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Chou CY, Chiang PC, Li CC, Chang JW, Lu PH, Hsu WF, Chang LC, Hsu JL, Wu MS, Wo AM. Improving the Purity of Extracellular Vesicles by Removal of Lipoproteins from Size Exclusion Chromatography- and Ultracentrifugation-Processed Samples Using Glycosaminoglycan-Functionalized Magnetic Beads. ACS APPLIED MATERIALS & INTERFACES 2024; 16:44386-44398. [PMID: 39149774 DOI: 10.1021/acsami.4c03869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Extracellular vesicles (EVs) are present in blood at much lower concentrations (5-6 orders of magnitude) compared to lipoprotein particles (LP). Because LP and EV overlap in size and density, isolating high-purity EVs is a significant challenge. While the current two-step sequential EV isolation process using size-expression chromatography (SEC) followed by a density gradient (DG) achieves high purity, the time-consuming ultracentrifugation (UC) step in DG hinders workflow efficiency. This paper introduces an optimized magnetic bead reagent, LipoMin, functionalized with glycosaminoglycans (GAGs), as a rapid alternative for LP removal during the second-step process in about 10 minutes. We evaluated LipoMin's efficacy on two sample types: (a) EV fractions isolated by size exclusion chromatography (SEC + LipoMin) and (b) the pellet obtained from ultracentrifugation (UC + LipoMin). The workflow is remarkably simple, involving a 10 min incubation with LipoMin followed by magnetic separation of the LP-depleted EV-containing supernatant. Results from enzyme-linked immunosorbent assay (ELISA) revealed that LipoMin removes 98.2% ApoB from SEC EV fractions, comparable to the LP removal ability of DG in the SEC + DG two-step process. Importantly, the EV yield (CD81 ELISA) remained at 93.0% and Western blot analysis confirmed that key EV markers, flotillin and CD81, were not compromised. Recombinant EV (rEV), an EV reference standard, was spiked into SEC EV fractions and recovered 89% of CD81 protein. For UC + LipoMin, ApoA1 decreased by 76.5% while retaining 90.7% of CD81. Notably, both colorectal cancer (CRC) and Alzheimer's disease (AD) samples processed by SEC + LipoMin and UC + LipoMin displayed clear expression of relevant EV and clinical markers. With a 10 min workflow (resulting in a 96% time saving compared to the traditional method), the LipoMin reagent offers a rapid and efficient alternative to DG for LP depletion, paving the way for a streamlined SEC + LipoMin two-step EV isolation process.
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Affiliation(s)
- Cheng-Yu Chou
- Institute of Applied Mechanics, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106319, Taiwan
| | | | - Chih-Chi Li
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106319, Taiwan
| | - Jheng-Wun Chang
- Institute of Applied Mechanics, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106319, Taiwan
| | - Po-Han Lu
- Institute of Applied Mechanics, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106319, Taiwan
| | - Wei-Fan Hsu
- Institute of Applied Mechanics, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106319, Taiwan
- Reliance Biosciences, Inc., New Taipei City 231023, Taiwan
| | - Li-Chun Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100225, Taiwan
- Health Management Center, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Jung-Lung Hsu
- Department of Neurology, New Taipei Municipal TuCheng Hospital, New Taipei City 236017, Taiwan
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Neuroscience Research Center, Chang-Gung University, Linkou, Taoyuan 33302, Taiwan
- Graduate Institute of Mind, Brain, & Consciousness, Taipei Medical University, Taipei 110301, Taiwan
| | - Ming-Shiang Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Andrew M Wo
- Institute of Applied Mechanics, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106319, Taiwan
- Reliance Biosciences, Inc., New Taipei City 231023, Taiwan
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2
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Saari H, Marttila H, Poranen MM, Oksanen HM, Zini J, Laitinen S. Inline Raman Spectroscopy Provides Versatile Molecular Monitoring for Platelet Extracellular Vesicle Purification with Anion-Exchange Chromatography. Int J Mol Sci 2024; 25:8130. [PMID: 39125704 PMCID: PMC11311901 DOI: 10.3390/ijms25158130] [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: 06/07/2024] [Revised: 07/18/2024] [Accepted: 07/20/2024] [Indexed: 08/12/2024] Open
Abstract
Extracellular vesicles (EVs) are relatively recently discovered biological nanoparticles that mediate intercellular communication. The development of new methods for the isolation and characterization of EVs is crucial to support further studies on these small and structurally heterogenous vesicles. New scalable production methods are also needed to meet the needs of future therapeutic applications. A reliable inline detection method for the EV manufacturing process is needed to ensure reproducibility and to identify any possible variations in real time. Here, we demonstrate the use of an inline Raman detector in conjunction with anion exchange chromatography for the isolation of EVs from human platelets. Anion-exchange chromatography can be easily coupled with multiple inline detectors and provides an alternative to size-based methods for separating EVs from similar-sized impurities, such as lipoprotein particles. Raman spectroscopy enabled us to identify functional groups in EV samples and trace EVs and impurities in different stages of the process. Our results show a notable separation of impurities from the EVs during anion-exchange chromatography and demonstrate the power of inline Raman spectroscopy. Compared to conventional EV analysis methods, the inline Raman approach does not require hands-on work and can provide detailed, real-time information about the sample and the purification process.
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Affiliation(s)
- Heikki Saari
- Finnish Red Cross, Blood Service, Härkälenkki 13, 01730 Vantaa, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00790 Helsinki, Finland
| | - Heli Marttila
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
| | - Jacopo Zini
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00790 Helsinki, Finland
- Timegate Instruments Ltd., Tutkijantie 7, 90590 Oulu, Finland
| | - Saara Laitinen
- Finnish Red Cross, Blood Service, Härkälenkki 13, 01730 Vantaa, Finland
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3
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Martínez-Díaz P, Parra A, Sanchez-López CM, Casas J, Lucas X, Marcilla A, Roca J, Barranco I. Small and Large Extracellular Vesicles of Porcine Seminal Plasma Differ in Lipid Profile. Int J Mol Sci 2024; 25:7492. [PMID: 39000599 PMCID: PMC11242203 DOI: 10.3390/ijms25137492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Seminal plasma contains a heterogeneous population of extracellular vesicles (sEVs) that remains poorly characterized. This study aimed to characterize the lipidomic profile of two subsets of differently sized sEVs, small (S-) and large (L-), isolated from porcine seminal plasma by size-exclusion chromatography and characterized by an orthogonal approach. High-performance liquid chromatography-high-resolution mass spectrometry was used for lipidomic analysis. A total of 157 lipid species from 14 lipid classes of 4 major categories (sphingolipids, glycerophospholipids, glycerolipids, and sterols) were identified. Qualitative differences were limited to two cholesteryl ester species present only in S-sEVs. L-sEVs had higher levels of all quantified lipid classes due to their larger membrane surface area. The distribution pattern was different, especially for sphingomyelins (more in S-sEVs) and ceramides (more in L-sEVs). In conclusion, this study reveals differences in the lipidomic profile of two subsets of porcine sEVs, suggesting that they differ in biogenesis and functionality.
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Affiliation(s)
- Pablo Martínez-Díaz
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Ana Parra
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Christian M Sanchez-López
- Àrea de Parasitologia, Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Universitat de València, 46100 Valencia, Spain
- Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Health Research Institute La Fe, Universitat de València, 46100 Valencia, Spain
| | - Josefina Casas
- Research Unit on BioActive Molecules (RUBAM), Institute for Advanced Chemistry (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Xiomara Lucas
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Antonio Marcilla
- Àrea de Parasitologia, Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Universitat de València, 46100 Valencia, Spain
- Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Health Research Institute La Fe, Universitat de València, 46100 Valencia, Spain
| | - Jordi Roca
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
| | - Isabel Barranco
- Department of Medicine and Animal Surgery, Faculty of Veterinary Science, University of Murcia, 30100 Murcia, Spain
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Lim W, Lee S, Koh M, Jo A, Park J. Recent advances in chemical biology tools for protein and RNA profiling of extracellular vesicles. RSC Chem Biol 2024; 5:483-499. [PMID: 38846074 PMCID: PMC11151817 DOI: 10.1039/d3cb00200d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/25/2024] [Indexed: 06/09/2024] Open
Abstract
Extracellular vesicles (EVs) are nano-sized vesicles secreted by cells that contain various cellular components such as proteins, nucleic acids, and lipids from the parent cell. EVs are abundant in body fluids and can serve as circulating biomarkers for a variety of diseases or as a regulator of various biological processes. Considering these characteristics of EVs, analysis of the EV cargo has been spotlighted for disease diagnosis or to understand biological processes in biomedical research. Over the past decade, technologies for rapid and sensitive analysis of EVs in biofluids have evolved, but detection and isolation of targeted EVs in complex body fluids is still challenging due to the unique physical and biological properties of EVs. Recent advances in chemical biology provide new opportunities for efficient profiling of the molecular contents of EVs. A myriad of chemical biology tools have been harnessed to enhance the analytical performance of conventional assays for better understanding of EV biology. In this review, we will discuss the improvements that have been achieved using chemical biology tools.
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Affiliation(s)
- Woojeong Lim
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
| | - Soyeon Lee
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
| | - Minseob Koh
- Department of Chemistry, Pusan National University Busan 46241 Republic of Korea
| | - Ala Jo
- Center for Nanomedicine, Institute for Basic Science Seoul 03722 Republic of Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
- Institute for Molecular Science and Fusion Technology, Kangwon National University Chuncheon 24341 Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University Chuncheon 24341 Republic of Korea
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Merij LB, da Silva LR, Palhinha L, Gomes MT, Dib PRB, Martins-Gonçalves R, Toledo-Quiroga K, Raposo-Nunes MA, Andrade FB, de Toledo Martins S, Nascimento ALR, Rocha VN, Alves LR, Bozza PT, de Oliveira Trugilho MR, Hottz ED. Density-based lipoprotein depletion improves extracellular vesicle isolation and functional analysis. J Thromb Haemost 2024; 22:1372-1388. [PMID: 38278418 DOI: 10.1016/j.jtha.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/07/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024]
Abstract
BACKGROUND Blood plasma is the main source of extracellular vesicles (EVs) in clinical studies aiming to identify biomarkers and to investigate pathophysiological processes, especially regarding EV roles in inflammation and thrombosis. However, EV isolation from plasma has faced the fundamental issue of lipoprotein contamination, representing an important bias since lipoproteins are highly abundant and modulate cell signaling, metabolism, and thromboinflammation. OBJECTIVES Here, we aimed to isolate plasma EVs after depleting lipoproteins, thereby improving sample purity and EV thromboinflammatory analysis. METHODS Density-based gradient ultracentrifugation (G-UC) was used for lipoprotein depletion before EV isolation from plasma through size-exclusion chromatography (SEC) or serial centrifugation (SC). Recovered EVs were analyzed by size, concentration, cellular source, ultrastructure, and bottom-up proteomics. RESULTS G-UC efficiently separated lipoproteins from the plasma, allowing subsequent EV isolation through SEC or SC. Combined analysis from EV proteomics, cholesterol quantification, and apoB-100 detection confirmed the significant reduction in lipoproteins from isolated EVs. Proteomic analysis identified similar gene ontology and cellular components in EVs, regardless of lipoprotein depletion, which was consistent with similar EV cellular sources, size, and ultrastructure by flow cytometry and transmission electron microscopy. Importantly, lipoprotein depletion increased the detection of less abundant proteins in EV proteome and enhanced thromboinflammatory responses of platelets and monocytes stimulated in vitro with EV isolates. CONCLUSION Combination of G-UC+SEC significantly reduced EV lipoprotein contamination without interfering in EV cellular source, gene ontology, and ultrastructure, allowing the recovery of highly pure EVs with potential implications for functional assays and proteomic and lipidomic analyses.
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Affiliation(s)
- Laura Botelho Merij
- Laboratory of Immunothrombosis, Department of Biochemistry, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Luana Rocha da Silva
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lohanna Palhinha
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Milena Tavares Gomes
- Laboratory of Immunothrombosis, Department of Biochemistry, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Paula Ribeiro Braga Dib
- Laboratory of Immunothrombosis, Department of Biochemistry, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Remy Martins-Gonçalves
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kemily Toledo-Quiroga
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Fernanda Brandi Andrade
- Laboratory of Immunothrombosis, Department of Biochemistry, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Sharon de Toledo Martins
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, ICC-Fiocruz, Curitiba, Paraná, Brazil
| | - Ana Lúcia Rosa Nascimento
- Laboratory of Ultrastructure and Tissue, Department of Histology and Embryology, State University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vinicius Novaes Rocha
- Laboratory of Veterinary Pathology and Histology, Department of Veterinary Medicine, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Lysangela Ronalte Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, ICC-Fiocruz, Curitiba, Paraná, Brazil
| | - Patrícia T Bozza
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, ICC-Fiocruz, Curitiba, Paraná, Brazil
| | - Monique Ramos de Oliveira Trugilho
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil; Center for Technological Development in Health, Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Eugenio D Hottz
- Laboratory of Immunothrombosis, Department of Biochemistry, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil.
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6
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Li Y, Zhang S, Liu C, Deng J, Tian F, Feng Q, Qin L, Bai L, Fu T, Zhang L, Wang Y, Sun J. Thermophoretic glycan profiling of extracellular vesicles for triple-negative breast cancer management. Nat Commun 2024; 15:2292. [PMID: 38480740 PMCID: PMC10937950 DOI: 10.1038/s41467-024-46557-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly metastatic and heterogeneous type of breast cancer with poor outcomes. Precise, non-invasive methods for diagnosis, monitoring and prognosis of TNBC are particularly challenging due to a paucity of TNBC biomarkers. Glycans on extracellular vesicles (EVs) hold the promise as valuable biomarkers, but conventional methods for glycan analysis are not feasible in clinical practice. Here, we report that a lectin-based thermophoretic assay (EVLET) streamlines vibrating membrane filtration (VMF) and thermophoretic amplification, allowing for rapid, sensitive, selective and cost-effective EV glycan profiling in TNBC plasma. A pilot cohort study shows that the EV glycan signature reaches 91% accuracy for TNBC detection and 96% accuracy for longitudinal monitoring of TNBC therapeutic response. Moreover, we demonstrate the potential of EV glycan signature for predicting TNBC progression. Our EVLET system lays the foundation for non-invasive cancer management by EV glycans.
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Affiliation(s)
- Yike Li
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Shaohua Zhang
- Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, 100071, China
| | - Chao Liu
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jinqi Deng
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Tian
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Feng
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Lili Qin
- Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, 100071, China
| | - Lixiao Bai
- Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, 100071, China
| | - Ting Fu
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou, Zhejiang, 310022, China
- Jiangsu Union Institute of Translational Medicine, Zhongdi Biotechnology Co., Ltd, Nanjing, Jiangsu, 211500, China
| | - Liqin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
| | - Yuguang Wang
- Department of General Dentistry II, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, 100081, China.
| | - Jiashu Sun
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Kawano K, Kuzuma Y, Yoshio K, Hosokawa K, Oosugi Y, Fujiwara T, Yokoyama F, Matsuzaki K. Extracellular-Vesicle Catch-and-Release Isolation System Using a Net-Charge Invertible Curvature-Sensing Peptide. Anal Chem 2024; 96:3754-3762. [PMID: 38402519 DOI: 10.1021/acs.analchem.3c03756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Extracellular vesicles (EVs) carry various informative components, including signaling proteins, transcriptional regulators, lipids, and nucleic acids. These components are utilized for cell-cell communication between donor and recipient cells. EVs have shown great promise as pharmaceutical-targeting vesicles and have attracted the attention of researchers in the fields of biological and medical science because of their importance as diagnostic and prognostic markers. However, the isolation and purification of EVs from cell-cultured media remain challenging. Ultracentrifugation is the most widely used method, but it requires specialized and expensive equipment. In the present study, we proposed a novel methodology to isolate EVs using a simple and convenient method, i.e., an EV catch-and-release isolation system (EV-CaRiS) using a net-charge invertible curvature-sensing peptide (NIC). Curvature-sensing peptides recognize vesicles by binding to lipid-packing defects on highly curved membranes regardless of the expression levels of biomarkers. NIC was newly designed to reversibly capture and release EVs in a pH-dependent manner. NIC allowed us to achieve reproducible EV isolation from three human cell lines on resin using a batch method and single-particle imaging of EVs containing the ubiquitous exosome markers CD63 and CD81 by total internal reflection fluorescence microscopy (TIRFM). EV-CaRiS was demonstrated as a simple and convenient methodology for EV isolation, and NIC is promising for applications in the single-particle analysis of EVs.
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Affiliation(s)
- Kenichi Kawano
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Kuzuma
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Koichi Yoshio
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenta Hosokawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuuto Oosugi
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fumiaki Yokoyama
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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8
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Leong SY, Lok WW, Goh KY, Ong HB, Tay HM, Su C, Kong F, Upadya M, Wang W, Radnaa E, Menon R, Dao M, Dalan R, Suresh S, Lim DWT, Hou HW. High-Throughput Microfluidic Extraction of Platelet-free Plasma for MicroRNA and Extracellular Vesicle Analysis. ACS NANO 2024; 18:6623-6637. [PMID: 38348825 DOI: 10.1021/acsnano.3c12862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Cell-free RNAs and extracellular vesicles (EVs) are valuable biomarkers in liquid biopsies, but they are prone to preanalytical variabilities such as nonstandardized centrifugation or ex vivo blood degradation. Herein, we report a high-throughput and label-free inertial microfluidic device (ExoArc) for isolation of platelet-free plasma from blood for RNA and EV analysis. Unlike conventional inertial microfluidic devices widely used for cell sorting, a submicrometer size cutoff (500 nm) was achieved which completely removed all leukocytes, RBCs, platelets, and cellular debris based on differential lateral migration induced by Dean vortices. The single-step operation also reduced platelet-associated miRNAs (∼2-fold) compared to centrifugation. We clinically validated ExoArc for plasma miRNA profiling (39 samples) and identified a 7-miRNA panel that detects non-small cell lung cancer with ∼90% sensitivity. ExoArc was also coupled with size exclusion chromatography (SEC) to isolate EVs within 50 min with ∼10-fold higher yield than ultracentrifugation. As a proof-of-concept for EV-based transcriptomics analysis, we performed miRNA analysis in healthy and type 2 diabetes mellitus (T2DM) subjects (n = 3 per group) by coupling ExoArc and ExoArc+SEC with quantitative polymerase chain reaction (RT-qPCR) assay. Among 293 miRNAs detected, plasmas and EVs showed distinct differentially expressed miRNAs in T2DM subjects. We further demonstrated automated in-line EV sorting from low volume culture media for continuous EV monitoring. Overall, the developed ExoArc offers a convenient centrifugation-free workflow to automate plasma and EV isolation for point-of-care diagnostics and quality control in EV manufacturing.
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Affiliation(s)
- Sheng Yuan Leong
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Wan Wei Lok
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Kah Yee Goh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583
| | - Hong Boon Ong
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Hui Min Tay
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Chengxun Su
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
| | - Fang Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Megha Upadya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Wei Wang
- Singapore Institute of Manufacturing Technology (SIMTech), Agency for Science, Technology and Research (A*STAR), Singapore 138634
| | - Enkhtuya Radnaa
- Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1062, United States
| | - Ramkumar Menon
- Department of Obstetrics and Gynecology, The University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1062, United States
| | - Ming Dao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
- Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rinkoo Dalan
- Endocrine and Diabetes, Tan Tock Seng Hospital, Singapore 308433
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232
| | - Subra Suresh
- Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- School of Material Science and Engineering, Nanyang Technological University, Singapore 639798
| | - Darren Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673
- Duke-NUS Medical School, Singapore 169857
| | - Han Wei Hou
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232
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9
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Hsia T, You DG, Politis MG, Batool SM, Ekanayake E, Lee H, Carter BS, Balaj L. Rigorous Comparison of Extracellular Vesicle Processing to Enhance Downstream Analysis for Glioblastoma Characterization. Adv Biol (Weinh) 2024; 8:e2300233. [PMID: 37670402 DOI: 10.1002/adbi.202300233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/28/2023] [Indexed: 09/07/2023]
Abstract
Extracellular vesicles (EVs) are highly sought after as a source of biomarkers for disease detection and monitoring. Tumor EV isolation, processing, and evaluation from biofluids is convoluted by EV heterogeneity and biological contaminants and is limited by technical processing efficacy. This study rigorously compares common bulk EV isolation workflows (size exclusion chromatography, SEC; membrane affinity, MA) alongside downstream RNA extraction protocols to investigate molecular analyte recovery. EV integrity and recovery is evaluated using a variety of technologies to quantify total intact EVs, total and surface proteins, and RNA purity and recovery. A comprehensive evaluation of each analyte is performed, with a specific emphasis on maintaining user (n = 2), biological (n = 3), and technical replicates (n≥3) under in vitro conditions. Subsequent study of tumor EV spike-in into healthy donor plasma samples is performed to further validate biofluid-derived EV purity and isolation for clinical application. Results show that EV surface integrity is considerably preserved in eluates from SEC-derived EVs, but RNA recovery and purity, as well as bulk protein isolation, is significantly improved in MA-isolated EVs. This study concludes that EV isolation and RNA extraction pipelines govern recovered analyte integrity, necessitating careful selection of processing modality to enhance recovery of the analyte of interest.
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Affiliation(s)
- Tiffaney Hsia
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Dong Gil You
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Michelle Garlin Politis
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Syeda Maheen Batool
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Emil Ekanayake
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
- Department of Neurosurgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
- Department of Neurosurgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
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10
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Yang R, Lou D, Xia K, Sun L, Zhu Q. A pH-Mediated Highly Selective System Enabling Simultaneous Analysis of Circulating RNAs Carried by Extracellular Vesicles and Lipoproteins. Anal Chem 2023; 95:18803-18813. [PMID: 38078945 DOI: 10.1021/acs.analchem.3c03924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Extracellular vesicles (EVs) and lipoproteins (LPPs) serve as important carriers of circulating miRNAs in peripheral blood, offering immense potential for disease diagnosis and therapeutic interventions. Due to their shared physicochemical attributes, EVs and LPPs are frequently coisolated, potentially leading to misunderstandings regarding their distinct functional roles in physiological and pathological processes. Here, we report a highly selective magnetic system based on the pH-mediated affinity displayed by cibacron blue (CB) toward EVs and LPPs, enabling successful separation and collection of these two nanoparticles without cross-contamination for subsequent circulating RNA analysis. First, we found that CB-modified magnetic beads (CBMBs) exhibit a strong affinity toward LPP particles while displaying little interaction with EVs in standard samples under physiological pH conditions. We further demonstrate that the affinity between CB molecules and bionanoparticles in plasma samples is highly pH-dependent. Specifically, CBMBs show affinities for both LPP and EV particles under neutral and acidic conditions. However, at basic pH levels, CB molecules selectively bind only to LPP particles. Consequently, the remaining EV particles present in plasma are subsequently isolated by using titanium dioxide-modified beads (TiMBs) through phospholipid affinity. The simultaneous analysis of the transcriptomic contents of EV and LPP reveals clear differences in their small RNA profiles, with the differentially expressed RNAs reflecting distinct biological processes. Significantly, in a proof-of-concept study, we successfully demonstrated a strong correlation between miRNAs carried by both EV and LPP particles with the occurrence of ocular neovascularization during the progression of diabetic retinopathy. The involved miRNAs may serve as potential biomarkers for DR diagnostics and severity classification. To sum up, this pH-mediated separation system is not only user-friendly but also highly compatible, rendering it a potent tool for probing the molecular compositions, biomarkers, and underlying biological mechanisms of EVs and LPPs.
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Affiliation(s)
- Rui Yang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Doudou Lou
- Jiangsu Institute for Food and Drug Control, Nanjing 210019, China
| | - Kangfu Xia
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230051, China
- Department of Clinical Laboratory, Lu'an People's Hospital of Anhui Province, Lu'an Hospital of Anhui Medical University, Lu'an 237005, China
| | - Lei Sun
- Department of Clinical Laboratory, Lu'an People's Hospital of Anhui Province, Lu'an Hospital of Anhui Medical University, Lu'an 237005, China
| | - Qingfu Zhu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
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11
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Kwak TJ, Son T, Hong JS, Winter UA, Jeong MH, McLean C, Weissleder R, Lee H, Castro CM, Im H. Electrokinetically enhanced label-free plasmonic sensing for rapid detection of tumor-derived extracellular vesicles. Biosens Bioelectron 2023; 237:115422. [PMID: 37301179 PMCID: PMC10527155 DOI: 10.1016/j.bios.2023.115422] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/02/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023]
Abstract
ANALYSIS of rare circulating extracellular vesicles (EV) from early cancers or different types of host cells requires extremely sensitive EV sensing technologies. Nanoplasmonic EV sensing technologies have demonstrated good analytical performances, but their sensitivity is often limited by EVs' diffusion to the active sensor surface for specific target EV capture. Here, we developed an advanced plasmonic EV platform with electrokinetically enhanced yields (KeyPLEX). The KeyPLEX system effectively overcomes diffusion-limited reactions with applied electroosmosis and dielectrophoresis forces. These forces bring EVs toward the sensor surface and concentrate them in specific areas. Using the keyPLEX, we showed significant improvements in detection sensitivity by ∼100-fold, leading to the sensitive detection of rare cancer EVs from human plasma samples in 10 min. The keyPLEX system could become a valuable tool for point-of-care rapid EV analysis.
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Affiliation(s)
- Tae Joon Kwak
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Taehwang Son
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Ursula Andrea Winter
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Mi Ho Jeong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Charlotte McLean
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Health Science, Northeastern University Boston, MA, 02115, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA, 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Cesar M Castro
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA, 02114, USA.
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12
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Saari H, Pusa R, Marttila H, Yliperttula M, Laitinen S. Development of tandem cation exchange chromatography for high purity extracellular vesicle isolation: The effect of ligand steric availability. J Chromatogr A 2023; 1707:464293. [PMID: 37579702 DOI: 10.1016/j.chroma.2023.464293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023]
Abstract
Purification of extracellular vesicles for research and therapeutic applications requires updated methodology to address the limitations of traditional ultracentrifugation and other size-based separation techniques. Their downfalls include induced extracellular vesicle aggregation, low yields, poor scalability and one-dimensionality of the separation process, as the size or sedimentation speed of extracellular vesicles is often the only selection criterion. Ion exchange chromatography is a promising alternative or supplementary method candidate, as it offers a different approach for extracellular vesicle separation, which is surface charge. For now, mostly anion exchange chromatography has been evaluated for extracellular vesicle purification, as it successfully relies on the strongly negative surface charge of extracellular vesicles. However, as extracellular vesicles are very complex in their structure, also cation exchange chromatography could be applicable, due to individual cationic domains on the extracellular vesicle surface. Here, we compare anion exchange chromatography to different types of cation exchange chromatography for the purification of platelet extracellular vesicle samples also containing plasma-derived impurities. We found that the choice of resin structure used for cation exchange chromatography is critical for binding platelet extracellular vesicles, as a conventional-type cation exchanger was found to only capture and elute less than 20% of extracellular vesicles. With the tentacle-type resin, it was possible to obtain comparable platelet extracellular vesicle yields (over 90%) with cation exchange chromatography compared to anion exchange chromatography, as well as superior purity, especially when it was combined to conventional cation exchange resin.
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Affiliation(s)
- Heikki Saari
- Finnish Red Cross Blood Service. Härkälenkki 13, 01730 Vantaa, Finland.
| | - Reetta Pusa
- Finnish Red Cross Blood Service. Härkälenkki 13, 01730 Vantaa, Finland
| | - Heli Marttila
- Molecular and Integrative Biosciences Research Programme, Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
| | - Marjo Yliperttula
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00790 Helsinki, Finland
| | - Saara Laitinen
- Finnish Red Cross Blood Service. Härkälenkki 13, 01730 Vantaa, Finland
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13
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van de Wakker SI, Meijers FM, Sluijter JPG, Vader P. Extracellular Vesicle Heterogeneity and Its Impact for Regenerative Medicine Applications. Pharmacol Rev 2023; 75:1043-1061. [PMID: 37280097 DOI: 10.1124/pharmrev.123.000841] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/20/2023] [Accepted: 05/01/2023] [Indexed: 06/08/2023] Open
Abstract
Extracellular vesicles (EVs) are cell-derived membrane-enclosed particles that are involved in physiologic and pathologic processes. EVs are increasingly being studied for therapeutic applications in the field of regenerative medicine. Therapeutic application of stem cell-derived EVs has shown great potential to stimulate tissue repair. However, the exact mechanisms through which they induce this effect have not been fully clarified. This may to a large extent be attributed to a lack of knowledge on EV heterogeneity. Recent studies suggest that EVs represent a heterogeneous population of vesicles with distinct functions. The heterogeneity of EVs can be attributed to differences in their biogenesis, and as such, they can be classified into distinct populations that can then be further subcategorized into various subpopulations. A better understanding of EV heterogeneity is crucial for elucidating their mechanisms of action in tissue regeneration. This review provides an overview of the latest insights on EV heterogeneity related to tissue repair, including the different characteristics that contribute to such heterogeneity and the functional differences among EV subtypes. It also sheds light on the challenges that hinder clinical translation of EVs. Additionally, innovative EV isolation techniques for studying EV heterogeneity are discussed. Improved knowledge of active EV subtypes would promote the development of tailored EV therapies and aid researchers in the translation of EV-based therapeutics to the clinic. SIGNIFICANCE STATEMENT: Within this review we discuss the differences in regenerative properties of extracellular vesicle (EV) subpopulations and implications of EV heterogeneity for development of EV-based therapeutics. We aim to provide new insights into which aspects are leading to heterogeneity in EV preparations and stress the importance of EV heterogeneity studies for clinical applications.
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Affiliation(s)
- Simonides Immanuel van de Wakker
- Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (S.I.V.D.W., F.M.M., J.P.G.S., P.V.) and CDL Research, University Medical Center Utrecht, The Netherlands (P.V.)
| | - Fleur Michelle Meijers
- Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (S.I.V.D.W., F.M.M., J.P.G.S., P.V.) and CDL Research, University Medical Center Utrecht, The Netherlands (P.V.)
| | - Joost Petrus Gerardus Sluijter
- Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (S.I.V.D.W., F.M.M., J.P.G.S., P.V.) and CDL Research, University Medical Center Utrecht, The Netherlands (P.V.)
| | - Pieter Vader
- Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, The Netherlands (S.I.V.D.W., F.M.M., J.P.G.S., P.V.) and CDL Research, University Medical Center Utrecht, The Netherlands (P.V.)
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14
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Hong J, Son T, Castro CM, Im H. CRISPR/Cas13a-Based MicroRNA Detection in Tumor-Derived Extracellular Vesicles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301766. [PMID: 37340600 PMCID: PMC10460892 DOI: 10.1002/advs.202301766] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/23/2023] [Indexed: 06/22/2023]
Abstract
MicroRNAs (miRNAs) in extracellular vesicles (EVs) play essential roles in cancer initiation and progression. Quantitative measurements of EV miRNAs are critical for cancer diagnosis and longitudinal monitoring. Traditional PCR-based methods, however, require multi-step procedures and remain as bulk analysis. Here, the authors introduce an amplification-free and extraction-free EV miRNA detection method using a CRISPR/Cas13a sensing system. CRISPR/Cas13a sensing components are encapsulated in liposomes and delivered them into EVs through liposome-EV fusion. This allows for accurately quantify specific miRNA-positive EV counts using 1 × 108 EVs. The authors show that miR-21-5p-positive EV counts are in the range of 2%-10% in ovarian cancer EVs, which is significantly higher than the positive EV counts from the benign cells (<0.65%). The result show an excellent correlation between bulk analysis with the gold-standard method, RT-qPCR. The authors also demonstrate multiplexed protein-miRNA analysis in tumor-derived EVs by capturing EpCAM-positive EVs and quantifying miR-21-5p-positive ones in the subpopulation, which show significantly higher counts in the plasma of cancer patients than healthy controls. The developed EV miRNA sensing system provides the specific miRNA detection method in intact EVs without RNA extraction and opens up the possibility of multiplexed single EV analysis for protein and RNA markers.
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Affiliation(s)
- Jae‐Sang Hong
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
| | - Taehwang Son
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
| | - Cesar M. Castro
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
- Cancer CenterMassachusetts General HospitalBostonMA02114USA
| | - Hyungsoon Im
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
- Department of RadiologyMassachusetts General HospitalBostonMA02114USA
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15
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Kashkanova AD, Blessing M, Reischke M, Baur J, Baur AS, Sandoghdar V, Van Deun J. Label-free discrimination of extracellular vesicles from large lipoproteins. J Extracell Vesicles 2023; 12:e12348. [PMID: 37489102 PMCID: PMC10366660 DOI: 10.1002/jev2.12348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/05/2023] [Accepted: 05/26/2023] [Indexed: 07/26/2023] Open
Abstract
Extracellular vesicles (EVs) are increasingly gaining interest as biomarkers and therapeutics. Accurate sizing and quantification of EVs remain problematic, given their nanometre size range and small scattering cross-sections. This is compounded by the fact that common EV isolation methods result in co-isolation of particles with comparable features. Especially in blood plasma, similarly-sized lipoproteins outnumber EVs to a great extent. Recently, interferometric nanoparticle tracking analysis (iNTA) was introduced as a particle analysis method that enables determining the size and refractive index of nanoparticles with high sensitivity and precision. In this work, we apply iNTA to differentiate between EVs and lipoproteins, and compare its performance to conventional nanoparticle tracking analysis (NTA). We show that iNTA can accurately quantify EVs in artificial EV-lipoprotein mixtures and in plasma-derived EV samples of varying complexity. Conventional NTA could not report on EV numbers, as it was not able to distinguish EVs from lipoproteins. iNTA has the potential to become a new standard for label-free EV characterization in suspension.
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Affiliation(s)
- Anna D. Kashkanova
- Max Planck Institute for the Science of LightErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
| | - Martin Blessing
- Max Planck Institute for the Science of LightErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
- Department of PhysicsFriedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
| | - Marie Reischke
- Max Planck Institute for the Science of LightErlangenGermany
| | - Jan‐Ole Baur
- Department of DermatologyUniversitätsklinikum Erlangen, Friedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
| | - Andreas S. Baur
- Department of DermatologyUniversitätsklinikum Erlangen, Friedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of LightErlangenGermany
- Max‐Planck‐Zentrum für Physik und MedizinErlangenGermany
- Department of PhysicsFriedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
| | - Jan Van Deun
- Department of DermatologyUniversitätsklinikum Erlangen, Friedrich‐Alexander‐Universität Erlangen‐NürnbergErlangenGermany
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16
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Benayas B, Morales J, Egea C, Armisén P, Yáñez‐Mó M. Optimization of extracellular vesicle isolation and their separation from lipoproteins by size exclusion chromatography. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e100. [PMID: 38939075 PMCID: PMC11080862 DOI: 10.1002/jex2.100] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 06/29/2024]
Abstract
Interest in the use of extracellular vesicles (EVs) as biomarkers of disease is rapidly growing. However, one main unsolved issue in the EV field is finding a technique able to eliminate non-EV contaminants present in biofluid samples in a one-step isolation protocol. Due to the expansion and value of size exclusion chromatography (SEC) as one of the best EV isolation methods, we have tested several agarose resins with different agarose percentages, bead sizes and crosslinking features to optimize EV isolation. For this optimization of SEC, we first employed conditioned media from a melanoma cell culture, a simpler sample in comparison to biological fluids, but which also contains abundant contaminants such as soluble protein and lipoproteins (LPPs). The distinct agaroses and the combinations of resins with different agarose percentages in the same column were tested. Soluble protein, EVs and LPPs levels from the different eluted fractions were quantitated by immunodetection or absorbance measurements. Samples were also analysed by NTA and TEM to verify the yield and the LPP contamination. Different percentages of agarose resins (2%, 4% and 6%) yielded samples with increasing LPP contamination respectively, which was not improved in the columns that combined them. Crosslinking of the agarose did not affect EV isolation yield nor the LPP contamination. In contrast, reducing the bead size greatly improved EV purity. We thus selected 4% Rapid Run Fine agarose beads as the resin that more efficiently isolated EVs with almost no contamination of other particles. Using blood plasma samples, this resin also demonstrated an improved capacity in the isolation of EVs from LPPs in comparison to the agaroses most commonly used in the field and differential ultracentrifugation.
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Affiliation(s)
- Beatriz Benayas
- Agarose Bead Technologies (ABT)Torrejón de ArdozMadridSpain
- Dept Biología MolecularUniversidad Autónoma de MadridIUBMCentro de Biología Molecular Severo Ochoa, IIS‐IPMadridSpain
| | - Joaquín Morales
- Dept Biología MolecularUniversidad Autónoma de MadridIUBMCentro de Biología Molecular Severo Ochoa, IIS‐IPMadridSpain
| | - Carolina Egea
- Agarose Bead Technologies (ABT)Torrejón de ArdozMadridSpain
| | - Pilar Armisén
- Agarose Bead Technologies (ABT)Torrejón de ArdozMadridSpain
| | - María Yáñez‐Mó
- Dept Biología MolecularUniversidad Autónoma de MadridIUBMCentro de Biología Molecular Severo Ochoa, IIS‐IPMadridSpain
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17
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Zhang Y, Dou Y, Liu Y, Di M, Bian H, Sun X, Yang Q. Advances in Therapeutic Applications of Extracellular Vesicles. Int J Nanomedicine 2023; 18:3285-3307. [PMID: 37346366 PMCID: PMC10281276 DOI: 10.2147/ijn.s409588] [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: 02/22/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023] Open
Abstract
Extracellular vesicles (EVs) are nanoscale bilayer phospholipid membrane vesicles released by cells. Contained large molecules such as nucleic acid, protein, and lipid, EVs are an integral part of cell communication. The contents of EVs vary based on the cell source and play an important role in both pathological and physiological conditions. EVs can be used as drugs or targets in disease treatment, and changes in the contents of EVs can indicate the progression of diseases. In recent years, with the continuous exploration of the structure, characteristics, and functions of EVs, the potential of engineered EVs for drug delivery and therapy being constantly explored. This review provides a brief overview of the structure, characteristics and functions of EVs, summarizes the advanced application of EVs and outlook on the prospect of it. It is our hope that this review will increase understanding of the current development of medical applications of EVs and help us overcome future challenges.
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Affiliation(s)
- Yiming Zhang
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin, People’s Republic of China
- Clinical School of Orthopedics, Tianjin Medical University, Tianjin, People’s Republic of China
| | - Yiming Dou
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin, People’s Republic of China
- Clinical School of Orthopedics, Tianjin Medical University, Tianjin, People’s Republic of China
| | - Yang Liu
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin, People’s Republic of China
- Clinical School of Orthopedics, Tianjin Medical University, Tianjin, People’s Republic of China
| | - Mingyuan Di
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin, People’s Republic of China
- Clinical School of Orthopedics, Tianjin Medical University, Tianjin, People’s Republic of China
| | - Hanming Bian
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin, People’s Republic of China
- Clinical School of Orthopedics, Tianjin Medical University, Tianjin, People’s Republic of China
| | - Xun Sun
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin, People’s Republic of China
- Clinical School of Orthopedics, Tianjin Medical University, Tianjin, People’s Republic of China
| | - Qiang Yang
- Department of Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin, People’s Republic of China
- Clinical School of Orthopedics, Tianjin Medical University, Tianjin, People’s Republic of China
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18
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Spitzberg JD, Ferguson S, Yang KS, Peterson HM, Carlson JCT, Weissleder R. Multiplexed analysis of EV reveals specific biomarker composition with diagnostic impact. Nat Commun 2023; 14:1239. [PMID: 36870999 PMCID: PMC9985597 DOI: 10.1038/s41467-023-36932-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Exosomes and extracellular vesicles (EV) are increasingly being explored as circulating biomarkers, but their heterogenous composition will likely mandate the development of multiplexed EV technologies. Iteratively multiplexed analyses of near single EVs have been challenging to implement beyond a few colors during spectral sensing. Here we developed a multiplexed analysis of EV technique (MASEV) to interrogate thousands of individual EVs during 5 cycles of multi-channel fluorescence staining for 15 EV biomarkers. Contrary to the common belief, we show that: several markers proposed to be ubiquitous are less prevalent than believed; multiple biomarkers concur in single vesicles but only in small fractions; affinity purification can lead to loss of rare EV subtypes; and deep profiling allows detailed analysis of EV, potentially improving the diagnostic content. These findings establish the potential of MASEV for uncovering fundamental EV biology and heterogeneity and increasing diagnostic specificity.
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Affiliation(s)
- Joshua D Spitzberg
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Scott Ferguson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Katherine S Yang
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Hannah M Peterson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Jonathan C T Carlson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA. .,Cancer Center, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA. .,Cancer Center, Massachusetts General Hospital, Boston, MA, 02114, USA. .,Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA.
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19
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Amarasinghe I, Phillips W, Hill AF, Cheng L, Helbig KJ, Willms E, Monson EA. Cellular communication through extracellular vesicles and lipid droplets. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e77. [PMID: 38938415 PMCID: PMC11080893 DOI: 10.1002/jex2.77] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 06/29/2024]
Abstract
Cellular communication is essential for effective coordination of biological processes. One major form of intercellular communication occurs via the release of extracellular vesicles (EVs). These vesicles mediate intercellular communication through the transfer of their cargo and are actively explored for their role in various diseases and their potential therapeutic and diagnostic applications. Conversely, lipid droplets (LDs) are vesicles that transfer cargo within cells. Lipid droplets play roles in various diseases and evidence for their ability to transfer cargo between cells is emerging. To date, there has been little interdisciplinary research looking at the similarities and interactions between these two classes of small lipid vesicles. This review will compare the commonalities and differences between EVs and LDs including their biogenesis and secretion, isolation and characterisation methodologies, composition, and general heterogeneity and discuss challenges and opportunities in both fields.
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Affiliation(s)
- Irumi Amarasinghe
- School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneAustralia
| | - William Phillips
- School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneAustralia
- La Trobe Institute for Molecular SciencesLa Trobe UniversityMelbourneAustralia
| | - Andrew F. Hill
- Institute for Health and SportVictoria UniversityFootscrayVictoriaAustralia
| | - Lesley Cheng
- School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneAustralia
- La Trobe Institute for Molecular SciencesLa Trobe UniversityMelbourneAustralia
| | - Karla J. Helbig
- School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneAustralia
| | - Eduard Willms
- School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneAustralia
- La Trobe Institute for Molecular SciencesLa Trobe UniversityMelbourneAustralia
| | - Ebony A. Monson
- School of Agriculture, Biomedicine and EnvironmentLa Trobe UniversityMelbourneAustralia
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20
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Jeong MH, Son T, Tae YK, Park CH, Lee HS, Chung MJ, Park JY, Castro CM, Weissleder R, Jo JH, Bang S, Im H. Plasmon-Enhanced Single Extracellular Vesicle Analysis for Cholangiocarcinoma Diagnosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205148. [PMID: 36698298 PMCID: PMC10015870 DOI: 10.1002/advs.202205148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/01/2023] [Indexed: 05/20/2023]
Abstract
Cholangiocarcinoma (CCA) is a fatal disease often detected late in unresectable stages. Currently, there are no effective diagnostic methods or biomarkers to detect CCA early with high confidence. Analysis of tumor-derived extracellular vesicles (tEVs) harvested from liquid biopsies can provide a new opportunity to achieve this goal. Here, an advanced nanoplasmonic sensing technology is reported, termed FLEX (fluorescence-amplified extracellular vesicle sensing technology), for sensitive and robust single EV analysis. In the FLEX assay, EVs are captured on a plasmonic gold nanowell surface and immunolabeled for cancer-associated biomarkers to identify tEVs. The underlying plasmonic gold nanowell structures then amplify EVs' fluorescence signals, an effective amplification process at the single EV level. The FLEX EV analysis revealed a wide heterogeneity of tEVs and their marker levels. FLEX also detected small tEVs not detected by conventional EV fluorescence imaging due to weak signals. Tumor markers (MUC1, EGFR, and EPCAM) are identified in CCA, and this marker combination is applied to detect tEVs in clinical bile samples. The FLEX assay detected CCA with an area under the curve of 0.93, significantly better than current clinical markers. The sensitive and accurate nanoplasmonic EV sensing technology can aid in early CCA diagnosis.
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Affiliation(s)
- Mi Ho Jeong
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
| | - Taehwang Son
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
| | - Yoo Keung Tae
- Division of GastroenterologyDepartment of Internal MedicineSeverance HospitalYonsei University College of MedicineSeoul03722Republic of Korea
| | - Chan Hee Park
- Division of GastroenterologyDepartment of Internal MedicineSeverance HospitalYonsei University College of MedicineSeoul03722Republic of Korea
| | - Hee Seung Lee
- Division of GastroenterologyDepartment of Internal MedicineSeverance HospitalYonsei University College of MedicineSeoul03722Republic of Korea
| | - Moon Jae Chung
- Division of GastroenterologyDepartment of Internal MedicineSeverance HospitalYonsei University College of MedicineSeoul03722Republic of Korea
| | - Jeong Youp Park
- Division of GastroenterologyDepartment of Internal MedicineSeverance HospitalYonsei University College of MedicineSeoul03722Republic of Korea
| | - Cesar M. Castro
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
- Cancer Center, Massachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
| | - Ralph Weissleder
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
- Cancer Center, Massachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
- Department of RadiologyMassachusetts General HospitalBostonMA02114USA
- Department of Systems BiologyHarvard Medical SchoolBostonMA02115USA
| | - Jung Hyun Jo
- Division of GastroenterologyDepartment of Internal MedicineSeverance HospitalYonsei University College of MedicineSeoul03722Republic of Korea
| | - Seungmin Bang
- Division of GastroenterologyDepartment of Internal MedicineSeverance HospitalYonsei University College of MedicineSeoul03722Republic of Korea
| | - Hyungsoon Im
- Center for Systems BiologyMassachusetts General HospitalBostonMA02114USA
- Department of RadiologyMassachusetts General HospitalBostonMA02114USA
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21
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Bracht JWP, Los M, van Eijndhoven MAJ, Bettin B, van der Pol E, Pegtel DM, Nieuwland R. Platelet removal from human blood plasma improves detection of extracellular vesicle-associated miRNA. J Extracell Vesicles 2023; 12:e12302. [PMID: 36788785 PMCID: PMC9929339 DOI: 10.1002/jev2.12302] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/12/2022] [Accepted: 01/04/2023] [Indexed: 02/16/2023] Open
Abstract
Human blood plasma prepared by centrifugation contains not only extracellular vesicles (EVs) but also platelets and erythrocyte ghosts (ery-ghosts). Here we studied whether analysis of miRNA associated with plasma EVs (EV-miRNA) is affected by the presence of platelets and ery-ghosts. EDTA blood was collected from healthy donors (n = 3), and plasma was prepared by the centrifugation protocol recommended by the International Society on Thrombosis and Haemostasis (ISTH), and by a centrifugation protocol from an EV-miRNA expert lab (non-ISTH protocol). EVs were isolated from plasma by size-exclusion chromatography CL-2B (SEC2B), and concentrations of platelets, activated platelets, ery-ghosts and EVs (150-1000 nm) were measured by calibrated flow cytometry. Two EV-associated miRNAs (let7a-5p and miR-21-5p), and one platelet-associated miRNA (miR-223-3p), were measured by qRT-PCR. Measurements were performed with and without filtration using 0.8 μm track-etched filters to remove platelets and ery-ghosts from plasma and EV-enriched SEC fractions. Plasma prepared by both centrifugation protocols contained platelets and ery-ghosts, which co-migrated with EVs into the EV-enriched SEC2B fractions. Filtration removed platelets and ery-ghosts (>97%; p ≤ 0.05) and did not affect the EV concentrations (p > 0.17). The miRNA concentrations were 2-4-fold overestimated due to the presence of platelets but not ery-ghosts. Thus, filtration of human plasma is expected to improve comparability and reproducibility of quantitative EV-miRNA studies. Therefore, we recommend to measure and report the plasma concentration of platelets for EV-miRNA studies, and to filter plasma before downstream analyses or storage in biobanks.
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Affiliation(s)
- Jillian W. P. Bracht
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam Cardiovascular Sciences, Atherosclerosis and Ischemic SyndromesAmsterdamThe Netherlands
| | - Mandy Los
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
| | - Monique A. J. van Eijndhoven
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, Boelelaan 1117AmsterdamThe Netherlands
| | - Britta Bettin
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
- Amsterdam UMC location University of Amsterdam, Department of Biomedical Engineering and Physics, Meibergdreef 9AmsterdamThe Netherlands
| | - Edwin van der Pol
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam Cardiovascular Sciences, Atherosclerosis and Ischemic SyndromesAmsterdamThe Netherlands
- Amsterdam UMC location University of Amsterdam, Department of Biomedical Engineering and Physics, Meibergdreef 9AmsterdamThe Netherlands
| | - D. Michiel Pegtel
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, Boelelaan 1117AmsterdamThe Netherlands
| | - Rienk Nieuwland
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam Cardiovascular Sciences, Atherosclerosis and Ischemic SyndromesAmsterdamThe Netherlands
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22
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Schiavello M, Vizio B, Bosco O, Pivetta E, Mariano F, Montrucchio G, Lupia E. Extracellular Vesicles: New Players in the Mechanisms of Sepsis- and COVID-19-Related Thromboinflammation. Int J Mol Sci 2023; 24:ijms24031920. [PMID: 36768242 PMCID: PMC9916541 DOI: 10.3390/ijms24031920] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
Sepsis and COVID-19 patients often manifest an imbalance in inflammation and coagulation, a complex pathological mechanism also named thromboinflammation, which strongly affects patient prognosis. Extracellular vesicles (EVs) are nanoparticles released by cells into extracellular space that have a relevant role in cell-to-cell communication. Recently, EVs have been shown to act as important players in a variety of pathologies, including cancer and cardiovascular disease. The biological properties of EVs in the mechanisms of thromboinflammation during sepsis and COVID-19 are still only partially known. Herein, we summarize the current experimental evidence on the role of EVs in thromboinflammation, both in bacterial sepsis and in COVID-19. A better understanding of EV involvement in these processes could be useful in describing novel diagnostic and therapeutic applications of EVs in these diseases.
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23
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Jeong MH, Son T, Im H. Plasmon-Enhanced Characterization of Single Extracellular Vesicles. Methods Mol Biol 2023; 2668:3-13. [PMID: 37140785 PMCID: PMC10394726 DOI: 10.1007/978-1-0716-3203-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Extracellular vesicles (EVs) represent heterogeneous populations of membrane-bound vesicles shed from almost all kinds of cells. Although superior to conventional methods, most newly developed EV sensing platforms still require a certain number of EVs, measuring bulk signals from a group of vesicles. A new analytical approach that enables single EV analysis could be extremely valuable for understanding EVs' subtypes, heterogeneity, and production dynamics during disease development and progression. Here, we describe a new nanoplasmonic sensing platform for sensitive single EV analysis. Termed nPLEX-FL (nano-plasmonic EV analysis with enhanced fluorescence detection), the system amplifies EVs' fluorescence signals using periodic gold nanohole structures, enabling sensitive, multiplexed analysis of single EVs.
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Affiliation(s)
- Mi Ho Jeong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Taehwang Son
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
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24
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Zhang S, Deng J, Li J, Tian F, Liu C, Fang L, Sun J. Advanced microfluidic technologies for isolating extracellular vesicles. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Hallal S, Tűzesi Á, Grau GE, Buckland ME, Alexander KL. Understanding the extracellular vesicle surface for clinical molecular biology. J Extracell Vesicles 2022; 11:e12260. [PMID: 36239734 PMCID: PMC9563386 DOI: 10.1002/jev2.12260] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 12/17/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid-membrane enclosed nanoparticles that play significant roles in health and disease. EVs are abundant in body fluids and carry an array of molecules (proteins, lipids, nucleic acids and glycans) that reflect the identity and activity of their cell-of-origin. While the advent of high throughput omics technologies has allowed in-depth characterisation of EV compositions, how these molecular species are spatially distributed within EV structures is not well appreciated. This is particularly true of the EV surface where a plethora of molecules are reported to be both integral and peripherally associated to the EV membrane. This coronal layer or 'atmosphere' that surrounds the EV membrane contributes to a large, highly interactive and dynamic surface area that is responsible for facilitating EV interactions with the extracellular environment. The EV coronal layer harbours surface molecules that reflect the identity of parent cells, which is likely a highly valuable property in the context of diagnostic liquid biopsies. In this review, we describe the current understanding of the mechanical, electrostatic and molecular properties of the EV surface that offer significant biomarker potential and contribute to a highly dynamic interactome.
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Affiliation(s)
- Susannah Hallal
- Neurosurgery DepartmentChris O'Brien LifehouseCamperdownNSWAustralia,Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia
| | - Ágota Tűzesi
- Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Georges E. Grau
- School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Michael E. Buckland
- Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Kimberley L. Alexander
- Neurosurgery DepartmentChris O'Brien LifehouseCamperdownNSWAustralia,Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
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26
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Kim K, Son T, Hong JS, Kwak TJ, Jeong MH, Weissleder R, Im H. Physisorption of Affinity Ligands Facilitates Extracellular Vesicle Detection with Low Non-Specific Binding to Plasmonic Gold Substrates. ACS APPLIED MATERIALS & INTERFACES 2022; 14:10.1021/acsami.2c07317. [PMID: 35653580 PMCID: PMC9715849 DOI: 10.1021/acsami.2c07317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Plasmonic biosensors are increasingly being used for the analysis of extracellular vesicles (EVs) originating from disease areas. However, the high non-specific binding of EVs to a gold-sensing surface has been a critical problem and hindered the true translational potential. Here, we report that direct antibody immobilization on the plasmonic gold surface via physisorption shows excellent capture of cancer-derived EVs with ultralow non-specific binding even at very high concentrations. Contrary to commonly used methods that involve thiol-based linker attachment and an EDC/sulfo-NHS reaction, we show a higher specific capture rate and >50-fold lower non-specific on citrate-capped plain and nanopatterned gold surfaces. The method provides a simple, fast, and reproducible means to functionalize plasmonic gold surfaces with antibodies for robust EV biosensing.
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Affiliation(s)
- Kihyeun Kim
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Taehwang Son
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Tae Joon Kwak
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Mi Ho Jeong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
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27
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Karimi N, Dalirfardouei R, Dias T, Lötvall J, Lässer C. Tetraspanins distinguish separate extracellular vesicle subpopulations in human serum and plasma - Contributions of platelet extracellular vesicles in plasma samples. J Extracell Vesicles 2022; 11:e12213. [PMID: 35524458 PMCID: PMC9077141 DOI: 10.1002/jev2.12213] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The ability to isolate extracellular vesicles (EVs) from blood is vital in the development of EVs as disease biomarkers. Both serum and plasma can be used, but few studies have compared these sources in terms of the type of EVs that are obtained. The aim of this study was to determine the presence of different subpopulations of EVs in plasma and serum. METHOD Blood was collected from healthy subjects, and plasma and serum were isolated in parallel. ACD or EDTA tubes were used for the collection of plasma, while serum was obtained in clot activator tubes. EVs were isolated utilising a combination of density cushion and SEC, a combination of density cushion and gradient or by a bead antibody capturing system (anti-CD63, anti-CD9 and anti-CD81 beads). The subpopulations of EVs were analysed by NTA, Western blot, SP-IRIS, conventional and nano flow cytometry, magnetic bead ELISA and mass spectrometry. Additionally, different isolation protocols for plasma were compared to determine the contribution of residual platelets in the analysis. RESULTS This study shows that a higher number of CD9+ EVs were present in EDTA-plasma compared to ACD-plasma and to serum, and the presence of CD41a on these EVs suggests that they were released from platelets. Furthermore, only a very small number of EVs in blood were double-positive for CD63 and CD81. The CD63+ EVs were enriched in serum, while CD81+ vesicles were the rarest subpopulation in both plasma and serum. Additionally, EDTA-plasma contained more residual platelets than ACD-plasma and serum, and two centrifugation steps were crucial to reduce the number of platelets in plasma prior to EV isolation. CONCLUSION These results show that human blood contains multiple subpopulations of EVs that carry different tetraspanins. Blood sampling methods, including the use of anti-coagulants and choice of centrifugation protocols, can affect EV analyses and should always be reported in detail.
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Affiliation(s)
- Nasibeh Karimi
- Krefting Research CentreDepartment of Internal Medicine and Clinical NutritionInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Razieh Dalirfardouei
- Krefting Research CentreDepartment of Internal Medicine and Clinical NutritionInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
- Endometrium and Endometriosis Research CenterHamadan University of Medical SciencesHamadanIran
- Faculty of MedicineDepartment of Medical BiotechnologyMashhad University of Medical SciencesMashhadIran
| | | | - Jan Lötvall
- Krefting Research CentreDepartment of Internal Medicine and Clinical NutritionInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Cecilia Lässer
- Krefting Research CentreDepartment of Internal Medicine and Clinical NutritionInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
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28
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Ferguson S, Yang KS, Zelga P, Liss AS, Carlson JCT, del Castillo CF, Weissleder R. Single-EV analysis (sEVA) of mutated proteins allows detection of stage 1 pancreatic cancer. SCIENCE ADVANCES 2022; 8:eabm3453. [PMID: 35452280 PMCID: PMC9032977 DOI: 10.1126/sciadv.abm3453] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/07/2022] [Indexed: 05/02/2023]
Abstract
Tumor cell-derived extracellular vesicles (EVs) are being explored as circulating biomarkers, but it is unclear whether bulk measurements will allow early cancer detection. We hypothesized that a single-EV analysis (sEVA) technique could potentially improve diagnostic accuracy. Using pancreatic cancer (PDAC), we analyzed the composition of putative cancer markers in 11 model lines. In parental PDAC cells positive for KRASmut and/or P53mut proteins, only ~40% of EVs were also positive. In a blinded study involving 16 patients with surgically proven stage 1 PDAC, KRASmut and P53mut protein was detectable at much lower levels, generally in <0.1% of vesicles. These vesicles were detectable by the new sEVA approach in 15 of the 16 patients. Using a modeling approach, we estimate that the current PDAC detection limit is at ~0.1-cm3 tumor volume, below clinical imaging capabilities. These findings establish the potential for sEVA for early cancer detection.
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Affiliation(s)
- Scott Ferguson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
| | - Katherine S. Yang
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
| | - Piotr Zelga
- Department of Surgery, Massachusetts General Hospital, 32 Fruit St, Boston, MA 02114, USA
| | - Andrew S. Liss
- Department of Surgery, Massachusetts General Hospital, 32 Fruit St, Boston, MA 02114, USA
| | - Jonathan C. T. Carlson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Carlos Fernandez del Castillo
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
- Department of Surgery, Massachusetts General Hospital, 32 Fruit St, Boston, MA 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
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29
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Morales-Sanfrutos J, Munoz J. UNRAVELLING THE COMPLEXITY OF THE EXTRACELLULAR VESICLE LANDSCAPE WITH ADVANCED PROTEOMICS. Expert Rev Proteomics 2022; 19:89-101. [PMID: 35290757 DOI: 10.1080/14789450.2022.2052849] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The field of extracellular vesicles (EVs) is rapidly advancing. This progress is fuelled by the potential applications of these agents as biomarkers and also as an attractive source to encapsulate therapeutics and other agents to target specific cells. AREAS COVERED Different types of EVs, including exosomes, and other nanoparticles have been identified in the last years with key regulatory functions in cell-cell communication. However, the techniques used for their purification possess inherent limitations, resulting in heterogeneous preparations contaminated by other EVs subtypes and nano-size structures. It is therefore urgent to deconvolute the molecular constituents present in each type of EVs in order to accurately ascribe their specific functions. In this context, proteomics can profile, not only the lumen proteins and surface markers, but also their post-translational modifications, which will inform on the mechanisms of cargo selection and sorting. EXPERT OPINION Mass spectrometry-based proteomics is now a mature technique and has started to deliver new insights in the EV field. Here, we review recent developments in sample preparation, mass spectrometry (MS) and computational analysis and discuss how these technological advances, in conjunction with improved purification protocols, could impact the proteomic characterization of the complex landscape of EVs and other secreted nanoparticles.
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Affiliation(s)
| | - Javier Munoz
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Cell Signaling and Clinical Proteomics Group. Biocruces Bizkaia Health Research Institute. 48903 Barkaldo, Spain.,Ikerbasque, Basque foundation for science, Bilbao, Spain
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30
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Woo HK, Cho YK, Lee CY, Lee H, Castro CM, Lee H. Characterization and modulation of surface charges to enhance extracellular vesicle isolation in plasma. Theranostics 2022; 12:1988-1998. [PMID: 35265194 PMCID: PMC8899565 DOI: 10.7150/thno.69094] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/13/2022] [Indexed: 01/03/2023] Open
Abstract
Extracellular vesicles (EVs) carry information inherited from parental cells, having significant potential for disease diagnosis. In blood, however, EVs are outnumbered >104-fold by low density lipoproteins (LDLs), yet similar in size and density. These fundamental disadvantages often cause LDL spillover into EV isolates, thus confounding assay results. We hypothesized that EVs can be further separated from LDLs based on electric charge: EVs and LDLs have different lipid composition, which can lead to differential surface charge densities. To test this hypothesis, we modeled and quantified the surface charge of EVs and LDLs, and used the information to optimally separate EVs from LDLs via ion-exchange chromatography. Methods: We built an enhanced dual-mode chromatography (eDMC) device which performed i) size-exclusion to remove particles smaller than EVs and LDLs and ii) cation-exchange in an acidic elution to retain LDLs longer than EVs. The performance of the eDMC, in comparison to size-exclusion only, was evaluated by analyzing the yield and purity of the isolated EVs. Results: By measuring and modeling zeta potentials at different buffer pH, we estimated surface charge densities of EVs (-6.2 mC/m2) and LDLs (-3.6 mC/m2), revealing that EVs are more negatively charged than LDLs. Furthermore, the charge difference between EVs and LDLs was maximal at a weak acidic condition (pH = 6.4). By applying these findings, we optimized eDMC operation to enrich EVs directly from plasma, depleting >99.8% of LPPs within 30 min. Minimizing LDL contamination improved analytical signals in EV molecular assays, including single vesicle imaging, bulk protein measurements, and mRNA detection. Conclusions: These developments will promote the translational value of the dual-mode separation - a fast, equipment-free, and non-biased way for EV isolation from plasma samples.
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Affiliation(s)
- Hyun-Kyung Woo
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Young Kwan Cho
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Chemistry, Kennedy College of Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, 01854, USA
| | - Chang Yeol Lee
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Haeun Lee
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Chemistry, Soongsil University, Seoul, 06978, Republic of Korea
| | - Cesar M. Castro
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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31
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Takov K, Teng IJ, Mayr M. Isolation of Circulating Extracellular Vesicles by High-Performance Size-Exclusion Chromatography. Methods Mol Biol 2022; 2504:31-40. [PMID: 35467277 DOI: 10.1007/978-1-0716-2341-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circulating extracellular vesicles (EVs) are gaining increased attention as carriers of proteins, nucleic acids, and lipids. Blood contains EVs from different cell sources that constitute an attractive target for biomarker studies. However, there is no consensus on the best approach to isolate EVs from blood. Non-EV proteins and lipoproteins in plasma/serum tend to contaminate isolated EVs and confound functional experiments. Here we describe a single-step, high-performance size-exclusion chromatography procedure for separation of EVs from most lipoproteins and non-EV proteins, and compare it to ultracentrifugation, still the most commonly used method for EV isolation.
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Affiliation(s)
- Kaloyan Takov
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK.
| | - I-Jou Teng
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK
| | - Manuel Mayr
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK.
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32
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Ashcroft J, Leighton P, Elliott TR, Hosgood SA, Nicholson ML, Kosmoliaptsis V. Extracellular vesicles in kidney transplantation: a state-of-the-art review. Kidney Int 2021; 101:485-497. [PMID: 34838864 DOI: 10.1016/j.kint.2021.10.038] [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] [Received: 08/09/2021] [Revised: 10/11/2021] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Kidney transplantation is the optimal treatment for patients with kidney failure; however, early detection and timely treatment of graft injury remain a challenge. Precise and noninvasive techniques of graft assessment and innovative therapeutics are required to improve kidney transplantation outcomes. Extracellular vesicles (EVs) are lipid bilayer-delimited particles with unique biosignatures and immunomodulatory potential, functioning as intermediaries of cell signalling. Promising evidence exists for the potential of EVs to develop precision diagnostics of graft dysfunction, and prognostic biomarkers for clinician decision making. The inherent targeting characteristics of EVs and their low immunogenic and toxicity profiles combined with their potential as vehicles for drug delivery make them ideal targets for development of therapeutics to improve kidney transplant outcomes. In this review, we summarize the current evidence for EVs in kidney transplantation, discuss common methodological principles of EV isolation and characterization, explore upcoming innovative approaches in EV research, and discuss challenges and opportunities to enable translation of research findings into clinical practice.
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Affiliation(s)
- James Ashcroft
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Philippa Leighton
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Tegwen R Elliott
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Sarah A Hosgood
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK
| | - Michael L Nicholson
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK.
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33
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Ter-Ovanesyan D, Norman M, Lazarovits R, Trieu W, Lee JH, Church GM, Walt DR. Framework for rapid comparison of extracellular vesicle isolation methods. eLife 2021; 10:70725. [PMID: 34783650 PMCID: PMC8651285 DOI: 10.7554/elife.70725] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/14/2021] [Indexed: 12/17/2022] Open
Abstract
Extracellular vesicles (EVs) are released by all cells into biofluids and hold great promise as reservoirs of disease biomarkers. One of the main challenges in studying EVs is a lack of methods to quantify EVs that are sensitive enough and can differentiate EVs from similarly sized lipoproteins and protein aggregates. We demonstrate the use of ultrasensitive, single-molecule array (Simoa) assays for the quantification of EVs using three widely expressed transmembrane proteins: the tetraspanins CD9, CD63, and CD81. Using Simoa to measure these three EV markers, as well as albumin to measure protein contamination, we were able to compare the relative efficiency and purity of several commonly used EV isolation methods in plasma and cerebrospinal fluid (CSF): ultracentrifugation, precipitation, and size exclusion chromatography (SEC). We further used these assays, all on one platform, to improve SEC isolation from plasma and CSF. Our results highlight the utility of quantifying EV proteins using Simoa and provide a rapid framework for comparing and improving EV isolation methods from biofluids.
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Affiliation(s)
| | - Maia Norman
- Wyss Institute for Biologically Inspired Engineering, Boston, United States.,Tufts University School of Medicine, Boston, United States.,Department of Pathology, Brigham and Women's Hospital, Boston, United States
| | - Roey Lazarovits
- Wyss Institute for Biologically Inspired Engineering, Boston, United States
| | - Wendy Trieu
- Wyss Institute for Biologically Inspired Engineering, Boston, United States
| | - Ju-Hyun Lee
- Wyss Institute for Biologically Inspired Engineering, Boston, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Boston, United States.,Harvard Medical School, Boston, United States
| | - David R Walt
- Wyss Institute for Biologically Inspired Engineering, Boston, United States.,Department of Pathology, Brigham and Women's Hospital, Boston, United States.,Harvard Medical School, Boston, United States
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34
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Kaddour H, Tranquille M, Okeoma CM. The Past, the Present, and the Future of the Size Exclusion Chromatography in Extracellular Vesicles Separation. Viruses 2021; 13:2272. [PMID: 34835078 PMCID: PMC8618570 DOI: 10.3390/v13112272] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 01/13/2023] Open
Abstract
Extracellular vesicles (EVs) are cell-derived membranous particles secreted by all cell types (including virus infected and uninfected cells) into the extracellular milieu. EVs carry, protect, and transport a wide array of bioactive cargoes to recipient/target cells. EVs regulate physiological and pathophysiological processes in recipient cells and are important in therapeutics/drug delivery. Despite these great attributes of EVs, an efficient protocol for EV separation from biofluids is lacking. Numerous techniques have been adapted for the separation of EVs with size exclusion chromatography (SEC)-based methods being the most promising. Here, we review the SEC protocols used for EV separation, and discuss opportunities for significant improvements, such as the development of novel particle purification liquid chromatography (PPLC) system capable of tandem purification and characterization of biological and synthetic particles with near-single vesicle resolution. Finally, we identify future perspectives and current issues to make PPLC a tool capable of providing a unified, automated, adaptable, yet simple and affordable particle separation resource.
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Affiliation(s)
- Hussein Kaddour
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Malik Tranquille
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Chioma M. Okeoma
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
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35
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Phillips W, Willms E, Hill AF. Understanding extracellular vesicle and nanoparticle heterogeneity: Novel methods and considerations. Proteomics 2021; 21:e2000118. [PMID: 33857352 PMCID: PMC8365743 DOI: 10.1002/pmic.202000118] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/22/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022]
Abstract
Extracellular vesicles (EVs) are a heterogeneous population of membrane-enclosed nanoparticles released by cells. They play a role in intercellular communication and are involved in numerous physiological and pathological processes. Cells release subpopulations of EVs with distinct composition and inherent biological function which overlap in size. Current size-based isolation methods are, therefore, not optimal to discriminate between functional EV subpopulations. In addition, EVs overlap in size with several other biological nanoparticles, such as lipoproteins and viruses. Proteomic analysis has allowed for more detailed study of EV composition, and EV isolation approaches based on this could provide a promising alternative for purification based on size. Elucidating EV heterogeneity and the characteristics and role of EV subpopulations will advance our understanding of EV biology and the role of EVs in health and disease. Here, we discuss current knowledge of EV composition, EV heterogeneity and advances in affinity based EV isolation tools.
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Affiliation(s)
- William Phillips
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Eduard Willms
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Andrew F. Hill
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
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36
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Review of Methodological Approaches to Human Milk Small Extracellular Vesicle Proteomics. Biomolecules 2021; 11:biom11060833. [PMID: 34204944 PMCID: PMC8228857 DOI: 10.3390/biom11060833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics can map extracellular vesicles (EVs), including exosomes, across disease states between organisms and cell types. Due to the diverse origin and cargo of EVs, tailoring methodological and analytical techniques can support the reproducibility of results. Proteomics scans are sensitive to in-sample contaminants, which can be retained during EV isolation procedures. Contaminants can also arise from the biological origin of exosomes, such as the lipid-rich environment in human milk. Human milk (HM) EVs and exosomes are emerging as a research interest in health and disease, though the experimental characterization and functional assays remain varied. Past studies of HM EV proteomes have used data-dependent acquisition methods for protein detection, however, improvements in data independent acquisition could allow for previously undetected EV proteins to be identified by mass spectrometry. Depending on the research question, only a specific population of proteins can be compared and measured using isotope and other labelling techniques. In this review, we summarize published HM EV proteomics protocols and suggest a methodological workflow with the end-goal of effective and reproducible analysis of human milk EV proteomes.
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37
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Recent advances on protein-based quantification of extracellular vesicles. Anal Biochem 2021; 622:114168. [PMID: 33741309 DOI: 10.1016/j.ab.2021.114168] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/27/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are secreted by almost all cells into the circulatory system and have the important function of intercellular communication. Ranging in size from 50 to 1000 nm, they are further classified based on origin, size, physical properties and function. EVs have shown the potential for studying various physiological and pathological processes, such as characterizing their parent cells with molecular markers that could further signify diseases. Proteins within EVs are the building blocks for the vesicles to function within a biological system. Isolation and proteomic profiling of EVs can advance the understanding of their biogenesis and functions, which can give further insight of how they can be used in clinical settings. However, the nanoscale size of EVs, which is much smaller than that of cells, comprises a major challenge for EV isolation and the characterization of their protein cargos. With the recent advances of bioanalytical techniques such as lab-on-a-chip devices and innovated flow cytometry, the quantification of EV proteins from a small number of vesicles down to the single vesicle level has been achieved, shining light on the promising applications of these small vesicles for early disease diagnosis and treatment monitoring. In this article, we first briefly review conventional EV protein determination technologies and their limitations, followed by detailed description and analysis of emerging technologies used for EV protein quantification, including optical, non-optical, microfluidic, and single vesicle detection methods. The pros and cons of these technologies are compared and the current challenges are outlined. Future perspectives and potential research directions of the EV protein analysis methods are discussed.
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38
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Liangsupree T, Multia E, Riekkola ML. Modern isolation and separation techniques for extracellular vesicles. J Chromatogr A 2020; 1636:461773. [PMID: 33316564 DOI: 10.1016/j.chroma.2020.461773] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023]
Abstract
Extracellular vesicles (EVs) are heterogenous membrane-bound vesicles released from various origins. EVs play a crucial role in cellular communication and mediate several physiological and pathological processes, highlighting their potential therapeutic and diagnostic applications. Due to the rapid increase in interests and needs to elucidate EV properties and functions, numerous isolation and separation approaches for EVs have been developed to overcome limitations of conventional techniques, such as ultracentrifugation. This review focuses on recently emerging and modern EV isolation and separation techniques, including size-, charge-, and affinity-based techniques while excluding ultracentrifugation and precipitation-based techniques due to their multiple limitations. The advantages and drawbacks of each technique are discussed together with insights into their applications. Emerging approaches all share similar features in terms of being time-effective, easy-to-operate, and capable of providing EVs with suitable and desirable purity and integrity for applications of interest. Combination and hyphenation of techniques have been used for EV isolation and separation to yield EVs with the best quality. The most recent development using an automated on-line system including selective affinity-based trapping unit and asymmetrical flow field-flow fractionation allows reliable isolation and fractionation of EV subpopulations from human plasma.
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Affiliation(s)
| | - Evgen Multia
- Department of Chemistry, P.O. Box 55, FI-00014 University of Helsinki, Finland
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39
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Sidhom K, Obi PO, Saleem A. A Review of Exosomal Isolation Methods: Is Size Exclusion Chromatography the Best Option? Int J Mol Sci 2020; 21:E6466. [PMID: 32899828 PMCID: PMC7556044 DOI: 10.3390/ijms21186466] [Citation(s) in RCA: 329] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) are membranous vesicles secreted by both prokaryotic and eukaryotic cells and play a vital role in intercellular communication. EVs are classified into several subtypes based on their origin, physical characteristics, and biomolecular makeup. Exosomes, a subtype of EVs, are released by the fusion of multivesicular bodies (MVB) with the plasma membrane of the cell. Several methods have been described in literature to isolate exosomes from biofluids including blood, urine, milk, and cell culture media, among others. While differential ultracentrifugation (dUC) has been widely used to isolate exosomes, other techniques including ultrafiltration, precipitating agents such as poly-ethylene glycol (PEG), immunoaffinity capture, microfluidics, and size-exclusion chromatography (SEC) have emerged as credible alternatives with pros and cons associated with each. In this review, we provide a summary of commonly used exosomal isolation techniques with a focus on SEC as an ideal methodology. We evaluate the efficacy of SEC to isolate exosomes from an array of biological fluids, with a particular focus on its application to adipose tissue-derived exosomes. We argue that exosomes isolated via SEC are relatively pure and functional, and that this methodology is reproducible, scalable, inexpensive, and does not require specialized equipment or user expertise. However, it must be noted that while SEC is a good candidate method to isolate exosomes, direct comparative studies are required to support this conclusion.
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Affiliation(s)
- Karim Sidhom
- Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of CHRIM, Winnipeg, MB R3E 3P4, Canada;
- Biology of Breathing Research Theme of CHRIM, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB R3E 3P4, Canada
| | - Patience O. Obi
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of CHRIM, Winnipeg, MB R3E 3P4, Canada;
- Biology of Breathing Research Theme of CHRIM, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB R3E 3P4, Canada
- Applied Health Sciences, Faculty of Graduate Studies, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Faculty of Kinesiology and Recreation Management, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayesha Saleem
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of CHRIM, Winnipeg, MB R3E 3P4, Canada;
- Biology of Breathing Research Theme of CHRIM, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB R3E 3P4, Canada
- Applied Health Sciences, Faculty of Graduate Studies, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Faculty of Kinesiology and Recreation Management, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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