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Moon MJ, Rai A, Sharma P, Fang H, McFadyen JD, Greening DW, Peter K. Differential effects of physiological agonists on the proteome of platelet-derived extracellular vesicles. Proteomics 2024:e2300391. [PMID: 38556629 DOI: 10.1002/pmic.202300391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024]
Abstract
Arterial thrombosis manifesting as heart attack and stroke is the leading cause of death worldwide. Platelets are central mediators of thrombosis that can be activated through multiple activation pathways. Platelet-derived extracellular vesicles (pEVs), also known as platelet-derived microparticles, are granular mixtures of membrane structures produced by platelets in response to various activating stimuli. Initial studies have attracted interest on how platelet agonists influence the composition of the pEV proteome. In the current study, we used physiological platelet agonists of varying potencies which reflect the microenvironments that platelets experience during thrombus formation: adenosine diphosphate, collagen, thrombin as well as a combination of thrombin/collagen to induce platelet activation and pEV generation. Proteomic profiling revealed that pEVs have an agonist-dependent altered proteome in comparison to their cells of origin, activated platelets. Furthermore, we found that various protein classes including those related to coagulation and complement (prothrombin, antithrombin, and plasminogen) and platelet activation (fibrinogen) are attributed to platelet EVs following agonist stimulation. This agonist-dependent altered proteome suggests that protein packaging is an active process that appears to occur without de novo protein synthesis. This study provides new information on the influence of physiological agonist stimuli on the biogenesis and proteome landscape of pEVs.
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Affiliation(s)
- Mitchell J Moon
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Alin Rai
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Prerna Sharma
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Haoyun Fang
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - James D McFadyen
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Haematology, Alfred Hospital, Melbourne, Victoria, Australia
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - David W Greening
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Karlheinz Peter
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Atherothrombosis and Vascular Biology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Department of Cardiology, Alfred Hospital, Melbourne, Victoria, Australia
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Tsagmo JM, Njiokou F, Dziedziech A, Rofidal V, Hem S, Geiger A. Protein abundance in the midgut of wild tsetse flies (Glossina palpalis palpalis) naturally infected by Trypanosoma congolense s.l. Med Vet Entomol 2023; 37:723-736. [PMID: 37357577 DOI: 10.1111/mve.12676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/08/2023] [Indexed: 06/27/2023]
Abstract
Tsetse flies (Glossina spp.) are major vectors of African trypanosomes, causing either Human or Animal African Trypanosomiasis (HAT or AAT). Several approaches have been developed to control the disease, among which is the anti-vector Sterile Insect Technique. Another approach to anti-vector strategies could consist of controlling the fly's vector competence through hitherto unidentified regulatory factors (genes, proteins, biological pathways, etc.). The present work aims to evaluate the protein abundance in the midgut of wild tsetse flies (Glossina palpalis palpalis) naturally infected by Trypanosoma congolense s.l. Infected and non-infected flies were sampled in two HAT/AAT foci in Southern Cameroon. After dissection, the proteomes from the guts of parasite-infected flies were compared to that of uninfected flies to identify quantitative and/or qualitative changes associated with infection. Among the proteins with increased abundance were fructose-1,6-biphosphatase, membrane trafficking proteins, death proteins (or apoptosis proteins) and SERPINs (inhibitor of serine proteases, enzymes considered as trypanosome virulence factors) that displayed the highest increased abundance. The present study, together with previous proteomic and transcriptomic studies on the secretome of trypanosomes from tsetse fly gut extracts, provides data to be explored in further investigations on, for example, mammal host immunisation or on fly vector competence modification via para-transgenic approaches.
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Affiliation(s)
- Jean Marc Tsagmo
- INTERTRYP, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
- Faculty of Science, University of Yaoundé I, Yaounde, Cameroon
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, Department of Parasites and Insect Vectors and INSERM U1201, Institut Pasteur, Paris, France
| | - Flobert Njiokou
- Faculty of Science, University of Yaoundé I, Yaounde, Cameroon
| | - Alexis Dziedziech
- Biology of Host-Parasite Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Valerie Rofidal
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Sonia Hem
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Anne Geiger
- INTERTRYP, Institut de Recherche pour le Développement, University of Montpellier, Montpellier, France
- Faculty of Science, University of Yaoundé I, Yaounde, Cameroon
- Center for Research on Filariasis and Other Tropical Diseases (CRFilMT), Yaounde, Cameroon
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3
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Shichkova P, Coggan JS, Markram H, Keller D. A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. Front Mol Neurosci 2021; 14:604559. [PMID: 34858137 PMCID: PMC8631404 DOI: 10.3389/fnmol.2021.604559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/05/2021] [Indexed: 12/12/2022] Open
Abstract
Accurate molecular concentrations are essential for reliable analyses of biochemical networks and the creation of predictive models for molecular and systems biology, yet protein and metabolite concentrations used in such models are often poorly constrained or irreproducible. Challenges of using data from different sources include conflicts in nomenclature and units, as well as discrepancies in experimental procedures, data processing and implementation of the model. To obtain a consistent estimate of protein and metabolite levels, we integrated and normalized data from a large variety of sources to calculate Adjusted Molecular Concentrations. We found a high degree of reproducibility and consistency of many molecular species across brain regions and cell types, consistent with tight homeostatic regulation. We demonstrated the value of this normalization with differential protein expression analyses related to neurodegenerative diseases, brain regions and cell types. We also used the results in proof-of-concept simulations of brain energy metabolism. The standardized Brain Molecular Atlas overcomes the obstacles of missing or inconsistent data to support systems biology research and is provided as a resource for biomolecular modeling.
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Affiliation(s)
- Polina Shichkova
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland
| | - Jay S Coggan
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland
| | - Henry Markram
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland.,Laboratory of Neural Microcircuitry, Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Daniel Keller
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland
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Kleinwort KJH, Hobmaier BF, Mayer R, Hölzel C, Degroote RL, Märtlbauer E, Hauck SM, Deeg CA. Mycobacterium avium subsp. paratuberculosis Proteome Changes Profoundly in Milk. Metabolites 2021; 11:metabo11080549. [PMID: 34436489 PMCID: PMC8399727 DOI: 10.3390/metabo11080549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) are detectable viable in milk and other dairy products. The molecular mechanisms allowing the adaptation of MAP in these products are still poorly understood. To obtain information about respective adaptation of MAP in milk, we differentially analyzed the proteomes of MAP cultivated for 48 h in either milk at 37 °C or 4 °C or Middlebrook 7H9 broth as a control. From a total of 2197 MAP proteins identified, 242 proteins were at least fivefold higher in abundance in milk. MAP responded to the nutritional shortage in milk with upregulation of 32% of proteins with function in metabolism and 17% in fatty acid metabolism/synthesis. Additionally, MAP upregulated clusters of 19% proteins with roles in stress responses and immune evasion, 19% in transcription/translation, and 13% in bacterial cell wall synthesis. Dut, MmpL4_1, and RecA were only detected in MAP incubated in milk, pointing to very important roles of these proteins for MAP coping with a stressful environment. Dut is essential and plays an exclusive role for growth, MmpL4_1 for virulence through secretion of specific lipids, and RecA for SOS response of mycobacteria. Further, 35 candidates with stable expression in all conditions were detected, which could serve as targets for detection. Data are available via ProteomeXchange with identifier PXD027444.
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Affiliation(s)
- Kristina J. H. Kleinwort
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, D-82152 Martinsried, Germany; (K.J.H.K.); (B.F.H.); (R.L.D.)
| | - Bernhard F. Hobmaier
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, D-82152 Martinsried, Germany; (K.J.H.K.); (B.F.H.); (R.L.D.)
| | - Ricarda Mayer
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, LMU Munich, D-85764 Oberschleißheim, Germany; (R.M.); (C.H.); (E.M.)
| | - Christina Hölzel
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, LMU Munich, D-85764 Oberschleißheim, Germany; (R.M.); (C.H.); (E.M.)
- Institute of Animal Breeding and Husbandry, Faculty of Agricultural and Nutritional Sciences, CAU Kiel, D-24098 Kiel, Germany
| | - Roxane L. Degroote
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, D-82152 Martinsried, Germany; (K.J.H.K.); (B.F.H.); (R.L.D.)
| | - Erwin Märtlbauer
- Chair of Hygiene and Technology of Milk, Department of Veterinary Sciences, LMU Munich, D-85764 Oberschleißheim, Germany; (R.M.); (C.H.); (E.M.)
| | - Stefanie M. Hauck
- Research Unit Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health, D-80939 Munich, Germany;
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, D-82152 Martinsried, Germany; (K.J.H.K.); (B.F.H.); (R.L.D.)
- Correspondence:
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Marcelino I, Holzmuller P, Coelho A, Mazzucchelli G, Fernandez B, Vachiéry N. Revisiting Ehrlichia ruminantium Replication Cycle Using Proteomics: The Host and the Bacterium Perspectives. Microorganisms 2021; 9:1144. [PMID: 34073568 DOI: 10.3390/microorganisms9061144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/28/2021] [Accepted: 05/07/2021] [Indexed: 12/16/2022] Open
Abstract
The Rickettsiales Ehrlichia ruminantium, the causal agent of the fatal tick-borne disease Heartwater, induces severe damage to the vascular endothelium in ruminants. Nevertheless, E. ruminantium-induced pathobiology remains largely unknown. Our work paves the way for understanding this phenomenon by using quantitative proteomic analyses (2D-DIGE-MS/MS, 1DE-nanoLC-MS/MS and biotin-nanoUPLC-MS/MS) of host bovine aorta endothelial cells (BAE) during the in vitro bacterium intracellular replication cycle. We detect 265 bacterial proteins (including virulence factors), at all time-points of the E. ruminantium replication cycle, highlighting a dynamic bacterium–host interaction. We show that E. ruminantium infection modulates the expression of 433 host proteins: 98 being over-expressed, 161 under-expressed, 140 detected only in infected BAE cells and 34 exclusively detected in non-infected cells. Cystoscape integrated data analysis shows that these proteins lead to major changes in host cell immune responses, host cell metabolism and vesicle trafficking, with a clear involvement of inflammation-related proteins in this process. Our findings led to the first model of E. ruminantium infection in host cells in vitro, and we highlight potential biomarkers of E. ruminantium infection in endothelial cells (such as ROCK1, TMEM16K, Albumin and PTPN1), which may be important to further combat Heartwater, namely by developing non-antibiotic-based strategies.
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Monkman J, Taheri T, Ebrahimi Warkiani M, O’Leary C, Ladwa R, Richard D, O’Byrne K, Kulasinghe A. High-Plex and High-Throughput Digital Spatial Profiling of Non-Small-Cell Lung Cancer (NSCLC). Cancers (Basel) 2020; 12:cancers12123551. [PMID: 33261133 PMCID: PMC7760230 DOI: 10.3390/cancers12123551] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Profiling the tumour microenvironment (TME) has been informative in understanding the underlying tumour-immune interactions. Multiplex immunohistochemistry (mIHC) coupled with molecular barcoding technologies have revealed greater insights into the TME. In this study, we utilised the Nanostring GeoMX Digital Spatial Profiler (DSP) platform to profile a non-small-cell lung cancer (NSCLC) tissue microarray for protein markers across immune cell profiling, immuno-oncology (IO) drug targets, immune activation status, immune cell typing, and pan-tumour protein modules. Regions of interest (ROIs) were selected that described tumour, TME, and normal adjacent tissue (NAT) compartments. Our data revealed that paired analysis (n = 18) of matched patient compartments indicate that the TME was significantly enriched in CD27, CD3, CD4, CD44, CD45, CD45RO, CD68, CD163, and VISTA relative to the tumour. Unmatched analysis indicated that the NAT (n = 19) was significantly enriched in CD34, fibronectin, IDO1, LAG3, ARG1, and PTEN when compared to the TME (n = 32). Univariate Cox proportional hazards indicated that the presence of cells expressing CD3 (hazard ratio (HR): 0.5, p = 0.018), CD34 (HR: 0.53, p = 0.004), and ICOS (HR: 0.6, p = 0.047) in tumour compartments were significantly associated with improved overall survival (OS). We implemented both high-plex and high-throughput methodologies to the discovery of protein biomarkers and molecular phenotypes within biopsy samples, and demonstrate the power of such tools for a new generation of pathology research.
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Affiliation(s)
- James Monkman
- School of Biomedical Sciences, Faculty of Health and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia; (J.M.); (C.O.); (D.R.); (K.O.)
- Translational Research Institute, Woolloongabba, QLD 4102, Australia
- Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD 4000, Australia
| | - Touraj Taheri
- Queensland Pathology, Herston, QLD 4006, Australia;
- School of Medicine, University of Queensland, Brisbane, QLD 4102, Australia;
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia;
| | - Connor O’Leary
- School of Biomedical Sciences, Faculty of Health and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia; (J.M.); (C.O.); (D.R.); (K.O.)
- Translational Research Institute, Woolloongabba, QLD 4102, Australia
- Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD 4000, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD 4102, Australia
| | - Rahul Ladwa
- School of Medicine, University of Queensland, Brisbane, QLD 4102, Australia;
- Princess Alexandra Hospital, Woolloongabba, QLD 4102, Australia
| | - Derek Richard
- School of Biomedical Sciences, Faculty of Health and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia; (J.M.); (C.O.); (D.R.); (K.O.)
- Translational Research Institute, Woolloongabba, QLD 4102, Australia
- Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD 4000, Australia
| | - Ken O’Byrne
- School of Biomedical Sciences, Faculty of Health and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia; (J.M.); (C.O.); (D.R.); (K.O.)
- Translational Research Institute, Woolloongabba, QLD 4102, Australia
- Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD 4000, Australia
- Princess Alexandra Hospital, Woolloongabba, QLD 4102, Australia
| | - Arutha Kulasinghe
- School of Biomedical Sciences, Faculty of Health and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia; (J.M.); (C.O.); (D.R.); (K.O.)
- Translational Research Institute, Woolloongabba, QLD 4102, Australia
- Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD 4000, Australia
- Institute of Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence:
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Kraemer BF, Geimer M, Franz-Wachtel M, Lamkemeyer T, Mannell H, Lindemann S. Extracellular Matrix-Specific Platelet Activation Leads to a Differential Translational Response and Protein De Novo Synthesis in Human Platelets. Int J Mol Sci 2020; 21:ijms21218155. [PMID: 33142786 PMCID: PMC7672557 DOI: 10.3390/ijms21218155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 02/08/2023] Open
Abstract
Platelets are exposed to extracellular matrix (ECM) proteins like collagen and laminin and to fibrinogen during acute vascular events. However, beyond hemostasis, platelets have the important capacity to migrate on ECM surfaces, but the translational response of platelets to different extracellular matrix stimuli is still not fully characterized. Using 2D-gel electrophoresis, confocal microscopy, polysome analysis and protein sequencing by mass spectrometry, we demonstrate that platelets show a differential expression profile of newly synthesized proteins on laminin, collagen or fibrinogen. In this context, we observed a characteristic, ECM-dependent translocation phenotype of translation initiation factor eIF4E to the ribosomal site. eIF4E accumulated in polysomes with increased binding of mRNA and co-localization with vinculin, leading to de novo synthesis of important cytoskeletal regulator proteins. As the first study, we included a proteome analysis of laminin-adherent platelets and interestingly identified upregulation of essentially important proteins that mediate cytoskeletal regulation and mobility in platelets, such as filamin A, talin, vinculin, gelsolin, coronin or kindlin-3. In summary, we demonstrate that platelet activation with extracellular matrix proteins results in a distinct stimulus-specific translational response of platelets that will help to improve our understanding of the regulation of platelet mobility and migration.
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Affiliation(s)
- Bjoern F. Kraemer
- Medizinische Klinik und Poliklinik I, Klinikum der Universität München, Marchioninistrasse 15, 81377 Munich, Germany;
| | - Marc Geimer
- Klinik für Anästhesie, Intensiv- und Notfallmedizin, Westpfalz Klinikum Kaiserslautern, Hellmut-Hartert Str. 1, 67655 Kaiserslautern, Germany;
| | - Mirita Franz-Wachtel
- Proteasome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany;
| | - Tobias Lamkemeyer
- Cluster of Excellence Cologne (CEDAD), Mass Spectrometry Facility at the Institute for Genetics, University of Köln, Josef-Stelzmann-Str. 26, 50931 Köln, Germany;
| | - Hanna Mannell
- Doctoral Programme of Clinical Pharmacy, University Hospital, Ludwig-Maximilians-University, Marchioninistr. 27, 81377 Munich, Germany;
- Institute of Cardiovascular Physiology and Pathophysiology Biomedical Center, Ludwig-Maximilians-University, Großhaderner Str. 9, 82152 Planegg, Germany
| | - Stephan Lindemann
- Philipps Universität Marburg, FB 20-Medizin, Baldingerstraße, 35032 Marburg, Germany
- Klinikum Warburg, Medizinische Klinik II, Hüffertstr. 50, 34414 Warburg, Germany
- Medizinische Klinik und Poliklinik III, Otfried-Muller-Str. 10, Universitätsklinikum Tübingen, 72076 Tübingen, Germany
- Correspondence:
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8
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Wang Y, Zhang H, Ma D, Deng X, Wu D, Li F, Wu Q, Liu H, Wang J. Hsp70 Is a Potential Therapeutic Target for Echovirus 9 Infection. Front Mol Biosci 2020; 7:146. [PMID: 32766279 PMCID: PMC7379509 DOI: 10.3389/fmolb.2020.00146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/11/2020] [Indexed: 11/13/2022] Open
Abstract
Echovirus is an important cause of viral pneumonia and encephalitis in infants, neonates, and young children worldwide. However, the exact mechanism of its pathogenesis is still not well understood. Here, we established an echovirus type 9 infection mice model, and performed two-dimensional gel electrophoresis (2DE) and tandem mass spectrometry (MS/MS)-based comparative proteomics analysis to investigate the differentially expressed host proteins in mice brain. A total of 21 differentially expressed proteins were identified by MS/MS. The annotation of the differentially expressed proteins by function using the UniProt and GO databases identified one viral protein (5%), seven cytoskeletal proteins (33%), six macromolecular biosynthesis and metabolism proteins (28%), two stress response and chaperone binding proteins (9%), and five other cellular proteins (25%). The subcellular locations of these proteins were mainly found in the cytoskeleton, cytoplasm, nucleus, mitochondria, and Golgi apparatus. The protein expression profiles and the results of quantitative RT-PCR in the detection of gene transcripts were found to complement each other. The differential protein interaction network was predicted using the STRING database. Of the identified proteins, heat shock protein 70 (Hsp70), showing consistent results in the proteomics and transcriptomic analyses, was analyzed through Western blotting to verify the reliability of differential protein expression data in this study. Further, evaluation of the function of Hsp70 using siRNA and quercetin, an inhibitor of Hsp70, showed that Hsp70 was necessary for the infection of echovirus type 9. This study revealed that echovirus infection could cause the differential expression of a series of host proteins, which is helpful to reveal the pathogenesis of viral infection and identify therapeutic drug targets. Additionally, our results suggest that Hsp70 could be a useful therapeutic host protein target for echovirus infection.
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Affiliation(s)
- Yang Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongbo Ma
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiang Deng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongdong Wu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fang Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiuge Wu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Correani V, Di Francesco L, Mignogna G, Fabrizi C, Leone S, Giorgi A, Passeri A, Casata R, Fumagalli L, Maras B, Schininà ME. Plasma Membrane Protein Profiling in Beta-Amyloid-Treated Microglia Cell Line. Proteomics 2017; 17. [PMID: 28815942 DOI: 10.1002/pmic.201600439] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 08/01/2017] [Indexed: 01/13/2023]
Abstract
In the responsiveness of microglia to toxic stimuli, plasma membrane proteins play a key role. In this study we treated with a synthetic beta amyloid peptide murine microglial cells metabolically differently labelled with stable isotope amino acids (SILAC). The plasma membrane was selectively enriched by a multi-stage aqueous two-phase partition system. We were able to identify by 1D-LC-MS/MS analyses 1577 proteins, most of them are plasma membrane proteins according to the Gene Ontology annotation. An unchanged level of amyloid receptors in this data set suggests that microglia preserve their responsiveness capability to the environment even after 24-h challenge with amyloid peptides. On the other hand, 14 proteins were observed to change their plasma membrane abundance to a statistically significant extent. Among these, we proposed as reliable biomarkers of the inflammatory microglia phenotype in AD damaged tissues MAP/microtubule affinity-regulating kinase 3 (MARK3), Interferon-induced transmembrane protein 3 (IFITM3), Annexins A5 and A7 (ANXA5, ANXA7) and Neuropilin-1 (NRP1), all proteins known to be involved in the inflammation processes and in microtubule network assembly rate.
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Affiliation(s)
- Virginia Correani
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Rome, Italy
| | - Laura Di Francesco
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Rome, Italy
| | - Giuseppina Mignogna
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Rome, Italy
| | - Cinzia Fabrizi
- Dipartimento di Scienze Anatomiche Istologiche, Medico-Legali e dell'Apparato Locomotore, Sapienza Università di Roma, Rome, Italy
| | - Stefano Leone
- Dipartimento di Scienze, Università Roma Tre, Rome, Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Rome, Italy
| | - Alessia Passeri
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Rome, Italy
| | - Roberto Casata
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Rome, Italy
| | - Lorenzo Fumagalli
- Dipartimento di Scienze Anatomiche Istologiche, Medico-Legali e dell'Apparato Locomotore, Sapienza Università di Roma, Rome, Italy
| | - Bruno Maras
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Rome, Italy
| | - M Eugenia Schininà
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Rome, Italy
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Lin H, Li B, Chen L, Ma Z, He K, Fan H. Differential Protein Analysis of IPEC-J2 Cells Infected with Porcine Epidemic Diarrhea Virus Pandemic and Classical Strains Elucidates the Pathogenesis of Infection. J Proteome Res 2017; 16:2113-2120. [PMID: 28506058 DOI: 10.1021/acs.jproteome.6b00957] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Porcine epidemic diarrhea (PED) re-emerged in China in late 2010 and has now become widespread. Accumulated evidence indicates that this large-scale outbreak of diarrhea was caused by variants of the highly virulent porcine epidemic diarrhea virus (PEDV). A pandemic PEDV YC2014 strain (YC2014) was isolated from clinical samples. An iTRAQ-based comparative quantitative proteomic study of IPEC-J2 cells infected with YC2014 and a classical CV777 strain (CV777) was performed to determine the differences between pandemic and classical PEDV strain infection. Totals of 353 and 299 differentially expressed proteins were identified upon YC2014 and CV777 infection, respectively. The canonical pathways and functional networks involved in both PEDV infections were analyzed. The results indicated that the PEDV suppressed protein synthesis of IPEC-J2 cells through down-regulation of the PI3K-AKT/mTOR signaling pathways. Infection with YC2014 could activate the JAK-STAT signaling pathway and the NF-κB pathway more intensively than CV777. YC2014 could activate NF-κB pathway more intensively than CV777. On the basis of differentially expressed proteins, we propose that PEDV might disrupt apoptosis and may elicit stronger inflammatory cascades as well. This study might contribute to an understanding of the pathogenesis of PEDV infection and aid in the development of effective preventive and control vaccines.
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Affiliation(s)
- Huixing Lin
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Bin Li
- Institute of Veterinary Medicine , Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lei Chen
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Zhe Ma
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Kongwang He
- Institute of Veterinary Medicine , Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hongjie Fan
- College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China
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Ren Z, Wang Y, Peng J, Zhang L, Xu W, Liang X, Zhao Q, Lu S. Protein expression of sensory and motor nerves: Two-dimensional gel electrophoresis and mass spectrometry. Neural Regen Res 2015; 7:369-75. [PMID: 25774177 PMCID: PMC4350121 DOI: 10.3969/j.issn.1673-5374.2012.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 01/05/2012] [Indexed: 01/12/2023] Open
Abstract
The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product (gi|55628), glyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylglutathione lyase, adenylate kinase isozyme 1, two unnamed proteins products (gi|55628 and gi|1334163), and poly(rC)-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.
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Affiliation(s)
- Zhiwu Ren
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China ; Medical College of Nankai University, Tianjin 300071, China
| | - Yu Wang
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Jiang Peng
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Li Zhang
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Wenjing Xu
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiangdang Liang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
| | - Qing Zhao
- Department of Orthopedics, First Affiliated Hospital of Chinese PLA General Hospital, Beijing 100037, China
| | - Shibi Lu
- Key Laboratory of People's Liberation Army, Institute of Orthopedics, Chinese PLA General Hospital, Beijing 100853, China
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Huang Q, Zhang J, Peng S, Du M, Ow S, Pu H, Pan C, Shen H. Proteomic analysis of perfluorooctane sulfonate-induced apoptosis in human hepatic cells using the iTRAQ technique. J Appl Toxicol 2013; 34:1342-51. [PMID: 24301089 DOI: 10.1002/jat.2963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 01/09/2023]
Abstract
Perfluorooctane sulfonate (PFOS) is one of the most commonly used perfluorinated compounds, whose environmental exposure has been associated with a number of adverse health outcomes. However, the molecular mechanisms involved in PFOS toxicity are still not well elucidated. In the present study, we applied iTRAQ labeling quantitative proteomic technology to investigate the differential protein expression profiles of non-tumor human hepatic cells (L-02) exposed to PFOS. A total of 18 proteins were differentially expressed in a dose-dependent manner in PFOS-treated cells versus the control. Among these, 11 proteins were up-regulated and 7 were down-regulated. Gene ontology analysis indicated that PFOS would exert toxic effects on L-02 cells by affecting multiple biological processes, including protein biosynthesis and degradation, mRNA processing and splicing, transcription, signal transduction and transport. Furthermore, the proteomic results especially proposed that the inhibition of HNRNPC, HUWE1 and UBQLN1, as well as the induction of PAF1 is involved in the activation of the p53 and c-myc signaling pathways, which then trigger the apoptotic process in L-02 cells exposed to PFOS. Overall, these data will aid our understanding of the mechanisms responsible for PFOS-mediated hepatotoxicity, and develop useful biomarkers for monitoring and evaluating PFOS contamination in the environment.
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Affiliation(s)
- Qingyu Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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13
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Abstract
The filamentous fungus Magnaporthe oryzae (M. oryzae) is the causative agent of rice blast disease and presents a significant threat to worldwide rice production. To establish the groundwork for future research on the pathogenic development of M. oryzae, a global proteomic study of conidia was performed. The filter aided sample preparation method (FASP) and anion StageTip fractionation combined with long, optimized shallow 210 min nanoLC gradients prior to mass spectrometry analysis on an Orbitrap XL was applied, which resulted in a doubling of protein identifications in comparison to our previous GeLC analysis. Herein, we report the identification of 2912 conidial proteins at a 1% protein false discovery rate (FDR) and we present the most extensive study performed on M. oryzae conidia to date. A similar distribution between identified proteins and the predicted proteome was observed when subcellular localization analysis was performed, suggesting the detected proteins build a representative portion of the predicted proteome. A higher percentage of cytoplasmic proteins (associated with translation, energy, and metabolism) were observed in the conidial proteome relative to the whole predicted proteome. Conversely, nuclear and extracellular proteins were less well represented in the conidial proteome. Further analysis by gene ontology revealed biological insights into identified proteins important for central metabolic processes and the physiology of conidia.
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Affiliation(s)
- Emine Gokce
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - William L. Franck
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina, 27695
| | - Yeonyee Oh
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina, 27695
| | - Ralph A. Dean
- Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina, 27695
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
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