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Vacchini A, Maffioli E, Di Silvestre D, Cancellieri C, Milanesi S, Nonnis S, Badanai S, Mauri P, Negri A, Locati M, Tedeschi G, Borroni EM. Phosphoproteomic mapping of CCR5 and ACKR2 signaling properties. Front Mol Biosci 2022; 9:1060555. [DOI: 10.3389/fmolb.2022.1060555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
ACKR2 is an atypical chemokine receptor which is structurally uncoupled from G proteins and is unable to activate signaling pathways used by conventional chemokine receptors to promote cell migration. Nonetheless, ACKR2 regulates inflammatory and immune responses by shaping chemokine gradients in tissues via scavenging inflammatory chemokines. To investigate the signaling pathways downstream to ACKR2, a quantitative SILAC-based phosphoproteomic analysis coupled with a systems biology approach with network analysis, was carried out on a HEK293 cell model expressing either ACKR2 or its conventional counterpart CCR5. The model was stimulated with the common agonist CCL3L1 for short (3 min) and long (30 min) durations. As expected, many of the identified proteins are known to participate in conventional signal transduction pathways and in the regulation of cytoskeleton dynamics. However, our analyses revealed unique phosphorylation and network signatures, suggesting roles for ACKR2 other than its scavenger activity. In conclusion, the mapping of phosphorylation events at a holistic level indicated that conventional and atypical chemokine receptors differ in signaling properties. This provides an unprecedented level of detail in chemokine receptor signaling and identifying potential targets for the regulation of ACKR2 and CCR5 function.
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Bae SH, Kim JH, Park TH, Lee K, Lee BI, Jang H. BMS794833 inhibits macrophage efferocytosis by directly binding to MERTK and inhibiting its activity. Exp Mol Med 2022; 54:1450-1460. [PMID: 36056187 PMCID: PMC9534909 DOI: 10.1038/s12276-022-00840-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/13/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023] Open
Abstract
Myeloid epithelial reproductive proto-oncogene tyrosine kinase (MERTK) plays an essential role in modulating cancer immune tolerance by regulating macrophage efferocytosis. Studies are underway to develop small-molecule chemicals that inhibit MERTK as cancer immunotherapeutic agents, but these efforts are in their early stages. This study identified BMS794833, whose primary targets are MET and VEGFR2, as a potent MERTK inhibitor and developed a real-time efferocytosis monitoring system. The X-ray cocrystal structure revealed that BMS794833 was in contact with the ATP-binding pocket and the allosteric back pocket, rendering MERTK inactive. Homogeneous time-resolved fluorescence kinetic and Western blotting analyses showed that BMS794833 competitively inhibited MERTK activity in vitro and inhibited the autophosphorylation of MERTK in macrophages. We developed a system to monitor MERTK-dependent efferocytosis in real time, and using this system, we confirmed that BMS794833 significantly inhibited the efferocytosis of differentiated macrophages. Finally, BMS794833 significantly inhibited efferocytosis in vivo in a mouse model. These data show that BMS794833 is a type II MERTK inhibitor that regulates macrophage efferocytosis. In addition, the real-time efferocytosis monitoring technology developed in this study has great potential for future applications.
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Affiliation(s)
- Seung-Hyun Bae
- Reasearch Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Jung-Hoon Kim
- Reasearch Institute, National Cancer Center, Goyang, 10408, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, 10408, Republic of Korea
| | - Tae Hyun Park
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kyeong Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Byung Il Lee
- Reasearch Institute, National Cancer Center, Goyang, 10408, Republic of Korea.
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, 10408, Republic of Korea.
| | - Hyonchol Jang
- Reasearch Institute, National Cancer Center, Goyang, 10408, Republic of Korea.
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, 10408, Republic of Korea.
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Wang S, Liu C, Ouyang W, Liu Y, Li C, Cheng Y, Su Y, Liu C, Yang L, Liu Y, Wang Z. Common Genes Involved in Autophagy, Cellular Senescence and the Inflammatory Response in AMD and Drug Discovery Identified via Biomedical Databases. Transl Vis Sci Technol 2021; 10:14. [PMID: 33510953 PMCID: PMC7804500 DOI: 10.1167/tvst.10.1.14] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/28/2020] [Indexed: 12/27/2022] Open
Abstract
Purpose Retinal pigment epithelial cell autophagy dysfunction, cellular senescence, and the retinal inflammatory response are key pathogenic factors in age-related macular degeneration (AMD), which has been reviewed in our previously work in 2019. This study aims to identify genes collectively involved in these three biological processes and target drugs in AMD. Methods The pubmed2ensembl database was used to perform text mining. The GeneCodis database was applied to analyze gene ontology biological process and the KEGG pathway. The STRING database was used to analyze protein–protein interaction analysis and hub genes were identified by the Cytoscape software. The Drug Gene Interaction Database was used to perform drug–gene interactions. Results We identified 62 genes collectively involved in AMD, autophagy, cellular senescence, and inflammatory response, 19 biological processes including 42 genes, 11 enriched KEGG pathways including 37 genes, and 12 hub genes step by step via the above biomedical databases. Finally, five hub genes (IL-6, VEGF-A, TP53, IL-1β, and transforming growth factor [TGF]-β1) and their specific interaction modes were identified, corresponding with 24 target drugs with therapeutic potential for AMD. Conclusions IL-6, VEGF-A, TP53, IL-1β, and TGF-β1 are pivotal in autophagy, cellular senescence, and the inflammatory response in AMD, corresponding with 24 drugs with therapeutic potential for AMD, providing definite molecular mechanisms for further research and new possibilities for AMD treatment in the future. Translational Relevance IL-6, VEGF-A, TP53, IL-1β, and TGF-β1 may be new targets for AMD gene therapy and drug development.
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Affiliation(s)
- Shoubi Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Chengxiu Liu
- Department of Ophthalmology, Affiliated Hospital of Qingdao University Medical College, Qingdao University, Qingdao, China
| | - Weijie Ouyang
- Eye Institute of Xiamen University, Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, School of Medicine, Xiamen University, Xiamen, China
| | - Ying Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Chaoyang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yaqi Cheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yaru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Chang Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Liu Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yurun Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhichong Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Valdés A, Bergström Lind S. Mass Spectrometry-Based Analysis of Time-Resolved Proteome Quantification. Proteomics 2019; 20:e1800425. [PMID: 31652013 DOI: 10.1002/pmic.201800425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/20/2019] [Indexed: 11/09/2022]
Abstract
The aspect of time is essential in biological processes and thus it is important to be able to monitor signaling molecules through time. Proteins are key players in cellular signaling and they respond to many stimuli and change their expression in many time-dependent processes. Mass spectrometry (MS) is an important tool for studying proteins, including their posttranslational modifications and their interaction partners-both in qualitative and quantitative ways. In order to distinguish the different trends over time, proteins, modification sites, and interacting proteins must be compared between different time points, and therefore relative quantification is preferred. In this review, the progress and challenges for MS-based analysis of time-resolved proteome dynamics are discussed. Further, aspects on model systems, technologies, sampling frequencies, and presentation of the dynamic data are discussed.
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Affiliation(s)
- Alberto Valdés
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, 28871, Alcalá de Henares, Madrid, Spain
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, 75124, Uppsala, Sweden
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Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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Dong M, Bian Y, Wang Y, Dong J, Yao Y, Deng Z, Qin H, Zou H, Ye M. Sensitive, Robust, and Cost-Effective Approach for Tyrosine Phosphoproteome Analysis. Anal Chem 2017; 89:9307-9314. [DOI: 10.1021/acs.analchem.7b02078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mingming Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Bian
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- Medical Research Center, The First Affiliated
Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenzhen Deng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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Tran TT, Strozynski M, Thiede B. Quantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/12/2017] [Accepted: 04/27/2017] [Indexed: 01/06/2023]
Affiliation(s)
- The Trung Tran
- Department of Biosciences; University of Oslo; Oslo Norway
| | | | - Bernd Thiede
- Department of Biosciences; University of Oslo; Oslo Norway
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Richter E, Mostertz J, Hochgräfe F. Proteomic discovery of host kinase signaling in bacterial infections. Proteomics Clin Appl 2016; 10:994-1010. [PMID: 27440122 PMCID: PMC5096009 DOI: 10.1002/prca.201600035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 06/08/2016] [Accepted: 07/18/2016] [Indexed: 12/15/2022]
Abstract
Protein phosphorylation catalyzed by protein kinases acts as a reversible molecular switch in signal transduction, providing a mechanism for the control of protein function in cellular processes. During microbial infection, cellular signaling essentially contributes to immune control to restrict the dissemination of invading pathogens within the host organism. However, pathogenic microbes compete for the control of host signaling to create a beneficial environment for successful invasion and infection. Although efforts to achieve a better understanding of the host–pathogen interaction and its molecular consequences have been made, there is urgent need for a comprehensive characterization of infection‐related host signaling processes. System‐wide and hypothesis‐free analysis of phosphorylation‐mediated host signaling during host–microbe interactions by mass spectrometry (MS)‐based methods is not only promising in view of a greater understanding of the pathogenesis of the infection but also may result in the identification of novel host targets for preventive or therapeutic intervention. Here, we review state‐of‐the‐art MS‐based techniques for the system‐wide identification and quantitation of protein phosphorylation and compare them to array‐based phosphoprotein analyses. We also provide an overview of how phosphoproteomics and kinomics have contributed to our understanding of protein kinase‐driven phosphorylation networks that operate during host–microbe interactions.
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Affiliation(s)
- Erik Richter
- Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, Greifswald, Germany
| | - Jörg Mostertz
- Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, Greifswald, Germany
| | - Falko Hochgräfe
- Competence Center Functional Genomics, Junior Research Group Pathoproteomics, University of Greifswald, Greifswald, Germany.
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Lochmatter C, Fischer R, Charles PD, Yu Z, Powrie F, Kessler BM. Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes. Sci Rep 2016; 6:24491. [PMID: 27080861 PMCID: PMC4832251 DOI: 10.1038/srep24491] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/30/2016] [Indexed: 12/15/2022] Open
Abstract
Interleukin (IL)-23 mediated signal transduction represents a major molecular mechanism underlying the pathology of inflammatory bowel disease, Crohn's disease and ulcerative colitis. In addition, emerging evidence supports the role of IL-23-driven Th17 cells in inflammation. Components of the IL-23 signaling pathway, such as IL-23R, JAK2 and STAT3, have been characterized, but elements unique to this network as compared to other interleukins have not been readily explored. In this study, we have undertaken an integrative phosphoproteomics approach to better characterise downstream signaling events. To this end, we performed and compared phosphopeptide and phosphoprotein enrichment methodologies after activation of T lymphocytes by IL-23. We demonstrate the complementary nature of the two phosphoenrichment approaches by maximizing the capture of phosphorylation events. A total of 8202 unique phosphopeptides, and 4317 unique proteins were identified, amongst which STAT3, PKM2, CDK6 and LASP-1 showed induction of specific phosphorylation not readily observed after IL-2 stimulation. Interestingly, quantitative analysis revealed predominant phosphorylation of pre-existing STAT3 nuclear subsets in addition to translocation of phosphorylated STAT3 within 30 min after IL-23 stimulation. After IL-23R activation, a small subset of PKM2 also translocates to the nucleus and may contribute to STAT3 phosphorylation, suggesting multiple cellular responses including metabolic adaptation.
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Affiliation(s)
- Corinne Lochmatter
- Kennedy Institute, Nuffield Department of Orthopedics Research Medical Science, Roosevelt Drive, Oxford OX3 7LF, UK
- Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Roman Fischer
- Kennedy Institute, Nuffield Department of Orthopedics Research Medical Science, Roosevelt Drive, Oxford OX3 7LF, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Philip D. Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Zhanru Yu
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Fiona Powrie
- Kennedy Institute, Nuffield Department of Orthopedics Research Medical Science, Roosevelt Drive, Oxford OX3 7LF, UK
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
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Dolai S, Sia KC, Robbins AK, Zhong L, Heatley SL, Vincent TL, Hochgräfe F, Sutton R, Kurmasheva RT, Revesz T, White DL, Houghton PJ, Smith MA, Teachey DT, Daly RJ, Raftery MJ, Lock RB. Quantitative Phosphotyrosine Profiling of Patient-Derived Xenografts Identifies Therapeutic Targets in Pediatric Leukemia. Cancer Res 2016; 76:2766-2777. [DOI: 10.1158/0008-5472.can-15-2786] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Phospho flow cytometry is a powerful technique for the detection of protein phosphorylation events that, like Western blotting, relies on phospho-epitope-specific antibodies. In contrast to the latter, however, multidimensional and directly quantifiable data is obtained at the single-cell level allowing separate analysis of small cell populations in complex cellular mixtures. Furthermore, up to 30 phospho-specific antibodies or antibodies identifying other posttranslational modifications in combination with cell surface markers can be analyzed in a single experiment. Utilizing a technique called fluorescent cell barcoding that enables combination of up to 64 samples into one tube for multiplex analysis and later data deconvolution, phospho flow cytometry is turned into a medium- to high-throughput technology.
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Affiliation(s)
- Jian Yin
- CAS Key Lab of Bio-Medical Diagnostics; Suzhou Institute of Biomedical Engineering and Technology; Chinese Academy of Sciences; Suzhou 215163 P.R. China
| | - Peng Miao
- CAS Key Lab of Bio-Medical Diagnostics; Suzhou Institute of Biomedical Engineering and Technology; Chinese Academy of Sciences; Suzhou 215163 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
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Hoedt E, Zhang G, Neubert TA. Stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomics. Adv Exp Med Biol 2014; 806:93-106. [PMID: 24952180 DOI: 10.1007/978-3-319-06068-2_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 540 First Avenue, New York, NY, 10016, USA
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