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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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2
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Wang Z, Zhou X, Kong Q, He H, Sun J, Qiu W, Zhang L, Yang M. Extracellular Vesicle Preparation and Analysis: A State-of-the-Art Review. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401069. [PMID: 38874129 DOI: 10.1002/advs.202401069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/11/2024] [Indexed: 06/15/2024]
Abstract
In recent decades, research on Extracellular Vesicles (EVs) has gained prominence in the life sciences due to their critical roles in both health and disease states, offering promising applications in disease diagnosis, drug delivery, and therapy. However, their inherent heterogeneity and complex origins pose significant challenges to their preparation, analysis, and subsequent clinical application. This review is structured to provide an overview of the biogenesis, composition, and various sources of EVs, thereby laying the groundwork for a detailed discussion of contemporary techniques for their preparation and analysis. Particular focus is given to state-of-the-art technologies that employ both microfluidic and non-microfluidic platforms for EV processing. Furthermore, this discourse extends into innovative approaches that incorporate artificial intelligence and cutting-edge electrochemical sensors, with a particular emphasis on single EV analysis. This review proposes current challenges and outlines prospective avenues for future research. The objective is to motivate researchers to innovate and expand methods for the preparation and analysis of EVs, fully unlocking their biomedical potential.
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Affiliation(s)
- Zesheng Wang
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Xiaoyu Zhou
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Qinglong Kong
- The Second Department of Thoracic Surgery, Dalian Municipal Central Hospital, Dalian, 116033, P. R. China
| | - Huimin He
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Jiayu Sun
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Wenting Qiu
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Liang Zhang
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Mengsu Yang
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
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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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Singhto N, Pongphitcha P, Jinawath N, Hongeng S, Chutipongtanate S. Extracellular Vesicles for Childhood Cancer Liquid Biopsy. Cancers (Basel) 2024; 16:1681. [PMID: 38730633 PMCID: PMC11083250 DOI: 10.3390/cancers16091681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Liquid biopsy involves the utilization of minimally invasive or noninvasive techniques to detect biomarkers in biofluids for disease diagnosis, monitoring, or guiding treatments. This approach is promising for the early diagnosis of childhood cancer, especially for brain tumors, where tissue biopsies are more challenging and cause late detection. Extracellular vesicles offer several characteristics that make them ideal resources for childhood cancer liquid biopsy. Extracellular vesicles are nanosized particles, primarily secreted by all cell types into body fluids such as blood and urine, and contain molecular cargos, i.e., lipids, proteins, and nucleic acids of original cells. Notably, the lipid bilayer-enclosed structure of extracellular vesicles protects their cargos from enzymatic degradation in the extracellular milieu. Proteins and nucleic acids of extracellular vesicles represent genetic alterations and molecular profiles of childhood cancer, thus serving as promising resources for precision medicine in cancer diagnosis, treatment monitoring, and prognosis prediction. This review evaluates the recent progress of extracellular vesicles as a liquid biopsy platform for various types of childhood cancer, discusses the mechanistic roles of molecular cargos in carcinogenesis and metastasis, and provides perspectives on extracellular vesicle-guided therapeutic intervention. Extracellular vesicle-based liquid biopsy for childhood cancer may ultimately contribute to improving patient outcomes.
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Affiliation(s)
- Nilubon Singhto
- Ramathibodi Comprehensive Cancer Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Pongpak Pongphitcha
- Bangkok Child Health Center, Bangkok Hospital Headquarters, Bangkok 10130, Thailand;
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan 10540, Thailand
- Integrative Computational Biosciences Center, Mahidol University, Nakon Pathom 73170, Thailand
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Somchai Chutipongtanate
- MILCH and Novel Therapeutics Laboratory, Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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Bai HH, Wang XF, Zhang BY, Liu W. A comparison of size exclusion chromatography-based tandem strategies for plasma exosome enrichment and proteomic analysis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:6245-6251. [PMID: 37955202 DOI: 10.1039/d3ay01704d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Proteomic analysis of exosomes from human plasma faces a tremendous challenge mainly due to the low abundance of the exosome itself and the complexity of the plasma matrix. Therefore, enrichment of exosomes from human plasma is an essential and indispensable step for large scale and in depth proteomic analysis. Size exclusion chromatography (SEC) is one of the most extensively used methods for exosome isolation from human plasma and many SEC-based tandem methods were established in order to increase the purity of the enriched exosomes and thus the accuracy of the proteomic analysis. To compare the advantages and disadvantages of the different isolation methods and subsequently to promote the establishment of a standardized method for plasma proteomic research, the capacities of the direct SEC method, the combination of SEC with ultracentrifugation (SEC-UC), ultrafiltration (SEC-UF), and titanium dioxide microspheres (SEC-TiO2) were systematically evaluated for exosome isolation from human plasma and thus proteomic analysis. The results demonstrated that the SEC-based tandem methods were superior to the direct SEC method in the purity of exosomes isolated from human plasma. Additionally, the SEC-UC method possessed the highest number of the total identified proteins and the overlapped proteins with the top 100 exosome markers in comparison with the other methods. The SEC-TiO2 method displayed the biggest capacity for plasma protein deleting. We expect that the research will have more beneficial values in the field of exosome research.
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Affiliation(s)
- H H Bai
- Department of Pharmacy, Beijing YouAn Hospital, Capital Medical University, Beijing 100069, PR China.
| | - X F Wang
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, PR China
| | - B Y Zhang
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, PR China
| | - W Liu
- Department of Pharmacy, Beijing YouAn Hospital, Capital Medical University, Beijing 100069, PR China.
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6
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Turner N, Abeysinghe P, Flay H, Meier S, Sadowski P, Mitchell MD. SWATH-MS Analysis of Blood Plasma and Circulating Small Extracellular Vesicles Enables Detection of Putative Protein Biomarkers of Fertility in Young and Aged Dairy Cows. J Proteome Res 2023; 22:3580-3595. [PMID: 37830897 DOI: 10.1021/acs.jproteome.3c00406] [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] [Indexed: 10/14/2023]
Abstract
The development of biomarkers of fertility could provide benefits for the genetic improvement of dairy cows. Circulating small extracellular vesicles (sEVs) show promise as diagnostic or prognostic markers since their cargo reflects the metabolic state of the cell of origin; thus, they mirror the physiological status of the host. Here, we employed data-independent acquisition mass spectrometry to survey the plasma and plasma sEV proteomes of two different cohorts of Young (Peripubertal; n = 30) and Aged (Primiparous; n = 20) dairy cows (Bos taurus) of high- and low-genetic merit of fertility and known pregnancy outcomes (ProteomeXchange data set identifier PXD042891). We established predictive models of fertility status with an area under the curve of 0.97 (sEV; p value = 3.302e-07) and 0.95 (plasma; p value = 6.405e-08). Biomarker candidates unique to high-fertility Young cattle had a sensitivity of 0.77 and specificity of 0.67 (*p = 0.0287). Low-fertility biomarker candidates uniquely identified in sEVs from Young and Aged cattle had a sensitivity and specificity of 0.69 and 1.0, respectively (***p = 0.0005). Our bioinformatics pipeline enabled quantification of plasma and circulating sEV proteins associated with fertility phenotype. Further investigations are warranted to validate this research in a larger population, which may lead to improved classification of fertility status in cattle.
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Affiliation(s)
- Natalie Turner
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Pevindu Abeysinghe
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Holly Flay
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Susanne Meier
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), QUT, Gardens Point Campus, 2 George Street, Brisbane City, Queensland 4000, Australia
| | - Murray D Mitchell
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
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Turner NP, Abeysinghe P, Sadowski P, Mitchell MD. Omics Analysis of Extracellular Vesicles Recovered from Infant Formula Products and Milk: Towards Personalized Infant Nutrition. Mol Nutr Food Res 2023; 67:e2300404. [PMID: 37562982 DOI: 10.1002/mnfr.202300404] [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: 07/26/2023] [Indexed: 08/12/2023]
Abstract
SCOPE Milk and milk products such as infant formula (IF) play a fundamental role in serving the nutritional needs of the developing infant. Extracellular vesicles (EVs) in human (HM) and cow milk (CM) contain molecular cargo such as proteins and micro(mi)RNAs that serve as functional messengers between cells and may be of importance to infant health. Most IF is derived from a CM protein base, however differences between HM and CM EV molecular cargo have not been extensively studied. METHODS AND RESULTS This study develops a pipeline using advanced proteomics and transcriptomics to enable cross-species comparison of milk and IF EVs. The number of nanoparticles per mL of IF is significantly reduced compared to unprocessed CM. 130 proteins and 514 miRNAs are differentially abundant between HM and CM EVs. While 90% of CM EV miRNAs are also identified in IF EVs, only 20% of CM EV proteins are identified in IF EVs. CONCLUSIONS This workflow identifies key species-specific differences that can be used to optimize IF recipes and enhance infant nutrition. Improved preservation of EV functional molecular cargo in IF products is of critical importance to retaining molecular drivers of good health and should be the focus of future investigations.
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Affiliation(s)
- Natalie P Turner
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD, 4101, Australia
| | - Pevindu Abeysinghe
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD, 4101, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), QUT, Gardens Point Campus, 2 George Street, Brisbane City, QLD, 4000, Australia
| | - Murray D Mitchell
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD, 4101, Australia
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Fan S, Poetsch A. Proteomic Research of Extracellular Vesicles in Clinical Biofluid. Proteomes 2023; 11:proteomes11020018. [PMID: 37218923 DOI: 10.3390/proteomes11020018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Extracellular vesicles (EVs), the lipid bilayer membranous structures of particles, are produced and released from almost all cells, including eukaryotes and prokaryotes. The versatility of EVs has been investigated in various pathologies, including development, coagulation, inflammation, immune response modulation, and cell-cell communication. Proteomics technologies have revolutionized EV studies by enabling high-throughput analysis of their biomolecules to deliver comprehensive identification and quantification with rich structural information (PTMs, proteoforms). Extensive research has highlighted variations in EV cargo depending on vesicle size, origin, disease, and other features. This fact has sparked activities to use EVs for diagnosis and treatment to ultimately achieve clinical translation with recent endeavors summarized and critically reviewed in this publication. Notably, successful application and translation require a constant improvement of methods for sample preparation and analysis and their standardization, both of which are areas of active research. This review summarizes the characteristics, isolation, and identification approaches for EVs and the recent advances in EVs for clinical biofluid analysis to gain novel knowledge by employing proteomics. In addition, the current and predicted future challenges and technical barriers are also reviewed and discussed.
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Affiliation(s)
- Shipan Fan
- School of Basic Medical Sciences, Nanchang University, Nanchang 330021, China
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang 330021, China
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Reymond S, Gruaz L, Sanchez JC. Depletion of abundant plasma proteins for extracellular vesicle proteome characterization: benefits and pitfalls. Anal Bioanal Chem 2023:10.1007/s00216-023-04684-w. [PMID: 37069444 DOI: 10.1007/s00216-023-04684-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/01/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023]
Abstract
Blood extracellular vesicles (EVs) play essential roles in cell-cell communication and their molecular cargo is a promising source of disease biomarkers. However, proteomic characterization of plasma-derived EVs is challenged by the presence of highly abundant plasma proteins, which limits the detection of less abundant proteins, and by the low number of EVs in biological fluids. The aim of this study was to investigate if the removal of abundant plasma proteins prior to EV isolation could improve plasma-derived EV characterization by LC-MS/MS and expand the proteome coverage. Plasma depletion was performed using a single-use spin column and EVs were isolated from only 100 µL of non-depleted and depleted plasma by size exclusion chromatography. Afterwards, EVs were characterized by nanoparticle tracking analysis and mass spectrometry-based proteomics using a data-independent acquisition approach. Depleted plasma-derived EVs had higher particle concentrations and particle-to-protein ratios. Depletion did increase the protein coverage with a higher number of identifications in EVs from depleted plasma (474 proteins) than from non-depleted (386 proteins). However, EVs derived from non-depleted plasma carried a slightly higher number of common EV markers. Overall, our findings suggest that plasma depletion prior to EV isolation by size exclusion chromatography provides higher yield and protein coverage, but slightly lower identification of EV markers. This study also showed the possibility to characterize the proteome of EVs derived from small plasma volumes, encouraging the clinical feasibility of the discovery of EV biomarkers.
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Affiliation(s)
- Sandrine Reymond
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| | - Lyssia Gruaz
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Charles Sanchez
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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10
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Abeysinghe P, Turner N, Mosaad E, Logan J, Mitchell MD. Dynamics of inflammatory cytokine expression in bovine endometrial cells exposed to cow blood plasma small extracellular vesicles (sEV) may reflect high fertility. Sci Rep 2023; 13:5425. [PMID: 37012302 PMCID: PMC10070242 DOI: 10.1038/s41598-023-32045-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
Aberrant inflammation in the endometrium impairs reproduction and leads to poor fertility. Small extracellular vesicles (sEV) are nanoparticles 30-200 nm in-size and contain transferable bioactive molecules that reflect the parent cell. Holstein-Friesian dairy cows with divergent genetic merit, high- (n = 10) and low-fertile (n = 10), were identified based on fertility breeding value (FBV), cow ovulation synchronization and postpartum anovulatory intervals (PPAI). In this study, we evaluated the effects of sEVs enriched from plasma of high-fertile (HF-EXO) and low-fertile (LF-EXO) dairy cows on inflammatory mediator expression by bovine endometrial epithelial (bEEL) and stromal (bCSC) cells. Exposure to HF-EXO in bCSC and bEEL cells yielded lower expression of PTGS1 and PTGS2 compared to the control. In bCSC cells exposed to HF-EXO, pro-inflammatory cytokine IL1-α was downregulated compared to the untreated control, IL-12α and IL-8 were downregulated compared to the LF-EXO treatment. Our findings demonstrate that sEVs interact with both endometrial epithelial and stromal cells to initiate differential gene expression, specifically genes relate to inflammation. Therefore, even subtle changes on the inflammatory gene cascade in the endometrium via sEV may affect reproductive performance and/or outcomes. Further, sEV from high-fertile animals acts in a unique direction to deactivate prostaglandin synthases in both bCSC and bEEL cells and deactivate pro-inflammatory cytokines in the endometrial stroma. The results suggest that circulating sEV may serve as a potential biomarker of fertility.
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Affiliation(s)
- Pevindu Abeysinghe
- School of Biomedical Sciences, Faculty of Health, Centre for Children's Health Research, Queensland University of Technology, Brisbane, QLD, 4029, Australia.
| | - Natalie Turner
- School of Biomedical Sciences, Faculty of Health, Centre for Children's Health Research, Queensland University of Technology, Brisbane, QLD, 4029, Australia
| | - Eman Mosaad
- School of Biomedical Sciences, Faculty of Health, Centre for Children's Health Research, Queensland University of Technology, Brisbane, QLD, 4029, Australia
| | - Jayden Logan
- School of Biomedical Sciences, Faculty of Health, Centre for Children's Health Research, Queensland University of Technology, Brisbane, QLD, 4029, Australia
| | - Murray D Mitchell
- School of Biomedical Sciences, Faculty of Health, Centre for Children's Health Research, Queensland University of Technology, Brisbane, QLD, 4029, Australia.
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11
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Gao J, Li A, Hu J, Feng L, Liu L, Shen Z. Recent developments in isolating methods for exosomes. Front Bioeng Biotechnol 2023; 10:1100892. [PMID: 36714629 PMCID: PMC9879965 DOI: 10.3389/fbioe.2022.1100892] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
Exosomes are the smallest extracellular vesicles that can be released by practically all cell types, and range in size from 30 nm to 150 nm. As the major marker of liquid biopsies, exosomes have great potential for disease diagnosis, therapy, and prognosis. However, their inherent heterogeneity, the complexity of biological fluids, and the presence of nanoscale contaminants make the isolation of exosomes a great challenge. Traditional isolation methods of exosomes are cumbersome and challenging with complex and time-consuming operations. In recent years, the emergence of microfluidic chips, nanolithography, electro-deposition, and other technologies has promoted the combination and innovation of the isolation methods. The application of these methods has brought very considerable benefits to the isolation of exosomes such as ultra-fast, portable integration, and low loss. There are significant functional improvements in isolation yield, isolation purity, and clinical applications. In this review, a series of methods for the isolation of exosomes are summarized, with emphasis on the emerging methods, and in-depth comparison and analysis of each method are provided, including their principles, merits, and demerits.
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Affiliation(s)
| | | | | | | | - Liu Liu
- *Correspondence: Zuojun Shen, ; Liu Liu,
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The exosome: a review of current therapeutic roles and capabilities in human reproduction. Drug Deliv Transl Res 2023; 13:473-502. [PMID: 35980542 PMCID: PMC9794547 DOI: 10.1007/s13346-022-01225-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 12/31/2022]
Abstract
Exosomes are nano-vesicles (30-150 nm) which may be useful as therapeutic delivery vehicles and as diagnostic biomarkers. Exosomes are produced naturally within the human body and therefore are not prone to immunogenicity effects which would otherwise destroy unelicited foreign bodies. Clinically, they have been regarded as ideal candidates for applications relating to biomarker developments for the early detection of different diseases. Furthermore, exosomes may be of interest as potential drug delivery vehicles, which may improve factors such as bioavailability of loaded molecular cargo, side effect profiles, off-target effects, and pharmacokinetics of drug molecules. In this review, the therapeutic potential of exosomes and their use as clinical biomarkers for early diagnostics will be explored, alongside exosomes as therapeutic delivery vehicles. This review will evaluate techniques for cargo loading, and the capacity of loaded exosomes to improve various reproductive disease states. It becomes important, therefore, to consider factors such as loading efficiency, loading methods, cell viability, exosomal sources, exosome isolation, and the potential therapeutic benefits of exosomes. Issues related to targeted drug delivery will also be discussed. Finally, the variety of therapeutic cargo and the application of appropriate loading methods is explored, in the context of establishing clinical utility. Exosomes have more recently been widely accpeted as potential tools for disease diagnostics and the targeted delivery of certain therapeutic molecules-and in due time exosomes will be utilised more commonly within the clinical setting. Specifically, exosomal biomarkers can be identified and related to various detrimental conditions which occur during pregnancy. Considering, this review will explore the potential future of exosomes as both diagnostic tools and therapeutic delivery vehicles to treat related conditions, including the challenges which exist towards incorporating exosomes within the clinical environment to benefit patients.
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