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Skoczylas Ł, Gawin M, Fochtman D, Widłak P, Whiteside TL, Pietrowska M. Immune capture and protein profiling of small extracellular vesicles from human plasma. Proteomics 2024; 24:e2300180. [PMID: 37713108 PMCID: PMC11046486 DOI: 10.1002/pmic.202300180] [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: 05/16/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Extracellular vesicles (EVs), the key players in inter-cellular communication, are produced by all cell types and are present in all body fluids. Analysis of the proteome content is an important approach in structural and functional studies of these vesicles. EVs circulating in human plasma are heterogeneous in size, cellular origin, and functions. This heterogeneity and the potential presence of contamination with plasma components such as lipoprotein particles and soluble plasma proteins represent a challenge in profiling the proteome of EV subsets by mass spectrometry. An immunocapture strategy prior to mass spectrometry may be used to isolate a homogeneous subpopulation of small EVs (sEV) with a specific endocytic origin from plasma or other biofluids. Immunocapture selectively separates EV subpopulations in biofluids based on the presence of a unique protein carried on the vesicle surface. The advantages and disadvantages of EV immune capture as a preparative step for mass spectrometry are discussed.
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Affiliation(s)
- Łukasz Skoczylas
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland
| | - Marta Gawin
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland
| | - Daniel Fochtman
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland
- Silesian University of Technology, 44-100 Gliwice, Poland
| | - Piotr Widłak
- Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Theresa L. Whiteside
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Monika Pietrowska
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland
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Zhang Q, Ren T, Cao K, Xu Z. Advances of machine learning-assisted small extracellular vesicles detection strategy. Biosens Bioelectron 2024; 251:116076. [PMID: 38340580 DOI: 10.1016/j.bios.2024.116076] [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: 09/05/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
Detection of extracellular vesicles (EVs), particularly small EVs (sEVs), is of great significance in exploring their physiological characteristics and clinical applications. The heterogeneity of sEVs plays a crucial role in distinguishing different types of cells and diseases. Machine learning, with its exceptional data processing capabilities, offers a solution to overcome the limitations of conventional detection methods for accurately classifying sEV subtypes and sources. Principal component analysis, linear discriminant analysis, partial least squares discriminant analysis, XGBoost, support vector machine, k-nearest neighbor, and deep learning, along with some combined methods such as principal component-linear discriminant analysis, have been successfully applied in the detection and identification of sEVs. This review focuses on machine learning-assisted detection strategies for cell identification and disease prediction via sEVs, and summarizes the integration of these strategies with surface-enhanced Raman scattering, electrochemistry, inductively coupled plasma mass spectrometry and fluorescence. The performance of different machine learning-based detection strategies is compared, and the advantages and limitations of various machine learning models are also evaluated. Finally, we discuss the merits and limitations of the current approaches and briefly outline the perspective of potential research directions in the field of sEV analysis based on machine learning.
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Affiliation(s)
- Qi Zhang
- Research Center for Analytical Sciences, Northeastern University, Shenyang, 110819, PR China
| | - Tingju Ren
- Research Center for Analytical Sciences, Northeastern University, Shenyang, 110819, PR China
| | - Ke Cao
- Research Center for Analytical Sciences, Northeastern University, Shenyang, 110819, PR China
| | - Zhangrun Xu
- Research Center for Analytical Sciences, Northeastern University, Shenyang, 110819, PR China.
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3
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Wu J, Li Z, Wu Y, Cui N. The crosstalk between exosomes and ferroptosis: a review. Cell Death Discov 2024; 10:170. [PMID: 38594265 PMCID: PMC11004161 DOI: 10.1038/s41420-024-01938-z] [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: 11/07/2023] [Revised: 03/17/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Exosomes are a subtype of extracellular vesicles composed of bioactive molecules, including nucleic acids, proteins, and lipids. Exosomes are generated by the fusion of intracellular multivesicular bodies (MVBs) with the cell membrane and subsequently released into the extracellular space to participate in intercellular communication and diverse biological processes within target cells. As a crucial mediator, exosomes have been implicated in regulating ferroptosis-an iron-dependent programmed cell death characterized by lipid peroxide accumulation induced by reactive oxygen species. The involvement of exosomes in iron, lipid, and amino acid metabolism contributes to their regulatory role in specific mechanisms underlying how exosomes modulate ferroptosis, which remains incompletely understood, and some related studies are still preliminary. Therefore, targeting the regulation of ferroptosis by exosomes holds promise for future clinical treatment strategies across various diseases. This review aims to provide insights into the pathophysiology and mechanisms governing the interaction between exosomes and ferroptosis and their implications in disease development and treatment to serve as a reference for further research.
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Affiliation(s)
- Jiao Wu
- Oncology Department of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhongyu Li
- Department of Internal Medicine, Eye Hospital China Academy of Chinese Medical Sciences, Beijing, China.
| | - Yu Wu
- Oncology Department of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Ning Cui
- Oncology Department of Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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Melachroinou K, Divolis G, Tsafaras G, Karampetsou M, Fortis S, Stratoulias Y, Papadopoulou G, Kriebardis AG, Samiotaki M, Vekrellis K. Endogenous Alpha-Synuclein is Essential for the Transfer of Pathology by Exosome-Enriched Extracellular Vesicles, Following Inoculation with Preformed Fibrils in vivo. Aging Dis 2024; 15:869-892. [PMID: 37548944 PMCID: PMC10917543 DOI: 10.14336/ad.2023.0614] [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: 04/07/2023] [Accepted: 06/14/2023] [Indexed: 08/08/2023] Open
Abstract
The main pathological hallmark of Parkinson's disease (PD) and related synucleinopathies is the presence of intracellular proteinaceous aggregates, enriched in the presynaptic protein alpha-Synuclein (α-Syn). α-Syn association with exosomes has been previously documented both as a physiological process of secretion and as a pathological process of disease transmission, however, critical information about the mechanisms governing this interplay is still lacking. To address this, we utilized the α-Syn preformed fibril (PFF) mouse model of PD, as a source of brain-derived exosome-enriched extracellular vesicles (ExE-EVs) and assessed their pathogenic capacity following intrastriatal injections in host wild type (WT) mouse brain. We further investigated the impact of the fibrillar α-Syn on the exosomal cargo independent of the endogenous α-Syn, by isolating ExE-EVs from PFF-injected α-Syn knockout mice. Although PFF inoculation does not alter the morphology, size distribution, and quantity of brain-derived ExE-EVs, it triggers changes in the exosomal proteome related to synaptic and mitochondrial function, as well as metabolic processes. Importantly, we showed that the presence of the endogenous α-Syn is essential for the ExE-EVs to acquire a pathogenic capacity, allowing them to mediate disease transmission by inducing phosphorylated-α-Syn pathology. Notably, misfolded α-Syn containing ExE-EVs when injected in WT mice were able to induce astrogliosis and synaptic alterations in the host brain, at very early stages of α-Syn pathology, preceding the formation of the insoluble α-Syn accumulations. Collectively, our data suggest that exosomal cargo defines their ability to spread α-Syn pathology.
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Affiliation(s)
- Katerina Melachroinou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Georgios Divolis
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - George Tsafaras
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Mantia Karampetsou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Sotirios Fortis
- Laboratory of Reliability and Quality Control in Laboratory Hematology (HemQcR), Department of Biomedical Sciences, School of Health & Welfare Sciences, University of West Attica (UniWA), Egaleo, Greece.
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece.
| | - Yannis Stratoulias
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Gina Papadopoulou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Anastasios G Kriebardis
- Laboratory of Reliability and Quality Control in Laboratory Hematology (HemQcR), Department of Biomedical Sciences, School of Health & Welfare Sciences, University of West Attica (UniWA), Egaleo, Greece.
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
| | - Kostas Vekrellis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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Pfeiffer A, Bandara G, Petersen JD, Falduto GH, Zimmerberg J, Metcalfe DD, Olivera A. Activation of the receptor KIT induces the secretion of exosome-like small extracellular vesicles. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e139. [PMID: 38938682 PMCID: PMC11080788 DOI: 10.1002/jex2.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 06/29/2024]
Abstract
The receptor tyrosine kinase (RTK) KIT and its ligand stem cell factor (SCF) are essential for human mast cell (huMC) survival and proliferation. HuMCs expressing oncogenic KIT variants secrete large numbers of extracellular vesicles (EVs). The role KIT plays in regulating EV secretion has not been examined. Here, we investigated the effects of stimulation or inhibition of KIT activity on the secretion of small EVs (sEVs). In huMCs expressing constitutively active KIT, the quantity and quality of secreted sEVs positively correlated with the activity status of KIT. SCF-mediated stimulation of KIT in huMCs or murine MCs, or of transiently expressed KIT in HeLa cells, enhanced the release of sEVs expressing exosome markers. In contrast, ligand-mediated stimulation of the RTK EGFR in HeLa cells did not affect sEV secretion. The release of sEVs induced by either constitutively active or ligand-activated KIT was remarkably decreased when cells were treated with KIT inhibitors, concomitant with reduced exosome markers in sEVs. Similarly, inhibition of oncogenic KIT signalling kinases like PI3K, and MAPK significantly reduced the secretion of sEVs. Thus, activation of KIT and its early signalling cascades stimulate the secretion of exosome-like sEVs in a regulated fashion, which may have implications for KIT-driven functions.
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Affiliation(s)
- Annika Pfeiffer
- Mast Cell Biology SectionLaboratory of Allergic DiseasesNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Geethani Bandara
- Mast Cell Biology SectionLaboratory of Allergic DiseasesNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Jennifer D. Petersen
- Section on Integrative BiophysicsDivision of Basic and Translational BiophysicsEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMarylandUSA
- Inherited Movement Disorders UnitNeurogenetics BranchNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMarylandUSA
| | - Guido H. Falduto
- Mast Cell Biology SectionLaboratory of Allergic DiseasesNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Joshua Zimmerberg
- Section on Integrative BiophysicsDivision of Basic and Translational BiophysicsEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMarylandUSA
| | - Dean D. Metcalfe
- Mast Cell Biology SectionLaboratory of Allergic DiseasesNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Ana Olivera
- Mast Cell Biology SectionLaboratory of Allergic DiseasesNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
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Molderings GJ, Afrin LB. A survey of the currently known mast cell mediators with potential relevance for therapy of mast cell-induced symptoms. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2023; 396:2881-2891. [PMID: 37243761 PMCID: PMC10567897 DOI: 10.1007/s00210-023-02545-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/29/2023]
Abstract
Mast cells (MCs) occupy a central role in immunological as well as non-immunological processes as reflected in the variety of the mediators by which MCs influence other cells. Published lists of MC mediators have all shown only subsets-usually quite small-of the full repertoire. The full repertoire of MC mediators released by exocytosis is comprehensively compiled here for the first time. The compilation of the data is essentially based on the largely cytokine-focused database COPE®, supplemented with data on the expression of substances in human MCs published in several articles, plus extensive research in the PubMed database. Three hundred and ninety substances could be identified as mediators of human MCs which can be secreted into the extracellular space by activation of the MC. This number might still be an underestimate of the actual number of MC mediators since, in principle, all substances produced by MCs can become mediators because of the possibility of their release by diffusion into the extracellular space, mast cell extracellular traps, and intercellular exchange via nanotubules. When human MCs release mediators in inappropriate manners, this may lead to symptoms in any or all organs/tissues. Thus, such MC activation disorders may clinically present with a myriad of potential combinations of symptoms ranging from trivial to disabling or even life-threatening. The present compilation can be consulted by physicians when trying to gain clarity about MC mediators which may be involved in patients with MC disease symptoms refractory to most therapies.
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Affiliation(s)
- Gerhard J Molderings
- Institute for Human Genetics, University Hospital of Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany.
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Biagiotti S, Abbas F, Montanari M, Barattini C, Rossi L, Magnani M, Papa S, Canonico B. Extracellular Vesicles as New Players in Drug Delivery: A Focus on Red Blood Cells-Derived EVs. Pharmaceutics 2023; 15:pharmaceutics15020365. [PMID: 36839687 PMCID: PMC9961903 DOI: 10.3390/pharmaceutics15020365] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The article is divided into several sections, focusing on extracellular vesicles' (EVs) nature, features, commonly employed methodologies and strategies for their isolation/preparation, and their characterization/visualization. This work aims to give an overview of advances in EVs' extensive nanomedical-drug delivery applications. Furthermore, considerations for EVs translation to clinical application are summarized here, before focusing the review on a special kind of extracellular vesicles, the ones derived from red blood cells (RBCEVs). Generally, employing EVs as drug carriers means managing entities with advantageous properties over synthetic vehicles or nanoparticles. Besides the fact that certain EVs also reveal intrinsic therapeutic characteristics, in regenerative medicine, EVs nanosize, lipidomic and proteomic profiles enable them to pass biologic barriers and display cell/tissue tropisms; indeed, EVs engineering can further optimize their organ targeting. In the second part of the review, we focus our attention on RBCEVs. First, we describe the biogenesis and composition of those naturally produced by red blood cells (RBCs) under physiological and pathological conditions. Afterwards, we discuss the current procedures to isolate and/or produce RBCEVs in the lab and to load a specific cargo for therapeutic exploitation. Finally, we disclose the most recent applications of RBCEVs at the in vitro and preclinical research level and their potential industrial exploitation. In conclusion, RBCEVs can be, in the near future, a very promising and versatile platform for several clinical applications and pharmaceutical exploitations.
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Affiliation(s)
- Sara Biagiotti
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy
| | - Faiza Abbas
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy
| | - Mariele Montanari
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy
| | - Chiara Barattini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy
- AcZon s.r.l., 40050 Monte San Pietro, BO, Italy
| | - Luigia Rossi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy
| | - Stefano Papa
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy
| | - Barbara Canonico
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy
- Correspondence:
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