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Vanderboom PM, Chawla Y, Dasari S, Kapoor I, Kumar SK, Nair KS, Gonsalves WI. Differences in the proteome within extracellular vesicles between premalignant and malignant plasma cell disorders. Eur J Haematol 2024; 113:351-356. [PMID: 38804098 PMCID: PMC11296916 DOI: 10.1111/ejh.14246] [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: 03/08/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Precursor plasma cell disorders such as monoclonal gammopathy of undetermined significance (MGUS) always precede the development of active malignancies such as multiple myeloma (MM). There is a need for novel biomarkers to identify those patients with such precursor plasma cell disorders who rapidly progress to MM. Plasma-derived extracellular vesicles (EVs) may serve as a reservoir of potential biomarkers that can shed light on the pathogenesis and disease biology of MM. METHODS This study isolated small EVs (SEVs) and large EVs (LEVs) from the platelet-poor peripheral blood plasma of MGUS (n = 9) and MM (n = 12) patients using the size exclusion chromatography-based method and evaluated their proteome using a label-free proteomics workflow. RESULTS In total, 2055 proteins were identified in SEVs, while 2794 proteins were identified in LEVs. The transferrin receptor (or CD71) protein was upregulated in both populations of EVs derived from MM patients compared to MGUS patients and was of prognostic significance. Similarly, three isoforms of serum amyloid A (SAA) protein, SAA1, SAA2, and SAA4, were also highly upregulated in SEVs within MM patients relative to MGUS patients. Finally, CD40 expression was also higher in the LEVs derived from MM patients than in MGUS patients. CONCLUSIONS This study demonstrates the feasibility of successfully isolating both SEVs and LEVs from the peripheral blood of patients with plasma cell disorders and quantifying protein biomarkers within these EVs that could be of prognostic and diagnostic interest.
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Affiliation(s)
- Patrick M. Vanderboom
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Isha Kapoor
- Hematology, Mayo Clinic, Rochester, MN 55905, USA
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Poupardin R, Wolf M, Maeding N, Paniushkina L, Geissler S, Bergese P, Witwer KW, Schallmoser K, Fuhrmann G, Strunk D. Advances in Extracellular Vesicle Research Over the Past Decade: Source and Isolation Method are Connected with Cargo and Function. Adv Healthc Mater 2024; 13:e2303941. [PMID: 38270559 DOI: 10.1002/adhm.202303941] [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: 11/10/2023] [Revised: 12/23/2023] [Indexed: 01/26/2024]
Abstract
The evolution of extracellular vesicle (EV) research has introduced nanotechnology into biomedical cell communication science while recognizing what is formerly considered cell "dust" as constituting an entirely new universe of cell signaling particles. To display the global EV research landscape, a systematic review of 20 364 original research articles selected from all 40 684 EV-related records identified in PubMed 2013-2022 is performed. Machine-learning is used to categorize the high-dimensional data and further dissected significant associations between EV source, isolation method, cargo, and function. Unexpected correlations between these four categories indicate prevalent experimental strategies based on cargo connectivity with function of interest being associated with certain EV sources or isolation strategies. Conceptually relevant association of size-based EV isolation with protein cargo and uptake function will guide strategic conclusions enhancing future EV research and product development. Based on this study, an open-source database is built to facilitate further analysis with conventional or AI tools to identify additional causative associations of interest.
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Affiliation(s)
- Rodolphe Poupardin
- Cell Therapy Institute, Paracelsus Medical University, Salzburg, 5020, Austria
| | - Martin Wolf
- Cell Therapy Institute, Paracelsus Medical University, Salzburg, 5020, Austria
| | - Nicole Maeding
- Cell Therapy Institute, Paracelsus Medical University, Salzburg, 5020, Austria
| | - Liliia Paniushkina
- Cell Therapy Institute, Paracelsus Medical University, Salzburg, 5020, Austria
- Departments of Molecular and Comparative Pathobiology and Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Sven Geissler
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, 25121, Italy
- INSTM - National Interuniversity Consortium of Materials Science and Technology, Firenze, 50121, Italy
- National Center for Gene Therapy and Drugs based on RNA Technology - CN3, Padova, 35122, Italy
| | - Kenneth W Witwer
- Departments of Molecular and Comparative Pathobiology and Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Katharina Schallmoser
- Institute of Transfusion Medicine, Paracelsus Medical University, Salzburg, 5020, Austria
| | - Gregor Fuhrmann
- Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Dirk Strunk
- Cell Therapy Institute, Paracelsus Medical University, Salzburg, 5020, Austria
- Institute of Transfusion Medicine, Paracelsus Medical University, Salzburg, 5020, Austria
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3
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Torres A, Bernardo L, Sánchez C, Morato E, Solana JC, Carrillo E. Comparing the Proteomic Profiles of Extracellular Vesicles Isolated using Different Methods from Long-term Stored Plasma Samples. Biol Proced Online 2024; 26:18. [PMID: 38898416 PMCID: PMC11188224 DOI: 10.1186/s12575-024-00243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND The lack of standardized protocols for isolating extracellular vesicles (EVs), especially from biobank-stored blood plasma, translates to limitations for the study of new biomarkers. This study examines whether a combination of current isolation methods could enhance the specificity and purity of isolated EVs for diagnosis and personalized medicine purposes. RESULTS EVs were isolated from healthy human plasma stored for one year by ultracentrifugation (UC), size exclusion chromatography (SEC), or SEC and UC combined (SEC + UC). The EV isolates were then characterized by transmission electron microscopy imaging, nanoparticle tracking analysis (NTA) and western blotting. Proteomic procedures were used to analyze protein contents. The presence of EV markers in all isolates was confirmed by western blotting yet this analysis revealed higher albumin expression in EVs-UC, suggesting plasma protein contamination. Proteomic analysis identified 542 proteins, SEC + UC yielding the most complex proteome at 364 proteins. Through gene ontology enrichment, we observed differences in the cellular components of EVs and plasma in that SEC + UC isolates featured higher proportions of EV proteins than those derived from the other two methods. Analysis of proteins unique to each isolation method served to identify 181 unique proteins for the combined approach, including those normally appearing in low concentrations in plasma. This indicates that with this combined method, it is possible to detect less abundant plasma proteins by proteomics in the resultant isolates. CONCLUSIONS Our findings reveal that the SEC + UC approach yields highly pure and diverse EVs suitable for comprehensive proteomic analysis with applications for the detection of new biomarkers in biobank-stored plasma samples.
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Affiliation(s)
- Ana Torres
- WHO Collaborating Centre for Leishmaniasis, Spanish National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Lorena Bernardo
- WHO Collaborating Centre for Leishmaniasis, Spanish National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Sánchez
- WHO Collaborating Centre for Leishmaniasis, Spanish National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Esperanza Morato
- Proteomics Facility, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose Carlos Solana
- WHO Collaborating Centre for Leishmaniasis, Spanish National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
| | - Eugenia Carrillo
- WHO Collaborating Centre for Leishmaniasis, Spanish National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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4
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Guerricchio L, Barile L, Bollini S. Evolving Strategies for Extracellular Vesicles as Future Cardiac Therapeutics: From Macro- to Nano-Applications. Int J Mol Sci 2024; 25:6187. [PMID: 38892376 PMCID: PMC11173118 DOI: 10.3390/ijms25116187] [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: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Cardiovascular disease represents the foremost cause of mortality and morbidity worldwide, with a steadily increasing incidence due to the growth of the ageing population. Cardiac dysfunction leading to heart failure may arise from acute myocardial infarction (MI) as well as inflammatory- and cancer-related chronic cardiomyopathy. Despite pharmacological progress, effective cardiac repair represents an unmet clinical need, with heart transplantation being the only option for end-stage heart failure. The functional profiling of the biological activity of extracellular vesicles (EVs) has recently attracted increasing interest in the field of translational research for cardiac regenerative medicine. The cardioprotective and cardioactive potential of human progenitor stem/cell-derived EVs has been reported in several preclinical studies, and EVs have been suggested as promising paracrine therapy candidates for future clinical translation. Nevertheless, some compelling aspects must be properly addressed, including optimizing delivery strategies to meet patient needs and enhancing targeting specificity to the cardiac tissue. Therefore, in this review, we will discuss the most relevant aspects of the therapeutic potential of EVs released by human progenitors for cardiovascular disease, with a specific focus on the strategies that have been recently implemented to improve myocardial targeting and administration routes.
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Affiliation(s)
- Laura Guerricchio
- Biology Unit, Department of Experimental Medicine (DIMES), University of Genova, 16132 Genova, Italy;
| | - Lucio Barile
- Cardiovascular Theranostics, Istituto Cardiocentro Ticino, Laboratories for Translational Research, Ente Ospedaliero Cantonale, CH-6500 Bellinzona, Switzerland;
- Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Sveva Bollini
- Biology Unit, Department of Experimental Medicine (DIMES), University of Genova, 16132 Genova, Italy;
- Cellular Oncology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
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5
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Li Y, Wang J, Chen W, Lu H, Zhang Y. Comprehensive review of MS-based studies on N-glycoproteome and N-glycome of extracellular vesicles. Proteomics 2024; 24:e2300065. [PMID: 37474487 DOI: 10.1002/pmic.202300065] [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: 04/02/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed particles that can be released by all type of cells. Whereas, as one of the most common post-translational modifications, glycosylation plays a vital role in various biological functions of EVs, such as EV biogenesis, sorting, and cellular recognition. Nevertheless, compared with studies on RNAs or proteins, those investigating the glycoconjugates of EVs are limited. An in-depth investigation of N-glycosylation of EVs can improve the understanding of the biological functions of EVs and help to exploit EVs from different perspectives. The general focus of studies on glycosylation of EVs primarily includes isolation and characterization of EVs, preparation of glycoproteome/glycome samples and MS analysis. However, the low content of EVs and non-standard separation methods for downstream analysis are the main limitations of these studies. In this review, we highlight the importance of glycopeptide/glycan enrichment and derivatization owing to the low abundance of glycoproteins and the low ionization efficiency of glycans. Diverse fragmentation patterns and professional analytical software are indispensable for analysing glycosylation via MS. Altogether, this review summarises recent studies on glycosylation of EVs, revealing the role of EVs in disease progression and their remarkable potential as biomarkers.
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Affiliation(s)
- Yang Li
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, P. R. China
| | - Jun Wang
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai, P. R. China
| | - Weiyu Chen
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai, P. R. China
| | - Haojie Lu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, P. R. China
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai, P. R. China
| | - Ying Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, P. R. China
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai, P. R. China
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6
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Mastrototaro L, Roden M. The effects of extracellular vesicles and their cargo on metabolism and its adaptation to physical exercise in insulin resistance and type 2 diabetes. Proteomics 2024; 24:e2300078. [PMID: 37525338 DOI: 10.1002/pmic.202300078] [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: 05/08/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Lifestyle modification represents the first-line strategy for the prevention and treatment of type 2 diabetes mellitus (T2DM), which is frequently associated with obesity and characterized by defective pancreatic insulin secretion and/or insulin resistance. Exercise training is an essential component of lifestyle modification and has been shown to ameliorate insulin resistance by reducing body fat mass and by enhancing skeletal muscle mitochondrial biogenesis and insulin-independent glucose uptake. Additionally, exercising stimulates the release of exerkines such as metabolites or cytokines, but also long non-coding RNA, microRNAs, cell-free DNA (cf-DNA), and extracellular vesicles (EVs), which contribute to inter-tissue communication. There is emerging evidence that EV number and content are altered in obesity and T2DM and may be involved in several metabolic processes, specifically either worsening or improving insulin resistance. This review summarizes the current knowledge on the metabolic effects of exercise training and on the potential role of humoral factors and EV as new biomarkers for early diagnosis and tailored treatment of T2DM.
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Affiliation(s)
- Lucia Mastrototaro
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Partner Düsseldorf, Neuherberg, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, Partner Düsseldorf, Neuherberg, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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7
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György B, Pálóczi K, Balbisi M, Turiák L, Drahos L, Visnovitz T, Koltai E, Radák Z. Effect of the 35 nm and 70 nm Size Exclusion Chromatography (SEC) Column and Plasma Storage Time on Separated Extracellular Vesicles. Curr Issues Mol Biol 2024; 46:4337-4357. [PMID: 38785532 PMCID: PMC11120626 DOI: 10.3390/cimb46050264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
The technical difficulty of separating extracellular vesicles (EVs) from plasma proteins in human blood presents a significant hurdle in EV research, particularly during nano ultra-high-performance liquid chromatography-tandem mass spectrometric (UHPLC-MS/MS) analysis, where detecting "vesicular" proteins among abundant plasma proteins is challenging. Standardisation is a pressing issue in EV research, prompting collaborative global efforts to address it. While the MISEV guidelines offer valuable recommendations, unanswered questions remain, particularly regarding sample storage. We compared size exclusion chromatography (SEC) columns with pore sizes of 35 nm and 70 nm to identify fractions with minimal contaminating proteins and the highest concentration of small EVs (sEVs). Following column selection, we explored potential differences in the quality and quantity of sEVs isolated from platelet-free plasma (PFP) after long-term storage at -80 °C (>2.5 years) compared to freshly drawn blood. Our methodologically rigorous study indicates that prolonged storage, under correct storage and processing conditions, does not compromise sEV quality. Both columns effectively isolated vesicles, with the 70 nm column exhibiting a higher abundance of "vesicular" proteins. We propose a relatively rapid and moderately efficient protocol for obtaining a comparatively pure sEV fraction from plasma, facilitating sEV processing in clinical trials.
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Affiliation(s)
- Bernadett György
- Research Centre for Molecular Exercise Science, Hungarian University of Sport Science, Alkotás u. 42-48, 1123 Budapest, Hungary; (B.G.); (E.K.)
| | - Krisztina Pálóczi
- Department of Genetics, Cell and Immunobiology, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (K.P.); (T.V.)
| | - Mirjam Balbisi
- Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (M.B.); (L.T.); (L.D.)
| | - Lilla Turiák
- Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (M.B.); (L.T.); (L.D.)
| | - László Drahos
- Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar Tudósok Körútja 2, 1117 Budapest, Hungary; (M.B.); (L.T.); (L.D.)
| | - Tamás Visnovitz
- Department of Genetics, Cell and Immunobiology, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (K.P.); (T.V.)
- Department of Plant Physiology and Molecular Plant Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary
| | - Erika Koltai
- Research Centre for Molecular Exercise Science, Hungarian University of Sport Science, Alkotás u. 42-48, 1123 Budapest, Hungary; (B.G.); (E.K.)
| | - Zsolt Radák
- Research Centre for Molecular Exercise Science, Hungarian University of Sport Science, Alkotás u. 42-48, 1123 Budapest, Hungary; (B.G.); (E.K.)
- Faculty of Sport Sciences, Waseda University, Tokorozawa 2-579-15, Japan
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8
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Paes Leme AF, Yokoo S, Normando AGC, Ormonde JVS, Domingues RR, Cruz FF, Silva PL, Souza BSF, Dos Santos CC, Castro-Faria-Neto H, Martins CM, Lopes-Pacheco M, Rocco PRM. Proteomics of serum-derived extracellular vesicles are associated with the severity and different clinical profiles of patients with COVID-19: An exploratory secondary analysis. Cytotherapy 2024; 26:444-455. [PMID: 38363248 DOI: 10.1016/j.jcyt.2024.02.001] [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: 11/12/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND AIMS Coronavirus disease 2019 (COVID-19) is characterized by a broad spectrum of clinical manifestations with the potential to progress to multiple organ dysfunction in severe cases. Extracellular vesicles (EVs) carry a range of biological cargoes, which may be used as biomarkers of disease state. METHODS An exploratory secondary analysis of the SARITA-2 and SARITA-1 datasets (randomized clinical trials on patients with mild and moderate/severe COVID-19) was performed. Serum-derived EVs were used for proteomic analysis to identify enriched biological processes and key proteins, thus providing insights into differences in disease severity. Serum-derived EVs were separated from patients with COVID-19 by size exclusion chromatography and nanoparticle tracking analysis was used to determine particle concentration and diameter. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed to identify and quantify protein signatures. Bioinformatics and multivariate statistical analysis were applied to distinguish candidate proteins associated with disease severity (mild versus moderate/severe COVID-19). RESULTS No differences were observed in terms of the concentration and diameter of enriched EVs between mild (n = 14) and moderate/severe (n = 30) COVID-19. A total of 414 proteins were found to be present in EVs, of which 360 were shared while 48 were uniquely present in severe/moderate compared to mild COVID-19. The main biological signatures in moderate/severe COVID-19 were associated with platelet degranulation, exocytosis, complement activation, immune effector activation, and humoral immune response. Von Willebrand factor, serum amyloid A-2 protein, histone H4 and H2A type 2-C, and fibrinogen β-chain were the most differentially expressed proteins between severity groups. CONCLUSION Exploratory proteomic analysis of serum-derived EVs from patients with COVID-19 detected key proteins related to immune response and activation of coagulation and complement pathways, which are associated with disease severity. Our data suggest that EV proteins may be relevant biomarkers of disease state and prognosis.
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Affiliation(s)
- Adriana F Paes Leme
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - Sami Yokoo
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - Ana Gabriela C Normando
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - João Vitor S Ormonde
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - Romenia Ramos Domingues
- Laboratório Nacional de Biociências - LNBio, Centro Nacional de Pesquisa em Energia e Materiais - CNPEM, Campinas, São Paulo, Brazil
| | - Fernanda F Cruz
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil; Rio de Janeiro Innovation Network in Nanosystems for Health-NanoSaúde, Research Support Foundation of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro L Silva
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil; Rio de Janeiro Innovation Network in Nanosystems for Health-NanoSaúde, Research Support Foundation of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno S F Souza
- Goncalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil; D'Or Institute for Research and Education (IDOR), Salvador, Bahia, Brazil; Center for Biotechnology and Cell Therapy, São Rafael Hospital, Salvador, Bahia, Brazil
| | - Claudia C Dos Santos
- The Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, Ontario, Canada; Institute of Medical Sciences and Interdepartmental Division of Critical Care, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Miquéias Lopes-Pacheco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Patricia R M Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil; Rio de Janeiro Innovation Network in Nanosystems for Health-NanoSaúde, Research Support Foundation of the State of Rio de Janeiro, Rio de Janeiro, Brazil.
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9
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Shahi S, Kang T, Fonseka P. Extracellular Vesicles in Pathophysiology: A Prudent Target That Requires Careful Consideration. Cells 2024; 13:754. [PMID: 38727289 PMCID: PMC11083420 DOI: 10.3390/cells13090754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Extracellular vesicles (EVs) are membrane-bound particles released by cells to perform multitudes of biological functions. Owing to their significant implications in diseases, the pathophysiological role of EVs continues to be extensively studied, leading research to neglect the need to explore their role in normal physiology. Despite this, many identified physiological functions of EVs, including, but not limited to, tissue repair, early development and aging, are attributed to their modulatory role in various signaling pathways via intercellular communication. EVs are widely perceived as a potential therapeutic strategy for better prognosis, primarily through utilization as a mode of delivery vehicle. Moreover, disease-associated EVs serve as candidates for the targeted inhibition by pharmacological or genetic means. However, these attempts are often accompanied by major challenges, such as off-target effects, which may result in adverse phenotypes. This renders the clinical efficacy of EVs elusive, indicating that further understanding of the specific role of EVs in physiology may enhance their utility. This review highlights the essential role of EVs in maintaining cellular homeostasis under different physiological settings, and also discusses the various aspects that may potentially hinder the robust utility of EV-based therapeutics.
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Affiliation(s)
| | | | - Pamali Fonseka
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; (S.S.); (T.K.)
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10
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Liu Y, Xiao S, Wang D, Qin C, Wei H, Li D. A review on separation and application of plant-derived exosome-like nanoparticles. J Sep Sci 2024; 47:e2300669. [PMID: 38651549 DOI: 10.1002/jssc.202300669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/25/2023] [Accepted: 01/04/2024] [Indexed: 04/25/2024]
Abstract
Exosomes-like nanoparticles (ELNs) (exosomes or extracellular vesicles) are vesicle-like bodies secreted by cells. Plant ELNs (PENs) are membrane vesicles secreted by plant cells, with a lipid bilayer as the basic skeleton, enclosing various active substances such as proteins and nucleic acids, which have many physiological and pathological functions. Recent studies have found that the PENs are widespread within different plant species and their biological functions are increasingly recognized. The effective separation method is also necessary for its function and application. Ultracentrifugation, sucrose density gradient ultracentrifugation, ultrafiltration, polymer-based precipitation methods, etc., are commonly used methods for plant exosome-like nanoparticle extraction. In recent years, emerging methods such as size exclusion chromatography, immunoaffinity capture-based technique, and microfluidic technology have shown advancements compared to traditional methods. The standardized separation process for PENs continues to evolve. In this review, we summarized the recent progress in the biogenesis, components, separation methods, and some functions of PENs. When the research on the separation method of PENs and their unique biological structure is further studied. A brand-new idea for the efficient separation and utilization of PENs can be provided in the future, which has a very broad prospect.
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Affiliation(s)
- Ying Liu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Siqiu Xiao
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Dianbing Wang
- Institute of Biophysics, Chinese Academy of Sciences, Research Center of Biomacromolecules, China Academy of Sciences, National Laboratory of Biomacromolecules, Beijing, China
| | - Chengyu Qin
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Hongling Wei
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Dewen Li
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, China
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11
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Chong MC, Shah AD, Schittenhelm RB, Silva A, James PF, Wu SSX, Howitt J. Acute exercise-induced release of innate immune proteins via small extracellular vesicles changes with aerobic fitness and age. Acta Physiol (Oxf) 2024; 240:e14095. [PMID: 38243724 DOI: 10.1111/apha.14095] [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: 06/13/2023] [Revised: 10/04/2023] [Accepted: 01/01/2024] [Indexed: 01/21/2024]
Abstract
AIM Physical exercise triggers the secretion of small extracellular vesicles (sEVs) into the circulation in humans, enabling signalling crosstalk between tissues. Exercise-derived EVs and their cargo have been proposed to mediate adaptations to exercise; however, our understanding of how exercise-derived EV protein cargo is modulated by factors such as aerobic fitness and age of an individual is currently unknown. Here, we examined the circulating sEV proteome following aerobic exercise in healthy males of different ages and aerobic fitness to understand exercise-induced EV response during the aging process. METHODS Twenty-eight healthy men completed a bout of 20-min cycling exercise at 70% estimated VO2peak . Small EVs were isolated from blood samples collected before and immediately after exercise, and then quantified using particle analysis and Western blotting. Small EV proteome was examined using quantitative proteomic analysis. RESULTS We identified a significant increase in 13 proteins in small plasma EVs following moderate-to-vigorous intensity exercise. We observed distinct changes in sEV proteome after exercise in young, mature, unfit, and fit individuals, highlighting the impact of aerobic fitness and age on sEV protein secretion. Functional enrichment and pathway analysis identified that the majority of the significantly altered sEV proteins are associated with the innate immune system, including proteins known to be damage-associated molecular patterns (DAMPs). CONCLUSION Together, our findings suggest that exercise-evoked acute stress can positively challenge the innate immune system through the release of signalling molecules such as DAMPs in sEVs, proposing a novel EV-based mechanism for moderate-to-vigorous intensity exercise in immune surveillance pathways.
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Affiliation(s)
- Mee Chee Chong
- School of Health Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Anup D Shah
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria, Australia
| | - Anabel Silva
- Exopharm Limited, Melbourne, Victoria, Australia
| | | | - Sam Shi Xuan Wu
- School of Health Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Jason Howitt
- School of Health Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Iverson Health Innovation Institute, Swinburne University of Technology, Hawthorn, Victoria, Australia
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12
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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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13
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Lattmann E, Räss L, Tognetti M, Gómez JMM, Lapaire V, Bruderer R, Reiter L, Feng Y, Steinmetz LM, Levesque MP. Size-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum. Cell Mol Life Sci 2024; 81:90. [PMID: 38353833 PMCID: PMC10867102 DOI: 10.1007/s00018-024-05137-y] [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: 04/23/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Extracellular vesicles (EVs) are important players in melanoma progression, but their use as clinical biomarkers has been limited by the difficulty of profiling blood-derived EV proteins with high depth of coverage, the requirement for large input amounts, and complex protocols. Here, we provide a streamlined and reproducible experimental workflow to identify plasma- and serum- derived EV proteins of healthy donors and melanoma patients using minimal amounts of sample input. SEC-DIA-MS couples size-exclusion chromatography to EV concentration and deep-proteomic profiling using data-independent acquisition. From as little as 200 µL of plasma per patient in a cohort of three healthy donors and six melanoma patients, we identified and quantified 2896 EV-associated proteins, achieving a 3.5-fold increase in depth compared to previously published melanoma studies. To compare the EV-proteome to unenriched blood, we employed an automated workflow to deplete the 14 most abundant proteins from plasma and serum and thereby approximately doubled protein group identifications versus native blood. The EV proteome diverged from corresponding unenriched plasma and serum, and unlike the latter, separated healthy donor and melanoma patient samples. Furthermore, known melanoma markers, such as MCAM, TNC, and TGFBI, were upregulated in melanoma EVs but not in depleted melanoma plasma, highlighting the specific information contained in EVs. Overall, EVs were significantly enriched in intact membrane proteins and proteins related to SNARE protein interactions and T-cell biology. Taken together, we demonstrated the increased sensitivity of an EV-based proteomic workflow that can be easily applied to larger melanoma cohorts and other indications.
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Affiliation(s)
- Evelyn Lattmann
- Department of Dermatology, University Hospital Zurich, University of Zurich, Schlieren, Switzerland
| | - Luca Räss
- Biognosys AG, Schlieren, Switzerland
| | | | - Julia M Martínez Gómez
- Department of Dermatology, University Hospital Zurich, University of Zurich, Schlieren, Switzerland
| | - Valérie Lapaire
- Department of Dermatology, University Hospital Zurich, University of Zurich, Schlieren, Switzerland
| | | | | | | | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Schlieren, Switzerland.
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14
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Kumar MA, Baba SK, Sadida HQ, Marzooqi SA, Jerobin J, Altemani FH, Algehainy N, Alanazi MA, Abou-Samra AB, Kumar R, Al-Shabeeb Akil AS, Macha MA, Mir R, Bhat AA. Extracellular vesicles as tools and targets in therapy for diseases. Signal Transduct Target Ther 2024; 9:27. [PMID: 38311623 PMCID: PMC10838959 DOI: 10.1038/s41392-024-01735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 02/06/2024] Open
Abstract
Extracellular vesicles (EVs) are nano-sized, membranous structures secreted into the extracellular space. They exhibit diverse sizes, contents, and surface markers and are ubiquitously released from cells under normal and pathological conditions. Human serum is a rich source of these EVs, though their isolation from serum proteins and non-EV lipid particles poses challenges. These vesicles transport various cellular components such as proteins, mRNAs, miRNAs, DNA, and lipids across distances, influencing numerous physiological and pathological events, including those within the tumor microenvironment (TME). Their pivotal roles in cellular communication make EVs promising candidates for therapeutic agents, drug delivery systems, and disease biomarkers. Especially in cancer diagnostics, EV detection can pave the way for early identification and offers potential as diagnostic biomarkers. Moreover, various EV subtypes are emerging as targeted drug delivery tools, highlighting their potential clinical significance. The need for non-invasive biomarkers to monitor biological processes for diagnostic and therapeutic purposes remains unfulfilled. Tapping into the unique composition of EVs could unlock advanced diagnostic and therapeutic avenues in the future. In this review, we discuss in detail the roles of EVs across various conditions, including cancers (encompassing head and neck, lung, gastric, breast, and hepatocellular carcinoma), neurodegenerative disorders, diabetes, viral infections, autoimmune and renal diseases, emphasizing the potential advancements in molecular diagnostics and drug delivery.
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Affiliation(s)
- Mudasir A Kumar
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Kashmir, 192122, India
| | - Sadaf K Baba
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Kashmir, 192122, India
| | - Hana Q Sadida
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Sara Al Marzooqi
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Jayakumar Jerobin
- Qatar Metabolic Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Faisal H Altemani
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Naseh Algehainy
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Mohammad A Alanazi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Abdul-Badi Abou-Samra
- Qatar Metabolic Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Kashmir, 192122, India
| | - Rashid Mir
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia.
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar.
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15
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Cervone DT, Moreno-Justicia R, Quesada JP, Deshmukh AS. Mass spectrometry-based proteomics approaches to interrogate skeletal muscle adaptations to exercise. Scand J Med Sci Sports 2024; 34:e14334. [PMID: 36973869 DOI: 10.1111/sms.14334] [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: 11/08/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 03/29/2023]
Abstract
Acute exercise and chronic exercise training elicit beneficial whole-body changes in physiology that ultimately depend on profound alterations to the dynamics of tissue-specific proteins. Since the work accomplished during exercise owes predominantly to skeletal muscle, it has received the majority of interest from exercise scientists that attempt to unravel adaptive mechanisms accounting for salutary metabolic effects and performance improvements that arise from training. Contemporary scientists are also beginning to use mass spectrometry-based proteomics, which is emerging as a powerful approach to interrogate the muscle protein signature in a more comprehensive manner. Collectively, these technologies facilitate the analysis of skeletal muscle protein dynamics from several viewpoints, including changes to intracellular proteins (expression proteomics), secreted proteins (secretomics), post-translational modifications as well as fiber-, cell-, and organelle-specific changes. This review aims to highlight recent literature that has leveraged new workflows and advances in mass spectrometry-based proteomics to further our understanding of training-related changes in skeletal muscle. We call attention to untapped areas in skeletal muscle proteomics research relating to exercise training and metabolism, as well as basic points of contention when applying mass spectrometry-based analyses, particularly in the study of human biology. We further encourage researchers to couple the hypothesis-generating and descriptive nature of omics data with functional analyses that propel our understanding of the complex adaptive responses in skeletal muscle that occur with acute and chronic exercise.
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Affiliation(s)
- Daniel T Cervone
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Roger Moreno-Justicia
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Júlia Prats Quesada
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Clinical Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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16
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Vallejo MC, Sarkar S, Elliott EC, Henry HR, Powell SM, Diaz Ludovico I, You Y, Huang F, Payne SH, Ramanadham S, Sims EK, Metz TO, Mirmira RG, Nakayasu ES. A proteomic meta-analysis refinement of plasma extracellular vesicles. Sci Data 2023; 10:837. [PMID: 38017024 PMCID: PMC10684639 DOI: 10.1038/s41597-023-02748-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Extracellular vesicles play major roles in cell-to-cell communication and are excellent biomarker candidates. However, studying plasma extracellular vesicles is challenging due to contaminants. Here, we performed a proteomics meta-analysis of public data to refine the plasma EV composition by separating EV proteins and contaminants into different clusters. We obtained two clusters with a total of 1717 proteins that were depleted of known contaminants and enriched in EV markers with independently validated 71% true-positive. These clusters had 133 clusters of differentiation (CD) antigens and were enriched with proteins from cell-to-cell communication and signaling. We compared our data with the proteins deposited in PeptideAtlas, making our refined EV protein list a resource for mechanistic and biomarker studies. As a use case example for this resource, we validated the type 1 diabetes biomarker proplatelet basic protein in EVs and showed that it regulates apoptosis of β cells and macrophages, two key players in the disease development. Our approach provides a refinement of the EV composition and a resource for the scientific community.
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Affiliation(s)
- Milene C Vallejo
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Emily C Elliott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Hayden R Henry
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Samantha M Powell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ivo Diaz Ludovico
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Fei Huang
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Sasanka Ramanadham
- Department of Cell, Developmental, and Integrative Biology, and Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Emily K Sims
- Department of Pediatrics, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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17
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McIlvenna LC, Whitham M. Exercise, healthy ageing, and the potential role of small extracellular vesicles. J Physiol 2023; 601:4937-4951. [PMID: 35388915 PMCID: PMC10952297 DOI: 10.1113/jp282468] [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: 11/30/2021] [Accepted: 03/29/2022] [Indexed: 11/08/2022] Open
Abstract
Extracellular vesicles (EVs) can be released from most cells in the body and act as intercellular messengers transferring information in their cargo to affect cellular function. A growing body of evidence suggests that a subset of EVs, referred to here as 'small extracellular vesicles' (sEVs), can accelerate or slow the processes of ageing and age-related diseases dependent on their molecular cargo and cellular origin. Continued exploration of the vast complexity of the sEV cargo aims to further characterise these systemic vehicles that may be targeted to ameliorate age-related pathologies. Marked progress in the development of mass spectrometry-based technologies means that it is now possible to characterise a significant proportion of the proteome of sEVs (surface and cargo) via unbiased proteomics. This information is vital for identifying biomarkers and the development of sEV-based therapeutics in the context of ageing. Although exercise and physical activity are prominent features in maintaining health in advancing years, the mechanisms responsible are unclear. A potential mechanism by which plasma sEVs released during exercise could influence ageing and senescence is via the increased delivery of cargo proteins that function as antioxidant enzymes or inhibitors of senescence. These have been observed to increase in sEVs following acute and chronic exercise, as identified via independent interrogation of high coverage, publicly available proteomic datasets. Establishing tropism and exchange of functionally active proteins by these processes represents a promising line of enquiry in implicating sEVs as biologically relevant mediators of the ageing process.
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Affiliation(s)
- Luke C. McIlvenna
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
| | - Martin Whitham
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
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18
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McIlvenna LC, Parker H, Seabright AP, Sale B, Anghileri G, Weaver SR, Lucas SJ, Whitham M. Single vesicle analysis reveals the release of tetraspanin positive extracellular vesicles into circulation with high intensity intermittent exercise. J Physiol 2023; 601:5093-5106. [PMID: 36855276 PMCID: PMC10953002 DOI: 10.1113/jp284047] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Small extracellular vesicles (sEVs) are released from all cell types and participate in the intercellular exchange of proteins, lipids, metabolites and nucleic acids. Proteomic, flow cytometry and nanoparticle tracking analyses suggest sEVs are released into circulation with exercise. However, interpretation of these data may be influenced by sources of bias introduced by different analytical approaches. Seven healthy participants carried out a high intensity intermittent training (HIIT) cycle protocol consisting of 4 × 30 s at a work-rate corresponding to 200% of individual max power (watts) interspersed by 4.5 min of active recovery. EDTA-treated blood was collected before and immediately after the final effort. Platelet-poor (PPP) and platelet-free (PFP) plasma was derived by one or two centrifugal spins at 2500 g, respectively (15 min, room temperature). Platelets were counted on an automated haemocytometer. Plasma samples were assessed with the Exoview R100 platform, which immobilises sEVs expressing common tetraspanin markers CD9, CD63, CD81 and CD41a on microfluidic chips and with the aid of fluorescence imaging, counts their abundance at a single sEV resolution, importantly, without a pre-isolation step. There was a lower number of platelets in the PFP than PPP, which was associated with a lower number of CD9, CD63 and CD41a positive sEVs. HIIT induced an increase in fluorescence counts in CD9, CD63 and CD81 positive sEVs in both PPP and PFP. These data support the concept that sEVs are released into circulation with exercise. Furthermore, platelet-free plasma is the preferred, representative analyte to study sEV dynamics and phenotype during exercise. KEY POINTS: Small extracellular vesicles (sEV) are nano-sized particles containing protein, metabolites, lipid and RNA that can be transferred from cell to cell. Previous findings implicate that sEVs are released into circulation with exhaustive, aerobic exercise, but since there is no gold standard method to isolate sEVs, these findings may be subject to bias introduced by different approaches. Here, we use a novel method to immobilise and image sEVs, at single-vesicle resolution, to show sEVs are released into circulation with high intensity intermittent exercise. Since platelet depletion of plasma results in a reduction in sEVs, platelet-free plasma is the preferred analyte to examine sEV dynamics and phenotype in the context of exercise.
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Affiliation(s)
- Luke C. McIlvenna
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
- Epigenetics & Cellular Senescence Group, Blizard Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Hannah‐Jade Parker
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
- MRC‐Versus Arthritis Centre for Musculoskeletal Ageing ResearchUniversity of BirminghamBirminghamUK
| | - Alex P. Seabright
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
| | - Benedict Sale
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
| | - Genevieve Anghileri
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
- School of Sport, Exercise and Health SciencesLoughborough UniversityLoughboroughUK
| | - Samuel R.C. Weaver
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
| | - Samuel J.E. Lucas
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
| | - Martin Whitham
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
- MRC‐Versus Arthritis Centre for Musculoskeletal Ageing ResearchUniversity of BirminghamBirminghamUK
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19
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Jaimes MSV, Liao C, Chen MM, Czosseck A, Lee T, Chou Y, Chen Y, Lin S, Lai JJ, Lundy DJ. Assessment of circulating extracellular vesicles from calorie-restricted mice and humans in ischaemic injury models. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e86. [PMID: 38938283 PMCID: PMC11080834 DOI: 10.1002/jex2.86] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/23/2023] [Accepted: 04/11/2023] [Indexed: 06/29/2024]
Abstract
Calorie restriction (CR) and fasting affect lifespan, disease susceptibility and response to acute injury across multiple animal models, including ischaemic injuries such as myocardial infarction or kidney hypoxia. The cargo and function of circulating extracellular vesicles (EV) respond to changes in host physiology, including exercise, injury, and other interventions. Thus, we hypothesised that EVs induced following CR may reflect some of the beneficial properties of CR itself. In a pilot study, EVs were isolated from mice following 21 days of 30 % CR, and from eight human donors after 72 h water-only fasting. EV size, concentration and morphology were profiled by NTA, western blot and cryoEM, and their function was assessed using multiple assays related to ischaemic diseases. We found that EVs from post-fasting samples better protected cardiac cells from hypoxia/reperfusion (H/R) injury compared to pre-fasting EVs. However, there was no difference when used to treat H/R-injured kidney epithelial cells. Post-fasting derived EVs slowed the rate of fibroblast migration and slightly reduced macrophage inflammatory gene expression compared to pre-fasting derived EVs. Lastly, we compared miRNA cargos of pre- and post-fasting human serum EVs and found significant changes in a small number of miRNAs. We conclude that fasting appears to influence EV cargo and function, with varied effects worthy of further exploration.
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Affiliation(s)
- Manuel S. V. Jaimes
- Graduate Institute of Biomedical Materials & Tissue EngineeringTaipei Medical UniversityTaipeiTaiwan
| | - Chia‐Te Liao
- Division of NephrologyDepartment of Internal MedicineShuang Ho HospitalTaipei Medical UniversityNew TaipeiTaiwan
- Division of NephrologyDepartment of Internal MedicineSchool of MedicineCollege of MedicineTaipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Urology and Kidney (TMU‐RCUK)Taipei Medical UniversityTaipeiTaiwan
| | - Max M. Chen
- Graduate Institute of Biomedical Materials & Tissue EngineeringTaipei Medical UniversityTaipeiTaiwan
| | - Andreas Czosseck
- Graduate Institute of Biomedical Materials & Tissue EngineeringTaipei Medical UniversityTaipeiTaiwan
| | - Tsung‐Lin Lee
- Division of NephrologyDepartment of Internal MedicineShuang Ho HospitalTaipei Medical UniversityNew TaipeiTaiwan
| | - Yu‐Hsiang Chou
- Division of NephrologyDepartment of Internal MedicineNational Taiwan University HospitalCollege of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Yung‐Ming Chen
- Division of NephrologyDepartment of Internal MedicineNational Taiwan University HospitalCollege of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Shuei‐Liong Lin
- Division of NephrologyDepartment of Internal MedicineNational Taiwan University HospitalCollege of MedicineNational Taiwan UniversityTaipeiTaiwan
- Graduate Institute of PhysiologyCollege of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - James J. Lai
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
- Department of Materials Science and EngineeringNational Taiwan University of Science and TechnologyTaipeiTaiwan
| | - David J. Lundy
- Graduate Institute of Biomedical Materials & Tissue EngineeringTaipei Medical UniversityTaipeiTaiwan
- International PhD Program in Biomedical EngineeringTaipei Medical UniversityTaipeiTaiwan
- Center for Cell TherapyTaipei Medical University HospitalTaipeiTaiwan
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20
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Ayilam Ramachandran R, Lemoff A, Robertson DM. Pseudomonas aeruginosa-Derived Extracellular Vesicles Modulate Corneal Inflammation: Role in Microbial Keratitis? Infect Immun 2023; 91:e0003623. [PMID: 36995231 PMCID: PMC10112165 DOI: 10.1128/iai.00036-23] [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: 01/21/2023] [Accepted: 02/16/2023] [Indexed: 03/31/2023] Open
Abstract
Pseudomonas aeruginosa keratitis occurs following trauma, in immunocompromised patients, and in otherwise healthy contact lens wearers. Characterized by a light-blocking infiltrate, P. aeruginosa keratitis is the most serious complication associated with contact lens wear and, in severe cases, can lead to vision loss. Bacterial extracellular vesicles (B EVs) are membrane-enclosed nanometer-scale particles secreted from bacteria and are packed with bioactive molecules. B EVs have been shown to mediate biological functions that regulate host pathogenic responses. In the present study, we isolated P. aeruginosa-derived EVs using size exclusion chromatography and compared the proteomic compositions and functional activities of P. aeruginosa-derived EVs and P. aeruginosa-derived free protein (FP) on corneal epithelial cells and neutrophils. Importantly, P. aeruginosa-derived EVs and FP exhibited unique protein profiles, with EVs being enriched in P. aeruginosa virulence proteins. P. aeruginosa-derived EVs promoted corneal epithelial cell secretion of interleukin-6 (IL-6) and IL-8, whereas these cytokines were not upregulated following treatment with FP. In contrast, FP had a negative effect on the host inflammatory response and impaired neutrophil killing. Both P. aeruginosa-derived EVs and FP promoted intracellular bacterial survival in corneal epithelial cells. Collectively, these data suggest that P. aeruginosa-derived EVs and FP may play a critical role in the pathogenesis of corneal infection by interfering with host innate immune defense mechanisms.
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Affiliation(s)
| | - Andrew Lemoff
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, Texas, USA
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21
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Aibaidula A(Z, Fain CE, Garcia LC, Wier A, Bouchal SM, Bauman MM, Jung MY, Sarkaria JN, Johnson AJ, Parney IF. Spectral flow cytometry identifies distinct nonneoplastic plasma extracellular vesicle phenotype in glioblastoma patients. Neurooncol Adv 2023; 5:vdad082. [PMID: 37638345 PMCID: PMC10457026 DOI: 10.1093/noajnl/vdad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Background Glioblastoma (GBM) is the most common malignant brain tumor and has a poor prognosis. Imaging findings at diagnosis and in response to treatment are nonspecific. Developing noninvasive assays to augment imaging would be helpful. Plasma extracellular vesicles (EVs) are a promising biomarker source for this. Here, we develop spectral flow cytometry techniques that demonstrate differences in bulk plasma EV phenotype between GBM patients and normal donors that could serve as the basis of a liquid biopsy. Methods Plasma EVs were stained for EV-associated tetraspanins (CD9/CD63/CD81), markers indicating cell of origin (CD11b/CD31/CD41a/CD45), and actin/phalloidin (to exclude cell debris). EVs were analyzed using spectral flow cytometry. Multiparametric analysis using t-distributed stochastic neighbor embedding (t-SNE) and self-organizing maps on flow cytometry data (FlowSOM) was performed comparing GBM and normal donor (ND) plasma EVs. Results Size exclusion chromatography plus spectral-based flow cytometer threshold settings enriched plasma EVs while minimizing background noise. GBM patients had increased CD9+, CD63+, CD81+, and myeloid-derived (CD11b+) EVs. Multiparametric analysis demonstrated distinct surface marker expression profiles in GBM plasma EVs compared to ND EVs. Fifteen plasma EV sub-populations differing in size and surface marker expression were identified, six enriched in GBM patients and two in normal donors. Conclusions Multiparametric analysis demonstrates that GBM patients have a distinct nonneoplastic plasma EV phenotype compared to ND. This simple rapid analysis can be performed without purifying tumor EVs and may serve as the basis of a liquid biopsy.
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Affiliation(s)
- Abudumijiti (Zack) Aibaidula
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Cori E Fain
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Luz Cumba Garcia
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Annelise Wier
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Samantha M Bouchal
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Megan M Bauman
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Mi-Yeon Jung
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Aaron J Johnson
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Ian F Parney
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
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22
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Catitti G, De Bellis D, Vespa S, Simeone P, Canonico B, Lanuti P. Extracellular Vesicles as Players in the Anti-Inflammatory Inter-Cellular Crosstalk Induced by Exercise Training. Int J Mol Sci 2022; 23:14098. [PMID: 36430575 PMCID: PMC9697937 DOI: 10.3390/ijms232214098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 07/28/2023] Open
Abstract
Extracellular Vesicles (EVs) are circulating particles surrounded by a plasma membrane carrying a cargo consisting of proteins, lipids, RNAs, and DNA fragments, stemming from the cells from which they originated. EV factors (i.e., miRNAs) play relevant roles in intercellular crosstalk, both locally and systemically. As EVs increasingly gained attention as potential carriers for targeted genes, the study of EV effects on the host immune response became more relevant. It has been demonstrated that EVs regulate the host immune response, executing both pro- and anti-inflammatory functions. It is also known that physical exercise triggers anti-inflammatory effects. This review underlines the role of circulating EVs as players in the anti-inflammatory events associated with the regulation of the host's immune response to physical exercise.
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Affiliation(s)
- Giulia Catitti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (G.C.); (D.D.B.); (S.V.); (P.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Domenico De Bellis
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (G.C.); (D.D.B.); (S.V.); (P.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Simone Vespa
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (G.C.); (D.D.B.); (S.V.); (P.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Pasquale Simeone
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (G.C.); (D.D.B.); (S.V.); (P.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Barbara Canonico
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy;
| | - Paola Lanuti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (G.C.); (D.D.B.); (S.V.); (P.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
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23
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Newman LA, Useckaite Z, Rowland A. Addressing MISEV guidance using targeted LC-MS/MS: A method for the detection and quantification of extracellular vesicle-enriched and contaminant protein markers from blood. JOURNAL OF EXTRACELLULAR BIOLOGY 2022; 1:e56. [PMID: 38938773 PMCID: PMC11080780 DOI: 10.1002/jex2.56] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/03/2022] [Accepted: 08/14/2022] [Indexed: 06/29/2024]
Abstract
Extracellular vesicles (EVs) are membrane-bound nanosized particles released by cells into bodily fluids containing an array of molecular cargo. Several characteristics, including stability and accessibility in biofluids such as blood and urine, make EVs and associated cargo attractive biomarkers and therapeutic tools. To promote robust characterisation of EV isolates, the minimal requirements for the study of extracellular vesicles (MISEV) guidelines recommend the analysis of proteins in EV samples, including positive EV-associated markers and negative contaminant markers based on commonly co-isolated components of the starting material. Western blot is conventionally used to address the guidelines; however, this approach is limited in terms of quantitation and throughput and requires larger volumes than typically available for patient samples. The increasing application of EVs as liquid biopsy in clinical contexts requires a high-throughput multiplexed approach for analysis of protein markers from small volumes of starting material. Here, we document the development and validation of a targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) assay for the quantification of markers associated with EVs and non-vesicle contaminants from human blood samples. The assay was highly sensitive, requiring only a fraction of the sample consumed for immunoblots, fully quantitative and high throughput. Application of the assay to EVs isolated by size exclusion chromatography (SEC) and precipitation revealed differences in yield, purity and recovery of subpopulations.
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Affiliation(s)
- Lauren A. Newman
- College of Medicine and Public HealthFlinders UniversityAdelaideSouth Australia
| | - Zivile Useckaite
- College of Medicine and Public HealthFlinders UniversityAdelaideSouth Australia
| | - Andrew Rowland
- College of Medicine and Public HealthFlinders UniversityAdelaideSouth Australia
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24
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Słomka A, Wang B, Mocan T, Horhat A, Willms AG, Schmidt-Wolf IGH, Strassburg CP, Gonzalez-Carmona MA, Lukacs-Kornek V, Kornek MT. Extracellular Vesicles and Circulating Tumour Cells - complementary liquid biopsies or standalone concepts? Theranostics 2022; 12:5836-5855. [PMID: 35966579 PMCID: PMC9373826 DOI: 10.7150/thno.73400] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/06/2022] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsies do promise a lot, but are they keeping it? In the past decade, additional novel biomarkers qualified to be called like that, of which, some took necessary hurdles resulting in FDA approval and clinical use. Some others are since a while around, well known and were once regarded to be a game changer in cancer diagnosis or cancer screening. But, during their clinical use limitations were observed from statistical significance and questions raised regarding their robustness, that eventually led to be dropped from associated clinical guidelines for certain applications including cancer diagnosis. The purpose of this review isn't to give a broad overview of all current liquid biopsy as biomarkers, weight them and promise a brighter future in cancer prevention, but rather to take a deeper look on two of those who do qualify to be called liquid biopsies now or then. These two are probably of greatest interest conceptually and methodically, and likely have the highest chances to be in clinical use soon, with a portfolio extension over their original conceptual usage. We aim to dig deeper beyond cancer diagnosis or cancer screening. Actually, we aim to review in depth extracellular vesicles (EVs) and compare with circulating tumour cells (CTCs). The latter methodology is partially FDA approved and in clinical use. We will lay out similarities as taking advantage of surface antigens on EVs and CTCs in case of characterization and quantification. But drawing readers' attention to downstream application based on capture/isolation methodology and simply on their overall nature, here apparently being living material eventually recoverable as CTCs are vs. dead material with transient effects on recipient cell as in case of EVs. All this we try to bring in perspective, compare and conclude towards which future direction we are aiming for, or should aim for. Do we announce a winner between CTCs vs EVs? No, but we provide good reasons to intensify research on them.
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Affiliation(s)
- Artur Słomka
- Department of Pathophysiology, Nicolaus Copernicus University in Toruń, Ludwik Rydygier Collegium Medicum in Bydgoszcz, 85-067 Bydgoszcz, Poland
| | - Bingduo Wang
- Department of Internal Medicine I, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany.,Institute of Molecular Medicine & Experimental Immunology, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany
| | - Tudor Mocan
- Octavian Fodor Institute for Gastroenterology and Hepatology, Iuliu Haţieganu, University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania
| | - Adelina Horhat
- Octavian Fodor Institute for Gastroenterology and Hepatology, Iuliu Haţieganu, University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania
| | - Arnulf G Willms
- Institute of Molecular Medicine & Experimental Immunology, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany.,Department of General, Visceral and Vascular Surgery, German Armed Forces Hospital Hamburg, 22049 Hamburg, Germany
| | - Ingo G H Schmidt-Wolf
- Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany
| | - Christian P Strassburg
- Department of Internal Medicine I, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany
| | - Maria A Gonzalez-Carmona
- Department of Internal Medicine I, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany
| | - Veronika Lukacs-Kornek
- Institute of Molecular Medicine & Experimental Immunology, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany
| | - Miroslaw T Kornek
- Department of Internal Medicine I, University Hospital Bonn of the Rheinische Friedrich-Wilhelms-University, 53127 Bonn, Germany
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25
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Identification of Target Proteins Involved in Cochlear Hair Cell Progenitor Cytotoxicity following Gentamicin Exposure. J Clin Med 2022; 11:jcm11144072. [PMID: 35887836 PMCID: PMC9319054 DOI: 10.3390/jcm11144072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Given the non-labile, terminal differentiation of inner-ear sensory cells, preserving their function is critical since sensory cell damage results in irreversible hearing loss. Gentamicin-induced cytotoxicity is one of the major causes of sensory cell damage and consequent sensorineural hearing loss. However, the precise molecular mechanisms and target proteins involved in ototoxicity are still unknown. The objective of the present study was to identify target proteins involved in gentamicin-induced cytotoxicity to better characterize the molecular pathways involved in sensory cell damage following ototoxic drug administration using House Ear Institute-Organ of Corti 1 (HEI-OC1) cells and high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). We identified several unique proteins involved in gentamicin-induced cytotoxicity, expression of which were further confirmed using confocal microscopy. Further investigation of these pathways can inform the design and discovery of novel treatment modalities to prevent sensory cell damage and preserve their function.
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26
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A Comparison of Blood Plasma Small Extracellular Vesicle Enrichment Strategies for Proteomic Analysis. Proteomes 2022; 10:proteomes10020019. [PMID: 35736799 PMCID: PMC9229025 DOI: 10.3390/proteomes10020019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
Proteomic analysis of small extracellular vesicles (sEVs) poses a significant challenge. A ‘gold-standard’ method for plasma sEV enrichment for downstream proteomic analysis is yet to be established. Methods were evaluated for their capacity to successfully isolate and enrich sEVs from plasma, minimise the presence of highly abundant plasma proteins, and result in the optimum representation of sEV proteins by liquid chromatography tandem mass spectrometry. Plasma from four cattle (Bos taurus) of similar physical attributes and genetics were used. Three methods of sEV enrichment were utilised: ultracentrifugation (UC), size-exclusion chromatography (SEC), and ultrafiltration (UF). These methods were combined to create four groups for methodological evaluation: UC + SEC, UC + SEC + UF, SEC + UC and SEC + UF. The UC + SEC method yielded the highest number of protein identifications (IDs). The SEC + UC method reduced plasma protein IDs compared to the other methods, but also resulted in the lowest number of protein IDs overall. The UC + SEC + UF method decreased sEV protein ID, particle number, mean and mode particle size, particle yield, and did not improve purity compared to the UC + SEC method. In this study, the UC + SEC method was the best method for sEV protein ID, purity, and overall particle yield. Our data suggest that the method and sequence of sEV enrichment strategy impacts protein ID, which may influence the outcome of biomarker discovery studies.
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27
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Chow LS, Gerszten RE, Taylor JM, Pedersen BK, van Praag H, Trappe S, Febbraio MA, Galis ZS, Gao Y, Haus JM, Lanza IR, Lavie CJ, Lee CH, Lucia A, Moro C, Pandey A, Robbins JM, Stanford KI, Thackray AE, Villeda S, Watt MJ, Xia A, Zierath JR, Goodpaster BH, Snyder MP. Exerkines in health, resilience and disease. Nat Rev Endocrinol 2022; 18:273-289. [PMID: 35304603 PMCID: PMC9554896 DOI: 10.1038/s41574-022-00641-2] [Citation(s) in RCA: 281] [Impact Index Per Article: 140.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/27/2022] [Indexed: 12/16/2022]
Abstract
The health benefits of exercise are well-recognized and are observed across multiple organ systems. These beneficial effects enhance overall resilience, healthspan and longevity. The molecular mechanisms that underlie the beneficial effects of exercise, however, remain poorly understood. Since the discovery in 2000 that muscle contraction releases IL-6, the number of exercise-associated signalling molecules that have been identified has multiplied. Exerkines are defined as signalling moieties released in response to acute and/or chronic exercise, which exert their effects through endocrine, paracrine and/or autocrine pathways. A multitude of organs, cells and tissues release these factors, including skeletal muscle (myokines), the heart (cardiokines), liver (hepatokines), white adipose tissue (adipokines), brown adipose tissue (baptokines) and neurons (neurokines). Exerkines have potential roles in improving cardiovascular, metabolic, immune and neurological health. As such, exerkines have potential for the treatment of cardiovascular disease, type 2 diabetes mellitus and obesity, and possibly in the facilitation of healthy ageing. This Review summarizes the importance and current state of exerkine research, prevailing challenges and future directions.
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Affiliation(s)
- Lisa S Chow
- Division of Diabetes Endocrinology and Metabolism, University of Minnesota, Minneapolis, MN, USA.
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Joan M Taylor
- Department of Pathology, McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Bente K Pedersen
- Centre of Inflammation and Metabolism/Centre for PA Research (CIM/CFAS), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Henriette van Praag
- Stiles-Nicholson Brain institute and Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, USA
| | - Scott Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN, USA
| | - Mark A Febbraio
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Zorina S Galis
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yunling Gao
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacob M Haus
- School of Kinesiology, University of Michigan, Ann Arbor, MI, USA
| | - Ian R Lanza
- Division of Endocrinology, Nutrition, and Metabolism, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Carl J Lavie
- Division of Cardiovascular Diseases, John Ochsner Heart and Vascular Institute, Ochsner Clinical School-the University of Queensland School of Medicine, New Orleans, LA, USA
| | - Chih-Hao Lee
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alejandro Lucia
- Faculty of Sport Sciences, Universidad Europea de Madrid, Madrid, Spain
- Research Institute Hospital 12 de Octubre ('imas12'), Madrid, Spain
- CIBER en Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Cedric Moro
- Institute of Metabolic and Cardiovascular Diseases, Team MetaDiab, Inserm UMR1297, Toulouse, France
- Toulouse III University-Paul Sabatier (UPS), Toulouse, France
| | - Ambarish Pandey
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeremy M Robbins
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kristin I Stanford
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Alice E Thackray
- National Centre for Sport and Exercise Medicine, School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Saul Villeda
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Matthew J Watt
- Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Victoria, Australia
| | - Ashley Xia
- Division of Diabetes, Endocrinology, & Metabolic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juleen R Zierath
- Department of Molecular Medicine and Surgery, Section for Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
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28
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Northrop-Albrecht EJ, Taylor WR, Huang BQ, Kisiel JB, Lucien F. Assessment of extracellular vesicle isolation methods from human stool supernatant. J Extracell Vesicles 2022; 11:e12208. [PMID: 35383410 PMCID: PMC8980777 DOI: 10.1002/jev2.12208] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/22/2022] [Accepted: 03/16/2022] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are of growing interest due to their potential diagnostic, disease surveillance, and therapeutic applications. While several studies have evaluated EV isolation methods in various biofluids, there are few if any data on these techniques when applied to stool. The latter is an ideal biospecimen for studying EVs and colorectal cancer (CRC) because the release of tumour markers by luminal exfoliation into stool occurs earlier than vascular invasion. Since EV release is a conserved mechanism, bacteria in stool contribute to the overall EV population. In this study, we assessed five EV separation methods (ultracentrifugation [UC], precipitation [EQ‐O, EQ‐TC], size exclusion chromatography [SEC], and ultrafiltration [UF]) for total recovery, reproducibility, purity, RNA composition, and protein expression in stool supernatant. CD63, TSG101, and ompA proteins were present in EV fractions from all methods except UC. Human (18s) and bacterial (16s) rRNA was detected in stool EV preparations. Enzymatic treatment prior to extraction is necessary to avoid non‐vesicular RNA contamination. Ultrafiltration had the highest recovery, RNA, and protein yield. After assessing purity further, SEC was the isolation method of choice. These findings serve as the groundwork for future studies that use high throughput omics technologies to investigate the potential of stool‐derived EVs as a source for novel biomarkers for early CRC detection.
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Affiliation(s)
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bing Q Huang
- Microscopy and Cell Analysis Core, Mayo Clinic, Rochester, Minnesota, USA
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Fabrice Lucien
- Department of Urology, Mayo Clinic, Rochester, Minnesota, USA
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