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Kudriavtsev A, Pastor B, Mirandola A, Pisareva E, Gricourt Y, Capdevila X, Thierry AR, Cuvillon P. Association of the immediate perioperative dynamics of circulating DNA levels and neutrophil extracellular traps formation in cancer patients. Precis Clin Med 2024; 7:pbae008. [PMID: 38699382 PMCID: PMC11062027 DOI: 10.1093/pcmedi/pbae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 05/05/2024] Open
Abstract
Objectives Elevated circulating DNA (cirDNA) concentrations were found to be associated with trauma or tissue damage which suggests involvement of inflammation or cell death in post-operative cirDNA release. We carried out the first prospective, multicenter study of the dynamics of cirDNA and neutrophil extracellular trap (NETs) markers during the perioperative period from 24 h before surgery up to 72 h after curative surgery in cancer patients. Methods We examined the plasma levels of two NETs protein markers [myeloperoxidase (MPO) and neutrophil elastase (NE)], as well as levels of cirDNA of nuclear (cir-nDNA) and mitochondrial (cir-mtDNA) origin in 29 colon, prostate, and breast cancer patients and in 114 healthy individuals (HI). Results The synergistic analytical information provided by these markers revealed that: (i) NETs formation contributes to post-surgery conditions; (ii) post-surgery cir-nDNA levels were highly associated with NE and MPO in colon cancer [r = 0.60 (P < 0.001) and r = 0.53 (P < 0.01), respectively], but not in prostate and breast cancer; (iii) each tumor type shows a specific pattern of cir-nDNA and NETs marker dynamics, but overall the pre- and post-surgery median values of cir-nDNA, NE, and MPO were significantly higher in cancer patients than in HI. Conclusion Taken as a whole, our work reveals the association of NETs formation with the elevated cir-nDNA release during a cancer patient's perioperative period, depending on surgical procedure or cancer type. By contrast, cir-mtDNA is poorly associated with NETs formation in the studied perioperative period, which would appear to indicate a different mechanism of release or suggest mitochondrial dysfunction.
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Affiliation(s)
- Andrei Kudriavtsev
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Brice Pastor
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
- Institut régional du Cancer de Montpellier, Montpellier 34298, France
| | - Alexia Mirandola
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Ekaterina Pisareva
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
| | - Yann Gricourt
- Department of Anaesthesiology and Pain Management, Centre Hospitalo-Universitaire (CHU) Carémeau, Place du Professeur Debré,Nîmes 30400, France
- University of Montpellier, Montpellier 34298, France
| | - Xavier Capdevila
- Division of Anaesthesia Intensive Care, Pain and Emergency Medicine, Montpellier University Hospital, Montpellier 34090, France
- Montpellier NeuroSciences Institute, INSERM U1298, University of Montpellier, Montpellier 34295, France
| | - Alain R Thierry
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier 34298, France
- Institut régional du Cancer de Montpellier, Montpellier 34298, France
| | - Philippe Cuvillon
- Department of Anaesthesiology and Pain Management, Centre Hospitalo-Universitaire (CHU) Carémeau, Place du Professeur Debré,Nîmes 30400, France
- University of Montpellier, Montpellier 34298, France
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Thierry AR. NETosis creates a link between diabetes and Long COVID. Physiol Rev 2024; 104:651-654. [PMID: 37855816 DOI: 10.1152/physrev.00032.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023] Open
Affiliation(s)
- Alain R Thierry
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, Montpellier, France
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3
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Cristol JP, Thierry AR, Bargnoux AS, Morena-Carrere M, Canaud B. Corrigendum: What is the role of the neutrophil extracellular traps in the cardiovascular disease burden associated with hemodialysis bioincompatibility? Front Med (Lausanne) 2024; 11:1393023. [PMID: 38533319 PMCID: PMC10964985 DOI: 10.3389/fmed.2024.1393023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fmed.2023.1268748.].
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Affiliation(s)
- Jean-Paul Cristol
- PhyMedExp, University of Montpellier, INSERM, CNRS, Department of Biochemistry and Hormonology, University Hospital Center of Montpellier, Montpellier, France
- Charles Mion Foundation, AIDER-Santé, Montpellier, France
| | - Alain R. Thierry
- Research Institute of Cancerology of Montpellier, INSERM, IRCM, ICM, University of Montpellier, Montpellier, France
| | - Anne-Sophie Bargnoux
- PhyMedExp, University of Montpellier, INSERM, CNRS, Department of Biochemistry and Hormonology, University Hospital Center of Montpellier, Montpellier, France
| | - Marion Morena-Carrere
- PhyMedExp, University of Montpellier, INSERM, CNRS, Department of Biochemistry and Hormonology, University Hospital Center of Montpellier, Montpellier, France
| | - Bernard Canaud
- School of Medicine, University of Montpellier, Montpellier, France
- MTX Consulting Int., Montpellier, France
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4
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Phillips D, Noble D. Reply from Daniel Phillips and Denis Noble. J Physiol 2024. [PMID: 38305416 DOI: 10.1113/jp286224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Affiliation(s)
- Daniel Phillips
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shefer A, Tutanov O, Belenikin M, Tsentalovich YP, Tamkovich S. Blood Plasma Circulating DNA-Protein Complexes: Involvement in Carcinogenesis and Prospects for Liquid Biopsy of Breast Cancer. J Pers Med 2023; 13:1691. [PMID: 38138918 PMCID: PMC10744380 DOI: 10.3390/jpm13121691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Circulating DNA (cirDNA) is a promising tool in translational medicine. However, studies of cirDNA have neglected its association with proteins, despite ample evidence that this interaction may affect the fate of DNA in the bloodstream and its molecular functions. The goal of the current study is to shed light on the differences between the proteomic cargos of histone-containing nucleoprotein complexes (NPCs) from healthy female (HFs) and breast cancer patients (BCPs), and to reveal the proteins involved in carcinogenesis. NPCs were isolated from the blood samples of HFs and BCPs using affinity chromatography. A total of 177 and 169 proteins were identified in NPCs from HFs and BCPs using MALDI-TOF mass spectrometry. A bioinformatics analysis revealed that catalytically active proteins, as well as proteins that bind nucleic acids and regulate the activity of receptors, are the most represented among the unique proteins of blood NPCs from HFs and BCPs. In addition, the proportion of proteins participating in ion channels and proteins binding proteins increases in the NPCs from BCP blood. However, the involvement in transport and signal transduction was greater in BCP NPCs compared to those from HFs. Gene ontology term (GO) analysis revealed that the NPC protein cargo from HF blood was enriched with proteins involved in the negative regulation of cell proliferation, and in BCP blood, proteins involved in EMT, invasion, and cell migration were observed. The combination of SPG7, ADRB1, SMCO4, PHF1, and PSMG1 NPC proteins differentiates BCPs from HFs with a sensitivity of 100% and a specificity of 80%. The obtained results indirectly indicate that, in tandem with proteins, blood cirDNA is an important part of intercellular communication, playing a regulatory and integrating role in the physiology of the body.
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Affiliation(s)
- Aleksei Shefer
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Oleg Tutanov
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA;
| | | | - Yuri P. Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
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7
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Cristol JP, Thierry AR, Bargnoux AS, Morena-Carrere M, Canaud B. What is the role of the neutrophil extracellular traps in the cardiovascular disease burden associated with hemodialysis bioincompatibility? Front Med (Lausanne) 2023; 10:1268748. [PMID: 38034546 PMCID: PMC10684960 DOI: 10.3389/fmed.2023.1268748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023] Open
Abstract
Despite significant progress in dialysis modalities, intermittent renal replacement therapy remains an "unphysiological" treatment that imperfectly corrects uremic disorders and may lead to low-grade chronic inflammation, neutrophil activation, and oxidative stress due to repetitive blood/membrane interactions contributing to the "remaining uremic syndrome" and cardiovascular disease burden of hemodialysis patients. Understanding dialysis bioincompatibility pathways still remains a clinical and biochemical challenge. Indeed, surrogate biomarkers of inflammation including C-reactive protein could not discriminate between all components involved in these complex pathways. A few examples may serve to illustrate the case. Cytokine release during dialysis sessions may be underestimated due to their removal using high-flux dialysis or hemodiafiltration modalities. Complement activation is recognized as a key event of bioincompatibility. However, it appears as an early and transient event with anaphylatoxin level normalization at the end of the dialysis session. Complement activation is generally assumed to trigger leukocyte stimulation leading to proinflammatory mediators' secretion and oxidative burst. In addition to being part of the innate immune response involved in eliminating physically and enzymatically microbes, the formation of Neutrophil Extracellular Traps (NETs), known as NETosis, has been recently identified as a major harmful component in a wide range of pathologies associated with inflammatory processes. NETs result from the neutrophil degranulation induced by reactive oxygen species overproduction via NADPH oxidase and consist of modified chromatin decorated with serine proteases, elastase, bactericidal proteins, and myeloperoxidase (MPO) that produces hypochlorite anion. Currently, NETosis remains poorly investigated as a sensitive and integrated marker of bioincompatibility in dialysis. Only scarce data could be found in the literature. Oxidative burst and NADPH oxidase activation are well-known events in the bioincompatibility phenomenon. NET byproducts such as elastase, MPO, and circulating DNA have been reported to be increased in dialysis patients more specifically during dialysis sessions, and were identified as predictors of poor outcomes. As NETs and MPO could be taken up by endothelium, NETs could be considered as a vascular memory of intermittent bioincompatibility phenomenon. In this working hypothesis article, we summarized the puzzle pieces showing the involvement of NET formation during hemodialysis and postulated that NETosis may act as a disease modifier and may contribute to the comorbid burden associated with dialysis bioincompatibility.
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Affiliation(s)
- Jean-Paul Cristol
- PhyMedExp, University of Montpellier, INSERM, CNRS, Department of Biochemistry and Hormonology, University Hospital Center of Montpellier, Montpellier, France
- Charles Mion Foundation, AIDER-Santé, Montpellier, France
| | - Alain R. Thierry
- Research Institute of Cancerology of Montpellier, INSERM, IRCM, ICM, University of Montpellier, Montpellier, France
| | - Anne-Sophie Bargnoux
- PhyMedExp, University of Montpellier, INSERM, CNRS, Department of Biochemistry and Hormonology, University Hospital Center of Montpellier, Montpellier, France
| | - Marion Morena-Carrere
- PhyMedExp, University of Montpellier, INSERM, CNRS, Department of Biochemistry and Hormonology, University Hospital Center of Montpellier, Montpellier, France
| | - Bernard Canaud
- School of Medicine, University of Montpellier, Montpellier, France
- MTX Consulting Int., Montpellier, France
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8
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Rosenberg S, Ben Cohen G, Kato S, Okamura R, Lippman SM, Kurzrock R. Concordance between cancer gene alterations in tumor and circulating tumor DNA correlates with poor survival in a real-world precision-medicine population. Mol Oncol 2023; 17:1844-1856. [PMID: 36694946 PMCID: PMC10483598 DOI: 10.1002/1878-0261.13383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/01/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Genomic analysis, performed on tumoral tissue DNA and on circulating tumor DNA (ctDNA) from blood, is the cornerstone of precision cancer medicine. Herein, we characterized the clinical prognostic implications of the concordance of alterations in major cancer genes between tissue- and blood-derived DNA in a pan-cancer cohort. The molecular profiles of both liquid (Guardant Health) and tissue (Foundation Medicine) biopsies from 433 patients were analyzed. Mutations and amplifications of cancer genes scored by these two tests were assessed. In 184 (42.5%) patients, there was at least one mutual gene alteration. The mean number of mutual gene-level alterations in the samples was 0.67 per patient (range: 0-5). A higher mutual gene-level alteration number correlated with shorter overall survival (OS). As confirmed in multivariable analysis, patients with ≥2 mutual gene-level alterations in blood and tissue had a hazard ratio (HR) of death of 1.49 (95% confidence interval [CI]=1-2.2; P=0.047), whereas patients with ≥3 mutual gene-level alterations had an HR of death 2.38 (95% CI=1.47-3.87; P=0.0005). Together, our results show that gene-level concordance between tissue DNA and ctDNA analysis is prevalent and is an independent factor predicting significantly shorter patient survival.
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Affiliation(s)
- Shai Rosenberg
- Gaffin Center for Neuro‐Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of MedicineHebrew University of JerusalemIsrael
- The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of MedicineHebrew University of JerusalemIsrael
| | - Gil Ben Cohen
- Gaffin Center for Neuro‐Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of MedicineHebrew University of JerusalemIsrael
- The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of MedicineHebrew University of JerusalemIsrael
| | - Shumei Kato
- Center for Personalized Cancer Therapy, Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
| | | | - Scott M. Lippman
- Center for Personalized Cancer Therapy, Moores Cancer CenterUniversity of California San DiegoLa JollaCAUSA
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Priyadharsini JV. Potential role of circulating bacterial DNA as diagnostic indicator of oral cancer. Future Microbiol 2023; 18:695-697. [PMID: 37477522 DOI: 10.2217/fmb-2022-0253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Affiliation(s)
- Jayaseelan Vijayashree Priyadharsini
- Clinical Genetics Lab, Center for Cellular & Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai, 600077, India
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Bryan SJ, Lee J, Gunu R, Jones A, Olaitan A, Rosenthal AN, Cutts RJ, Garcia-Murillas I, Turner N, Lalondrelle S, Bhide SA. Circulating HPV DNA as a Biomarker for Pre-Invasive and Early Invasive Cervical Cancer: A Feasibility Study. Cancers (Basel) 2023; 15:cancers15092590. [PMID: 37174056 PMCID: PMC10177194 DOI: 10.3390/cancers15092590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/29/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND High-risk HPV infection is responsible for >99% of cervix cancers (CC). In persistent infections that lead to cancer, the tumour breaches the basement membrane, releasing HPV-DNA into the bloodstream (cHPV-DNA). A next-generation sequencing assay (NGS) for detection of plasma HPV circulating DNA (cHPV-DNA) has demonstrated high sensitivity and specificity in patients with locally advanced cervix cancers. We hypothesised that cHPV-DNA is detectable in early invasive cervical cancers but not in pre-invasive lesions (CIN). METHODS Blood samples were collected from patients with CIN (n = 52) and FIGO stage 1A-1B CC (n = 12) prior to treatment and at follow-up. DNA extraction from plasma, followed by NGS, was used for the detection of cHPV-DNA. RESULTS None of the patients with pre-invasive lesions were positive for CHPV-DNA. In invasive tumours, plasma from one patient (10%) reached the threshold of positivity for cHPV-DNA in plasma. CONCLUSION Low detection of cHPV-DNA in early CC may be explained by small tumour size, poorer access to lymphatics and circulation, and therefore little shedding of cHPV-DNA in plasma at detectable levels. The detection rate of cHPV-DNA in patients with early invasive cervix cancer using even the most sensitive of currently available technologies lacks adequate sensitivity for clinical utility.
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Affiliation(s)
- Stacey J Bryan
- UCL Elizabeth Garrett Anderson Institute for Women's Health, Faculty of Population Health Sciences, University College London, Medical School Building, 74 Huntley Street, London WC1E 6AU, UK
| | - Jen Lee
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
| | - Richard Gunu
- Translational Research Lab, Department of Women's Cancer, IfWH, Ground Floor POGB, 72 Huntley Street, London WC1E 6DD, UK
| | - Allison Jones
- Translational Research Lab, Department of Women's Cancer, IfWH, Ground Floor POGB, 72 Huntley Street, London WC1E 6DD, UK
| | - Adeola Olaitan
- UCL Elizabeth Garrett Anderson Institute for Women's Health, Faculty of Population Health Sciences, University College London, Medical School Building, 74 Huntley Street, London WC1E 6AU, UK
| | - Adam N Rosenthal
- UCL Elizabeth Garrett Anderson Institute for Women's Health, Faculty of Population Health Sciences, University College London, Medical School Building, 74 Huntley Street, London WC1E 6AU, UK
| | - Ros J Cutts
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
| | - Isaac Garcia-Murillas
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
| | - Nick Turner
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
| | | | - Shreerang A Bhide
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
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Tutanov O, Shefer A, Tsentalovich Y, Tamkovich S. Comparative Analysis of Molecular Functions and Biological Role of Proteins from Cell-Free DNA-Protein Complexes Circulating in Plasma of Healthy Females and Breast Cancer Patients. Int J Mol Sci 2023; 24:ijms24087279. [PMID: 37108441 PMCID: PMC10138639 DOI: 10.3390/ijms24087279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Cell-free DNA (cfDNA) circulates in the bloodstream packed in membrane-coated structures (such as apoptotic bodies) or bound to proteins. To identify proteins involved in the formation of deoxyribonucleoprotein complexes circulating in the blood, native complexes were isolated using affinity chromatography with immobilized polyclonal anti-histone antibodies from plasma of healthy females (HFs) and breast cancer patients (BCPs). It was found that the nucleoprotein complexes (NPCs) from HF plasma samples contained shorter DNA fragments (~180 bp) than BCP NPCs. However, the share of DNA in the NPCs from cfDNA in blood plasma in HFs and BCPs did not differ significantly, as well as the share of NPC protein from blood plasma total protein. Proteins were separated by SDS-PAGE and identified by MALDI-TOF mass spectrometry. Bioinformatic analysis showed that in the presence of a malignant tumor, the proportion of proteins involved in ion channels, protein binding, transport, and signal transduction increased in the composition of blood-circulating NPCs. Moreover, 58 (35%) proteins are differentially expressed in a number of malignant neoplasms in the NPCs of BCPs. Identified NPC proteins from BCP blood can be recommended for further testing as breast cancer diagnostic/prognostic biomarkers or as being useful in developing gene-targeted therapy approaches.
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Affiliation(s)
- Oleg Tutanov
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksei Shefer
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Yuri Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
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13
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Lalondrelle S, Lee J, Cutts RJ, Garcia Murillas I, Matthews N, Turner N, Harrington K, Vroobel K, Moretti E, Bhide SA. Predicting Response to Radical Chemoradiotherapy with Circulating HPV DNA (cHPV-DNA) in Locally Advanced Uterine Cervix Cancer. Cancers (Basel) 2023; 15:1387. [PMID: 36900180 PMCID: PMC10000151 DOI: 10.3390/cancers15051387] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND The majority of locally advanced cervical cancers (LaCC) are causally related to HPV. We sought to investigate the utility of an ultra-sensitive HPV-DNA next generation sequencing (NGS) assay-panHPV-detect-in LaCC treated with chemoradiotherapy, as a marker of treatment response and persistent disease. METHOD Serial blood samples were collected from 22 patients with LaCC before, during and after chemoradiation. The presence of circulating HPV-DNA was correlated with clinical and radiological outcomes. RESULTS The panHPV-detect test demonstrated a sensitivity and specificity of 88% (95% CI-70-99%) and 100% (95% CI-30-100%), respectively, and correctly identified the HPV-subtype (16, 18, 45, 58). After a median follow up of 16 months, and three relapses all had detectable cHPV-DNA at 3 months post-CRT despite complete response on imaging. Another four patients with radiological partial or equivocal response and undetectable cHPV-DNA at the 3-month time point did not go on to develop relapse. All patients with radiological CR and undetectable cHPV-DNA at 3-months remained disease free. CONCLUSIONS These results demonstrate that the panHPV-detect test shows high sensitivity and specificity for detecting cHPV-DNA in plasma. The test has potential applications in assessment of the response to CRT and in monitoring for relapse, and these initial findings warrant validation in a larger cohort.
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Affiliation(s)
- Susan Lalondrelle
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
- The Royal Marsden Hospital, Downs Road, Sutton SM2 5PT, UK
| | - Jen Lee
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | | | | | - Nik Matthews
- Imperial College London, South Kengsington Campus, SW7 2AZ, UK
| | - Nicholas Turner
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
- The Royal Marsden Hospital, Downs Road, Sutton SM2 5PT, UK
| | - Kevin Harrington
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
- The Royal Marsden Hospital, Downs Road, Sutton SM2 5PT, UK
| | - Katherine Vroobel
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
- The Royal Marsden Hospital, Downs Road, Sutton SM2 5PT, UK
| | - Emily Moretti
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
- The Royal Marsden Hospital, Downs Road, Sutton SM2 5PT, UK
| | - Shreerang A. Bhide
- The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
- The Royal Marsden Hospital, Fulham Road, London SW3 6JJ, UK
- The Royal Marsden Hospital, Downs Road, Sutton SM2 5PT, UK
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14
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Thierry A. Circulating DNA fragmentomics and cancer screening. Cell Genom 2023; 3:100242. [PMID: 36777187 PMCID: PMC9903826 DOI: 10.1016/j.xgen.2022.100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The high fragmentation of nuclear circulating DNA (cirDNA) relies on chromatin organization and protection or packaging within mononucleosomes, the smallest and the most stabilized structure in the bloodstream. The detection of differing size patterns, termed fragmentomics, exploits information about the nucleosomal packing of DNA. Fragmentomics not only implies size pattern characterization but also considers the positioning and occupancy of nucleosomes, which result in cirDNA fragments being protected and persisting in the circulation. Fragmentomics can determine tissue of origin and distinguish cancer-derived cirDNA. The screening power of fragmentomics has been considerably strengthened in the omics era, as shown in the ongoing development of sophisticated technologies assisted by machine learning. Fragmentomics can thus be regarded as a strategy for characterizing cancer within individuals and offers an alternative or a synergistic supplement to mutation searches, methylation, or nucleosome positioning. As such, it offers potential for improving diagnostics and cancer screening.
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Affiliation(s)
- A.R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, and ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France,Corresponding author
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Pisareva E, Badiou S, Mihalovičová L, Mirandola A, Pastor B, Kudriavtsev A, Berger M, Roubille C, Fesler P, Klouche K, Cristol J, Thierry AR. Persistence of neutrophil extracellular traps and anticardiolipin auto-antibodies in post-acute phase COVID-19 patients. J Med Virol 2023; 95:e28209. [PMID: 36226380 PMCID: PMC9874393 DOI: 10.1002/jmv.28209] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Accepted: 10/03/2022] [Indexed: 01/27/2023]
Abstract
In the early phase of the pandemic, we were among the first to postulate that neutrophil extracellular traps (NETs) play a key role in COVID-19 pathogenesis. This exploratory prospective study based on 279 individuals showed that plasma levels of neutrophil elastase, myeloperoxidase and circulating DNA of nuclear and mitochondrial origins in nonsevere (NS), severe (S) and postacute phase (PAP) COVID-19 patients were statistically different as compared to the levels in healthy individuals, and revealed the high diagnostic power of these NETs markers in respect to the disease severity. The diagnostic power of NE, MPO, and cir-nDNA as determined by the Area Under Receiver Operating Curves (AUROC) was 0.95, 097, and 0.64; 0.99, 1.0, and 0.82; and 0.94, 1.0, and 0.93, in NS, S, and PAP patient subgroups, respectively. In addition, a significant fraction of NS, S as well as of PAP patients exhibited aCL IgM/IgG and anti-B2GP IgM/IgG positivity. We first demonstrate persistence of these NETs markers in PAP patients and consequently of sustained innate immune response imbalance, and a prolonged low-level pro-thrombotic potential activity highlighting the need to monitor these markers in all COVID-19 PAP individuals, to investigate postacute COVID-19 pathogenesis following intensive care, and to better identify which medical resources will ensure complete patient recovery.
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Affiliation(s)
- Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Institut Régional du Cancer de MontpellierUniversité de MontpellierMontpellierFrance
| | - Stephanie Badiou
- Department of Biochemistry and Hormonology, INSERM, CNRS, University Hospital Center of MontpellierUniversity of Montpellier, PhyMedExpMontpellierFrance
| | - Lucia Mihalovičová
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Institut Régional du Cancer de MontpellierUniversité de MontpellierMontpellierFrance
- Faculty of Medicine, Institute of Molecular BiomedicineComenius UniversityBratislavaSlovakia
| | - Alexia Mirandola
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Institut Régional du Cancer de MontpellierUniversité de MontpellierMontpellierFrance
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Institut Régional du Cancer de MontpellierUniversité de MontpellierMontpellierFrance
| | - Andrei Kudriavtsev
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Institut Régional du Cancer de MontpellierUniversité de MontpellierMontpellierFrance
| | - Marie Berger
- Department of Internal Medicine, INSERM U1046, CNRS, Montpellier University Hospital, Montpellier, PhyMedExpUniversity of MontpellierMontpellierFrance
| | - Camille Roubille
- Department of Internal Medicine, INSERM U1046, CNRS, Montpellier University Hospital, Montpellier, PhyMedExpUniversity of MontpellierMontpellierFrance
| | - Pierre Fesler
- Department of Internal Medicine, INSERM U1046, CNRS, Montpellier University Hospital, Montpellier, PhyMedExpUniversity of MontpellierMontpellierFrance
| | - Kada Klouche
- Intensive Care Medicine Department, INSERM, CNRS, Lapeyronie HospitalUniversity Hospital of Montpellier, France, and PhyMedExp, University of MontpellierMontpellierFrance
| | - Jean‐Paul Cristol
- Department of Biochemistry and Hormonology, INSERM, CNRS, University Hospital Center of MontpellierUniversity of Montpellier, PhyMedExpMontpellierFrance
| | - Alain R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Institut Régional du Cancer de MontpellierUniversité de MontpellierMontpellierFrance
- Montpellier Cancer Institute (ICM)MontpellierFrance
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17
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Park MA, Zaw T, Yoder SJ, Gomez M, Genilo-Delgado M, Basinski T, Katende E, Dam A, Mok SRS, Monteiro A, Mohammadi A, Jeong DK, Jiang K, Centeno BA, Hodul P, Malafa M, Fleming J, Chen DT, Mo Q, Teer JK, Permuth JB. A pilot study to evaluate tissue- and plasma-based DNA driver mutations in a cohort of patients with pancreatic intraductal papillary mucinous neoplasms. G3 (Bethesda) 2022; 13:6861874. [PMID: 36454217 PMCID: PMC9911050 DOI: 10.1093/g3journal/jkac314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/22/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
Intraductal papillary mucinous neoplasms (IPMNs) are precursor lesions to pancreatic ductal adenocarcinoma that are challenging to manage due to limited imaging, cytologic, and molecular markers that accurately classify lesions, grade of dysplasia, or focus of invasion preoperatively. The objective of this pilot study was to determine the frequency and type of DNA mutations in a cohort of surgically resected, pathologically confirmed IPMN, and to determine if concordant mutations are detectable in paired pretreatment plasma samples. Formalin-fixed paraffin-embedded (FFPE) tissue from 46 surgically resected IPMNs (31 low-grade, 15 high-grade) and paired plasma from a subset of 15 IPMN cases (10 low-grade, 5 high-grade) were subjected to targeted mutation analysis using a QIAseq Targeted DNA Custom Panel. Common driver mutations were detected in FFPE from 44 of 46 (95.6%) IPMN cases spanning all grades; the most common DNA mutations included: KRAS (80%), RNF43 (24%), and GNAS (43%). Of note, we observed a significant increase in the frequency of RNF43 mutations from low-grade to high-grade IPMNs associated or concomitant with invasive carcinoma (trend test, P = 0.01). Among the subset of cases with paired plasma, driver mutations identified in the IPMNs were not detected in circulation. Overall, our results indicate that mutational burden for IPMNs is a common occurrence, even in low-grade IPMNs. Furthermore, although blood-based biopsies are an attractive, noninvasive method for detecting somatic DNA mutations, the QIAseq panel was not sensitive enough to detect driver mutations that existed in IPMN tissue using paired plasma in the volume we were able to retrieve for this retrospective study.
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Affiliation(s)
| | | | - Sean J Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Maria Gomez
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Maria Genilo-Delgado
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Toni Basinski
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Esther Katende
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Aamir Dam
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Shaffer R S Mok
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Alvaro Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Amir Mohammadi
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Daniel K Jeong
- Department of Diagnostic Imaging and Interventional Radiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Kun Jiang
- Department of Anatomic Pathology, H. Lee Moffitt Cancer & Research Institute, Tampa, FL 33620, USA
| | - Barbara A Centeno
- Department of Anatomic Pathology, H. Lee Moffitt Cancer & Research Institute, Tampa, FL 33620, USA
| | - Pamela Hodul
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Mokenge Malafa
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Jason Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA
| | - Dung-Tsa Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer & Research Institute, Tampa, FL 33620, USA
| | - Qianxing Mo
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer & Research Institute, Tampa, FL 33620, USA
| | | | - Jennifer B Permuth
- Corresponding author: Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33620, USA.
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18
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Galoș D, Gorzo A, Balacescu O, Sur D. Clinical Applications of Liquid Biopsy in Colorectal Cancer Screening: Current Challenges and Future Perspectives. Cells 2022; 11:3493. [PMID: 36359889 PMCID: PMC9657568 DOI: 10.3390/cells11213493] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) represents the third most prevalent cancer worldwide and a leading cause of mortality among the population of western countries. However, CRC is frequently a preventable malignancy due to various screening tests being available. While failing to obtain real-time data, current screening methods (either endoscopic or stool-based tests) also require disagreeable preparation protocols and tissue sampling through invasive procedures, rendering adherence to CRC screening programs suboptimal. In this context, the necessity for novel, less invasive biomarkers able to identify and assess cancer at an early stage is evident. Liquid biopsy comes as a promising minimally invasive diagnostic tool, able to provide comprehensive information on tumor heterogeneity and dynamics during carcinogenesis. This review focuses on the potential use of circulating tumor cells (CTCs), circulating nucleic acids (CNAs) and extracellular vesicles as emerging liquid biopsy markers with clinical application in the setting of CRC screening. The review also examines the opportunity to implement liquid biopsy analysis during everyday practice and provides highlights on clinical trials researching blood tests designed for early cancer diagnosis. Additionally, the review explores potential applications of liquid biopsies in the era of immunotherapy.
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Affiliation(s)
- Diana Galoș
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
| | - Alecsandra Gorzo
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
| | - Ovidiu Balacescu
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
| | - Daniel Sur
- Department of Medical Oncology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, 400015 Cluj-Napoca, Romania
- Department of Medical Oncology, University of Medicine and Pharmacy “Iuliu Hațieganu”, 400012 Cluj-Napoca, Romania
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19
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Abstract
Circulating cell-free mitochondrial DNA (ccf-mtDNA) released upon cell injury or death stimulates diverse pattern recognition receptors to activate innate immune responses and initiate systemic inflammation. In this review, we discuss the temporal changes of ccf-mtDNA during pregnancy and its potential contribution to adverse pregnancy outcomes in pregnancy complications.
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Affiliation(s)
- Jessica L Bradshaw
- Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, Texas, United States
| | - Spencer C Cushen
- Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, Texas, United States.,Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, United States
| | - Nicole R Phillips
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Styliani Goulopoulou
- Department of Physiology and Anatomy, University of North Texas Health Science Center, Fort Worth, Texas, United States
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20
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Millon L, Caillot D, Berceanu A, Bretagne S, Lanternier F, Morio F, Letscher-Bru V, Dalle F, Denis B, Alanio A, Boutoille D, Bougnoux ME, Botterel F, Chouaki T, Charbonnier A, Ader F, Dupont D, Bellanger AP, Rocchi S, Scherer E, Gbaguidi-Haore H, Herbrecht R. Evaluation of serum Mucorales PCR for the diagnosis of Mucormycoses: The MODIMUCOR prospective trial. Clin Infect Dis 2022; 75:777-785. [PMID: 34986227 DOI: 10.1093/cid/ciab1066] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Early diagnosis and prompt initiation of specific antifungal treatment is essential for improving the prognosis of mucormycosis. We aimed to assess the performance of serum Mucorales quantitative PCR (qPCR) for the early diagnosis and follow-up of mucormycosis. METHODS We prospectively enrolled 232 patients with suspicion of invasive mold disease, evaluated using standard imaging and mycological procedures. Thirteen additional patients with proven or probable mucormycosis were included to analyze DNA load kinetics. Serum samples were collected twice-a-week for Mucorales qPCR tests targeting the Mucorales species Lichtheimia, Rhizomucor and Mucor/Rhizopus. RESULTS The sensitivity was 85·2%, specificity 89·8%, and positive and negative likelihood ratios 8·3 and 0·17, respectively in this prospective study. The first Mucorales qPCR-positive serum was observed a median of four days (IQR, 0-9) before sampling of the first mycological or histological positive specimen and a median of one day (IQR, (-2)-6) before the first imaging was performed. Negativity of Mucorales qPCR within seven days after liposomal-amphotericin B initiation was associated with an 85% lower 30-day mortality rate (adjusted hazard Ratio = 0·15, 95%CI [0·03-0·73], p = 0·02). CONCLUSION Our study argues for the inclusion of qPCR for the detection of circulating Mucorales DNA for mucormycosis diagnosis and follow-up after treatment initiation. Positive results should be added to the criteria for the consensual definitions from the European Organization for the Research and Treatment of Cancer/ Mycoses Study Group Education and Research Consortium (EORTC/MSGERC), as already done for Aspergillus PCR.
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Affiliation(s)
- Laurence Millon
- Laboratoire de Parasitologie-Mycologie, CHU Besançon, Besançon, France.,UMR 6249 CNRS Chrono-Environnement, Univ Bourgogne Franche-Comté, Besançon, France
| | - Denis Caillot
- Department of Clinical Hematology, CHU Dijon, Dijon, France
| | - Ana Berceanu
- Service d'Hematologie, CHU Besançon, Besançon, France
| | - Stéphane Bretagne
- Institut Pasteur, CNRS, Molecular Mycology Unit, National Reference Center for Invasive Mycoses & Antifungals, UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint Louis, AP-HP, Paris, France.,Université de Paris, Paris, France
| | - Fanny Lanternier
- Institut Pasteur, CNRS, Molecular Mycology Unit, National Reference Center for Invasive Mycoses & Antifungals, UMR2000, Paris, France.,Université de Paris, Paris, France.,Necker Pasteur Center for Infectious Diseases and Tropical Medicine, Hôpital Necker Enfants malades, AP-HP, IHU Imagine, Paris, France
| | - Florent Morio
- Laboratoire de Parasitologie-Mycologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 - IICiMed, Nantes Université, Nantes, France
| | - Valérie Letscher-Bru
- Laboratoire de Parasitologie et de Mycologie Médicale, Hôpitaux Universitaires de Strasbourg Strasbourg, France
| | - Frédéric Dalle
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire Gérard Mack, Dijon France.,UMR PAM Univ Bourgogne Franche-Comté - AgroSup Dijon - Equipe Vin, Aliment, Microbiologie, Stress, Dijon, France
| | - Blandine Denis
- Infectious Diseases Department, APHP, Saint-Louis Hospital, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, CNRS, Molecular Mycology Unit, National Reference Center for Invasive Mycoses & Antifungals, UMR2000, Paris, France.,Laboratoire de Parasitologie-Mycologie, Hôpital Saint Louis, AP-HP, Paris, France.,Université de Paris, Paris, France
| | - David Boutoille
- Unité Maladies Infectieuses et Tropicales, CHU Nantes, Nantes, France
| | - Marie-Elisabeth Bougnoux
- Parasitology-Mycology Unit, Necker Enfants Malades Hospital, APHP, Paris, France.,Fungal Biology and Pathogenicity Unit - INRA USC 2019. Institut Pasteur, Paris, France
| | - Françoise Botterel
- EA Dynamyc 7380 UPEC, ENVA, Faculté de Médecine, Créteil, France.,Unité de Parasitologie - Mycologie, Département de Virologie, Bactériologie-Hygiène, Mycologie-Parasitologie, DHU VIC, CHU Henri Mondor, Créteil, France
| | - Taieb Chouaki
- Laboratoire de Parasitologie et Mycologie Médicales, Centre de Biologie Humaine, CHU Amiens Picardie, Amiens, France.,Equipe AGIR : Agents Infectieux, Résistance et Chimiothérapie UR4294, Université de Picardie Jules Verne, Amiens, France
| | - Amandine Charbonnier
- Department of Clinical Hematology and Cellular Therapy, Amiens University Medical Center, Amiens, France
| | - Florence Ader
- Hospices Civils de Lyon, Département des Maladies Infectieuses et Tropicales, F-69004, Lyon, France
| | - Damien Dupont
- Institut des Agents Infectieux, Parasitologie Mycologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Anne-Pauline Bellanger
- Laboratoire de Parasitologie-Mycologie, CHU Besançon, Besançon, France.,UMR 6249 CNRS Chrono-Environnement, Univ Bourgogne Franche-Comté, Besançon, France
| | - Steffi Rocchi
- Laboratoire de Parasitologie-Mycologie, CHU Besançon, Besançon, France.,UMR 6249 CNRS Chrono-Environnement, Univ Bourgogne Franche-Comté, Besançon, France
| | - Emeline Scherer
- Laboratoire de Parasitologie-Mycologie, CHU Besançon, Besançon, France.,UMR 6249 CNRS Chrono-Environnement, Univ Bourgogne Franche-Comté, Besançon, France
| | - Houssein Gbaguidi-Haore
- UMR 6249 CNRS Chrono-Environnement, Univ Bourgogne Franche-Comté, Besançon, France.,Infection Control Department, CHU Besançon, Besançon, France
| | - Raoul Herbrecht
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France.,Service d'Hématologie, Institut de Cancérologie Strasbourg Europe (ICANS), Strasbourg, France
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21
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Manne A, Woods E, Tsung A, Mittra A. Biliary Tract Cancers: Treatment Updates and Future Directions in the Era of Precision Medicine and Immuno-Oncology. Front Oncol 2021; 11:768009. [PMID: 34868996 PMCID: PMC8634105 DOI: 10.3389/fonc.2021.768009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/13/2021] [Indexed: 12/12/2022] Open
Abstract
The effective management of biliary tract cancers (BTCs) has been hampered by limited options for systemic therapy. In recent years, the focus on precision medicine has made technologies such as next-generation sequencing (NGS) accessible to clinicians to identify targetable mutations in BTCs in tumor tissue (primarily) as well as blood, and to treat them with targeted therapies when possible. It has also expanded our understanding of functional pathways associated with genetic alterations and opened doors for identifying novel targets for treatment. Recent advances in the precision medicine approach allowed us to identify new molecular markers in BTCs, such as epigenetic changes (methylation and histone modification) and non-DNA markers such as messenger RNA, microRNA, and long non-coding RNA. It also made detecting these markers from non-traditional sources such as blood, urine, bile, and cytology (from fine-needle aspiration and biliary brushings) possible. As these tests become more accessible, we can see the integration of different molecular markers from all available sources to aid physicians in diagnosing, assessing prognosis, predicting tumor response, and screening BTCs. Currently, there are a handful of approved targeted therapies and only one class of immunotherapy agents (immune checkpoint inhibitors or ICIs) to treat BTCs. Early success with new targets, vascular endothelial growth factor receptor (VEGFR), HER2, protein kinase receptor, and Dickkopf-1 (DKK1); new drugs for known targets, fibroblast growth factor receptors (FGFRs) such as futabatinib, derazantinib, and erdafitinib; and ICIs such as durvalumab and tremelimumab is encouraging. Novel immunotherapy agents such as bispecific antibodies (bintrafusp alfa), arginase inhibitors, vaccines, and cellular therapy (chimeric antigen receptor-T cell or CAR-T, natural killer cells, tumor-infiltrating lymphocytes) have the potential to improve outcomes of BTCs in the coming years.
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Affiliation(s)
- Ashish Manne
- Department of Internal Medicine, Division of Medical Oncology at the Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Edward Woods
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Allan Tsung
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Cancer Hospital and Solove Research Institute, Columbus, OH, United States
| | - Arjun Mittra
- Department of Internal Medicine, Division of Medical Oncology at the Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
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22
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Cédile O, Veyhe SR, Hansen MH, Titlestad K, Nyvold CG. Investigation of circulating DNA integrity after blood collection. Biotechniques 2021; 71:550-555. [PMID: 34645292 DOI: 10.2144/btn-2020-0167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Method summary Concentrations of circulating DNA in blood plasma were compared using NanoDrop, Qubit, quantitative PCR and Bioanalyzer, and DNA integrity was evaluated with the Bioanalyzer according to the time of plasma preparation.
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Affiliation(s)
- Oriane Cédile
- Haematology-Pathology Research Laboratory, Research Unit for Haematology & Research Unit for Pathology, University of Southern Denmark & Odense University Hospital, Odense, Denmark.,OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
| | | | - Marcus Høy Hansen
- Haematology-Pathology Research Laboratory, Research Unit for Haematology & Research Unit for Pathology, University of Southern Denmark & Odense University Hospital, Odense, Denmark
| | - Kjell Titlestad
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Charlotte Guldborg Nyvold
- Haematology-Pathology Research Laboratory, Research Unit for Haematology & Research Unit for Pathology, University of Southern Denmark & Odense University Hospital, Odense, Denmark.,OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
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23
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Rocchi S, Scherer E, Mengoli C, Alanio A, Botterel F, Bougnoux ME, Bretagne S, Cogliati M, Cornu M, Dalle F, Damiani C, Denis J, Fuchs S, Gits-Muselli M, Hagen F, Halliday C, Hare R, Iriart X, Klaassen C, Lackner M, Lengerova M, Letscher-Bru V, Morio F, Nourrisson C, Posch W, Sendid B, Springer J, Willinger B, White PL, Barnes RA, Cruciani M, Donnelly JP, Loeffler J, Millon L. Interlaboratory evaluation of Mucorales PCR assays for testing serum specimens: A study by the fungal PCR Initiative and the Modimucor study group. Med Mycol 2021; 59:126-138. [PMID: 32534456 DOI: 10.1093/mmy/myaa036] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/14/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
Interlaboratory evaluations of Mucorales qPCR assays were developed to assess the reproducibility and performance of methods currently used. The participants comprised 12 laboratories from French university hospitals (nine of them participating in the Modimucor study) and 11 laboratories participating in the Fungal PCR Initiative. For panel 1, three sera were each spiked with DNA from three different species (Rhizomucor pusillus, Lichtheimia corymbifera, Rhizopus oryzae). For panel 2, six sera with three concentrations of R. pusillus and L. corymbifera (1, 10, and 100 genomes/ml) were prepared. Each panel included a blind negative-control serum. A form was distributed with each panel to collect results and required technical information, including DNA extraction method, sample volume used, DNA elution volume, qPCR method, qPCR template input volume, qPCR total reaction volume, qPCR platform, and qPCR reagents used. For panel 1, assessing 18 different protocols, qualitative results (positive or negative) were correct in 97% of cases (70/72). A very low interlaboratory variability in Cq values (SD = 1.89 cycles) were observed. For panel 2 assessing 26 different protocols, the detection rates were high (77-100%) for 5/6 of spiked serum. There was a significant association between the qPCR platform and performance. However, certain technical steps and optimal combinations of factors may also impact performance. The good reproducibility and performance demonstrated in this study support the use of Mucorales qPCR as part of the diagnostic strategy for mucormycosis.
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Affiliation(s)
- S Rocchi
- Parasitology - Mycology, University Hospital Besançon, Besançon, France.,UMR6249 CNRS Chrono-Environnement, University of Bourgogne Franche-Comté, Besançon, Besançon, France
| | - E Scherer
- Parasitology - Mycology, University Hospital Besançon, Besançon, France.,UMR6249 CNRS Chrono-Environnement, University of Bourgogne Franche-Comté, Besançon, Besançon, France
| | - C Mengoli
- Molecular Medicine, University of Padova, Padova, Italy
| | - A Alanio
- Institut Pasteur, CNRS, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Molecular Mycology Unit, UMR2000, Paris, France.,Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal hospitals, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, France
| | - F Botterel
- EA Dynamyc 7380 UPEC, ENVA, Faculté de Médecine de Créteil, 8 rue du Général Sarrail 94010 Créteil, France.,Unité de Parasitologie - Mycologie, Département de Virologie, Bactériologie-Hygiène, Mycologie-Parasitologie, DHU VIC, CHU Henri Mondor, AP-HP, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France
| | - M E Bougnoux
- Parasitology-Mycology Unit, Necker Enfants Malades Hospital, APHP, Paris, France.,Fungal Biology and Pathogenicity Unit - INRA USC 2019. Institut Pasteur, Paris, France
| | - S Bretagne
- Institut Pasteur, CNRS, National Reference Center for Invasive Mycoses and Antifungals (NRCMA), Molecular Mycology Unit, UMR2000, Paris, France.,Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal hospitals, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, France
| | - M Cogliati
- Lab. Medical Mycology, Dip. Scienze Biomediche per la Salute, Università degli Studi di Milano, Milano, Italy
| | - M Cornu
- Inserm U1285, Univ. Lille, UMR CNRS 8576- UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - F Dalle
- Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire Gérard Mack, Dijon France.,UMR PAM Univ Bourgogne Franche-Comté - AgroSup Dijon - Equipe Vin, Aliment, Microbiologie, Stress, Dijon, France
| | - C Damiani
- Laboratoire de Parasitologie et Mycologie Médicales, Centre de Biologie Humaine, CHU Amiens Picardie, France.,Equipe AGIR: Agents Infectieux, Résistance et Chimiothérapie UR4294, Université de Picardie Jules Verne, Amiens, France
| | - J Denis
- Laboratoire de Parasitologie et de Mycologie Médicale, Hôpitaux Universitaires de Strasbourg. 1 Place de l'Hôpital, 67000 Strasbourg, France
| | - S Fuchs
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - M Gits-Muselli
- Parasitology-Mycology Laboratory, Lariboisière Saint-Louis Fernand Widal hospitals, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Université de Paris, France
| | - F Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - C Halliday
- Clinical Mycology Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, NSW Health Pathology, Westmead, NSW, 2145, Australia
| | - R Hare
- Mycology Unit, Department for Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - X Iriart
- Service de Parasitologie-Mycologie, CHU Toulouse, Toulouse, France.,Centre de Physiopathologie de Toulouse Purpan (CPTP), Université de Toulouse, CNRS, INSERM, UPS, Toulouse, France
| | - C Klaassen
- Department of Medical Microbiology & Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - M Lackner
- Institut for Hygiene and Medical Microbiology, Medical University of Innsbruck (MUI), Austria
| | - M Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - V Letscher-Bru
- Laboratoire de Parasitologie et de Mycologie Médicale, Hôpitaux Universitaires de Strasbourg. 1 Place de l'Hôpital, 67000 Strasbourg, France
| | - F Morio
- Laboratoire de Parasitologie-Mycologie, CHU Nantes, Nantes, France.,Département de Parasitologie et Mycologie Médicale, EA1155 - IICiMed, Nantes Université, Nantes, France
| | - C Nourrisson
- Laboratoire de Parasitologie-Mycologie, CHU Clermont-Ferrand, 3IHP, France
| | - W Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - B Sendid
- Inserm U1285, Univ. Lille, UMR CNRS 8576- UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - J Springer
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Wuerzburg, Germany
| | - B Willinger
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna
| | - P L White
- Mycology Reference Laboratory, Public Health Wales Microbiology, Cardiff, United Kingdom
| | - R A Barnes
- Medical Microbiology and Infectious Diseases, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - M Cruciani
- Infectious Diseases Unit, ULSS 20 Verona, Italy
| | - J P Donnelly
- Division of Infectious Diseases, San Antonio Center for Medical Mycology, San Antonio, Texas, United States of America
| | - J Loeffler
- Department of Internal Medicine II, WÜ4i, University Hospital Wuerzburg, Wuerzburg, Germany
| | - L Millon
- Parasitology - Mycology, University Hospital Besançon, Besançon, France.,UMR6249 CNRS Chrono-Environnement, University of Bourgogne Franche-Comté, Besançon, Besançon, France
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24
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Pastor B, André T, Henriques J, Trouilloud I, Tournigand C, Jary M, Mazard T, Louvet C, Azan S, Bauer A, Roch B, Sanchez C, Vernerey D, Thierry AR, Adenis A. Monitoring levels of circulating cell-free DNA in patients with metastatic colorectal cancer as a potential biomarker of responses to regorafenib treatment. Mol Oncol 2021; 15:2401-2411. [PMID: 33934494 PMCID: PMC8410523 DOI: 10.1002/1878-0261.12972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/09/2021] [Accepted: 04/20/2021] [Indexed: 12/25/2022] Open
Abstract
Circulating cell‐free DNA (cfDNA) contains circulating tumor DNA (ctDNA), which can be obtained from serial liquid biopsies to enable tumor genome analysis throughout the course of treatment. We investigated cfDNA and mutant ctDNA as potential biomarkers to predict the best outcomes of regorafenib‐treated metastatic colorectal cancer (mCRC) patients. We analyzed longitudinally collected plasma cfDNA of 43 mCRC patients prospectively enrolled in the phase II TEXCAN trial by IntPlex qPCR. Qualitative (KRAS, NRAS, BRAFV600E mutations) and quantitative (total cfDNA concentration, mutant ctDNA concentration, mutant ctDNA fraction) parameters were correlated with overall survival (OS) and progression‐free survival (PFS). When examined as classes or continuous variables, the concentrations of total cfDNA, mutant ctDNA, and, partly, mutant ctDNA fraction prior to regorafenib treatment correlated with OS. Patients with baseline cfDNA > 26 ng·mL−1 had shorter OS than those with cfDNA value below this threshold (4.0 vs 6.9 months; log‐rank P = 0.0366). Patients with baseline mutant ctDNA > 2 ng·mL−1 had shorter OS than those with mutant ctDNA below this threshold (log‐rank P = 0.0154). We show that pretreatment cfDNA and mutant ctDNA levels may identify mCRC patients that may benefit from regorafenib treatment.
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Affiliation(s)
- Brice Pastor
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France
| | - Thierry André
- Department of Medical Oncology, Saint-Antoine University Hospital, Sorbonne University, Paris, France.,Oncology Multidisciplinary Research Group (GERCOR), Paris, France
| | - Julie Henriques
- Methodology and Quality of Life Unit in Oncology, Besançon University Hospital, France
| | - Isabelle Trouilloud
- Department of Medical Oncology, Saint-Antoine University Hospital, Sorbonne University, Paris, France.,Oncology Multidisciplinary Research Group (GERCOR), Paris, France
| | - Christophe Tournigand
- Oncology Multidisciplinary Research Group (GERCOR), Paris, France.,Medical Oncology Service, Henri Mondor Hospital, AP-HP, Université Paris Est Créteil Créteil, France
| | - Marine Jary
- Oncology Multidisciplinary Research Group (GERCOR), Paris, France.,INSERM, Etablissement Français du Sang Bourgogne Franche-Comté, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Bourgogne Franche-Comté University, Besançon, France.,Department of Medical Oncology, Besançon University Hospital, France
| | - Thibault Mazard
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France.,Department of Medical Oncology, Montpellier Cancer Institute (ICM), France
| | - Christophe Louvet
- Oncology Multidisciplinary Research Group (GERCOR), Paris, France.,Department of Medical Oncology, Institut Monsouris, Paris, France
| | - Simon Azan
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France
| | - Audrey Bauer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France
| | - Benoit Roch
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France.,Department of Thoracic Oncology, Montpellier University Hospital, Université de Montpellier, France
| | - Cynthia Sanchez
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France
| | - Dewi Vernerey
- Oncology Multidisciplinary Research Group (GERCOR), Paris, France.,Methodology and Quality of Life Unit in Oncology, Besançon University Hospital, France
| | - Alain R Thierry
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France.,Department of Medical Oncology, Montpellier Cancer Institute (ICM), France
| | - Antoine Adenis
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France.,Department of Medical Oncology, Montpellier Cancer Institute (ICM), France
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25
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Guo Q, Hua Y. The assessment of circulating cell-free DNA as a diagnostic tool for breast cancer: an updated systematic review and meta-analysis of quantitative and qualitative ssays. Clin Chem Lab Med 2021; 59:1479-1500. [PMID: 33951758 DOI: 10.1515/cclm-2021-0193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES This updated meta-analysis aimed to assess the diagnostic accuracy of circulating cell-free DNA (cfDNA) in breast cancer (BC). CONTENT An extensive systematic search was performed in PubMed, Scopus, Embase, and Science Direct databases to retrieve all related literature. Various diagnostic estimates, including sensitivity (SE), specificity (SP), likelihood ratios (LRs), diagnostic odds ratio (DOR), and area under the curve (AUC) of summary receiver operating characteristic (sROC) curve, were also calculated using bivariate linear mixed models. SUMMARY In this meta-analysis, 57 unique articles (130 assays) on 4246 BC patients and 2,952 controls, were enrolled. For quantitative approaches, pooled SE, SP, PLR, NLR, DOR, and AUC were obtained as 0.80, 0.88, 6.7, 0.23, 29, and 0.91, respectively. Moreover, for qualitative approaches, pooled SE and SP for diagnostic performance were obtained as 0.36 and 0.98, respectively. In addition, PLR was 14.9 and NLR was 0.66. As well, the combined DOR was 23, and the AUC was 0.79. OUTLOOK Regardless of promising SE and SP, analysis of LRs suggested that quantitative assays are not robust enough neither for BC confirmation nor for its exclusion. On the other hand, qualitative assays showed satisfying performance only for confirming the diagnosis of BC, but not for its exclusion. Furthermore, qualitative cfDNA assays showed a better diagnostic performance in patients at the advanced stage of cancer, which represented no remarkable clinical significance as a biomarker for early detection.
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Affiliation(s)
- Qingfeng Guo
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
| | - Yuming Hua
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
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26
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Chen C, Chen C, Sadeghi M. Evaluation of cell-free DNA accuracy as diagnostic biomarker for prostate cancer: A systematic review and meta-analysis. Biotechnol Appl Biochem 2021; 69:749-766. [PMID: 33749048 DOI: 10.1002/bab.2149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/15/2021] [Indexed: 12/09/2022]
Abstract
PURPOSE This updated meta-analysis aimed to assess the diagnostic performance of circulating cell-free DNA (cf-DNA) for prostate cancer (PCa). METHODS A systematic search was conducted in PubMed, Scopus, Web of Science, and Embase databases to retrieve related studies. Several diagnostic estimates, including sensitivity (SE), specificity (SP), likelihood ratios (LRs), and diagnostic odds ratio (DOR) were also used to perform the meta-synthesis. Additionally, the area under hierarchical summary receiver operating characteristic curves (AU-HSROC) was used as a global measure of test accuracy. RESULTS Twenty-nine unique articles were enrolled in the meta-analysis. Pooled SE and SP for overall accuracy of cf-DNA in PCa were obtained as 0.54 (95% CI: 0.47-0.61) and 0.92 (95% CI: 0.88-0.95), respectively. Positive LR (PLR) was 6.8 (95% CI: 4.9-9.5, I2 : 92.98%) and negative LR (NLR) was 0.5 (95% CI: 0.43-0.58). Pooled DOR was 13.56 (95% CI: 9.49-19.37) and the AU-HSROC was 0.83 (95% CI: 0.79-0.86). CONCLUSION The present study suggested that cf-DNA assays have comparable SE as well as remarkably higher SP (qualitative assays) than common biomarkers in the detection of PCa like prostate-specific antigen (PSA). In addition, cf-DNA assays have better performance in PCa confirmation and almost similar performance to PSA in excluding PCa patients.
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Affiliation(s)
- Caixia Chen
- Department of Laboratory Medicine, Henan Provincial People's Hospital, Zhengzhou, China
| | - Chunfeng Chen
- Department of the Third Affiliated Hospital, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Morteza Sadeghi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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27
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Guan G, Wang Y, Sun Q, Wang L, Xie F, Yan J, Huang H, Liu H. Utility of urinary ctDNA to monitoring minimal residual disease in early breast cancer patients. Cancer Biomark 2021; 28:111-119. [PMID: 32176625 DOI: 10.3233/cbm-190523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Cancer recurrence for patients with early breast cancer is significant. Patients will benefit from more non-invasive modes of monitoring and we aim to study the feasibility of urinary circulating tumor DNA (ctDNA) to monitor for residual disease (MRD). METHODS In this longitudinal study, 300 early breast cancer patients were recruited prospectively. Measurements were taken prior to treatment and at different time points thereafter for a total of 8 measurements. Comparisons were made with healthy volunteers and patients without detectable mutations in urine specimens. Disease free relapse were correlated to both urinary DNA quantity and ctDNA concentration. RESULTS Baseline index measurements showed 38% of patients with detectable mutations. The concordance with biopsy tissues was 97.3%. Overall, breast cancer patients had higher urinary DNA compared with healthy volunteers. Over time, fluctuations in urinary DNA was negligible in healthy volunteers, indicating the stability of the marker. Among the patients with detectable mutations, we observed that higher urinary DNA quantity measurements at 6-month and patients with positive mutations were associated with greater risk of relapse. Hazard ratios for patients in this category was 1.65 (95% CI 1.26-2.16) and 1.98 (95% CI 1.48-2.63) respectively. CONCLUSION Urinary DNA offers non-invasive probing and real-time monitoring of breast cancer relapse. Our results demonstrated clear clinical relevance in breast cancer and significant risk profiling of early breast cancer patients. This potentially aids to complement current cancer relapse monitoring and may help in early intervention.
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Affiliation(s)
- Gege Guan
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China.,Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Yuehua Wang
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China.,Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Qiushi Sun
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Ling Wang
- Department of General Surgery, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Fei Xie
- Department of General Surgery, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Jiayin Yan
- Department of General Surgery, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Huajun Huang
- Department of General Surgery, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Huijie Liu
- Department of General Surgery, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
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Masood M, Grimm S, El-Bahrawy M, Yagüe E. TMEFF2: A Transmembrane Proteoglycan with Multifaceted Actions in Cancer and Disease. Cancers (Basel) 2020; 12:cancers12123862. [PMID: 33371267 PMCID: PMC7766544 DOI: 10.3390/cancers12123862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/25/2022] Open
Abstract
Simple Summary We recently came across an intriguing protein while screening for tumour-specific apoptosis inducers. It is known as the transmembrane protein with an EGF-like and two Follistatin-like domains 2 (TMEFF2). The gene was identified and characterized by five different groups almost simultaneously around 2000. Physiological function of TMEFF2 is elusive; however, the protein is reported to be involved in wide-ranging physiological and pathological functions including neuroprotection in Alzheimer’s diseases, interferon induction and one-carbon metabolism. Moreover, the TMEFF2 promoter and 5′-upstream regions harbour a CpG island which is progressively methylated upon progression in a wide variety of cancers. Numerous primary publications suggest the methylation of TMEFF2 as a prognostic and even diagnostic marker in different cancers. The primary literature regarding TMEFF2 is distributed far and wide, and despite having more than 150 primary publications mentioning TMEFF2 (or its aliases) in the title or abstract on PubMed, a comprehensive literature review is not available. We believe the reason behind this is firstly the sheer diversity of subjects of these publications and secondly the numerous primary publications reporting contradictory information about TMEFF2, especially when it comes to its oncogenic versus the onco-suppressive roles. The interest in TMEFF2 is growing again; PubMed returning at least 60 publications mentioning TMEFF2 (or its aliases) within the last year. We have made a laborious effort and written a comprehensive review article on TMEFF2 where we have not only compiled and contextualized the information regarding it but also critically analysed the information in the major primary publications. In addition, we have proposed some answers to the apparent TMEFF2 disagreements on its function. This information could serve as a valuable tool for readers not only about TMEFF2 but also on the dual role of type-I transmembrane proteoglycans (harbouring Follistatin-like domains) in oncogenesis and onco-suppression. Abstract Transmembrane protein with an EGF-like and two Follistatin-like domains 2 (TMEFF2) is a 374-residue long type-I transmembrane proteoglycan which is proteolytically shed from the cell surface. The protein is involved in a range of functions including metabolism, neuroprotection, apoptosis, embryonic development, onco-suppression and endocrine function. TMEFF2 is methylated in numerous cancers, and an inverse correlation with the stage, response to therapy and survival outcome has been observed. Moreover, TMEFF2 methylation increases with breast, colon and gastric cancer progression. TMEFF2 is methylated early during oncogenesis in breast and colorectal cancer, and the detection of methylated free-circulating TMEFF2 DNA has been suggested as a potential diagnostic tool. The TMEFF2 downregulation signature equals and sometimes outperforms the Gleason and pathological scores in prostate cancer. TMEFF2 is downregulated in glioma and cotricotropinomas, and it impairs the production of adrenocorticotropic hormone in glioma cells. Interestingly, through binding the amyloid β protein, its precursor and derivatives, TMEFF2 provides neuroprotection in Alzheimer’s disease. Despite undergoing extensive investigation over the last two decades, the primary literature regarding TMEFF2 is incoherent and offers conflicting information, in particular, the oncogenic vs. onco-suppressive role of TMEFF2 in prostate cancer. For the first time, we have compiled, contextualised and critically analysed the vast body of TMEFF2-related literature and answered the apparent discrepancies regarding its function, tissue expression, intracellular localization and oncogenic vs. onco-suppressive role.
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Affiliation(s)
- Motasim Masood
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK;
| | - Stefan Grimm
- Department of Medicine, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK;
| | - Mona El-Bahrawy
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
- Correspondence: (M.E.-B.); (E.Y.); Tel.: +44-(0)77-7157-4968 (M.E.B.); +44-(0)20-7594-2802 (E.Y.)
| | - Ernesto Yagüe
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK;
- Correspondence: (M.E.-B.); (E.Y.); Tel.: +44-(0)77-7157-4968 (M.E.B.); +44-(0)20-7594-2802 (E.Y.)
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Lockney NA, Henderson R, Swarts SG, Zhang Z, Zhang B, Li J, Zlotecki RA, Morris CG, Casey-Sawicki K, Okunieff P. Circulating Cell-Free DNA Correlates with Body Integral Dose and Radiation Modality in Prostate Cancer. Int J Part Ther 2020; 7:21-30. [PMID: 33274254 PMCID: PMC7707322 DOI: 10.14338/ijpt-20-00033.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 12/25/2022] Open
Abstract
Purpose The RadTox assay measures circulating cell-free DNA released in response to radiotherapy (RT)-induced tissue damage. The primary objectives for this clinical trial were to determine whether cell-free DNA numbers measured by the RadTox assay are (1) correlated with body integral dose, (2) lower with proton RT compared with photon RT, and (3) higher with larger prostate cancer RT fields. Patients and Methods Patients planned to receive proton or photon RT for nonmetastatic prostate cancer in the setting of an intact prostate or postprostatectomy were eligible for the trial. Plasma was collected pre-RT and at 5 additional daily collection points beginning 24 hours after the initiation of RT. Data from 54 evaluable patients were analyzed to examine any correlations among RadTox scores with body-integral dose, RT modality (photon versus proton), and RT field size (prostate or prostate bed versus whole pelvis). Results Body integral dose was significantly associated with the peak post-RT RadTox score (P = .04). Patients who received photon RT had a significant increase in peak post-RT RadTox score (P = .04), average post-RT RadTox score (P = .04), and day-2 RadTox score (all minus the pre-RT values for each patient) as compared with patients who received proton RT. Field size was not significantly associated with RadTox score. Conclusion RadTox is correlated with body integral dose and correctly predicts which patients receive proton versus photon RT. Data collection remains ongoing for patient-reported RT toxicity outcomes to determine whether RadTox scores are correlated with toxicity.
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Affiliation(s)
- Natalie A Lockney
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Randal Henderson
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Steven G Swarts
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Zhenhuan Zhang
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Bingrong Zhang
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Jennifer Li
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Robert A Zlotecki
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Christopher G Morris
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Katherine Casey-Sawicki
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
| | - Paul Okunieff
- Department of Radiation Oncology, University of Florida College of Medicine, Gainesville and Jacksonville, FL, USA
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Chan RWY, Serpas L, Ni M, Volpi S, Hiraki LT, Tam LS, Rashidfarrokhi A, Wong PCH, Tam LHP, Wang Y, Jiang P, Cheng ASH, Peng W, Han DSC, Tse PPP, Lau PK, Lee WS, Magnasco A, Buti E, Sisirak V, AlMutairi N, Chan KCA, Chiu RWK, Reizis B, Lo YMD. Plasma DNA Profile Associated with DNASE1L3 Gene Mutations: Clinical Observations, Relationships to Nuclease Substrate Preference, and In Vivo Correction. Am J Hum Genet 2020; 107:882-894. [PMID: 33022220 PMCID: PMC7674998 DOI: 10.1016/j.ajhg.2020.09.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/16/2020] [Indexed: 12/30/2022] Open
Abstract
Plasma DNA fragmentomics is an emerging area in cell-free DNA diagnostics and research. In murine models, it has been shown that the extracellular DNase, DNASE1L3, plays a role in the fragmentation of plasma DNA. In humans, DNASE1L3 deficiency causes familial monogenic systemic lupus erythematosus with childhood onset and anti-dsDNA reactivity. In this study, we found that human patients with DNASE1L3 disease-associated gene variations showed aberrations in size and a reduction of a "CC" end motif of plasma DNA. Furthermore, we demonstrated that DNA from DNASE1L3-digested cell nuclei showed a median length of 153 bp with CC motif frequencies resembling plasma DNA from healthy individuals. Adeno-associated virus-based transduction of Dnase1l3 into Dnase1l3-deficient mice restored the end motif profiles to those seen in the plasma DNA of wild-type mice. Our findings demonstrate that DNASE1L3 is an important player in the fragmentation of plasma DNA, which appears to act in a cell-extrinsic manner to regulate plasma DNA size and motif frequency.
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Affiliation(s)
- Rebecca W Y 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
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Meng Ni
- 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
| | - Stefano Volpi
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy; Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili (DINOGMI), Università degli Studi di Genova, 16132 Genova, Italy
| | - Linda T Hiraki
- Division of Rheumatology, The Hospital for Sick Children, Toronto, ON M5G 1X5, Canada
| | - Lai-Shan Tam
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Ali Rashidfarrokhi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Priscilla C H Wong
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Lydia H P Tam
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Yueyang Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - 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
| | - Alice S H 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
| | - 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
| | - Diana S C Han
- 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
| | - Patty P P 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
| | - Pik Ki Lau
- 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
| | - Alberto Magnasco
- Division of Nephrology, Dialysis and Transplantation, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Elisa Buti
- Nefrologia e Dialisi, Azienda Ospedaliero Universitaria Meyer, 50139 Firenze, Italy
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpt, Université de Bordeaux, 33076 Bordeaux, France
| | - Nora AlMutairi
- Sabah Hospital, Jaber Al Ahmad Al Jaber Al Sabah Hospital, Kuwait
| | - 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
| | - 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
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - 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.
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Grabuschnig S, Bronkhorst AJ, Holdenrieder S, Rosales Rodriguez I, Schliep KP, Schwendenwein D, Ungerer V, Sensen CW. Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms. Int J Mol Sci 2020; 21:E8062. [PMID: 33137955 DOI: 10.3390/ijms21218062] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.
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Lamy PJ, van der Leest P, Lozano N, Becht C, Duboeuf F, Groen HJM, Hilgers W, Pourel N, Rifaela N, Schuuring E, Alix-Panabières C. Mass Spectrometry as a Highly Sensitive Method for Specific Circulating Tumor DNA Analysis in NSCLC: A Comparison Study. Cancers (Basel) 2020; 12:cancers12103002. [PMID: 33081150 PMCID: PMC7602843 DOI: 10.3390/cancers12103002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary We compared the UltraSEEK™ Lung Panel on the MassARRAY® System (Agena Bioscience) with the FDA-approved Cobas® EGFR Mutation Test v2 for the detection of EGFR mutations in liquid biopsies of NSCLC patients, accompanied with preanalytical sample assessment using the novel Liquid IQ® Panel. For the detection of relevant predictive mutations using the UltraSEEK™ Lung Panel, an input of over 10 ng showed 100% concordance with Cobas® EGFR Mutation Test v2 and detection of all tissue confirmed mutations. In case of lower ccfDNA input, the risk of missing clinically relevant mutations should be considered. The use of a preanalytical ccfDNA quality control assay such as the Liquid IQ® Panel is recommended to confidently interpret results, avoiding bias induced by non-specific genomic DNA and low input of specific tumoral ccfDNA fragments. Abstract Plasma-based tumor mutational profiling is arising as a reliable approach to detect primary and therapy-induced resistance mutations required for accurate treatment decision making. Here, we compared the FDA-approved Cobas® EGFR Mutation Test v2 with the UltraSEEK™ Lung Panel on the MassARRAY® System on detection of EGFR mutations, accompanied with preanalytical sample assessment using the novel Liquid IQ® Panel. 137 cancer patient-derived cell-free plasma samples were analyzed with the Cobas® and UltraSEEK™ tests. Liquid IQ® analysis was initially validated (n = 84) and used to determine ccfDNA input for all samples. Subsequently, Liquid IQ® results were applied to harmonize ccfDNA input for the Cobas® and UltraSEEK™ tests for 63 NSCLC patients. The overall concordance between the Cobas® and UltraSEEK™ tests was 86%. The Cobas® test detected more EGFR exon19 deletions and L858R mutations, while the UltraSEEK™ test detected more T790M mutations. A 100% concordance in both the clinical (n = 137) and harmonized (n = 63) cohorts was observed when >10 ng of ccfDNA was used as determined by the Liquid IQ® Panel. The Cobas® and UltraSEEK™ tests showed similar sensitivity in EGFR mutation detection, particularly when ccfDNA input was sufficient. It is recommended to preanalytically determine the ccfDNA concentration accurately to ensure sufficient input for reliable interpretation and treatment decision making.
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Affiliation(s)
- Pierre-Jean Lamy
- Biopathologie et Génétique des Cancers, Institute d’Analyse Médicale Imagenome, Inovie, 6 Rue Fontenille, 34000 Montpellier, France;
- Correspondence: ; Tel.: +33-430-053-100
| | - Paul van der Leest
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Nicolas Lozano
- Biopathologie et Génétique des Cancers, Institute d’Analyse Médicale Imagenome, Inovie, 6 Rue Fontenille, 34000 Montpellier, France;
| | - Catherine Becht
- Oncologie Médicale, Clinique Clémenville, 25 rue Clémenville, 34000 Montpellier, France; (C.B.); (F.D.)
| | - Frédérique Duboeuf
- Oncologie Médicale, Clinique Clémenville, 25 rue Clémenville, 34000 Montpellier, France; (C.B.); (F.D.)
| | - Harry J. M. Groen
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Werner Hilgers
- Oncologie Médicale, Institute Sainte Catherine, 250 Chemin de Baigne Pieds, 84918 Avignon, France; (W.H.); (N.P.)
| | - Nicolas Pourel
- Oncologie Médicale, Institute Sainte Catherine, 250 Chemin de Baigne Pieds, 84918 Avignon, France; (W.H.); (N.P.)
| | - Naomi Rifaela
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Catherine Alix-Panabières
- Laboratoire de Cellules Rares Circulantes, University Medical Center of Montpellier, 641, Avenue du Doyen Gaston GIRAUD, 34093 Montpellier, France;
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Lam D, Clark S, Stirzaker C, Pidsley R. Advances in Prognostic Methylation Biomarkers for Prostate Cancer. Cancers (Basel) 2020; 12:E2993. [PMID: 33076494 PMCID: PMC7602626 DOI: 10.3390/cancers12102993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/24/2022] Open
Abstract
There is a major clinical need for accurate biomarkers for prostate cancer prognosis, to better inform treatment strategies and disease monitoring. Current clinically recognised prognostic factors, including prostate-specific antigen (PSA) levels, lack sensitivity and specificity in distinguishing aggressive from indolent disease, particularly in patients with localised intermediate grade prostate cancer. There has therefore been a major focus on identifying molecular biomarkers that can add prognostic value to existing markers, including investigation of DNA methylation, which has a known role in tumorigenesis. In this review, we will provide a comprehensive overview of the current state of DNA methylation biomarker studies in prostate cancer prognosis, and highlight the advances that have been made in this field. We cover the numerous studies into well-established candidate genes, and explore the technological transition that has enabled hypothesis-free genome-wide studies and the subsequent discovery of novel prognostic genes.
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Affiliation(s)
- Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
| | - Susan Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; (D.L.); (S.C.); (C.S.)
- St. Vincent’s Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia
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Sundquist K, Sundquist J, Hedelius A, Memon AA. Diagnostic potential of circulating cell-free nuclear and mitochondrial DNA for several cancer types and nonmalignant diseases: A study on suspected cancer patients. Mol Carcinog 2020; 59:1362-1370. [PMID: 33051887 PMCID: PMC7702094 DOI: 10.1002/mc.23261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/31/2020] [Accepted: 09/27/2020] [Indexed: 11/30/2022]
Abstract
Circulating cell‐free nuclear DNA (nDNA) has been implicated in individual cancer types with a diagnostic value; however, the role of cell‐free mitochondrial DNA (mtDNA) in cancers is controversial. We aimed to investigate and compare the diagnostic potential of both nDNA and mtDNA for multiple cancers and to investigate their ability to distinguish multiple cancers from healthy controls and from nonmalignant diseases. We also investigated the prognostic value of both nDNA and mtDNA. The absolute copy number of circulating DNAs in suspected cancer patients (n = 286) referred to a cancer diagnostic center and healthy controls (n = 109) was quantified by droplet digital polymerase chain reaction. Among the suspected cancer patients, 66 (23%) were diagnosed with various cancers, 193 (67%) with nonmalignant diseases, and 27 (10%) with no active disease. Levels of nDNA were significantly higher in cancers (copies/μl; mean ± SD, 21.0 ± 14.2) as compared with nonmalignant diseases (15.2 ± 10.0) and controls (9.3 ± 4.1). In contrast, levels of mtDNA were significantly lower in cancers (copies/μl; mean ± SD, 68,557 ± 66,663) and nonmalignant diseases (60,174 ± 55,831) as compared with controls (98,714 ± 77,789). Receiver operating curve analysis showed that nDNA not only could distinguish multiple cancers from controls (area under curve [AUC] = 0.78; 95% confidence interval [CI] = 0.70–0.86) but also from nonmalignant diseases (AUC = 0.68; 95% CI = 0.59–0.76). However, mtDNA could only differentiate cancers from controls (AUC = 0.65; 95% CI = 0.56–0.73). Higher levels of nDNA were also associated with increased mortality in the cancer patients (hazard ratio = 2.3; 95% CI = 1.1–4.7). Circulating cell‐free nDNA, but not the mtDNA, could distinguish multiple cancers from nonmalignant diseases and was associated with poor survival of cancer patients.
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Affiliation(s)
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Anna Hedelius
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Ashfaque A Memon
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
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Thierry AR, Roch B. Neutrophil Extracellular Traps and By-Products Play a Key Role in COVID-19: Pathogenesis, Risk Factors, and Therapy. J Clin Med 2020; 9:E2942. [PMID: 32933031 PMCID: PMC7565044 DOI: 10.3390/jcm9092942] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/04/2020] [Accepted: 09/06/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding of the pathogenesis of the coronavirus disease-2019 (COVID-19) remains incomplete, particularly in respect to the multi-organ dysfunction it may cause. We were the first to report the analogous biological and physiological features of COVID-19 pathogenesis and the harmful amplification loop between inflammation and tissue damage induced by the dysregulation of neutrophil extracellular traps (NETs) formation. Given the rapid evolution of this disease, the nature of its symptoms, and its potential lethality, we hypothesize that COVID-19 progresses under just such an amplifier loop, leading to a massive, uncontrolled inflammation process. Here, we describe in-depth the correlations of COVID-19 symptoms and biological features with those where uncontrolled NET formation is implicated in various sterile or infectious diseases. General clinical conditions, as well as numerous pathological and biological features, are analogous with NETs deleterious effects. Among NETs by-products implicated in COVID-19 pathogenesis, one of the most significant appears to be elastase, in accelerating virus entry and inducing hypertension, thrombosis and vasculitis. We postulate that severe acute respiratory syndrome-coronavirus 2 (SARS-CoV2) may evade innate immune response, causing uncontrolled NETs formation and multi-organ failure. In addition, we point to indicators that NETS-associated diseases are COVID-19 risk factors. Acknowledging that neutrophils are the principal origin of extracellular and circulating DNA release, we nonetheless, explain why targeting NETs rather than neutrophils themselves may in practice be a better strategy. This paper also offers an in-depth review of NET formation, function and pathogenic dysregulation, as well as of current and prospective future therapies to control NETopathies. As such, it enables us also to suggest new therapeutic strategies to fight COVID-19. In combination with or independent of the latest tested approaches, we propose the evaluation, in the short term, of treatments with DNase-1, with the anti-diabetic Metformin, or with drugs targeting elastase (i.e., Silvelestat). With a longer perspective, we also advocate a significant increase in research on the development of toll-like receptors (TLR) and C-type lectin-like receptors (CLEC) inhibitors, NET-inhibitory peptides, and on anti-IL-26 therapies.
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Affiliation(s)
- Alain R. Thierry
- Research Institute of Cancerology of Montpellier, INSERM U1194, IRCM, ICM, Montpellier University, F-34298 Montpellier, France
| | - Benoit Roch
- Respiratory Medicine, University Hospital of Montpellier, Montpellier University, F-34298 Montpellier, France;
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Condappa A, McGrowder D, Aiken W, McLaughlin W, Gossell-Williams M. Evaluation of Plasma Circulating Cell Free DNA Concentration and Integrity in Patients with Prostate Cancer in Jamaica: A Preliminary Study. Diseases 2020; 8:diseases8030034. [PMID: 32906694 PMCID: PMC7564624 DOI: 10.3390/diseases8030034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 01/05/2023] Open
Abstract
Background: Cell free circulating DNA (cfcDNA) is a promising diagnostic tool for prostate cancer (PCa). This study aimed to measure the cfcDNA concentration and integrity in PCa patients using quantitative polymerase chain reaction (qPCR) analysis. This study also assessed the correlation between these molecular biomarkers with total prostate-specific antigen (PSA), Gleason score, prostate volume, and age. Methods: Eleven PCa patients and 9 persons with benign prostatic hyperplasia (BPH) were recruited. Blood samples were collected before prostate biopsy and plasma quantified by qPCR amplification of the ALU 115 DNA sequence, with the ratio of ALU 247 to ALU 115 reflecting cfcDNA integrity. Results: There were no significant differences in median, interquartile range (IQR) cfcDNA concentration or cfcDNA integrity between the patients with PCa (47.9 (214.93) ng/mL; 0.61 (0.49)) and persons with BPH (41.5 (55.13) ng/mL, p = 0.382; 0.67 (0.45), p = 0.342). A weakly positive correlation exists between cfcDNA concentration and total PSA (r = 0.200, p = 0.555) but not with age or Gleason score in PCa patients. Conclusion: cfcDNA concentration was relatively nonsignificantly higher in PCa patients in comparison to persons with BPH, whereas cfcDNA integrity was similar in both groups. Though limited in sample size, this study shows that cfcDNA concentration may be a potentially valuable noninvasive biomarker for the diagnosis of PCa.
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Affiliation(s)
- Andrew Condappa
- Department of Basic Medical Sciences (Pharmacology Section), Faculty of Medical Sciences, The University of the West Indies, Kingston 7, Jamaica; (A.C.); (M.G.-W.)
| | - Donovan McGrowder
- Department of Pathology, Faculty of Medical Sciences, The University of the West Indies, Kingston 7, Jamaica
- Correspondence:
| | - William Aiken
- Department of Surgery, Radiology, Anaesthesia and Intensive Care, Section of Surgery, Urology Division, Faculty of Medical Sciences, The University of the West Indies, Kingston 7, Jamaica;
| | - Wayne McLaughlin
- Department of Basic Medical Sciences (Molecular Biology Section), Faculty of Medical Sciences, The University of the West Indies, Kingston 7, Jamaica;
| | - Maxine Gossell-Williams
- Department of Basic Medical Sciences (Pharmacology Section), Faculty of Medical Sciences, The University of the West Indies, Kingston 7, Jamaica; (A.C.); (M.G.-W.)
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Tanos R, Tosato G, Otandault A, Al Amir Dache Z, Pique Lasorsa L, Tousch G, El Messaoudi S, Meddeb R, Diab Assaf M, Ychou M, Du Manoir S, Pezet D, Gagnière J, Colombo P, Jacot W, Assénat E, Dupuy M, Adenis A, Mazard T, Mollevi C, Sayagués JM, Colinge J, Thierry AR. Machine Learning-Assisted Evaluation of Circulating DNA Quantitative Analysis for Cancer Screening. Adv Sci (Weinh) 2020; 7:2000486. [PMID: 32999827 PMCID: PMC7509651 DOI: 10.1002/advs.202000486] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/30/2020] [Indexed: 05/24/2023]
Abstract
While the utility of circulating cell-free DNA (cfDNA) in cancer screening and early detection have recently been investigated by testing genetic and epigenetic alterations, here, an original approach by examining cfDNA quantitative and structural features is developed. First, the potential of cfDNA quantitative and structural parameters is independently demonstrated in cell culture, murine, and human plasma models. Subsequently, these variables are evaluated in a large retrospective cohort of 289 healthy individuals and 983 patients with various cancer types; after age resampling, this evaluation is done independently and the variables are combined using a machine learning approach. Implementation of a decision tree prediction model for the detection and classification of healthy and cancer patients shows unprecedented performance for 0, I, and II colorectal cancer stages (specificity, 0.89 and sensitivity, 0.72). Consequently, the methodological proof of concept of using both quantitative and structural biomarkers, and classification with a machine learning method are highlighted, as an efficient strategy for cancer screening. It is foreseen that the classification rate may even be improved by the addition of such biomarkers to fragmentomics, methylation, or the detection of genetic alterations. The optimization of such a multianalyte strategy with this machine learning method is therefore warranted.
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Huang Y, Mu J, Qi L, Ge W, Fang X, Song Y, Yuan Y, Zheng S. Diverse fragment lengths dismiss size selection for serum cell-free DNA: a comparative study of serum and plasma samples. Clin Chem Lab Med 2020; 58:1451-1459. [PMID: 32229658 DOI: 10.1515/cclm-2020-0078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/25/2020] [Indexed: 01/09/2023]
Abstract
Background The objective of this study was to determine the features of fragment length for circulating cell-free DNA (cfDNA) from plasma and serum samples. Methods Plasma and serum samples from different sources were randomly collected. Circulating cfDNA was extracted and purified by a precipitation-enriched and spin-column-based kit. The concentration of the purified DNA was immediately measured by a highly sensitive dsDNA quantitative assay, and then the fragment length was analyzed by capillary electrophoresis. The abundance of a specific fragment was estimated by the area under curve (AUC) for the fragment peak in the capillary electrophoresis. Results A total of 199 plasma and 117 serum samples were extracted and analyzed. The average yield of cfDNA from the serum samples (131.67 ng/mL) was significantly higher than that from the plasma samples (32.78 ng/mL, p < 0.001). The average abundance of the 20-400 bp fragments in plasma cfDNA (84.4%) was significantly higher than that of serum cfDNA (51.9%, p < 0.001). Fragment peaks in serum cfDNA always presented in regions around 190 bp, 430 bp, and 630 bp, but plasma cfDNA generally showed a sharp peak in the 165-190 bp region and a much lower peak in the 300<uni-2013;400 bp region. Large fragments in plasma cfDNA were longer than 1000 bp and peaked around the 3000<uni-2013;4000 bp region while the large fragments in serum cfDNA were always shorter and peaked around the 1000 bp region. Conclusions The fragment lengths of serum cfDNA and plasma cfDNA have very different features. Fragment size selection is suitable for plasma cfDNA but may not apply to serum cfDNA.
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Affiliation(s)
- Yanqin Huang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, P.R. China
| | - Jiayi Mu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, P.R. China
| | - Lina Qi
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, P.R. China
| | - Weiting Ge
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, P.R. China
| | - Xuefeng Fang
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Yongmao Song
- Department of Colorectal Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang,P.R. China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province), The Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road,Hangzhou, Zhejiang Province,P.R. China, Phone: +8657187784501, Fax: +8657187214404
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Thierry A, Roch B. SARS-CoV2 may evade innate immune response, causing uncontrolled neutrophil extracellular traps formation and multi-organ failure. Clin Sci (Lond) 2020; 134:1295-300. [PMID: 32543703 DOI: 10.1042/cs20200531] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/14/2022]
Abstract
We demonstrate that the general clinical conditions, risk factors and numerous pathological and biological features of COVID-19 are analogous with various disorders caused by the uncontrolled formation of neutrophil extracellular traps and their by-products. Given the rapid evolution of this disease's symptoms and its lethality, we hypothesize that SARS-CoV2 evades innate immune response causing COVID-19 progresses under just such an amplifier loop, leading to a massive, uncontrolled inflammation process. This work allows us to propose new strategies for treating the pandemic.
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Otandault A, Anker P, Al Amir Dache Z, Guillaumon V, Meddeb R, Pastor B, Pisareva E, Sanchez C, Tanos R, Tousch G, Schwarzenbach H, Thierry AR. Recent advances in circulating nucleic acids in oncology. Ann Oncol 2020; 30:374-384. [PMID: 30753271 DOI: 10.1093/annonc/mdz031] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) is one of the fastest growing and most exciting areas in oncology in recent years. Its potential clinical uses cover now each phase of cancer patient management care (predictive information, detection of the minimal residual disease, early detection of resistance, treatment monitoring, recurrence surveillance, and cancer early detection/screening). This review relates the recent advances in the application of circulating DNA or RNA in oncology building on unpublished or initial findings/work presented at the 10th international symposium on circulating nucleic acids in plasma and serum held in Montpellier from the 20th to the 22nd of September 2017. This year, presenters revealed their latest data and crucial observations notably in relation to (i) the circulating cell-free (cfDNA) structure and implications regarding their optimal detection; (ii) their role in the metastatic or immunological processes; (iii) evaluation of miRNA panels for cancer patient follow up; (iv) the detection of the minimal residual disease; (v) the evaluation of a screening tests for cancer using cfDNA analysis; and (vi) elements of preanalytical guidelines. This work reviews the recent progresses in the field brought to light in the meeting, as well as in the most important reports from the literature, past and present. It proposes a broader picture of the basic research and its potential, and of the implementation and current challenges in the use of circulating nucleic acids in oncology.
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Affiliation(s)
- A Otandault
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - P Anker
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - Z Al Amir Dache
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - V Guillaumon
- Regional Institute of Cancer of Montpellier, Montpellier; SIRIC, Integrated Cancer Research Site, Montpellier, France
| | - R Meddeb
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - B Pastor
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - E Pisareva
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - C Sanchez
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - R Tanos
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - G Tousch
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - H Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - A R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier.
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Bande Rodríguez MF, Fernandez Marta B, Lago Baameiro N, Santiago-Varela M, Silva-Rodríguez P, Blanco-Teijeiro MJ, Pardo Perez M, Piñeiro Ces A. Blood Biomarkers of Uveal Melanoma: Current Perspectives. Clin Ophthalmol 2020; 14:157-169. [PMID: 32021081 PMCID: PMC6980862 DOI: 10.2147/opth.s199064] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/09/2020] [Indexed: 12/21/2022] Open
Abstract
The detection of metastases in patients with a diagnosis of uveal melanoma (UM) is a controversial issue. While only 1% of the patients have detectable metastases at the time of diagnosis, up to 30% of them will develop liver metastases within 5 years of treatment. UM spreads hematogenously, therefore, blood biomarkers may be helpful for prognosis and monitoring the disease progression. Despite the great progress achieved thanks to the genetic analysis of UM biopsies, this is an invasive technique and is limited by the heterogeneity of the tumor. The present review considers the current understanding in the field regarding biomarkers for the diagnosis and prognosis of UM and its metastasis, primarily to the liver. General covered topics include non-conventional markers such as proteins previously identified in cutaneous melanoma and UM cell lines, circulating tumor cells, microRNAs (miRNA), and circulating DNA, and how each may be critical in the development of novel blood biomarkers for UM.
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Affiliation(s)
- Manuel F Bande Rodríguez
- Unidad de Retina Quirúrgica y Tumores Intraoculares del Adulto (URQTIA), Servicio de Oftalmología Xerencia de Xestión Integrada de Santiago de Compostela, SERGAS, Santiago de Compostela, Spain.,Tumores Intraoculares en el Adulto, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Beatriz Fernandez Marta
- Unidad de Retina Quirúrgica y Tumores Intraoculares del Adulto (URQTIA), Servicio de Oftalmología Xerencia de Xestión Integrada de Santiago de Compostela, SERGAS, Santiago de Compostela, Spain
| | - Nerea Lago Baameiro
- Grupo Obesidómica, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Maria Santiago-Varela
- Unidad de Retina Quirúrgica y Tumores Intraoculares del Adulto (URQTIA), Servicio de Oftalmología Xerencia de Xestión Integrada de Santiago de Compostela, SERGAS, Santiago de Compostela, Spain.,Tumores Intraoculares en el Adulto, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Paula Silva-Rodríguez
- Tumores Intraoculares en el Adulto, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica, Clinical University Hospital, SERGAS, Santiago de Compostela 15705, Spain
| | - María Jose Blanco-Teijeiro
- Unidad de Retina Quirúrgica y Tumores Intraoculares del Adulto (URQTIA), Servicio de Oftalmología Xerencia de Xestión Integrada de Santiago de Compostela, SERGAS, Santiago de Compostela, Spain.,Tumores Intraoculares en el Adulto, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Maria Pardo Perez
- Grupo Obesidómica, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Antonio Piñeiro Ces
- Unidad de Retina Quirúrgica y Tumores Intraoculares del Adulto (URQTIA), Servicio de Oftalmología Xerencia de Xestión Integrada de Santiago de Compostela, SERGAS, Santiago de Compostela, Spain.,Tumores Intraoculares en el Adulto, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Eun YG, Yoon YJ, Won KY, Lee YC. Circulating Tumor DNA in Saliva in an Orthotopic Head and Neck Cancer Mouse Model. Anticancer Res 2020; 40:191-199. [PMID: 31892567 DOI: 10.21873/anticanres.13940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 11/10/2022]
Abstract
AIM To evaluate the feasibility of conducting studies of saliva circulating tumor DNA (ctDNA) as a biomarker of metastasis or recurrence in our orthotopic head and neck cancer (HNC) mouse model. MATERIALS AND METHODS A mouse model of recurrence or metastasis after tongue cancer resection was developed. Blood and saliva were collected at baseline and at the establishment of recurrence or metastasis. Real-time polymerase chain reaction was performed to quantify human long interspersed element (hLINE) in samples to assess the amount of ctDNA. RESULTS In our model, salivary hLINE increased as the cancer developed and decreased after surgery. Plasma hLINE was significantly elevated in mice with metastasis. The presence of tongue cancer recurrence in mice was more correlated with hLINE concentration in saliva than in plasma. CONCLUSION In our orthotopic model, salivary ctDNA better reflected tumor development and recurrence than did plasma ctDNA.
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Affiliation(s)
- Young-Gyu Eun
- Department of Otolaryngology-Head & Neck Surgery, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Yu Jin Yoon
- Department of Otolaryngology-Head & Neck Surgery, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Kyu Yeoun Won
- Department of Pathology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Young Chan Lee
- Department of Otolaryngology-Head & Neck Surgery, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
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Parameshwaran K, Sharma P, Rajendra S, Stelzer-Braid S, Xuan W, Rawlinson WD. Circulating human papillomavirus DNA detection in Barrett's dysplasia and esophageal adenocarcinoma. Dis Esophagus 2019; 32:5532832. [PMID: 31313804 DOI: 10.1093/dote/doz064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/12/2019] [Accepted: 06/22/2019] [Indexed: 02/07/2023]
Abstract
There is evidence to suggest that human papillomaviruses (HPV) are associated with Barrett's dysplasia and esophageal adenocarcinoma. In other HPV-linked cancers such as cervical and oropharyngeal cancer, circulating HPV DNA is a potential biomarker to assist in tumor diagnosis and management. This study aimed to determine whether circulating HPV DNA was detectable in patients with Barrett's dysplasia and esophageal adenocarcinoma, and if so, whether there is any correlation with esophageal tissue HPV status. Plasma from 138 patients representing esophageal adenocarcinoma (N = 41), Barrett's dysplasia (N = 48) and hospital controls (N = 49) were analyzed for the presence of circulating HPV DNA using droplet-digital PCR targeting the E7 gene of HPV types 16 and 18. Circulating HPV DNA was detected in 11/138 (8.0%) study subjects including 1/49 (2.0%) hospital controls, 4/48 (8.3%) Barrett's dysplasia patients, and 6/41 (14.6%) esophageal adenocarcinoma patients. Detection of circulating HPV DNA was higher in patients with HPV-positive esophageal tissue (6/35, 17.1%) compared to those with HPV-negative specimens (5/103; 4.9%) (OR = 4.06; 95% CI 1.15-14.25; P = 0.020). The highest rates of detection occurred in esophageal adenocarcinoma patients, particularly those with invasive tumors that had breached the esophageal submucosa, had regional lymph node involvement or metastatic disease. Circulating HPV DNA was detectable in a subset of Barrett's dysplasia and esophageal adenocarcinoma patients. Detection was associated with tissue HPV positivity and possibly disease severity.
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Affiliation(s)
- K Parameshwaran
- Gastro-Intestinal Viral Oncology Group, Ingham Institute for Applied Medical Research.,South Western Sydney Clinical School
| | - P Sharma
- Gastro-Intestinal Viral Oncology Group, Ingham Institute for Applied Medical Research.,South Western Sydney Clinical School
| | - S Rajendra
- Gastro-Intestinal Viral Oncology Group, Ingham Institute for Applied Medical Research.,South Western Sydney Clinical School.,Department of Gastroenterology & Hepatology, Bankstown-Lidcombe Hospital, South Western Sydney Local Health Network, Bankstown, Sydney
| | - S Stelzer-Braid
- School of Medical Sciences, School of Biotechnology and Biomolecular Sciences, School of Women's and Children's Health, Faculties of Medicine and Science, University of New South Wales.,Serology and Virology Division (SAViD) NSW Health Pathology, Microbiology Department, Randwick NSW, Australia
| | - W Xuan
- South Western Sydney Clinical School.,Ingham Institute for Applied Medical Research
| | - W D Rawlinson
- School of Medical Sciences, School of Biotechnology and Biomolecular Sciences, School of Women's and Children's Health, Faculties of Medicine and Science, University of New South Wales.,Serology and Virology Division (SAViD) NSW Health Pathology, Microbiology Department, Randwick NSW, Australia
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45
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Mercier T, Reynders M, Beuselinck K, Guldentops E, Maertens J, Lagrou K. Serial Detection of Circulating Mucorales DNA in Invasive Mucormycosis: A Retrospective Multicenter Evaluation. J Fungi (Basel) 2019; 5:jof5040113. [PMID: 31816976 PMCID: PMC6958450 DOI: 10.3390/jof5040113] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022] Open
Abstract
Invasive mucormycosis is a fungal infection with high mortality. Early diagnosis and initiation of appropriate treatment is essential to improve survival. However, current diagnostic tools suffer from low sensitivity, leading to delayed or missed diagnoses. Recently, several PCR assays for the detection of Mucorales DNA have been developed. We retrospectively assessed the diagnostic and kinetic properties of a commercial Mucorales PCR assay (MucorGenius®, PathoNostics) on serial blood samples from patients with culture-positive invasive mucormycosis and found an overall sensitivity of 75%. Importantly, a positive test preceded a positive culture result by up to 81 days (median eight days, inter-quartile range 1.75–16.25). After initiation of appropriate therapy, the average levels of circulating DNA decreased after one week and stabilized after two weeks. In conclusion, detection of circulating Mucorales DNA appears to be a good, fast diagnostic test that often precedes the final diagnosis by several days to weeks. This test could be especially useful in cases in which sampling for culture or histopathology is not feasible.
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Affiliation(s)
- Toine Mercier
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, 3000 Leuven, Belgium
- Correspondence:
| | - Marijke Reynders
- Department of Laboratory Medicine, Medical Microbiology, AZ St Jan Bruges, 8000 Bruges, Belgium
| | - Kurt Beuselinck
- Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Ellen Guldentops
- Department of Hematology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Johan Maertens
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, 3000 Leuven, Belgium
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46
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Jiang F, Yang X, He X, Yang M. Circulating DNA, a Potentially Sensitive and Specific Diagnostic Tool for Future Medicine. Dose Response 2019; 17:1559325819891010. [PMID: 31827416 PMCID: PMC6886285 DOI: 10.1177/1559325819891010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 11/28/2022] Open
Abstract
Liquid biopsy has the great potential of detecting early diseases before deterioration and is valued for screening abnormalities at early stage. In oncology, circulating DNA derived from shed cancer cells reflects the tissue of origin, so it could be used to locate tissue sites during early screening. However, the heterogenous parameters of different types limit the clinical application, making it inaccessible to encompass all the cancer types. Instead, for reproducible scenario as pregnancy, fetal cell-free DNA has been well utilized for screening aneuploidies. Noninvasive and convenient as is, it would be of great value in the next decades far more than early diagnosis. This review recapitulates the discovery and development of tumor and fetal cell-free DNA. The common factors are also present that could be taken into consideration when collecting, transporting, and preserving samples. Meanwhile, several protocols used for purifying cell-free DNA, either classic ones or through commercial kits, are compared carefully. In addition, the development of technologies for analyzing cell-free DNA have been summarized and discussed in detail, especially some up-to-date approaches. At the end, the potential prospect of circulating DNA is bravely depicted. In summary, although there would be a lot of efforts before it’s prevalent, cell-free DNA remains a promising tool in point-of-care diagnostic medicine.
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Affiliation(s)
- Fan Jiang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiaoxiao Yang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiping He
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Mingming Yang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Winter H, Kaisaki PJ, Harvey J, Giacopuzzi E, Ferla MP, Pentony MM, Knight SJ, Sharma RA, Taylor JC, McCullagh JS. Identification of Circulating Genomic and Metabolic Biomarkers in Intrahepatic Cholangiocarcinoma. Cancers (Basel) 2019; 11:E1895. [PMID: 31795195 PMCID: PMC6966597 DOI: 10.3390/cancers11121895] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is an aggressive cancer arising from the bile ducts with a need for earlier diagnosis and a greater range of treatment options. KRAS/NRAS mutations are common in ICC tumours and 6-32% of patients also have isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) gene mutations associated with metabolic changes. This feasibility study investigated sequencing circulating tumour DNA (ctDNA) combined with metabolite profiling of plasma as a method for biomarker discovery in ICC patients. Plasma was collected from four ICC patients receiving radio-embolisation and healthy controls at multiple time points. ctDNA was sequenced using Ampliseq cancer hotspot panel-v2 on Ion Torrent PGM for single nucleotide variants (SNV) detection and with Illumina whole genome sequencing for copy number variants (CNV) and further targeted examination for SNVs. Untargeted analysis of metabolites from patient and control plasma was performed using liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-MS/MS). Metabolite identification was performed using multi-parameter comparisons with analysis of authentic standards, and univariate statistical analysis was performed to identify differences in metabolite abundance between patient and control samples. Recurrent somatic SNVs and CNVs were identified in ctDNA from three out of four patients that included both NRAS and IDH1 mutations linked to ICC. Plasma metabolite analysis revealed biomarker metabolites associated with ICC and in particular 2-hydroxyglutarate (2-HG) levels were elevated in both samples from the only patient showing a variant allele in IDH1. A reduction in the number of CNVs was observed with treatment. This study demonstrates that ctDNA and metabolite levels can be identified and correlated in ICC patient blood samples and differentiated from healthy controls. We conclude that combining genomic and metabolic analysis of plasma offers an effective approach to biomarker identification with potential for disease stratification and early detection studies.
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Affiliation(s)
- Helen Winter
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (H.W.); (P.J.K.); (E.G.); (M.P.F.); (M.M.P.); (J.C.T.)
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK;
- Bristol Cancer Institute, Horfield Rd, Bristol BS2 8ED, UK
| | - Pamela J. Kaisaki
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (H.W.); (P.J.K.); (E.G.); (M.P.F.); (M.M.P.); (J.C.T.)
| | - Joe Harvey
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK;
| | - Edoardo Giacopuzzi
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (H.W.); (P.J.K.); (E.G.); (M.P.F.); (M.M.P.); (J.C.T.)
| | - Matteo P. Ferla
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (H.W.); (P.J.K.); (E.G.); (M.P.F.); (M.M.P.); (J.C.T.)
| | - Melissa M. Pentony
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (H.W.); (P.J.K.); (E.G.); (M.P.F.); (M.M.P.); (J.C.T.)
| | - Samantha J.L. Knight
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (H.W.); (P.J.K.); (E.G.); (M.P.F.); (M.M.P.); (J.C.T.)
| | - Ricky A. Sharma
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK;
- NIHR University College London Hospitals Biomedical Research Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Jenny C. Taylor
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (H.W.); (P.J.K.); (E.G.); (M.P.F.); (M.M.P.); (J.C.T.)
| | - James S.O. McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK;
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48
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Tamkovich S, Laktionov P. Cell-surface-bound circulating DNA in the blood: Biology and clinical application. IUBMB Life 2019; 71:1201-1210. [PMID: 31091350 DOI: 10.1002/iub.2070] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/17/2019] [Indexed: 01/04/2023]
Abstract
Cell-surface-bound extracellular DNA (csbDNA) is present on the outer membrane of blood cells, including both red blood cells and leukocytes. Although less well characterized than cell-free DNA (cfDNA) in plasma and serum, leukocyte and red blood cell csbDNA form a considerable fraction of the blood extracellular nucleic acids pool, with typically at least comparable amount of DNA occurring bound to the outer surface of cells as compared with circulating free DNA in plasma. The cellular origin of csbDNA is not clear; however, as with cfDNA, in patients with cancer a proportion is derived from the tumor, thus making it potentially a useful source of DNA for cancer diagnosis, prognosis, and monitoring. © 2019 IUBMB Life, 71(9):1201-1210, 2019.
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Affiliation(s)
- Svetlana Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk National Research State University, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
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49
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Abstract
The clinical utility of tissue biopsies in cancer management will continue to expand, especially with the evolving role of targeted therapies. "Liquid biopsy" refers to testing a patient's biofluid samples such as blood or urine to detect tumor-derived molecules and cells that can be used diagnostically and prognostically in the assessment of cancer. Many proof-of-concept and pilot studies have shown the clinical potential of liquid biopsies as diagnostic and prognostic markers which would provide a surrogate for the conventional "solid biopsy". In this review, we focus on three methods of liquid biopsy-circulating tumor cells, extracellular vesicles, and circulating tumor DNA-to provide a landscape view of their clinical applicability in cancer management and research.
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Affiliation(s)
- Matthew Scarlotta
- 1 Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Cem Simsek
- 2 Division of Gastroenterology and Hepatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Amy K Kim
- 2 Division of Gastroenterology and Hepatology, Johns Hopkins School of Medicine, Baltimore, Maryland
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50
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Gutierrez J, Guimaraes AO, Lewin-Koh N, Berhanu A, Xu M, Cao Y, Kim J, Yan D, Chang JK, Dinoso JB, Koss CA, Clemenzi-Allen A, Chambers HF, Peck MC, Baruch A, Rosenberger CM. Sustained Circulating Bacterial Deoxyribonucleic Acid Is Associated With Complicated Staphylococcus aureus Bacteremia. Open Forum Infect Dis 2019; 6:ofz090. [PMID: 31024970 PMCID: PMC6475589 DOI: 10.1093/ofid/ofz090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/20/2019] [Indexed: 11/15/2022] Open
Abstract
Background Staphylococcus aureus (SA) bacteremia often requires a long treatment duration with antibiotics to prevent relapse due to the ability of SA to establish reservoirs of infection in sites such as heart and bone. These metastatic sites of infection cannot be serially sampled to monitor the clearance of SA infection. This study aimed to establish a link between persistence of circulating SA deoxyribonucleic acid (SA-DNA) and tissue reservoirs in patients with SA bacteremia. Methods A highly sensitive quantitative polymerase chain reaction was used to measure whole blood SA-DNA and plasma-derived SA cell-free DNA (SA-cfDNA) in a set of longitudinal samples from 73 patients with confirmed SA bacteremia and correlated with clinical features. Results Blood SA-DNA was detected for longer than the duration of positive blood cultures. Longer duration of circulating bacterial DNA was observed in complicated SA bacteremia infections, such as endocarditis and osteoarticular infections, compared with uncomplicated bloodstream infections. In contrast, traditional blood cultures demonstrated similar time to clearance regardless of foci of infection. Plasma-derived SA-cfDNA showed concordance with blood SA-DNA levels. Baseline levels of SA-DNA were higher in patients presenting with greater clinical severity and complicated bacteremia. Conclusions Prolonged levels of circulating SA-DNA in patients with complicated tissue reservoirs after clearance of blood cultures observed in this single-center study should be validated in additional cohorts to assess the potential utility for monitoring clearance of infection in patients with SA bacteremia.
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Affiliation(s)
| | | | | | | | - Min Xu
- Genentech, Inc., South San Francisco, California
| | - Yi Cao
- Genentech, Inc., South San Francisco, California
| | - Janice Kim
- Genentech, Inc., South San Francisco, California
| | - Donghong Yan
- Genentech, Inc., South San Francisco, California
| | | | | | | | | | | | | | - Amos Baruch
- Genentech, Inc., South San Francisco, California
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