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Molinar-Inglis O, Wozniak JM, Grimsey NJ, Orduña-Castillo L, Cheng N, Lin Y, Gonzalez Ramirez ML, Birch CA, Lapek JD, Gonzalez DJ, Trejo J. Phosphoproteomic analysis of thrombin- and p38 MAPK-regulated signaling networks in endothelial cells. J Biol Chem 2022; 298:101801. [PMID: 35257745 PMCID: PMC8987612 DOI: 10.1016/j.jbc.2022.101801] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 01/11/2023] Open
Abstract
Endothelial dysfunction is a hallmark of inflammation and is mediated by inflammatory factors that signal through G protein–coupled receptors including protease-activated receptor-1 (PAR1). PAR1, a receptor for thrombin, signals via the small GTPase RhoA and myosin light chain intermediates to facilitate endothelial barrier permeability. PAR1 also induces endothelial barrier disruption through a p38 mitogen-activated protein kinase–dependent pathway, which does not integrate into the RhoA/MLC pathway; however, the PAR1-p38 signaling pathways that promote endothelial dysfunction remain poorly defined. To identify effectors of this pathway, we performed a global phosphoproteome analysis of thrombin signaling regulated by p38 in human cultured endothelial cells using multiplexed quantitative mass spectrometry. We identified 5491 unique phosphopeptides and 2317 phosphoproteins, four distinct dynamic phosphoproteome profiles of thrombin-p38 signaling, and an enrichment of biological functions associated with endothelial dysfunction, including modulators of endothelial barrier disruption and a subset of kinases predicted to regulate p38-dependent thrombin signaling. Using available antibodies to detect identified phosphosites of key p38-regulated proteins, we discovered that inhibition of p38 activity and siRNA-targeted depletion of the p38α isoform increased basal phosphorylation of extracellular signal–regulated protein kinase 1/2, resulting in amplified thrombin-stimulated extracellular signal–regulated protein kinase 1/2 phosphorylation that was dependent on PAR1. We also discovered a role for p38 in the phosphorylation of α-catenin, a component of adherens junctions, suggesting that this phosphorylation may function as an important regulatory process. Taken together, these studies define a rich array of thrombin- and p38-regulated candidate proteins that may serve important roles in endothelial dysfunction.
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Takahashi M, Lio CWJ, Campeau A, Steger M, Ay F, Mann M, Gonzalez DJ, Jain M, Sharma S. The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway. Nat Immunol 2021; 22:485-496. [PMID: 33767426 PMCID: PMC8300883 DOI: 10.1038/s41590-021-00896-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023]
Abstract
Evasion of host immunity is a hallmark of cancer; however, mechanisms linking oncogenic mutations and immune escape are incompletely understood. Through loss-of-function screening of 1,001 tumor suppressor genes, we identified death-associated protein kinase 3 (DAPK3) as a previously unrecognized driver of anti-tumor immunity through the stimulator of interferon genes (STING) pathway of cytosolic DNA sensing. Loss of DAPK3 expression or kinase activity impaired STING activation and interferon (IFN)-β-stimulated gene induction. DAPK3 deficiency in IFN-β-producing tumors drove rapid growth and reduced infiltration of CD103+CD8α+ dendritic cells and cytotoxic lymphocytes, attenuating the response to cancer chemo-immunotherapy. Mechanistically, DAPK3 coordinated post-translational modification of STING. In unstimulated cells, DAPK3 inhibited STING K48-linked poly-ubiquitination and proteasome-mediated degradation. After cGAMP stimulation, DAPK3 was required for STING K63-linked poly-ubiquitination and STING-TANK-binding kinase 1 interaction. Comprehensive phospho-proteomics uncovered a DAPK3-specific phospho-site on the E3 ligase LMO7, critical for LMO7-STING interaction and STING K63-linked poly-ubiquitination. Thus, DAPK3 is an essential kinase for STING activation that drives tumor-intrinsic innate immunity and tumor immune surveillance.
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Affiliation(s)
| | - Chan-Wang J Lio
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Anaamika Campeau
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Martin Steger
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Evotec München GmbH, Martinsried, Germany
| | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Mohit Jain
- Department of Pharmacology, University of California, San Diego, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Sonia Sharma
- La Jolla Institute for Immunology, La Jolla, CA, USA.
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5
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Xi L, Zhang Z, Herold S, Kassem S, Wu XN, Schulze WX. Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates. Methods Mol Biol 2021; 2358:1-16. [PMID: 34270043 DOI: 10.1007/978-1-0716-1625-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sarah Kassem
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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6
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Wozniak JM, Mills RH, Olson J, Caldera JR, Sepich-Poore GD, Carrillo-Terrazas M, Tsai CM, Vargas F, Knight R, Dorrestein PC, Liu GY, Nizet V, Sakoulas G, Rose W, Gonzalez DJ. Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic Signatures. Cell 2020; 182:1311-1327.e14. [PMID: 32888495 PMCID: PMC7494005 DOI: 10.1016/j.cell.2020.07.040] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022]
Abstract
Staphylococcus aureus bacteremia (SaB) causes significant disease in humans, carrying mortality rates of ∼25%. The ability to rapidly predict SaB patient responses and guide personalized treatment regimens could reduce mortality. Here, we present a resource of SaB prognostic biomarkers. Integrating proteomic and metabolomic techniques enabled the identification of >10,000 features from >200 serum samples collected upon clinical presentation. We interrogated the complexity of serum using multiple computational strategies, which provided a comprehensive view of the early host response to infection. Our biomarkers exceed the predictive capabilities of those previously reported, particularly when used in combination. Last, we validated the biological contribution of mortality-associated pathways using a murine model of SaB. Our findings represent a starting point for the development of a prognostic test for identifying high-risk patients at a time early enough to trigger intensive monitoring and interventions.
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Affiliation(s)
- Jacob M Wozniak
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert H Mills
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua Olson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - J R Caldera
- Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gregory D Sepich-Poore
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marvic Carrillo-Terrazas
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chih-Ming Tsai
- Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rob Knight
- Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - George Y Liu
- Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Victor Nizet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - George Sakoulas
- Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Warren Rose
- School of Pharmacy, School of Medicine and Public Health University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Medicine, School of Medicine and Public Health University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative to Halt Antibiotic-Resistant Microbes, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
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7
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Wozniak JM, Silva TA, Thomas D, Siqueira-Neto JL, McKerrow JH, Gonzalez DJ, Calvet CM. Molecular dissection of Chagas induced cardiomyopathy reveals central disease associated and druggable signaling pathways. PLoS Negl Trop Dis 2020; 14:e0007980. [PMID: 32433643 PMCID: PMC7279607 DOI: 10.1371/journal.pntd.0007980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/08/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Chagas disease, the clinical presentation of T. cruzi infection, is a major human health concern. While the acute phase of Chagas disease is typically asymptomatic and self-resolving, chronically infected individuals suffer numerous sequelae later in life. Cardiomyopathies in particular are the most severe consequence of chronic Chagas disease and cannot be reversed solely by parasite load reduction. To prioritize new therapeutic targets, we unbiasedly interrogated the host signaling events in heart tissues isolated from a Chagas disease mouse model using quantitative, multiplexed proteomics. We defined the host response to infection at both the proteome and phospho-proteome levels. The proteome showed an increase in the immune response and a strong repression of several mitochondrial proteins. Complementing the proteome studies, the phospho-proteomic survey found an abundance of phospho-site alterations in plasma membrane and cytoskeletal proteins. Bioinformatic analysis of kinase activity provided substantial evidence for the activation of NDRG2 and JNK/p38 kinases during Chagas disease. A significant activation of DYRK2 and AMPKA2 and the inhibition of casein family kinases were also predicted. We concluded our analyses by linking the diseased heart proteome profile to known therapeutic interventions, uncovering a potential to target mitochondrial proteins, secreted immune effectors and core kinases for the treatment of chronic Chagas disease. Together, this study provides molecular insight into host proteome and phospho-proteome responses to T. cruzi infection in the heart for the first time, highlighting pathways that can be further validated for functional contributions to disease and suitability as drug targets.
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Affiliation(s)
- Jacob M. Wozniak
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
- Department of Pharmacology; University of California San Diego; La Jolla, CA, United States of America
| | - Tatiana Araújo Silva
- Cellular Ultrastructure Laboratory; Oswaldo Cruz Institute, FIOCRUZ; Rio de Janeiro, RJ, Brazil
| | - Diane Thomas
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
| | - David J. Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
- Department of Pharmacology; University of California San Diego; La Jolla, CA, United States of America
- * E-mail: (DJG); (CMC)
| | - Claudia M. Calvet
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla, CA, United States of America
- Cellular Ultrastructure Laboratory; Oswaldo Cruz Institute, FIOCRUZ; Rio de Janeiro, RJ, Brazil
- * E-mail: (DJG); (CMC)
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8
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Manzano-Román R, Fuentes M. Relevance and proteomics challenge of functional posttranslational modifications in Kinetoplastid parasites. J Proteomics 2020; 220:103762. [PMID: 32244008 DOI: 10.1016/j.jprot.2020.103762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/06/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
Abstract
Protozoan parasitic infections are health, social and economic issues impacting both humans and animals, with significant morbidity and mortality worldwide. Protozoan parasites have complicated life cycles with both intracellular and extracellular forms. As a consequence, protozoan adapt to changing environments in part through a dynamic enzyme-catalyzed process leading to reversible posttranslational modifications (PTMs). The characterization by proteomics approaches reveals the critical role of the PTMs of the proteins involved in host-pathogen interaction. The complexity of PTMs characterization is increased by the high diversity, stoichiometry, dynamic and also co-existence of several PTMs in the same moieties which crosstalk between them. Here, we review how to understand the complexity and the essential role of PTMs crosstalk in order to provide a new hallmark for vaccines developments, immunotherapies and personalized medicine. In addition, the importance of these motifs in the biology and biological cycle of kinetoplastid parasites is highlighted with key examples showing the potential to act as targets against protozoan diseases.
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Affiliation(s)
- R Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain..
| | - M Fuentes
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain.; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain
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