolation that considers both ccf-nDNA and ccf-mtDNA. We initially optimized human plasma digestion and extraction conditions for maximal recovery of these DNAs using a magnetic bead-based isolation method. However, when we incorporated this method onto a high-throughput platform, initial experiments found that DNA isolated from identical human plasma samples displayed plate edge effects resulting in low ccf-mtDNA reproducibility, whereas ccf-nDNA was less affected. Therefore, we developed a detailed protocol optimized for both ccf-mtDNA and ccf-nDNA recovery that uses a magnetic bead-based isolation process on an automated 96-well platform. Overall, we calculate an improved efficiency of recovery of ∼95-fold for ccf-mtDNA and 20-fold for ccf-nDNA when compared with the initial procedure. Digestion conditions, liquid-handling characteristics, and magnetic particle processor programming all contributed to increased recovery without detectable positional effects. To our knowledge, this is the first high-throughput approach optimized for ccf-mtDNA and ccf-nDNA recovery and serves as an important starting point for clinical studies.
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Affiliation(s)
- Sarah A Ware
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nikita Desai
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mabel Lopez
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel Leach
- Optimize Laboratory Consultants, LLC, Lansdale, Pennsylvania, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Luca Giordano
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Martin Picard
- Division of Behavioral Medicine, Departments of Psychiatry and Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Brett A Kaufman
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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Blood Levels of Free-Circulating Mitochondrial DNA in Septic Shock and Postsurgical Systemic Inflammation and Its Influence on Coagulation: A Secondary Analysis of a Prospective Observational Study. J Clin Med 2020; 9:jcm9072056. [PMID: 32629885 PMCID: PMC7408641 DOI: 10.3390/jcm9072056] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/29/2022] Open
Abstract
Major surgery is regularly associated with clinical signs of systemic inflammation, which potentially affects the rapid identification of sepsis. Therefore, this secondary analysis of an observational study aims to determine whether NADH dehydrogenase 1 (ND1) mitochondrial DNA (mtDNA) could be used as a potential biomarker for the discrimination between septic shock and postsurgical systemic inflammation. Overall, 80 patients were included (septic shock (n = 20), cardiac artery bypass grafting (CABG, n = 20), major abdominal surgery (MAS, n = 20), and matched controls (CTRL, n = 20)). Quantitative PCR was performed to measure ND1 mtDNA. Thromboelastography was used to analyze the coagulatory system. Free-circulating ND1 mtDNA levels were significantly higher in septic shock patients compared to patients suffering from post-surgical inflammation ({copies/µL}: CTRL: 1208 (668-2685); septic shock: 3823 (2170-7318); CABG: 1272 (417-2720); and MAS: 1356 (694-2845); CTRL vs. septic shock: p < 0.001; septic shock vs. CABG: p < 0.001; septic shock vs. MAS: p = 0.006; CABG vs. MAS: p = 0.01). ND1 mtDNA levels in CABG patients showed a strong positive correlation with fibrinogen (correlation coefficient [r]= 0.57, p < 0.001) and fibrinogen-dependent thromboelastographic assays (maximum clot firmness, EXTEM: r = 0.35, p = 0.01; INTEM: r = 0.31, p = 0.02; FIBTEM: r = 0.46, p < 0.001). In conclusion, plasma levels of free-circulating ND1 mtDNA were increased in septic shock patients and were discriminative between sepsis and surgery-induced inflammation. Furthermore, this study showed an association between ND1 mtDNA and a fibrinogen-dependent pro-coagulatory shift in cardiac surgical patients.
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Morandi A, Zusi C, Corradi M, Takemoto K, Contreas G, Olivieri F, Fornari E, Maffeis C. Circulating mitochondrial DNA is decreased in children and adolescents with obesity and/or insulin resistance. Acta Diabetol 2020; 57:623-625. [PMID: 31953686 DOI: 10.1007/s00592-019-01471-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/23/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Anita Morandi
- Pediatric Diabetes and Metabolic Disorders Unit, University Hospital of Verona, Verona, Italy.
| | - Chiara Zusi
- Pediatric Diabetes and Metabolic Disorders Unit, University Hospital of Verona, Verona, Italy
| | - Massimiliano Corradi
- Pediatric Diabetes and Metabolic Disorders Unit, University Hospital of Verona, Verona, Italy
| | - Koji Takemoto
- Department of Pediatrics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Giovanna Contreas
- Pediatric Diabetes and Metabolic Disorders Unit, University Hospital of Verona, Verona, Italy
| | - Francesca Olivieri
- Pediatric Diabetes and Metabolic Disorders Unit, University Hospital of Verona, Verona, Italy
| | - Elena Fornari
- Pediatric Diabetes and Metabolic Disorders Unit, University Hospital of Verona, Verona, Italy
| | - Claudio Maffeis
- Pediatric Diabetes and Metabolic Disorders Unit, University Hospital of Verona, Verona, Italy
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Cancer epithelia-derived mitochondrial DNA is a targetable initiator of a paracrine signaling loop that confers taxane resistance. Proc Natl Acad Sci U S A 2020; 117:8515-8523. [PMID: 32238563 PMCID: PMC7165425 DOI: 10.1073/pnas.1910952117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The work provides a conceptual advance in functionally defining the cross talk of tumor epithelia with cancer-associated fibroblastic cells contributing to tumor progression and therapeutic resistance. Independent of protein-based signaling molecules, prostate cancer cells secreted mitochondrial DNA to induce associated fibroblasts to generate anaphylatoxin C3a to support tumor progression in a positive feedback loop. Interestingly, the standard of care chemotherapy, docetaxel, used to treat castrate-resistant prostate cancer was found to further potentiate this paracrine-signaling axis to mediate therapeutic resistance. Blocking anaphylatoxin C3a signaling cooperatively sensitized prostate cancer tumors to docetaxel. We reveal that docetaxel resistance is not a cancer cell-autonomous phenomena and that targeting an immune modulator derived from cancer-associated fibroblasts can limit the expansion of docetaxel-resistant tumors. Stromal-epithelial interactions dictate cancer progression and therapeutic response. Prostate cancer (PCa) cells were identified to secrete greater concentration of mitochondrial DNA (mtDNA) compared to noncancer epithelia. Based on the recognized coevolution of cancer-associated fibroblasts (CAF) with tumor progression, we tested the role of cancer-derived mtDNA in a mechanism of paracrine signaling. We found that prostatic CAF expressed DEC205, which was not expressed by normal tissue-associated fibroblasts. DEC205 is a transmembrane protein that bound mtDNA and contributed to pattern recognition by Toll-like receptor 9 (TLR9). Complement C3 was the dominant gene targeted by TLR9-induced NF-κB signaling in CAF. The subsequent maturation complement C3 maturation to anaphylatoxin C3a was dependent on PCa epithelial inhibition of catalase in CAF. In a syngeneic tissue recombination model of PCa and associated fibroblast, the antagonism of the C3a receptor and the fibroblastic knockout of TLR9 similarly resulted in immune suppression with a significant reduction in tumor progression, compared to saline-treated tumors associated with wild-type prostatic fibroblasts. Interestingly, docetaxel, a common therapy for advanced PCa, further promoted mtDNA secretion in cultured epithelia, mice, and PCa patients. The antiapoptotic signaling downstream of anaphylatoxin C3a signaling in tumor cells contributed to docetaxel resistance. The inhibition of C3a receptor sensitized PCa epithelia to docetaxel in a synergistic manner. Tumor models of human PCa epithelia with CAF expanded similarly in mice in the presence or absence of docetaxel. The combination therapy of docetaxel and C3 receptor antagonist disrupted the mtDNA/C3a paracrine loop and restored docetaxel sensitivity.
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Increased level of circulating cell-free mitochondrial DNA due to a single bout of strenuous physical exercise. Eur J Appl Physiol 2020; 120:897-905. [PMID: 32088743 PMCID: PMC7125245 DOI: 10.1007/s00421-020-04330-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/17/2020] [Indexed: 01/26/2023]
Abstract
Purpose Physical exercise is reported to affect the immune response in various ways. Thus, the levels of pro-inflammatory cytokines as well as the abundance of circulating leukocytes are changed. In this study, the occurence of circulating cell-free mitochondrial DNA (cfmtDNA) and nuclear DNA (nDNA) was investigated in connection with a single bout of strenuous physical exercise. Methods Healthy volunteers performed a controlled ergo-spirometry cycle test and venous blood samples were taken at different time-points to analyze the concentration of blood components before, during and after the test. The number of circulating leukocytes was measured, as well as secretion of the soluble urokinase activator receptor (suPAR). Results Cf-mtDNA significantly increased during exercise, compared to baseline values and after 30 and 90 min of rest. Circulating leukocytes increased during exercise, but returned to baseline levels afterwards. Surface expression of the urokinase plasminogen activating receptor (uPAR) on neutrophils decreased significantly during exercise. The concentration of suPAR tended to increase during exercise but only significantly after 90 min of rest. Conclusion Increased concentration of cf-mtDNA indicates that cell damage takes place during high intensity training. Hypoxia and tissue damage are likely causes of cf-mtDNA from muscle cells. The levels of cf-mtDNA remain high during the initial rest, due to the decreasing numbers of leukocytes normally clearing the plasma from cf-mtDNA. The increased levels of suPAR further emphasize that strenuous physical exercise causes a reaction similar to inflammation. Further studies are needed to detect the source of increased cf-mtDNA and the corresponding increase of suPAR liberation.
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Al Amir Dache Z, Otandault A, Tanos R, Pastor B, Meddeb R, Sanchez C, Arena G, Lasorsa L, Bennett A, Grange T, El Messaoudi S, Mazard T, Prevostel C, Thierry AR. Blood contains circulating cell-free respiratory competent mitochondria. FASEB J 2020; 34:3616-3630. [PMID: 31957088 DOI: 10.1096/fj.201901917rr] [Citation(s) in RCA: 220] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 11/11/2022]
Abstract
Mitochondria are considered as the power-generating units of the cell due to their key role in energy metabolism and cell signaling. However, mitochondrial components could be found in the extracellular space, as fragments or encapsulated in vesicles. In addition, this intact organelle has been recently reported to be released by platelets exclusively in specific conditions. Here, we demonstrate for the first time, that blood preparation with resting platelets, contains whole functional mitochondria in normal physiological state. Likewise, we show, that normal and tumor cultured cells are able to secrete their mitochondria. Using serial centrifugation or filtration followed by polymerase chain reaction-based methods, and Whole Genome Sequencing, we detect extracellular full-length mitochondrial DNA in particles over 0.22 µm holding specific mitochondrial membrane proteins. We identify these particles as intact cell-free mitochondria using fluorescence-activated cell sorting analysis, fluorescence microscopy, and transmission electron microscopy. Oxygen consumption analysis revealed that these mitochondria are respiratory competent. In view of previously described mitochondrial potential in intercellular transfer, this discovery could greatly widen the scope of cell-cell communication biology. Further steps should be developed to investigate the potential role of mitochondria as a signaling organelle outside the cell and to determine whether these circulating units could be relevant for early detection and prognosis of various diseases.
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Affiliation(s)
- Zahra Al Amir Dache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Amaëlle Otandault
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Rita Tanos
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Romain Meddeb
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Giuseppe Arena
- Gustave Roussy Cancer Campus, INSERM U1030, Villejuif, 94805, France
| | - Laurence Lasorsa
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Andrew Bennett
- Institut Jacques Monod, Université Paris Diderot, Paris, France
| | - Thierry Grange
- Institut Jacques Monod, Université Paris Diderot, Paris, France
| | - Safia El Messaoudi
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Thibault Mazard
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Corinne Prevostel
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
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van der Pol Y, Mouliere F. Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA. Cancer Cell 2019; 36:350-368. [PMID: 31614115 DOI: 10.1016/j.ccell.2019.09.003] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022]
Abstract
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic alterations, but only a minor fraction of tumor-derived cell-free DNA (cfDNA) fragments exhibit mutations. The cellular processes occurring in cancer development mark the chromatin. These epigenetic marks are reflected by modifications in the cfDNA methylation, fragment size, and structure. In this review, we describe how going beyond DNA sequence information alone, by analyzing cfDNA epigenetic and immune signatures, boosts the potential of liquid biopsy for the early detection of cancer.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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Wang HC, Lin YT, Hsu SY, Tsai NW, Lai YR, Su BYJ, Kung CT, Lu CH. Serial plasma DNA levels as predictors of outcome in patients with acute traumatic cervical spinal cord injury. J Transl Med 2019; 17:329. [PMID: 31570098 PMCID: PMC6771086 DOI: 10.1186/s12967-019-2084-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 09/23/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Acute traumatic cervical spinal cord injury (SCI) is a leading cause of disability in adolescents and young adults worldwide. Evidence from previous studies suggests that circulating cell-free DNA is associated with severity following acute injury. The present study determined whether plasma DNA levels in acute cervical SCI are predictive of outcome. METHODS In present study, serial plasma nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) levels were obtained from 44 patients with acute traumatic cervical SCI at five time points from day 1 to day 180 post-injury. Control blood samples were obtained from 66 volunteers. RESULTS Data showed a significant increase in plasma nDNA and mtDNA concentrations at admission in SCI patients compared to the control group. Plasma nDNA levels at admission, but not plasma mtDNA levels, were significantly associated with the Japanese Orthopaedic Association (JOA) score and Injury Severity Score in patients with acute traumatic cervical SCI. In patients with non-excellent outcomes, plasma nDNA increased significantly at days 1, 14 and 30 post-injury. Furthermore, its level at day 14 was independently associated with outcome. Higher plasma nDNA levels at the chosen cutoff point (> 45.6 ng/ml) predicted poorer outcome with a sensitivity of 78.9% and a specificity of 78.4%. CONCLUSIONS These results indicate JOA score performance and plasma nDNA levels reflect the severity of spinal cord injury. Therefore, the plasma nDNA assays can be considered as potential neuropathological markers in patients with acute traumatic cervical SCI.
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Affiliation(s)
- Hung-Chen Wang
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yu-Tsai Lin
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shih-Yuan Hsu
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Nai-Wen Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta Pei Road, Niao Sung Dist., Kaohsiung, Taiwan
| | - Yun-Ru Lai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta Pei Road, Niao Sung Dist., Kaohsiung, Taiwan
| | - Ben Yu-Jih Su
- Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Te Kung
- Department of Emergency Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Cheng-Hsien Lu
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta Pei Road, Niao Sung Dist., Kaohsiung, Taiwan. .,Department of Biological Science, National Sun Yat-Sen University, Kaohsiung, Taiwan. .,Department of Neurology, Xiamen Chang Gung Memorial Hospital, Xiamen, Fujian, China.
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Extracellular Mitochondrial DNA and N-Formyl Peptides in Trauma and Critical Illness: A Systematic Review. Crit Care Med 2019; 46:2018-2028. [PMID: 30113320 DOI: 10.1097/ccm.0000000000003381] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Extracellular mitochondrial DNA and N-formyl peptides released following tissue damage may contribute to systemic inflammation through stimulation of the innate immune system. In this review, we evaluate existing in vivo human data regarding a role for mitochondrial DNA and N-formyl peptides in producing systemic inflammation in trauma and critical illness, investigate the utility of these molecules in risk prediction and clinical decision support, and provide suggestions for standardization of future research. DATA SOURCES PubMed, Embase (1971-2017). STUDY SELECTION Studies measuring extracellular mitochondrial DNA and/or N-formyl peptides in acutely ill patients. DATA EXTRACTION Fifty-four studies were analyzed. Data extracted included article characteristics, methods, results, and performance in clinical prediction. DATA SYNTHESIS The most common patient types investigated were trauma (19 studies) and sepsis (eight). In studies comparing patient mitochondrial DNA or N-formyl peptide levels to healthy controls, 38 (90.5%) reported significantly elevated mitochondrial DNA levels in patients at first reported time point, as did the one study making this comparison for N-formyl peptides. Nine studies (81.8%) reported significantly elevated plasma/serum mitochondrial DNA levels in at least one time point in patients who developed inflammatory complications of their primary pathology compared with patients without inflammatory complications. For the ability of mitochondrial DNA to predict complications or outcomes, the area under the curve was 0.7 or greater in 84.6% of receiver operating characteristic curves, and 92.9% of odds, adjusted odds, risk, and hazard ratios were statistically significant. CONCLUSIONS Extracellular mitochondrial DNA levels are elevated early in patients' hospital courses in many acute illnesses and are higher in patients who develop inflammatory complications. Elevated mitochondrial DNA levels may be clinically useful in risk prediction and clinical decision support systems. Further research is needed to determine the role of extracellular N-formyl peptides in systemic inflammation and their possible clinical utility.
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50
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Ma MJL, Zhang H, Jiang P, Sin STK, Lam WKJ, Cheng SH, Lee WS, Gai W, Tse OYO, Peng W, Wong J, Raghupathy R, Wong RSM, Sahota D, Leung TY, Chan KCA, Chiu RWK, Lo YMD. Topologic Analysis of Plasma Mitochondrial DNA Reveals the Coexistence of Both Linear and Circular Molecules. Clin Chem 2019; 65:1161-1170. [PMID: 31263037 DOI: 10.1373/clinchem.2019.308122] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/21/2019] [Indexed: 12/31/2022]
Abstract
Abstract
BACKGROUND
Cellular mitochondrial DNA (mtDNA) is organized as circular, covalently closed and double-stranded DNA. Studies have demonstrated the presence of short mtDNA fragments in plasma. It is not known whether circular mtDNA might concurrently exist with linear mtDNA in plasma.
METHODS
We elucidated the topology of plasma mtDNA using restriction enzyme BfaI cleavage signatures on mtDNA fragment ends to differentiate linear and circular mtDNA. mtDNA fragments with both ends carrying BfaI cleavage signatures were defined as circular-derived mtDNA, whereas those with no cleavage signature or with 1 cleavage signature were defined as linear-derived mtDNA. An independent assay using exonuclease V to remove linear DNA followed by restriction enzyme MspI digestion was used for confirming the conclusions based on BfaI cleavage analysis. We analyzed the presence of BfaI cleavage signatures on plasma DNA ends in nonhematopoietically and hematopoietically derived DNA molecules by sequencing plasma DNA of patients with liver transplantation and bone marrow transplantation.
RESULTS
Both linear and circular mtDNA coexisted in plasma. In patients with liver transplantation, donor-derived (i.e., liver) mtDNA molecules were mainly linear (median fraction, 91%; range, 75%–97%), whereas recipient-derived (i.e., hematopoietic) mtDNA molecules were mainly circular (median fraction, 88%; range, 77%–93%). The proportion of linear mtDNA was well correlated with liver DNA contribution in the plasma DNA pool (r = 0.83; P value = 0.0008). Consistent data were obtained from a bone marrow transplantation recipient in whom the donor-derived (i.e., hematopoietic) mtDNA molecules were predominantly circular.
CONCLUSIONS
Linear and circular mtDNA molecules coexist in plasma and may have different tissue origins.
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Affiliation(s)
- Mary-Jane L Ma
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Haiqiang Zhang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Sarah T K Sin
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wai Kei Jacky Lam
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Suk Hang Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wing-Shan Lee
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wanxia Gai
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - O Y Olivia Tse
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wenlei Peng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Radha Raghupathy
- Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Raymond S M Wong
- Sir Y.K. Pao Centre for Cancer and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong SAR, China
| | - Daljit Sahota
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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