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Mann M, Brasier AR. Evolution of proteomics technologies for understanding respiratory syncytial virus pathogenesis. Expert Rev Proteomics 2021; 18:379-394. [PMID: 34018899 PMCID: PMC8277732 DOI: 10.1080/14789450.2021.1931130] [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: 03/05/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
Introduction: Respiratory syncytial virus (RSV) is a major human pathogen associated with long term morbidity. RSV replication occurs primarily in the epithelium, producing a complex cellular response associated with acute inflammation and long-lived changes in pulmonary function and allergic disease. Proteomics approaches provide important insights into post-transcriptional regulatory processes including alterations in cellular complexes regulating the coordinated innate response and epigenome.Areas covered: Peer-reviewed proteomics studies of host responses to RSV infections and proteomics techniques were analyzed. Methodologies identified include 1)." bottom-up" discovery proteomics, 2). Organellar proteomics by LC-gel fractionation; 3). Dynamic changes in protein interaction networks by LC-MS; and 4). selective reaction monitoring MS. We introduce recent developments in single-cell proteomics, top-down mass spectrometry, and photo-cleavable surfactant chemistries that will have impact on understanding how RSV induces extracellular matrix (ECM) composition and airway remodeling.Expert opinion: RSV replication induces global changes in the cellular proteome, dynamic shifts in nuclear proteins, and remodeling of epigenetic regulatory complexes linked to the innate response. Pathways discovered by proteomics technologies have led to deeper mechanistic understanding of the roles of heat shock proteins, redox response, transcriptional elongation complex remodeling and ECM secretion remodeling in host responses to RSV infections and pathological sequelae.
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Affiliation(s)
- Morgan Mann
- Department of Internal Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, USA
| | - Allan R Brasier
- Department of Internal Medicine and Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison, Madison, WI, USA
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2
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Zhao Y, Tian B, Sun H, Zhang J, Zhang Y, Ivannikov M, Motamedi M, Liu Z, Zhou J, Kaphalia L, Calhoun WJ, Maroto R, Brasier AR. Pharmacoproteomics reveal novel protective activity of bromodomain containing 4 inhibitors on vascular homeostasis in TLR3-mediated airway remodeling. J Proteomics 2019; 205:103415. [PMID: 31195152 DOI: 10.1016/j.jprot.2019.103415] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/23/2019] [Accepted: 06/09/2019] [Indexed: 12/19/2022]
Abstract
Small molecule inhibitors of the epigenetic regulator bromodomain-containing protein 4 (BRD4) are potential therapeutics for viral and allergen-induced airway remodeling. A limitation of their preclinical advancement is the lack of detailed understanding of mechanisms of action and biomarkers of effect. We report a systems-level pharmacoproteomics in a standardized murine model of toll-like receptor TLR3-NFκB/RelA innate inflammation in the absence or presence of a highly selective BRD4 inhibitor (ZL0454) or nonselective bromodomain and extraterminal domain inhibitor (JQ1). Proteomics of bronchoalveolar lavage fluid (BALF) secretome and exosomal proteins from this murine model revealed increased, selective, capillary leak associated with pericyte-myofibroblast transition, a phenomenon blocked by BRD4 inhibitors. BALF proteomics also suggested that ZL0454 better reduced the vascular leakage and extracellular matrix deposition than JQ1. A significant subset of inflammation-mediated remodeling factors was also identified in a mouse model of idiopathic pulmonary fibrosis produced by bleomycin. BALF exosome analysis indicated that BRD4 inhibitors reduced the induction of exosomes enriched in coagulation factors whose presence correlated with interstitial fibrin deposition. Finally, BALF samples from humans with severe asthma demonstrated similar upregulations of ORM2, APCS, SPARCL1, FGA, and FN1, suggesting their potential as biomarkers for early detection of airway remodeling and/or monitoring of therapy response. SIGNIFICANCE: Repetitive and chronic viral upper respiratory tract infections trigger toll-like receptor (TLR)3-NFκB/RelA mediated airway remodeling which is linked to a progressive decline in pulmonary function in patients with asthma and chronic obstructive pulmonary disease. Small molecule inhibitors of the epigenetic regulator bromodomain-containing protein 4 (BRD4) are potential therapeutics for viral and allergen-induced airway remodeling. A limitation of their preclinical advancement is the lack of detailed understanding of mechanisms of action and biomarkers of effect. Our study revealed that the activation of (TLR)3-NFκB/RelA pathway in the lung induced an elevation in coagulation, complement, and platelet factors, indicating the increased vascular leak during airway remodeling. The mechanism of vascular leakage was chronic inflammation-induced pericyte-myofibroblast transition, which was blocked by BRD4 inhibitors. Finally, proteomics analysis of the bronchoalveolar lavage fluid samples from humans with severe asthma demonstrated similar findings that we observed in the animal model.
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Affiliation(s)
- Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA; Institute for Translational Sciences, UTMB, Galveston, TX, USA; Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA.
| | - Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA; Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Jing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | | | | | - Zhiqing Liu
- Department of Pharmacology and Toxicology, UTMB, Galveston, TX, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, UTMB, Galveston, TX, USA
| | - Lata Kaphalia
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - William J Calhoun
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA; Institute for Translational Sciences, UTMB, Galveston, TX, USA; Sealy Center for Molecular Medicine, UTMB, Galveston, TX, USA
| | - Rosario Maroto
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Allan R Brasier
- Institute for Clinical and Translational Research, University of Wisconsin-Madison, Madison, WI, USA
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3
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Bregenzer ME, Horst EN, Mehta P, Novak CM, Raghavan S, Snyder CS, Mehta G. Integrated cancer tissue engineering models for precision medicine. PLoS One 2019; 14:e0216564. [PMID: 31075118 PMCID: PMC6510431 DOI: 10.1371/journal.pone.0216564] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tumors are not merely cancerous cells that undergo mindless proliferation. Rather, they are highly organized and interconnected organ systems. Tumor cells reside in complex microenvironments in which they are subjected to a variety of physical and chemical stimuli that influence cell behavior and ultimately the progression and maintenance of the tumor. As cancer bioengineers, it is our responsibility to create physiologic models that enable accurate understanding of the multi-dimensional structure, organization, and complex relationships in diverse tumor microenvironments. Such models can greatly expedite clinical discovery and translation by closely replicating the physiological conditions while maintaining high tunability and control of extrinsic factors. In this review, we discuss the current models that target key aspects of the tumor microenvironment and their role in cancer progression. In order to address sources of experimental variation and model limitations, we also make recommendations for methods to improve overall physiologic reproducibility, experimental repeatability, and rigor within the field. Improvements can be made through an enhanced emphasis on mathematical modeling, standardized in vitro model characterization, transparent reporting of methodologies, and designing experiments with physiological metrics. Taken together these considerations will enhance the relevance of in vitro tumor models, biological understanding, and accelerate treatment exploration ultimately leading to improved clinical outcomes. Moreover, the development of robust, user-friendly models that integrate important stimuli will allow for the in-depth study of tumors as they undergo progression from non-transformed primary cells to metastatic disease and facilitate translation to a wide variety of biological and clinical studies.
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Affiliation(s)
- Michael E. Bregenzer
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Eric N. Horst
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Pooja Mehta
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Caymen M. Novak
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Shreya Raghavan
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Catherine S. Snyder
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Geeta Mehta
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Rogel Cancer Center, School of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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4
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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5
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Leyman B, Huysmans H, Mc Cafferty S, Combes F, Cox E, Devriendt B, Sanders NN. Comparison of the Expression Kinetics and Immunostimulatory Activity of Replicating mRNA, Nonreplicating mRNA, and pDNA after Intradermal Electroporation in Pigs. Mol Pharm 2018; 15:377-384. [PMID: 29297692 DOI: 10.1021/acs.molpharmaceut.7b00722] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthetic mRNA is becoming increasingly popular as an alternative to pDNA-based gene therapy. Currently, multiple synthetic mRNA platforms have been developed. In this study we investigated the expression kinetics and the changes in mRNA encoding cytokine and chemokine levels following intradermal electroporation in pigs of pDNA, self-replicating mRNA, and modified and unmodified mRNA. The self-replicating mRNA tended to induce the highest protein expression, followed by pDNA, modified mRNA, and unmodified mRNA. Interestingly, the self-replicating mRNA was able to maintain its high expression levels during at least 12 days. In contrast, the expression of pDNA and the nonreplicating mRNAs dropped after respectively one and two days. Six days after intradermal electroporation a dose-dependent expression was observed for all vectors. Again, also at lower doses, the self-replicating mRNA tended to show the highest expression. All the mRNA vectors, including the modified mRNA, induced elevated levels of mRNA encoding cytokines and chemokines in the porcine skin after intradermal electroporation, while no such response was noticed after intradermal electroporation of the pDNA vector.
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Affiliation(s)
- Bregje Leyman
- Faculty of Veterinary Medicine, Department of Nutrition, Genetics, and Ethology, Laboratory for Gene Therapy, Ghent University , Heidestraat 19, 9820 Merelbeke, Belgium
| | - Hanne Huysmans
- Faculty of Veterinary Medicine, Department of Nutrition, Genetics, and Ethology, Laboratory for Gene Therapy, Ghent University , Heidestraat 19, 9820 Merelbeke, Belgium
| | - Séan Mc Cafferty
- Faculty of Veterinary Medicine, Department of Nutrition, Genetics, and Ethology, Laboratory for Gene Therapy, Ghent University , Heidestraat 19, 9820 Merelbeke, Belgium.,Cancer Research Institute (CRIG), Ghent University , 9820 Merelbeke, Belgium
| | - Francis Combes
- Faculty of Veterinary Medicine, Department of Nutrition, Genetics, and Ethology, Laboratory for Gene Therapy, Ghent University , Heidestraat 19, 9820 Merelbeke, Belgium.,Cancer Research Institute (CRIG), Ghent University , 9820 Merelbeke, Belgium
| | - Eric Cox
- Faculty of Veterinary Medicine, Department of Virology, Parasitology, and Immunology, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Bert Devriendt
- Faculty of Veterinary Medicine, Department of Virology, Parasitology, and Immunology, Ghent University , Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Niek N Sanders
- Faculty of Veterinary Medicine, Department of Nutrition, Genetics, and Ethology, Laboratory for Gene Therapy, Ghent University , Heidestraat 19, 9820 Merelbeke, Belgium.,Cancer Research Institute (CRIG), Ghent University , 9820 Merelbeke, Belgium
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6
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Sun W, Tang M, Sun Y, Xu Y, Zheng H. Effective sludge dewatering technique using the combination of Fenton's reagent and CPAM. CAN J CHEM ENG 2017. [DOI: 10.1002/cjce.23069] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wenquan Sun
- College of Urban Construction; Nanjing Tech University; Nanjing, 211800 China
- Jiangsu Key Laboratory of Industrial Water-Conservation & Emission Reduction, College of Environment; Nanjing Tech University; Nanjing, 211800 China
| | - Mengdan Tang
- College of Urban Construction; Nanjing Tech University; Nanjing, 211800 China
| | - Yongjun Sun
- College of Urban Construction; Nanjing Tech University; Nanjing, 211800 China
- Jiangsu Key Laboratory of Industrial Water-Conservation & Emission Reduction, College of Environment; Nanjing Tech University; Nanjing, 211800 China
| | - Yanhua Xu
- Jiangsu Key Laboratory of Industrial Water-Conservation & Emission Reduction, College of Environment; Nanjing Tech University; Nanjing, 211800 China
| | - Huaili Zheng
- Key laboratory of the Three Gorges Reservoir Region's Eco-Environment, State Ministry of Education; Chongqing University; Chongqing, 400045 China
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7
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Zhang Y, Sun H, Zhang J, Brasier AR, Zhao Y. Quantitative Assessment of the Effects of Trypsin Digestion Methods on Affinity Purification-Mass Spectrometry-based Protein-Protein Interaction Analysis. J Proteome Res 2017; 16:3068-3082. [PMID: 28726418 DOI: 10.1021/acs.jproteome.7b00432] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Affinity purification-mass spectrometry (AP-MS) has become the method of choice for discovering protein-protein interactions (PPIs) under native conditions. The success of AP-MS depends on the efficiency of trypsin digestion and the recovery of the tryptic peptides for MS analysis. Several different protocols have been used for trypsin digestion of protein complexes in AP-MS studies, but no systematic studies have been conducted on the impact of trypsin digestion conditions on the identification of PPIs. Here, we used NFκB/RelA and Bromodomain-containing protein 4 (BRD4) as baits and test five distinct trypsin digestion methods (two using "on-beads," three using "elution-digestion" protocols). Although the performance of the trypsin digestion protocols change slightly depending on the different baits, antibodies and cell lines used, we found that elution-digestion methods consistently outperformed on-beads digestion methods. The high-abundance interactors can be identified universally by all five methods, but the identification of low-abundance RelA interactors is significantly affected by the choice of trypsin digestion method. We also found that different digestion protocols influence the selected reaction monitoring (SRM)-MS quantification of PPIs, suggesting that optimization of trypsin digestion conditions may be required for robust targeted analysis of PPIs.
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Affiliation(s)
- Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Jing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
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8
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Tian B, Yang J, Zhao Y, Ivanciuc T, Sun H, Garofalo RP, Brasier AR. BRD4 Couples NF-κB/RelA with Airway Inflammation and the IRF-RIG-I Amplification Loop in Respiratory Syncytial Virus Infection. J Virol 2017; 91:e00007-17. [PMID: 28077651 PMCID: PMC5331805 DOI: 10.1128/jvi.00007-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 01/09/2023] Open
Abstract
The airway mucosa expresses protective interferon (IFN) and inflammatory cytokines in response to respiratory syncytial virus (RSV) infection. In this study, we examine the role of bromodomain containing 4 (BRD4) in mediating this innate immune response in human small airway epithelial cells. We observe that RSV induces BRD4 to complex with NF-κB/RelA. BRD4 is functionally required for expression of the NF-κB-dependent inflammatory gene regulatory network (GRN), including the IFN response factor 1 (IRF1) and IRF7, which mediate a cross talk pathway for RIG-I upregulation. Mechanistically, BRD4 is required for cyclin-dependent kinase 9 (CDK9) recruitment and phospho-Ser 2 carboxy-terminal domain (CTD) RNA polymerase (Pol) II formation on the promoters of IRF1, IRF7, and RIG-I, producing their enhanced expression by transcriptional elongation. We also find that BRD4 independently regulates CDK9/phospho-Ser 2 CTD RNA Pol II recruitment to the IRF3-dependent IFN-stimulated genes (ISGs). In vivo, poly(I·C)-induced neutrophilia and mucosal chemokine production are blocked by a small-molecule BRD4 bromodomain inhibitor. Similarly, BRD4 inhibition reduces RSV-induced neutrophilia, mucosal CXC chemokine expression, activation of the IRF7-RIG-I autoamplification loop, mucosal IFN expression, and airway obstruction. RSV infection activates BRD4 acetyltransferase activity on histone H3 Lys (K) 122, demonstrating that RSV infection activates BRD4 in vivo These data validate BRD4 as a major effector of RSV-induced inflammation and disease. BRD4 is required for coupling NF-κB to expression of inflammatory genes and the IRF-RIG-I autoamplification pathway and independently facilitates antiviral ISG expression. BRD4 inhibition may be a strategy to reduce exuberant virus-induced mucosal airway inflammation.IMPORTANCE In the United States, 2.1 million children annually require medical attention for RSV infections. A first line of defense is the expression of the innate gene network by infected epithelial cells. Expression of the innate response requires the recruitment of transcriptional elongation factors to rapidly induce innate response genes through an unknown mechanism. We discovered that RSV infection induces a complex of bromodomain containing 4 (BRD4) with NF-κB and cyclin-dependent kinase 9 (CDK9). BRD4 is required for stable CDK9 binding, phospho-Ser 2 RNA Pol II formation, and histone acetyltransferase activity. Inhibition of BRD4 blocks Toll-like receptor 3 (TLR3)-dependent neutrophilia and RSV-induced inflammation, demonstrating its importance in the mucosal innate response in vivo Our study shows that BRD4 plays a central role in inflammation and activation of the IRF7-RIG-I amplification loop vital for mucosal interferon expression. BRD4 inhibition may be a strategy for modulating exuberant mucosal airway inflammation.
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Affiliation(s)
- Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jun Yang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Teodora Ivanciuc
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Roberto P Garofalo
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, USA
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9
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Zhao Y, Jamaluddin M, Zhang Y, Sun H, Ivanciuc T, Garofalo RP, Brasier AR. Systematic Analysis of Cell-Type Differences in the Epithelial Secretome Reveals Insights into the Pathogenesis of Respiratory Syncytial Virus-Induced Lower Respiratory Tract Infections. THE JOURNAL OF IMMUNOLOGY 2017; 198:3345-3364. [PMID: 28258195 DOI: 10.4049/jimmunol.1601291] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/23/2017] [Indexed: 11/19/2022]
Abstract
Lower respiratory tract infections from respiratory syncytial virus (RSV) are due, in part, to secreted signals from lower airway cells that modify the immune response and trigger airway remodeling. To understand this process, we applied an unbiased quantitative proteomics analysis of the RSV-induced epithelial secretory response in cells representative of the trachea versus small airway bronchiolar cells. A workflow was established using telomerase-immortalized human epithelial cells that revealed highly reproducible cell type-specific differences in secreted proteins and nanoparticles (exosomes). Approximately one third of secretome proteins are exosomal; the remainder are from lysosomal and vacuolar compartments. We applied this workflow to three independently derived primary human cultures from trachea versus bronchioles. A total of 577 differentially expressed proteins from control supernatants and 966 differentially expressed proteins from RSV-infected cell supernatants were identified at a 1% false discovery rate. Fifteen proteins unique to RSV-infected primary human cultures from trachea were regulated by epithelial-specific ets homologous factor. A total of 106 proteins unique to RSV-infected human small airway epithelial cells was regulated by the transcription factor NF-κB. In this latter group, we validated the differential expression of CCL20/macrophage-inducible protein 3α, thymic stromal lymphopoietin, and CCL3-like 1 because of their roles in Th2 polarization. CCL20/macrophage-inducible protein 3α was the most active mucin-inducing factor in the RSV-infected human small airway epithelial cell secretome and was differentially expressed in smaller airways in a mouse model of RSV infection. These studies provide insights into the complexity of innate responses and regional differences in the epithelial secretome participating in RSV lower respiratory tract infection-induced airway remodeling.
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Affiliation(s)
- Yingxin Zhao
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555.,Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555.,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555; and
| | - Mohammad Jamaluddin
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555.,Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Teodora Ivanciuc
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555
| | - Roberto P Garofalo
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555.,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555; and.,Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555
| | - Allan R Brasier
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555; .,Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555.,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555; and
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10
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Coordinate activities of BRD4 and CDK9 in the transcriptional elongation complex are required for TGFβ-induced Nox4 expression and myofibroblast transdifferentiation. Cell Death Dis 2017; 8:e2606. [PMID: 28182006 PMCID: PMC5386453 DOI: 10.1038/cddis.2016.434] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/15/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Transdifferentiation of quiescent dermal fibroblasts to secretory myofibroblasts has a central role in wound healing and pathological scar formation. This myofibroblast transdifferentiation process involves TGFβ-induced de novo synthesis of alpha smooth muscle cell actin (αSMA)+ fibers that enhance contractility as well as increased expression of extracellular matrix (ECM) proteins, including collagen and fibronectin. These processes are mediated upstream by the reactive oxygen species (ROS)-producing enzyme Nox4, whose induction by TGFβ is incompletely understood. In this study, we demonstrate that Nox4 is involved in αSMA+ fiber formation and collagen production in primary human dermal fibroblasts (hDFs) using a small-molecule inhibitor and siRNA-mediated silencing. Furthermore, TGFβ-induced signaling via Smad3 is required for myofibroblast transformation and Nox4 upregulation. Immunoprecipitation-selected reaction monitoring (IP-SRM) assays of the activated Smad3 complex suggest that it couples with the epigenetic reader and transcription co-activator bromodomain and extraterminal (BET) domain containing protein 4 (BRD4) to promote Nox4 transcription. In addition, cyclin-dependent kinase 9 (CDK9), a component of positive transcription elongation factor, binds to BRD4 after TGFβ stimulation and is also required for RNA polymerase II phosphorylation and Nox4 transcription regulation. Surprisingly, BRD4 depletion decreases myofibroblast differentiation but does not affect collagen or fibronectin expression in primary skin fibroblasts, whereas knockdown of CDK9 decreases all myofibroblast genes. We observe enhanced numbers and persistence of myofibroblast formation and TGFβ signaling in hypertrophic scars. BRD4 inhibition reverses hypertrophic skin fibroblast transdifferentiation to myofibroblasts. Our data indicate that BRD4 and CDK9 have independent, coordinated roles in promoting the myofibroblast transition and suggest that inhibition of the Smad3-BRD4 pathway may be a useful strategy to limit hypertrophic scar formation after burn injury.
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11
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Vlahopoulos SA. Aberrant control of NF-κB in cancer permits transcriptional and phenotypic plasticity, to curtail dependence on host tissue: molecular mode. Cancer Biol Med 2017; 14:254-270. [PMID: 28884042 PMCID: PMC5570602 DOI: 10.20892/j.issn.2095-3941.2017.0029] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The role of the transcription factor NF-κB in shaping the cancer microenvironment is becoming increasingly clear. Inflammation alters the activity of enzymes that modulate NF-κB function, and causes extensive changes in genomic chromatin that ultimately drastically alter cell-specific gene expression. NF-κB regulates the expression of cytokines and adhesion factors that control interactions among adjacent cells. As such, NF-κB fine tunes tissue cellular composition, as well as tissues' interactions with the immune system. Therefore, NF-κB changes the cell response to hormones and to contact with neighboring cells. Activating NF-κB confers transcriptional and phenotypic plasticity to a cell and thereby enables profound local changes in tissue function and composition. Research suggests that the regulation of NF-κB target genes is specifically altered in cancer. Such alterations occur not only due to mutations of NF-κB regulatory proteins, but also because of changes in the activity of specific proteostatic modules and metabolic pathways. This article describes the molecular mode of NF-κB regulation with a few characteristic examples of target genes.
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Affiliation(s)
- Spiros A Vlahopoulos
- The First Department of Pediatrics, University of Athens, Horemeio Research Laboratory, Athens 11527, Greece
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12
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Vialas V, Colomé-Calls N, Abian J, Aloria K, Alvarez-Llamas G, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Barderas MG, Blanco F, Casal JI, Casas V, de la Torre C, Chicano-Gálvez E, Elortza F, Espadas G, Estanyol JM, Fernandez-Irigoyen J, Fernandez-Puente P, Fidalgo MJ, Fuentes M, Gay M, Gil C, Hainard A, Hernaez ML, Ibarrola N, Kopylov AT, Lario A, Lopez JA, López-Lucendo M, Marcilla M, Marina-Ramírez A, Marko-Varga G, Martín L, Mora MI, Morato-López E, Muñoz J, Odena MA, de Oliveira E, Orera I, Ortea I, Pasquarello C, Ray KB, Rezeli M, Ruppen I, Sabidó E, Del Pino MMS, Sancho J, Santamaría E, Vazquez J, Vilaseca M, Vivanco F, Walters JJ, Zgoda VG, Corrales FJ, Canals F, Paradela A. A multicentric study to evaluate the use of relative retention times in targeted proteomics. J Proteomics 2016; 152:138-149. [PMID: 27989941 DOI: 10.1016/j.jprot.2016.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/27/2016] [Accepted: 10/24/2016] [Indexed: 12/19/2022]
Abstract
Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results obtained in this study, dimensionless retention time values (iRTs) demonstrated to be a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups both intra- and inter-laboratories. iRT values also showed very low variability over long time periods. Furthermore, parallel quantitative analyses showed a high reproducibility despite the variety of experimental strategies used, either MRM (multiple reaction monitoring) or pseudoMRM, and the diversity of analytical platforms employed. BIOLOGICAL SIGNIFICANCE From the very beginning of proteomics as an analytical science there has been a growing interest in developing standardized methods and experimental procedures in order to ensure the highest quality and reproducibility of the results. In this regard, the recent (2012) introduction of the dimensionless retention time concept has been a significant advance. In our multicentric (28 laboratories) study we explore the usefulness of this concept in the context of a targeted proteomics experiment, demonstrating that dimensionless retention time values is a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups.
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Affiliation(s)
- Vital Vialas
- ProteoRed-ISCIII, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Núria Colomé-Calls
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Joaquín Abian
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona 08036, Spain
| | - Kerman Aloria
- Department of Biochemistry and Molecular Biology, University of the Basque Country-UPV/EHU, Leioa 48940, Spain
| | | | - Oreto Antúnez
- ProteoRed-ISCIII, SCSIE Universitat de Valencia, Burjassot 46100, Spain
| | - Jesus M Arizmendi
- ProteoRed-ISCIII, University of the Basque Country-UPV/EHU, Leioa 48940, Spain
| | - Mikel Azkargorta
- ProteoRed-ISCIII, CIC bioGUNE, Science and Technology Park of Bizkaia, Derio, Spain
| | | | - María G Barderas
- ProteoRed-ISCIII, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | | | - J Ignacio Casal
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Vanessa Casas
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona 08036, Spain
| | - Carolina de la Torre
- ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Eduardo Chicano-Gálvez
- ProteoRed-ISCIII, Maimonides Institute for Biomedical Research and Universidad de Córdoba, Córdoba 14004, Spain
| | - Felix Elortza
- ProteoRed-ISCIII, CIC bioGUNE, Science and Technology Park of Bizkaia, Derio, Spain
| | - Guadalupe Espadas
- ProteoRed-ISCIII, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Josep M Estanyol
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, Barcelona 08036, Spain
| | | | | | - María José Fidalgo
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, Barcelona 08036, Spain
| | - Manuel Fuentes
- ProteoRed-ISCIII, Cancer Research Center, University of Salamanca-CSIC, IBSAL, Salamanca 37007, Spain
| | - Marina Gay
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
| | - Concha Gil
- ProteoRed-ISCIII, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Alexandre Hainard
- Proteomics Core Facility CMU, University of Geneva, Geneva, Switzerland
| | | | - Nieves Ibarrola
- ProteoRed-ISCIII, Cancer Research Center, University of Salamanca-CSIC, IBSAL, Salamanca 37007, Spain
| | - Arthur T Kopylov
- Orekhovich Institute of Biomedical Chemistry RAMS, Moscow 119121, Russian Federation
| | - Antonio Lario
- ProteoRed-ISCIII, IPBLN (CSIC), Armilla, Granada, Spain
| | - Juan Antonio Lopez
- ProteoRed-ISCIII, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - María López-Lucendo
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Miguel Marcilla
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), Madrid 28049, Spain
| | | | - Gyorgy Marko-Varga
- Centre of Excellence in Biological and Medical Mass spectrometry, Lund University, Lund, Sweden
| | - Luna Martín
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Maria I Mora
- ProteoRed-ISCIII, CIMA, University of Navarra, Pamplona 31008, Spain
| | | | - Javier Muñoz
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | | | | | - Irene Orera
- ProteoRed-ISCIII, Instituto Aragonés de Ciencias de la Salud, Zaragoza 50009, Spain
| | - Ignacio Ortea
- ProteoRed-ISCIII, Maimonides Institute for Biomedical Research and Universidad de Córdoba, Córdoba 14004, Spain
| | - Carla Pasquarello
- Proteomics Core Facility CMU, University of Geneva, Geneva, Switzerland
| | | | - Melinda Rezeli
- Centre of Excellence in Biological and Medical Mass spectrometry, Lund University, Lund, Sweden
| | - Isabel Ruppen
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Eduard Sabidó
- ProteoRed-ISCIII, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - Jaime Sancho
- ProteoRed-ISCIII, IPBLN (CSIC), Armilla, Granada, Spain
| | - Enrique Santamaría
- ProteoRed-ISCIII, Navarrabiomed Biomedical Research Center-IdiSNa, Pamplona, Spain
| | - Jesus Vazquez
- ProteoRed-ISCIII, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Marta Vilaseca
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
| | | | | | - Victor G Zgoda
- Orekhovich Institute of Biomedical Chemistry RAMS, Moscow 119121, Russian Federation
| | | | - Francesc Canals
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain.
| | - Alberto Paradela
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), Madrid 28049, Spain.
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13
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Tian B, Zhao Y, Sun H, Zhang Y, Yang J, Brasier AR. BRD4 mediates NF-κB-dependent epithelial-mesenchymal transition and pulmonary fibrosis via transcriptional elongation. Am J Physiol Lung Cell Mol Physiol 2016; 311:L1183-L1201. [PMID: 27793799 DOI: 10.1152/ajplung.00224.2016] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/25/2016] [Indexed: 02/08/2023] Open
Abstract
Chronic epithelial injury triggers a TGF-β-mediated cellular transition from normal epithelium into a mesenchymal-like state that produces subepithelial fibrosis and airway remodeling. Here we examined how TGF-β induces the mesenchymal cell state and determined its mechanism. We observed that TGF-β stimulation activates an inflammatory gene program controlled by the NF-κB/RelA signaling pathway. In the mesenchymal state, NF-κB-dependent immediate-early genes accumulate euchromatin marks and processive RNA polymerase. This program of immediate-early genes is activated by enhanced expression, nuclear translocation, and activating phosphorylation of the NF-κB/RelA transcription factor on Ser276, mediated by a paracrine signal. Phospho-Ser276 RelA binds to the BRD4/CDK9 transcriptional elongation complex, activating the paused RNA Pol II by phosphorylation on Ser2 in its carboxy-terminal domain. RelA-initiated transcriptional elongation is required for expression of the core epithelial-mesenchymal transition transcriptional regulators SNAI1, TWIST1, and ZEB1 and mesenchymal genes. Finally, we observed that pharmacological inhibition of BRD4 can attenuate experimental lung fibrosis induced by repetitive TGF-β challenge in a mouse model. These data provide a detailed mechanism for how activated NF-κB and BRD4 control epithelial-mesenchymal transition initiation and transcriptional elongation in model airway epithelial cells in vitro and in a murine pulmonary fibrosis model in vivo. Our data validate BRD4 as an in vivo target for the treatment of pulmonary fibrosis associated with inflammation-coupled remodeling in chronic lung diseases.
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Affiliation(s)
- Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; .,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas.,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas; and.,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Jun Yang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas.,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas.,Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas; and.,Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas
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14
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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15
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Zhao Y, Tian B, Sadygov RG, Zhang Y, Brasier AR. Integrative proteomic analysis reveals reprograming tumor necrosis factor signaling in epithelial mesenchymal transition. J Proteomics 2016; 148:126-38. [PMID: 27461979 DOI: 10.1016/j.jprot.2016.07.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/07/2016] [Accepted: 07/12/2016] [Indexed: 12/29/2022]
Abstract
UNLABELLED The airway epithelium is a semi-impermeable barrier whose disruption by growth factor reprogramming is associated with chronic airway diseases of humans. Transforming growth factor beta (TGFβ)-induced epithelial mesenchymal transition (EMT) plays important roles in airway remodeling characteristic of idiopathic lung fibrosis, asthma and chronic obstructive pulmonary disease (COPD). Inflammation of the airways leads to airway injury and tumor necrosis factor alpha (TNFα) plays an important pro-inflammatory role. Little systematic information about the effects of EMT on TNFα signaling is available. Using an in vitro model of TGFβ-induced EMT in primary human small airway epithelial cells (hSAECs), we applied quantitative proteomics and phosphoprotein profiling to understand the molecular mechanism of EMT and the impact of EMT on innate inflammatory responses. We quantified 7925 proteins and 1348 phosphorylation sites by stable isotope labeling with iTRAQ technology. We found that cellular response to TNFα is cell state dependent and the relative TNFα response in mesenchymal state is highly compressed. Combined bioinformatics analyses of proteome and phosphoproteome indicate that the EMT state is associated with reprogramming of kinome, signaling cascade of upstream transcription regulators, phosphor-networks, and NF-κB dependent cell signaling. BIOLOGICAL SIGNIFICANCE Epithelial mesenchymal transition and inflammation have important implications for clinical and physiologic manifestations of chronic airway diseases such as severe asthma, COPD, and lung fibrosis. Little systematic information on the interplay between EMT and innate inflammation is available. This study combined quantitative proteomics and phosphorproteomics approach to obtain systems-level insight into the upstream transcription regulators involved in the TGFβ-induced EMT in primary human small airway epithelial cells and to elucidate how EMT impacts on the TNFα signaling pathways. The proteomics and phosphoproteomics analysis indicates that many signaling pathways involved in TGFβ-induced EMT and EMT has profound reprogramming effects on innate inflammation response.
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Affiliation(s)
- Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, United States; Institute for Translational Sciences, UTMB, Galveston, TX, United States; Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States.
| | - Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, United States; Institute for Translational Sciences, UTMB, Galveston, TX, United States; Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States
| | - Rovshan G Sadygov
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States; Department of Biochemistry & Molecular Biology, UTMB, Galveston, TX, United States
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, United States
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, United States; Institute for Translational Sciences, UTMB, Galveston, TX, United States; Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States.
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16
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Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, Yin J, Coon JJ. Neucode Labels for Multiplexed, Absolute Protein Quantification. Anal Chem 2016; 88:3295-303. [PMID: 26882330 PMCID: PMC5141612 DOI: 10.1021/acs.analchem.5b04773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We describe a new method to accomplish multiplexed, absolute protein quantification in a targeted fashion. The approach draws upon the recently developed neutron encoding (NeuCode) metabolic labeling strategy and parallel reaction monitoring (PRM). Since PRM scanning relies upon high-resolution tandem mass spectra for targeted protein quantification, incorporation of multiple NeuCode labeled peptides permits high levels of multiplexing that can be accessed from high-resolution tandem mass spectra. Here we demonstrate this approach in cultured cells by monitoring a viral infection and the corresponding viral protein production over many infection time points in a single experiment. In this context the NeuCode PRM combination affords up to 30 channels of quantitative information in a single MS experiment.
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Affiliation(s)
- Gregory K Potts
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Emily A Voigt
- Department of Chemical and Biological Engineering, University of Wisconsin , Madison, Wisconsin 53706, United States
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Derek J Bailey
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Christopher M Rose
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin , Madison, Wisconsin 53706, United States
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
- Genome Center of Wisconsin, University of Wisconsin , Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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Zhao Y, Brasier AR. Qualification and Verification of Protein Biomarker Candidates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:493-514. [DOI: 10.1007/978-3-319-41448-5_23] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Zhao Y, Valbuena G, Walker DH, Gazi M, Hidalgo M, DeSousa R, Oteo JA, Goez Y, Brasier AR. Endothelial Cell Proteomic Response to Rickettsia conorii Infection Reveals Activation of the Janus Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT)-Inferferon Stimulated Gene (ISG)15 Pathway and Reprogramming Plasma Membrane Integrin/Cadherin Signaling. Mol Cell Proteomics 2015; 15:289-304. [PMID: 26560068 DOI: 10.1074/mcp.m115.054361] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 11/06/2022] Open
Abstract
Rickettsia conorii is the etiologic agent of Mediterranean spotted fever, a re-emerging infectious disease with significant mortality. This Gram-negative, obligately intracellular pathogen is transmitted via tick bites, resulting in disseminated vascular endothelial cell infection with vascular leakage. In the infected human, Rickettsia conorii infects endothelial cells, stimulating expression of cytokines and pro-coagulant factors. However, the integrated proteomic response of human endothelial cells to R. conorii infection is not known. In this study, we performed quantitative proteomic profiling of primary human umbilical vein endothelial cells (HUVECs) with established R conorii infection versus those stimulated with endotoxin (LPS) alone. We observed differential expression of 55 proteins in HUVEC whole cell lysates. Of these, we observed induction of signal transducer and activator of transcription (STAT)1, MX dynamin-like GTPase (MX1), and ISG15 ubiquitin-like modifier, indicating activation of the JAK-STAT signaling pathway occurs in R. conorii-infected HUVECs. The down-regulated proteins included those involved in the pyrimidine and arginine biosynthetic pathways. A highly specific biotinylated cross-linking enrichment protocol was performed to identify dysregulation of 11 integral plasma membrane proteins that included up-regulated expression of a sodium/potassium transporter and down-regulation of α-actin 1. Analysis of Golgi and soluble Golgi fractions identified up-regulated proteins involved in platelet-endothelial adhesion, phospholipase activity, and IFN activity. Thirty four rickettsial proteins were identified with high confidence in the Golgi, plasma membrane, or secreted protein fractions. The host proteins associated with rickettsial infections indicate activation of interferon-STAT signaling pathways; the disruption of cellular adhesion and alteration of antigen presentation pathways in response to rickettsial infections are distinct from those produced by nonspecific LPS stimulation. These patterns of differentially expressed proteins suggest mechanisms of pathogenesis as well as methods for diagnosis and monitoring Rickettsia infections.
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Affiliation(s)
- Yingxin Zhao
- From the Departments of ‡Internal Medicine and §Institute for Translational Sciences, and ¶Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555-1060
| | | | | | | | - Marylin Hidalgo
- the **Microbiology Department, Faculty of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Rita DeSousa
- the ‡‡Centre for the Study of Vectors and Infectious Diseases Dr. Francisco Cambournac, National Institute of Health Dr. Ricardo Jorge, Águas de Moura, Av. Padre Cruz, Lisbon, 1649-016, Portugal, and
| | - Jose Antonio Oteo
- the §§Centre of Rickettsiosis and Arthropod-Borne Diseases, Hospital San Pedro-Centro de Investigation Biomedical de la Rioja (CIBIR), Logroño, La Rioja, 26006, Spain
| | | | - Allan R Brasier
- From the Departments of ‡Internal Medicine and §Institute for Translational Sciences, and ¶Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555-1060,
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19
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Iwanaszko M, Kimmel M. NF-κB and IRF pathways: cross-regulation on target genes promoter level. BMC Genomics 2015; 16:307. [PMID: 25888367 PMCID: PMC4430024 DOI: 10.1186/s12864-015-1511-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 03/31/2015] [Indexed: 12/30/2022] Open
Abstract
Background The NF-κB and IRF transcription factor families are major players in inflammation and antiviral response and act as two major effectors of the innate immune response (IIR). The regulatory mechanisms of activation of these two pathways and their interactions during the IIR are only partially known. Results Our in silico findings report that there is cross-regulation between both pathways at the level of gene transcription regulation, mediated by the presence of binding sites for both factors in promoters of genes essential for these pathways. These findings agree with recent experimental data reporting crosstalk between pathways activated by RIG-I and TLR3 receptors in response to pathogens. Conclusions We present an extended crosstalk diagram of the IRF - NF-κB pathways. We conclude that members of the NF-κB family may directly impact regulation of IRF family, while IRF members impact regulation of NF-κB family rather indirectly, via other transcription factors such as AP-1 and SP1. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1511-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Iwanaszko
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland. .,Department of Statistics, Rice University, Houston, TX, USA. .,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Marek Kimmel
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland. .,Department of Statistics, Rice University, Houston, TX, USA.
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20
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Zhang CC, Li R, Jiang H, Lin S, Rogalski JC, Liu K, Kast J. Development and application of a quantitative multiplexed small GTPase activity assay using targeted proteomics. J Proteome Res 2015; 14:967-76. [PMID: 25569337 DOI: 10.1021/pr501010v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Small GTPases are a family of key signaling molecules that are ubiquitously expressed in various types of cells. Their activity is often analyzed by western blot, which is limited by its multiplexing capability, the quality of isoform-specific antibodies, and the accuracy of quantification. To overcome these issues, a quantitative multiplexed small GTPase activity assay has been developed. Using four different binding domains, this assay allows the binding of up to 12 active small GTPase isoforms simultaneously in a single experiment. To accurately quantify the closely related small GTPase isoforms, a targeted proteomic approach, i.e., selected/multiple reaction monitoring, was developed, and its functionality and reproducibility were validated. This assay was successfully applied to human platelets and revealed time-resolved coactivation of multiple small GTPase isoforms in response to agonists and differential activation of these isoforms in response to inhibitor treatment. This widely applicable approach can be used for signaling pathway studies and inhibitor screening in many cellular systems.
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Affiliation(s)
- Cheng-Cheng Zhang
- The Biomedical Research Centre, ∥The Centre for Blood Research, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
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Simicevic J, Moniatte M, Hamelin R, Ahrné E, Deplancke B. A mammalian transcription factor-specific peptide repository for targeted proteomics. Proteomics 2015; 15:752-6. [DOI: 10.1002/pmic.201400355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/17/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Jovan Simicevic
- Biozentrum; University of Basel; Basel Switzerland
- Laboratory of Systems Biology and Genetics; Institute of Bioengineering; School of Life Sciences; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Marc Moniatte
- Proteomics Core Facility; School of Life Sciences; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Romain Hamelin
- Proteomics Core Facility; School of Life Sciences; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Erik Ahrné
- Biozentrum; University of Basel; Basel Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics; Institute of Bioengineering; School of Life Sciences; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
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22
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Ray S, Zhao Y, Jamaluddin M, Edeh CB, Lee C, Brasier AR. Inducible STAT3 NH2 terminal mono-ubiquitination promotes BRD4 complex formation to regulate apoptosis. Cell Signal 2014; 26:1445-55. [PMID: 24657799 PMCID: PMC4067092 DOI: 10.1016/j.cellsig.2014.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/24/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Signal Transducers and Activator of Transcription-3 (STAT3) are latent transcription factors that are regulated by post-translational modifications (PTMs) in response to cellular activation by the IL-6 superfamily of cytokines to regulate cell cycle progression and/or apoptosis. Here we observe that STAT3 is inducibly mono-ubiquitinated and investigate its consequences. Using domain mapping and highly specific selected reaction monitoring-mass spectrometric assays, we identify lysine (K) 97 in its NH2-terminal domain as the major mono-ubiquitin conjugation site. We constructed a mono-ubiquitinated mimic consisting of a deubiquitinase-resistant monomeric ubiquitin fused to the NH2 terminus of STAT3 (ubiquitinated-STAT3 FP). In complex assays of ectopically expressed ubi-STAT3-FP, we observed enhanced complex formation with bromodomain-containing protein 4 (BRD4), a component of the activated positive transcriptional elongation factor (P-TEFb) complex. Chromatin immunoprecipitation experiments in STAT3(+/-) and STAT3(-/-) MEFs showed BRD4 recruitment to STAT3-dependent suppressor of cytokine signaling-3 gene (SOCS3). The effect of a selective small molecule inhibitor of BRD4, JQ1, to inhibit SOCS3 expression demonstrated the functional role of BRD4 for STAT3-dependent transcription. Additionally, ectopic ubiquitinated-STAT3 FP expression upregulated BCL2, BCL2L1, APEX1, SOD2, CCND1 and MYC expression indicating the role of ubiquitinated STAT3 in anti-apoptosis and cellular proliferation. Finally we observed that ubiquitinated-STAT3 FP suppressed TNFα-induced apoptotic cell death, indicating the functional importance of mono-ubiquitinated STAT3 in antiapoptotic gene expression. We conclude that STAT3 mono-ubiquitination is a key trigger in BRD4-dependent antiapoptotic and pro-proliferative gene expression programs. Thus, inhibiting the STAT3 mono-ubiquitination-BRD4 pathway may be a novel therapeutic target for the treatment of STAT3-dependent proliferative diseases.
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Affiliation(s)
- Sutapa Ray
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Yingxin Zhao
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Mohammad Jamaluddin
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Chukwudi B Edeh
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Chang Lee
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Allan R Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, United States.
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Fang L, Choudhary S, Zhao Y, Edeh CB, Yang C, Boldogh I, Brasier AR. ATM regulates NF-κB-dependent immediate-early genes via RelA Ser 276 phosphorylation coupled to CDK9 promoter recruitment. Nucleic Acids Res 2014; 42:8416-32. [PMID: 24957606 PMCID: PMC4117761 DOI: 10.1093/nar/gku529] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ataxia-telangiectasia mutated (ATM), a member of the phosphatidylinositol 3 kinase-like kinase family, is a master regulator of the double strand DNA break-repair pathway after genotoxic stress. Here, we found ATM serves as an essential regulator of TNF-induced NF-kB pathway. We observed that TNF exposure of cells rapidly induced DNA double strand breaks and activates ATM. TNF-induced ROS promote nuclear IKKγ association with ubiquitin and its complex formation with ATM for nuclear export. Activated cytoplasmic ATM is involved in the selective recruitment of the E3-ubiquitin ligase β-TrCP to phospho-IκBα proteosomal degradation. Importantly, ATM binds and activates the catalytic subunit of protein kinase A (PKAc), ribosmal S6 kinase that controls RelA Ser 276 phosphorylation. In ATM knockdown cells, TNF-induced RelA Ser 276 phosphorylation is significantly decreased. We further observed decreased binding and recruitment of the transcriptional elongation complex containing cyclin dependent kinase-9 (CDK9; a kinase necessary for triggering transcriptional elongation) to promoters of NF-κB-dependent immediate-early cytokine genes, in ATM knockdown cells. We conclude that ATM is a nuclear damage-response signal modulator of TNF-induced NF-κB activation that plays a key scaffolding role in IκBα degradation and RelA Ser 276 phosphorylation. Our study provides a mechanistic explanation of decreased innate immune response associated with A-T mutation.
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Affiliation(s)
- Ling Fang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), 301 University Blvd, Galveston, TX 77555 USA Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555, USA
| | - Sanjeev Choudhary
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), 301 University Blvd, Galveston, TX 77555 USA Sealy Center for Molecular Medicine, UTMB, 301 University Blvd, Galveston, TX 77555, USA Institute for Translational Sciences, UTMB, 301 University Blvd, Galveston, TX 77555, USA
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), 301 University Blvd, Galveston, TX 77555 USA Sealy Center for Molecular Medicine, UTMB, 301 University Blvd, Galveston, TX 77555, USA Institute for Translational Sciences, UTMB, 301 University Blvd, Galveston, TX 77555, USA
| | - Chukwudi B Edeh
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), 301 University Blvd, Galveston, TX 77555 USA
| | - Chunying Yang
- Department of Radiation Oncology, Houston Methodist Research Institute, Weill Cornell University, Houston, TX 77030, USA
| | - Istvan Boldogh
- Sealy Center for Molecular Medicine, UTMB, 301 University Blvd, Galveston, TX 77555, USA Department of Microbiology and Immunology, UTMB, 301 University Blvd, Galveston, TX 77555, USA
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), 301 University Blvd, Galveston, TX 77555 USA Sealy Center for Molecular Medicine, UTMB, 301 University Blvd, Galveston, TX 77555, USA Institute for Translational Sciences, UTMB, 301 University Blvd, Galveston, TX 77555, USA
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24
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Bertolusso R, Tian B, Zhao Y, Vergara L, Sabree A, Iwanaszko M, Lipniacki T, Brasier AR, Kimmel M. Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise. PLoS One 2014; 9:e93396. [PMID: 24710104 PMCID: PMC3977818 DOI: 10.1371/journal.pone.0093396] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/04/2014] [Indexed: 01/01/2023] Open
Abstract
We present an integrated dynamical cross-talk model of the epithelial innate immune response (IIR) incorporating RIG-I and TLR3 as the two major pattern recognition receptors (PRR) converging on the RelA and IRF3 transcriptional effectors. bioPN simulations reproduce biologically relevant gene-and protein abundance measurements in response to time course, gene silencing and dose-response perturbations both at the population and single cell level. Our computational predictions suggest that RelA and IRF3 are under auto- and cross-regulation. We predict, and confirm experimentally, that RIG-I mRNA expression is controlled by IRF7. We also predict the existence of a TLR3-dependent, IRF3-independent transcription factor (or factors) that control(s) expression of MAVS, IRF3 and members of the IKK family. Our model confirms the observed dsRNA dose-dependence of oscillatory patterns in single cells, with periods of 1-3 hr. Model fitting to time series, matched by knockdown data suggests that the NF-κB module operates in a different regime (with different coefficient values) than in the TNFα-stimulation experiments. In future studies, this model will serve as a foundation for identification of virus-encoded IIR antagonists and examination of stochastic effects of viral replication. Our model generates simulated time series, which reproduce the noisy oscillatory patterns of activity (with 1-3 hour period) observed in individual cells. Our work supports the hypothesis that the IIR is a phenomenon that emerged by evolution despite highly variable responses at an individual cell level.
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Affiliation(s)
- Roberto Bertolusso
- Department of Statistics, Rice University, Houston, Texas, United States of America
| | - Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
| | - Leoncio Vergara
- Center for Biomedical Engineering, UTMB, Galveston, Texas, United States of America
| | - Aqeeb Sabree
- Department of Statistics, Rice University, Houston, Texas, United States of America
| | - Marta Iwanaszko
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Allan R. Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, Texas, United States of America
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
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25
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Garbis SD, Townsend PA. Proteomics of human prostate cancer biospecimens: the global, systems-wide perspective for Protein markers with potential clinical utility. Expert Rev Proteomics 2014; 10:337-54. [DOI: 10.1586/14789450.2013.827408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Brasier AR, Zhao Y. Measurement of the innate immune response in the airway. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 795:233-54. [PMID: 24162913 DOI: 10.1007/978-1-4614-8603-9_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Asthma is an idiopathic disease associated with episodic inflammation and reversible airway obstruction that is triggered by environmental agents. Allergic and infectious agents trigger asthmatic exacerbations through the innate immune response (IIR). The IIR is activated by sentinel cells in the airways to elaborate inflammatory cytokines and protective mucosal interferons whose actions are designed to limit the spread of the organism, as well as to activate the adaptive immune response. We address the structure of the IIR pathway in sentinel cells of the airway and describe observations on its dysregulation. The IIR is triggered in a cell-type specific manner by germline-encoded pathogen recognition receptors (PPRs) including plasma membrane Toll-like receptors (TLRs) and the cytoplasmic Retinoic Acid-inducible Gene (RIG)-I-like RNA helicases, and protein kinase R (PKR). Although their mechanisms of intracellular signaling differ, both pathways converge on a small group of transcriptional effectors, nuclear factor-κB (NF-κB), IFN regulatory factor (IRF), and signal transducer and activator of transcription (STAT). We describe several distinct techniques to quantitate the IIR including assays based on quantitative real-time PCR (Q-RT-PCR) of NF-κB and IRF3-regulated genes, multiplex bead-based analysis of secreted proteins/cytokines and more recent developments in targeted, quantitative selected reaction monitoring (SRM)-mass spectrometry (MS). Application of these methods for quantitation of the IIR will further our understanding of the role of the IIR in asthma and its contribution to disease heterogeneity.
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Affiliation(s)
- Allan R Brasier
- University of Texas Medical Branch, 8.128 Medical Research Building, 301 University Blvd, Galveston, TX, USA,
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27
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Brasier AR. Identification of innate immune response endotypes in asthma: implications for personalized medicine. Curr Allergy Asthma Rep 2013; 13:462-8. [PMID: 23793609 PMCID: PMC3778047 DOI: 10.1007/s11882-013-0363-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Asthma is an idiopathic disease characterized by episodic inflammation and reversible airway obstruction triggered by exposure to environmental agents. Because this disease is heterogeneous in onset, exacerbations, inflammatory states, and response to therapy, there is intense interest in developing personalized approaches to its management. Of focus in this review, the recognition that a component of the pathophysiology of asthma is mediated by inflammation has implications for understanding its etiology and individualizing its therapy. Despite understanding how Th2 polarization mediates asthma exacerbations by aeroallergen exposure, we do not yet fully understand how RNA virus infections produce asthmatic exacerbations. This review will summarize the explosion of information that has revealed how patterns produced by RNA virus infection trigger the innate immune response (IIR) in sentinel airway cells. When the IIR is triggered, these cells elaborate inflammatory cytokines and protective mucosal interferons whose actions activate long-lived adaptive immunity and limit organismal replication. Recent work has shown the multifaceted way that dysregulation of the IIR is linked to viral-induced exacerbation, steroid insensitivity, and T helper polarization of adaptive immunity. New developments in quantitative proteomics now enable accurate identification of subgroups of individuals that demonstrate activation of IIR ("innate endotype"). Potential applications to clinical research are proposed. Together, these developments open realistic prospects for how identification of the IIR endotype may inform asthma therapy in the future.
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Affiliation(s)
- Allan R Brasier
- Institute for Translational Sciences, Department of Internal Medicine, Sealy Center for Molecular Medicine, 8.128 Medical Research Building, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1060, USA,
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28
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Tian B, Zhao Y, Kalita M, Edeh CB, Paessler S, Casola A, Teng MN, Garofalo RP, Brasier AR. CDK9-dependent transcriptional elongation in the innate interferon-stimulated gene response to respiratory syncytial virus infection in airway epithelial cells. J Virol 2013; 87:7075-92. [PMID: 23596302 PMCID: PMC3676079 DOI: 10.1128/jvi.03399-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 04/08/2013] [Indexed: 12/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a negative-sense single-stranded RNA virus responsible for lower respiratory tract infections. During infection, the presence of double-stranded RNA (dsRNA) activates the interferon (IFN) regulatory factor 3 (IRF3) transcription factor, an event triggering expression of immediate early, IFN-stimulated genes (ISGs). We examine the role of transcriptional elongation in control of IRF3-dependent ISG expression. RSV infection induces ISG54, ISG56, and CIG5 gene expression in an IRF3-dependent manner demonstrated by IRF3 small interfering RNA (siRNA) silencing in both A549 epithelial cells and IRF3(-/-) MEFs. ISG expression was mediated by the recruitment of IRF3, CDK9, polymerase II (Pol II), and phospho-Ser(2) carboxy-terminal domain (CTD) Pol II to the IFN-stimulated response element (ISRE) binding sites of the IRF3-dependent ISG promoters in native chromatin. We find that RSV infection enhances the activated fraction of cyclin-dependent kinase 9 (CDK9) by promoting its association with bromodomain 4 (BRD4) and disrupting its association with the inhibitory 7SK small nuclear RNA. The requirement of CDK9 activity for ISG expression was shown by siRNA-mediated silencing of CDK9 and by a selective CDK9 inhibitor in A549 cells. In contrast, RSV-induced beta interferon (IFN-β) expression is not influenced by CDK9 inhibition. Using transcript-selective quantitative real-time reverse transcription-PCR (Q-RT-PCR) assays for the ISG54 gene, we observed that RSV induces transition from short to fully spliced mRNA transcripts and that this transition is blocked by CDK9 inhibition in both A549 and primary human small airway epithelial cells. These data indicate that transcription elongation plays a major role in RSV-induced ISG expression and is mediated by IRF3-dependent recruitment of activated CDK9. CDK9 activity may be a target for immunomodulation in RSV-induced lung disease.
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Affiliation(s)
| | - Yingxin Zhao
- Department of Internal Medicine,
- Institute for Translational Sciences,
- Sealy Center for Molecular Medicine,
| | | | | | | | - Antonella Casola
- Institute for Translational Sciences,
- Sealy Center for Molecular Medicine,
- Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Michael N. Teng
- Joy McCann Culverhouse Airway Disease Research Center, Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - Roberto P. Garofalo
- Institute for Translational Sciences,
- Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Allan R. Brasier
- Department of Internal Medicine,
- Institute for Translational Sciences,
- Sealy Center for Molecular Medicine,
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