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Karim AF, Sande OJ, Tomechko SE, Ding X, Li M, Maxwell S, Ewing RM, Harding CV, Rojas RE, Chance MR, Boom WH. Proteomics and Network Analyses Reveal Inhibition of Akt-mTOR Signaling in CD4 + T Cells by Mycobacterium tuberculosis Mannose-Capped Lipoarabinomannan. Proteomics 2017; 17:1700233. [PMID: 28994205 PMCID: PMC5725663 DOI: 10.1002/pmic.201700233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/13/2017] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis (Mtb) cell wall glycolipid mannose-capped lipoarabinomannan (ManLAM) inhibits CD4+ T-cell activation by inhibiting proximal T-cell receptor (TCR) signaling when activated by anti-CD3. To understand the impact of ManLAM on CD4+ T-cell function when both the TCR-CD3 complex and major costimulator CD28 are engaged, we performed label-free quantitative MS and network analysis. Mixed-effect model analysis of peptide intensity identified 149 unique peptides representing 131 proteins that were differentially regulated by ManLAM in anti-CD3- and anti-CD28-activated CD4+ T cells. Crosstalker, a novel network analysis tool identified dysregulated translation, TCA cycle, and RNA metabolism network modules. PCNA, Akt, mTOR, and UBC were found to be bridge node proteins connecting these modules of dysregulated proteins. Altered PCNA expression and cell cycle analysis showed arrest at the G2M phase. Western blot confirmed that ManLAM inhibited Akt and mTOR phosphorylation, and decreased expression of deubiquitinating enzymes Usp9x and Otub1. Decreased NF-κB phosphorylation suggested interference with CD28 signaling through inhibition of the Usp9x-Akt-mTOR pathway. Thus, ManLAM induced global changes in the CD4+ T-cell proteome by affecting Akt-mTOR signaling, resulting in broad functional impairment of CD4+ T-cell activation beyond inhibition of proximal TCR-CD3 signaling.
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Affiliation(s)
- Ahmad F. Karim
- Department of MedicineUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOHUSA
| | - Obondo J. Sande
- Department of MedicineUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
| | - Sara E. Tomechko
- Center for Proteomics & BioinformaticsCase Western Reserve UniversityClevelandOHUSA
| | - Xuedong Ding
- Department of MedicineUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
| | - Ming Li
- Center for Proteomics & BioinformaticsCase Western Reserve UniversityClevelandOHUSA
| | - Sean Maxwell
- Center for Proteomics & BioinformaticsCase Western Reserve UniversityClevelandOHUSA
| | - Rob M. Ewing
- Centre for Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Clifford V. Harding
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOHUSA
- Department of PathologyUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
| | - Roxana E. Rojas
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOHUSA
| | - Mark R. Chance
- Center for Proteomics & BioinformaticsCase Western Reserve UniversityClevelandOHUSA
- Department of NutritionSchool of MedicineCase Western Reserve UniversityClevelandOHUSA
| | - W. Henry Boom
- Department of MedicineUniversity Hospitals Cleveland Medical CenterCase Western Reserve UniversityClevelandOHUSA
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOHUSA
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Abstract
Proper differentiation of naïve T helper cells into functionally distinct subsets is of critical importance to human health. Consequently, the process is tightly controlled by a complex intracellular signalling network. To dissect the regulatory principles of this network, immunologists have early on embraced system-wide transcriptomics tools, leading to identification of large panels of potential regulatory factors. In contrast, the use of proteomics approaches in T helper cell research has been notably rare, and to this date relatively few high-throughput datasets have been reported. Here, we discuss the importance of such research and envision the possibilities afforded by mass spectrometry-based proteomics in the near future.
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Affiliation(s)
- Tapio Lönnberg
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
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Chen Z, Lönnberg T, Lahesmaa R. Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets. Scand J Immunol 2013; 78:172-80. [PMID: 23679154 DOI: 10.1111/sji.12071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 05/11/2013] [Indexed: 01/22/2023]
Abstract
Current knowledge of helper T cell differentiation largely relies on data generated from mouse studies. To develop therapeutical strategies combating human diseases, understanding the molecular mechanisms how human naïve T cells differentiate to functionally distinct T helper (Th) subsets as well as studies on human differentiated Th cell subsets is particularly valuable. Systems biology approaches provide a holistic view of the processes of T helper differentiation, enable discovery of new factors and pathways involved and generation of new hypotheses to be tested to improve our understanding of human Th cell differentiation and immune-mediated diseases. Here, we summarize studies where high-throughput systems biology approaches have been exploited to human primary T cells. These studies reveal new factors and signalling pathways influencing T cell differentiation towards distinct subsets, important for immune regulation. Such information provides new insights into T cell biology and into targeting immune system for therapeutic interventions.
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Affiliation(s)
- Z Chen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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Li H, Zhang XY, Wu TJ, Cheng W, Liu X, Jiang TT, Wen J, Li J, Ma QL, Hua ZC. Endoplasmic reticulum stress regulates rat mandibular cartilage thinning under compressive mechanical stress. J Biol Chem 2013; 288:18172-83. [PMID: 23603905 DOI: 10.1074/jbc.m112.407296] [Citation(s) in RCA: 55] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Compressive mechanical stress-induced cartilage thinning has been characterized as a key step in the progression of temporomandibular joint diseases, such as osteoarthritis. However, the regulatory mechanisms underlying this loss have not been thoroughly studied. Here, we used an established animal model for loading compressive mechanical stress to induce cartilage thinning in vivo. The mechanically stressed mandibular chondrocytes were then isolated to screen potential candidates using a proteomics approach. A total of 28 proteins were identified that were directly or indirectly associated with endoplasmic reticulum stress, including protein disulfide-isomerase, calreticulin, translationally controlled tumor protein, and peptidyl-prolyl cis/trans-isomerase protein. The altered expression of these candidates was validated at both the mRNA and protein levels. The induction of endoplasmic reticulum stress by mechanical stress loading was confirmed by the activation of endoplasmic reticulum stress markers, the elevation of the cytoplasmic Ca(2+) level, and the expansion of endoplasmic reticulum membranes. More importantly, the use of a selective inhibitor to block endoplasmic reticulum stress in vivo reduced the apoptosis observed at the early stages of mechanical stress loading and inhibited the proliferation observed at the later stages of mechanical stress loading. Accordingly, the use of the inhibitor significantly restored cartilage thinning. Taken together, these results demonstrated that endoplasmic reticulum stress is significantly activated in mechanical stress-induced mandibular cartilage thinning and, more importantly, that endoplasmic reticulum stress inhibition alleviates this loss, suggesting a novel pharmaceutical strategy for the treatment of mechanical stress-induced temporomandibular joint diseases.
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Affiliation(s)
- Huang Li
- School of Stomatology and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, 30 Zhongyang Road, Nanjing 210009, China.
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Lichtenfels R, Rappl G, Hombach AA, Recktenwald CV, Dressler SP, Abken H, Seliger B. A proteomic view at T cell costimulation. PLoS One 2012; 7:e32994. [PMID: 22539942 PMCID: PMC3335147 DOI: 10.1371/journal.pone.0032994] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 02/07/2012] [Indexed: 12/31/2022] Open
Abstract
The "two-signal paradigm" in T cell activation predicts that the cooperation of "signal 1," provided by the T cell receptor (TCR) through engagement of major histocompatility complex (MHC)-presented peptide, with "signal 2″ provided by costimulatory molecules, the prototype of which is CD28, is required to induce T cell effector functions. While the individual signalling pathways are well understood, little is known about global changes in the proteome pattern during TCR/CD28-mediated activation. Therefore, comparative 2-DE-based proteome analyses of CD3(+) CD69(-) resting T cells versus cells incubated with (i) the agonistic anti-CD3 antibody OKT3 mimicking signal 1 in absence or presence of IL-2 and/or with (ii) the agonistic antibody 15E8 triggering CD28-mediated signaling were performed. Differentially regulated spots were defined leading to the identification of proteins involved in the regulation of the metabolism, shaping and maintenance of the cytoskeleton and signal transduction. Representative members of the differentially expressed protein families, such as calmodulin (CALM), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), L-lactate dehydrogenase (LDH), Rho GDP-dissociation inhibitor 2 (GDIR2), and platelet basic protein (CXCL7), were independently verified by flow cytometry. Data provide a detailed map of individual protein alterations at the global proteome level in response to TCR/CD28-mediated T cell activation.
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Affiliation(s)
- Rudolf Lichtenfels
- Institute of Medical Immunology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Gunter Rappl
- Center for Molecular Medicine Cologne (CMMC) and Tumor Genetics Section, Clinic I Internal Medicine, University Cologne, Cologne, Germany
| | - Andreas A. Hombach
- Center for Molecular Medicine Cologne (CMMC) and Tumor Genetics Section, Clinic I Internal Medicine, University Cologne, Cologne, Germany
| | | | - Sven P. Dressler
- Institute of Medical Immunology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Hinrich Abken
- Center for Molecular Medicine Cologne (CMMC) and Tumor Genetics Section, Clinic I Internal Medicine, University Cologne, Cologne, Germany
| | - Barbara Seliger
- Institute of Medical Immunology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
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Pirooznia N, Hasannia S, Taghdir M, Rahbarizadeh F, Eskandani M. The construction of chimeric T-Cell receptor with spacer base of modeling study of VHH and MUC1 interaction. J Biomed Biotechnol 2011; 2011:578128. [PMID: 21869862 DOI: 10.1155/2011/578128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 05/24/2011] [Accepted: 06/02/2011] [Indexed: 01/07/2023] Open
Abstract
Adaptive cell immunotherapy with the use of chimeric receptors leads to the best and most specific response against tumors. Chimeric receptors consist of a signaling fragment, extracellular spacer, costimulating domain, and an antibody. Antibodies cause immunogenicity; therefore, VHH is a good replacement for ScFv in chimeric receptors. Since peptide sequences have an influence on chimeric receptors, the effect of peptide domains on each other's conformation were investigated. CD3Zeta, CD28, VHH and CD8α, and FcgIIα are used as signaling moieties, costimulating domain, antibody, and spacers, respectively. To investigate the influence of the ligation of spacers on the conformational structure of VHH, models of VHH were constructed. Molecular dynamics simulation was run to study the influence of the presence of spacers on the conformational changes in the binding sites of VHH. Root mean square deviation and root mean square fluctuation of critical segments in the binding site showed no noticeable differences with those in the native VHH. Results from molecular docking revealed that the presence of spacer FcgIIα causes an increasing effect on VHH with MUC1 interaction. Each of the constructs was transformed into the Jurkat E6.1. Expression analysis and evaluation of their functions were examined. The results showed good expression and function.
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Abstract
CD4(+)CD25(+) regulatory T-cells (Treg cells) are an important subset of T-cells that functions to negatively control immune responses to self or non-self antigens. Depletion of CD4(+)CD25(+) Treg cells leads to the occurrence of lymphoproliferative autoimmune diseases in animals and humans. Therefore, CD4(+)CD25(+) Treg cells must be tightly regulated in the physiologic situation. In this article, we try to summarize the regulating pathways of the development, survival, and function of CD4(+)CD25(+) Treg cells at multiple levels and multiple pathways, including the dendritic cells, costimulatory signals, cytokines, as well as intracellular signals.
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Affiliation(s)
- Yanyan Qu
- Transplantation Biology Research Division, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Thadikkaran L, Rufer N, Benay C, Crettaz D, Tissot JD. Methods for human CD8(+) T lymphocyte proteome analysis. Methods Mol Biol 2008; 484:45-65. [PMID: 18592172 DOI: 10.1007/978-1-59745-398-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
T lymphocytes, including cytotoxic CD8(+) T cells, are important cells involved in immunology, as they can destroy infected or tumor cells. We describe here a detailed protocol starting from CD8(+) T lymphocytes isolation for T cell culture followed by total protein extraction or subcellular fractionation, like nuclei isolation. We also describe well-defined biochemistry and cell biology methods adapted to T lymphocytes, showing the importance of using the method best suited to answering the question addressed. All these techniques would be very helpful to immunologists willing to study underlying biological processes related to T lymphocytes.
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