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Torres-Puig S, Crespo-Pomar S, Akarsu H, Yimthin T, Cippà V, Démoulins T, Posthaus H, Ruggli N, Kuhnert P, Labroussaa F, Jores J. Functional surface expression of immunoglobulin cleavage systems in a candidate Mycoplasma vaccine chassis. Commun Biol 2024; 7:779. [PMID: 38942984 PMCID: PMC11213901 DOI: 10.1038/s42003-024-06497-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024] Open
Abstract
The Mycoplasma Immunoglobulin Binding/Protease (MIB-MIP) system is a candidate 'virulence factor present in multiple pathogenic species of the Mollicutes, including the fast-growing species Mycoplasma feriruminatoris. The MIB-MIP system cleaves the heavy chain of host immunoglobulins, hence affecting antigen-antibody interactions and potentially facilitating immune evasion. In this work, using -omics technologies and 5'RACE, we show that the four copies of the M. feriruminatoris MIB-MIP system have different expression levels and are transcribed as operons controlled by four different promoters. Individual MIB-MIP gene pairs of M. feriruminatoris and other Mollicutes were introduced in an engineered M. feriruminatoris strain devoid of MIB-MIP genes and were tested for their functionality using newly developed oriC-based plasmids. The two proteins are functionally expressed at the surface of M. feriruminatoris, which confirms the possibility to display large membrane-associated proteins in this bacterium. However, functional expression of heterologous MIB-MIP systems introduced in this engineered strain from phylogenetically distant porcine Mollicutes like Mesomycoplasma hyorhinis or Mesomycoplasma hyopneumoniae could not be achieved. Finally, since M. feriruminatoris is a candidate for biomedical applications such as drug delivery, we confirmed its safety in vivo in domestic goats, which are the closest livestock relatives to its native host the Alpine ibex.
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Affiliation(s)
- Sergi Torres-Puig
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
| | - Silvia Crespo-Pomar
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Hatice Akarsu
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Thatcha Yimthin
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Valentina Cippà
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Thomas Démoulins
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Horst Posthaus
- Institute of Animal Pathology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Nicolas Ruggli
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
- Institute of Virology and Immunology IVI, Sensemattstrasse 293, 3147, Mittelhäusern, Schweiz
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Fabien Labroussaa
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, 3001, Bern, Switzerland
- French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Lyon Laboratory, VetAgro Sup, UMR Animal Mycoplasmosis, University of Lyon, Lyon, France
| | - Jörg Jores
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, 3001, Bern, Switzerland.
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2
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Müller J, Boubaker G, Müller N, Uldry AC, Braga-Lagache S, Heller M, Hemphill A. Investigating Antiprotozoal Chemotherapies with Novel Proteomic Tools-Chances and Limitations: A Critical Review. Int J Mol Sci 2024; 25:6903. [PMID: 39000012 PMCID: PMC11241152 DOI: 10.3390/ijms25136903] [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: 05/31/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Identification of drug targets and biochemical investigations on mechanisms of action are major issues in modern drug development. The present article is a critical review of the classical "one drug"-"one target" paradigm. In fact, novel methods for target deconvolution and for investigation of resistant strains based on protein mass spectrometry have shown that multiple gene products and adaptation mechanisms are involved in the responses of pathogens to xenobiotics rather than one single gene or gene product. Resistance to drugs may be linked to differential expression of other proteins than those interacting with the drug in protein binding studies and result in complex cell physiological adaptation. Consequently, the unraveling of mechanisms of action needs approaches beyond proteomics. This review is focused on protozoan pathogens. The conclusions can, however, be extended to chemotherapies against other pathogens or cancer.
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Affiliation(s)
- Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Ghalia Boubaker
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Norbert Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Sophie Braga-Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggass-Strasse 122, 3012 Bern, Switzerland
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3
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Pais MA, Papanikolaou A, Hoyos IA, Nißler R, De Brot S, Gogos A, Rieben R, Constantinescu MA, Matter MT, Herrmann IK, Lese I. Bioglass/ceria nanoparticle hybrids for the treatment of seroma: a comparative long-term study in rats. Front Bioeng Biotechnol 2024; 12:1363126. [PMID: 38532882 PMCID: PMC10963406 DOI: 10.3389/fbioe.2024.1363126] [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: 01/02/2024] [Accepted: 02/23/2024] [Indexed: 03/28/2024] Open
Abstract
Background: Seroma formation is a common postoperative complication. Fibrin-based glues are typically employed in an attempt to seal the cavity. Recently, the first nanoparticle (NP)-based treatment approaches have emerged. Nanoparticle dispersions can be used as tissue glues, capitalizing on a phenomenon known as 'nanobridging'. In this process, macromolecules such as proteins physically adsorb onto the NP surface, leading to macroscopic adhesion. Although significant early seroma reduction has been shown, little is known about long-term efficacy of NPs. The aim of this study was to assess the long-term effects of NPs in reducing seroma formation, and to understand their underlying mechanism. Methods: Seroma was surgically induced bilaterally in 20 Lewis rats. On postoperative day (POD) 7, seromas were aspirated on both sides. In 10 rats, one side was treated with NPs, while the contralateral side received only NP carrier solution. In the other 10 rats, one side was treated with fibrin glue, while the other was left untreated. Seroma fluid, blood and tissue samples were obtained at defined time points. Biochemical, histopathological and immunohistochemical assessments were made. Results: NP-treated sides showed no macroscopically visible seroma formation after application on POD 7, in stark contrast to the fibrin-treated sides, where 60% of the rats had seromas on POD 14, and 50% on POD 21. At the endpoint (POD 42), sides treated with nanoparticles (NPs) exhibited significant macroscopic differences compared to other groups, including the absence of a cavity, and increased fibrous adhesions. Histologically, there were more macrophage groupings and collagen type 1 (COL1) deposits in the superficial capsule on NP-treated sides. Conclusion: NPs not only significantly reduced early manifestations of seroma and demonstrated an anti-inflammatory response, but they also led to increased adhesion formation over the long term, suggesting a decreased risk of seroma recurrence. These findings highlight both the adhesive properties of NPs and their potential for clinical therapy.
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Affiliation(s)
- Michael-Alexander Pais
- Department of Plastic and Hand Surgery, Inselspital, University Hospital Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Athanasios Papanikolaou
- Department of Plastic and Hand Surgery, Inselspital, University Hospital Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Isabel Arenas Hoyos
- Department of Plastic and Hand Surgery, Inselspital, University Hospital Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Robert Nißler
- Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), StGallen, Switzerland
- Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
- Ingenuity Lab, University Hospital Balgrist and University of Zurich, Zurich, Switzerland
| | - Simone De Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Alexander Gogos
- Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), StGallen, Switzerland
| | - Robert Rieben
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Mihai A. Constantinescu
- Department of Plastic and Hand Surgery, Inselspital, University Hospital Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Martin T. Matter
- Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), StGallen, Switzerland
- Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
| | - Inge K. Herrmann
- Department of Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), StGallen, Switzerland
- Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland
- Ingenuity Lab, University Hospital Balgrist and University of Zurich, Zurich, Switzerland
| | - Ioana Lese
- Department of Plastic and Hand Surgery, Inselspital, University Hospital Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
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Kumar MA, Baba SK, Sadida HQ, Marzooqi SA, Jerobin J, Altemani FH, Algehainy N, Alanazi MA, Abou-Samra AB, Kumar R, Al-Shabeeb Akil AS, Macha MA, Mir R, Bhat AA. Extracellular vesicles as tools and targets in therapy for diseases. Signal Transduct Target Ther 2024; 9:27. [PMID: 38311623 PMCID: PMC10838959 DOI: 10.1038/s41392-024-01735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 02/06/2024] Open
Abstract
Extracellular vesicles (EVs) are nano-sized, membranous structures secreted into the extracellular space. They exhibit diverse sizes, contents, and surface markers and are ubiquitously released from cells under normal and pathological conditions. Human serum is a rich source of these EVs, though their isolation from serum proteins and non-EV lipid particles poses challenges. These vesicles transport various cellular components such as proteins, mRNAs, miRNAs, DNA, and lipids across distances, influencing numerous physiological and pathological events, including those within the tumor microenvironment (TME). Their pivotal roles in cellular communication make EVs promising candidates for therapeutic agents, drug delivery systems, and disease biomarkers. Especially in cancer diagnostics, EV detection can pave the way for early identification and offers potential as diagnostic biomarkers. Moreover, various EV subtypes are emerging as targeted drug delivery tools, highlighting their potential clinical significance. The need for non-invasive biomarkers to monitor biological processes for diagnostic and therapeutic purposes remains unfulfilled. Tapping into the unique composition of EVs could unlock advanced diagnostic and therapeutic avenues in the future. In this review, we discuss in detail the roles of EVs across various conditions, including cancers (encompassing head and neck, lung, gastric, breast, and hepatocellular carcinoma), neurodegenerative disorders, diabetes, viral infections, autoimmune and renal diseases, emphasizing the potential advancements in molecular diagnostics and drug delivery.
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Affiliation(s)
- Mudasir A Kumar
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Kashmir, 192122, India
| | - Sadaf K Baba
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Kashmir, 192122, India
| | - Hana Q Sadida
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Sara Al Marzooqi
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Jayakumar Jerobin
- Qatar Metabolic Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Faisal H Altemani
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Naseh Algehainy
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Mohammad A Alanazi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Abdul-Badi Abou-Samra
- Qatar Metabolic Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Kashmir, 192122, India
| | - Rashid Mir
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia.
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar.
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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: 0] [Impact Index Per Article: 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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6
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Pilotto F, Douthwaite C, Diab R, Ye X, Al Qassab Z, Tietje C, Mounassir M, Odriozola A, Thapa A, Buijsen RAM, Lagache S, Uldry AC, Heller M, Müller S, van Roon-Mom WMC, Zuber B, Liebscher S, Saxena S. Early molecular layer interneuron hyperactivity triggers Purkinje neuron degeneration in SCA1. Neuron 2023; 111:2523-2543.e10. [PMID: 37321222 PMCID: PMC10431915 DOI: 10.1016/j.neuron.2023.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/17/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Toxic proteinaceous deposits and alterations in excitability and activity levels characterize vulnerable neuronal populations in neurodegenerative diseases. Using in vivo two-photon imaging in behaving spinocerebellar ataxia type 1 (Sca1) mice, wherein Purkinje neurons (PNs) degenerate, we identify an inhibitory circuit element (molecular layer interneurons [MLINs]) that becomes prematurely hyperexcitable, compromising sensorimotor signals in the cerebellum at early stages. Mutant MLINs express abnormally elevated parvalbumin, harbor high excitatory-to-inhibitory synaptic density, and display more numerous synaptic connections on PNs, indicating an excitation/inhibition imbalance. Chemogenetic inhibition of hyperexcitable MLINs normalizes parvalbumin expression and restores calcium signaling in Sca1 PNs. Chronic inhibition of mutant MLINs delayed PN degeneration, reduced pathology, and ameliorated motor deficits in Sca1 mice. Conserved proteomic signature of Sca1 MLINs, shared with human SCA1 interneurons, involved the higher expression of FRRS1L, implicated in AMPA receptor trafficking. We thus propose that circuit-level deficits upstream of PNs are one of the main disease triggers in SCA1.
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Affiliation(s)
- Federica Pilotto
- Department of Neurology, Inselspital University Hospital, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Christopher Douthwaite
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig-Maximilians University Munich, Martinsried, Germany
| | - Rim Diab
- Department of Neurology, Inselspital University Hospital, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - XiaoQian Ye
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig-Maximilians University Munich, Martinsried, Germany
| | - Zahraa Al Qassab
- Department of Neurology, Inselspital University Hospital, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Christoph Tietje
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig-Maximilians University Munich, Martinsried, Germany
| | - Meriem Mounassir
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig-Maximilians University Munich, Martinsried, Germany
| | | | - Aishwarya Thapa
- Department of Neurology, Inselspital University Hospital, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Ronald A M Buijsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sophie Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Stefan Müller
- Flow Cytometry and Cell sorting, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Benoît Zuber
- Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Sabine Liebscher
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig-Maximilians University Munich, Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; University Hospital Cologne, Deptartment of Neurology, Cologne, Germany.
| | - Smita Saxena
- Department of Neurology, Inselspital University Hospital, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland.
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7
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Ye X, Cui X, Zhang L, Wu Q, Sui X, He A, Zhang X, Xu R, Tian R. Combination of automated sample preparation and micro-flow LC-MS for high-throughput plasma proteomics. Clin Proteomics 2023; 20:3. [PMID: 36611134 PMCID: PMC9824974 DOI: 10.1186/s12014-022-09390-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Non-invasive detection of blood-based markers is a critical clinical need. Plasma has become the main sample type for clinical proteomics research because it is easy to obtain and contains measurable protein biomarkers that can reveal disease-related physiological and pathological changes. Many efforts have been made to improve the depth of its identification, while there is an increasing need to improve the throughput and reproducibility of plasma proteomics analysis in order to adapt to the clinical large-scale sample analysis. METHODS We have developed and optimized a robust plasma analysis workflow that combines an automated sample preparation platform with a micro-flow LC-MS-based detection method. The stability and reproducibility of the workflow were systematically evaluated and the workflow was applied to a proof-of-concept plasma proteome study of 30 colon cancer patients from three age groups. RESULTS This workflow can analyze dozens of samples simultaneously with high reproducibility. Without protein depletion and prefractionation, more than 300 protein groups can be identified in a single analysis with micro-flow LC-MS system on a Orbitrap Exploris 240 mass spectrometer, including quantification of 35 FDA approved disease markers. The quantitative precision of the entire workflow was acceptable with median CV of 9%. The preliminary proteomic analysis of colon cancer plasma from different age groups could be well separated with identification of potential colon cancer-related biomarkers. CONCLUSIONS This workflow is suitable for the analysis of large-scale clinical plasma samples with its simple and time-saving operation, and the results demonstrate the feasibility of discovering significantly changed plasma proteins and distinguishing different patient groups.
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Affiliation(s)
- Xueting Ye
- grid.440218.b0000 0004 1759 7210The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 China ,grid.258164.c0000 0004 1790 3548The First Affiliated Hospital, Jinan University, Guangzhou, 510632 China ,grid.263817.90000 0004 1773 1790Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xiaozhen Cui
- grid.263817.90000 0004 1773 1790Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Luobin Zhang
- grid.440218.b0000 0004 1759 7210The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 China
| | - Qiong Wu
- grid.263817.90000 0004 1773 1790Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xintong Sui
- grid.263817.90000 0004 1773 1790Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055 China
| | - An He
- grid.263817.90000 0004 1773 1790Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xinyou Zhang
- grid.440218.b0000 0004 1759 7210The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 China
| | - Ruilian Xu
- grid.440218.b0000 0004 1759 7210The Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, 518020 China
| | - Ruijun Tian
- grid.263817.90000 0004 1773 1790Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055 China
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8
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AmiA and AliA peptide ligands are secreted by Klebsiella pneumoniae and inhibit growth of Streptococcus pneumoniae. Sci Rep 2022; 12:22268. [PMID: 36564446 PMCID: PMC9789142 DOI: 10.1038/s41598-022-26838-z] [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: 06/30/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniae colonizes the human nasopharynx, a multi-species microbial niche. Pneumococcal Ami-AliA/AliB oligopeptide permease is an ABC transporter involved in environmental sensing with peptides AKTIKITQTR, FNEMQPIVDRQ, and AIQSEKARKHN identified as ligands of its substrate binding proteins AmiA, AliA, and AliB, respectively. These sequences match ribosomal proteins of multiple bacterial species, including Klebsiella pneumoniae. By mass spectrometry, we identified such peptides in the Klebsiella pneumoniae secretome. AmiA and AliA peptide ligands suppressed pneumococcal growth, but the effect was dependent on peptide length. Growth was suppressed for diverse pneumococci, including antibiotic-resistant strains, but not other bacterial species tested, with the exception of Streptococcus pseudopneumoniae, whose growth was suppressed by the AmiA peptide ligand. By multiple sequence alignments and protein and peptide binding site predictions, for AmiA we have identified the location of an amino acid in the putative binding site whose mutation appears to result in loss of response to the peptide. Our results indicate that pneumococci sense the presence of Klebsiella pneumoniae peptides in the environment.
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9
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Tracking matricellular protein SPARC in extracellular vesicles as a non-destructive method to evaluate lipid-based antifibrotic treatments. Commun Biol 2022; 5:1155. [PMID: 36310239 PMCID: PMC9618575 DOI: 10.1038/s42003-022-04123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
Uncovering the complex cellular mechanisms underlying hepatic fibrogenesis could expedite the development of effective treatments and noninvasive diagnosis for liver fibrosis. The biochemical complexity of extracellular vesicles (EVs) and their role in intercellular communication make them an attractive tool to look for biomarkers as potential alternative to liver biopsies. We developed a solid set of methods to isolate and characterize EVs from differently treated human hepatic stellate cell (HSC) line LX-2, and we investigated their biological effect onto naïve LX-2, proving that EVs do play an active role in fibrogenesis. We mined our proteomic data for EV-associated proteins whose expression correlated with HSC treatment, choosing the matricellular protein SPARC as proof-of-concept for the feasibility of fluorescence nanoparticle-tracking analysis to determine an EV-based HSCs’ fibrogenic phenotype. We thus used EVs to directly evaluate the efficacy of treatment with S80, a polyenylphosphatidylcholines-rich lipid, finding that S80 reduces the relative presence of SPARC-positive EVs. Here we correlated the cellular response to lipid-based antifibrotic treatment to the relative presence of a candidate protein marker associated with the released EVs. Along with providing insights into polyenylphosphatidylcholines treatments, our findings pave the way for precise and less invasive diagnostic analyses of hepatic fibrogenesis. A method is developed to isolate and characterize extracellular vesicles (EVs) from human hepatic stellate cells and proteomics reveals that the matricellular protein SPARC may be used as an EV marker after lipid-based antifibrotic treatment.
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10
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Domanski M, Dedic E, Pérez ME, Cléry A, Campagne S, Uldry AC, Braga S, Heller M, Rabl J, Afanasyev P, Boehringer D, Nováček J, Allain FT, Mühlemann O. 40S hnRNP particles are a novel class of nuclear biomolecular condensates. Nucleic Acids Res 2022; 50:6300-6312. [PMID: 35687109 PMCID: PMC9226511 DOI: 10.1093/nar/gkac457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Heterogenous nuclear ribonucleoproteins (hnRNPs) are abundant proteins implicated in various steps of RNA processing that assemble on nuclear RNA into larger complexes termed 40S hnRNP particles. Despite their initial discovery 55 years ago, our understanding of these intriguing macromolecular assemblies remains limited. Here, we report the biochemical purification of native 40S hnRNP particles and the determination of their complete protein composition by label-free quantitative mass spectrometry, identifying A-group and C-group hnRNPs as the major protein constituents. Isolated 40S hnRNP particles dissociate upon RNA digestion and can be reconstituted in vitro on defined RNAs in the presence of the individual protein components, demonstrating a scaffolding role for RNA in nucleating particle formation. Finally, we revealed their nanometer scale, condensate-like nature, promoted by intrinsically disordered regions of A-group hnRNPs. Collectively, we identify nuclear 40S hnRNP particles as novel dynamic biomolecular condensates.
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Affiliation(s)
- Michal Domanski
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Maria Escura Pérez
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Antoine Cléry
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Sébastien Campagne
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Anne-Christine Uldry
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Sophie Braga
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Manfred Heller
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Julius Rabl
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Daniel Boehringer
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiří Nováček
- Cryo-Electron Microscopy and Tomography Core Facility, Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Frédéric T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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11
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Ilic N, Bojic-Trbojevic Z, Lundström-Stadelmann B, Cujic D, Mitic I, Gruden-Movsesijan A. Immunomodulatory components of Trichinella spiralis excretory-secretory products with lactose-binding specificity. EXCLI JOURNAL 2022; 21:793-813. [PMID: 35949491 PMCID: PMC9360477 DOI: 10.17179/excli2022-4954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/31/2022] [Indexed: 11/06/2022]
Abstract
The immunomodulatory potential of Trichinella spiralis muscle larvae excretory-secretory products (ES L1) has been well documented in vitro on dendritic cells (DCs) and in animal models of autoimmune diseases. ES L1 products possess the potential to induce tolerogenic DCs and consequently trigger regulatory mechanisms that maintain immune homeostasis. The use of ES L1 as a potential treatment for various inflammatory disorders proved to be beneficial in animal models, although the precise immunomodulatory factors have not yet been identified. This study aimed at the isolation and characterization of ES L1 components that possess galectin family member properties. Galectin-1-like proteins (TsGal-1-like) were isolated from ES L1 based on the assumption of the existence of a lactose-specific carbohydrate-recognition domain and were recognized by anti-galectin-1 antibodies in Western blot. This TsGal-1-like isolate, similar to galectin-1, induced DCs with tolerogenic properties and hence, the capacity to polarize T cell response towards a regulatory type. This was reflected by a significantly increased percentage of CD4+CD25+Foxp3+ regulatory T cells and significantly increased expression of IL-10 and TGF-β within this cell population. Proteomic analysis of TsGal-1-like isolate by mass spectrometry identified nineteen proteins, seven with annotated function after blast analysis against a database for T. spiralis and the UniProt database. To our surprise, none of the identified proteins possesses homology with known galectin family members. Nevertheless, the isolated components of ES L1 possess certain galectin-1 properties, such as specific lactose binding and the potential to elicit a regulatory immune response, so it would be worth further investigating the structure of sugar binding within isolated proteins and its biological significance.
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Affiliation(s)
- Natasa Ilic
- University of Belgrade, Institute for the Application of Nuclear Energy, Banatska 31b, 11080 Belgrade, Serbia
| | - Zanka Bojic-Trbojevic
- University of Belgrade, Institute for the Application of Nuclear Energy, Banatska 31b, 11080 Belgrade, Serbia
| | - Britta Lundström-Stadelmann
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
| | - Danica Cujic
- University of Belgrade, Institute for the Application of Nuclear Energy, Banatska 31b, 11080 Belgrade, Serbia
| | - Ivana Mitic
- University of Belgrade, Institute for the Application of Nuclear Energy, Banatska 31b, 11080 Belgrade, Serbia
| | - Alisa Gruden-Movsesijan
- University of Belgrade, Institute for the Application of Nuclear Energy, Banatska 31b, 11080 Belgrade, Serbia,*To whom correspondence should be addressed: Alisa Gruden-Movsesijan, University of Belgrade, Institute for the Application of Nuclear Energy, Banatska 31b, 11080 Belgrade, Serbia; Tel.: +381 641510389, E-mail:
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12
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Uldry AC, Maciel-Dominguez A, Jornod M, Buchs N, Braga-Lagache S, Brodard J, Jankovic J, Bonadies N, Heller M. Effect of Sample Transportation on the Proteome of Human Circulating Blood Extracellular Vesicles. Int J Mol Sci 2022; 23:ijms23094515. [PMID: 35562906 PMCID: PMC9099550 DOI: 10.3390/ijms23094515] [Citation(s) in RCA: 10] [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: 03/24/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 02/01/2023] Open
Abstract
Circulating extracellular vesicles (cEV) are released by many kinds of cells and play an important role in cellular communication, signaling, inflammation modulation, coagulation, and tumor growth. cEV are of growing interest, not only as biomarkers, but also as potential treatment targets. However, very little is known about the effect of transporting biological samples from the clinical ward to the diagnostic laboratory, notably on the protein composition. Pneumatic tube systems (PTS) and human carriers (C) are both routinely used for transport, subjecting the samples to different ranges of mechanical forces. We therefore investigated qualitatively and quantitatively the effect of transport by C and PTS on the human cEV proteome and particle size distribution. We found that samples transported by PTS were subjected to intense, irregular, and multidirectional shocks, while those that were transported by C mostly underwent oscillations at a ground frequency of approximately 4 Hz. PTS resulted in the broadening of nanoparticle size distribution in platelet-free (PFP) but not in platelet-poor plasma (PPP). Cell-type specific cEV-associated protein abundances remained largely unaffected by the transport type. Since residual material of lymphocytes, monocytes, and platelets seemed to dominate cEV proteomes in PPP, it was concluded that PFP should be preferred for any further analyses. Differential expression showed that the impact of the transport method on cEV-associated protein composition was heterogeneous and likely donor-specific. Correlation analysis was nonetheless able to detect that vibration dose, shocks, and imparted energy were associated with different terms depending on the transport, namely in C with cytoskeleton-regulated cell organization activity, and in PTS with a release of extracellular vesicles, mainly from organelle origin, and specifically from mitochondrial structures. Feature selection algorithm identified proteins which, when considered together with the correlated protein-protein interaction network, could be viewed as surrogates of network clusters.
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Affiliation(s)
- Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; (A.-C.U.); (A.M.-D.); (M.J.); (N.B.); (S.B.-L.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Anabel Maciel-Dominguez
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; (A.-C.U.); (A.M.-D.); (M.J.); (N.B.); (S.B.-L.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Maïwenn Jornod
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; (A.-C.U.); (A.M.-D.); (M.J.); (N.B.); (S.B.-L.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Natasha Buchs
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; (A.-C.U.); (A.M.-D.); (M.J.); (N.B.); (S.B.-L.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Sophie Braga-Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; (A.-C.U.); (A.M.-D.); (M.J.); (N.B.); (S.B.-L.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Justine Brodard
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (J.B.); (J.J.)
| | - Jovana Jankovic
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (J.B.); (J.J.)
| | - Nicolas Bonadies
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (J.B.); (J.J.)
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland; (A.-C.U.); (A.M.-D.); (M.J.); (N.B.); (S.B.-L.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
- Correspondence: ; Tel.: +41-31-684-04-82
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Besançon H, Larpin Y, Babiychuk VS, Köffel R, Babiychuk EB. Engineered Liposomes Protect Immortalized Immune Cells from Cytolysins Secreted by Group A and Group G Streptococci. Cells 2022; 11:cells11010166. [PMID: 35011729 PMCID: PMC8749993 DOI: 10.3390/cells11010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 12/10/2022] Open
Abstract
The increasing antibiotic resistance of bacterial pathogens fosters the development of alternative, non-antibiotic treatments. Antivirulence therapy, which is neither bacteriostatic nor bactericidal, acts by depriving bacterial pathogens of their virulence factors. To establish a successful infection, many bacterial pathogens secrete exotoxins/cytolysins that perforate the host cell plasma membrane. Recently developed liposomal nanotraps, mimicking the outer layer of the targeted cell membranes, serve as decoys for exotoxins, thus diverting them from attacking host cells. In this study, we develop a liposomal nanotrap formulation that is capable of protecting immortalized immune cells from the whole palette of cytolysins secreted by Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis—important human pathogens that can cause life-threatening bacteremia. We show that the mixture of cholesterol-containing liposomes with liposomes composed exclusively of phospholipids is protective against the combined action of all streptococcal exotoxins. Our findings pave the way for further development of liposomal antivirulence therapy in order to provide more efficient treatment of bacterial infections, including those caused by antibiotic resistant pathogens.
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14
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Anastasi F, Dilillo M, Pellegrini D, McDonnell LA. Isolation and Proteomic Analysis of Mouse Serum Small Extracellular Vesicles for Individual Subject Analysis. Methods Mol Biol 2022; 2504:41-54. [PMID: 35467278 DOI: 10.1007/978-1-0716-2341-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Proteomics characterization of blood and circulating material has been extensively explored for the study of pathological states. In particular, circulating small extracellular vesicles (sEV, diameter: 30-150 nm) are known to play an important role in intercellular communication processes, and proteomics profiling has been explored to develop minimally invasive assays for disease monitoring and diagnosis. Due to the genetic and physiological similarities between the two species, and also on account of their shorter life span and rapid disease progression, rodent models are the most commonly used animal model for many human diseases. Such models have provided invaluable insight into the molecular mechanisms of disease progression, candidate drug efficacy, therapy monitoring, and biomarkers research.Longitudinal investigations, in which individuals are monitored over periods of time, are more able to resolve molecular changes during disease progression because they circumvent the inter-individual variation. Longitudinal investigations of rodent models are challenging because of the limited amount of blood that can be withdrawn at each time; the American Association of Veterinary Science stipulates that fortnightly sampling should be limited to a maximum of 10% of the total blood volume. For adult mice this corresponds to approximately 75 μL of serum. We developed an approach for the isolation and characterization of serum sEV proteins from just 50 μL of serum, for longitudinal studies of disease mouse models. This chapter describes in detail the steps and considerations involved in the sEV isolation, morphological characterization, and proteome profiling by mass spectrometry.
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Affiliation(s)
- Federica Anastasi
- NEST Laboratories, Scuola Normale Superiore, Pisa, Italy
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | | | - Davide Pellegrini
- NEST Laboratories, Scuola Normale Superiore, Pisa, Italy
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
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15
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Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM. Advances and Utility of the Human Plasma Proteome. J Proteome Res 2021; 20:5241-5263. [PMID: 34672606 PMCID: PMC9469506 DOI: 10.1021/acs.jproteome.1c00657] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Michal Maes
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Maria Pernemalm
- Department of Oncology and Pathology/Science for Life Laboratory, Karolinska Institutet, 171 65 Stockholm, Sweden
| | | | - Natasha Letunica
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Yves Vandenbrouck
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, B207 SCSB Building, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Philipp E Geyer
- OmicEra Diagnostics GmbH, Behringstr. 6, 82152 Planegg, Germany
| | - Vera Ignjatovic
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
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16
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Hallal M, Braga-Lagache S, Jankovic J, Simillion C, Bruggmann R, Uldry AC, Allam R, Heller M, Bonadies N. Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA). BMC Cancer 2021; 21:789. [PMID: 34238254 PMCID: PMC8268341 DOI: 10.1186/s12885-021-08479-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/10/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Despite the introduction of targeted therapies, most patients with myeloid malignancies will not be cured and progress. Genomics is useful to elucidate the mutational landscape but remains limited in the prediction of therapeutic outcome and identification of targets for resistance. Dysregulation of phosphorylation-based signaling pathways is a hallmark of cancer, and therefore, kinase-inhibitors are playing an increasingly important role as targeted treatments. Untargeted phosphoproteomics analysis pipelines have been published but show limitations in inferring kinase-activities and identifying potential biomarkers of response and resistance. METHODS We developed a phosphoproteomics workflow based on titanium dioxide phosphopeptide enrichment with subsequent analysis by liquid chromatography tandem mass spectrometry (LC-MS). We applied a novel Kinase-Activity Enrichment Analysis (KAEA) pipeline on differential phosphoproteomics profiles, which is based on the recently published SetRank enrichment algorithm with reduced false positive rates. Kinase activities were inferred by this algorithm using an extensive reference database comprising five experimentally validated kinase-substrate meta-databases complemented with the NetworKIN in-silico prediction tool. For the proof of concept, we used human myeloid cell lines (K562, NB4, THP1, OCI-AML3, MOLM13 and MV4-11) with known oncogenic drivers and exposed them to clinically established kinase-inhibitors. RESULTS Biologically meaningful over- and under-active kinases were identified by KAEA in the unperturbed human myeloid cell lines (K562, NB4, THP1, OCI-AML3 and MOLM13). To increase the inhibition signal of the driving oncogenic kinases, we exposed the K562 (BCR-ABL1) and MOLM13/MV4-11 (FLT3-ITD) cell lines to either Nilotinib or Midostaurin kinase inhibitors, respectively. We observed correct detection of expected direct (ABL, KIT, SRC) and indirect (MAPK) targets of Nilotinib in K562 as well as indirect (PRKC, MAPK, AKT, RPS6K) targets of Midostaurin in MOLM13/MV4-11, respectively. Moreover, our pipeline was able to characterize unexplored kinase-activities within the corresponding signaling networks. CONCLUSIONS We developed and validated a novel KAEA pipeline for the analysis of differential phosphoproteomics MS profiling data. We provide translational researchers with an improved instrument to characterize the biological behavior of kinases in response or resistance to targeted treatment. Further investigations are warranted to determine the utility of KAEA to characterize mechanisms of disease progression and treatment failure using primary patient samples.
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Affiliation(s)
- Mahmoud Hallal
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sophie Braga-Lagache
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Jovana Jankovic
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cedric Simillion
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ramanjaneyulu Allam
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Manfred Heller
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Nicolas Bonadies
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.
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17
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Ahn SB, Kamath KS, Mohamedali A, Noor Z, Wu JX, Pascovici D, Adhikari S, Cheruku HR, Guillemin GJ, McKay MJ, Nice EC, Baker MS. Use of a Recombinant Biomarker Protein DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins. J Proteome Res 2021; 20:2374-2389. [PMID: 33752330 DOI: 10.1021/acs.jproteome.0c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). In this proof-of-concept study, we employed a mixture of selected recombinant proteins in DDA libraries to subsequently identify (not quantify) cancer-associated low abundance plasma proteins using SWATH/DIA. The exemplar DDA recombinant protein spectral library (rPSL) was derived from tryptic digestion of 36 recombinant human proteins that had been previously implicated as possible cancer biomarkers from both our own and other studies. The rPSL was then used to identify proteins from nondepleted colorectal cancer (CRC) EDTA plasmas by SWATH-MS. Most (32/36) of the proteins used in the rPSL were reliably identified from CRC plasma samples, including 8 proteins (i.e., BTC, CXCL10, IL1B, IL6, ITGB6, TGFα, TNF, TP53) not previously detected using high-stringency protein inference MS according to PeptideAtlas. The rPSL SWATH-MS protocol was compared to DDA-MS using MARS-depleted and postdigestion peptide fractionated plasmas (here referred to as a human plasma DDA library). Of the 32 proteins identified using rPSL SWATH, only 12 could be identified using DDA-MS. The 20 additional proteins exclusively identified using the rPSL SWATH approach were almost exclusively lower abundance (i.e., <10 ng/mL) proteins. To mitigate justified FDR concerns, and to replicate a more typical library creation approach, the DDA rPSL library was merged with a human plasma DDA library and SWATH identification repeated using such a merged library. The majority (33/36) of the low abundance plasma proteins added from the rPSL were still able to be identified using such a merged library when high-stringency HPP Guidelines v3.0 protein inference criteria were applied to our data set. The MS data set has been deposited to ProteomeXchange Consortium via the PRIDE partner repository (PXD022361).
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Affiliation(s)
- Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Karthik S Kamath
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Zainab Noor
- ProCan, Children's Medical Research Institute, The University of Sydney, Westmead, Newtown, NSW 2042, Australia
| | - Jemma X Wu
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Subash Adhikari
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Harish R Cheruku
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Gilles J Guillemin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
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18
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Terkelsen T, Pernemalm M, Gromov P, Børresen-Dale AL, Krogh A, Haakensen VD, Lethiö J, Papaleo E, Gromova I. High-throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers. Mol Oncol 2021; 15:429-461. [PMID: 33176066 PMCID: PMC7858121 DOI: 10.1002/1878-0261.12850] [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] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 08/13/2020] [Accepted: 11/09/2020] [Indexed: 12/24/2022] Open
Abstract
Despite significant advancements in breast cancer (BC) research, clinicians lack robust serological protein markers for accurate diagnostics and tumor stratification. Tumor interstitial fluid (TIF) accumulates aberrantly externalized proteins within the local tumor space, which can potentially gain access to the circulatory system. As such, TIF may represent a valuable starting point for identifying relevant tumor-specific serological biomarkers. The aim of the study was to perform comprehensive proteomic profiling of TIF to identify proteins associated with BC tumor status and subtype. A liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of 35 TIFs of three main subtypes: luminal (19), Her2 (4), and triple-negative (TNBC) (12) resulted in the identification of > 8800 proteins. Unsupervised hierarchical clustering segregated the TIF proteome into two major clusters, luminal and TNBC/Her2 subgroups. High-grade tumors enriched with tumor infiltrating lymphocytes (TILs) were also stratified from low-grade tumors. A consensus analysis approach, including differential abundance analysis, selection operator regression, and random forest returned a minimal set of 24 proteins associated with BC subtypes, receptor status, and TIL scoring. Among them, a panel of 10 proteins, AGR3, BCAM, CELSR1, MIEN1, NAT1, PIP4K2B, SEC23B, THTPA, TMEM51, and ULBP2, was found to stratify the tumor subtype-specific TIFs. In particular, upregulation of BCAM and CELSR1 differentiates luminal subtypes, while upregulation of MIEN1 differentiates Her2 subtypes. Immunohistochemistry analysis showed a direct correlation between protein abundance in TIFs and intratumor expression levels for all 10 proteins. Sensitivity and specificity were estimated for this protein panel by using an independent, comprehensive breast tumor proteome dataset. The results of this analysis strongly support our data, with eight of the proteins potentially representing biomarkers for stratification of BC subtypes. Five of the most representative proteomics databases currently available were also used to estimate the potential for these selected proteins to serve as putative serological markers.
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Affiliation(s)
- Thilde Terkelsen
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Maria Pernemalm
- Cancer Proteomics Mass Spectrometry, Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Pavel Gromov
- Breast Cancer Biology Group, Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Anna-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Anders Krogh
- Department of Computer Science, University of Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Denmark
| | - Vilde D Haakensen
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Janne Lethiö
- Cancer Proteomics Mass Spectrometry, Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.,Translational Disease System Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - Irina Gromova
- Breast Cancer Biology Group, Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
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19
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Mallia A, Gianazza E, Zoanni B, Brioschi M, Barbieri SS, Banfi C. Proteomics of Extracellular Vesicles: Update on Their Composition, Biological Roles and Potential Use as Diagnostic Tools in Atherosclerotic Cardiovascular Diseases. Diagnostics (Basel) 2020; 10:diagnostics10100843. [PMID: 33086718 PMCID: PMC7588996 DOI: 10.3390/diagnostics10100843] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) are lipid-bound vesicles released from cells under physiological and pathological conditions. Basing on biogenesis, dimension, content and route of secretion, they can be classified into exosomes, microvesicles (MVs) and apoptotic bodies. EVs have a key role as bioactive mediators in intercellular communication, but they are also involved in other physiological processes like immune response, blood coagulation, and tissue repair. The interest in studying EVs has increased over the years due to their involvement in several diseases, such as cardiovascular diseases (CVDs), and their potential role as biomarkers in diagnosis, therapy, and in drug delivery system development. Nowadays, the improvement of mass spectrometry (MS)-based techniques allows the characterization of the EV protein composition to deeply understand their role in several diseases. In this review, a critical overview is provided on the EV’s origin and physical properties, as well as their emerging functional role in both physiological and disease conditions, focusing attention on the role of exosomes in CVDs. The most important cardiac exosome proteomic studies will be discussed giving a qualitative and quantitative characterization of the exosomal proteins that could be used in future as new potential diagnostic markers or targets for specific therapies.
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20
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Tunset ME, Haslene-Hox H, Van Den Bossche T, Vaaler AE, Sulheim E, Kondziella D. Extracellular vesicles in patients in the acute phase of psychosis and after clinical improvement: an explorative study. PeerJ 2020; 8:e9714. [PMID: 32995075 PMCID: PMC7501784 DOI: 10.7717/peerj.9714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/23/2020] [Indexed: 12/28/2022] Open
Abstract
Extracellular vesicles (EVs) are cell-derived structures that transport proteins, lipids and nucleic acids between cells, thereby affecting the phenotype of the recipient cell. As the content of EVs reflects the status of the originating cell, EVs can have potential as biomarkers. Identifying EVs, including their cells of origin and their cargo, may provide insights in the pathophysiology of psychosis. Here, we present an in-depth analysis and proteomics of EVs from peripheral blood in patients (n = 25) during and after the acute phase of psychosis. Concentration and protein content of EVs in psychotic patients were twofold higher than in 25 age- and sex-matched healthy controls (p < 0.001 for both concentration and protein content), and the diameter of EVs was larger in patients (p = 0.02). Properties of EVs did not differ significantly in blood sampled during and after the acute psychotic episode. Proteomic analyses on isolated EVs from individual patients revealed 1,853 proteins, whereof 45 were brain-elevated proteins. Of these, five proteins involved in regulation of plasticity of glutamatergic synapses were significantly different in psychotic patients compared to controls; neurogranin (NRGN), neuron-specific calcium-binding protein hippocalcin (HPCA), kalirin (KALRN), beta-adducin (ADD2) and ankyrin-2 (ANK2). To summarize, our results show that peripheral EVs in psychotic patients are different from those in healthy controls and point at alterations on the glutamatergic system. We suggest that EVs allow investigation of blood-borne brain-originating biological material and that their role as biomarkers in patients with psychotic disorders is worthy of further exploration.
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Affiliation(s)
- Mette Elise Tunset
- Department of Østmarka- Division of Mental Healthcare, St. Olavs University Hospital, Trondheim, Norway.,Department of Mental Health- Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hanne Haslene-Hox
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway
| | - Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Arne Einar Vaaler
- Department of Østmarka- Division of Mental Healthcare, St. Olavs University Hospital, Trondheim, Norway.,Department of Mental Health- Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Einar Sulheim
- Department of Biotechnology and Nanomedicine, SINTEF, Trondheim, Norway.,Department of Physics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Daniel Kondziella
- Department of Neurology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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21
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Martin DR, Witten JC, Tan CD, Rodriguez ER, Blackstone EH, Pettersson GB, Seifert DE, Willard BB, Apte SS. Proteomics identifies a convergent innate response to infective endocarditis and extensive proteolysis in vegetation components. JCI Insight 2020; 5:135317. [PMID: 32544089 DOI: 10.1172/jci.insight.135317] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Infective endocarditis is a life-threatening infection of heart valves and adjacent structures characterized by vegetations on valves and other endocardial surfaces, with tissue destruction and risk of embolization. We used high-resolution mass spectrometry to define the proteome of staphylococcal and non-staphylococcal vegetations and Terminal Amine Isotopic Labeling of Substrates (TAILS) to define their proteolytic landscapes. These approaches identified over 2000 human proteins in staphylococcal and non-staphylococcal vegetations. Individual vegetation proteomes demonstrated comparable profiles of quantitatively major constituents that overlapped with serum, platelet, and neutrophil proteomes. Staphylococcal vegetation proteomes resembled one another more than the proteomes of non-staphylococcal vegetations. TAILS demonstrated extensive proteolysis within vegetations, with numerous previously undescribed cleavages. Several proteases and pathogen-specific proteins, including virulence factors, were identified in most vegetations. Proteolytic peptides in fibronectin and complement C3 were identified as potential infective endocarditis biomarkers. Overlap of staphylococcal and non-staphylococcal vegetation proteomes suggests a convergent thrombotic and immune response to endocardial infection by diverse pathogens. However, the differences between staphylococcal and non-staphylococcal vegetations and internal variance within the non-staphylococcal group indicate that additional pathogen- or patient-specific effects exist. Pervasive proteolysis of vegetation components may arise from vegetation-intrinsic proteases and destabilize vegetations, contributing to embolism.
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Affiliation(s)
- Daniel R Martin
- Department of Biomedical Engineering, Lerner Research Institute
| | - James C Witten
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | - Carmela D Tan
- Department of Pathology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, and
| | - E Rene Rodriguez
- Department of Pathology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, and
| | - Eugene H Blackstone
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | - Gosta B Pettersson
- Department of Thoracic and Cardiovascular Surgery, Miller Family Heart and Vascular Institute
| | | | - Belinda B Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Suneel S Apte
- Department of Biomedical Engineering, Lerner Research Institute
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22
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Daurat M, Nguyen C, Dominguez Gil S, Sol V, Chaleix V, Charnay C, Raehm L, El Cheikh K, Morère A, Bernasconi M, Timpanaro A, Garcia M, Cunin F, Roessler J, Durand JO, Gary-Bobo M. The mannose 6-phosphate receptor targeted with porphyrin-based periodic mesoporous organosilica nanoparticles for rhabdomyosarcoma theranostics. Biomater Sci 2020; 8:3678-3684. [DOI: 10.1039/d0bm00586j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Periodic mesoporous organosilica nanoparticles targeted to the mannose 6-phosphate receptor for rhabdomyosarcoma photodynamic therapy using a pulsed laser.
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Affiliation(s)
- Morgane Daurat
- NanoMedSyn Avenue Charles Flahault
- Montpellier Cedex 05
- France
| | | | | | - Vincent Sol
- Laboratoire PEIRENE
- EA 7500
- Université de Limoges
- Faculté des Sciences et Techniques
- 87060 Limoges
| | - Vincent Chaleix
- Laboratoire PEIRENE
- EA 7500
- Université de Limoges
- Faculté des Sciences et Techniques
- 87060 Limoges
| | | | | | | | - Alain Morère
- IBMM
- UMR 5247 CNRS
- UM-Faculté de Pharmacie
- Montpellier Cedex 05
- France
| | - Michele Bernasconi
- Division of Pediatric Hematology/Oncology
- Department of Pediatrics
- Inselspital
- Bern University Hospital
- Department for BioMedical Research (DBMR)
| | - Andrea Timpanaro
- Division of Pediatric Hematology/Oncology
- Department of Pediatrics
- Inselspital
- Bern University Hospital
- Department for BioMedical Research (DBMR)
| | - Marcel Garcia
- NanoMedSyn Avenue Charles Flahault
- Montpellier Cedex 05
- France
| | | | - Jochen Roessler
- Division of Pediatric Hematology/Oncology
- Department of Pediatrics
- Inselspital
- Bern University Hospital
- Department for BioMedical Research (DBMR)
| | | | - Magali Gary-Bobo
- IBMM
- UMR 5247 CNRS
- UM-Faculté de Pharmacie
- Montpellier Cedex 05
- France
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23
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An Update on Isolation Methods for Proteomic Studies of Extracellular Vesicles in Biofluids. Molecules 2019; 24:molecules24193516. [PMID: 31569778 PMCID: PMC6803898 DOI: 10.3390/molecules24193516] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid bilayer enclosed particles which present in almost all types of biofluids and contain specific proteins, lipids, and RNA. Increasing evidence has demonstrated the tremendous clinical potential of EVs as diagnostic and therapeutic tools, especially in biofluids, since they can be detected without invasive surgery. With the advanced mass spectrometry (MS), it is possible to decipher the protein content of EVs under different physiological and pathological conditions. Therefore, MS-based EV proteomic studies have grown rapidly in the past decade for biomarker discovery. This review focuses on the studies that isolate EVs from different biofluids and contain MS-based proteomic analysis. Literature published in the past decade (2009.1-2019.7) were selected and summarized with emphasis on isolation methods of EVs and MS analysis strategies, with the aim to give an overview of MS-based EV proteomic studies and provide a reference for future research.
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24
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Hou R, Li Y, Sui Z, Yuan H, Yang K, Liang Z, Zhang L, Zhang Y. Advances in exosome isolation methods and their applications in proteomic analysis of biological samples. Anal Bioanal Chem 2019; 411:5351-5361. [PMID: 31267193 DOI: 10.1007/s00216-019-01982-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/02/2019] [Accepted: 06/14/2019] [Indexed: 12/20/2022]
Abstract
Exosomes are membrane-bound vesicles secreted by cells, and contain various important biological molecules, such as lipids, proteins, messenger RNAs, microRNAs, and noncoding RNAs. Emerging evidence demonstrates that proteomic analysis of exosomes is of great significance in studying metabolic diseases, tumor metastasis, immune regulation, and so forth. However, exosome proteomic analysis has high requirements with regard to the purity of collected exosomes. Here recent advances in the methods for isolating exosomes and their applications in proteomic analysis are summarized. Graphical abstract.
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Affiliation(s)
- Rui Hou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
| | - Yilan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
| | - Huiming Yuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China.
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
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25
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The Dual Prey-Inactivation Strategy of Spiders-In-Depth Venomic Analysis of Cupiennius salei. Toxins (Basel) 2019; 11:toxins11030167. [PMID: 30893800 PMCID: PMC6468893 DOI: 10.3390/toxins11030167] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/14/2019] [Indexed: 02/08/2023] Open
Abstract
Most knowledge of spider venom concerns neurotoxins acting on ion channels, whereas proteins and their significance for the envenomation process are neglected. The here presented comprehensive analysis of the venom gland transcriptome and proteome of Cupiennius salei focusses on proteins and cysteine-containing peptides and offers new insight into the structure and function of spider venom, here described as the dual prey-inactivation strategy. After venom injection, many enzymes and proteins, dominated by α-amylase, angiotensin-converting enzyme, and cysteine-rich secretory proteins, interact with main metabolic pathways, leading to a major disturbance of the cellular homeostasis. Hyaluronidase and cytolytic peptides destroy tissue and membranes, thus supporting the spread of other venom compounds. We detected 81 transcripts of neurotoxins from 13 peptide families, whereof two families comprise 93.7% of all cysteine-containing peptides. This raises the question of the importance of the other low-expressed peptide families. The identification of a venom gland-specific defensin-like peptide and an aga-toxin-like peptide in the hemocytes offers an important clue on the recruitment and neofunctionalization of body proteins and peptides as the origin of toxins.
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26
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V'kovski P, Gerber M, Kelly J, Pfaender S, Ebert N, Braga Lagache S, Simillion C, Portmann J, Stalder H, Gaschen V, Bruggmann R, Stoffel MH, Heller M, Dijkman R, Thiel V. Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. eLife 2019; 8:42037. [PMID: 30632963 PMCID: PMC6372286 DOI: 10.7554/elife.42037] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/11/2019] [Indexed: 12/31/2022] Open
Abstract
Positive-sense RNA viruses hijack intracellular membranes that provide niches for viral RNA synthesis and a platform for interactions with host proteins. However, little is known about host factors at the interface between replicase complexes and the host cytoplasm. We engineered a biotin ligase into a coronaviral replication/transcription complex (RTC) and identified >500 host proteins constituting the RTC microenvironment. siRNA-silencing of each RTC-proximal host factor demonstrated importance of vesicular trafficking pathways, ubiquitin-dependent and autophagy-related processes, and translation initiation factors. Notably, detection of translation initiation factors at the RTC was instrumental to visualize and demonstrate active translation proximal to replication complexes of several coronaviruses. Collectively, we establish a spatial link between viral RNA synthesis and diverse host factors of unprecedented breadth. Our data may serve as a paradigm for other positive-strand RNA viruses and provide a starting point for a comprehensive analysis of critical virus-host interactions that represent targets for therapeutic intervention. Coronaviruses can infect the nose and throat and are a main cause of the common cold. Infections are usually mild and short-lived, but sometimes they can turn nasty. In 2002 and 2012, two dangerous new coronaviruses emerged and caused diseases known as SARS and MERS. These viruses caused much more serious symptoms and in some cases proved deadly. The question is, why are some coronaviruses more dangerous than others? Scientists know that the body's response to virus infection can make a difference to whether someone had mild or severe disease. So, to understand why some coronaviruses cause a cold and others kill, they also need to learn how people react to virus infection. Coronaviruses hijack membranes inside cells and turn them into virus factories. Within these factories, the viruses build molecular machinery called replicase complexes to copy their genetic code, which is needed for the next generation of virus particles. The viruses steal and repurpose proteins from their host cell that will assist in the copying process. However, scientists do not yet know which host proteins are essential for the virus to multiply. So, to find out, V’kovski et al. developed a way to tag any host protein that came near the virus factories. The new technique involved attaching an enzyme called a biotin ligase to the replicase complex. This enzyme acts as a molecular label gun, attaching a chemical tag to any protein that comes within ten nanometres. The label gun revealed that more than 500 different proteins come into contact with the replicase complex. To find out what these proteins were doing, the next step was to switch off their genes one by one. This revealed the key cell machinery that coronaviruses hijack when they are replicating. It included the cell's cargo transport system, the waste disposal system, and the protein production system. Using these systems allows the viruses to copy their genetic code next to machines that can turn it straight into viral proteins. These new results provide clues about which proteins viruses actually need from their host cells. They also do not just apply to coronaviruses. Other viruses use similar strategies to complete their infection cycle. These findings could help researchers to understand more generally about how viruses multiply. In the future, this knowledge could lead to new ways to combat virus infections.
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Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Markus Gerber
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna Kelly
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit, SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Stephanie Pfaender
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sophie Braga Lagache
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Cedric Simillion
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.,Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Véronique Gaschen
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Michael H Stoffel
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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27
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Barrachina MN, Calderón-Cruz B, Fernandez-Rocca L, García Á. Application of Extracellular Vesicles Proteomics to Cardiovascular Disease: Guidelines, Data Analysis, and Future Perspectives. Proteomics 2019; 19:e1800247. [PMID: 30467982 DOI: 10.1002/pmic.201800247] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/09/2018] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are a heterogeneous population of vesicles composed of a lipid bilayer that carry a large repertoire of molecules including proteins, lipids, and nucleic acids. In this review, some guidelines for plasma-derived EVs isolation, characterization, and proteomic analysis, and the application of the above to cardiovascular disease (CVD) studies are provided. For EVs analysis, blood samples should be collected using a 21-gauge needle, preferably in citrate tubes, and plasma stored for up to 1 year at -80°, using a single freeze-thaw cycle. For proteomic applications, differential centrifugation (including ultracentrifugation steps) is a good option for EVs isolation. EVs characterization is done by transmission electron microscopy, particle enumeration techniques (nanoparticle-tracking analysis, dynamic light scattering), and flow cytometry. Regarding the proteomics strategy, a label-free and gel-free quantitative method is a good choice due to its accuracy and because it minimizes the amount of sample required for clinical applications. Besides the above, main EVs proteomic findings in cardiovascular-related diseases are presented and analyzed in this review, paying especial attention to overlapping results between studies. The latter might offer new insights into the clinical relevance and potential of novel EVs biomarkers identified to date in the context of CVD.
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Affiliation(s)
- Maria N Barrachina
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade Santiago de Compostela, Santiago de Compostela, 15782, Spain.,Instituto de Investigación, Sanitaria de Santiago (IDIS), Santiago de Compostela, 15706, Spain
| | - Beatriz Calderón-Cruz
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade Santiago de Compostela, Santiago de Compostela, 15782, Spain.,Instituto de Investigación, Sanitaria de Santiago (IDIS), Santiago de Compostela, 15706, Spain
| | - Lucía Fernandez-Rocca
- Clinical Analysis Laboratory, Maciel Hospital, Faculty of Chemistry, University of the Republic, Montevideo, 11000, Uruguay
| | - Ángel García
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade Santiago de Compostela, Santiago de Compostela, 15782, Spain.,Instituto de Investigación, Sanitaria de Santiago (IDIS), Santiago de Compostela, 15706, Spain
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Buchs N, Braga-Lagache S, Uldry AC, Brodard J, Debonneville C, Reynard JS, Heller M. Absolute Quantification of Grapevine Red Blotch Virus in Grapevine Leaf and Petiole Tissues by Proteomics. FRONTIERS IN PLANT SCIENCE 2018; 9:1735. [PMID: 30555495 PMCID: PMC6281998 DOI: 10.3389/fpls.2018.01735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/08/2018] [Indexed: 05/17/2023]
Abstract
Grapevine red blotch is a recently identified viral disease that was first recognized in the Napa Valley of California. Infected plants showed foliar symptoms similar to leafroll, another grapevine viral disease, on vines testing negative for known grapevine leafroll-associated virus. Later, the Grapevine red blotch virus (GRBV) was independently discovered in the US states of California and New York and was demonstrated to be the causal agent of red blotch disease. Due to its wide occurrence in the United States, vector transmission, and impacts on grape industry, this virus has the potential to cause serious economic losses. Despite numerous attempts, it has yet not been possible to isolate or visualize viral particles from GRBV-infected plants, thereby hampering the development of a serological assay that would facilitate GRBV detection in grapevine. In this work, mass spectrometry approaches were applied in order to quantify GRBV in infected plants and identify potential biomarkers for viral infection. We present for the first time the physical detection on the protein level of the two GRBV genes V1 (coat protein) and V2 in grapevine tissue lysates. The GRBV coat protein load in petioles was determined to be in the range of 100-900 million copies per milligram wet weight by using three heavy isotope labeled reference peptides as internal standards. In leaves on the other hand, the V1 copy number per unit wet tissue weight appeared to be about six times lower than in petioles, and about 300 times lower in terms of protein concentration in the extractable protein mass, albeit these estimations could only be made with one reference peptide detectable in leaf extracts. Moreover, we found in leaf and petiole extracts of GRBV-infected plants a consistent upregulation of several enzymes involved in flavonoid biosynthesis by label-free shotgun proteomics, indicating the activation of a defense mechanism against GRBV, a plant response already described for Grapevine leafroll-associated virus infection on the transcriptome level. Finally and importantly, we identified some other microorganisms belonging to the grapevine leaf microbiota, two bacterial species (Novosphingobium sp. Rr 2-17 and Methylobacterium) and one virus, Grapevine rupestris stem pitting-associated virus.
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Affiliation(s)
- Natasha Buchs
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sophie Braga-Lagache
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Justine Brodard
- Institute for Plant Production Science, Agroscope, Nyon, Switzerland
| | | | | | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
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Shi C, Ulke-Lemée A, Deng J, Batulan Z, O'Brien ER. Characterization of heat shock protein 27 in extracellular vesicles: a potential anti-inflammatory therapy. FASEB J 2018; 33:1617-1630. [PMID: 30188755 DOI: 10.1096/fj.201800987r] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Previously, we reported that elevated serum levels of heat shock protein 27 (HSP27) are predictive of a lower risk of having a heart attack, stroke, or death from cardiovascular disease. Moreover, augmenting HSP27 (or the murine ortholog, HSP25) attenuated experimental atherogenesis, reduced inflammation, and lowered cholesterol levels. Recently, we noted that HSP27 activates NF-κB via TLR-4, resulting in attenuation of plaque inflammation; however, the precise anti-atherosclerosis mechanisms mediated by extracellular HSP27 are incompletely understood. Our purpose in this study was to investigate the existence of HSP27 in extracellular vesicles (EVs) and whether HSP27 elicited atheroprotective effects on target cells. Here, we provide evidence that HSP27 localizes to EVs derived from THP-1 cells using transmission electron microscopy (TEM) and immunogold labeling, Western blotting, ELISA, and fluorescence-activated cell sorting. TEM imaging indicated that HSP27 is found at the exosomal membrane. Multiple reactor monitor-mass spectrometric analysis of large vesicles, which included microparticles and exosomes, isolated from human plasma, also led to detection of HSP27 using the unique signature peptide, R.LFDQAFGLPR.L. Studies using THP-1 and human embryonic kidney cells show that HSP27-laden exosomes significantly stimulated NF-κB activation ( P < 0.001) and release of IL-10 ( P < 0.0001), suggesting that HSP27 may be important exosomal cargo with beneficial anti-inflammatory effects.-Shi, C., Ulke-Lemée, A., Deng, J., Batulan, Z., O'Brien, E. R. Characterization of heat shock protein 27 in extracellular vesicles: a potential anti-inflammatory therapy.
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Affiliation(s)
- Chunhua Shi
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Annegret Ulke-Lemée
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jingti Deng
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Zarah Batulan
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Edward R O'Brien
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Østergaard O, Nielsen CT, Tanassi JT, Iversen LV, Jacobsen S, Heegaard NHH. Distinct proteome pathology of circulating microparticles in systemic lupus erythematosus. Clin Proteomics 2017. [PMID: 28649187 PMCID: PMC5479039 DOI: 10.1186/s12014-017-9159-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background The pathogenesis of systemic lupus erythematosus (SLE) is poorly understood but has been linked to defective clearance of subcellular particulate material from the circulation. This study investigates the origin, formation, and specificity of circulating microparticles (MPs) in patients with SLE based on comprehensive MP proteome profiling using patients with systemic sclerosis (SSc) and healthy donors (HC) as controls. Methods We purified MPs from platelet-poor plasma using differential centrifugation of samples from SLE (n = 45), SSc (n = 38), and two sets of HC (n = 35, n = 25). MP proteins were identified and quantitated after trypsin digestion by liquid chromatography-tandem mass spectrometry. The abundance of specific proteins was compared between the groups using univariate statistics and false discovery rate correction for multiple comparisons. Specific proteins and protein ratios were explored for diagnostic and disease activity information using receiver-operating characteristic curves and by analysis of correlations of protein abundance with disease activity scores. Results We identify and quantitate more than 1000 MP proteins and show that a subpopulation of SLE-MPs (which we propose to call luposomes) are highly specific for SLE, i.e. not found in MP preparations from HC or patients with another autoimmune, systemic disease, SSc. In SLE-MPs platelet proteins and mitochondrial proteins are significantly diminished, cytoskeletal proteins deranged, and glycolytic enzymes and apoptotic proteins significantly increased. Conclusions Normal MPs are efficiently removed in SLE, but aberrant MPs, derived from non-lymphoid leukocytes, are less efficiently removed and abundantly produced leading to an altered MP proteome in SLE. The data suggest that an abnormal generation of MPs may partake in the pathology of SLE and that new diagnostic, monitoring, and treatment strategies targeting these processes may be advantageous. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9159-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ole Østergaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - Christoffer Tandrup Nielsen
- Copenhagen Lupus and Vasculitis Clinic, Centre for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Julia T Tanassi
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - Line V Iversen
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Jacobsen
- Copenhagen Lupus and Vasculitis Clinic, Centre for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels H H Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, Odense, Denmark
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