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Miller CL, Herrmann M, Carter DRF, Turner N, Samuel P, Patel BA. Monitoring the electroactive cargo of extracellular vesicles can differentiate various cancer cell lines. Biosens Bioelectron 2024; 254:116224. [PMID: 38513539 DOI: 10.1016/j.bios.2024.116224] [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: 12/20/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 03/23/2024]
Abstract
Extracellular vesicles (EVs) are pivotal in cell-to-cell communication due to the array of cargo contained within these vesicles. EVs are considered important biomarkers for identification of disease, however most measurement approaches have focused on monitoring specific surface macromolecular targets. Our study focuses on exploring the electroactive component present within cargo from EVs obtained from various cancer and non-cancer cell lines using a disk carbon fiber microelectrode. Variations in the presence of oxidizable components were observed when the total cargo from EVs were measured, with the highest current detected in EVs from MCF7 cells. There were differences observed in the types of oxidizable species present within EVs from MCF7 and A549 cells. Single entity measurements showed clear spikes due to the detection of oxidizable cargo within EVs from MCF7 and A549 cells. These studies highlight the promise of monitoring EVs through the presence of varying electroactive components within the cargo and can drive a wave of new strategies towards specific detection of EVs for diagnosis and prognosis of various diseases.
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Affiliation(s)
- Chloe L Miller
- School of Applied Sciences, Italy; Centre for Lifelong Health, University of Brighton, Brighton, BN2 4GJ, UK
| | - Mareike Herrmann
- School of Applied Sciences, Italy; Centre for Lifelong Health, University of Brighton, Brighton, BN2 4GJ, UK
| | - David R F Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, OX3 0BP, UK
| | - Nicholas Turner
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Priya Samuel
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, OX3 0BP, UK
| | - Bhavik Anil Patel
- School of Applied Sciences, Italy; Centre for Lifelong Health, University of Brighton, Brighton, BN2 4GJ, UK.
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2
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Akbar N, Braithwaite AT, Corr EM, Koelwyn GJ, van Solingen C, Cochain C, Saliba AE, Corbin A, Pezzolla D, Møller Jørgensen M, Bæk R, Edgar L, De Villiers C, Gunadasa-Rohling M, Banerjee A, Paget D, Lee C, Hogg E, Costin A, Dhaliwal R, Johnson E, Krausgruber T, Riepsaame J, Melling GE, Shanmuganathan M, Bock C, Carter DRF, Channon KM, Riley PR, Udalova IA, Moore KJ, Anthony DC, Choudhury RP. Rapid neutrophil mobilization by VCAM-1+ endothelial cell-derived extracellular vesicles. Cardiovasc Res 2023; 119:236-251. [PMID: 35134856 PMCID: PMC10022859 DOI: 10.1093/cvr/cvac012] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/28/2022] [Indexed: 01/25/2023] Open
Abstract
AIMS Acute myocardial infarction rapidly increases blood neutrophils (<2 h). Release from bone marrow, in response to chemokine elevation, has been considered their source, but chemokine levels peak up to 24 h after injury, and after neutrophil elevation. This suggests that additional non-chemokine-dependent processes may be involved. Endothelial cell (EC) activation promotes the rapid (<30 min) release of extracellular vesicles (EVs), which have emerged as an important means of cell-cell signalling and are thus a potential mechanism for communicating with remote tissues. METHODS AND RESULTS Here, we show that injury to the myocardium rapidly mobilizes neutrophils from the spleen to peripheral blood and induces their transcriptional activation prior to arrival at the injured tissue. Time course analysis of plasma-EV composition revealed a rapid and selective increase in EVs bearing VCAM-1. These EVs, which were also enriched for miRNA-126, accumulated preferentially in the spleen where they induced local inflammatory gene and chemokine protein expression, and mobilized splenic-neutrophils to peripheral blood. Using CRISPR/Cas9 genome editing, we generated VCAM-1-deficient EC-EVs and showed that its deletion removed the ability of EC-EVs to provoke the mobilization of neutrophils. Furthermore, inhibition of miRNA-126 in vivo reduced myocardial infarction size in a mouse model. CONCLUSIONS Our findings show a novel EV-dependent mechanism for the rapid mobilization of neutrophils to peripheral blood from a splenic reserve and establish a proof of concept for functional manipulation of EV-communications through genetic alteration of parent cells.
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Affiliation(s)
- Naveed Akbar
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
| | - Adam T Braithwaite
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
| | - Emma M Corr
- NYU Cardiovascular Research Center, Department of Medicine, Division of Cardiology, School of Medicine, New York University School of Medicine, 435 E 30th St. New York, NY 10016, USA
| | - Graeme J Koelwyn
- NYU Cardiovascular Research Center, Department of Medicine, Division of Cardiology, School of Medicine, New York University School of Medicine, 435 E 30th St. New York, NY 10016, USA
| | - Coen van Solingen
- NYU Cardiovascular Research Center, Department of Medicine, Division of Cardiology, School of Medicine, New York University School of Medicine, 435 E 30th St. New York, NY 10016, USA
| | - Clément Cochain
- Comprehensive Heart Failure Center, University Hospital Wurzburg, Anstalt des öffentlichen Rechts Josef-Schneider-Straße 2 97080 Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Inhoffenstraße 7 38124 Braunschweig, Würzburg, Germany
| | - Alastair Corbin
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7FY, UK
| | - Daniela Pezzolla
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
| | - Malene Møller Jørgensen
- Department of Clinical Immunology, Aalborg University Hospital, Urbansgade 32-36, DK-9000, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, Aalborg, Denmark
| | - Rikke Bæk
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, Aalborg, Denmark
| | - Laurienne Edgar
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
| | - Carla De Villiers
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building Parks Road, OX1 3PT, Oxford, UK
| | - Mala Gunadasa-Rohling
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building Parks Road, OX1 3PT, Oxford, UK
| | - Abhirup Banerjee
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
| | - Daan Paget
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
| | - Charlotte Lee
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
| | - Eleanor Hogg
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
| | - Adam Costin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Raman Dhaliwal
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, Vienna, Austria
| | - Joey Riepsaame
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Genevieve E Melling
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington Campus Oxford OX3 0BP, UK
- Institute of Clinical Sciences, School of Biomedical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mayooran Shanmuganathan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
- The OxAMI Study is detailed in the Supplementary Acknowledgments
- Acute Vascular Imaging Centre, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, BT88 1090, Vienna, Austria
| | - David R F Carter
- Department of Biological and Medical Sciences, Oxford Brookes University, Headington Campus Oxford OX3 0BP, UK
| | - Keith M Channon
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
- The OxAMI Study is detailed in the Supplementary Acknowledgments
- Acute Vascular Imaging Centre, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building Parks Road, OX1 3PT, Oxford, UK
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7FY, UK
| | - Kathryn J Moore
- NYU Cardiovascular Research Center, Department of Medicine, Division of Cardiology, School of Medicine, New York University School of Medicine, 435 E 30th St. New York, NY 10016, USA
| | - Daniel C Anthony
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Robin P Choudhury
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine University of Oxford Level 6, West Wing John Radcliffe Hospital Headington Oxford OX3 9DU, UK
- The OxAMI Study is detailed in the Supplementary Acknowledgments
- Acute Vascular Imaging Centre, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
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van Niel G, Carter DRF, Clayton A, Lambert DW, Raposo G, Vader P. Challenges and directions in studying cell-cell communication by extracellular vesicles. Nat Rev Mol Cell Biol 2022; 23:369-382. [PMID: 35260831 DOI: 10.1038/s41580-022-00460-3] [Citation(s) in RCA: 316] [Impact Index Per Article: 158.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles (EVs) are increasingly recognized as important mediators of intercellular communication. They have important roles in numerous physiological and pathological processes, and show considerable promise as novel biomarkers of disease, as therapeutic agents and as drug delivery vehicles. Intriguingly, however, understanding of the cellular and molecular mechanisms that govern the many observed functions of EVs remains far from comprehensive, at least partly due to technical challenges in working with these small messengers. Here, we highlight areas of consensus as well as contentious issues in our understanding of the intracellular and intercellular journey of EVs: from biogenesis, release and dynamics in the extracellular space, to interaction with and uptake by recipient cells. We define knowledge gaps, identify key questions and challenges, and make recommendations on how to address these.
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Affiliation(s)
- Guillaume van Niel
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France. .,GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
| | - David R F Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK.,Evox Therapeutics Limited, Oxford Science Park, Oxford, UK
| | - Aled Clayton
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Daniel W Lambert
- School of Clinical Dentistry, The University of Sheffield, Sheffield, UK.,Neuroscience Institute, The University of Sheffield, Sheffield, UK.,Healthy Lifespan Institute, The University of Sheffield, Sheffield, UK
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France.,Institut Curie, PSL Research University, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Pieter Vader
- CDL Research, University Medical Center Utrecht, Utrecht, Netherlands. .,Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht, Netherlands.
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4
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Melling GE, Conlon R, Pantazi P, Dellar ER, Samuel P, Baena-Lopez LA, Simpson JC, Carter DRF. Confocal microscopy analysis reveals that only a small proportion of extracellular vesicles are successfully labelled with commonly utilised staining methods. Sci Rep 2022; 12:262. [PMID: 34997141 PMCID: PMC8741769 DOI: 10.1038/s41598-021-04225-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 07/07/2021] [Accepted: 11/24/2021] [Indexed: 12/14/2022] Open
Abstract
Assessing genuine extracellular vesicle (EV) uptake is crucial for understanding the functional roles of EVs. This study measured the bona fide labelling of EVs utilising two commonly used fluorescent dyes, PKH26 and C5-maleimide-Alexa633. MCF7 EVs tagged with mEmerald-CD81 were isolated from conditioned media by size exclusion chromatography (SEC) and characterised using Nanoparticle Tracking Analysis (NTA), Transmission Electron Microscopy (TEM), MACsPlex immunocapture assay and immunoblots. These fluorescently tagged EVs were subsequently stained with C5-maleimide-Alexa633 or PKH26, according to published protocols. Colocalisation of dual-labelled EVs was assessed by confocal microscopy and quantified using the Rank-Weighted Colocalisation (RWC) algorithm. We observed strikingly poor colocalisation between mEmerald-CD81-tagged EVs and C5-Maleimide-Alexa633 (5.4% ± 1.8) or PKH26 (4.6% ± 1.6), that remained low even when serum was removed from preparations. Our data confirms previous work showing that some dyes form contaminating aggregates. Furthermore, uptake studies showed that maleimide and mEmerald-CD81-tagged EVs can be often located into non-overlapping subcellular locations. By using common methods to isolate and stain EVs we observed that most EVs remained unstained and most dye signal does not appear to be EV associated. Our work shows that there is an urgent need for optimisation and standardisation in how EV researchers use these tools to assess genuine EV signals.
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Affiliation(s)
- Genevieve E Melling
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Institute of Clinical Sciences, School of Biomedical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ross Conlon
- Cell Screening Laboratory, School of Biology and Environmental Science, University College Dublin, Science Centre West, Belfield, Dublin 4, Ireland
| | - Paschalia Pantazi
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Institute of Reproductive and Developmental Biology, Imperial College London, Hammersmith Campus, London, UK
| | - Elizabeth R Dellar
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Priya Samuel
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Luis Alberto Baena-Lopez
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Jeremy C Simpson
- Cell Screening Laboratory, School of Biology and Environmental Science, University College Dublin, Science Centre West, Belfield, Dublin 4, Ireland.
| | - David R F Carter
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
- Evox Therapeutics Ltd, Oxford Science Park, Medawar Centre, Robert Robinson Avenue, Oxford, OX4 4HG, UK.
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5
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Couch Y, Buzàs EI, Vizio DD, Gho YS, Harrison P, Hill AF, Lötvall J, Raposo G, Stahl PD, Théry C, Witwer KW, Carter DRF. A brief history of nearly EV-erything - The rise and rise of extracellular vesicles. J Extracell Vesicles 2021; 10:e12144. [PMID: 34919343 PMCID: PMC8681215 DOI: 10.1002/jev2.12144] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [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: 05/19/2021] [Revised: 08/06/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Extracellular vesicles (EVs) are small cargo-bearing vesicles released by cells into the extracellular space. The field of EVs has grown exponentially over the past two decades; this growth follows the realisation that EVs are not simply a waste disposal system as had originally been suggested by some, but also a complex cell-to-cell communication mechanism. Indeed, EVs have been shown to transfer functional cargo between cells and can influence several biological processes. These small biological particles are also deregulated in disease. As we approach the 75th anniversary of the first experiments in which EVs were unknowingly isolated, it seems right to take stock and look back on how the field started, and has since exploded into its current state. Here we review the early experiments, summarise key findings that have propelled the field, describe the growth of an organised EV community, discuss the current state of the field, and identify key challenges that need to be addressed.
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Affiliation(s)
- Yvonne Couch
- Acute Stroke Programme, Radcliffe Department of MedicineUniversity of Oxford, John Radcliffe Hospital, Headley Way, HeadingtonOxfordUK
| | - Edit I. Buzàs
- Department of Genetics, Cell‐ and ImmunobiologySemmelweis UniversityBudapestHungary
- ELKH‐SE Immune‐Proteogenomics Extracellular Vesicle Research GroupBudapestHungary
- HCEMM‐SU Extracellular Vesicles Research GroupBudapestHungary
| | - Dolores Di Vizio
- Department of SurgeryPathology & Laboratory MedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Yong Song Gho
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Paul Harrison
- Institute of Inflammation and AgeingCollege of Medical and Dental SciencesUniversity of BirminghamEdgbastonBirminghamUK
| | - Andrew F. Hill
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Jan Lötvall
- Krefting Research CentreInstitute of Medicine Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Graça Raposo
- Institut CurieParis Sciences et Lettres Research UniversityCentre National de la Recherche Scientifique UMR144, Structure and Membrane CompartmentsParisFrance
| | - Philip D. Stahl
- Department of Cell BiologyWashington University School of MedicineSt LouisMissouriUSA
| | - Clotilde Théry
- INSERM U932Institut CurieParis Sciences et Lettres Research UniversityParisFrance
| | - Kenneth W. Witwer
- Molecular and Comparative Pathobiology and Neurology, and The Richman Family Precision Medicine Center of Excellence in Alzheimer’s DiseaseThe Johns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - David R. F. Carter
- Department of Biological and Medical SciencesFaculty of Health and Life SciencesOxford Brookes UniversityOxfordUK
- Evox Therapeutics LimitedOxford Science ParkOxfordOX4 4HGUK
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6
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Verweij FJ, Balaj L, Boulanger CM, Carter DRF, Compeer EB, D'Angelo G, El Andaloussi S, Goetz JG, Gross JC, Hyenne V, Krämer-Albers EM, Lai CP, Loyer X, Marki A, Momma S, Nolte-'t Hoen ENM, Pegtel DM, Peinado H, Raposo G, Rilla K, Tahara H, Théry C, van Royen ME, Vandenbroucke RE, Wehman AM, Witwer K, Wu Z, Wubbolts R, van Niel G. The power of imaging to understand extracellular vesicle biology in vivo. Nat Methods 2021; 18:1013-1026. [PMID: 34446922 PMCID: PMC8796660 DOI: 10.1038/s41592-021-01206-3] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023]
Abstract
Extracellular vesicles (EVs) are nano-sized lipid bilayer vesicles released by virtually every cell type. EVs have diverse biological activities, ranging from roles in development and homeostasis to cancer progression, which has spurred the development of EVs as disease biomarkers and drug nanovehicles. Owing to the small size of EVs, however, most studies have relied on isolation and biochemical analysis of bulk EVs separated from biofluids. Although informative, these approaches do not capture the dynamics of EV release, biodistribution, and other contributions to pathophysiology. Recent advances in live and high-resolution microscopy techniques, combined with innovative EV labeling strategies and reporter systems, provide new tools to study EVs in vivo in their physiological environment and at the single-vesicle level. Here we critically review the latest advances and challenges in EV imaging, and identify urgent, outstanding questions in our quest to unravel EV biology and therapeutic applications.
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Affiliation(s)
- Frederik J Verweij
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France.
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - David R F Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
- Evox Therapeutics Limited, Oxford Science Park, Oxford, UK
| | - Ewoud B Compeer
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Gisela D'Angelo
- Institut Curie, PSL Research University, CNRS, UMR144 Cell Biology and Cancer, Paris, France
| | - Samir El Andaloussi
- Evox Therapeutics Limited, Oxford Science Park, Oxford, UK
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jacky G Goetz
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Equipe Labellisée Ligue contre le Cancer, Strasbourg, France
| | | | - Vincent Hyenne
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Equipe Labellisée Ligue contre le Cancer, Strasbourg, France
- CNRS SNC5055, Strasbourg, France
| | - Eva-Maria Krämer-Albers
- Johannes Gutenberg-Universität Mainz, Institute of Developmental Biology and Neurobiology, Mainz, Germany
| | - Charles P Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Xavier Loyer
- Université de Paris, PARCC, INSERM, Paris, France
| | - Alex Marki
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Stefan Momma
- Institute of Neurology (Edinger Institute), Goethe-University, Frankfurt am Main, Germany
| | - Esther N M Nolte-'t Hoen
- Department of Biomolecular Health Sciences, Faculty of veterinary medicine, Utrecht University, Utrecht, the Netherlands
| | - D Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144 Cell Biology and Cancer, Paris, France
| | - Kirsi Rilla
- University of Eastern Finland, Institute of Biomedicine, Kuopio, Finland
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Clotilde Théry
- Institut Curie, PSL Research University, INSERM U932, Immunity and Cancer, Paris, France
| | | | - Roosmarijn E Vandenbroucke
- VIB Center for Inflammation Research and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Ann M Wehman
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Kenneth Witwer
- Department of Molecular and Comparative Pathobiology and Neurology and the Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China
- Medical School, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China
| | - Richard Wubbolts
- Department of Biomolecular Health Sciences, Faculty of veterinary medicine, Utrecht University, Utrecht, the Netherlands
| | - Guillaume van Niel
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France.
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
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7
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Fontana F, Carollo E, Melling GE, Carter DRF. Extracellular Vesicles: Emerging Modulators of Cancer Drug Resistance. Cancers (Basel) 2021; 13:749. [PMID: 33670185 PMCID: PMC7916933 DOI: 10.3390/cancers13040749] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 01/13/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) have recently emerged as crucial modulators of cancer drug resistance. Indeed, it has been shown that they can directly sequester anti-tumor drugs, decreasing their effective concentration at target sites. Moreover, they facilitate the horizontal transfer of specific bioactive cargoes able to regulate proliferative, apoptotic, and stemness programs in recipient cells, potentially conferring a resistant phenotype to drug-sensitive cancer cells. Finally, EVs can mediate the communication between the tumor and both stromal and immune cells within the microenvironment, promoting treatment escape. In this context, clarifying the EV-driven resistance mechanisms might improve not only tumor diagnosis and prognosis but also therapeutic outcomes. Detailed cellular and molecular events occurring during the development of EV-mediated cancer drug resistance are described in this review article.
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Affiliation(s)
- Fabrizio Fontana
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti 9, 20133 Milan, Italy
| | - Emanuela Carollo
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, UK; (E.C.); (G.E.M.)
| | - Genevieve E. Melling
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, UK; (E.C.); (G.E.M.)
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - David R. F. Carter
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, UK; (E.C.); (G.E.M.)
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8
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Welsh JA, van der Pol E, Bettin BA, Carter DRF, Hendrix A, Lenassi M, Langlois MA, Llorente A, van de Nes AS, Nieuwland R, Tang V, Wang L, Witwer KW, Jones JC. Towards defining reference materials for measuring extracellular vesicle refractive index, epitope abundance, size and concentration. J Extracell Vesicles 2020; 9:1816641. [PMID: 33062218 PMCID: PMC7534292 DOI: 10.1080/20013078.2020.1816641] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Accurate characterization of extracellular vesicles (EVs) is critical to explore their diagnostic and therapeutic applications. As the EV research field has developed, so too have the techniques used to characterize them. The development of reference materials are required for the standardization of these techniques. This work, initiated from the ISEV 2017 Biomarker Workshop in Birmingham, UK, and with further discussion during the ISEV 2019 Standardization Workshop in Ghent, Belgium, sets out to elucidate which reference materials are required and which are currently available to standardize commonly used analysis platforms for characterizing EV refractive index, epitope abundance, size and concentration. Due to their predominant use among EV researchers, a particular focus is placed on the optical methods nanoparticle tracking analysis and flow cytometry.
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Affiliation(s)
- Joshua A Welsh
- Translational Nanobiology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Edwin van der Pol
- Vesicle Observation Center, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Biomedical Engineering & Physics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Britta A Bettin
- Vesicle Observation Center, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - David R F Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University Hospital, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Metka Lenassi
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marc-André Langlois
- University of Ottawa Flow Cytometry and Virometry Core Facility, Ottawa, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Ottawa Center for Infection, Immunity and Inflammation, Ottawa, Canada
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Norway
| | | | - Rienk Nieuwland
- Vesicle Observation Center, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands.,Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Vera Tang
- University of Ottawa Flow Cytometry and Virometry Core Facility, Ottawa, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Lili Wang
- National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
| | - Kenneth W Witwer
- Departments of Molecular and Comparative Pathobiology and Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer C Jones
- Translational Nanobiology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, USA
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9
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Börger V, Weiss DJ, Anderson JD, Borràs FE, Bussolati B, Carter DRF, Dominici M, Falcón-Pérez JM, Gimona M, Hill AF, Hoffman AM, de Kleijn D, Levine BL, Lim R, Lötvall J, Mitsialis SA, Monguió-Tortajada M, Muraca M, Nieuwland R, Nowocin A, O'Driscoll L, Ortiz LA, Phinney DG, Reischl I, Rohde E, Sanzenbacher R, Théry C, Toh WS, Witwer KW, Lim SK, Giebel B. International Society for Extracellular Vesicles and International Society for Cell and Gene Therapy statement on extracellular vesicles from mesenchymal stromal cells and other cells: considerations for potential therapeutic agents to suppress coronavirus disease-19. Cytotherapy 2020; 22:482-485. [PMID: 32425691 PMCID: PMC7229942 DOI: 10.1016/j.jcyt.2020.05.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 02/08/2023]
Abstract
STATEMENT The International Society for Cellular and Gene Therapies (ISCT) and the International Society for Extracellular Vesicles (ISEV) recognize the potential of extracellular vesicles (EVs, including exosomes) from mesenchymal stromal cells (MSCs) and possibly other cell sources as treatments for COVID-19. Research and trials in this area are encouraged. However, ISEV and ISCT do not currently endorse the use of EVs or exosomes for any purpose in COVID-19, including but not limited to reducing cytokine storm, exerting regenerative effects or delivering drugs, pending the generation of appropriate manufacturing and quality control provisions, pre-clinical safety and efficacy data, rational clinical trial design and proper regulatory oversight.
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Affiliation(s)
- Verena Börger
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daniel J Weiss
- Department of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Johnathon D Anderson
- Department of Otolaryngology, Stem Cell Program, University of California, Davis, Davis, California, USA
| | - Francesc E Borràs
- REMAR-IVECAT Group, Health Science Research Institute Germans Trias i Pujol (IGTP), Can Ruti Campus, and Nephrology Service, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - David R F Carter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Massimo Dominici
- Department of Medical and Surgical Sciences of Children and Adults, University Hospital of Modena, Modena, Italy
| | - Juan M Falcón-Pérez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain; Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Mario Gimona
- GMP Unit and EV-TT Transfer Center, Spinal Cord Injury & Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University (PMU), Salzburg, Austria
| | - Andrew F Hill
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Andrew M Hoffman
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dominique de Kleijn
- Department of Vascular Surgery, University Medical Center Utrecht and Netherlands Heart Institute, Utrecht, the Netherlands
| | - Bruce L Levine
- Center for Cellular Immunotherapies at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rebecca Lim
- Department of Obstetrics and Gynaecology, Hudson Institute of Medical Research, Monash University and The Ritchie Centre, Melbourne, Australia
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - S Alex Mitsialis
- Department of Pediatrics, Harvard Medical School and Boston Children's Hospital, Boston, Massachusetts, USA
| | - Marta Monguió-Tortajada
- ICREC Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Can Ruti Campus, and Cardiology Service, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Maurizio Muraca
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry and Vesicle Observation Center, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Anna Nowocin
- Biotherapeutics, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Lorraine O'Driscoll
- School of Pharmacy and Pharmaceutical Sciences and Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Luis A Ortiz
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Donald G Phinney
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, USA
| | - Ilona Reischl
- Federal Office for Safety in Health Care (BASG) and Austrian Agency for Health and Food Safety (AGES), Institute Surveillance, Vienna, Austria
| | - Eva Rohde
- Department of Transfusion Medicine, University Hospital, Salzburger Landeskliniken GesmbH (SALK), Salzburg, Austria; GMP Unit, Spinal Cord Injury & Tissue Regeneration Centre Salzburg (SCI-TReCS), Paracelsus Medical University (PMU), Salzburg, Austria
| | - Ralf Sanzenbacher
- Section Tissue Engineering and Cell Therapeutics, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Clotilde Théry
- Institut Curie/INSERM U932/PSL Research University, Paris, France
| | - Wei Seong Toh
- Faculty of Dentistry, National University of Singapore, Singapore
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - Sai Kiang Lim
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore.
| | - Bernd Giebel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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10
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Bartelli TF, Senda de Abrantes LL, Freitas HC, Thomas AM, Silva JM, Albuquerque GE, Araújo LF, Branco GP, de Amorim MG, Serpa MS, Takenaka IKTM, Souza DT, Monção LO, Moda BS, Valieris R, Defelicibus A, Borges R, Drummond RD, Alves FIA, Santos MNP, Bobrovnitchaia IG, Elhaik E, Coelho LGV, Khayat A, Demachki S, Assumpção PP, Santiago KM, Torrezan GT, Carraro DM, Peres SV, Calsavara VF, Burbano R, Nóbrega CR, Baladão GPP, Pereira ACC, Gatti CM, Fagundes MA, Araújo MS, Miranda TV, Barbosa MS, Cardoso DMM, Carneiro LC, Brito AM, Ramos AFPL, Silva LLL, Pontes JC, Tiengo T, Arantes PE, Santana V, Cordeiro M, Sant’Ana RO, Andrade HB, Anaissi AKM, Sampaio SV, Abdallah EA, Chinen LTD, Braun AC, Flores BCT, Mello CAL, Claro LCL, Sztokfisz CZ, Altamirano CC, Carter DRF, Jesus VHF, Riechelmann R, Medina T, Gollob KJ, Martins VR, Setúbal JC, Pelosof AG, Coimbra FJ, Costa-Jr WL, Silva IT, Nunes DN, Curado MP, Dias-Neto E. Genomics and epidemiology for gastric adenocarcinomas (GE4GAC): a Brazilian initiative to study gastric cancer. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41241-019-0081-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abstract
Gastric cancer (GC) is the fifth most common type of cancer worldwide with high incidences in Asia, Central, and South American countries. This patchy distribution means that GC studies are neglected by large research centers from developed countries. The need for further understanding of this complex disease, including the local importance of epidemiological factors and the rich ancestral admixture found in Brazil, stimulated the implementation of the GE4GAC project. GE4GAC aims to embrace epidemiological, clinical, molecular and microbiological data from Brazilian controls and patients with malignant and pre-malignant gastric disease. In this letter, we summarize the main goals of the project, including subject and sample accrual and current findings.
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11
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Debrand E, Chakalova L, Miles J, Dai YF, Goyenechea B, Dye S, Osborne CS, Horton A, Harju-Baker S, Pink RC, Caley D, Carter DRF, Peterson KR, Fraser P. An intergenic non-coding RNA promoter required for histone modifications in the human β-globin chromatin domain. PLoS One 2019; 14:e0217532. [PMID: 31412036 PMCID: PMC6693763 DOI: 10.1371/journal.pone.0217532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/22/2019] [Indexed: 12/05/2022] Open
Abstract
Transcriptome analyses show a surprisingly large proportion of the mammalian genome is transcribed; much more than can be accounted for by genes and introns alone. Most of this transcription is non-coding in nature and arises from intergenic regions, often overlapping known protein-coding genes in sense or antisense orientation. The functional relevance of this widespread transcription is unknown. Here we characterize a promoter responsible for initiation of an intergenic transcript located approximately 3.3 kb and 10.7 kb upstream of the adult-specific human β-globin genes. Mutational analyses in β-YAC transgenic mice show that alteration of intergenic promoter activity results in ablation of H3K4 di- and tri-methylation and H3 hyperacetylation extending over a 30 kb region immediately downstream of the initiation site, containing the adult δ- and β-globin genes. This results in dramatically decreased expression of the adult genes through position effect variegation in which the vast majority of definitive erythroid cells harbor inactive adult globin genes. In contrast, expression of the neighboring ε- and γ-globin genes is completely normal in embryonic erythroid cells, indicating a developmentally specific variegation of the adult domain. Our results demonstrate a role for intergenic non-coding RNA transcription in the propagation of histone modifications over chromatin domains and epigenetic control of β-like globin gene transcription during development.
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Affiliation(s)
- Emmanuel Debrand
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Lyubomira Chakalova
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Joanne Miles
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Yan-Feng Dai
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Beatriz Goyenechea
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Sandra Dye
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Cameron S. Osborne
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Alice Horton
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Susanna Harju-Baker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Ryan C. Pink
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Daniel Caley
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - David R. F. Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Kenneth R. Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Peter Fraser
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
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12
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Clayton A, Buschmann D, Byrd JB, Carter DRF, Cheng L, Compton C, Daaboul G, Devitt A, Falcon-Perez JM, Gardiner C, Gustafson D, Harrison P, Helmbrecht C, Hendrix A, Hill A, Hoffman A, Jones JC, Kalluri R, Kang JY, Kirchner B, Lässer C, Lawson C, Lenassi M, Levin C, Llorente A, Martens-Uzunova ES, Möller A, Musante L, Ochiya T, Pink RC, Tahara H, Wauben MHM, Webber JP, Welsh JA, Witwer KW, Yin H, Nieuwland R. Summary of the ISEV workshop on extracellular vesicles as disease biomarkers, held in Birmingham, UK, during December 2017. J Extracell Vesicles 2018; 7:1473707. [PMID: 31162490 PMCID: PMC5965025 DOI: 10.1080/20013078.2018.1473707] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [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: 01/30/2018] [Accepted: 04/28/2018] [Indexed: 01/06/2023] Open
Abstract
This report summarises the presentations and activities of the ISEV Workshop on extracellular vesicle biomarkers held in Birmingham, UK during December 2017. Among the key messages was broad agreement about the importance of biospecimen science. Much greater attention needs to be paid towards the provenance of collected samples. The workshop also highlighted clear gaps in our knowledge about pre-analytical factors that alter extracellular vesicles (EVs). The future utility of certified standards for credentialing of instruments and software, to analyse EV and for tracking the influence of isolation steps on the structure and content of EVs were also discussed. Several example studies were presented, demonstrating the potential utility for EVs in disease diagnosis, prognosis, longitudinal serial testing and stratification of patients. The conclusion of the workshop was that more effort focused on pre-analytical issues and benchmarking of isolation methods is needed to strengthen collaborations and advance more effective biomarkers.
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Affiliation(s)
- Aled Clayton
- Tissue Microenvironment Group, School of Medicine, Cardiff University, Cardiff, UK
| | - Dominik Buschmann
- Division of Animal Physiology and Immunology, Technical University of Munich and Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
| | - J Brian Byrd
- Department of Internal Medicine, University of Michigan, 5570C MSRB II, Ann Arbor, USA
| | - David R F Carter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Lesley Cheng
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Carolyn Compton
- SkySong Center for Innovation, Arizona State University, Scottsdale, AZ, USA
| | | | - Andrew Devitt
- School of Life & Health Sciences, Aston University, Birmingham, UK
| | - Juan Manuel Falcon-Perez
- Exosomes Laboratory & Metabolomics Platform, CIC bioGUNE, CIBEREHD, IKERBASQUE Research Foundation, Derio, Spain
| | - Chris Gardiner
- Research Department of Haematology, Haemostasis Research, University College London, London, UK
| | - Dakota Gustafson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Paul Harrison
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and experimental Cancer Research, Ghent University, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium
| | - Andrew Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Andrew Hoffman
- Regenerative Medicine Laboratory, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Jennifer C Jones
- Department of Vaccine Branch, National Cancer Institute, Bethesda, MD, USA
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ji Yoon Kang
- Korea Institute of Science and Technology, Center for Bio-microsystems, Seoul, S. Korea
| | - Benedikt Kirchner
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Cecilia Lässer
- Institute of Medicine at Sahlgrenska Academy Krefting Research Centre University of Gothenburg, Gothenburg, Sweden
| | - Charlotte Lawson
- Department of Comparative Biomedical Sciences, Royal Veterinary College Royal College Street, London, UK
| | - Metka Lenassi
- Institute of Biochemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Carina Levin
- Afula and The Bruce Rappaport Faculty of Medicine, Emek Medical Center, Technion, Haifa, Israel
| | - Alicia Llorente
- Department of Molecular Cell Biology, Oslo University Hospital, Oslo, Norway
| | | | - Andreas Möller
- Tumour Microenvironment Laboratory, Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, Australia
| | - Luca Musante
- Department of Medicine, Division of Nephrology, University of Virginia, Charlottesville, VA, USA
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Ryan C Pink
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Institute and Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima City, Japan
| | - Marca H M Wauben
- Faculty of Veterinary Medicine, Dept. Biochemistry & Cell Biology, Utrecht University, Utrecht, The Netherlands
| | - Jason P Webber
- Tissue Microenvironment Group, School of Medicine, Cardiff University, Cardiff, UK
| | - Joshua A Welsh
- Department of Vaccine Branch, National Cancer Institute, Bethesda, MD, USA
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins Institute for NanoBio Technology, Johns Hopkins University, Baltimore, USA
| | - Hang Yin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Rienk Nieuwland
- Department Laboratory Experimental Clinical Chemistry, Academic Medical Center, University of Amsterdam, DE, Amsterdam, The Netherlands
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13
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Wei Z, Batagov AO, Carter DRF, Krichevsky AM. Fetal Bovine Serum RNA Interferes with the Cell Culture derived Extracellular RNA. Sci Rep 2016; 6:31175. [PMID: 27503761 PMCID: PMC4977539 DOI: 10.1038/srep31175] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/13/2016] [Indexed: 12/17/2022] Open
Abstract
Fetal bovine serum (FBS) has been used in eukaryotic cell cultures for decades. However, little attention has been paid to the biological effects associated with RNA content of FBS on cell cultures. Here, using RNA sequencing, we demonstrate that FBS contains a diverse repertoire of protein-coding and regulatory RNA species, including mRNA, miRNA, rRNA, and snoRNA. The majority of them (>70%) are retained even after extended ultracentrifugation in the preparations of vesicle-depleted FBS (vdFBS) commonly utilized in the studies of extracellular vesicles (EV) and intercellular communication. FBS-associated RNA is co-isolated with cell-culture derived extracellular RNA (exRNA) and interferes with the downstream RNA analysis. Many evolutionally conserved FBS-derived RNA species can be falsely annotated as human or mouse transcripts. Notably, specific miRNAs abundant in FBS, such as miR-122, miR-451a and miR-1246, have been previously reported as enriched in cell-culture derived EVs, possibly due to the confounding effect of the FBS. Analysis of publically available exRNA datasets supports the notion of FBS contamination. Furthermore, FBS transcripts can be taken up by cultured cells and affect the results of highly sensitive gene expression profiling technologies. Therefore, precautions for experimental design are warranted to minimize the interference and misinterpretations caused by FBS-derived RNA.
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Affiliation(s)
- Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Arsen O Batagov
- Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, Singapore 138671, Singapore
| | - David R F Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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14
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Carter JM, Baker SC, Pink R, Carter DRF, Collins A, Tomlin J, Gibbs M, Breuker CJ. Unscrambling butterfly oogenesis. BMC Genomics 2013; 14:283. [PMID: 23622113 PMCID: PMC3654919 DOI: 10.1186/1471-2164-14-283] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/05/2013] [Indexed: 12/16/2022] Open
Abstract
Background Butterflies are popular model organisms to study physiological mechanisms
underlying variability in oogenesis and egg provisioning in response to
environmental conditions. Nothing is known, however, about; the
developmental mechanisms governing butterfly oogenesis, how polarity in the
oocyte is established, or which particular maternal effect genes regulate
early embryogenesis. To gain insights into these developmental mechanisms
and to identify the conserved and divergent aspects of butterfly oogenesis,
we analysed a de novo ovarian transcriptome of the Speckled Wood
butterfly Pararge aegeria (L.), and compared the results with known
model organisms such as Drosophila melanogaster and Bombyx
mori. Results A total of 17306 contigs were annotated, with 30% possibly novel or highly
divergent sequences observed. Pararge aegeria females expressed
74.5% of the genes that are known to be essential for D.
melanogaster oogenesis. We discuss the genes involved in all
aspects of oogenesis, including vitellogenesis and choriogenesis, plus those
implicated in hormonal control of oogenesis and transgenerational hormonal
effects in great detail. Compared to other insects, a number of significant
differences were observed in; the genes involved in stem cell maintenance
and differentiation in the germarium, establishment of oocyte polarity, and
in several aspects of maternal regulation of zygotic development. Conclusions This study provides valuable resources to investigate a number of divergent
aspects of butterfly oogenesis requiring further research. In order to fully
unscramble butterfly oogenesis, we also now also have the resources to
investigate expression patterns of oogenesis genes under a range of
environmental conditions, and to establish their function.
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Affiliation(s)
- Jean-Michel Carter
- Evolutionary Developmental Biology Research Group, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford, OX3 0BP, UK
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15
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Al-Mayah AHJ, Irons SL, Pink RC, Carter DRF, Kadhim MA. Possible role of exosomes containing RNA in mediating nontargeted effect of ionizing radiation. Radiat Res 2012; 177:539-45. [PMID: 22612287 DOI: 10.1667/rr2868.1] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Communication between irradiated and un-irradiated (bystander) cells can cause damage in cells that are not directly targeted by ionizing radiation, a process known as the bystander effect. Bystander effects can also lead to chromosomal/genomic instability within the progeny of bystander cells, similar to the progeny of directly irradiated cells. The factors that mediate this cellular communication can be transferred between cells via gap junctions or released into the extracellular media following irradiation, but their nature has not been fully characterized. In this study we tested the hypothesis that the bystander effect mediator contains an RNA molecule that may be carried by exosomes. MCF7 cells were irradiated with 2 Gy of X rays and the extracellular media was harvested. RNase treatment abrogated the ability of the media to induce early and late chromosomal damage in bystander cells. Furthermore, treatment of bystander cells with exosomes isolated from this media increased the levels of genomic damage. These results suggest that the bystander effect, and genomic instability, are at least in part mediated by exosomes and implicate a role for RNA.
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Affiliation(s)
- Ammar H J Al-Mayah
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, United Kingdom
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16
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Pink RC, Bailey TA, Iputo JE, Sammon AM, Woodman AC, Carter DRF. Molecular basis for maize as a risk factor for esophageal cancer in a South African population via a prostaglandin E2 positive feedback mechanism. Nutr Cancer 2011; 63:714-21. [PMID: 21667399 DOI: 10.1080/01635581.2011.570893] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The incidence of squamous cancer of the esophagus varies up to a hundredfold in different regions of the world. In Transkei, South Africa, a particularly high incidence of the disease is observed. We have previously proposed an association between a maize-rich diet and elevated levels of intragastric prostaglandin E2 production (PGE(2)). Here we investigate the molecular mechanisms by which a high-maize diet could lead to increased incidence of squamous cancer of the esophagus. We confirm that levels of PGE(2) are high (606.8 pg/ml) in the gastric fluid of individuals from Transkei. We also show that treatment of esophageal cells with linoleic acid, which is found at high levels in maize and is a precursor to PGE(2), leads to increased cell proliferation. Similarly, treatment of cells with PGE(2) or with gastric fluid from Transkeians also leads to increased proliferation. Our data suggest that the high levels of PGE(2) associated with a maize-rich diet stimulate cell division and induce the enzyme COX 2, resulting in a positive feedback mechanism that predisposes the esophagus to carcinoma.
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Affiliation(s)
- Ryan C Pink
- Cranfield Health, Cranfield University, Cranfield, Bedfordshire, United Kingdom.
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Pink RC, Eskiw CH, Caley DP, Carter DRF. Analysis of β-globin chromatin micro-environment using a novel 3C variant, 4Cv. PLoS One 2010; 5. [PMID: 20927371 PMCID: PMC2947503 DOI: 10.1371/journal.pone.0013045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 09/07/2010] [Indexed: 12/13/2022] Open
Abstract
Higher order chromatin folding is critical to a number of developmental processes, including the regulation of gene expression. Recently developed biochemical techniques such as RNA TRAP and chromosome conformation capture (3C) have provided us with the tools to probe chromosomal structures. These techniques have been applied to the β-globin locus, revealing a complex pattern of interactions with regions along the chromosome that the gene resides on. However, biochemical and microscopy data on the nature of β-globin interactions with other chromosomes is contradictory. Therefore we developed a novel 4C variant, Complete-genome 3C by vectorette amplification (4Cv), which allows an unbiased and quantitative method to examine chromosomal structure. We have used 4Cv to study the microenvironment of the β-globin locus in mice and show that a significant proportion of the interactions of β-globin are inter-chromosomal. Furthermore, our data show that in the liver, where the gene is active, β-globin is more likely to interact with other chromosomes, compared to the brain where the gene is silent and is more likely to interact with other regions along the same chromosome. Our data suggest that transcriptional activation of the β-globin locus leads to a change in nuclear position relative to the chromosome territory.
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Affiliation(s)
- Ryan C Pink
- School of Life Sciences, Oxford Brookes University, Oxford, United Kingdom
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Abstract
The way in which the genome of a multicellular organism can orchestrate the differentiation of trillions of cells and many organs, all from a single fertilized egg, is the subject of intense study. Different cell types can be defined by the networks of genes they express. This differential expression is regulated at the epigenetic level by chromatin modifications, such as DNA and histone methylation, which interact with structural and enzymatic proteins, resulting in the activation or silencing of any given gene. While detailed mechanisms are emerging on the role of different chromatin modifications and how these functions are effected at the molecular level, it is still unclear how their deposition across the epigenomic landscape is regulated in different cells. A raft of recent evidence is accumulating that implicates long noncoding RNAs (lncRNAs) in these processes. Most genomes studied to date undergo widespread transcription, the majority of which is not translated into proteins. In this review, we will describe recent work suggesting that lncRNAs are more than transcriptional "noise", but instead play a functional role by acting as tethers and guides to bind proteins responsible for modifying chromatin and mediating their deposition at specific genomic locations. We suggest that lncRNAs are at the heart of developmental regulation, determining the epigenetic status and transcriptional network in any given cell type, and that they provide a means to integrate external differentiation cues with dynamic nuclear responses through the regulation of a metastable epigenome. Better characterization of the lncRNA-protein "interactome" may eventually lead to a new molecular toolkit, allowing researchers and clinicians to modulate the genome at the epigenetic level to treat conditions such as cancer.
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Eskiw CH, Rapp A, Carter DRF, Cook PR. RNA polymerase II activity is located on the surface of protein-rich transcription factories. J Cell Sci 2008; 121:1999-2007. [PMID: 18495842 DOI: 10.1242/jcs.027250] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We used electron spectroscopic imaging to map nucleoplasmic transcription sites in human cells at unprecedented resolution. HeLa cells were permeabilised, nascent transcripts were extended in BrUTP by approximately 40 nucleotides and the resulting BrRNA immunolabelled with gold particles before structures were viewed. Nascent RNA is almost invariably associated with polymorphic and nitrogen-rich (but phosphorus-poor) structures with a diameter of approximately 87 nm and mass of 10 MDa (calculated by reference to nucleosomes with known numbers of phosphorus and nitrogen atoms). Structures with similar atomic signatures and diameters were observed using correlative microscopy and in unpermeabilised cells. Our results are consistent with RNA synthesis occurring on the surface of these huge protein-rich transcription factories.
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