1
|
Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
Collapse
Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
2
|
Ramalhete L, Araújo R, Ferreira A, Calado CRC. Exosomes and microvesicles in kidney transplantation: the long road from trash to gold. Pathology 2024; 56:1-10. [PMID: 38071158 DOI: 10.1016/j.pathol.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 01/24/2024]
Abstract
Kidney transplantation significantly enhances the survival rate and quality of life of patients with end-stage kidney disease. The ability to predict post-transplantation rejection events in their early phases can reduce subsequent allograft loss. Therefore, it is critical to identify biomarkers of rejection processes that can be acquired on routine analysis of samples collected by non-invasive or minimally invasive procedures. It is also important to develop new therapeutic strategies that facilitate optimisation of the dose of immunotherapeutic drugs and the induction of allograft immunotolerance. This review explores the challenges and opportunities offered by extracellular vesicles (EVs) present in biofluids in the discovery of biomarkers of rejection processes, as drug carriers and in the induction of immunotolerance. Since EVs are highly complex structures and their composition is affected by the parent cell's metabolic status, the importance of defining standardised methods for isolating and characterising EVs is also discussed. Understanding the major bottlenecks associated with all these areas will promote the further investigation of EVs and their translation into a clinical setting.
Collapse
Affiliation(s)
- Luis Ramalhete
- Blood and Transplantation Center of Lisbon, Instituto Português do Sangue e da Transplantação, Alameda das Linhas de Torres, Lisbon, Portugal; NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal; iNOVA4Health - Advancing Precision Medicine, RG11: Reno-Vascular Diseases Group, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal.
| | - Ruben Araújo
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Aníbal Ferreira
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal; Centro Hospitalar Universitário Lisboa Central, Hospital Curry Cabral, Serviço de Nefrologia, NOVA Medical School, Lisbon, Portugal
| | - Cecília R C Calado
- ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, Lisbon, Portugal; CIMOSM - Centro de Investigação em Modelação e Otimização de Sistemas Multifuncionais, Lisbon, Portugal
| |
Collapse
|
3
|
Singh AD, Patnam S, Manocha A, Bashyam L, Rengan AK, Sasidhar MV. Polyethylene glycol-based isolation of urinary extracellular vesicles, an easily adoptable protocol. MethodsX 2023; 11:102310. [PMID: 37608961 PMCID: PMC10440582 DOI: 10.1016/j.mex.2023.102310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023] Open
Abstract
Urine is a highly advantageous biological specimen for biomarker research and is a non-invasive source. Most of the urinary biomarkers are non-specific, volatile and need extensive validation before clinical adoption. Extracellular vesicles are secreted by almost all cells and are involved in homoeostasis, intercellular communication, and cellular processes in healthy and pathophysiological states. Urinary extracellular vesicles (UEVs) are released from the urogenital system and mirror the molecular processes of physiological and pathological states of their source cells. Therefore, UEVs serve as a valuable source of biomarkers for the non-invasive diagnosis of various pathologies. They hold a promising source of multiplex biomarkers suitable for prognosis, diagnosis, and therapy monitoring. UEVs are easily accessible, non-invasive, and suited for longitudinal sampling. Although various techniques are available for isolating UEVs, there is yet to be a consensus on a standard and ideal protocol. We have optimized an efficient, reliable, and easily adoptable polyethylene glycol (PEG) based UEV isolation technique following MISEV guidelines. The method is suitable for various downstream applications of UEVs. This could be a cost-effective, consistent, and accessible procedure for many clinical labs and is most suited for longitudinal analysis. Adopting the protocol will pave the way for establishing UEVs as the ideal biomarker source. •Urine can be collected non-invasively and repeatedly, hence a very useful specimen for biomarker discovery. Urinary EVs (UEVs), derived from urine, offer a stable diagnostic tool, but standardised isolation and analysis approaches are warranted.•To have enough UEVs for any study, large volumes of urine sample are necessary, which limits different isolation methods by cost, yield, and time.•The protocol developed could help researchers by offering a cost-effective and dependable UEV isolation method and may lay the foundation for UEVs adoption in clinical space.
Collapse
Affiliation(s)
- Anula Divyash Singh
- Apollo Hospitals Educational and Research Foundation (AHERF), Hyderabad, India
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad (IITH), Kandi, Hyderabad, India
| | - Sreekanth Patnam
- Apollo Hospitals Educational and Research Foundation (AHERF), Hyderabad, India
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad (IITH), Kandi, Hyderabad, India
| | - Anisha Manocha
- Department of Histopathology, Apollo Hospitals, Hyderabad, India
| | - Leena Bashyam
- Genomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Aravind Kumar Rengan
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad (IITH), Kandi, Hyderabad, India
| | - Manda Venkata Sasidhar
- Apollo Hospitals Educational and Research Foundation (AHERF), Hyderabad, India
- Urvogelbio Private Ltd, Hyderabad, India
| |
Collapse
|
4
|
Verscheure E, Stierum R, Schlünssen V, Lund Würtz AM, Vanneste D, Kogevinas M, Harding BN, Broberg K, Zienolddiny-Narui S, Erdem JS, Das MK, Makris KC, Konstantinou C, Andrianou X, Dekkers S, Morris L, Pronk A, Godderis L, Ghosh M. Characterization of the internal working-life exposome using minimally and non-invasive sampling methods - a narrative review. ENVIRONMENTAL RESEARCH 2023; 238:117001. [PMID: 37683788 DOI: 10.1016/j.envres.2023.117001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023]
Abstract
During recent years, we are moving away from the 'one exposure, one disease'-approach in occupational settings and towards a more comprehensive approach, taking into account the totality of exposures during a life course by using an exposome approach. Taking an exposome approach however is accompanied by many challenges, one of which, for example, relates to the collection of biological samples. Methods used for sample collection in occupational exposome studies should ideally be minimally invasive, while at the same time sensitive, and enable meaningful repeated sampling in a large population and over a longer time period. This might be hampered in specific situations e.g., people working in remote areas, during pandemics or with flexible work hours. In these situations, using self-sampling techniques might offer a solution. Therefore, our aim was to identify existing self-sampling techniques and to evaluate the applicability of these techniques in an occupational exposome context by conducting a literature review. We here present an overview of current self-sampling methodologies used to characterize the internal exposome. In addition, the use of different biological matrices was evaluated and subdivided based on their level of invasiveness and applicability in an occupational exposome context. In conclusion, this review and the overview of self-sampling techniques presented herein can serve as a guide in the design of future (occupational) exposome studies while circumventing sample collection challenges associated with exposome studies.
Collapse
Affiliation(s)
- Eline Verscheure
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rob Stierum
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | - Vivi Schlünssen
- Department of Public Health, Research unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Anne Mette Lund Würtz
- Department of Public Health, Research unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Dorian Vanneste
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Manolis Kogevinas
- Environment and Health over the Lifecourse Program, ISGlobal, Barcelona, Spain
| | - Barbara N Harding
- Environment and Health over the Lifecourse Program, ISGlobal, Barcelona, Spain
| | - Karin Broberg
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Mrinal K Das
- National Institute of Occupational Health, Oslo, Norway
| | - Konstantinos C Makris
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Corina Konstantinou
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Xanthi Andrianou
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Susan Dekkers
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | | | - Anjoeka Pronk
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | - Lode Godderis
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium; Idewe, External Service for Prevention and Protection at work, Heverlee, Belgium.
| | - Manosij Ghosh
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium.
| |
Collapse
|
5
|
Barreiro K, Dwivedi OP, Rannikko A, Holthöfer H, Tuomi T, Groop PH, Puhka M. Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles-From Pre-Analytical Obstacles to Biomarker Research. Genes (Basel) 2023; 14:1415. [PMID: 37510317 PMCID: PMC10379145 DOI: 10.3390/genes14071415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Urinary extracellular vesicles (uEV) hold non-invasive RNA biomarkers for genitourinary tract diseases. However, missing knowledge about reference genes and effects of preanalytical choices hinder biomarker studies. We aimed to assess how preanalytical variables (urine storage temperature, isolation workflow) affect diabetic kidney disease (DKD)-linked miRNAs or kidney-linked miRNAs and mRNAs (kidney-RNAs) in uEV isolates and to discover stable reference mRNAs across diverse uEV datasets. We studied nine raw and normalized sequencing datasets including healthy controls and individuals with prostate cancer or type 1 diabetes with or without albuminuria. We focused on kidney-RNAs reviewing literature for DKD-linked miRNAs from kidney tissue, cell culture and uEV/urine experiments. RNAs were analyzed by expression heatmaps, hierarchical clustering and selecting stable mRNAs with normalized counts (>200) and minimal coefficient of variation. Kidney-RNAs were decreased after urine storage at -20 °C vs. -80 °C. Isolation workflows captured kidney-RNAs with different efficiencies. Ultracentrifugation captured DKD -linked miRNAs that separated healthy and diabetic macroalbuminuria groups. Eleven mRNAs were stably expressed across the datasets. Hence, pre-analytical choices had variable effects on kidney-RNAs-analyzing kidney-RNAs complemented global correlation, which could fade differences in some relevant RNAs. Replicating prior DKD-marker results and discovery of candidate reference mRNAs encourages further uEV biomarker studies.
Collapse
Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, EV and HiPREP Core, University of Helsinki, 00290 Helsinki, Finland
| | - Om Prakash Dwivedi
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Urology, University of Helsinki, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Harry Holthöfer
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, 214 28 Malmö, Sweden
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki, Finland
- Endocrinology, Abdominal Centre, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Nephrology, University of Helsinki, Helsinki University Hospital, 00290 Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, EV and HiPREP Core, University of Helsinki, 00290 Helsinki, Finland
| |
Collapse
|
6
|
Van Dorpe S, Lippens L, Boiy R, Pinheiro C, Vergauwen G, Rappu P, Miinalainen I, Tummers P, Denys H, De Wever O, Hendrix A. Integrating automated liquid handling in the separation workflow of extracellular vesicles enhances specificity and reproducibility. J Nanobiotechnology 2023; 21:157. [PMID: 37208684 DOI: 10.1186/s12951-023-01917-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Extracellular vesicles (EV) are extensively studied in human body fluids as potential biomarkers for numerous diseases. Major impediments of EV-based biomarker discovery include the specificity and reproducibility of EV sample preparation as well as intensive manual labor. We present an automated liquid handling workstation for the density-based separation of EV from human body fluids and compare its performance to manual handling by (in)experienced researchers. RESULTS Automated versus manual density-based separation of trackable recombinant extracellular vesicles (rEV) spiked in PBS significantly reduces variability in rEV recovery as quantified by fluorescent nanoparticle tracking analysis and ELISA. To validate automated density-based EV separation from complex body fluids, including blood plasma and urine, we assess reproducibility, recovery, and specificity by mass spectrometry-based proteomics and transmission electron microscopy. Method reproducibility is the highest in the automated procedure independent of the matrix used. While retaining (in urine) or enhancing (in plasma) EV recovery compared to manual liquid handling, automation significantly reduces the presence of body fluid specific abundant proteins in EV preparations, including apolipoproteins in plasma and Tamm-Horsfall protein in urine. CONCLUSIONS In conclusion, automated liquid handling ensures cost-effective EV separation from human body fluids with high reproducibility, specificity, and reduced hands-on time with the potential to enable larger-scale biomarker studies.
Collapse
Affiliation(s)
- Sofie Van Dorpe
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Gynecology, Ghent University Hospital, Ghent, Belgium
| | - Lien Lippens
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Robin Boiy
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Cláudio Pinheiro
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Glenn Vergauwen
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Gynecology, Ghent University Hospital, Ghent, Belgium
| | - Pekka Rappu
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Philippe Tummers
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Gynecology, Ghent University Hospital, Ghent, Belgium
| | - Hannelore Denys
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
| |
Collapse
|
7
|
Fan S, Poetsch A. Proteomic Research of Extracellular Vesicles in Clinical Biofluid. Proteomes 2023; 11:proteomes11020018. [PMID: 37218923 DOI: 10.3390/proteomes11020018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Extracellular vesicles (EVs), the lipid bilayer membranous structures of particles, are produced and released from almost all cells, including eukaryotes and prokaryotes. The versatility of EVs has been investigated in various pathologies, including development, coagulation, inflammation, immune response modulation, and cell-cell communication. Proteomics technologies have revolutionized EV studies by enabling high-throughput analysis of their biomolecules to deliver comprehensive identification and quantification with rich structural information (PTMs, proteoforms). Extensive research has highlighted variations in EV cargo depending on vesicle size, origin, disease, and other features. This fact has sparked activities to use EVs for diagnosis and treatment to ultimately achieve clinical translation with recent endeavors summarized and critically reviewed in this publication. Notably, successful application and translation require a constant improvement of methods for sample preparation and analysis and their standardization, both of which are areas of active research. This review summarizes the characteristics, isolation, and identification approaches for EVs and the recent advances in EVs for clinical biofluid analysis to gain novel knowledge by employing proteomics. In addition, the current and predicted future challenges and technical barriers are also reviewed and discussed.
Collapse
Affiliation(s)
- Shipan Fan
- School of Basic Medical Sciences, Nanchang University, Nanchang 330021, China
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang 330021, China
| |
Collapse
|
8
|
Neumair J, D'Ercole C, De March M, Elsner M, Seidel M, de Marco A. Macroporous Epoxy-Based Monoliths Functionalized with Anti-CD63 Nanobodies for Effective Isolation of Extracellular Vesicles in Urine. Int J Mol Sci 2023; 24:ijms24076131. [PMID: 37047104 PMCID: PMC10094263 DOI: 10.3390/ijms24076131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Extracellular vesicles (EVs) have enormous potential for the implementation of liquid biopsy and as effective drug delivery means, but the fulfilment of these expectations requires overcoming at least two bottlenecks relative to their purification, namely the finalization of reliable and affordable protocols for: (i) EV sub-population selective isolation and (ii) the scalability of their production/isolation from complex biological fluids. In this work, we demonstrated that these objectives can be achieved by a conceptually new affinity chromatography platform composed of a macroporous epoxy monolith matrix functionalized with anti-CD63 nanobodies with afflux of samples and buffers regulated through a pump. Such a system successfully captured and released integral EVs from urine samples and showed negligible unspecific binding for circulating proteins. Additionally, size discrimination of eluted EVs was achieved by different elution approaches (competitive versus pH-dependent). The physical characteristics of monolith material and the inexpensive production of recombinant nanobodies make scaling-up the capture unit feasible and affordable. Additionally, the availability of nanobodies for further specific EV biomarkers will allow for the preparation of monolithic affinity filters selective for different EV subclasses.
Collapse
Affiliation(s)
- Julia Neumair
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Claudia D'Ercole
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, P.O. Box 301, SI-5000 Nova Gorica, Slovenia
| | - Matteo De March
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, P.O. Box 301, SI-5000 Nova Gorica, Slovenia
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael Seidel
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, P.O. Box 301, SI-5000 Nova Gorica, Slovenia
| |
Collapse
|
9
|
Li L, Mussack V, Görgens A, Pepeldjiyska E, Hartz AS, Aslan H, Rackl E, Rank A, Schmohl J, El Andaloussi S, Pfaffl MW, Schmetzer H. The potential role of serum extracellular vesicle derived small RNAs in AML research as non-invasive biomarker. NANOSCALE ADVANCES 2023; 5:1691-1705. [PMID: 36926576 PMCID: PMC10012871 DOI: 10.1039/d2na00959e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Extracellular vesicles (EV) are cell-derived vesicles released by all cells in health and disease. Accordingly, EVs are also released by cells in acute myeloid leukemia (AML), a hematologic malignancy characterized by uncontrolled growth of immature myeloid cells, and these EVs likely carry markers and molecular cargo reflecting the malignant transformation occurring in diseased cells. Monitoring antileukemic or proleukemic processes during disease development and treatment is essential. Therefore, EVs and EV-derived microRNA (miRNA) from AML samples were explored as biomarkers to distinguish disease-related patterns ex vivo or in vivo. METHODOLOGY EVs were purified from serum of healthy (H) volunteers and AML patients by immunoaffinity. EV surface protein profiles were analyzed by multiplex bead-based flow cytometry (MBFCM) and total RNA was isolated from EVs prior to miRNA profiling via small RNA sequencing. RESULTS MBFCM revealed different surface protein patterns in H versus AML EVs. miRNA analysis showed individual as well as highly dysregulated patterns in H and AML samples. CONCLUSIONS In this study, we provide a proof-of-concept for the discriminative potential of EV derived miRNA profiles as biomarkers in H versus AML samples.
Collapse
Affiliation(s)
- Lin Li
- Immune-Modulation, Medical Department III, University Hospital of Munich Marchioninistraße 15 81377 Munich Germany +49 89 4400 76137 +49 89 4400 73137
| | - Veronika Mussack
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
| | - André Görgens
- Department of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institutet Stockholm Sweden
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen Essen Germany
| | - Elena Pepeldjiyska
- Immune-Modulation, Medical Department III, University Hospital of Munich Marchioninistraße 15 81377 Munich Germany +49 89 4400 76137 +49 89 4400 73137
| | - Anne Sophie Hartz
- Immune-Modulation, Medical Department III, University Hospital of Munich Marchioninistraße 15 81377 Munich Germany +49 89 4400 76137 +49 89 4400 73137
| | - Hazal Aslan
- Immune-Modulation, Medical Department III, University Hospital of Munich Marchioninistraße 15 81377 Munich Germany +49 89 4400 76137 +49 89 4400 73137
| | - Elias Rackl
- Immune-Modulation, Medical Department III, University Hospital of Munich Marchioninistraße 15 81377 Munich Germany +49 89 4400 76137 +49 89 4400 73137
| | - Andreas Rank
- Department of Hematology and Oncology, University Hospital of Augsburg Augsburg Germany
| | - Jörg Schmohl
- Department of Hematology and Oncology, Hospital of Stuttgart Stuttgart Germany
| | - Samir El Andaloussi
- Department of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institutet Stockholm Sweden
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
| | - Helga Schmetzer
- Immune-Modulation, Medical Department III, University Hospital of Munich Marchioninistraße 15 81377 Munich Germany +49 89 4400 76137 +49 89 4400 73137
| |
Collapse
|
10
|
Comparative analysis of magnetically activated cell sorting and ultracentrifugation methods for exosome isolation. PLoS One 2023; 18:e0282238. [PMID: 36854030 PMCID: PMC9974127 DOI: 10.1371/journal.pone.0282238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
Mesenchymal stem cell-derived exosomes regulate cell migration, proliferation, differentiation, and synthesis of the extracellular matrix, giving great potential for the treatment of different diseases. The ultracentrifugation method is the gold standard method for exosome isolation due to the simple protocol, and high yield, but presents low purity and requires specialized equipment. Amelioration of technical optimization is required for quick and reliable confinement of exosomes to translate them to the clinic as cell therapeutics In this study, we hypothesized that magnetically activated cell sorting may provide, an effective, reliable, and rapid tool for exosome isolation when compared to ultracentrifugation. We, therefore, aimed to compare the efficiency of magnetically activated cell sorting and ultracentrifugation for human mesenchymal stem cell-derived exosome isolation from culture media by protein quantification, surface biomarker, size, number, and morphological analysis. Magnetically activated cell sorting provided a higher purity and amount of exosomes that carry visible magnetic beads when compared to ultracentrifugation. The particle number of the magnetically activated cell sorting group was higher than the ultracentrifugation. In conclusion, magnetically activated cell sorting presents a quick, and reliable method to collect and present human mesenchymal stem cell exosomes to clinics at high purity for potential cellular therapeutic approaches. The novel isolation and purification method may be extended to different clinical protocols using different autogenic or allogeneic cell sources.
Collapse
|
11
|
Importance and implications of exosomes in nephrology and urology. Pflugers Arch 2023; 475:153-166. [PMID: 36399151 PMCID: PMC9849294 DOI: 10.1007/s00424-022-02771-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
Abstract
Exosomes are extracellular vesicles that are formed by two invaginations of the plasma membrane and can be released by all eukaryotic cells. Because of their bioactive contents, including nucleic acids and proteins, exosomes can activate a variety of functions in their recipient cells. Due to the plethora of physiological and pathophysiological functions, exosomes have received a lot of attention from researchers over the past few years. However, there is still no consensus regarding isolation and characterization protocols of exosomes and their subtypes. This heterogeneity poses a lot of methodical challenges but also offers new clinical opportunities simultaneously. So far, exosome-based research is still mostly limited to preclinical experiments and early-stage clinical trials since the translation of experimental findings remains difficult. Exosomes could potentially play an important role as future diagnostic and prognostic agents and might also be part of the development of new treatment strategies. Therefore, they have previously been investigated in a variety of nephrological and urological conditions such as acute kidney injury or prostate cancer.
Collapse
|
12
|
Identifying stable reference genes in polyethene glycol precipitated urinary extracellular vesicles for RT-qPCR-based gene expression studies in renal graft dysfunction patients. Transpl Immunol 2022; 75:101715. [PMID: 36122652 DOI: 10.1016/j.trim.2022.101715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Urinary extracellular vesicles (UEVs) hold RNA in their cargo and are potential sources of biomarkers for gene expression studies. The most used technique for gene-expression studies is quantitative polymerase chain reaction (qPCR). It is critical to use stable reference genes (RGs) as internal controls for normalising gene expression data, which aren't currently available for UEVs. METHODS UEVs were precipitated from urine of graft dysfunction patients and healthy controls by Polyethylene glycol, Mn6000 (PEG6K). Vesicular characterisation confirmed the presence of UEVs. Gene expression levels of five commonly used RGs, i.e., Beta-2-Microglobulin (B2M), ribosomal-protein-L13a (RPL13A), Peptidylprolyl-Isomerase-A (PPIA), hydroxymethylbilane synthase (HMBS), and glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) were quantified, and their stability was established through the RefFinder. The stability of identified RGs was validated by quantification of Perforin and granzyme B, signature molecules of renal graft dysfunction. RESULTS Urine precipitated with 12% 6 K PEG yielded round and double-membraned UEVs of size ranging from 30 to 100 nm, as confirmed through transmission electron microscopy. Nanoparticle tracking analysis (59 ± 22 nm) and Dynamic-light-scattering (78 ± 56.5 nm) confirmed their size profile. Semi-quantitative Exocheck antibody array demonstrated the presence of EV protein markers in UEV. Using the comparative ΔCт method and RefFinder analysis, B2M (1.6) and RPL13A (1.8) genes emerged as the most stable reference genes. Validation of target gene expression in renal graft dysfunction patients confirmed the efficiency of B2M and RPL13A through significant upregulation compared to other RGs. CONCLUSIONS Our study identified and validated B2M and RPL13A as optimal RGs for mRNA quantification studies in the UEVs of patients with renal graft dysfunction.
Collapse
|
13
|
Earle A, Bessonny M, Benito J, Huang K, Parker H, Tyler E, Crawford B, Khan N, Armstrong B, Stamatikos A, Garimella S, Clay-Gilmour A. Urinary Exosomal MicroRNAs as Biomarkers for Obesity-Associated Chronic Kidney Disease. J Clin Med 2022; 11:jcm11185271. [PMID: 36142918 PMCID: PMC9502686 DOI: 10.3390/jcm11185271] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
The early detection of chronic kidney disease (CKD) is key to reducing the burden of disease and rising costs of care. This need has spurred interest in finding new biomarkers for CKD. Ideal bi-omarkers for CKD should be: easy to measure; stable; reliably detected, even when interfering substances are present; site-specific based on the type of injury (tubules vs. glomeruli); and its changes in concentration should correlate with disease risk or outcome. Currently, no single can-didate biomarker fulfills these criteria effectively, and the mechanisms underlying kidney fibrosis are not fully understood; however, there is growing evidence in support of microRNA-mediated pro-cesses. Specifically, urinary exosomal microRNAs may serve as biomarkers for kidney fibrosis. In-creasing incidences of obesity and the recognition of obesity-associated CKD have increased interest in the interplay of obesity and CKD. In this review, we provide: (1) an overview of the current scope of CKD biomarkers within obese individuals to elucidate the genetic pathways unique to obesi-ty-related CKD; (2) a review of microRNA expression in obese individuals with kidney fibrosis in the presence of comorbidities, such as diabetes mellitus and hypertension; (3) a review of thera-peutic processes, such as diet and exercise, that may influence miR-expression in obesity-associated CKD; (4) a review of the technical aspects of urinary exosome isolation; and (5) future areas of research.
Collapse
Affiliation(s)
- Angel Earle
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Madison Bessonny
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Josh Benito
- Prisma Health, Pediatric Nephrology, Greenville, SC 29615, USA
| | - Kun Huang
- Department of Food, Nutrition, and Packaging Sciences, College of Agriculture, Forestry & Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Hannah Parker
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Emily Tyler
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Brittany Crawford
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Nabeeha Khan
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Bridget Armstrong
- Department of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Alexis Stamatikos
- Department of Food, Nutrition, and Packaging Sciences, College of Agriculture, Forestry & Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Sudha Garimella
- Prisma Health, Pediatric Nephrology, Greenville, SC 29615, USA
| | - Alyssa Clay-Gilmour
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
- Correspondence:
| |
Collapse
|
14
|
Park S, Moon HY. Urinary extracellular vesicle as a potential biomarker of exercise-induced fatigue in young adult males. Eur J Appl Physiol 2022; 122:2175-2188. [PMID: 35781843 PMCID: PMC9463341 DOI: 10.1007/s00421-022-04995-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/18/2022] [Indexed: 11/30/2022]
Abstract
Purpose Previous studies have suggested that circulating extracellular vesicles (EVs) arise after high intensity exercise and urine could reflect the plasma proteome. Herein, we investigated the characteristic of urinary EVs from healthy young adult males who had completed a maximal effort exercise test. Methods Thirteen healthy men completed a 20 m shuttle run test (20 m SRT). Fresh urine samples were collected at first morning, right after, and 1 h rest after 20 m SRT. Also, blood lactate, heart rate, rating of perceived exertion, and blood pressure were measured before, right after, and 1 h rest after 20 m SRT. Urinary EVs were analyzed using Exoview instrument and microRNAs (miRNAs) sequencing on urinary EVs were performed. Results Urinary EVs increased significantly after exercise and returned to baseline value after 1 h of rest. miRNA sequencing on urinary EV revealed alterations in four miRNAs (1 up and 3 down) and nine miRNAs (2 up and 7 down) in pre- vs. post- and post- vs. post-1 h samples, respectively. Lastly, bioinformatic analysis of urinary EV miRNA suggests that predicted target genes could affect PI3K-Akt, mitogen-activated protein kinase, and insulin pathways by exercise. Conclusions Exercise to voluntary exhaustion increased the number of EVs in urine. Also, miRNAs in urinary EVs were altered after exercise. These findings could indicate the possibility of using the urinary EVs as a novel biomarker of acute exercise-induced fatigue.
Collapse
Affiliation(s)
- Suhong Park
- Department of Physical Education, Seoul National University, Seoul, Republic of Korea
| | - Hyo Youl Moon
- Department of Physical Education, Seoul National University, Seoul, Republic of Korea. .,Institute of Sport Science, Seoul National University, 71-1, 407, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
| |
Collapse
|
15
|
He N, Thippabhotla S, Zhong C, Greenberg Z, Xu L, Pessetto Z, Godwin AK, Zeng Y, He M. Nano pom-poms prepared exosomes enable highly specific cancer biomarker detection. Commun Biol 2022; 5:660. [PMID: 35787656 PMCID: PMC9253007 DOI: 10.1038/s42003-022-03598-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 06/16/2022] [Indexed: 01/27/2023] Open
Abstract
Extracellular vesicles (EVs), particularly nano-sized small EV exosomes, are emerging biomarker sources. However, due to heterogeneous populations secreted from diverse cell types, mapping exosome multi-omic molecular information specifically to their pathogenesis origin for cancer biomarker identification is still extraordinarily challenging. Herein, we introduced a novel 3D-structured nanographene immunomagnetic particles (NanoPoms) with unique flower pom-poms morphology and photo-click chemistry for specific marker-defined capture and release of intact exosome. This specific exosome isolation approach leads to the expanded identification of targetable cancer biomarkers with enhanced specificity and sensitivity, as demonstrated by multi-omic exosome analysis of bladder cancer patient tissue fluids using the next generation sequencing of somatic DNA mutations, miRNAs, and the global proteome (Data are available via ProteomeXchange with identifier PXD034454). The NanoPoms prepared exosomes also exhibit distinctive in vivo biodistribution patterns, highlighting the highly viable and integral quality. The developed method is simple and straightforward, which is applicable to nearly all types of biological fluids and amenable for enrichment, scale up, and high-throughput exosome isolation.
Collapse
Affiliation(s)
- Nan He
- Department of Chemical and Petroleum Engineering, Bioengineering Program, University of Kansas, Lawrence, KS, 66045, USA
- Clara Biotech Inc., Lawrence, KS, 66047, USA
| | - Sirisha Thippabhotla
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS, 66045, USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS, 66045, USA
| | - Zachary Greenberg
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Ziyan Pessetto
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- University of Kansas Cancer Center, Kansas City, KS, 66160, USA
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, FL, 32603, USA
| | - Mei He
- Department of Chemical and Petroleum Engineering, Bioengineering Program, University of Kansas, Lawrence, KS, 66045, USA.
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
| |
Collapse
|
16
|
Yakubovich EI, Polischouk AG, Evtushenko VI. Principles and Problems of Exosome Isolation from Biological Fluids. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022; 16:115-126. [PMID: 35730027 PMCID: PMC9202659 DOI: 10.1134/s1990747822030096] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/03/2022]
Abstract
Exosomes, the subclass of small membrane extracellular vesicles, have great diagnostic and therapeutic potential, but the lack of standardized methods for their efficient isolation and analysis limits the introduction of exosomal technologies into clinical practice. This review discusses the problems associated with the isolation of exosomes from biological fluids, as well as the principles of traditional and alternative methods of isolation. The aim of the presented review is to illustrate the variety of approaches based on the physical and biochemical properties of exosomes that can be used for exosome isolation. The advantages and disadvantages of different methods are discussed.
Collapse
Affiliation(s)
- E. I. Yakubovich
- Granov Russian Research Center for Radiology and Surgical Technologies, Ministry of Health of the Russian Federation, 197758 St. Petersburg, Russia
| | - A. G. Polischouk
- Granov Russian Research Center for Radiology and Surgical Technologies, Ministry of Health of the Russian Federation, 197758 St. Petersburg, Russia
| | - V. I. Evtushenko
- Granov Russian Research Center for Radiology and Surgical Technologies, Ministry of Health of the Russian Federation, 197758 St. Petersburg, Russia
| |
Collapse
|
17
|
Lee HK, Lee BR, Lee TJ, Lee CM, Li C, O'Connor PM, Dong Z, Kwon SH. Differential release of extracellular vesicle tRNA from oxidative stressed renal cells and ischemic kidneys. Sci Rep 2022; 12:1646. [PMID: 35102218 PMCID: PMC8803936 DOI: 10.1038/s41598-022-05648-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/14/2022] [Indexed: 11/09/2022] Open
Abstract
While urine-based liquid biopsy has expanded to the analyses of extracellular nucleic acids, the potential of transfer RNA (tRNA) encapsulated within extracellular vesicles has not been explored as a new class of urine biomarkers for kidney injury. Using rat kidney and mouse tubular cell injury models, we tested if extracellular vesicle-loaded tRNA and their m1A (N1-methyladenosine) modification reflect oxidative stress of kidney injury and determined the mechanism of tRNA packaging into extracellular vesicles. We determined a set of extracellular vesicle-loaded, isoaccepting tRNAs differentially released after ischemia-reperfusion injury and oxidative stress. Next, we found that m1A modification of extracellular vesicle tRNAs, despite an increase of the methylated tRNAs in intracellular vesicles, showed little or no change under oxidative stress. Mechanistically, oxidative stress decreases tRNA loading into intracellular vesicles while the tRNA-loaded vesicles are accumulated due to decreased release of the vesicles from the cell surface. Furthermore, Maf1-mediated transcriptional repression of the tRNAs decreases the cargo availability for extracellular vesicle release in response to oxidative stress. Taken together, our data support that release of extracellular vesicle tRNAs reflects oxidative stress of kidney tubules which might be useful to detect ischemic kidney injury and could lead to rebalance protein translation under oxidative stress.
Collapse
Affiliation(s)
- Hee Kyung Lee
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Byung Rho Lee
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Chang Min Lee
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Chenglong Li
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Paul M O'Connor
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
- Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Sang-Ho Kwon
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA.
| |
Collapse
|
18
|
Puhka M, Thierens L, Nicorici D, Forsman T, Mirtti T, af Hällström T, Serkkola E, Rannikko A. Exploration of Extracellular Vesicle miRNAs, Targeted mRNAs and Pathways in Prostate Cancer: Relation to Disease Status and Progression. Cancers (Basel) 2022; 14:cancers14030532. [PMID: 35158801 PMCID: PMC8833493 DOI: 10.3390/cancers14030532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Prostate cancer lacks non-invasive specific biomarkers for aggressive disease. Urinary extracellular vesicles (uEV) could provide such markers; however, due to technical challenges, little is known regarding the pathogenesis pathways reflected in uEV. We performed a miRNA, target mRNA and pathway study focused on uEV, exploring the differences between cancer (1) status groups (Gleason score) and (2) progression groups. The uEV provided a surprisingly comprehensive presentation of differentially expressed miRNAs, target mRNAs and pathogenesis pathways. The miRNAs associated with prostate cancer status or progression were mostly unique, but still targeted overlapping sets of signalling, resistance, hormonal and immune pathways. Interestingly, mRNA targets of the key miRNAs (miR-892a, miR-223-3p, miR-146a-5p) were widely expressed in both uEV and plasma EV from PCa patients. The study thus suggests that uEV carry a vast presentation of PCa status and progression-linked RNAs that are worth further exploration in large personalized medicine trials. Abstract Background: Prostate cancer (PCa) lacks non-invasive specific biomarkers for aggressive disease. We studied the potential of urinary extracellular vesicles (uEV) as a liquid PCa biopsy by focusing on the micro RNA (miRNA) cargo, target messenger RNA (mRNA) and pathway analysis. Methods: We subjected uEV samples from 31 PCa patients (pre-prostatectomy) to miRNA sequencing and matched uEV and plasma EV (pEV) from three PCa patients to mRNA sequencing. EV quality control was performed by electron microscopy, Western blotting and particle and RNA analysis. We compared miRNA expression based on PCa status (Gleason Score) and progression (post-prostatectomy follow-up) and confirmed selected miRNAs by quantitative PCR. Expression of target mRNAs was mapped in matched EV. Results: Quality control showed typical small uEV, pEV, RNA and EV-protein marker enriched samples. Comparisons between PCa groups revealed mostly unique differentially expressed miRNAs. However, they targeted comprehensive and largely overlapping sets of cancer and progression-associated signalling, resistance, hormonal and immune pathways. Quantitative PCR confirmed changes in miR-892a (Gleason Score 7 vs. ≥8), miR-223-3p (progression vs. no progression) and miR-146a-5p (both comparisons). Their target mRNAs were expressed widely in PCa EV. Conclusions: PCa status and progression-linked RNAs in uEV are worth exploration in large personalized medicine trials.
Collapse
Affiliation(s)
- Maija Puhka
- HiPrep and EV Core, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00290 Helsinki, Finland;
- Correspondence: (M.P.); (A.R.)
| | - Lisse Thierens
- HiPrep and EV Core, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00290 Helsinki, Finland;
| | - Daniel Nicorici
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Tarja Forsman
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Tuomas Mirtti
- Department of Pathology, HUS Diagnostic Centre, Helsinki University Hospital, 00290 Helsinki, Finland;
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | | | - Elina Serkkola
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Urology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
- Correspondence: (M.P.); (A.R.)
| |
Collapse
|
19
|
Li L, Görgens A, Mussack V, Pepeldjiyska E, Hartz AS, Rank A, Schmohl J, Krämer D, Andaloussi SE, Pfaffl MW, Schmetzer H. Description and optimization of a multiplex bead-based flow cytometry method (MBFCM) to characterize extracellular vesicles in serum samples from patients with hematological malignancies. Cancer Gene Ther 2022; 29:1600-1615. [PMID: 35477770 PMCID: PMC9663305 DOI: 10.1038/s41417-022-00466-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/25/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023]
Abstract
Extracellular Vesicles (EVs) are membranous vesicles produced by all cells under physiological and pathological conditions. In hematological malignancies, tumor-derived EVs might reprogram the bone marrow environment, suppress antileukemic immunity, mediate drug resistance and interfere with immunotherapies. EVs collected from the serum of leukemic samples might correlate with disease stage, drug-/immunological resistance, or might correlate with antileukemic immunity/immune response. Special EV surface protein patterns in serum have the potential as noninvasive biomarker candidates to distinguish several disease-related patterns ex vivo or in vivo. EVs were isolated from the serum of acute myeloid leukemia (AML), acute lymphoid leukemia (ALL), chronic lymphoid leukemia (CLL) patients, and healthy volunteers. EVs were characterized by transmission electron microscopy and fluorescence nanoparticle tracking analysis, and EV surface protein profiles were analyzed by multiplex bead-based flow cytometry to identify tumor- or immune system-related EVs of AML, ALL, CLL, and healthy samples. Aiming to provide proof-of-concept evidence and methodology for the potential role of serum-derived EVs as biomarkers in leukemic versus healthy samples in this study, we hope to pave the way for future detection of promising biomarkers for imminent disease progression and the identification of potential targets to be used in a therapeutic strategy.
Collapse
Affiliation(s)
- Lin Li
- grid.411095.80000 0004 0477 2585Working-group: Immune-Modulation, Medical Department III, University Hospital of Munich, Munich, Germany
| | - André Görgens
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Veronika Mussack
- grid.6936.a0000000123222966Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Elena Pepeldjiyska
- grid.411095.80000 0004 0477 2585Working-group: Immune-Modulation, Medical Department III, University Hospital of Munich, Munich, Germany
| | - Anne Sophie Hartz
- grid.411095.80000 0004 0477 2585Working-group: Immune-Modulation, Medical Department III, University Hospital of Munich, Munich, Germany
| | - Andreas Rank
- grid.419801.50000 0000 9312 0220Department of Hematology and Oncology, University Hospital of Augsburg, Augsburg, Germany
| | - Jörg Schmohl
- Department of Hematology and Oncology, Hospital of Stuttgart, Stuttgart, Germany
| | - Doris Krämer
- Department of Heamatology, Oncology and Palliative Care, Ameos Klinikum Mitte, Bremerhaven, Germany
| | - Samir El Andaloussi
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael W. Pfaffl
- grid.6936.a0000000123222966Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Helga Schmetzer
- grid.411095.80000 0004 0477 2585Working-group: Immune-Modulation, Medical Department III, University Hospital of Munich, Munich, Germany
| |
Collapse
|
20
|
Choi D, Kim S, Woo J, Lee H, Kim H, Jeon JS, Noh H, Han DC, Kim SH, Cho HC, Choi JS, Bae YU, Kwon SH. Weight Change Alters the Small RNA Profile of Urinary Extracellular Vesicles in Obesity. Obes Facts 2022; 15:292-301. [PMID: 35008090 PMCID: PMC9021654 DOI: 10.1159/000521730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/27/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Various kidney diseases reportedly show different urinary extracellular vesicle (EV) RNA profiles. Although obesity is one of the main causes of chronic kidney disease, the expression pattern of urinary EV RNA in obesity is uncertain. Our aim was to sequence the small RNA profiles of urinary EVs in obese patients before and after weight reduction and compare them to those of healthy volunteers (HVs). METHODS We recruited age-sex-matched obese patients and HVs. The small RNA profiles of urinary EVs were analyzed using RNA sequencing. To evaluate the effect of weight reduction, small RNA profiles of urinary EVs 6 months after bariatric surgery were also analyzed. RESULTS The proportion of urinary EVs transfer RNA and microRNA of obese patients differed from that of HVs. Obese patients showed differential expression of 1,343 small RNAs in urinary EVs compared to HVs (fold change ≥2 and p value <0.05). Among those, 61 small RNAs were upregulated in obese patients and downregulated after weight reduction, whereas 167 small RNAs were downregulated in obese patients and upregulated after weight reduction. RNA sequencing revealed the correlation between the specific urinary EV small RNAs and clinical parameters including body weight, low-density lipoprotein cholesterol, triglyceride, high-density lipoprotein cholesterol, serum glucose, estimated glomerular filtration rate, and albuminuria. CONCLUSION Obese patients showed distinct urinary EV small RNA profiles compared to HVs. Weight reduction altered urinary EV small-RNA profiles in obese patients.
Collapse
Affiliation(s)
- Dughyun Choi
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Sewon Kim
- Macrogen Inc., Seoul, Republic of Korea
- ROKIT Genomics, Seoul, Republic of Korea
| | | | - Haekyung Lee
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Hyoungnae Kim
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Jin Seok Jeon
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Hyunjin Noh
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Dong Cheol Han
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Sang Hyun Kim
- Department of Surgery, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Ho Chan Cho
- Department of Clinical Endocrinology, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Jong-Soo Choi
- Research Institute, Biosolyx Co. Ltd., Daegu, Republic of Korea
| | - Yun-Ui Bae
- Department of Clinical Endocrinology, Keimyung University School of Medicine, Daegu, Republic of Korea
- *Yun-Ui Bae,
| | - Soon Hyo Kwon
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
- **Soon Hyo Kwon,
| |
Collapse
|
21
|
Reithmair M, Lindemann A, Mussack V, Pfaffl MW. Isolation and Characterization of Urinary Extracellular Vesicles for MicroRNA Biomarker Signature Development with Reference to MISEV Compliance. Methods Mol Biol 2022; 2504:113-133. [PMID: 35467283 DOI: 10.1007/978-1-0716-2341-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Urine bears high potential for serving as biomarker repository for renal and urinary tract associated disorders. Besides various metabolites and salts, urine carries extracellular vesicles (EVs)-a heterogeneous group of cell-derived mediators comprising proteins, lipids, and nucleic acids such as microRNAs (miRNAs). Particularly, EV-derived miRNA biomarkers have already been identified for numerous disorders such as sepsis, various blood and solid cancer entities, respiratory and renal diseases. However, study results are often incomparable due to poorly reported EV separation and miRNA isolation protocols and emphasize the need for standardization and reproducibility. To ensure valid EV-derived miRNA biomarker findings from urine, a step-by-step protocol compliant with the "Minimal Information for Studies of Extracellular Vesicles" (MISEV) is outlined in the following paragraphs. Actually, an immunoaffinity-based EV separation method followed by EV characterization, quantification, and normalization, as well as consecutive miRNA isolation and miRNA profiling by small RNA sequencing, are described.
Collapse
Affiliation(s)
- Marlene Reithmair
- Institute of Human Genetics, University Hospital Munich, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Anja Lindemann
- Institute of Human Genetics, University Hospital Munich, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Veronika Mussack
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| |
Collapse
|
22
|
Single Extracellular Vesicle Analysis Performed by Imaging Flow Cytometry and Nanoparticle Tracking Analysis Evaluate the Accuracy of Urinary Extracellular Vesicle Preparation Techniques Differently. Int J Mol Sci 2021; 22:ijms222212436. [PMID: 34830318 PMCID: PMC8620260 DOI: 10.3390/ijms222212436] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
Small extracellular vesicles isolated from urine (uEVs) are increasingly recognized as potential biomarkers. Meanwhile, different uEV preparation strategies exist. Conventionally, the performance of EV preparation methods is evaluated by single particle quantification, Western blot, and electron microscopy. Recently, we introduced imaging flow cytometry (IFCM) as a next-generation single EV analysis technology. Here, we analyzed uEV samples obtained with different preparation procedures using nanoparticle tracking analysis (NTA), semiquantitative Western blot, and IFCM. IFCM analyses demonstrated that urine contains a predominant CD9+ sEV population, which exceeds CD63+ and CD81+ sEV populations. Furthermore, we demonstrated that the storage temperature of urine samples negatively affects the recovery of CD9+ sEVs. Although overall reduced, the highest CD9+ sEV recovery was obtained from urine samples stored at −80 °C and the lowest from those stored at −20 °C. Upon comparing the yield of the different uEV preparations, incongruencies between NTA and IFCM data became apparent. Results obtained by both NTA and IFCM were consistent with Western blot analyses for EV marker proteins; however, NTA results correlated with the amount of the impurity marker uromodulin. Despite demonstrating that the combination of ultrafiltration and size exclusion chromatography appears as a reliable uEV preparation technique, our data challenge the soundness of traditional NTA for the evaluation of different EV preparation methods.
Collapse
|
23
|
Barreiro K, Dwivedi OP, Valkonen S, Groop P, Tuomi T, Holthofer H, Rannikko A, Yliperttula M, Siljander P, Laitinen S, Serkkola E, af Hällström T, Forsblom C, Groop L, Puhka M. Urinary extracellular vesicles: Assessment of pre-analytical variables and development of a quality control with focus on transcriptomic biomarker research. J Extracell Vesicles 2021; 10:e12158. [PMID: 34651466 PMCID: PMC8517090 DOI: 10.1002/jev2.12158] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/06/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
Urinary extracellular vesicles (uEV) are a topical source of non-invasive biomarkers for health and diseases of the urogenital system. However, several challenges have become evident in the standardization of uEV pipelines from collection of urine to biomarker analysis. Here, we studied the effect of pre-analytical variables and developed means of quality control for uEV isolates to be used in transcriptomic biomarker research. We included urine samples from healthy controls and individuals with type 1 or type 2 diabetes and normo-, micro- or macroalbuminuria and isolated uEV by ultracentrifugation. We studied the effect of storage temperature (-20°C vs. -80°C), time (up to 4 years) and storage format (urine or isolated uEV) on quality of uEV by nanoparticle tracking analysis, electron microscopy, Western blotting and qPCR. Urinary EV RNA was compared in terms of quantity, quality, and by mRNA or miRNA sequencing. To study the stability of miRNA levels in samples isolated by different methods, we created and tested a list of miRNAs commonly enriched in uEV isolates. uEV and their transcriptome were preserved in urine or as isolated uEV even after long-term storage at -80°C. However, storage at -20°C degraded particularly the GC-rich part of the transcriptome and EV protein markers. Transcriptome was preserved in RNA samples extracted with and without DNAse, but read distributions still showed some differences in e.g. intergenic and intronic reads. MiRNAs commonly enriched in uEV isolates were stable and concordant between different EV isolation methods. Analysis of never frozen uEV helped to identify surface characteristics of particles by EM. In addition to uEV, qPCR assays demonstrated that uEV isolates commonly contained polyoma viruses. Based on our results, we present recommendations how to store and handle uEV isolates for transcriptomics studies that may help to expedite standardization of the EV biomarker field.
Collapse
Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Om Prakash Dwivedi
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Sami Valkonen
- EV Group, Molecular and Integrative Biosciences Research ProgramFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Research and DevelopmentFinnish Red Cross Blood ServiceHelsinkiFinland
- Drug Research ProgramDivision of Pharmaceutical BiosciencesFaculty of PharmacyUniversity of HelsinkiHelsinkiFinland
| | - Per‐Henrik Groop
- Folkhälsan Institute of GeneticsFolkhälsan Research CenterHelsinkiFinland
- Department of NephrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of DiabetesCentral Clinical SchoolMonash UniversityMelbourneAustralia
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Clinical SciencesLund University Diabetes CenterMalmöSweden
- Skåne University HospitalLund UniversityMalmöSweden
- Abdominal Center, EndocrinologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Harry Holthofer
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Antti Rannikko
- Department of UrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program in Systems OncologyFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Marjo Yliperttula
- Drug Research ProgramDivision of Pharmaceutical BiosciencesFaculty of PharmacyUniversity of HelsinkiHelsinkiFinland
| | - Pia Siljander
- EV Group, Molecular and Integrative Biosciences Research ProgramFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- CURED, Drug Research ProgramDivision of Pharmaceutical BiosciencesFaculty of PharmacyUniversity of HelsinkiHelsinkiFinland
- EV‐coreFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Saara Laitinen
- Research and DevelopmentFinnish Red Cross Blood ServiceHelsinkiFinland
| | | | | | - Carol Forsblom
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- Folkhälsan Institute of GeneticsFolkhälsan Research CenterHelsinkiFinland
- Department of NephrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program for Clinical and Molecular MetabolismFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Leif Groop
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- Department of Clinical SciencesLund University Diabetes CenterMalmöSweden
- Skåne University HospitalLund UniversityMalmöSweden
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- HiPrep and EV CoreInstitute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| |
Collapse
|
24
|
Buschmann D, Mussack V, Byrd JB. Separation, characterization, and standardization of extracellular vesicles for drug delivery applications. Adv Drug Deliv Rev 2021; 174:348-368. [PMID: 33964356 PMCID: PMC8217305 DOI: 10.1016/j.addr.2021.04.027] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/25/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
Extracellular vesicles (EVs) are membranous nanovesicles secreted from living cells, shuttling macromolecules in intercellular communication and potentially possessing intrinsic therapeutic activity. Due to their stability, low immunogenicity, and inherent interaction with recipient cells, EVs also hold great promise as drug delivery vehicles. Indeed, they have been used to deliver nucleic acids, proteins, and small molecules in preclinical investigations. Furthermore, EV-based drugs have entered early clinical trials for cancer or neurodegenerative diseases. Despite their appeal as delivery vectors, however, EV-based drug delivery progress has been hampered by heterogeneity of sample types and methods as well as a persistent lack of standardization, validation, and comprehensive reporting. This review highlights specific requirements for EVs in drug delivery and describes the most pertinent approaches for separation and characterization. Despite residual uncertainties related to pharmacodynamics, pharmacokinetics, and potential off-target effects, clinical-grade, high-potency EV drugs might be achievable through GMP-compliant workflows in a highly standardized environment.
Collapse
Affiliation(s)
- Dominik Buschmann
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Veronika Mussack
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - James Brian Byrd
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| |
Collapse
|
25
|
Urinary Extracellular Vesicles: Uncovering the Basis of the Pathological Processes in Kidney-Related Diseases. Int J Mol Sci 2021; 22:ijms22126507. [PMID: 34204452 PMCID: PMC8234687 DOI: 10.3390/ijms22126507] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/27/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022] Open
Abstract
Intercellular communication governs multicellular interactions in complex organisms. A variety of mechanisms exist through which cells can communicate, e.g., cell-cell contact, the release of paracrine/autocrine soluble molecules, or the transfer of extracellular vesicles (EVs). EVs are membrane-surrounded structures released by almost all cell types, acting both nearby and distant from their tissue/organ of origin. In the kidney, EVs are potent intercellular messengers released by all urinary system cells and are involved in cell crosstalk, contributing to physiology and pathogenesis. Moreover, urine is a reservoir of EVs coming from the circulation after crossing the glomerular filtration barrier—or originating in the kidney. Thus, urine represents an alternative source for biomarkers in kidney-related diseases, potentially replacing standard diagnostic techniques, including kidney biopsy. This review will present an overview of EV biogenesis and classification and the leading procedures for isolating EVs from body fluids. Furthermore, their role in intra-nephron communication and their use as a diagnostic tool for precision medicine in kidney-related disorders will be discussed.
Collapse
|
26
|
Corrêa RR, Juncosa EM, Masereeuw R, Lindoso RS. Extracellular Vesicles as a Therapeutic Tool for Kidney Disease: Current Advances and Perspectives. Int J Mol Sci 2021; 22:ijms22115787. [PMID: 34071399 PMCID: PMC8198688 DOI: 10.3390/ijms22115787] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) have been described as important mediators of cell communication, regulating several physiological processes, including tissue recovery and regeneration. In the kidneys, EVs derived from stem cells have been shown to support tissue recovery in diverse disease models and have been considered an interesting alternative to cell therapy. For this purpose, however, several challenges remain to be overcome, such as the requirement of a high number of EVs for human therapy and the need for optimization of techniques for their isolation and characterization. Moreover, the kidney’s complexity and the pathological process to be treated require that EVs present a heterogeneous group of molecules to be delivered. In this review, we discuss the recent advances in the use of EVs as a therapeutic tool for kidney diseases. Moreover, we give an overview of the new technologies applied to improve EVs’ efficacy, such as novel methods of EV production and isolation by means of bioreactors and microfluidics, bioengineering the EV content and the use of alternative cell sources, including kidney organoids, to support their transfer to clinical applications.
Collapse
Affiliation(s)
- Raphael Rodrigues Corrêa
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil;
| | - Estela Mancheño Juncosa
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands;
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands;
- Correspondence: (R.M.); (R.S.L.); Tel.: +31-30-253-3529 (R.M.); Tel.: +55-21-3938-6520 (R.S.L.)
| | - Rafael Soares Lindoso
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil;
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands;
- National Institute of Science and Technology for Regenerative Medicine-REGENERA, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Correspondence: (R.M.); (R.S.L.); Tel.: +31-30-253-3529 (R.M.); Tel.: +55-21-3938-6520 (R.S.L.)
| |
Collapse
|
27
|
Malenica M, Vukomanović M, Kurtjak M, Masciotti V, dal Zilio S, Greco S, Lazzarino M, Krušić V, Perčić M, Jelovica Badovinac I, Wechtersbach K, Vidović I, Baričević V, Valić S, Lučin P, Kojc N, Grabušić K. Perspectives of Microscopy Methods for Morphology Characterisation of Extracellular Vesicles from Human Biofluids. Biomedicines 2021; 9:603. [PMID: 34073297 PMCID: PMC8228884 DOI: 10.3390/biomedicines9060603] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are nanometric membranous structures secreted from almost every cell and present in biofluids. Because EV composition reflects the state of its parental tissue, EVs possess an enormous diagnostic/prognostic potential to reveal pathophysiological conditions. However, a prerequisite for such usage of EVs is their detailed characterisation, including visualisation which is mainly achieved by atomic force microscopy (AFM) and electron microscopy (EM). Here we summarise the EV preparation protocols for AFM and EM bringing out the main challenges in the imaging of EVs, both in their natural environment as biofluid constituents and in a saline solution after EV isolation. In addition, we discuss approaches for EV imaging and identify the potential benefits and disadvantages when different AFM and EM methods are applied, including numerous factors that influence the morphological characterisation, standardisation, or formation of artefacts. We also demonstrate the effects of some of these factors by using cerebrospinal fluid as an example of human biofluid with a simpler composition. Here presented comparison of approaches to EV imaging should help to estimate the current state in morphology research of EVs from human biofluids and to identify the most efficient pathways towards the standardisation of sample preparation and microscopy modes.
Collapse
Affiliation(s)
- Mladenka Malenica
- Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, HR-51000 Rijeka, Croatia; (V.K.); (P.L.); (K.G.)
| | - Marija Vukomanović
- Advanced Materials Department, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia; (M.V.); (M.K.)
| | - Mario Kurtjak
- Advanced Materials Department, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia; (M.V.); (M.K.)
| | - Valentina Masciotti
- CNR-IOM Istituto Officina dei Materiali-Consiglio Nazionale delle Ricerche c/Area Scinece Park, Basovizza, I-34149 Trieste, Italy; (V.M.); (S.d.Z.); (M.L.)
| | - Simone dal Zilio
- CNR-IOM Istituto Officina dei Materiali-Consiglio Nazionale delle Ricerche c/Area Scinece Park, Basovizza, I-34149 Trieste, Italy; (V.M.); (S.d.Z.); (M.L.)
| | | | - Marco Lazzarino
- CNR-IOM Istituto Officina dei Materiali-Consiglio Nazionale delle Ricerche c/Area Scinece Park, Basovizza, I-34149 Trieste, Italy; (V.M.); (S.d.Z.); (M.L.)
| | - Vedrana Krušić
- Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, HR-51000 Rijeka, Croatia; (V.K.); (P.L.); (K.G.)
| | - Marko Perčić
- Faculty of Engineering, University of Rijeka, HR-51000 Rijeka, Croatia;
- Centre for Micro- and Nanosciences and Technologies, University of Rijeka, HR-51000 Rijeka, Croatia;
| | - Ivana Jelovica Badovinac
- Centre for Micro- and Nanosciences and Technologies, University of Rijeka, HR-51000 Rijeka, Croatia;
- Department of Physics, University of Rijeka, HR-51000 Rijeka, Croatia
| | - Karmen Wechtersbach
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.W.); (N.K.)
| | - Ivona Vidović
- Department of Biotechnology, University of Rijeka, HR-51000 Rijeka, Croatia; (I.V.); (V.B.)
| | - Vanja Baričević
- Department of Biotechnology, University of Rijeka, HR-51000 Rijeka, Croatia; (I.V.); (V.B.)
| | - Srećko Valić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, HR-51000 Rijeka, Croatia;
- Division of Physical Chemistry, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia
| | - Pero Lučin
- Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, HR-51000 Rijeka, Croatia; (V.K.); (P.L.); (K.G.)
| | - Nika Kojc
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (K.W.); (N.K.)
| | - Kristina Grabušić
- Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, HR-51000 Rijeka, Croatia; (V.K.); (P.L.); (K.G.)
| |
Collapse
|
28
|
Karttunen J, Stewart SE, Kalmar L, Grant AJ, Karet Frankl FE, Williams TL. Size-Exclusion Chromatography Separation Reveals That Vesicular and Non-Vesicular Small RNA Profiles Differ in Cell Free Urine. Int J Mol Sci 2021; 22:ijms22094881. [PMID: 34063036 PMCID: PMC8124894 DOI: 10.3390/ijms22094881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/22/2021] [Accepted: 04/30/2021] [Indexed: 12/26/2022] Open
Abstract
Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases. We aimed to identify the optimal method for isolating small (<200 nm) EVs from human urine prior to small RNA analysis. EVs from filtered healthy volunteer urine were concentrated using three methods: ultracentrifugation (UC); a precipitation-based kit (PR); and ultrafiltration (UF). EVs were further purified by size-exclusion chromatography (SEC). EV preparations were analysed with transmission electron microscopy (TEM), Western blotting, nanoparticle tracking analysis (NTA) and an Agilent Bioanalyzer Small RNA kit. UF yielded the highest number of particles both before and after SEC. Small RNA analysis from UF-concentrated urine identified two major peaks at 10–40 nucleotides (nt) and 40–80 nt. In contrast, EV preparations obtained after UC, PR or SEC combined with any concentrating method, contained predominantly 40–80 nt sized small RNA. Protein fractions from UF+SEC contained small RNA of 10–40 nt in size (consistent with miRNAs). These data indicate that most of the microRNA-sized RNAs in filtered urine are not associated with small-sized EVs, and highlights the importance of removing non-vesicular proteins and RNA from urine EV preparations prior to small RNA analysis.
Collapse
Affiliation(s)
- Jenni Karttunen
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.K.); (L.K.); (A.J.G.)
| | - Sarah E. Stewart
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK;
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Lajos Kalmar
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.K.); (L.K.); (A.J.G.)
| | - Andrew J. Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.K.); (L.K.); (A.J.G.)
| | | | - Tim L. Williams
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (J.K.); (L.K.); (A.J.G.)
- Correspondence:
| |
Collapse
|
29
|
Erdbrügger U, Blijdorp CJ, Bijnsdorp IV, Borràs FE, Burger D, Bussolati B, Byrd JB, Clayton A, Dear JW, Falcón‐Pérez JM, Grange C, Hill AF, Holthöfer H, Hoorn EJ, Jenster G, Jimenez CR, Junker K, Klein J, Knepper MA, Koritzinsky EH, Luther JM, Lenassi M, Leivo J, Mertens I, Musante L, Oeyen E, Puhka M, van Royen ME, Sánchez C, Soekmadji C, Thongboonkerd V, van Steijn V, Verhaegh G, Webber JP, Witwer K, Yuen PS, Zheng L, Llorente A, Martens‐Uzunova ES. Urinary extracellular vesicles: A position paper by the Urine Task Force of the International Society for Extracellular Vesicles. J Extracell Vesicles 2021; 10:e12093. [PMID: 34035881 PMCID: PMC8138533 DOI: 10.1002/jev2.12093] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/26/2021] [Accepted: 04/22/2021] [Indexed: 12/17/2022] Open
Abstract
Urine is commonly used for clinical diagnosis and biomedical research. The discovery of extracellular vesicles (EV) in urine opened a new fast-growing scientific field. In the last decade urinary extracellular vesicles (uEVs) were shown to mirror molecular processes as well as physiological and pathological conditions in kidney, urothelial and prostate tissue. Therefore, several methods to isolate and characterize uEVs have been developed. However, methodological aspects of EV separation and analysis, including normalization of results, need further optimization and standardization to foster scientific advances in uEV research and a subsequent successful translation into clinical practice. This position paper is written by the Urine Task Force of the Rigor and Standardization Subcommittee of ISEV consisting of nephrologists, urologists, cardiologists and biologists with active experience in uEV research. Our aim is to present the state of the art and identify challenges and gaps in current uEV-based analyses for clinical applications. Finally, recommendations for improved rigor, reproducibility and interoperability in uEV research are provided in order to facilitate advances in the field.
Collapse
|
30
|
Detection and Investigation of Extracellular Vesicles in Serum and Urine Supernatant of Prostate Cancer Patients. Diagnostics (Basel) 2021; 11:diagnostics11030466. [PMID: 33800141 PMCID: PMC7998238 DOI: 10.3390/diagnostics11030466] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
Prostate Cancer (PCa) is one of the most frequently identified urological cancers. PCa patients are often over-diagnosed due to still not highly specific diagnostic methods. The need for more accurate diagnostic tools to prevent overestimated diagnosis and unnecessary treatment of patients with non-malignant conditions is clear, and new markers and methods are strongly desirable. Extracellular vesicles (EVs) hold great promises as liquid biopsy-based markers. Despite the biological and technical issues present in their detection and study, these particles can be found highly abundantly in the biofluid and encompass a wealth of macromolecules that have been reported to be related to many physiological and pathological processes, including cancer onset, metastasis spreading, and treatment resistance. The present study aims to perform a technical feasibility study to develop a new workflow for investigating EVs from several biological sources. Serum and urinary supernatant EVs of PCa, benign prostatic hyperplasia (BPH) patients, and healthy donors were isolated and investigated by a fast, easily performable, and cost-effective cytofluorimetric approach for a multiplex detection of 37 EV-antigens. We also observed significant alterations in serum and urinary supernatant EVs potentially related to BPH and PCa, suggesting a potential clinical application of this workflow.
Collapse
|
31
|
Mussack V, Wittmann G, Pfaffl MW. On the trail of blood doping-microRNA fingerprints to monitor autologous blood transfusions in vivo. Am J Hematol 2021; 96:338-353. [PMID: 33326140 DOI: 10.1002/ajh.26078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022]
Abstract
Autologous blood doping refers to the illegal re-transfusion of any quantities of blood or blood components with blood donor and recipient being the same person. The re-transfusion of stored erythrocyte concentrates is particularly attractive to high-performance athletes as this practice improves their oxygen capacity excessively. However, there is still no reliable detection method available. Analyzing circulating microRNA profiles of human subjects that underwent monitored autologous blood transfusions seems to be a highly promising approach to develop novel biomarkers for autologous blood doping. In this exploratory study, we randomly divided 30 healthy males into two different treatment groups and one control group and sampled whole blood at several time points at baseline, after whole blood donation and after transfusion of erythrocyte concentrates. Hematological variables were recorded and analyzed following the adaptive model of the Athlete Biological Passport. microRNA profiles were examined by small RNA sequencing and comprehensive multivariate data analyses, revealing microRNA fingerprints that reflect the sampling time point and transfusion volume. Neither individual microRNAs nor a signature of transfusion-dependent microRNAs reached superior sensitivity at 100% specificity compared to the Athlete Biological Passport (≤11% 6 h after transfusion versus ≤44% 2 days after transfusion). However, the window of autologous blood doping detection was different. Due to the heterogenous nature of doping, with athletes frequently combining multiple medications in order to both gain a competitive advantage and interfere with known testing methods, the true applicability of the molecular signature remains to be validated in real anti-doping testings.
Collapse
Affiliation(s)
- Veronika Mussack
- Animal Physiology and Immunology School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
| | - Georg Wittmann
- Department for Transfusion Medicine, Cell therapeutics and Haemostaseology University Hospital LMU Munich Germany
| | - Michael W. Pfaffl
- Animal Physiology and Immunology School of Life Sciences Weihenstephan, Technical University of Munich Freising Germany
| |
Collapse
|
32
|
Budgude P, Kale V, Vaidya A. Cryopreservation of mesenchymal stromal cell-derived extracellular vesicles using trehalose maintains their ability to expand hematopoietic stem cells in vitro. Cryobiology 2021; 98:152-163. [PMID: 33253747 DOI: 10.1016/j.cryobiol.2020.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 02/08/2023]
Abstract
The multitude of clinical trials using mesenchymal stromal cells (MSCs) has underscored their significance as a promising cell source for regenerative therapies. Most studies have however shown that MSCs get entrapped into the microvasculature of lungs, liver and spleen. In addition to intercellular communication, MSCs exert their effects in a paracrine manner by secretion of extracellular vesicles (EVs). The therapeutic effects of MSC-derived EVs have been examined in several diseases such as hepatic failure, liver injury, hematopoiesis etc. Therefore, optimization of cryopreservation strategies for the long-term storage of functional EVs could help in the development of off-the-shelf biologics. The aim of this study was to develop an optimal cryopreservation strategy for the efficient storage of both types of EVs - Microvesicles (MVs) and exosomes, independently, and to further examine the effect of the cryopreserved EVs on the ex vivo expansion of HSCs. MVs and exosomes were separately cryopreserved at different temperatures using PBS or PBS supplemented with trehalose (pTRE), and these cryopreserved EVs were then assessed for their functionality after revival. We found that addition of trehalose during cryopreservation helped in maintaining the morphology and functionality of the EVs, as assessed by their HSC-supportive potential, ability to expand phenotypically defined HSCs and ability to maintain the chemotactic migration potential of the HSCs co-cultured with them. This strategy could prove to be beneficial for facilitating the use of EVs as cell-free ready-to-use biologics for the ex vivo expansion of HSCs and in regenerative medicine.
Collapse
Affiliation(s)
- Pallavi Budgude
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, 412115, India; Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, 412115, India
| | - Vaijayanti Kale
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, 412115, India
| | - Anuradha Vaidya
- Symbiosis Centre for Stem Cell Research, Symbiosis International (Deemed University), Pune, 412115, India; Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, 412115, India.
| |
Collapse
|
33
|
Maggio S, Polidori E, Ceccaroli P, Cioccoloni A, Stocchi V, Guescini M. Current Methods for the Isolation of Urinary Extracellular Vesicles. Methods Mol Biol 2021; 2292:153-172. [PMID: 33651360 DOI: 10.1007/978-1-0716-1354-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Extracellular vesicles (EVs) are small membrane-bound particles released into extracellular space by almost all cell types, and found in body fluids like blood, urine, and saliva. Mounting evidence has demonstrated the clinical potential of EVs as diagnostic and therapeutic tools to analyse physiological/pathological processes due to their ability to transport biomolecules secreted from diverse tissues of an individual.For example, the urinary EVs (uEVs), released from all regions of the kidney's nephron and from other cells that line the urinary tract, retain proteomic and transcriptomic markers specific to their cell of origin representing a valuable tool for kidney disease diagnosis.Despite the numerous efforts in developing suitable methods to separate EVs from biofluids, providing material of high purity and low variability poses a limit to clinical translation.This chapter focuses on advantages and disadvantages of several EV isolation methodologies, and provides examples of uEV isolation protocols based on time, cost, and equipment considerations, as well as the sample requirements for any downstream analyses.
Collapse
Affiliation(s)
- Serena Maggio
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Emanuela Polidori
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Paola Ceccaroli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Andrea Cioccoloni
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Vilberto Stocchi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Michele Guescini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy.
| |
Collapse
|
34
|
Barreiro K, Dwivedi OP, Leparc G, Rolser M, Delic D, Forsblom C, Groop P, Groop L, Huber TB, Puhka M, Holthofer H. Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease. J Extracell Vesicles 2020; 10:e12038. [PMID: 33437407 PMCID: PMC7789228 DOI: 10.1002/jev2.12038] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/20/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
Urinary Extracellular Vesicles (uEV) have emerged as a source for biomarkers of kidney damage, holding potential to replace the conventional invasive techniques including kidney biopsy. However, comprehensive studies characterizing uEV isolation methods with patient samples are rare. Here we compared performance of three established uEV isolation workflows for their subsequent use in transcriptomics analysis for biomarker discovery in diabetic kidney disease. We collected urine samples from individuals with type 1 diabetes with macroalbuminuria and healthy controls. We isolated uEV by Hydrostatic Filtration Dialysis (HFD), ultracentrifugation (UC), and a commercial kit- based isolation method (NG), each with different established urine clearing steps. Purified EVs were analysed by electron microscopy, nanoparticle tracking analysis, and Western blotting. Isolated RNAs were subjected to miRNA and RNA sequencing. HFD and UC samples showed close similarities based on mRNA sequencing data. NG samples had a lower number of reads and different mRNA content compared to HFD or UC. For miRNA sequencing data, satisfactory miRNA counts were obtained by all methods, but miRNA contents differed slightly. This suggests that the isolation workflows enrich specific subpopulations of miRNA-rich uEV preparation components. Our data shows that HFD,UC and the kit-based method are suitable methods to isolate uEV for miRNA-seq. However, only HFD and UC were suitable for mRNA-seq in our settings.
Collapse
Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Om Prakash Dwivedi
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - German Leparc
- Boehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Marcel Rolser
- Boehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Denis Delic
- Boehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre MannheimUniversity of HeidelbergHeidelbergGermany
| | - Carol Forsblom
- Folkhälsan Institute of GeneticsFolkhälsan Research CenterHelsinkiFinland
- Abdominal Center, NephrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program for Clinical and Molecular Metabolism, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Per‐Henrik Groop
- Folkhälsan Institute of GeneticsFolkhälsan Research CenterHelsinkiFinland
- Abdominal Center, NephrologyUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
- Research Program for Clinical and Molecular Metabolism, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Diabetes, Central Clinical SchoolMonash UniversityMelbourneVICAustralia
| | - Leif Groop
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Tobias B. Huber
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Harry Holthofer
- Institute for Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
- III Department of MedicineUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| |
Collapse
|
35
|
Dong L, Zieren RC, Horie K, Kim C, Mallick E, Jing Y, Feng M, Kuczler MD, Green J, Amend SR, Witwer KW, de Reijke TM, Cho Y, Pienta KJ, Xue W. Comprehensive evaluation of methods for small extracellular vesicles separation from human plasma, urine and cell culture medium. J Extracell Vesicles 2020; 10:e12044. [PMID: 33489012 PMCID: PMC7810129 DOI: 10.1002/jev2.12044] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/22/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
One of the challenges that restricts the evolving extracellular vesicle (EV) research field is the lack of a consensus method for EV separation. This may also explain the diversity of the experimental results, as co-separated soluble proteins and lipoproteins may impede the interpretation of experimental findings. In this study, we comprehensively evaluated the EV yields and sample purities of three most popular EV separation methods, ultracentrifugation, precipitation and size exclusion chromatography combined with ultrafiltration, along with a microfluidic tangential flow filtration device, Exodisc, in three commonly used biological samples, cell culture medium, human urine and plasma. Single EV phenotyping and density-gradient ultracentrifugation were used to understand the proportion of true EVs in particle separations. Our findings suggest Exodisc has the best EV yield though it may co-separate contaminants when the non-EV particle levels are high in input materials. We found no 100% pure EV preparations due to the overlap of their size and density with many non-EV particles in biofluids. Precipitation has the lowest sample purity, regardless of sample type. The purities of the other techniques may vary in different sample types and are largely dependent on their working principles and the intrinsic composition of the input sample. Researchers should choose the proper separation method according to the sample type, downstream analysis and their working scenarios.
Collapse
Affiliation(s)
- Liang Dong
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Urology, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Richard C. Zieren
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Urology, Amsterdam UMCUniversity of AmsterdamAmsterdamthe Netherlands
| | - Kengo Horie
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of UrologyGifu University Graduate School of MedicineGifuJapan
| | - Chi‐Ju Kim
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical Engineering, School of Life SciencesUlsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
| | - Emily Mallick
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Yuezhou Jing
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Mingxiao Feng
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Morgan D. Kuczler
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jordan Green
- Department of Biomedical Engineering, Institute for NanoBioTechnology, and Translational Tissue Engineering CenterJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Sarah R. Amend
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Kenneth W. Witwer
- Department of Molecular and Comparative PathobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Theo M. de Reijke
- Department of Urology, Amsterdam UMCUniversity of AmsterdamAmsterdamthe Netherlands
| | - Yoon‐Kyoung Cho
- Department of Biomedical Engineering, School of Life SciencesUlsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
- Center for Soft and Living MatterInstitute for Basic Science (IBS)UlsanRepublic of Korea
| | - Kenneth J. Pienta
- The Brady Urological InstituteJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Wei Xue
- Department of Urology, Renji HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| |
Collapse
|
36
|
Analysis of RNA yield in extracellular vesicles isolated by membrane affinity column and differential ultracentrifugation. PLoS One 2020; 15:e0238545. [PMID: 33156858 PMCID: PMC7647092 DOI: 10.1371/journal.pone.0238545] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EV) have attracted much attention as potential biomarkers due to their protein, RNA and other nucleic acid content. The most common method used for EV isolation is differential ultracentrifugation (DU), however given the DU technical difficulties, other more practical methods have surged, such as membrane-affinity column commercial kits. Here, we assessed one commercial kit in terms of EV recovery and EV-derived RNA yield and compared it with a DU protocol. Our data shows that the commercial kit preparation results in a lower count of EV-like structures and a reduced expression of EV markers when compared to DU samples. Thus, apparently suggesting that the commercial kit had a lower EV yield. However, these findings did not reflect on RNA yield, which was greater with the commercial kit, even after an enzymatic treatment with proteinase K and RNAse A. We conclude that the kit has a higher EV-derived RNA yield in comparison to our DU protocol, suggesting that it may be the method of choice for RNA sequencing purposes.
Collapse
|
37
|
Dhondt B, Lumen N, De Wever O, Hendrix A. Preparation of Multi-omics Grade Extracellular Vesicles by Density-Based Fractionation of Urine. STAR Protoc 2020; 1:100073. [PMID: 33111109 PMCID: PMC7580105 DOI: 10.1016/j.xpro.2020.100073] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The multidimensional cargo of extracellular vesicles (EV) released in urine is a reflection of the pathophysiological processes occurring within their cells and tissues of origin in the urogenital system. Here, we describe a step-by-step protocol for density-based separation of urinary EV with high specificity and repeatability. The implementation of integrative omics allows the study of the molecular complexity of highly purified urinary EV, supporting the identification of EV-specific functions and biomarkers. For complete details on the use and execution of this protocol, please refer to Dhondt et al. (2020).
Collapse
Affiliation(s)
- Bert Dhondt
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Nicolaas Lumen
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| |
Collapse
|
38
|
La Salvia S, Gunasekaran PM, Byrd JB, Erdbrügger U. Extracellular Vesicles in Essential Hypertension: Hidden Messengers. Curr Hypertens Rep 2020; 22:76. [PMID: 32880744 DOI: 10.1007/s11906-020-01084-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW Hypertension affects about half of all Americans, yet in the vast majority of cases, the factors causing the hypertension cannot be clearly delineated. Developing a more precise understanding of the molecular pathogenesis of HTN and its various phenotypes is therefore a pressing priority. Circulating and urinary extracellular vesicles (EVs) are potential novel candidates as biomarkers and bioactivators in HTN. EVs are a heterogeneous population of small membrane fragments shed from various cell types into various body fluids. As EVs carry protein, RNA, and lipids, they also play a role as effectors and novel cell-to-cell communicators. In this review, we discuss the diagnostic, functional, and regenerative role of EVs in essential HTN and focus on EV protein and RNA cargo as the most extensively studied EV cargo. RECENT FINDINGS The field of EVs in HTN is still a young one and earlier studies have not used the novel EV detection tools currently available. More rigor and transparency in EV research are needed. Current data suggest that EVs represent potential novel biomarkers in HTN. EVs correlate with HTN severity and possibly end-organ damage. However, it has yet to be discerned which specific subtype(s) of EV reflects best HTN pathophysiology. Evolving studies are also showing that EVs might be novel regulators in vascular and renal tubular function and also be therapeutic. RNA in EVs has been studied in the context of hypertension, largely in the form of studies of miRNA, which are reviewed herein. Beyond miRNAs, mRNA in urinary EVs changed in response to sodium loading in humans. EVs represent promising novel biomarkers and bioactivators in essential HTN. Novel tools are being developed to apply more rigor in EV research including more in vivo models and translation to humans.
Collapse
Affiliation(s)
- Sabrina La Salvia
- Department of Internal Medicine, Division of Nephrology, University of Virginia Health System, 1300 Jefferson Park Avenue, Charlottesville, VA, 22908-0133, USA.
| | - Pradeep Moon Gunasekaran
- Department of Internal Medicine, Division of Cardiovascular Medicine, Medical School, University of Michigan Medical School, 5570C MSRB II, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109, USA
| | - James Brian Byrd
- Department of Internal Medicine, Division of Cardiovascular Medicine, Medical School, University of Michigan Medical School, 5570C MSRB II, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109, USA
| | - Uta Erdbrügger
- Department of Internal Medicine, Division of Nephrology, University of Virginia Health System, 1300 Jefferson Park Avenue, Charlottesville, VA, 22908-0133, USA
| |
Collapse
|
39
|
Torres Crigna A, Fricke F, Nitschke K, Worst T, Erb U, Karremann M, Buschmann D, Elvers-Hornung S, Tucher C, Schiller M, Hausser I, Gebert J, Bieback K. Inter-Laboratory Comparison of Extracellular Vesicle Isolation Based on Ultracentrifugation. Transfus Med Hemother 2020; 48:48-59. [PMID: 33708052 DOI: 10.1159/000508712] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/07/2020] [Indexed: 12/19/2022] Open
Abstract
Background/Aims Extracellular vesicles (EVs), including microvesicles and exosomes, deliver bioactive cargo mediating intercellular communication in physiological and pathological conditions. EVs are increasingly investigated as therapeutic agents and targets, but also as disease biomarkers. However, a definite consensus regarding EV isolation methods is lacking, which makes it intricate to standardize research practices and eventually reach a desirable level of data comparability. In our study, we performed an inter-laboratory comparison of EV isolation based on a differential ultracentrifugation protocol carried out in 4 laboratories in 2 independent rounds of isolation. Methods Conditioned medium of colorectal cancer cells was prepared and pooled by 1 person and distributed to each of the participating laboratories for isolation according to a pre-defined protocol. After EV isolation in each laboratory, quantification and characterization of isolated EVs was collectively done by 1 person having the highest expertise in the respective test method: Western blot, flow cytometry (fluorescence-activated cell sorting [FACS], nanoparticle tracking analysis (NTA), and transmission electron microscopy (TEM). Results EVs were visualized with TEM, presenting similar cup-shaped and spherical morphology and sizes ranging from 30 to 150 nm. NTA results showed similar size ranges of particles in both isolation rounds. EV preparations showed high purity by the expression of EV marker proteins CD9, CD63, CD81, Alix, and TSG101, and the lack of calnexin. FACS analysis of EVs revealed intense staining for CD63 and CD81 but lower levels for CD9 and TSG101. Preparations from 1 laboratory presented significantly lower particle numbers (p < 0.0001), most probably related to increased processing time. However, even when standardizing processing time, particle yields still differed significantly between groups, indicating inter-laboratory differences in the efficiency of EV isolation. Importantly, no relation was observed between centrifugation speed/k-factor and EV yield. Conclusions Our findings demonstrate that quantitative differences in EV yield might be due to equipment- and operator-dependent technical variability in ultracentrifugation-based EV isolation. Furthermore, our study emphasizes the need to standardize technical parameters such as the exact run speed and k-factor in order to transfer protocols between different laboratories. This hints at substantial inter-laboratory biases that should be assessed in multi-centric studies.
Collapse
Affiliation(s)
- Adriana Torres Crigna
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Donor Service Baden-Württemberg-Hessen, Mannheim, Germany
| | - Fabia Fricke
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Katja Nitschke
- Department of Urology and Urosurgery, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Worst
- Department of Urology and Urosurgery, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Division Signaling and Functional Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Ulrike Erb
- Department of Pediatrics, Pediatric Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael Karremann
- Department of Pediatrics, Pediatric Oncology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Dominik Buschmann
- Department of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Susanne Elvers-Hornung
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Donor Service Baden-Württemberg-Hessen, Mannheim, Germany
| | - Christine Tucher
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Schiller
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Department of Internal Medicine, Kliniken Hochfranken, Naila, Germany
| | - Ingrid Hausser
- EM-Lab, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Karen Bieback
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Donor Service Baden-Württemberg-Hessen, Mannheim, Germany
| |
Collapse
|
40
|
Khalyfa A, Castro-Grattoni AL, Gozal D. Cardiovascular morbidities of obstructive sleep apnea and the role of circulating extracellular vesicles. Ther Adv Respir Dis 2020; 13:1753466619895229. [PMID: 31852426 PMCID: PMC6923690 DOI: 10.1177/1753466619895229] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Obstructive sleep apnea (OSA) is characterized by recurrent upper airway collapse
during sleep resulting in impaired blood gas exchange, namely intermittent
hypoxia (IH) and hypercapnia, fragmented sleep (SF), increased oxidative stress
and systemic inflammation. Among a myriad of potential associated morbidities,
OSA has been particularly implicated as mechanistically contributing to the
prevalence and severity of cardiovascular diseases (CVD). However, the benefits
of continuous positive airway pressure (CPAP), which is generally employed in
OSA treatment, to either prevent or improve CVD outcomes remain unconvincing,
suggesting that the pathophysiological mechanisms underlying the incremental CVD
risk associated with OSA are not clearly understood. One of the challenges in
development of non-invasive diagnostic assays is the ability to identify
clinically and mechanistically relevant biomarkers. Circulating extracellular
vesicles (EVs) and their cargos reflect underlying changes in cellular
homeostasis and can provide insights into how cells and systems cope with
physiological perturbations by virtue of the identity and abundance of miRNAs,
mRNAs, proteins, and lipids that are packaged in the EVs under normal as well as
diseased states, such as OSA. EVs can not only provide unique insights into
coordinated cellular responses at the organ or systemic level, but can also
serve as reporters of the effects of OSA in CVD, either by their properties
enabling regeneration and repair of injured vascular cells or by damaging them.
Here, we highlight recent progress in the pathological CVD consequences of OSA,
and explore the putative roles of EVs in OSA-associated CVD, along with emerging
diagnostic and therapeutic opportunities. The reviews of this paper are available via the supplemental material
section.
Collapse
Affiliation(s)
- Abdelnaby Khalyfa
- Department of Child Health and the Child Health Research Institute, University of Missouri School of Medicine, Columbia, MO, USA
| | - Anabel L Castro-Grattoni
- Department of Child Health and the Child Health Research Institute, University of Missouri School of Medicine, Columbia, MO, USA
| | - David Gozal
- Department of Child Health and MU Women's and Children's Hospital, University of Missouri School of Medicine, 400 N. Keene Street, Suite 010, Columbia, MO 65201, USA
| |
Collapse
|
41
|
Lu Y, Liu D, Feng Q, Liu Z. Diabetic Nephropathy: Perspective on Extracellular Vesicles. Front Immunol 2020; 11:943. [PMID: 32582146 PMCID: PMC7283536 DOI: 10.3389/fimmu.2020.00943] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Diabetic nephropathy (DN) is a major microvascular complication of diabetes mellitus. It is the most frequent cause of end-stage renal disease with no definitive therapy available so far. Extracellular vesicles (EVs), including exosomes, microvesicles, and apoptotic bodies, are nano- and micron-sized heterogeneous vesicles that can be secreted by almost all cell types. Importantly, EVs contain many biologically active materials, such as RNAs, DNAs, proteins, and lipids, from their parental cells, which can be transported to their recipient cells to mediate intercellular communication and signaling. Accumulating studies demonstrated that EVs, mainly exosomes and microvesicles, participated in the pathophysiological process of DN. Recently emerging studies also found that the contents of EVs in the urine (miRNAs, mRNAs, and proteins) could be used as potential biomarkers for DN. Therefore, in this mini-review, the generation, isolation methods, and biological function of EVs were introduced, and then the current information about the mechanism and the diagnostic value in the development of DN was summarized. Moreover, the review also discussed the future challenges of exploring the role of EVs in kidney disease.
Collapse
Affiliation(s)
- Yanfang Lu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Dongwei Liu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Qi Feng
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| | - Zhangsuo Liu
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, China.,Core Unit of National Clinical Medical Research Center of Kidney Disease, Zhengzhou, China
| |
Collapse
|
42
|
Abstract
Extracellular vesicles (EVs) play an important role in cell-to-cell communication by carrying molecular messages that reflect physiological and pathological conditions of the parent cells. EVs have been identified in all body fluids; and among them, urine stands out as a sample that is easy and inexpensive to obtain and can be collected over time to monitor changes. Various protocols have been established to study urinary extracellular vesicles (UEVs) and they have shown great potential as a biomarker source for clinical applications, not only for urological, but also non-urological diseases. Due to the high variability and low reproducibility of pre-analytical and analytical methods for UEVs, establishing a standardized protocol remains a challenge in the field of diagnosis. Here, we review UEV studies and present the techniques that are most commonly used, those that have been applied as new developments, and those that have the most potential for future applications. The workflow procedures from the sampling step to the qualitative and quantitative analysis steps are summarized along with advantages and disadvantages of the methodologies, in order to give consideration for choosing the most promising and suitable method to analyze human UEVs.
Collapse
Affiliation(s)
- Piyawan Paisrisarn
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
| | - Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University.,Japan Science and Technology Agency (JST), PRESTO.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University.,Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology
| |
Collapse
|