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Fekry B, Ugartemendia L, Esnaola NF, Goetzl L. Extracellular Vesicles, Circadian Rhythms, and Cancer: A Comprehensive Review with Emphasis on Hepatocellular Carcinoma. Cancers (Basel) 2024; 16:2552. [PMID: 39061191 PMCID: PMC11274441 DOI: 10.3390/cancers16142552] [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: 06/20/2024] [Revised: 07/12/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024] Open
Abstract
This review comprehensively explores the complex interplay between extracellular vesicles (ECVs)/exosomes and circadian rhythms, with a focus on the role of this interaction in hepatocellular carcinoma (HCC). Exosomes are nanovesicles derived from cells that facilitate intercellular communication by transporting bioactive molecules such as proteins, lipids, and RNA/DNA species. ECVs are implicated in a range of diseases, where they play crucial roles in signaling between cells and their surrounding environment. In the setting of cancer, ECVs are known to influence cancer initiation and progression. The scope of this review extends to all cancer types, synthesizing existing knowledge on the various roles of ECVs. A unique aspect of this review is the emphasis on the circadian-controlled release and composition of exosomes, highlighting their potential as biomarkers for early cancer detection and monitoring metastasis. We also discuss how circadian rhythms affect multiple cancer-related pathways, proposing that disruptions in the circadian clock can alter tumor development and treatment response. Additionally, this review delves into the influence of circadian clock components on ECV biogenesis and their impact on reshaping the tumor microenvironment, a key component driving HCC progression. Finally, we address the potential clinical applications of ECVs, particularly their use as diagnostic tools and drug delivery vehicles, while considering the challenges associated with clinical implementation.
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Affiliation(s)
- Baharan Fekry
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (L.U.); (L.G.)
| | - Lierni Ugartemendia
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (L.U.); (L.G.)
| | - Nestor F. Esnaola
- Division of Surgical Oncology and Gastrointestinal Surgery, Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA;
| | - Laura Goetzl
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (L.U.); (L.G.)
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2
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Peregrino ES, Castañeda-Casimiro J, Vázquez-Flores L, Estrada-Parra S, Wong-Baeza C, Serafín-López J, Wong-Baeza I. The Role of Bacterial Extracellular Vesicles in the Immune Response to Pathogens, and Therapeutic Opportunities. Int J Mol Sci 2024; 25:6210. [PMID: 38892397 PMCID: PMC11172497 DOI: 10.3390/ijms25116210] [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: 05/01/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Pathogenic bacteria have several mechanisms to evade the host's immune response and achieve an efficient infection. Bacterial extracellular vesicles (EVs) are a relevant cellular communication mechanism, since they can interact with other bacterial cells and with host cells. In this review, we focus on the EVs produced by some World Health Organization (WHO) priority Gram-negative and Gram-positive pathogenic bacteria; by spore-producing bacteria; by Mycobacterium tuberculosis (a bacteria with a complex cell wall); and by Treponema pallidum (a bacteria without lipopolysaccharide). We describe the classification and the general properties of bacterial EVs, their role during bacterial infections and their effects on the host immune response. Bacterial EVs contain pathogen-associated molecular patterns that activate innate immune receptors, which leads to cytokine production and inflammation, but they also contain antigens that induce the activation of B and T cell responses. Understanding the many effects of bacterial EVs on the host's immune response can yield new insights on the pathogenesis of clinically important infections, but it can also lead to the development of EV-based diagnostic and therapeutic strategies. In addition, since EVs are efficient activators of both the innate and the adaptive immune responses, they constitute a promising platform for vaccine development.
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Affiliation(s)
- Eliud S. Peregrino
- Posgrado en Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (E.S.P.); (J.C.-C.)
| | - Jessica Castañeda-Casimiro
- Posgrado en Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (E.S.P.); (J.C.-C.)
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (S.E.-P.); (J.S.-L.)
| | - Luis Vázquez-Flores
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (L.V.-F.); (C.W.-B.)
| | - Sergio Estrada-Parra
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (S.E.-P.); (J.S.-L.)
| | - Carlos Wong-Baeza
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (L.V.-F.); (C.W.-B.)
| | - Jeanet Serafín-López
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (S.E.-P.); (J.S.-L.)
| | - Isabel Wong-Baeza
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (S.E.-P.); (J.S.-L.)
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3
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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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Bandu R, Oh JW, Kim KP. Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry-based analysis. Proteomics 2024; 24:e2300062. [PMID: 38829178 DOI: 10.1002/pmic.202300062] [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: 06/11/2023] [Revised: 02/20/2024] [Accepted: 03/18/2024] [Indexed: 06/05/2024]
Abstract
Extracellular vesicles (EVs) are membrane-surrounded vesicles released by various cell types into the extracellular microenvironment. Although EVs vary in size, biological function, and components, their importance in cancer progression and the potential use of EV molecular species to serve as novel cancer biomarkers have become increasingly evident. Cancer cells actively release EVs into surrounding tissues, which play vital roles in cancer progression and metastasis, including invasion and immune modulation. EVs released by cancer cells are usually chosen as a gateway in the search for biomarkers for cancer. In this review, we mainly focused on molecular profiling of EV protein constituents from breast cancer, emphasizing mass spectrometry (MS)-based proteomic approaches. To further investigate the potential use of EVs as a source of breast cancer biomarkers, we have discussed the use of these proteins as predictive marker candidates. Besides, we have also summarized the key characteristics of EVs as potential therapeutic targets in breast cancer and provided significant information on their implications in breast cancer development and progression. Information provided in this review may help understand the recent progress in understanding EV biology and their potential role as new noninvasive biomarkers as well as emerging therapeutic opportunities and associated challenges.
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Affiliation(s)
- Raju Bandu
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jae Won Oh
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, Republic of Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, Republic of Korea
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Kong M, Hong DH, Paudel S, Yoon NE, Jung BH, Kim M, Kim TH, Jeong J, Choi D, Lee H. Metabolomics and miRNA profiling reveals feature of gallbladder cancer-derived biliary extracellular vesicles. Biochem Biophys Res Commun 2024; 705:149724. [PMID: 38432111 DOI: 10.1016/j.bbrc.2024.149724] [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: 11/22/2023] [Revised: 02/07/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Although there are several studies in the development of various human cancers, the role of exosomes is poorly understood in the progression of gallbladder cancer. This study aims to characterize the metabolic changes occurring in exosomes obtained from patients with gallbladder cancer compared with those from other gallbladder disease groups. METHODS Biliary exosomes were isolated from healthy donors (n = 3) and from patients with gallbladder cancer (n = 3), gallbladder polyps (n = 4), or cholecystitis (n = 3) using a validated exosome isolation kit. Afterward, we performed miRNA profiling and untargeted metabolomic analysis of the exosomes. The results were validated by integrating the results of the miRNA and metabolomic analyses. RESULTS The gallbladder cancer group exhibited a significant reduction in the levels of multiple unsaturated phosphatidylethanolamines and phosphatidylcholines compared to the normal group, which resulted in the loss of exosome membrane integrity. Additionally, the gallbladder cancer group demonstrated significant overexpression of miR-181c and palmitic acid, and decreased levels of conjugated deoxycholic acid, all of which are strongly associated with the activation of the PI3K/AKT pathway. CONCLUSIONS Our findings demonstrate that the contents of exosomes are disease-specific, particularly in gallbladder cancer, and that altered metabolites convey critical information regarding their phenotype. We believe that our metabolomic and miRNA profiling results may provide important insights into the development of gallbladder cancer.
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Affiliation(s)
- Mingyu Kong
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 130-701, Republic of Korea
| | - Da Hee Hong
- Research Institute of Regenerative Medicine and Stem Cells, Hanyang University, Seoul, 04763, Republic of Korea; Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, Republic of Korea
| | - Sanjita Paudel
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Na Eun Yoon
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Byung Hwa Jung
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Myounghoi Kim
- Research Institute of Regenerative Medicine and Stem Cells, Hanyang University, Seoul, 04763, Republic of Korea
| | - Tae Hun Kim
- Research Institute of Regenerative Medicine and Stem Cells, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jaemin Jeong
- Department of Biohealth Convergence, College of Natural Sciences, Seoul Women's University, Seoul, 01797, Republic of Korea.
| | - Dongho Choi
- Research Institute of Regenerative Medicine and Stem Cells, Hanyang University, Seoul, 04763, Republic of Korea; Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, Republic of Korea; Department of HY-KIST Bio-convergence, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Hyunbeom Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of HY-KIST Bio-convergence, Hanyang University, Seoul, 04763, Republic of Korea.
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Baptista Pereira P, Torrejón E, Ferreira I, Carvalho AS, Teshima A, Sousa-Lima I, Beck HC, Costa-Silva B, Matthiesen R, Macedo MP, de Oliveira RM. Proteomic Profiling of Plasma- and Gut-Derived Extracellular Vesicles in Obesity. Nutrients 2024; 16:736. [PMID: 38474865 DOI: 10.3390/nu16050736] [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: 01/08/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Obesity entails metabolic alterations across multiple organs, highlighting the role of inter-organ communication in its pathogenesis. Extracellular vesicles (EVs) are communication agents in physiological and pathological conditions, and although they have been associated with obesity comorbidities, their protein cargo in this context remains largely unknown. To decipher the messages encapsulated in EVs, we isolated plasma-derived EVs from a diet-induced obese murine model. Obese plasma EVs exhibited a decline in protein diversity while control EVs revealed significant enrichment in protein-folding functions, highlighting the importance of proper folding in maintaining metabolic homeostasis. Previously, we revealed that gut-derived EVs' proteome holds particular significance in obesity. Here, we compared plasma and gut EVs and identified four proteins exclusively present in the control state of both EVs, revealing the potential for a non-invasive assessment of gut health by analyzing blood-derived EVs. Given the relevance of post-translational modifications (PTMs), we observed a shift in chromatin-related proteins from glycation to acetylation in obese gut EVs, suggesting a regulatory mechanism targeting DNA transcription during obesity. This study provides valuable insights into novel roles of EVs and protein PTMs in the intricate mechanisms underlying obesity, shedding light on potential biomarkers and pathways for future research.
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Affiliation(s)
- Pedro Baptista Pereira
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Estefania Torrejón
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Inês Ferreira
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Akiko Teshima
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Inês Sousa-Lima
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Hans Christian Beck
- Centre for Clinical Proteomics, Department of Clinical Biochemistry, Odense University Hospital, DK-5000 Odense, Denmark
| | - Bruno Costa-Silva
- Champalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisboa, Portugal
| | - Rune Matthiesen
- Computational and Experimental Biology Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Maria Paula Macedo
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Rita Machado de Oliveira
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
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Wang W, Sun H, Duan H, Sheng G, Tian N, Liu D, Sun Z. Isolation and usage of exosomes in central nervous system diseases. CNS Neurosci Ther 2024; 30:e14677. [PMID: 38497529 PMCID: PMC10945885 DOI: 10.1111/cns.14677] [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: 09/18/2023] [Revised: 02/10/2024] [Accepted: 03/01/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Exosomes are vesicles secreted by all types of mammalian cells. They are characterized by a double-layered lipid membrane structure. They serve as carriers for a plethora of signal molecules, including DNA, RNA, proteins, and lipids. Their unique capability of effortlessly crossing the blood-brain barrier underscores their critical role in the progression of various neurological disorders. This includes, but is not limited to, diseases such as Alzheimer's, Parkinson's, and ischemic stroke. Establishing stable and mature methods for isolating exosomes is a prerequisite for the study of exosomes and their biomedical significance. The extraction technologies of exosomes include differential centrifugation, density gradient centrifugation, size exclusion chromatography, ultrafiltration, polymer coprecipitation, immunoaffinity capture, microfluidic, and so forth. Each extraction technology has its own advantages and disadvantages, and the extraction standards of exosomes have not been unified internationally. AIMS This review aimed to showcase the recent advancements in exosome isolation techniques and thoroughly compare the advantages and disadvantages of different methods. Furthermore, the significant research progress made in using exosomes for diagnosing and treating central nervous system (CNS) diseases has been emphasized. CONCLUSION The varying isolation methods result in differences in the concentration, purity, and size of exosomes. The efficient separation of exosomes facilitates their widespread application, particularly in the diagnosis and treatment of CNS diseases.
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Affiliation(s)
- Wenjing Wang
- Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijingChina
| | - Hong Sun
- Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijingChina
- Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
| | - Huijuan Duan
- Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
| | - Gang Sheng
- Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijingChina
| | - Na Tian
- Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijingChina
| | - Dingyi Liu
- Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijingChina
| | - Zhaogang Sun
- Beijing Chest Hospital Affiliated to Capital Medical UniversityBeijingChina
- Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijingChina
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Arntz OJ, Thurlings RM, Blaney Davidson EN, Jansen PWTC, Vermeulen M, Koenders MI, van der Kraan PM, van de Loo FAJ. Profiling of plasma extracellular vesicles identifies proteins that strongly associate with patient's global assessment of disease activity in rheumatoid arthritis. Front Med (Lausanne) 2024; 10:1247778. [PMID: 38274452 PMCID: PMC10808582 DOI: 10.3389/fmed.2023.1247778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/30/2023] [Indexed: 01/27/2024] Open
Abstract
Background Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic synovial inflammation and cartilage/bone damage. Intercellular messengers such as IL-1 and TNF play a crucial role in the pathophysiology of RA but have limited diagnostic and prognostic values. Therefore, we assessed whether the protein content of the recently discovered extracellular vesicles (EVs), which have gained attention in the pathogenesis of RA, correlates with disease activity parameters in RA patients. Methods We identified and quantified proteins in plasma-derived EVs (pEVs), isolated by size exclusion chromatography from 17 RA patients by mass spectrophotometry (MS). Quantified protein levels were correlated with laboratory and clinical parameters and the patient's own global assessment of their disease activity (PGA-VAS). In a second MS run, the pEV proteins of nine other RA patients were quantified and compared to those from nine healthy controls (HC). Results No differences were observed in the concentration, size, and protein content of pEVs from RA patients. Proteomics revealed >95% overlapping proteins in RA-pEVs, compared to HC-pEVs (data are available via ProteomeXchange with identifier PXD046058). Remarkably, in both runs, the level of far more RA-pEV proteins correlated positively to PGA-VAS than to either clinical or laboratory parameters. Interestingly, all observed PGA-VAS positively correlated RA-pEV proteins were associated with the actin-cytoskeleton linker proteins, ezrin, and moesin. Conclusion Our observation suggests that PGA-VAS (loss of vitality) may have a different underlying pathological mechanism in RA, possibly related to enhanced muscle actin-cytoskeleton activity. Furthermore, our study contributes to the growing awareness and evidence that pEVs contain valuable biomarkers for diseases, with added value for RA patients.
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Affiliation(s)
- Onno J. Arntz
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rogier M. Thurlings
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Pascal W. T. C. Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Marije I. Koenders
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Fons A. J. van de Loo
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, Netherlands
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9
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Anastasi F, Botto A, Immordino B, Giovannetti E, McDonnell LA. Proteomics analysis of circulating small extracellular vesicles: Focus on the contribution of EVs to tumor metabolism. Cytokine Growth Factor Rev 2023; 73:3-19. [PMID: 37652834 DOI: 10.1016/j.cytogfr.2023.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
The term small extracellular vesicle (sEV) is a comprehensive term that includes any type of cell-derived, membrane-delimited particle that has a diameter < 200 nm, and which includes exosomes and smaller microvesicles. sEVs transfer bioactive molecules between cells and are crucial for cellular homeostasis and particularly during tumor development, where sEVs provide important contributions to the formation of the premetastic niche and to their altered metabolism. sEVs are thus legitimate targets for intervention and have also gained increasing interest as an easily accessible source of biomarkers because they can be rapidly isolated from serum/plasma and their molecular cargo provides information on their cell-of origin. To target sEVs that are specific for a given cell/disease it is essential to identify EV surface proteins that are characteristic of that cell/disease. Mass-spectrometry based proteomics is widely used for the identification and quantification of sEV proteins. The methods used for isolating the sEVs, preparing the sEV sample for proteomics analysis, and mass spectrometry analysis, can have a strong influence on the results and requires careful consideration. This review provides an overview of the approaches used for sEV proteomics and discusses the inherent compromises regarding EV purity versus depth of coverage. Additionally, it discusses the practical applications of the methods to unravel the involvement of sEVs in regulating the metabolism of pancreatic ductal adenocarcinoma (PDAC). The metabolic reprogramming in PDAC includes enhanced glycolysis, elevated glutamine metabolism, alterations in lipid metabolism, mitochondrial dysfunction and hypoxia, all of which are crucial in promoting tumor cell growth. A thorough understanding of these metabolic adaptations is imperative for the development of targeted therapies to exploit PDAC's vulnerabilities.
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Affiliation(s)
- Federica Anastasi
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy; National Enterprise for NanoScience and NanoTechnology, Scuola Normale Superiore, Pisa, Italy; BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | - Asia Botto
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy; Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Benoit Immordino
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy; Scuola Superiore Sant'Anna, Pisa, Italy
| | - Elisa Giovannetti
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy; Department of Medical Oncology, Amsterdam UMC, Cancer Center Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy.
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10
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Park SH, Lee EK, Yim J, Lee MH, Lee E, Lee YS, Seo W. Exosomes: Nomenclature, Isolation, and Biological Roles in Liver Diseases. Biomol Ther (Seoul) 2023; 31:253-263. [PMID: 37095734 PMCID: PMC10129856 DOI: 10.4062/biomolther.2022.161] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 04/26/2023] Open
Abstract
The biogenesis and biological roles of extracellular vesicles (EVs) in the progression of liver diseases have attracted considerable attention in recent years. EVs are membrane-bound nanosized vesicles found in different types of body fluids and contain various bioactive materials, including proteins, lipids, nucleic acids, and mitochondrial DNA. Based on their origin and biogenesis, EVs can be classified as apoptotic bodies, microvesicles, and exosomes. Among these, exosomes are the smallest EVs (30-150 nm in diameter), which play a significant role in cell-to-cell communication and epigenetic regulation. Moreover, exosomal content analysis can reveal the functional state of the parental cell. Therefore, exosomes can be applied to various purposes, including disease diagnosis and treatment, drug delivery, cell-free vaccines, and regenerative medicine. However, exosome-related research faces two major limitations: isolation of exosomes with high yield and purity and distinction of exosomes from other EVs (especially microvesicles). No standardized exosome isolation method has been established to date; however, various exosome isolation strategies have been proposed to investigate their biological roles. Exosome-mediated intercellular communications are known to be involved in alcoholic liver disease and nonalcoholic fatty liver disease development. Damaged hepatocytes or nonparenchymal cells release large numbers of exosomes that promote the progression of inflammation and fibrogenesis through interactions with neighboring cells. Exosomes are expected to provide insight on the progression of liver disease. Here, we review the biogenesis of exosomes, exosome isolation techniques, and biological roles of exosomes in alcoholic liver disease and nonalcoholic fatty liver disease.
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Affiliation(s)
- Seol Hee Park
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea
| | - Eun Kyeong Lee
- College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - Joowon Yim
- College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - Min Hoo Lee
- College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - Eojin Lee
- College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - Young-Sun Lee
- Department of Internal Medicine, Korea University Medical Center, Seoul 08308, Republic of Korea
| | - Wonhyo Seo
- College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
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11
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Sojka DR, Abramowicz A, Adamiec-Organiściok M, Karnas E, Mielańczyk Ł, Kania D, Blamek S, Telka E, Scieglinska D. Heat shock protein A2 is a novel extracellular vesicle-associated protein. Sci Rep 2023; 13:4734. [PMID: 36959387 PMCID: PMC10036471 DOI: 10.1038/s41598-023-31962-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 03/25/2023] Open
Abstract
70-kDa Heat Shock Proteins (HSPA/HSP70) are chaperones playing a central role in the proteostasis control mechanisms. Their basal expression can be highly elevated as an adaptive response to environmental and pathophysiological stress conditions. HSPA2, one of poorly characterised chaperones of the HSPA/HSP70 family, has recently emerged as epithelial cells differentiation-related factor. It is also commonly expressed in cancer cells, where its functional significance remains unclear. Previously, we have found that proteotoxic stress provokes a decrease in HSPA2 levels in cancer cells. In the present study we found that proteasome inhibition-related loss of HSPA2 from cancer cells neither is related to a block in the gene transcription nor does it relate to increased autophagy-mediated disposals of the protein. Proteotoxic stress stimulated extracellular release of HSPA2 in extracellular vesicles (EVs). Interestingly, EVs containing HSPA2 are also released by non-stressed cancer and normal cells. In human urinary EVs levels of HSPA2 were correlated with the levels of TSG101, one of the main EVs markers. We conclude that HSPA2 may constitute basic components of EVs. Nevertheless, its specific role in EVs and cell-to-cell communication requires further investigation.
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Affiliation(s)
- Damian Robert Sojka
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15, 44-102, Gliwice, Poland
| | - Agata Abramowicz
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15, 44-102, Gliwice, Poland
| | - Małgorzata Adamiec-Organiściok
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15, 44-102, Gliwice, Poland
- Department of Systems Biology and Engineering, Silesian University of Technology, Institute of Automatic Control, Akademicka 16, 44-100, Gliwice, Poland
| | - Elżbieta Karnas
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7 St., 30-387, Kraków, Poland
| | - Łukasz Mielańczyk
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Daria Kania
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15, 44-102, Gliwice, Poland
| | - Sławomir Blamek
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15, 44-102, Gliwice, Poland
| | - Ewa Telka
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15, 44-102, Gliwice, Poland
| | - Dorota Scieglinska
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15, 44-102, Gliwice, Poland.
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12
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Bai Z, Ma X, Yan R, Lei W, Zhang Y, Ren Y, Liu S. Metabolomic profiling of early inactive hepatic alveolar and cystic echinococcosis. Acta Trop 2023; 242:106875. [PMID: 36940858 DOI: 10.1016/j.actatropica.2023.106875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 03/23/2023]
Abstract
Hepatic alveolar echinococcosis (AE) and cystic echinococcosis (CE) are severe helminthic zoonoses and leading causes of parasitic liver damage. They pose a high mortality risk due to invisible clinical signs, especially at the early inactive stage. However, the specific metabolic profiles induced by inactive AE and CE lesions remain largely unclear. Therefore, we used gas chromatography-mass spectrometry-based metabolomic profiling to identify the global metabolic variations in AE and CE patient sera to differentiate between the two diseases and reveal the mechanisms underlying their pathogenesis. In addition, specific serum biomarkers of inactive hepatic AE and CE were screened using receiver operating curves, which can contribute to the clinical diagnosis of both diseases, especially in the earlier phase. These differential metabolites are involved in glycine, serine, tyrosine, and phenylalanine metabolism. Further analysis of key metabolic pathways showed that inactive AE lesions strongly alter amino acid metabolism in the host. CE lesions have an altered metabolism of oxidative stress response. These changes suggest these metabolite-associated pathways can serve as biomarkers to distinguish individuals with inactive AE and CE from healthy populations. This study also investigated the differences in serum metabolic profiles in patients with CE and AE. The biomarkers identified belonged to different metabolic pathways, including lipid, carnitine, androgen, and bile acid metabolism. Taken together, by investigating the different phenotypes of CE and AE with metabolomic profiling, serum biomarkers facilitating early diagnosis were identified.
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Affiliation(s)
- Zhenzhong Bai
- Research Center for High-Altitude Medicine, Medical College, Qinghai University, Xining, Qinghai, China 810001
| | - Xiao Ma
- Department of Hydatid Disease Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China, 810001
| | - Ranran Yan
- Research Center for High-Altitude Medicine, Medical College, Qinghai University, Xining, Qinghai, China 810001
| | - Wen Lei
- Department of Hydatid Disease Prevention and Control, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China, 810001
| | - Yifan Zhang
- Department of Medical Imaging PET-CT Center, Qinghai Provincial People's Hospital, Xining, Qinghai, China, 810001
| | - Yanming Ren
- Research Center for High-Altitude Medicine, Medical College, Qinghai University, Xining, Qinghai, China 810001.
| | - Shou Liu
- Research Center for High-Altitude Medicine, Medical College, Qinghai University, Xining, Qinghai, China 810001; Department of Public Health, Plateau Medical Research Center, Medical College, Qinghai University, Xining, Qinghai, China, 810001.
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13
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Huang X, Liu B, Guo S, Guo W, Liao K, Hu G, Shi W, Kuss M, Duryee MJ, Anderson DR, Lu Y, Duan B. SERS spectroscopy with machine learning to analyze human plasma derived sEVs for coronary artery disease diagnosis and prognosis. Bioeng Transl Med 2023; 8:e10420. [PMID: 36925713 PMCID: PMC10013764 DOI: 10.1002/btm2.10420] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/02/2022] [Accepted: 09/18/2022] [Indexed: 11/12/2022] Open
Abstract
Coronary artery disease (CAD) is one of the major cardiovascular diseases and represents the leading causes of global mortality. Developing new diagnostic and therapeutic approaches for CAD treatment are critically needed, especially for an early accurate CAD detection and further timely intervention. In this study, we successfully isolated human plasma small extracellular vesicles (sEVs) from four stages of CAD patients, that is, healthy control, stable plaque, non-ST-elevation myocardial infarction, and ST-elevation myocardial infarction. Surface-enhanced Raman scattering (SERS) measurement in conjunction with five machine learning approaches, including Quadratic Discriminant Analysis, Support Vector Machine (SVM), K-Nearest Neighbor, Artificial Neural network, were then applied for the classification and prediction of the sEV samples. Among these five approaches, the overall accuracy of SVM shows the best predication results on both early CAD detection (86.4%) and overall prediction (92.3%). SVM also possesses the highest sensitivity (97.69%) and specificity (95.7%). Thus, our study demonstrates a promising strategy for noninvasive, safe, and high accurate diagnosis for CAD early detection.
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Affiliation(s)
- Xi Huang
- Department of Electrical and Computer EngineeringUniversity of Nebraska LincolnLincolnNebraskaUSA
| | - Bo Liu
- Mary & Dick Holland Regenerative Medicine ProgramUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Division of Cardiovascular Medicine, Department of Internal MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Shenghan Guo
- Department of Industrial and Systems EngineeringRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- School of Manufacturing Systems and NetworksArizona State UniversityMesaArizonaUSA
| | - Weihong Guo
- Department of Industrial and Systems EngineeringRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Ke Liao
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Guoku Hu
- Department of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Wen Shi
- Mary & Dick Holland Regenerative Medicine ProgramUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Division of Cardiovascular Medicine, Department of Internal MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Mitchell Kuss
- Mary & Dick Holland Regenerative Medicine ProgramUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Division of Cardiovascular Medicine, Department of Internal MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Michael J. Duryee
- Division of Rheumatology, Department of Internal MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Daniel R. Anderson
- Division of Cardiovascular Medicine, Department of Internal MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Yongfeng Lu
- Department of Electrical and Computer EngineeringUniversity of Nebraska LincolnLincolnNebraskaUSA
| | - Bin Duan
- Mary & Dick Holland Regenerative Medicine ProgramUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Department of Surgery, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
- Department of Mechanical and Materials EngineeringUniversity of Nebraska‐LincolnLincolnNebraskaUSA
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14
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The updated role of exosomal proteins in the diagnosis, prognosis, and treatment of cancer. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1390-1400. [PMID: 36138197 PMCID: PMC9535014 DOI: 10.1038/s12276-022-00855-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/29/2022] [Accepted: 07/21/2022] [Indexed: 11/08/2022]
Abstract
Exosomes are vesicles encompassed by a lipid bilayer that are released by various living cells. Exosomal proteins are encapsulated within the membrane or embedded on the surface. As an important type of exosome cargo, exosomal proteins can reflect the physiological status of the parent cell and play an essential role in cell-cell communication. Exosomal proteins can regulate tumor development, including tumor-related immune regulation, microenvironment reconstruction, angiogenesis, epithelial-mesenchymal transition, metastasis, etc. The features of exosomal proteins can provide insight into exosome generation, targeting, and biological function and are potential sources of markers for cancer diagnosis, prognosis, and treatment. Here, we summarize the effects of exosomal proteins on cancer biology, the latest progress in the application of exosomal proteins in cancer diagnosis and prognosis, and the potential contribution of exosomal proteins in cancer therapeutics and vaccines.
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15
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Hepatitis Viruses Control Host Immune Responses by Modifying the Exosomal Biogenesis Pathway and Cargo. Int J Mol Sci 2022; 23:ijms231810862. [PMID: 36142773 PMCID: PMC9505460 DOI: 10.3390/ijms231810862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The development of smart immune evasion mechanisms is crucial for the establishment of acute and chronic viral hepatitis. Hepatitis is a major health problem worldwide arising from different causes, such as pathogens, metabolic disorders, and xenotoxins, with the five hepatitis viruses A, B, C, D, and E (HAV, HBV, HCV, HDV, and HEV) representing the majority of the cases. Most of the hepatitis viruses are considered enveloped. Recently, it was reported that the non-enveloped HAV and HEV are, in reality, quasi-enveloped viruses exploiting exosomal-like biogenesis mechanisms for budding. Regardless, all hepatitis viruses use exosomes to egress, regulate, and eventually escape from the host immune system, revealing another key function of exosomes apart from their recognised role in intercellular communication. This review will discuss how the hepatitis viruses exploit exosome biogenesis and transport capacity to establish successful infection and spread. Then, we will outline the contribution of exosomes in viral persistence and liver disease progression.
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16
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Magnetic guanidyl-functionalized covalent organic framework composite: a platform for specific capture and isolation of phosphopeptides and exosomes. Mikrochim Acta 2022; 189:330. [PMID: 35969309 DOI: 10.1007/s00604-022-05394-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/20/2022] [Indexed: 10/15/2022]
Abstract
A guanidine-functionalized (GF) covalent organic framework (COF) nanocomposite has been developed by a post-synthetic approach for specific capture and separation of phosphopeptides and exosomes. The abundant binding sites on COF can immobilize a large number of gold nanoparticles (AuNPs), which can be used to react with amino groups to graft polyethyleneimine (PEI). Finally, Fe3O4@COF@Au@PEI-GF is obtained through the reaction of PEI and guanidyl group for phosphopeptides and exosomes detection. This composite shows a low detection limit (0.02 fmol), size exclusion effect (β-casein digests:Albumin from bovine serum protein = 1:10,000), good reusability (10 cycles), and high selectivity (β-casein digests:Albumin from bovine serum digests = 1:10,000). For complex biological sample, 4 phosphopeptides can be successfully identified from human serum. Furthermore, for the first time, we used guanidyl-functionalized probe to capture exosomes in human serum, providing a new method for enriching exosomes. The above experiments showed that Fe3O4@COF@Au@PEI-GF not only effectively enrich phosphopeptides and remove macromolecular proteins, but also successfully separate and capture exosomes. This demonstrates the great potential of this composite for the specific enrichment of phosphopeptides and isolation of exosomes.
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17
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Zebrowska A, Jelonek K, Mondal S, Gawin M, Mrowiec K, Widłak P, Whiteside T, Pietrowska M. Proteomic and Metabolomic Profiles of T Cell-Derived Exosomes Isolated from Human Plasma. Cells 2022; 11:1965. [PMID: 35741093 PMCID: PMC9222142 DOI: 10.3390/cells11121965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023] Open
Abstract
Exosomes that are released by T cells are key messengers involved in immune regulation. However, the molecular profiling of these vesicles, which is necessary for understanding their functions, requires their isolation from a very heterogeneous mixture of extracellular vesicles that are present in the human plasma. It has been shown that exosomes that are produced by T cells could be isolated from plasma by immune capture using antibodies that target the CD3 antigen, which is a key component of the TCR complex that is present in all T lymphocytes. Here, we demonstrate that CD3(+) exosomes that are isolated from plasma can be used for high-throughput molecular profiling using proteomics and metabolomics tools. This profiling allowed for the identification of proteins and metabolites that differentiated the CD3(+) from the CD3(-) exosome fractions that were present in the plasma of healthy donors. Importantly, the proteins and metabolites that accumulated in the CD3(+) vesicles reflected the known molecular features of T lymphocytes. Hence, CD3(+) exosomes that are isolated from human plasma by immune capture could serve as a "T cell biopsy".
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Affiliation(s)
- Aneta Zebrowska
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland; (A.Z.); (K.J.); (M.G.); (K.M.)
| | - Karol Jelonek
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland; (A.Z.); (K.J.); (M.G.); (K.M.)
| | - Sujan Mondal
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA;
| | - Marta Gawin
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland; (A.Z.); (K.J.); (M.G.); (K.M.)
| | - Katarzyna Mrowiec
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland; (A.Z.); (K.J.); (M.G.); (K.M.)
| | - Piotr Widłak
- Clinical Research Support Centre, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Theresa 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 Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Monika Pietrowska
- Maria Sklodowska-Curie National Research Institute of Oncology, 44-102 Gliwice, Poland; (A.Z.); (K.J.); (M.G.); (K.M.)
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18
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Li D, Yao X, Yue J, Fang Y, Cao G, Midgley AC, Nishinari K, Yang Y. Advances in Bioactivity of MicroRNAs of Plant-Derived Exosome-Like Nanoparticles and Milk-Derived Extracellular Vesicles. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6285-6299. [PMID: 35583385 DOI: 10.1021/acs.jafc.2c00631] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
MicroRNA (miRNA) is a class of small noncoding RNA involved in physiological and pathological processes via the regulation of gene expression. Naked miRNAs are unstable and liable to degradation by RNases. Exosome-like nanoparticles (ELNs) secreted by plants and extracellular vesicles (EVs) found in milk are abundant in miRNAs, which can be carried by ELNs and EVs to target cells to exert their bioactivities. In this review, we describe the current understanding of miRNAs in plant ELNs and milk EVs, summarize their important roles in regulation of inflammation, intestinal barrier, tumors, and infantile immunological functions, and also discuss the adverse effect of EV miRNAs on human health. Additionally, we prospect recent challenges centered around ELN and EV miRNAs for interventional applications and provide insights of grain-derived ELNs and miRNAs interventional use in human health. Overall, plant ELNs and milk EVs can transfer miRNAs to mitigate the pathological status of recipient cells by mediating the expression of target genes but may also exert some side effects. More studies are required to elucidate the in-depth understanding of potential interventional effects of ELN and EV miRNAs on human health.
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Affiliation(s)
- Dan Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Xiaolin Yao
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Jianxiong Yue
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Yapeng Fang
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guifang Cao
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
| | - Adam C Midgley
- Key Laboratory of Bioactive Materials (MoE), College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Katsuyoshi Nishinari
- Glyn O. Phillips Hydrocolloid Research Centre, School of Bioengineering and Food Science, Hubei University of Technology, Wuhan 430068, China
| | - Yongli Yang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, P. R. China
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Gan J, Zeng X, Wang X, Wu Y, Lei P, Wang Z, Yang C, Hu Z. Effective Diagnosis of Prostate Cancer Based on mRNAs From Urinary Exosomes. Front Med (Lausanne) 2022; 9:736110. [PMID: 35402423 PMCID: PMC8983915 DOI: 10.3389/fmed.2022.736110] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 03/01/2022] [Indexed: 12/16/2022] Open
Abstract
Background Novel non-invasive biomarkers are urgently required to improve the diagnostic sensitivity and specificity of prostate cancer (PCa). Therefore, the diagnostic value of following candidate genes (ERG, PCA3, ARV7, PSMA, CK19, and EpCAM) were estimated by testing mRNAs from urinary exosomes of patients with primary PCa. Methods Exosomes were obtained using size-exclusion chromatography (SEC), out of which RNAs were extracted, then analyzed by quantitative reverse transcription-polymerase chain reaction according to manufacturer's protocol. Results The expression of urinary exosomal ERG, PCA3, PSMA, CK19, and EpCAM were significantly increased in patients with PCa compared with healthy males. In addition, the levels of urinary exosomal ERG, ARV7, and PSMA were intimately correlated with the Gleason score in PCa patients (P < 0.05). The receiver operating characteristic curves (ROCs) showed that urinary exosomal ERG, PCA3, PSMA, CK19, and EpCAM were able to distinguish patients with PCa from healthy individuals with the area under the curve (AUC) of 0.782, 0.783, 0.772, 0.731, and 0.739, respectively. Urinary exosomal PCA3 and PSMA distinguished PCa patients from healthy individuals with an AUC of 0.870. Combination of urinary exosomal PCA3, PSMA with serum PSA and PI-RADS achieved higher AUC compared with PSA alone (0.914 and 0.846, respectively). Kaplan-Meier curves demonstrated that PCA3, ARV7, and EpCAM were associated in androgen-deprivation therapy (ADT) failure time which is defined as from the initiation of ADT in hormone-sensitive stage to the development of castration-resistant prostate cancer. Conclusion These findings suggested that mRNAs from urinary exosomes have the potential in serving as novel and non-invasive indicators for PCa diagnosis and prediction.
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Affiliation(s)
- Jiahua Gan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Zeng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ya Wu
- Wuhan YZY Medical Science and Technology Co., Ltd., Wuhan, China
| | - Ping Lei
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunguang Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Radiation-Induced Bystander Effect Mediated by Exosomes Involves the Replication Stress in Recipient Cells. Int J Mol Sci 2022; 23:ijms23084169. [PMID: 35456987 PMCID: PMC9029583 DOI: 10.3390/ijms23084169] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Exosomes released by irradiated cells mediate the radiation-induced bystander effect, which is manifested by DNA breaks detected in recipient cells; yet, the specific mechanism responsible for the generation of chromosome lesions remains unclear. In this study, naive FaDu head and neck cancer cells were stimulated with exosomes released by irradiated (a single 2 Gy dose) or mock-irradiated cells. Maximum accumulation of gamma H2A.X foci, a marker of DNA breaks, was detected after one hour of stimulation with exosomes from irradiated donors, the level of which was comparable to the one observed in directly irradiated cells (a weaker wave of the gamma H2A.X foci accumulation was also noted after 23 h of stimulation). Exosomes from irradiated cells, but not from control ones, activated two stress-induced protein kinases: ATM and ATR. Noteworthy is that while direct irradiation activated only ATM, both ATM and ATR were activated by two factors known to induce the replication stress: hydroxyurea and camptothecin (with subsequent phosphorylation of gamma H2A.X). One hour of stimulation with exosomes from irradiated cells suppressed DNA synthesis in recipient cells and resulted in the subsequent nuclear accumulation of RNA:DNA hybrids, which is an indicator of impaired replication. Interestingly, the abovementioned effects were observed before a substantial internalization of exosomes, which may suggest a receptor-mediated mechanism. It was observed that after one hour of stimulation with exosomes from irradiated donors, phosphorylation of several nuclear proteins, including replication factors and regulators of heterochromatin remodeling as well as components of multiple intracellular signaling pathways increased. Hence, we concluded that the bystander effect mediated by exosomes released from irradiated cells involves the replication stress in recipient cells.
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21
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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22
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Proteomic and Biochemical Analysis of Extracellular Vesicles Isolated from Blood Serum of Patients with Melanoma. SEPARATIONS 2022. [DOI: 10.3390/separations9040086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background: Malignant melanoma is the most serious type of skin cancer with the highest mortality rate. Extracellular vesicles (EVs) have potential as new tumor markers that could be used as diagnostic and prognostic markers for early detection of melanoma. Methods: EVs were purified from the blood serum of melanoma patients using two methods—ultracentrifugation and PEG precipitation—and analyzed by mass spectrometry and immunoblot. Results: We identified a total of 585 unique proteins; 334 proteins were detected in PEG-precipitated samples and 515 in UC-purified EVs. EVs purified from patients varied in their size and concentration in different individuals. EVs obtained from stage II and III patients were, on average, smaller and more abundant than others. Detailed analysis of three potential biomarkers—SERPINA3, LGALS3BP, and gelsolin—revealed that the expression of SERPINA3 and LGALS3BP was higher in melanoma patients than healthy controls, while gelsolin exhibited higher expression in healthy controls. Conclusion: We suggest that all three proteins might have potential to be used as biomarkers, but a number of issues, such as purification of EVs, standardization, and validation of methods suitable for everyday clinical settings, still need to be addressed.
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Morales-Sanfrutos J, Munoz J. UNRAVELLING THE COMPLEXITY OF THE EXTRACELLULAR VESICLE LANDSCAPE WITH ADVANCED PROTEOMICS. Expert Rev Proteomics 2022; 19:89-101. [PMID: 35290757 DOI: 10.1080/14789450.2022.2052849] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The field of extracellular vesicles (EVs) is rapidly advancing. This progress is fuelled by the potential applications of these agents as biomarkers and also as an attractive source to encapsulate therapeutics and other agents to target specific cells. AREAS COVERED Different types of EVs, including exosomes, and other nanoparticles have been identified in the last years with key regulatory functions in cell-cell communication. However, the techniques used for their purification possess inherent limitations, resulting in heterogeneous preparations contaminated by other EVs subtypes and nano-size structures. It is therefore urgent to deconvolute the molecular constituents present in each type of EVs in order to accurately ascribe their specific functions. In this context, proteomics can profile, not only the lumen proteins and surface markers, but also their post-translational modifications, which will inform on the mechanisms of cargo selection and sorting. EXPERT OPINION Mass spectrometry-based proteomics is now a mature technique and has started to deliver new insights in the EV field. Here, we review recent developments in sample preparation, mass spectrometry (MS) and computational analysis and discuss how these technological advances, in conjunction with improved purification protocols, could impact the proteomic characterization of the complex landscape of EVs and other secreted nanoparticles.
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Affiliation(s)
| | - Javier Munoz
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Cell Signaling and Clinical Proteomics Group. Biocruces Bizkaia Health Research Institute. 48903 Barkaldo, Spain.,Ikerbasque, Basque foundation for science, Bilbao, Spain
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24
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Liu S, Tian W, Ma Y, Li J, Yang J, Li B. Serum exosomal proteomics analysis of lung adenocarcinoma to discover new tumor markers. BMC Cancer 2022; 22:279. [PMID: 35291954 PMCID: PMC8925168 DOI: 10.1186/s12885-022-09366-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Among the most aggressive and rapidly lethal types of lung cancer, lung adenocarcinoma is the most common type. Exosomes, as a hot area, play an influential role in cancer. By using proteomics analysis, we aimed to identify potential markers of lung adenocarcinoma in serum. METHODS In our study, we used the ultracentrifugation method to isolate serum exosomes. The Liquid chromatography-mass spectrometry (LC-MS) and bioinformatics analysis were used to identify potential serum exosomal proteins with altered expression among patients with advanced lung adenocarcinoma, early lung adenocarcinoma, and healthy controls. A western blot (WB) was performed to confirm the above differential expression levels in a separate serum sample-isolated exosome, and immunohistochemistry (IHC) staining was conducted to detect expression levels of the above differential proteins of serum exosomes in lung adenocarcinoma tissues and adjacent tissues. Furthermore, we compared different expression models of the above differential proteins in serum and exosomes. RESULT According to the ITGAM (Integrin alpha M chain) and CLU (Clusterin) were differentially expressed in serum exosomes among different groups as well as tumor tissues and adjacent tissues. ITGAM was significantly and specifically enriched in exosomes. As compared to serum, CLU did not appear to be significantly enriched in exosomes. ITGAM and CLU were identified as serum exosomal protein markers of lung adenocarcinoma. CONCLUSIONS This study can provide novel ideas and a research basis for targeting lung adenocarcinoma treatment as a preliminary study.
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Affiliation(s)
- Shanshan Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China.,Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Wenjuan Tian
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China.,Internal Medicine Laboratory, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China
| | - Yuefeng Ma
- Department of Thoracic Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Jiaji Li
- The Second Clinical Medical College, Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi, 712046, P. R. China
| | - Jun Yang
- Department of Pathology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Burong Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China.
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25
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Saumell-Esnaola M, Delgado D, García del Caño G, Beitia M, Sallés J, González-Burguera I, Sánchez P, López de Jesús M, Barrondo S, Sánchez M. Isolation of Platelet-Derived Exosomes from Human Platelet-Rich Plasma: Biochemical and Morphological Characterization. Int J Mol Sci 2022; 23:ijms23052861. [PMID: 35270001 PMCID: PMC8911307 DOI: 10.3390/ijms23052861] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 02/07/2023] Open
Abstract
Platelet-Rich Plasma (PRP) is enriched in molecular messengers with restorative effects on altered tissue environments. Upon activation, platelets release a plethora of growth factors and cytokines, either in free form or encapsulated in exosomes, which have been proven to promote tissue repair and regeneration. Translational research on the potential of exosomes as a safe nanosystem for therapeutic cargo delivery requires standardizing exosome isolation methods along with their molecular and morphological characterization. With this aim, we isolated and characterized the exosomes released by human PRP platelets. Western blot analysis revealed that CaCl2-activated platelets (PLT-Exos-Ca2+) released more exosomes than non-activated ones (PLT-Exos). Moreover, PLT-Exos-Ca2+ exhibited a molecular signature that meets the most up-to-date biochemical criteria for platelet-derived exosomes and possessed morphological features typical of exosomes as assessed by transmission electron microscopy. Array analysis of 105 analytes including growth factors and cytokines showed that PLT-Exos-Ca2+ exhibited lower levels of most analytes compared to PLT-Exos, but relatively higher levels of those consistently validated as components of the protein cargo of platelet exosomes. In summary, the present study provides new insights into the molecular composition of human platelet-derived exosomes and validates a method for isolating highly pure platelet exosomes as a basis for future preclinical studies in regenerative medicine and drug delivery.
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Affiliation(s)
- Miquel Saumell-Esnaola
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.S.-E.); (M.L.d.J.); (S.B.)
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
| | - Diego Delgado
- Advanced Biological Therapy Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain; (D.D.); (M.B.); (P.S.)
| | - Gontzal García del Caño
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
- Department of Neurosciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Maider Beitia
- Advanced Biological Therapy Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain; (D.D.); (M.B.); (P.S.)
| | - Joan Sallés
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.S.-E.); (M.L.d.J.); (S.B.)
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029 Madrid, Spain
- Correspondence: (J.S.); (M.S.); Tel.: +34-945-013114 (J.S.); +34-945-252077 (M.S.)
| | - Imanol González-Burguera
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
- Department of Neurosciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Pello Sánchez
- Advanced Biological Therapy Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain; (D.D.); (M.B.); (P.S.)
| | - Maider López de Jesús
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.S.-E.); (M.L.d.J.); (S.B.)
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
| | - Sergio Barrondo
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.S.-E.); (M.L.d.J.); (S.B.)
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029 Madrid, Spain
| | - Mikel Sánchez
- Advanced Biological Therapy Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain; (D.D.); (M.B.); (P.S.)
- Arthroscopic Surgery Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain
- Correspondence: (J.S.); (M.S.); Tel.: +34-945-013114 (J.S.); +34-945-252077 (M.S.)
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26
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Strybel U, Marczak L, Zeman M, Polanski K, Mielańczyk Ł, Klymenko O, Samelak-Czajka A, Jackowiak P, Smolarz M, Chekan M, Zembala-Nożyńska E, Widlak P, Pietrowska M, Wojakowska A. Molecular Composition of Serum Exosomes Could Discriminate Rectal Cancer Patients with Different Responses to Neoadjuvant Radiotherapy. Cancers (Basel) 2022; 14:993. [PMID: 35205741 PMCID: PMC8870712 DOI: 10.3390/cancers14040993] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/21/2022] Open
Abstract
Identification of biomarkers that could be used for the prediction of the response to neoadjuvant radiotherapy (neo-RT) in locally advanced rectal cancer remains a challenge addressed by different experimental approaches. Exosomes and other classes of extracellular vesicles circulating in patients' blood represent a novel type of liquid biopsy and a source of cancer biomarkers. Here, we used a combined proteomic and metabolomic approach based on mass spectrometry techniques for studying the molecular components of exosomes isolated from the serum of rectal cancer patients with different responses to neo-RT. This allowed revealing several proteins and metabolites associated with common pathways relevant for the response of rectal cancer patients to neo-RT, including immune system response, complement activation cascade, platelet functions, metabolism of lipids, metabolism of glucose, and cancer-related signaling pathways. Moreover, the composition of serum-derived exosomes and a whole serum was analyzed in parallel to compare the biomarker potential of both specimens. Among proteins that the most properly discriminated good and poor responders were GPLD1 (AUC = 0.85, accuracy of 74%) identified in plasma as well as C8G (AUC = 0.91, accuracy 81%), SERPINF2 (AUC = 0.91, accuracy 79%) and CFHR3 (AUC = 0.90, accuracy 81%) identified in exosomes. We found that the proteome component of serum-derived exosomes has the highest capacity to discriminate samples of patients with different responses to neo-RT when compared to the whole plasma proteome and metabolome. We concluded that the molecular components of exosomes are associated with the response of rectal cancer patients to neo-RT and could be used for the prediction of such response.
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Affiliation(s)
- Urszula Strybel
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland; (U.S.); (L.M.); (A.S.-C.); (P.J.)
| | - Lukasz Marczak
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland; (U.S.); (L.M.); (A.S.-C.); (P.J.)
| | - Marcin Zeman
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.Z.); (M.S.); (M.C.); (E.Z.-N.); (M.P.)
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK;
| | - Łukasz Mielańczyk
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland; (Ł.M.); (O.K.)
| | - Olesya Klymenko
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland; (Ł.M.); (O.K.)
| | - Anna Samelak-Czajka
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland; (U.S.); (L.M.); (A.S.-C.); (P.J.)
| | - Paulina Jackowiak
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland; (U.S.); (L.M.); (A.S.-C.); (P.J.)
| | - Mateusz Smolarz
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.Z.); (M.S.); (M.C.); (E.Z.-N.); (M.P.)
| | - Mykola Chekan
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.Z.); (M.S.); (M.C.); (E.Z.-N.); (M.P.)
| | - Ewa Zembala-Nożyńska
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.Z.); (M.S.); (M.C.); (E.Z.-N.); (M.P.)
| | - Piotr Widlak
- Clinical Research Support Centre, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Monika Pietrowska
- Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.Z.); (M.S.); (M.C.); (E.Z.-N.); (M.P.)
| | - Anna Wojakowska
- Department of Biomedical Proteomics, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Poland; (U.S.); (L.M.); (A.S.-C.); (P.J.)
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27
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Improving Isolation of Extracellular Vesicles by Utilizing Nanomaterials. MEMBRANES 2021; 12:membranes12010055. [PMID: 35054584 PMCID: PMC8780510 DOI: 10.3390/membranes12010055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 01/04/2023]
Abstract
Extracellular vesicles (EVs) as the new form of cellular communication have been demonstrated their potential use for disease diagnosis, prognosis and treatment. EVs are vesicles with a lipid bilayer and are present in various biofluids, such as blood, saliva and urine. Therefore, EVs have emerged as one of the most appealing sources for the discovery of clinical biomarkers. However, isolation of the target EVs from different biofluids is required for the use of EVs as diagnostic and therapeutic entities in clinical settings. Owing to their unique properties and versatile functionalities, nanomaterials have been widely investigated for EV isolation with the aim to provide rapid, simple, and efficient EV enrichment. Herein, this review presents the progress of nanomaterial-based isolations for EVs over the past five years (from 2017 to 2021) and discusses the use of nanomaterials for EV isolations based on the underlying mechanism in order to offer insights into the design of nanomaterials for EV isolations.
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28
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Azkargorta M, Iloro I, Escobes I, Cabrera D, Falcon-Perez JM, Elortza F, Royo F. Human Serum Extracellular Vesicle Proteomic Profile Depends on the Enrichment Method Employed. Int J Mol Sci 2021; 22:ijms222011144. [PMID: 34681804 PMCID: PMC8540106 DOI: 10.3390/ijms222011144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 12/16/2022] Open
Abstract
The proteomic profiling of serum samples supposes a challenge due to the large abundance of a few blood proteins in comparison with other circulating proteins coming from different tissues and cells. Although the sensitivity of protein detection has increased enormously in the last years, specific strategies are still required to enrich less abundant proteins and get rid of abundant proteins such as albumin, lipoproteins, and immunoglobulins. One of the alternatives that has become more promising is to characterize circulating extracellular vesicles from serum samples that have great interest in biomedicine. In the present work, we enriched the extracellular vesicles fraction from human serum by applying different techniques, including ultracentrifugation, size-exclusion chromatography, and two commercial precipitation methods based on different mechanisms of action. To improve the performance and efficacy of the techniques to promote purity of the preparations, we have employed a small volume of serum samples (<100 mL). The comparative proteomic profiling of the enriched preparations shows that ultracentrifugation procedure yielded a larger and completely different set of proteins than other techniques, including mitochondrial and ribosome related proteins. The results showed that size exclusion chromatography carries over lipoprotein associated proteins, while a polymer-based precipitation kit has more affinity for proteins associated with granules of platelets. The precipitation kit that targets glycosylation molecules enriches differentially protein harboring glycosylation sites, including immunoglobulins and proteins of the membrane attack complex.
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Affiliation(s)
- Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Iraide Escobes
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Diana Cabrera
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Juan M. Falcon-Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Correspondence: (F.E.); (F.R.)
| | - Felix Royo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Correspondence: (F.E.); (F.R.)
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Shao D, Huang L, Wang Y, Cui X, Li Y, Wang Y, Ma Q, Du W, Cui J. HBFP: a new repository for human body fluid proteome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6395039. [PMID: 34642750 PMCID: PMC8516408 DOI: 10.1093/database/baab065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Body fluid proteome has been intensively studied as a primary source for disease
biomarker discovery. Using advanced proteomics technologies, early research
success has resulted in increasingly accumulated proteins detected in different
body fluids, among which many are promising biomarkers. However, despite a
handful of small-scale and specific data resources, current research is clearly
lacking effort compiling published body fluid proteins into a centralized and
sustainable repository that can provide users with systematic analytic tools. In
this study, we developed a new database of human body fluid proteome (HBFP) that
focuses on experimentally validated proteome in 17 types of human body fluids.
The current database archives 11 827 unique proteins reported by 164
scientific publications, with a maximal false discovery rate of 0.01 on both the
peptide and protein levels since 2001, and enables users to query, analyze and
download protein entries with respect to each body fluid. Three unique features
of this new system include the following: (i) the protein annotation page
includes detailed abundance information based on relative qualitative measures
of peptides reported in the original references, (ii) a new score is calculated
on each reported protein to indicate the discovery confidence and (iii) HBFP
catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of
nine amino acids according to the Human Proteome Project Data Interpretation
Guidelines, while the remaining 4473 proteins have more than two unique peptides
without given sequence information. As an important resource for human protein
secretome, we anticipate that this new HBFP database can be a powerful tool that
facilitates research in clinical proteomics and biomarker discovery. Database URL:https://bmbl.bmi.osumc.edu/HBFP/
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Affiliation(s)
- Dan Shao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA.,Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China.,Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xueteng Cui
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yufei Li
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yao Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 310G Lincoln tower, 1800 cannon drive, Columbus, OH 43210, USA
| | - Wei Du
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA
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30
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Apostolopoulou M, Mastrototaro L, Hartwig S, Pesta D, Straßburger K, de Filippo E, Jelenik T, Karusheva Y, Gancheva S, Markgraf D, Herder C, Nair KS, Reichert AS, Lehr S, Müssig K, Al-Hasani H, Szendroedi J, Roden M. Metabolic responsiveness to training depends on insulin sensitivity and protein content of exosomes in insulin-resistant males. SCIENCE ADVANCES 2021; 7:eabi9551. [PMID: 34623918 PMCID: PMC8500512 DOI: 10.1126/sciadv.abi9551] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
High-intensity interval training (HIIT) improves cardiorespiratory fitness (VO2max), but its impact on metabolism remains unclear. We hypothesized that 12-week HIIT increases insulin sensitivity in males with or without type 2 diabetes [T2D and NDM (nondiabetic humans)]. However, despite identically higher VO2max, mainly insulin-resistant (IR) persons (T2D and IR NDM) showed distinct alterations of circulating small extracellular vesicles (SEVs) along with lower inhibitory metabolic (protein kinase Cε activity) or inflammatory (nuclear factor κB) signaling in muscle of T2D or IR NDM, respectively. This is related to the specific alterations in SEV proteome reflecting down-regulation of the phospholipase C pathway (T2D) and up-regulated antioxidant capacity (IR NDM). Thus, SEV cargo may contribute to modulating the individual metabolic responsiveness to exercise training in humans.
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Affiliation(s)
- Maria Apostolopoulou
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- 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, München-Neuherberg, Germany
| | - 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, München-Neuherberg, Germany
| | - Sonja Hartwig
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
- Institute for Clinical Biochemistry and Pathobiochemistry German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Dominik Pesta
- 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, München-Neuherberg, Germany
| | - Klaus Straßburger
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Elisabetta de Filippo
- 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, München-Neuherberg, Germany
| | - Tomas Jelenik
- 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, München-Neuherberg, Germany
| | - Yanislava Karusheva
- 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, München-Neuherberg, Germany
| | - Sofiya Gancheva
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- 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, München-Neuherberg, Germany
| | - Daniel Markgraf
- 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, München-Neuherberg, Germany
| | - Christian Herder
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- 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, München-Neuherberg, Germany
| | - K. Sreekumaran Nair
- Division of Endocrinology, Diabetes and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - Andreas S. Reichert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Stefan Lehr
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
- Institute for Clinical Biochemistry and Pathobiochemistry German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Karsten Müssig
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- 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, München-Neuherberg, Germany
| | - Hadi Al-Hasani
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
- Institute for Clinical Biochemistry and Pathobiochemistry German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Julia Szendroedi
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- 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, München-Neuherberg, Germany
- Department of Internal Medicine, Heidelberg University, Heidelberg, Germany
| | - Michael Roden
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- 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, München-Neuherberg, Germany
- Corresponding author.
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Zhu J, Zhang J, Ji X, Tan Z, Lubman DM. Column-based Technology for CD9-HPLC Immunoaffinity Isolation of Serum Extracellular Vesicles. J Proteome Res 2021; 20:4901-4911. [PMID: 34473505 DOI: 10.1021/acs.jproteome.1c00549] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Serum-derived extracellular vesicles (EVs) are a promising source of biomarkers; however, major challenges in EV separation and proteomic profiling remain for isolating EVs from a small amount, that is, on the microliter scale, of human serum while minimizing the contamination of blood proteins and lipoprotein particles coeluting in EV preparations. Herein we have developed a column-based CD9-antibody-immobilized high-performance liquid chromatography immunoaffinity chromatography(CD9-HPLC-IAC) technology for EV isolation from a microliter scale of serum for downstream proteomic analysis. The CD9-HPLC-IAC method achieved EV isolation from 40 μL of serum in 30 min with a yield of 8.0 × 109 EVs, where EVs were further processed with a postcolumn cleaning step using the 50 kDa molecular weight cut-off filter for the buffer exchange, concentration, and reduction of potentially coeluting serum proteins. In total, 482 proteins were identified in EVs by using liquid chromatography tandem mass spectrometry, including the common exosomal markers such as CD63, CD81, CD82, Alix, and TSG101. The statistical analysis of EV protein content showed that the top 10 serum proteins in EVs were significantly decreased by using the CD9-HPLC-IAC method compared with the use of ultracentrifugation (p = 0.001) and size exclusion chromatography (p = 0.009), and apolipoproteins were significantly reduced 4.8-fold compared with the SEC method (p < 0.001). The result demonstrates the potential of the CD9-HPLC-IAC method for the efficient isolation and proteomic characterization of EVs from a microscale volume of serum.
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Affiliation(s)
- Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Xiaohui Ji
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States.,Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
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Reale A, Khong T, Mithraprabhu S, Spencer A. Translational Potential of RNA Derived From Extracellular Vesicles in Multiple Myeloma. Front Oncol 2021; 11:718502. [PMID: 34513695 PMCID: PMC8429596 DOI: 10.3389/fonc.2021.718502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/04/2021] [Indexed: 12/20/2022] Open
Abstract
The cross-talk between tumour cells and stromal cells is a hallmark of multiple myeloma (MM), a blood cancer that still remains incurable despite increased knowledge of its biology and advances in its treatment. Extracellular vesicles (EVs) derived from both tumour and stromal cells have been shown to play an important role in mediating this cross-talk ultimately favouring MM progression and drug resistance. Furthermore, EVs and their content including RNA (EV-RNA) have been successfully isolated from blood and are being explored as liquid biomarkers in MM with the potential to improve diagnosis and monitoring modalities with a minimally-invasive and repeatable analysis, i.e. liquid biopsy. In this review, we describe both the role of EV-RNA in defining the biological features of MM and their potential translational relevance as liquid biomarkers, therapeutic targets and delivery systems. We also discuss the limitations and technical challenges related to the isolation and characterization of EVs and provide a perspective on the future of MM-derived EV-RNA in translational research.
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Affiliation(s)
- Antonia Reale
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University/Alfred Health, Melbourne, VIC, Australia
| | - Tiffany Khong
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University/Alfred Health, Melbourne, VIC, Australia
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University/Alfred Health, Melbourne, VIC, Australia
| | - Andrew Spencer
- Myeloma Research Group, Australian Centre for Blood Diseases, Central Clinical School, Monash University/Alfred Health, Melbourne, VIC, Australia.,Malignant Haematology and Stem Cell Transplantation, The Alfred Hospital, and Department of Clinical Haematology, Monash University, Melbourne, VIC, Australia
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33
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A Comprehensive Insight into the Role of Exosomes in Viral Infection: Dual Faces Bearing Different Functions. Pharmaceutics 2021; 13:pharmaceutics13091405. [PMID: 34575480 PMCID: PMC8466084 DOI: 10.3390/pharmaceutics13091405] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) subtype, exosome is an extracellular nano-vesicle that sheds from cells’ surface and originates as intraluminal vesicles during endocytosis. Firstly, it was thought to be a way for the cell to get rid of unwanted materials as it loaded selectively with a variety of cellular molecules, including RNAs, proteins, and lipids. However, it has been found to play a crucial role in several biological processes such as immune modulation, cellular communication, and their role as vehicles to transport biologically active molecules. The latest discoveries have revealed that many viruses export their viral elements within cellular factors using exosomes. Hijacking the exosomal pathway by viruses influences downstream processes such as viral propagation and cellular immunity and modulates the cellular microenvironment. In this manuscript, we reviewed exosomes biogenesis and their role in the immune response to viral infection. In addition, we provided a summary of how some pathogenic viruses hijacked this normal physiological process. Viral components are harbored in exosomes and the role of these exosomes in viral infection is discussed. Understanding the nature of exosomes and their role in viral infections is fundamental for future development for them to be used as a vaccine or as a non-classical therapeutic strategy to control several viral infections.
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Wu Q, Poulsen SB, Murali SK, Grimm PR, Su XT, Delpire E, Welling PA, Ellison DH, Fenton RA. Large-Scale Proteomic Assessment of Urinary Extracellular Vesicles Highlights Their Reliability in Reflecting Protein Changes in the Kidney. J Am Soc Nephrol 2021; 32:2195-2209. [PMID: 34230103 PMCID: PMC8729841 DOI: 10.1681/asn.2020071035] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/12/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Urinary extracellular vesicles (uEVs) are secreted into urine by cells from the kidneys and urinary tract. Although changes in uEV proteins are used for quantitative assessment of protein levels in the kidney or biomarker discovery, whether they faithfully reflect (patho)physiologic changes in the kidney is a matter of debate. METHODS Mass spectrometry was used to compare in an unbiased manner the correlations between protein levels in uEVs and kidney tissue from the same animal. Studies were performed on rats fed a normal or high K+ diet. RESULTS Absolute quantification determined a positive correlation (Pearson R=0.46 or 0.45, control or high K+ respectively, P<0.0001) between the approximately 1000 proteins identified in uEVs and corresponding kidney tissue. Transmembrane proteins had greater positive correlations relative to cytoplasmic proteins. Proteins with high correlations (R>0.9), included exosome markers Tsg101 and Alix. Relative quantification highlighted a monotonic relationship between altered transporter/channel abundances in uEVs and the kidney after dietary K+ manipulation. Analysis of genetic mouse models also revealed correlations between uEVs and kidney. CONCLUSION This large-scale unbiased analysis identifies uEV proteins that track the abundance of the parent proteins in the kidney. The data form a novel resource for the kidney community and support the reliability of using uEV protein changes to monitor specific physiologic responses and disease mechanisms.
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Affiliation(s)
- Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | | | - Paul R. Grimm
- Departments of Medicine and Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Xiao-Tong Su
- Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Paul A. Welling
- Departments of Medicine and Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - David H. Ellison
- Department of Medicine, Oregon Health & Science University, Portland, Oregon
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35
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Ledreux A, Thomas S, Hamlett ED, Trautman C, Gilmore A, Rickman Hager E, Paredes DA, Margittai M, Fortea J, Granholm AC. Small Neuron-Derived Extracellular Vesicles from Individuals with Down Syndrome Propagate Tau Pathology in the Wildtype Mouse Brain. J Clin Med 2021; 10:3931. [PMID: 34501378 PMCID: PMC8432237 DOI: 10.3390/jcm10173931] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/28/2021] [Indexed: 12/11/2022] Open
Abstract
Individuals with Down syndrome (DS) exhibit Alzheimer's disease (AD) pathology at a young age, including amyloid plaques and neurofibrillary tangles (NFTs). Tau pathology can spread via extracellular vesicles, such as exosomes. The cargo of neuron-derived small extracellular vesicles (NDEVs) from individuals with DS contains p-Tau at an early age. The goal of the study was to investigate whether NDEVs isolated from the blood of individuals with DS can spread Tau pathology in the brain of wildtype mice. We purified NDEVs from the plasma of patients with DS-AD and controls and injected small quantities using stereotaxic surgery into the dorsal hippocampus of adult wildtype mice. Seeding competent Tau conformers were amplified in vitro from DS-AD NDEVs but not NDEVs from controls. One month or 4 months post-injection, we examined Tau pathology in mouse brains. We found abundant p-Tau immunostaining in the hippocampus of the mice injected with DS-AD NDEVs compared to injections of age-matched control NDEVs. Double labeling with neuronal and glial markers showed that p-Tau staining was largely found in neurons and, to a lesser extent, in glial cells and that p-Tau immunostaining was spreading along the corpus callosum and the medio-lateral axis of the hippocampus. These studies demonstrate that NDEVs from DS-AD patients exhibit Tau seeding capacity and give rise to tangle-like intracellular inclusions.
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Affiliation(s)
- Aurélie Ledreux
- Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA; (S.T.); (C.T.); (A.G.); (D.A.P.); (A.-C.G.)
| | - Sarah Thomas
- Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA; (S.T.); (C.T.); (A.G.); (D.A.P.); (A.-C.G.)
| | - Eric D. Hamlett
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Camille Trautman
- Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA; (S.T.); (C.T.); (A.G.); (D.A.P.); (A.-C.G.)
| | - Anah Gilmore
- Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA; (S.T.); (C.T.); (A.G.); (D.A.P.); (A.-C.G.)
| | - Emily Rickman Hager
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208, USA; (E.R.H.); (M.M.)
| | - Daniel A. Paredes
- Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA; (S.T.); (C.T.); (A.G.); (D.A.P.); (A.-C.G.)
| | - Martin Margittai
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208, USA; (E.R.H.); (M.M.)
| | - Juan Fortea
- Hospital de la Santa Creu i Sant Pau and Catalan Down Syndrome Foundation, 08041 Barcelona, Spain;
| | - Ann-Charlotte Granholm
- Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA; (S.T.); (C.T.); (A.G.); (D.A.P.); (A.-C.G.)
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Extracellular Vesicle Separation Techniques Impact Results from Human Blood Samples: Considerations for Diagnostic Applications. Int J Mol Sci 2021; 22:ijms22179211. [PMID: 34502122 PMCID: PMC8431127 DOI: 10.3390/ijms22179211] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/14/2023] Open
Abstract
Extracellular vesicles (EVs) are reminiscent of their cell of origin and thus represent a valuable source of biomarkers. However, for EVs to be used as biomarkers in clinical practice, simple, comparable, and reproducible analytical methods must be applied. Although progress is being made in EV separation methods for human biofluids, the implementation of EV assays for clinical diagnosis and common guidelines are still lacking. We conducted a comprehensive analysis of established EV separation techniques from human serum and plasma, including ultracentrifugation and size exclusion chromatography (SEC), followed by concentration using (a) ultracentrifugation, (b) ultrafiltration, or (c) precipitation, and immunoaffinity isolation. We analyzed the size, number, protein, and miRNA content of the obtained EVs and assessed the functional delivery of EV cargo. Our results demonstrate that all methods led to an adequate yield of small EVs. While no significant difference in miRNA content was observed for the different separation methods, ultracentrifugation was best for subsequent flow cytometry analysis. Immunoaffinity isolation is not suitable for subsequent protein analyses. SEC + ultracentrifugation showed the best functional delivery of EV cargo. In summary, combining SEC with ultracentrifugation gives the highest yield of pure and functional EVs and allows reliable analysis of both protein and miRNA contents. We propose this combination as the preferred EV isolation method for biomarker studies from human serum or plasma.
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37
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Qu X, Leung TCN, Ngai SM, Tsai SN, Thakur A, Li WK, Lee Y, Leung L, Ng TH, Yam J, Lan L, Lau EHL, Wong EWY, Chan JYK, Meehan K. Proteomic Analysis of Circulating Extracellular Vesicles Identifies Potential Biomarkers for Lymph Node Metastasis in Oral Tongue Squamous Cell Carcinoma. Cells 2021; 10:2179. [PMID: 34571828 PMCID: PMC8468562 DOI: 10.3390/cells10092179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Lymph node metastasis is the most reliable indicator of a poor prognosis for patients with oral tongue cancers. Currently, there are no biomarkers to predict whether a cancer will spread in the future if it has not already spread at the time of diagnosis. The aim of this study was to quantitatively profile the proteomes of extracellular vesicles (EVs) isolated from blood samples taken from patients with oral tongue squamous cell carcinoma with and without lymph node involvement and non-cancer controls. EVs were enriched using size exclusion chromatography (SEC) from pooled plasma samples of patients with non-nodal and nodal oral tongue squamous cell carcinoma (OTSCC) and non-cancer controls. Protein cargo was quantitatively profiled using isobaric labelling (iTRAQ) and two-dimensional high-performance liquid chromatography followed by tandem mass spectrometry. We identified 208 EV associated proteins and, after filtering, generated a short list of 136 proteins. Over 85% of the EV-associated proteins were associated with the GO cellular compartment term "extracellular exosome". Comparisons between non-cancer controls and oral tongue squamous cell carcinoma with and without lymph node involvement revealed 43 unique candidate EV-associated proteins with deregulated expression patterns. The shortlisted EV associated proteins described here may be useful discriminatory biomarkers for differentiating OTSCC with and without nodal disease or non-cancer controls.
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Affiliation(s)
- Xinyu Qu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Thomas C. N. Leung
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (T.C.N.L.); (S.-M.N.); (S.-N.T.)
| | - Sai-Ming Ngai
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (T.C.N.L.); (S.-M.N.); (S.-N.T.)
| | - Sau-Na Tsai
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (T.C.N.L.); (S.-M.N.); (S.-N.T.)
| | - Abhimanyu Thakur
- Department of Neuroscience, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China; (A.T.); (Y.L.)
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China;
- Ben May Department for Cancer Research, Pritzker School of Molecular Engineering, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Wing-Kar Li
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China;
| | - Youngjin Lee
- Department of Neuroscience, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China; (A.T.); (Y.L.)
| | - Leanne Leung
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Tung-Him Ng
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China; (T.-H.N.); (J.Y.)
| | - Judy Yam
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China; (T.-H.N.); (J.Y.)
| | - Linlin Lan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Eric H. L. Lau
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Eddy W. Y. Wong
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Jason Y. K. Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Katie Meehan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
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The Lipid Composition of Serum-Derived Small Extracellular Vesicles in Participants of a Lung Cancer Screening Study. Cancers (Basel) 2021; 13:cancers13143414. [PMID: 34298629 PMCID: PMC8307680 DOI: 10.3390/cancers13143414] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/29/2021] [Accepted: 07/06/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Molecular components of extracellular vesicles present in serum are potential biomarkers of lung cancer, however, none of them have been validated in the context of an actual early detection of lung cancer. Here, we compared the lipid profiles of vesicles obtained from participants in a lung cancer screening study, including patients with screening-detected cancer and individuals with benign pulmonary nodules or without pathological changes. A few lipids whose levels were different between compared groups were detected, including ceramide Cer(42:1) upregulated in vesicles from cancer patients. Furthermore, a high heterogeneity of lipid profiles of extracellular vesicles was observed, which impaired the performance of classification models based on specific compounds. Abstract Molecular components of exosomes and other classes of small extracellular vesicles (sEV) present in human biofluids are potential biomarkers with possible applicability in the early detection of lung cancer. Here, we compared the lipid profiles of serum-derived sEV from three groups of lung cancer screening participants: individuals without pulmonary alterations, individuals with benign lung nodules, and patients with screening-detected lung cancer (81 individuals in each group). Extracellular vesicles and particles were purified from serum by size-exclusion chromatography, and a fraction enriched in sEV and depleted of low-density lipoproteins (LDLs) was selected (similar sized vesicles was observed in all groups: 70–100 nm). The targeted mass-spectrometry-based approach enabled the detection of 352 lipids, including 201 compounds used in quantitative analyses. A few compounds, exemplified by Cer(42:1), i.e., a ceramide whose increased plasma/serum level was reported in different pathological conditions, were upregulated in vesicles from cancer patients. On the other hand, the contribution of phosphatidylcholines with poly-unsaturated acyl chains was reduced in vesicles from lung cancer patients. Cancer-related features detected in serum-derived sEV were different than those of the corresponding whole serum. A high heterogeneity of lipid profiles of sEV was observed, which markedly impaired the performance of classification models based on specific compounds (the three-state classifiers showed an average AUC = 0.65 and 0.58 in the training and test subsets, respectively).
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39
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Signore M, Alfonsi R, Federici G, Nanni S, Addario A, Bertuccini L, Aiello A, Di Pace AL, Sperduti I, Muto G, Giacobbe A, Collura D, Brunetto L, Simone G, Costantini M, Crinò L, Rossi S, Tabolacci C, Diociaiuti M, Merlino T, Gallucci M, Sentinelli S, Papalia R, De Maria R, Bonci D. Diagnostic and prognostic potential of the proteomic profiling of serum-derived extracellular vesicles in prostate cancer. Cell Death Dis 2021; 12:636. [PMID: 34155195 PMCID: PMC8215487 DOI: 10.1038/s41419-021-03909-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 12/16/2022]
Abstract
Extracellular vesicles (EVs) and their cargo represent an intriguing source of cancer biomarkers for developing robust and sensitive molecular tests by liquid biopsy. Prostate cancer (PCa) is still one of the most frequent and deadly tumor in men and analysis of EVs from biological fluids of PCa patients has proven the feasibility and the unprecedented potential of such an approach. Here, we exploited an antibody-based proteomic technology, i.e. the Reverse-Phase Protein microArrays (RPPA), to measure key antigens and activated signaling in EVs isolated from sera of PCa patients. Notably, we found tumor-specific protein profiles associated with clinical settings as well as candidate markers for EV-based tumor diagnosis. Among others, PD-L1, ERG, Integrin-β5, Survivin, TGF-β, phosphorylated-TSC2 as well as partners of the MAP-kinase and mTOR pathways emerged as differentially expressed endpoints in tumor-derived EVs. In addition, the retrospective analysis of EVs from a 15-year follow-up cohort generated a protein signature with prognostic significance. Our results confirm that serum-derived EV cargo may be exploited to improve the current diagnostic procedures while providing potential prognostic and predictive information. The approach proposed here has been already applied to tumor entities other than PCa, thus proving its value in translational medicine and paving the way to innovative, clinically meaningful tools.
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Affiliation(s)
- Michele Signore
- RPPA Unit, Proteomics Area, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Romina Alfonsi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Simona Nanni
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore Largo F. Vito 1, 00168, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Antonio Addario
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Bertuccini
- RPPA Unit, Proteomics Area, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Aurora Aiello
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore Largo F. Vito 1, 00168, Rome, Italy
| | - Anna Laura Di Pace
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Giovanni Muto
- Department of Urology, Humanitas University, Turin, Italy.,Department of Urology, S. Giovanni Bosco Hospital, Turin, Italy
| | - Alessandro Giacobbe
- Department of Urology, Humanitas University, Turin, Italy.,Department of Urology, S. Giovanni Bosco Hospital, Turin, Italy
| | - Devis Collura
- Department of Urology, Humanitas University, Turin, Italy.,Department of Urology, S. Giovanni Bosco Hospital, Turin, Italy
| | - Lidia Brunetto
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Simone
- Department of Urology-IRCCS Regina Elena National Cancer Institute of Rome, Rome, Italy
| | - Manuela Costantini
- Department of Urology-IRCCS Regina Elena National Cancer Institute of Rome, Rome, Italy
| | - Lucio Crinò
- Department of Oncology, IRST-Meldola, Meldola, Italy
| | - Stefania Rossi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Claudio Tabolacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Diociaiuti
- Department of Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Tania Merlino
- IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | - Michele Gallucci
- Department of Urology-IRCCS Regina Elena National Cancer Institute of Rome, Rome, Italy.,Department of Urology, Sapienza University of Rome, Rome, Italy
| | | | | | - Ruggero De Maria
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore Largo F. Vito 1, 00168, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Désirée Bonci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy. .,IRCCS, Regina Elena National Cancer Institute, Rome, Italy.
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40
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Richter R, Lehr CM. Extracellular vesicles as novel assay tools to study cellular interactions of anti-infective compounds - A perspective. Adv Drug Deliv Rev 2021; 173:492-503. [PMID: 33857554 DOI: 10.1016/j.addr.2021.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Sudden outbreaks of novel infectious diseases and the persistent evolution of antimicrobial resistant pathogens make it necessary to develop specific tools to quickly understand pathogen-cell interactions and to study appropriate drug delivery strategies. Extracellular vesicles (EVs) are cell-specific biogenic transport systems, which are gaining more and more popularity as either diagnostic markers or drug delivery systems. Apart from that, there are emerging possibilities for EVs as tools to study drug penetration, drug-membrane interactions as well as pathogen-membrane interactions. However, it appears that the potential of EVs for such applications has not been fully exploited yet. Considering the vast variety of cells that can be involved in an infection, vesicle-based analytical methods are just emerging and the number of reported applications is still relatively small. Aim of this review is to discuss the current state of the art of EV-based assays, especially in the context of antimicrobial research and therapy, and to present some new perspectives for a more exhaustive and creative exploration in the future.
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Affiliation(s)
- Robert Richter
- Department of Drug Delivery Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Claus-Michael Lehr
- Department of Drug Delivery Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
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Human Plasma Extracellular Vesicle Isolation and Proteomic Characterization for the Optimization of Liquid Biopsy in Multiple Myeloma. Methods Mol Biol 2021; 2261:151-191. [PMID: 33420989 DOI: 10.1007/978-1-0716-1186-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer cells secrete membranous extracellular vesicles (EVs) which contain specific oncogenic molecular cargo (including oncoproteins, oncopeptides, and RNA) into their microenvironment and the circulation. As such, EVs including exosomes (small EVs) and microvesicles (large EVs) represent important circulating biomarkers for various diseases, including cancer and its progression. These circulating biomarkers offer a potentially minimally invasive and repeatable targets for analysis (liquid biopsy) that could aid in the diagnosis, risk stratification, and monitoring of cancer. Although their potential as cancer biomarkers has been promising, the identification and quantification of EVs in clinical samples remain challenging. Like EVs, other types of circulating biomarkers (including cell-free nucleic acids, cf-NAs; or circulating tumor cells, CTCs) may represent a complementary or alternative approach to cancer diagnosis. In the context of multiple myeloma (MM), a systemic cancer type that causes cancer cells to accumulate in the bone marrow, the specific role for EVs as biomarkers for diagnosis and monitoring remains undefined. Tumor heterogeneity along with the various subtypes of MM (such as non-secretory MM) that cannot be monitored using conventional testing (e.g. sequential serological testing and bone marrow biopsies) render liquid biopsy and circulating tumor-derived EVs a promising approach. In this protocol, we describe the isolation and purification of EVs from peripheral blood plasma (PBPL) collected from healthy donors and patients with MM for a biomarker discovery strategy. Our results demonstrate detection of circulating EVs from as little as 1 mL of MM patients' PBPL. High-resolution mass spectrometry (MS)-based proteomics promises to provide new avenues in identifying novel markers for detection, monitoring, and therapeutic intervention of disease. We describe biophysical characterization and quantitative proteomic profiling of disease-specific circulating EVs which may provide important implications for the development of cancer diagnostics in MM.
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42
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Raman Spectral Signatures of Serum-Derived Extracellular Vesicle-Enriched Isolates May Support the Diagnosis of CNS Tumors. Cancers (Basel) 2021; 13:cancers13061407. [PMID: 33808766 PMCID: PMC8003579 DOI: 10.3390/cancers13061407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023] Open
Abstract
Investigating the molecular composition of small extracellular vesicles (sEVs) for tumor diagnostic purposes is becoming increasingly popular, especially for diseases for which diagnosis is challenging, such as central nervous system (CNS) malignancies. Thorough examination of the molecular content of sEVs by Raman spectroscopy is a promising but hitherto barely explored approach for these tumor types. We attempt to reveal the potential role of serum-derived sEVs in diagnosing CNS tumors through Raman spectroscopic analyses using a relevant number of clinical samples. A total of 138 serum samples were obtained from four patient groups (glioblastoma multiforme, non-small-cell lung cancer brain metastasis, meningioma and lumbar disc herniation as control). After isolation, characterization and Raman spectroscopic assessment of sEVs, the Principal Component Analysis-Support Vector Machine (PCA-SVM) algorithm was performed on the Raman spectra for pairwise classifications. Classification accuracy (CA), sensitivity, specificity and the Area Under the Curve (AUC) value derived from Receiver Operating Characteristic (ROC) analyses were used to evaluate the performance of classification. The groups compared were distinguishable with 82.9-92.5% CA, 80-95% sensitivity and 80-90% specificity. AUC scores in the range of 0.82-0.9 suggest excellent and outstanding classification performance. Our results support that Raman spectroscopic analysis of sEV-enriched isolates from serum is a promising method that could be further developed in order to be applicable in the diagnosis of CNS tumors.
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Reale A, Carmichael I, Xu R, Mithraprabhu S, Khong T, Chen M, Fang H, Savvidou I, Ramachandran M, Bingham N, Simpson RJ, Greening DW, Spencer A. Human myeloma cell- and plasma-derived extracellular vesicles contribute to functional regulation of stromal cells. Proteomics 2021; 21:e2000119. [PMID: 33580572 DOI: 10.1002/pmic.202000119] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Circulating small extracellular vesicles (sEV) represent promising non-invasive biomarkers that may aid in the diagnosis and risk-stratification of multiple myeloma (MM), an incurable blood cancer. Here, we comprehensively isolated and characterized sEV from human MM cell lines (HMCL) and patient-derived plasma (psEV) by specific EV-marker enrichment and morphology. Importantly, we demonstrate that HMCL-sEV are readily internalised by stromal cells to functionally modulate proliferation. psEV were isolated using various commercial approaches and pre-analytical conditions (collection tube types, storage conditions) assessed for sEV yield and marker enrichment. Functionally, MM-psEV was shown to regulate stromal cell proliferation and migration. In turn, pre-educated stromal cells favour HMCL adhesion. psEV isolated from patients with both pre-malignant plasma cell disorders (monoclonal gammopathy of undetermined significance [MGUS]; smouldering MM [SMM]) and MM have a similar ability to promote cell migration and adhesion, suggesting a role for both malignant and pre-malignant sEV in disease progression. Proteomic profiling of MM-psEV (305 proteins) revealed enrichment of oncogenic factors implicated in cell migration and adhesion, in comparison to non-disease psEV. This study describes a protocol to generate morphologically-intact and biologically functional sEV capable of mediating the regulation of stromal cells, and a model for the characterization of tumour-stromal cross-talk by sEV in MM.
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Affiliation(s)
- Antonia Reale
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Irena Carmichael
- Monash Micro Imaging-AMREP, Monash University, Melbourne, Victoria, Australia
| | - Rong Xu
- Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Nanobiotechnology Laboratory, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Tiffany Khong
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Maoshan Chen
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia
| | - Haoyun Fang
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Ioanna Savvidou
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Malarmathy Ramachandran
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Nicholas Bingham
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Richard J Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - David W Greening
- Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Andrew Spencer
- Myeloma Research Group, Australian Centre for Blood Diseases, Monash University/Alfred Health, Melbourne, Victoria, Australia.,Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Malignant Haematology and Stem Cell Transplantation, The Alfred Hospital, and Department of Clinical Haematology, Monash University, Melbourne, Victoria, Australia
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Mathew B, Mansuri MS, Williams KR, Nairn AC. Exosomes as Emerging Biomarker Tools in Neurodegenerative and Neuropsychiatric Disorders-A Proteomics Perspective. Brain Sci 2021; 11:258. [PMID: 33669482 PMCID: PMC7922222 DOI: 10.3390/brainsci11020258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Exosomes are synthesized and secreted by different cell types and contain proteins, lipids, metabolites and RNA species that reflect the physiological status of the cell of origin. As such, exosomes are increasingly being used as a novel reservoir for disease biomarker discovery. However, isolation of exosomes can be challenging due to their nonuniformity of shape and variable tissue of origin. Moreover, various analytical techniques used for protein detection and quantitation remain insensitive to the low amounts of protein isolated from exosomes. Despite these challenges, techniques to improve proteomic yield and increase protein dynamic range continue to improve at a rapid rate. In this review, we highlight the importance of exosome proteomics in neurodegenerative and neuropsychiatric disorders and the associated technical difficulties. Furthermore, current progress and technological advancements in exosome proteomics research are discussed with an emphasis on disease-associated protein biomarkers.
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Affiliation(s)
- Boby Mathew
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; (B.M.); (K.R.W.)
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA
| | - M. Shahid Mansuri
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; (B.M.); (K.R.W.)
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Kenneth R. Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; (B.M.); (K.R.W.)
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Angus C. Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; (B.M.); (K.R.W.)
- Department of Psychiatry, Yale University, 34 Park Street, 3rd Floor Research, New Haven, CT 06508, USA
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2020 White Paper on Recent Issues in Bioanalysis: BMV of Hybrid Assays, Acoustic MS, HRMS, Data Integrity, Endogenous Compounds, Microsampling and Microbiome ( Part 1 - Recommendations on Industry/Regulators Consensus on BMV of Biotherapeutics by LCMS, Advanced Application in Hybrid Assays, Regulatory Challenges in Mass Spec, Innovation in Small Molecules, Peptides and Oligos). Bioanalysis 2021; 13:203-238. [PMID: 33470871 DOI: 10.4155/bio-2020-0324] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The 14th edition of the Workshop on Recent Issues in Bioanalysis (14th WRIB) was held virtually on June 15-29, 2020 with an attendance of over 1000 representatives from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations, and regulatory agencies worldwide. The 14th WRIB included three Main Workshops, seven Specialized Workshops that together spanned 11 days in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccine. Moreover, a comprehensive vaccine assays track; an enhanced cytometry track and updated Industry/Regulators consensus on BMV of biotherapeutics by Mass Spectrometry (hybrid assays, LCMS and HRMS) were special features in 2020. As in previous years, this year's WRIB continued to gather a wide diversity of international industry opinion leaders and regulatory authority experts working on both small and large molecules to facilitate sharing and discussions focused on improving quality, increasing regulatory compliance and achieving scientific excellence on bioanalytical issues. This 2020 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the Global Bioanalytical Community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2020 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication covers the recommendations on (Part 1) Hybrid Assays, Innovation in Small Molecules, & Regulated Bioanalysis. Part 2A (BAV, PK LBA, Flow Cytometry Validation and Cytometry Innovation), Part 2B (Regulatory Input) and Part 3 (Vaccine, Gene/Cell Therapy, NAb Harmonization and Immunogenicity) are published in volume 13 of Bioanalysis, issues 5, and 6 (2021), respectively.
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Dual size-exclusion chromatography for efficient isolation of extracellular vesicles from bone marrow derived human plasma. Sci Rep 2021; 11:217. [PMID: 33436891 PMCID: PMC7804108 DOI: 10.1038/s41598-020-80514-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/15/2020] [Indexed: 01/08/2023] Open
Abstract
Isolation of pure extracellular vesicles (EVs), especially from blood, has been a major challenge in the field of EV research. The presence of lipoproteins and soluble proteins often hinders the isolation of high purity EVs upon utilization of conventional separation methods. To circumvent such problems, we designed a single-step dual size-exclusion chromatography (dSEC) column for effective isolation of highly pure EVs from bone marrow derived human plasma. With an aim to select appropriate column design parameters, we analyzed the physiochemical properties of the major substances in bone marrow derived plasma, which include EVs, lipoproteins, and soluble proteins. Based on these findings, we devised a novel dSEC column with two different types of porous beads sequentially stacked each other for efficient separation of EVs from other contaminants. The newly developed dSEC columns exhibited better performance in isolating highly pure EVs from AML plasma in comparison to conventional isolation methods.
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Wu SC, Kuo PJ, Rau CS, Wu YC, Wu CJ, Lu TH, Lin CW, Tsai CW, Hsieh CH. Subpopulations of exosomes purified via different exosomal markers carry different microRNA contents. Int J Med Sci 2021; 18:1058-1066. [PMID: 33456364 PMCID: PMC7807189 DOI: 10.7150/ijms.52768] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022] Open
Abstract
The heterogeneity of exosome populations presents a great challenge to their study. The current study was designed to investigate the potential heterogeneity miRNA contents in circulating exosomes purified via different exosomal markers. In this study, exosomes from the serum of C57BL/6 mice after cecum ligation and perforation (CLP) or sham operation were isolated by precipitation using ExoQuick-TC and affinity purified with anti-Rab5b, anti-CD9, anti-CD31, and anti-CD44 antibodies using the Exo-Flow Exosome Capture kit to collect exosome subpopulations. RNA extracted from the exosomes isolated by ExoQuick-TC were profiled by next-generation sequencing (NGS). Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was also employed to determine the expression profiles of four representative exosomal miRNAs (mmu-miR-486-5p, mmu-miR-10a-5p, mmu-miR-143-3p, and mmu-miR-25-3p) selected from the NGS analysis. The results revealed that the expression patterns of these miRNAs in exosomes isolated by ExoQuick-TC as determined by RT-qPCR and NGS were similar, showing upregulation of mmu-miR-10a-5p and mmu-miR-143-3p but downregulation of mmu-miR-25-3p and mmu-miR-486-5p following CLP when compared to the levels in exosomes from sham control mice. However, their expression levels in the antibody-captured exosome subpopulations varied. The miRNAs in the exosomes captured by anti-Rab5b or anti-CD9 antibodies were more similar to those isolated by ExoQuick-TC than to those captured by anti-CD44 antibodies. However, there were no significant differences in these four miRNAs in CD31-captured exosomes. This study demonstrated that purification with different exosomal markers allows the collection of different exosome subpopulations with various miRNA contents. The results of this study demonstrate the heterogeneity of circulating exosomes and suggest the importance of stratifying exosome subpopulations when using circulating exosomes as biomarkers or investigating exosome function. In addition, this study also emphasized the necessity of using a consistent exosome marker across different samples as detecting biomarkers.
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Affiliation(s)
- Shao-Chun Wu
- Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Pao-Jen Kuo
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Cheng-Shyuan Rau
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Yi-Chan Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Chia-Jung Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Tsu-Hsiang Lu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Chia-Wei Lin
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Chia-Wen Tsai
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
| | - Ching-Hua Hsieh
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taiwan
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Marchisio M, Simeone P, Bologna G, Ercolino E, Pierdomenico L, Pieragostino D, Ventrella A, Antonini F, Del Zotto G, Vergara D, Celia C, Di Marzio L, Del Boccio P, Fontana A, Bosco D, Miscia S, Lanuti P. Flow Cytometry Analysis of Circulating Extracellular Vesicle Subtypes from Fresh Peripheral Blood Samples. Int J Mol Sci 2020; 22:ijms22010048. [PMID: 33374539 PMCID: PMC7793062 DOI: 10.3390/ijms22010048] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 01/04/2023] Open
Abstract
Extracellular vesicles (EVs) are released by shedding during different physiological processes and are increasingly thought to be new potential biomarkers. However, the impact of pre-analytical processing phases on the final measurement is not predictable and for this reason, the translation of basic research into clinical practice has been precluded. Here we have optimized a simple procedure in combination with polychromatic flow cytometry (PFC), to identify, classify, enumerate, and separate circulating EVs from different cell origins. This protocol takes advantage of a lipophilic cationic dye (LCD) able to probe EVs. Moreover, the application of the newly optimized PFC protocol here described allowed the obtainment of repeatable EVs counts. The translation of this PFC protocol to fluorescence-activated cell sorting allowed us to separate EVs from fresh peripheral blood samples. Sorted EVs preparations resulted particularly suitable for proteomic analyses, which we applied to study their protein cargo. Here we show that LCD staining allowed PFC detection and sorting of EVs from fresh body fluids, avoiding pre-analytical steps of enrichment that could impact final results. Therefore, LCD staining is an essential step towards the assessment of EVs clinical significance.
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Affiliation(s)
- Marco Marchisio
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Pasquale Simeone
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Giuseppina Bologna
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Eva Ercolino
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Laura Pierdomenico
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
| | - Damiana Pieragostino
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
- Department of Innovative Technologies in Medicine & Dentistry, University G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy
| | - Alessia Ventrella
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Francesca Antonini
- Department of Research and Diagnostics, IRCCS Giannina Gaslini, 16147 Genova, Italy; (F.A.); (G.D.Z.)
| | - Genny Del Zotto
- Department of Research and Diagnostics, IRCCS Giannina Gaslini, 16147 Genova, Italy; (F.A.); (G.D.Z.)
| | - Daniele Vergara
- Laboratory of Clinical Proteomics, “Giovanni Paolo II” Hospital, 73100 ASL-Lecce, Italy;
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Christian Celia
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Luisa Di Marzio
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Piero Del Boccio
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Antonella Fontana
- Department of Pharmacy, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (A.V.); (C.C.); (L.D.M.); (A.F.)
| | - Domenico Bosco
- Department of Biomorphological Science, Molecular Genetic Institute, Italian National Research Council, 66100 Chieti, Italy;
| | - Sebastiano Miscia
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
- Correspondence: ; Tel.: +39-0871541391
| | - Paola Lanuti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (M.M.); (P.S.); (G.B.); (E.E.); (L.P.); (P.L.)
- Center for Advanced Studies and Technology (C.A.S.T.), University “G. d’Annunzio”, Chieti-Pescara, 66100 Chieti, Italy; (D.P.); (P.D.B.)
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49
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Anastasi F, Greco F, Dilillo M, Vannini E, Cappello V, Baroncelli L, Costa M, Gemmi M, Caleo M, McDonnell LA. Proteomics analysis of serum small extracellular vesicles for the longitudinal study of a glioblastoma multiforme mouse model. Sci Rep 2020; 10:20498. [PMID: 33235327 PMCID: PMC7686310 DOI: 10.1038/s41598-020-77535-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/09/2020] [Indexed: 12/25/2022] Open
Abstract
Longitudinal analysis of disease models enables the molecular changes due to disease progression or therapeutic intervention to be better resolved. Approximately 75 µl of serum can be drawn from a mouse every 14 days. To date no methods have been reported that are able to analyze the proteome of small extracellular vesicles (sEV’s) from such low serum volumes. Here we report a method for the proteomics analysis of sEV's from 50 µl of serum. Two sEV isolation procedures were first compared; precipitation based purification (PPT) and size exclusion chromatography (SEC). The methodological comparison confirmed that SEC led to purer sEV’s both in terms of size and identified proteins. The procedure was then scaled down and the proteolytic digestion further optimized. The method was then applied to a longitudinal study of serum-sEV proteome changes in a glioblastoma multiforme (GBM) mouse model. Serum was collected at multiple time points, sEV’s isolated and their proteins analyzed. The protocol enabled 274 protein groups to be identified and quantified. The longitudinal analysis revealed 25 deregulated proteins in GBM serum sEV's including proteins previously shown to be associated with GBM progression and metastasis (Myh9, Tln-1, Angpt1, Thbs1).
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Affiliation(s)
- Federica Anastasi
- NEST Laboratories, Scuola Normale Superiore, 56127, Pisa, Italy.,Fondazione Pisana per la Scienza ONLUS, 56107, San Giuliano Terme, PI, Italy
| | - Francesco Greco
- Fondazione Pisana per la Scienza ONLUS, 56107, San Giuliano Terme, PI, Italy.,Institute of Life Sciences, Sant'Anna School of Advanced Studies, 56127, Pisa, Italy
| | - Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS, 56107, San Giuliano Terme, PI, Italy
| | - Eleonora Vannini
- CNR, Neuroscience Institute, 56124, Pisa, Italy.,Fondazione Umberto Veronesi, 20122, Milano, Italy
| | - Valentina Cappello
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation @NEST, 56127, Pisa, Italy
| | - Laura Baroncelli
- CNR, Neuroscience Institute, 56124, Pisa, Italy.,IRCCS Fondazione Stella Maris, 56018, Calambrone, PI, Italy
| | - Mario Costa
- CNR, Neuroscience Institute, 56124, Pisa, Italy
| | - Mauro Gemmi
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation @NEST, 56127, Pisa, Italy
| | - Matteo Caleo
- CNR, Neuroscience Institute, 56124, Pisa, Italy.,Department of Biomedical Sciences, University of Padua, 335122, Padua, Italy
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza ONLUS, 56107, San Giuliano Terme, PI, Italy.
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50
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Chitoiu L, Dobranici A, Gherghiceanu M, Dinescu S, Costache M. Multi-Omics Data Integration in Extracellular Vesicle Biology-Utopia or Future Reality? Int J Mol Sci 2020; 21:ijms21228550. [PMID: 33202771 PMCID: PMC7697477 DOI: 10.3390/ijms21228550] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) are membranous structures derived from the endosomal system or generated by plasma membrane shedding. Due to their composition of DNA, RNA, proteins, and lipids, EVs have garnered a lot of attention as an essential mechanism of cell-to-cell communication, with various implications in physiological and pathological processes. EVs are not only a highly heterogeneous population by means of size and biogenesis, but they are also a source of diverse, functionally rich biomolecules. Recent advances in high-throughput processing of biological samples have facilitated the development of databases comprised of characteristic genomic, transcriptomic, proteomic, metabolomic, and lipidomic profiles for EV cargo. Despite the in-depth approach used to map functional molecules in EV-mediated cellular cross-talk, few integrative methods have been applied to analyze the molecular interplay in these targeted delivery systems. New perspectives arise from the field of systems biology, where accounting for heterogeneity may lead to finding patterns in an apparently random pool of data. In this review, we map the biological and methodological causes of heterogeneity in EV multi-omics data and present current applications or possible statistical methods for integrating such data while keeping track of the current bottlenecks in the field.
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Affiliation(s)
- Leona Chitoiu
- Ultrastructural Pathology and Bioimaging Laboratory, ‘Victor Babeș’ National Institute of Pathology, Bucharest 050096, Romania; (L.C.); (M.G.)
| | - Alexandra Dobranici
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest 050095, Romania; (A.D.); (M.C.)
| | - Mihaela Gherghiceanu
- Ultrastructural Pathology and Bioimaging Laboratory, ‘Victor Babeș’ National Institute of Pathology, Bucharest 050096, Romania; (L.C.); (M.G.)
- Department of Cellular, Molecular Biology and Histology, ‘Carol Davila’ University of Medicine and Pharmacy, Bucharest 050474, Romania
| | - Sorina Dinescu
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest 050095, Romania; (A.D.); (M.C.)
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest 050663, Romania
- Correspondence:
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest 050095, Romania; (A.D.); (M.C.)
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest 050663, Romania
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