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Guo J, Wang F, Huang Y, He H, Tan W, Yi M, Egelman EH, Xu B. Cell spheroid creation by transcytotic intercellular gelation. NATURE NANOTECHNOLOGY 2023; 18:1094-1104. [PMID: 37217766 PMCID: PMC10525029 DOI: 10.1038/s41565-023-01401-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/14/2023] [Indexed: 05/24/2023]
Abstract
Cell spheroids bridge the discontinuity between in vitro systems and in vivo animal models. However, inducing cell spheroids by nanomaterials remains an inefficient and poorly understood process. Here we use cryogenic electron microscopy to determine the atomic structure of helical nanofibres self-assembled from enzyme-responsive D-peptides and fluorescent imaging to show that the transcytosis of D-peptides induces intercellular nanofibres/gels that potentially interact with fibronectin to enable cell spheroid formation. Specifically, D-phosphopeptides, being protease resistant, undergo endocytosis and endosomal dephosphorylation to generate helical nanofibres. On secretion to the cell surface, these nanofibres form intercellular gels that act as artificial matrices and facilitate the fibrillogenesis of fibronectins to induce cell spheroids. No spheroid formation occurs without endo- or exocytosis, phosphate triggers or shape switching of the peptide assemblies. This study-coupling transcytosis and morphological transformation of peptide assemblies-demonstrates a potential approach for regenerative medicine and tissue engineering.
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Affiliation(s)
- Jiaqi Guo
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Yimeng Huang
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
| | - Bing Xu
- Department of Chemistry, Brandeis University, Waltham, MA, USA.
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2
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Knecht S, Eberl HC, Kreisz N, Ugwu UJ, Starikova T, Kuster B, Wilhelm S. An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics. Mol Cell Proteomics 2023; 22:100636. [PMID: 37597723 PMCID: PMC10518356 DOI: 10.1016/j.mcpro.2023.100636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS-based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry-based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science.
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Affiliation(s)
- Sascha Knecht
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - H Christian Eberl
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany
| | - Norbert Kreisz
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Ukamaka Juliet Ugwu
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tatiana Starikova
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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3
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Sun J, Li Q, Ding Y, Wei D, Hadisurya M, Luo Z, Gu Z, Chen B, Tao WA. Profiling Phosphoproteome Landscape in Circulating Extracellular Vesicles from Microliters of Biofluids through Functionally Tunable Paramagnetic Separation. Angew Chem Int Ed Engl 2023; 62:e202305668. [PMID: 37216424 PMCID: PMC11019431 DOI: 10.1002/anie.202305668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Many biological processes are regulated through dynamic protein phosphorylation. Monitoring disease-relevant phosphorylation events in circulating biofluids is highly appealing but also technically challenging. We introduce here a functionally tunable material and a strategy, extracellular vesicles to phosphoproteins (EVTOP), which achieves one-pot extracellular vesicles (EVs) isolation, extraction, and digestion of EV proteins, and enrichment of phosphopeptides, with only a trace amount of starting biofluids. EVs are efficiently isolated by magnetic beads functionalized with TiIV ions and a membrane-penetrating peptide, octa-arginine R8 + , which also provides the hydrophilic surface to retain EV proteins during lysis. Subsequent on-bead digestion concurrently converts EVTOP to TiIV ion-only surface for efficient enrichment of phosphopeptides for phosphoproteomic analyses. The streamlined, ultra-sensitive platform enabled us to quantify 500 unique EV phosphopeptides with only a few μL of plasma and over 1200 phosphopeptides with 100 μL of cerebrospinal fluid (CSF). We explored its clinical application of monitoring the outcome of chemotherapy of primary central nervous system lymphoma (PCNSL) patients with a small volume of CSF, presenting a powerful tool for broad clinical applications.
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Affiliation(s)
- Jie Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Qing Li
- Department of Hematology, Huashan Hospital, Shanghai, China
| | - Yajie Ding
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Marco Hadisurya
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
| | - Zhuojun Luo
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Bobin Chen
- Department of Hematology, Huashan Hospital, Shanghai, China
| | - W. Andy Tao
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
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4
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Wu X, Liu YK, Iliuk AB, Tao WA. Mass spectrometry-based phosphoproteomics in clinical applications. Trends Analyt Chem 2023; 163:117066. [PMID: 37215489 PMCID: PMC10195102 DOI: 10.1016/j.trac.2023.117066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.
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Affiliation(s)
- Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
| | - W. Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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5
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Phosphorylation of IGFBP-3 by Casein Kinase 2 Blocks Its Interaction with Hyaluronan, Enabling HA-CD44 Signaling Leading to Increased NSCLC Cell Survival and Cisplatin Resistance. Cells 2023; 12:cells12030405. [PMID: 36766747 PMCID: PMC9913475 DOI: 10.3390/cells12030405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 01/27/2023] Open
Abstract
Cisplatin is a platinum agent used in the treatment of non-small cell lung cancer (NSCLC). Much remains unknown regarding the basic operative mechanisms underlying cisplatin resistance in NSCLC. In this study, we found that phosphorylation of IGFBP-3 by CK2 (P-IGFBP-3) decreased its binding to hyaluronan (HA) but not to IGF-1 and rendered the protein less effective at reducing cell viability or increasing apoptosis than the non-phosphorylated protein with or without cisplatin in the human NSCLC cell lines, A549 and H1299. Our data suggest that blocking CD44 signaling augmented the effects of cisplatin and that IGFBP-3 was more effective at inhibiting HA-CD44 signaling than P-IGFBP-3. Blocking CK2 activity and HA-CD44 signaling increased cisplatin sensitivity and more effectively blocked the PI3K and AKT activities and the phospho/total NFκB ratio and led to increased p53 activation in A549 cells. Increased cell sensitivity to cisplatin was observed upon co-treatment with inhibitors targeted against PI3K, AKT, and NFκB while blocking p53 activity decreased A549 cell sensitivity to cisplatin. Our findings shed light on a novel mechanism employed by CK2 in phosphorylating IGFBP-3 and increasing cisplatin resistance in NSCLC. Blocking phosphorylation of IGFBP-3 by CK2 may be an effective strategy to increase NSCLC sensitivity to cisplatin.
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Jia Q, Huang Z, Wang G, Sun X, Wu Y, Yang B, Yang T, Liu J, Li P, Li J. Osteopontin: An important protein in the formation of kidney stones. Front Pharmacol 2022; 13:1036423. [DOI: 10.3389/fphar.2022.1036423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
The incidence of kidney stones averages 10%, and the recurrence rate of kidney stones is approximately 10% at 1 year, 35% at 5 years, 50% at 10 years, and 75% at 20 years. However, there is currently a lack of good medicines for the prevention and treatment of kidney stones. Osteopontin (OPN) is an important protein in kidney stone formation, but its role is controversial, with some studies suggesting that it inhibits stone formation, while other studies suggest that it can promote stone formation. OPN is a highly phosphorylated protein, and with the deepening of research, there is growing evidence that it promotes stone formation, and the phosphorylated protein is believed to have adhesion effect, promote stone aggregation and nucleation. In addition, OPN is closely related to immune cell infiltration, such as OPN as a pro-inflammatory factor, which can activate mast cells (degranulate to release various inflammatory factors), macrophages (differentiated into M1 macrophages), and T cells (differentiated into T1 cells) etc., and these inflammatory cells play a role in kidney damage and stone formation. In short, OPN mainly exists in the phosphorylated form in kidney stones, plays an important role in the formation of stones, and may be an important target for drug therapy of kidney stones.
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7
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Translational proteomics and phosphoproteomics: Tissue to extracellular vesicles. Adv Clin Chem 2022; 112:119-153. [PMID: 36642482 DOI: 10.1016/bs.acc.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We are currently experiencing a rapidly developing era in terms of translational and clinical medical sciences. The relatively mature state of nucleic acid examination has significantly improved our understanding of disease mechanism and therapeutic potential of personalized treatment, but misses a large portion of phenotypic disease information. Proteins, in particular phosphorylation events that regulates many cellular functions, could provide real-time information for disease onset, progression and treatment efficacy. The technical advances in liquid chromatography and mass spectrometry have realized large-scale and unbiased proteome and phosphoproteome analyses with disease relevant samples such as tissues. However, tissue biopsy still has multiple shortcomings, such as invasiveness of sample collection, potential health risk for patients, difficulty in protein preservation and extreme heterogeneity. Recently, extracellular vesicles (EVs) have offered a great promise as a unique source of protein biomarkers for non-invasive liquid biopsy. Membranous EVs provide stable preservation of internal proteins and especially labile phosphoproteins, which is essential for effective routine biomarker detection. To aid efficient EV proteomic and phosphoproteomic analyses, recent developments showcase clinically-friendly EV techniques, facilitating diagnostic and therapeutic applications. Ultimately, we envision that with streamlined sample preparation from tissues and EVs proteomics and phosphoproteomics analysis will become routine in clinical settings.
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8
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Hallal S, Tűzesi Á, Grau GE, Buckland ME, Alexander KL. Understanding the extracellular vesicle surface for clinical molecular biology. J Extracell Vesicles 2022; 11:e12260. [PMID: 36239734 PMCID: PMC9563386 DOI: 10.1002/jev2.12260] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 12/17/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid-membrane enclosed nanoparticles that play significant roles in health and disease. EVs are abundant in body fluids and carry an array of molecules (proteins, lipids, nucleic acids and glycans) that reflect the identity and activity of their cell-of-origin. While the advent of high throughput omics technologies has allowed in-depth characterisation of EV compositions, how these molecular species are spatially distributed within EV structures is not well appreciated. This is particularly true of the EV surface where a plethora of molecules are reported to be both integral and peripherally associated to the EV membrane. This coronal layer or 'atmosphere' that surrounds the EV membrane contributes to a large, highly interactive and dynamic surface area that is responsible for facilitating EV interactions with the extracellular environment. The EV coronal layer harbours surface molecules that reflect the identity of parent cells, which is likely a highly valuable property in the context of diagnostic liquid biopsies. In this review, we describe the current understanding of the mechanical, electrostatic and molecular properties of the EV surface that offer significant biomarker potential and contribute to a highly dynamic interactome.
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Affiliation(s)
- Susannah Hallal
- Neurosurgery DepartmentChris O'Brien LifehouseCamperdownNSWAustralia,Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia
| | - Ágota Tűzesi
- Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Georges E. Grau
- School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Michael E. Buckland
- Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
| | - Kimberley L. Alexander
- Neurosurgery DepartmentChris O'Brien LifehouseCamperdownNSWAustralia,Brainstorm Brain Cancer Research, Brain and Mind CentreThe University of SydneyNSWAustralia,Neuropathology DepartmentRoyal Prince Alfred HospitalCamperdownNSWAustralia,School of Medical SciencesFaculty of Medicine & HealthThe University of SydneyCamperdownNSWAustralia
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9
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Huang Z, Wang G, Yang B, Li P, Yang T, Wu Y, Yang X, Liu J, Li J. Mechanism of ketotifen fumarate inhibiting renal calcium oxalate stone formation in SD rats. Biomed Pharmacother 2022; 151:113147. [PMID: 35643070 DOI: 10.1016/j.biopha.2022.113147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/02/2022] [Accepted: 05/15/2022] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES To investigate the inhibitory effect of ketotifen fumarate (KFA), a mast cell membrane stabilizer, on renal calcium oxalate stone (CaOx) formation and its possible molecular mechanism. METHODS We used the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database for functional and pathway enrichment analyses of osteopontin (OPN), CD44 and fibronectin (FN). Blood biochemistry, reactive oxygen species ratio (ROS), mast cells, proteins (CD44, OPN and FN) and OPN receptor integrin family genes were detected by ELISA, flow cytometry, immunohistochemistry and RT-QPCR, respectively. RESULTS The crystal area of CaOx in the KFA and Control group was significantly smaller than that in the Model group. The number of activated mast cells, the expression levels of OPN and CD44 in the Control and KFA groups were significantly lower than those in the Model group, and the percentage of ROS in the KFA group was also significantly lower than that in the Model group. The mRNA expression levels of ITGB1, ITGA9, ITGAV and ITGA4 genes in the prominent OPN receptor integrin family increased significantly in the Model group. CONCLUSIONS Ketotifen can effectively inhibit the crystal formation of CaOx and reduce the inflammatory response of tissue in SD rats. The mechanism may be to reduce the infiltration and activation of mast cells in renal tissue and down-regulate the expression of OPN, CD44 and FN in renal tubules and renal interstitium. And affect the synthesis of integrins (ITGA9, ITGA4, ITGAV, ITGB1, ITGB3 and ITGB5) and ROS.
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Affiliation(s)
- Ziye Huang
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China
| | - Guang Wang
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China
| | - Bowei Yang
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China
| | - Pei Li
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China
| | - Tongxin Yang
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China
| | - Yuyun Wu
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China
| | - Xing Yang
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China
| | - Jianhe Liu
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China.
| | - Jiongming Li
- The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan 650101, PR China.
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10
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Rui X, Cui M, Martewicz S, Hu M, Gagliano O, Elvassore N, Luni C. Extracellular phosphoprotein regulation is affected by culture system scale-down. Biochim Biophys Acta Gen Subj 2022; 1866:130165. [PMID: 35513203 DOI: 10.1016/j.bbagen.2022.130165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Phosphorylated proteins are known to be present in multiple body fluids in normal conditions, and abnormally accumulated under some pathological conditions. The biological significance of their role in the extracellular space has started being elucidated only recently, for example in bone mineralization, neural development, and coagulation. Here, we address some criticalities of conventional culture systems for the study of the extracellular regulation of phosphorylation. METHODS We make use of microfluidics to scale-down the culture volume to a size comparable to the interstitial spaces occurring in vivo. The phosphoprotein content of conditioned media was analyzed by a colorimetric assay that detects global phosphorylation. RESULTS We found that miniaturization of the culture system increases phosphoprotein accumulation. Moreover, we demonstrated that in conventional culture systems dilution affects the extent of the phosphorylation reactions occurring within the extracellular space. On the other hand, in microfluidics the phosphorylation status was not affected by addition of adenosine triphosphate (ATP) and FAM20C Golgi Associated Secretory Pathway Kinase (FAM20C) ectokinase, as if their concentration was already not limiting for the phosphorylation reaction to occur. CONCLUSIONS The volume of the extracellular environment plays a role in the process of extracellular phosphorylation due to its effect on the concentration of substrates, enzymes and co-factors. GENERAL SIGNIFICANCE Thus, the biological role of extracellular phosphoregulation may be better appreciated within a microfluidic culture system.
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Affiliation(s)
- Xue Rui
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Meihua Cui
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, China
| | - Sebastian Martewicz
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, China
| | - Manli Hu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, China
| | - Onelia Gagliano
- Department of Industrial Engineering, University of Padova, Padova 35131, Italy; Venetian Institute of Molecular Medicine, Padova 35129, Italy
| | - Nicola Elvassore
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, China; Department of Industrial Engineering, University of Padova, Padova 35131, Italy; Venetian Institute of Molecular Medicine, Padova 35129, Italy; Stem Cells & Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Camilla Luni
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, China; Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, Bologna 40131, Italy.
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11
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A not so lonesome kinase secreted by platelets. Blood 2022; 139:8-9. [PMID: 34989772 DOI: 10.1182/blood.2021013533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
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12
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Song XJ, Zhou HY, Sun YY, Huang HC. Phosphorylation and Glycosylation of Amyloid-β Protein Precursor: The Relationship to Trafficking and Cleavage in Alzheimer's Disease. J Alzheimers Dis 2021; 84:937-957. [PMID: 34602469 DOI: 10.3233/jad-210337] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder in the central nervous system, and this disease is characterized by extracellular senile plaques and intracellular neurofibrillary tangles. Amyloid-β (Aβ) peptide is the main constituent of senile plaques, and this peptide is derived from the amyloid-β protein precursor (AβPP) through the successive cleaving by β-site AβPP-cleavage enzyme 1 (BACE1) and γ-secretase. AβPP undergoes the progress of post-translational modifications, such as phosphorylation and glycosylation, which might affect the trafficking and the cleavage of AβPP. In the recent years, about 10 phosphorylation sites of AβPP were identified, and they play complex roles in glycosylation modification and cleavage of AβPP. In this article, we introduced the transport and the cleavage pathways of AβPP, then summarized the phosphorylation and glycosylation sites of AβPP, and further discussed the links and relationship between phosphorylation and glycosylation on the pathways of AβPP trafficking and cleavage in order to provide theoretical basis for AD research.
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Affiliation(s)
- Xi-Jun Song
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing, China.,Research Institute of Functional Factors and Brain Science, Beijing Union University, Beijing, China
| | - He-Yan Zhou
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing, China.,Research Institute of Functional Factors and Brain Science, Beijing Union University, Beijing, China
| | - Yu-Ying Sun
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing, China.,Research Institute of Functional Factors and Brain Science, Beijing Union University, Beijing, China
| | - Han-Chang Huang
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University, Beijing, China.,Research Institute of Functional Factors and Brain Science, Beijing Union University, Beijing, China
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13
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Phosphorylated Osteopontin Secreted from Cancer Cells Induces Cancer Cell Motility. Biomolecules 2021; 11:biom11091323. [PMID: 34572536 PMCID: PMC8470647 DOI: 10.3390/biom11091323] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/30/2021] [Accepted: 09/04/2021] [Indexed: 12/22/2022] Open
Abstract
Osteopontin (OPN) plays a pivotal role in cancer cell invasion and metastasis. Although OPN has a large number of phosphorylation sites, the functional significance of OPN phosphorylation in cancer cell motility remains unclear. In this study, we attempted to investigate whether phosphorylated OPN secreted from cancer cells affect cancer cell migration. Quantitative PCR and Western blot analyses revealed that MDA-MB435S, A549, and H460 cells highly expressed OPN, whereas the OPN expression levels in H358, MIAPaca-2, and Panc-1 cells were quite low or were not detected. Compared with the cancer cell lines with a low OPN expression, the high OPN-expressing cancer cell lines displayed a higher cell migration, and the cell migration was suppressed by the anti-OPN antibody. This was confirmed by the OPN overexpression in H358 cancer cells with a low endogenous OPN. Phos-tag ELISA showed that phosphorylated OPN was abundant in the cell culture media of A549 and H460 cells, but not in those of MDA-MB435S cells. Moreover, the A549 and H460 cell culture media, as well as the MDA-MB435S cell culture media with a kinase treatment increased cancer cell motility, both of which were abrogated by phosphatase treatment or anti-OPN antibodies. These results suggest that phosphorylated OPN secreted from cancer cells regulates cancer cell motility.
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14
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Proteolytic processing of secretory pathway kinase Fam20C by site-1 protease promotes biomineralization. Proc Natl Acad Sci U S A 2021; 118:2100133118. [PMID: 34349020 DOI: 10.1073/pnas.2100133118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Family with sequence similarity 20C (Fam20C), the major protein kinase in the secretory pathway, generates the vast majority of the secreted phosphoproteome. However, the regulatory mechanisms of Fam20C transport, secretion, and function remain largely unexplored. Here, we show that Fam20C exists as a type II transmembrane protein within the secretory compartments, with its N-terminal signal peptide-like region serving as a membrane anchor for Golgi retention. The secretion and kinase activity of Fam20C are governed by site-1 protease (S1P), a key regulator of cholesterol homeostasis. We find that only mature Fam20C processed by S1P functions in osteoblast differentiation and mineralization. Together, our findings reveal a unique mechanism for Fam20C secretion and activation via proteolytic regulation, providing a molecular link between biomineralization and lipid metabolism.
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15
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Mateos B, Holzinger J, Conrad-Billroth C, Platzer G, Żerko S, Sealey-Cardona M, Anrather D, Koźmiński W, Konrat R. Hyperphosphorylation of Human Osteopontin and Its Impact on Structural Dynamics and Molecular Recognition. Biochemistry 2021; 60:1347-1355. [PMID: 33876640 PMCID: PMC8154273 DOI: 10.1021/acs.biochem.1c00050] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein phosphorylation is an abundant post-translational modification (PTM) and an essential modulator of protein functionality in living cells. Intrinsically disordered proteins (IDPs) are particular targets of PTM protein kinases due to their involvement in fundamental protein interaction networks. Despite their dynamic nature, IDPs are far from having random-coil conformations but exhibit significant structural heterogeneity. Changes in the molecular environment, most prominently in the form of PTM via phosphorylation, can modulate these structural features. Therefore, how phosphorylation events can alter conformational ensembles of IDPs and their interactions with binding partners is of great interest. Here we study the effects of hyperphosphorylation on the IDP osteopontin (OPN), an extracellular target of the Fam20C kinase. We report a full characterization of the phosphorylation sites of OPN using a combined nuclear magnetic resonance/mass spectrometry approach and provide evidence for an increase in the local flexibility of highly phosphorylated regions and the ensuing overall structural elongation. Our study emphasizes the simultaneous importance of electrostatic and hydrophobic interactions in the formation of compact substates in IDPs and their relevance for molecular recognition events.
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Affiliation(s)
- Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
| | - Julian Holzinger
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
| | - Clara Conrad-Billroth
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
| | - Gerald Platzer
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093 Warsaw, Poland
| | | | - Dorothea Anrather
- Mass Spectrometry Facility, Max Perutz Laboratories, Vienna BioCenter Campus 5, Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02093 Warsaw, Poland
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Max Perutz Labs, Vienna BioCenter Campus 5, 1030 Vienna, Austria
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16
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Strittmatter T, Egli S, Bertschi A, Plieninger R, Bojar D, Xie M, Fussenegger M. Gene switch for l-glucose-induced biopharmaceutical production in mammalian cells. Biotechnol Bioeng 2021; 118:2220-2233. [PMID: 33629358 DOI: 10.1002/bit.27730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/23/2021] [Accepted: 02/17/2021] [Indexed: 12/11/2022]
Abstract
In this study, we designed and built a gene switch that employs metabolically inert l-glucose to regulate transgene expression in mammalian cells via d-idonate-mediated control of the bacterial regulator LgnR. To this end, we engineered a metabolic cascade in mammalian cells to produce the inducer molecule d-idonate from its precursor l-glucose by ectopically expressing the Paracoccus species 43P-derived catabolic enzymes LgdA, LgnH, and LgnI. To obtain ON- and OFF-switches, we fused LgnR to the human transcriptional silencer domain Krüppel associated box (KRAB) and the viral trans-activator domain VP16, respectively. Thus, these artificial transcription factors KRAB-LgnR or VP16-LgnR modulated cognate promoters containing LgnR-specific binding sites in a d-idonate-dependent manner as a direct result of l-glucose metabolism. In a proof-of-concept experiment, we show that the switches can control production of the model biopharmaceutical rituximab in both transiently and stably transfected HEK-293T cells, as well as CHO-K1 cells. Rituximab production reached 5.9 µg/ml in stably transfected HEK-293T cells and 3.3 µg/ml in stably transfected CHO-K1 cells.
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Affiliation(s)
- Tobias Strittmatter
- Department of Biosystems, Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sabina Egli
- Department of Biosystems, Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Adrian Bertschi
- Department of Biosystems, Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Richard Plieninger
- Department of Biosystems, Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel Bojar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Mingqi Xie
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Martin Fussenegger
- Department of Biosystems, Science and Engineering, ETH Zurich, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse, Basel, Switzerland
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17
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Atali S, Dorandish S, Devos J, Williams A, Price D, Taylor J, Guthrie J, Heyl D, Evans HG. Interaction of amyloid beta with humanin and acetylcholinesterase is modulated by ATP. FEBS Open Bio 2020; 10:2805-2823. [PMID: 33145964 PMCID: PMC7714071 DOI: 10.1002/2211-5463.13023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/24/2020] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Humanin (HN) is known to bind amyloid beta (Aβ)‐inducing cytoprotective effects, while binding of acetylcholinesterase (AChE) to Aβ increases its aggregation and cytotoxicity. Previously, we showed that binding of HN to Aβ blocks aggregation induced by AChE and that HN decreases but does not abolish Aβ‐AChE interactions in A549 cell media. Here, we set out to shed light on factors that modulate the interactions of Aβ with HN and AChE. We found that binding of either HN or AChE to Aβ is not affected by heparan sulfate, while ATP, thought to reduce misfolding of Aβ, weakened interactions between AChE and Aβ but strengthened those between Aβ and HN. Using media from either A549 or H1299 lung cancer cells, we observed that more HN was bound to Aβ upon addition of ATP, while levels of AChE in a complex with Aβ were decreased by ATP addition to A549 cell media. Exogenous addition of ATP to either A549 or H1299 cell media increased interactions of endogenous HN with Aβ to a comparable extent despite differences in AChE expression in the two cell lines, and this was correlated with decreased binding of exogenously added HN to Aβ. Treatment with exogenous ATP had no effect on cell viability under all conditions examined. Exogenously added ATP did not affect viability of cells treated with AChE‐immunodepleted media, and there was no apparent protection against the cytotoxicity resulting from immunodepletion of HN. Moreover, exogenously added ATP had no effect on the relative abundance of oligomer versus total Aβ in either cell line.
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Affiliation(s)
- Sarah Atali
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Sadaf Dorandish
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Jonathan Devos
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Asana Williams
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Deanna Price
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Jaylen Taylor
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Jeffrey Guthrie
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Deborah Heyl
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Hedeel Guy Evans
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
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18
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Örd M, Faustova I, Loog M. The sequence at Spike S1/S2 site enables cleavage by furin and phospho-regulation in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV. Sci Rep 2020; 10:16944. [PMID: 33037310 PMCID: PMC7547067 DOI: 10.1038/s41598-020-74101-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022] Open
Abstract
The Spike protein of the novel coronavirus SARS-CoV2 contains an insertion 680SPRRAR↓SV687 forming a cleavage motif RxxR for furin-like enzymes at the boundary of S1/S2 subunits. Cleavage at S1/S2 is important for efficient viral entry into target cells. The insertion is absent in other CoV-s of the same clade, including SARS-CoV1 that caused the 2003 outbreak. However, an analogous cleavage motif was present at S1/S2 of the Spike protein of the more distant Middle East Respiratory Syndrome coronavirus MERS-CoV. We show that a crucial third arginine at the left middle position, comprising a motif RRxR is required for furin recognition in vitro, while the general motif RxxR in common with MERS-CoV is not sufficient for cleavage. Further, we describe a surprising finding that the two serines at the edges of the insert SPRRAR↓SV can be efficiently phosphorylated by proline-directed and basophilic protein kinases. Both phosphorylations switch off furin’s ability to cleave the site. Although phospho-regulation of secreted proteins is still poorly understood, further studies, supported by a recent report of ten in vivo phosphorylated sites in the Spike protein of SARS-CoV2, could potentially uncover important novel regulatory mechanisms for SARS-CoV2.
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Affiliation(s)
- Mihkel Örd
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Ilona Faustova
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia.
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19
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Abstract
Enzymatic reactions and noncovalent (i.e., supramolecular) interactions are two fundamental nongenetic attributes of life. Enzymatic noncovalent synthesis (ENS) refers to a process where enzymatic reactions control intermolecular noncovalent interactions for spatial organization of higher-order molecular assemblies that exhibit emergent properties and functions. Like enzymatic covalent synthesis (ECS), in which an enzyme catalyzes the formation of covalent bonds to generate individual molecules, ENS is a unifying theme for understanding the functions, morphologies, and locations of molecular ensembles in cellular environments. This review intends to provide a summary of the works of ENS within the past decade and emphasize ENS for functions. After comparing ECS and ENS, we describe a few representative examples where nature uses ENS, as a rule of life, to create the ensembles of biomacromolecules for emergent properties/functions in a myriad of cellular processes. Then, we focus on ENS of man-made (synthetic) molecules in cell-free conditions, classified by the types of enzymes. After that, we introduce the exploration of ENS of man-made molecules in the context of cells by discussing intercellular, peri/intracellular, and subcellular ENS for cell morphogenesis, molecular imaging, cancer therapy, and other applications. Finally, we provide a perspective on the promises of ENS for developing molecular assemblies/processes for functions. This review aims to be an updated introduction for researchers who are interested in exploring noncovalent synthesis for developing molecular science and technologies to address societal needs.
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Affiliation(s)
- Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Adrianna N Shy
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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20
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Positive surface charge of GluN1 N-terminus mediates the direct interaction with EphB2 and NMDAR mobility. Nat Commun 2020; 11:570. [PMID: 31996679 PMCID: PMC6989673 DOI: 10.1038/s41467-020-14345-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
Localization of the N-methyl-D-aspartate type glutamate receptor (NMDAR) to dendritic spines is essential for excitatory synaptic transmission and plasticity. Rather than remaining trapped at synaptic sites, NMDA receptors undergo constant cycling into and out of the postsynaptic density. Receptor movement is constrained by protein-protein interactions with both the intracellular and extracellular domains of the NMDAR. The role of extracellular interactions on the mobility of the NMDAR is poorly understood. Here we demonstrate that the positive surface charge of the hinge region of the N-terminal domain in the GluN1 subunit of the NMDAR is required to maintain NMDARs at dendritic spine synapses and mediates the direct extracellular interaction with a negatively charged phospho-tyrosine on the receptor tyrosine kinase EphB2. Loss of the EphB-NMDAR interaction by either mutating GluN1 or knocking down endogenous EphB2 increases NMDAR mobility. These findings begin to define a mechanism for extracellular interactions mediated by charged domains.
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21
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Izzi V, Koivunen J, Rappu P, Heino J, Pihlajaniemi T. Integration of Matrisome Omics: Towards System Biology of the Tumor Matrisome. EXTRACELLULAR MATRIX OMICS 2020. [DOI: 10.1007/978-3-030-58330-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Frandsen KEH, Tovborg M, Jørgensen CI, Spodsberg N, Rosso MN, Hemsworth GR, Garman EF, Grime GW, Poulsen JCN, Batth TS, Miyauchi S, Lipzen A, Daum C, Grigoriev IV, Johansen KS, Henrissat B, Berrin JG, Lo Leggio L. Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases. J Biol Chem 2019; 294:17117-17130. [PMID: 31471321 DOI: 10.1074/jbc.ra119.009223] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/22/2019] [Indexed: 01/13/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class Agaricomycetes, associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, LsAA9B, a naturally occurring protein from Lentinus similis The LsAA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of LsAA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass.
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Affiliation(s)
- Kristian E H Frandsen
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark.,INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | | | | | | | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Glyn R Hemsworth
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.,Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Geoffrey W Grime
- The Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford GU2 7XH, United Kingdom
| | | | - Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shingo Miyauchi
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720
| | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, 13009 Marseille, France.,INRA, USC 1408 AFMB, 13009 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Université, UMR1163 BBF (Biodiversité et Biotechnologie Fongiques), 13009 Marseille, France
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
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23
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Amann T, Schmieder V, Faustrup Kildegaard H, Borth N, Andersen MR. Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms. Biotechnol Bioeng 2019; 116:2778-2796. [PMID: 31237682 DOI: 10.1002/bit.27101] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/27/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022]
Abstract
The number of approved biopharmaceuticals, where product quality attributes remain of major importance, is increasing steadily. Within the available variety of expression hosts, the production of biopharmaceuticals faces diverse limitations with respect to posttranslational modifications (PTM), while different biopharmaceuticals demand different forms and specifications of PTMs for proper functionality. With the growing toolbox of genetic engineering technologies, it is now possible to address general as well as host- or biopharmaceutical-specific product quality obstacles. In this review, we present diverse expression systems derived from mammalians, bacteria, yeast, plants, and insects as well as available genetic engineering tools. We focus on genes for knockout/knockdown and overexpression for meaningful approaches to improve biopharmaceutical PTMs and discuss their applicability as well as future trends in the field.
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Affiliation(s)
- Thomas Amann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valerie Schmieder
- acib GmbH-Austrian Centre of Industrial Biotechnology, Graz, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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24
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Eriksson O, Mohlin C, Nilsson B, Ekdahl KN. The Human Platelet as an Innate Immune Cell: Interactions Between Activated Platelets and the Complement System. Front Immunol 2019; 10:1590. [PMID: 31354729 PMCID: PMC6635567 DOI: 10.3389/fimmu.2019.01590] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
Platelets play an essential role in maintaining homeostasis in the circulatory system after an injury by forming a platelet thrombus, but they also occupy a central node in the intravascular innate immune system. This concept is supported by their extensive interactions with immune cells and the cascade systems of the blood. In this review we discuss the close relationship between platelets and the complement system and the role of these interactions during thromboinflammation. Platelets are protected from complement-mediated damage by soluble and membrane-expressed complement regulators, but they bind several complement components on their surfaces and trigger complement activation in the fluid phase. Furthermore, localized complement activation may enhance the procoagulant responses of platelets through the generation of procoagulant microparticles by insertion of sublytic amounts of C5b9 into the platelet membrane. We also highlight the role of post-translational protein modifications in regulating the complement system and the critical role of platelets in driving these reactions. In particular, modification of disulfide bonds by thiol isomerases and protein phosphorylation by extracellular kinases have emerged as important mechanisms to fine-tune complement activity in the platelet microenvironment. Lastly, we describe disorders with perturbed complement activation where part of the clinical presentation includes uncontrolled platelet activation that results in thrombocytopenia, and illustrate how complement-targeting drugs are alleviating the prothrombotic phenotype in these patients. Based on these clinical observations, we discuss the role of limited complement activation in enhancing platelet activation and consider how these drugs may provide opportunities for further dissecting the complex interactions between complement and platelets.
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Affiliation(s)
- Oskar Eriksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Camilla Mohlin
- Linnaeus Center of Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden
| | - Bo Nilsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kristina N. Ekdahl
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Linnaeus Center of Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden
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25
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Yalak G, Shiu JY, Schoen I, Mitsi M, Vogel V. Phosphorylated fibronectin enhances cell attachment and upregulates mechanical cell functions. PLoS One 2019; 14:e0218893. [PMID: 31291285 PMCID: PMC6619657 DOI: 10.1371/journal.pone.0218893] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/11/2019] [Indexed: 01/29/2023] Open
Abstract
A large number of extracellular matrix proteins have been found in phosphorylated states, yet little is known about how the phosphorylation of extracellular matrix proteins might affect cell functions. We thus tested the hypothesis whether the phosphorylation of fibronectin, a major adhesion protein, affects cell behavior. Controlled in vitro phosphorylation of fibronectin by a casein kinase II (CKII) significantly upregulated cell traction forces and total strain energy generated by fibroblasts on nanopillar arrays, and consequently other elementary cell functions including cell spreading and metabolic activity. Mass spectrometry of plasma fibronectin from healthy human donors then identified a constitutively phosphorylated site in the C-terminus, and numerous other residues that became phosphorylated by the CKII kinase in vitro. Our findings open up novel strategies for translational applications including targeting diseased ECM, or to develop assays that probe the phosphorylation state of the ECM or blood as potential cancer markers.
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Affiliation(s)
- Garif Yalak
- Laboratory of Applied Mechanobiology, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Jau-Ye Shiu
- Laboratory of Applied Mechanobiology, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Ingmar Schoen
- Laboratory of Applied Mechanobiology, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Maria Mitsi
- Laboratory of Applied Mechanobiology, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
- * E-mail:
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26
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Park BC, Reese M, Tagliabracci VS. Thinking outside of the cell: Secreted protein kinases in bacteria, parasites, and mammals. IUBMB Life 2019; 71:749-759. [PMID: 30941842 DOI: 10.1002/iub.2040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 01/02/2023]
Abstract
Previous decades have seen an explosion in our understanding of protein kinase function in human health and disease. Hundreds of unique kinase structures have been solved, allowing us to create generalized rules for catalysis, assign roles of communities within the catalytic core, and develop specific drugs for targeting various pathways. Although our understanding of intracellular kinases has developed at a fast rate, our exploration into extracellular kinases has just begun. In this review, we will cover the secreted protein kinase families found in humans, bacteria, and parasites. © 2019 IUBMB Life, 71(6):749-759, 2019.
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Affiliation(s)
- Brenden C Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Reese
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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27
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Sathe G, Na CH, Renuse S, Madugundu A, Albert M, Moghekar A, Pandey A. Phosphotyrosine profiling of human cerebrospinal fluid. Clin Proteomics 2018; 15:29. [PMID: 30220890 PMCID: PMC6136184 DOI: 10.1186/s12014-018-9205-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Background Cerebrospinal fluid (CSF) is an important source of potential biomarkers that affect the brain. Biomarkers for neurodegenerative disorders are needed to assist in diagnosis, monitoring disease progression and evaluating efficacy of therapies. Recent studies have demonstrated the involvement of tyrosine kinases in neuronal cell death. Thus, neurodegeneration in the brain is related to altered tyrosine phosphorylation of proteins in the brain and identification of abnormally phosphorylated tyrosine peptides in CSF has the potential to ascertain candidate biomarkers for neurodegenerative disorders. Methods In this study, we used an antibody-based tyrosine phosphopeptide enrichment method coupled with high resolution Orbitrap Fusion Tribrid Lumos Fourier transform mass spectrometer to catalog tyrosine phosphorylated peptides from cerebrospinal fluid. The subset of identified tyrosine phosphorylated peptides was also validated using parallel reaction monitoring (PRM)-based targeted approach. Results To date, there are no published studies on global profiling of phosphotyrosine modifications of CSF proteins. We carried out phosphotyrosine profiling of CSF using an anti-phosphotyrosine antibody-based enrichment and analysis using high resolution Orbitrap Fusion Lumos mass spectrometer. We identified 111 phosphotyrosine peptides mapping to 66 proteins, which included 24 proteins which have not been identified in CSF previously. We then validated a set of 5 tyrosine phosphorylated peptides in an independent set of CSF samples from cognitively normal subjects, using a PRM-based targeted approach. Conclusions The findings from this deep phosphotyrosine profiling of CSF samples have the potential to identify novel disease-related phosphotyrosine-containing peptides in CSF. Electronic supplementary material The online version of this article (10.1186/s12014-018-9205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gajanan Sathe
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,7Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
| | - Chan Hyun Na
- 3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,6Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Anil Madugundu
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,7Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
| | - Marilyn Albert
- 4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Abhay Moghekar
- 4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Akhilesh Pandey
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,5Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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Klichkhanov NK, Dzhafarova AM. The Kinetics of Thermal Denaturation of Acetylcholinesterase of the Rat Red Blood Cell Membrane during Moderate Hypothermia. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918040103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Biological role of site-specific O-glycosylation in cell adhesion activity and phosphorylation of osteopontin. Biochem J 2018; 475:1583-1595. [PMID: 29626154 DOI: 10.1042/bcj20170205] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 02/08/2018] [Accepted: 04/03/2018] [Indexed: 01/13/2023]
Abstract
Osteopontin (OPN) is an extracellular glycosylated phosphoprotein that promotes cell adhesion by interacting with several integrin receptors. We previously reported that an OPN mutant lacking five O-glycosylation sites (Thr134/Thr138/Thr143/Thr147/Thr152) in the threonine/proline-rich region increased cell adhesion activity and phosphorylation compared with the wild type. However, the role of O-glycosylation in cell adhesion activity and phosphorylation of OPN remains to be clarified. Here, we show that site-specific O-glycosylation in the threonine/proline-rich region of OPN affects its cell adhesion activity and phosphorylation independently and/or synergistically. Using site-directed mutagenesis, we found that OPN mutants with substitution sets of Thr134/Thr138 or Thr143/Thr147/Thr152 had decreased and increased cell adhesion activity, respectively. In contrast, the introduction of a single mutation into the O-glycosylation sites had no effect on OPN cell adhesion activity. An adhesion assay using function-blocking antibodies against αvβ3 and β1 integrins, as well as αvβ3 integrin-overexpressing A549 cells, revealed that site-specific O-glycosylation affected the association of OPN with the two integrins. Phosphorylation analyses using phos-tag and LC-MS/MS indicated that phosphorylation levels and sites were influenced by the O-glycosylation status, although the number of O-glycosylation sites was not correlated with the phosphorylation level in OPN. Furthermore, a correlation analysis between phosphorylation level and cell adhesion activity in OPN mutants with the site-specific O-glycosylation showed that they were not always correlated. These results provide conclusive evidence of a novel regulatory mechanism of cell adhesion activity and phosphorylation of OPN by site-specific O-glycosylation.
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fam20C participates in the shell formation in the pearl oyster, Pinctada fucata. Sci Rep 2018; 8:3563. [PMID: 29476076 PMCID: PMC5824888 DOI: 10.1038/s41598-018-21797-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 02/12/2018] [Indexed: 12/16/2022] Open
Abstract
Kinase-family with sequence similarity 20, member C (Fam20C) is a protein kinase, which can phosphorylate biomineralization related proteins in vertebrate animals. However, the function of Fam20C in invertebrate animals especially the role in biomineralization is still unknown. Herein, we cloned the cDNA of fam20C from the pearl oyster, Pinctada fucata. It is showed that the expression of fam20C in the mantle edge was much higher than other tissues. In situ hybridization showed that fam20C was expressed mostly in the outer epithelial cells of the middle fold, indicating it may play important roles in the shell formation. Besides, fam20C expression increased greatly in the D-shape stage of pearl oyster development, when the shell was first formed. During the shell repair process, the expression level of fam20C increased 1.5 times at 6 h after shell notching. Knockdown of fam20C in vivo by RNA interference resulted in abnormally stacking of calcium carbonate crystals at the edges of nacre tablets, showing direct evidence that fam20C participates in the shell formation. This study provides an insight into the role of kinase protein in the shell formation in mollusk and broaden our understanding of biomineralization mechanism.
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Maddala R, Skiba NP, Rao PV. Vertebrate Lonesome Kinase Regulated Extracellular Matrix Protein Phosphorylation, Cell Shape, and Adhesion in Trabecular Meshwork Cells. J Cell Physiol 2017; 232:2447-2460. [PMID: 27591737 PMCID: PMC5462548 DOI: 10.1002/jcp.25582] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022]
Abstract
Glaucoma, a leading cause of irreversible blindness, is commonly associated with elevated intraocular pressure (IOP) due to impaired aqueous humor (AH) drainage through the trabecular meshwork (TM). Although dysregulated production and organization of extracellular matrix (ECM) is presumed to increase resistance to AH outflow and elevate IOP by altering TM cell contractile and adhesive properties, it is not known whether regulation of ECM protein phosphorylation via the secretory vertebrate lonesome kinase (VLK) influences TM cellular characteristics. Here, we tested this possibility. Experiments carried out in this study reveal that the 32 kDa protein is a prominent VLK isoform detectable in lysates and conditioned media (CM) of human TM cells. Increased levels of VLK were observed in CM of TM cells subjected to cyclic mechanical stretch, or treated with dexamethasone, TGF-β2, and TM cells expressing constitutively active RhoA GTPase. Downregulation of VLK expression in TM cells using siRNA decreased tyrosine phosphorylation (TyrP) of ECM proteins and focal adhesions, and induced changes in cell shape in association with reduced levels of actin stress fibers and phospho-paxillin. VLK was also demonstrated to regulate TGF-β2-induced TyrP of ECM proteins. Taken together, these results suggest that VLK secretion can be regulated by external cues, intracellular signal proteins, and mechanical stretch, and VLK can in turn regulate TyrP of ECM proteins secreted by TM cells and control cell shape, actin stress fibers, and focal adhesions. These observations indicate a potential role for VLK in homeostasis of AH outflow and IOP, and in the pathobiology of glaucoma. J. Cell. Physiol. 232: 2447-2460, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rupalatha Maddala
- Department of Ophthalmology, Duke University School of Medicine. Durham, NC. USA. 27710
| | - Nikolai P. Skiba
- Department of Ophthalmology, Duke University School of Medicine. Durham, NC. USA. 27710
| | - Ponugoti Vasantha Rao
- Department of Ophthalmology, Duke University School of Medicine. Durham, NC. USA. 27710
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine. Durham, NC. USA. 27710
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Hanamura K, Washburn HR, Sheffler-Collins SI, Xia NL, Henderson N, Tillu DV, Hassler S, Spellman DS, Zhang G, Neubert TA, Price TJ, Dalva MB. Extracellular phosphorylation of a receptor tyrosine kinase controls synaptic localization of NMDA receptors and regulates pathological pain. PLoS Biol 2017; 15:e2002457. [PMID: 28719605 PMCID: PMC5515392 DOI: 10.1371/journal.pbio.2002457] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/12/2017] [Indexed: 11/18/2022] Open
Abstract
Extracellular phosphorylation of proteins was suggested in the late 1800s when it was demonstrated that casein contains phosphate. More recently, extracellular kinases that phosphorylate extracellular serine, threonine, and tyrosine residues of numerous proteins have been identified. However, the functional significance of extracellular phosphorylation of specific residues in the nervous system is poorly understood. Here we show that synaptic accumulation of GluN2B-containing N-methyl-D-aspartate receptors (NMDARs) and pathological pain are controlled by ephrin-B-induced extracellular phosphorylation of a single tyrosine (p*Y504) in a highly conserved region of the fibronectin type III (FN3) domain of the receptor tyrosine kinase EphB2. Ligand-dependent Y504 phosphorylation modulates the EphB-NMDAR interaction in cortical and spinal cord neurons. Furthermore, Y504 phosphorylation enhances NMDAR localization and injury-induced pain behavior. By mediating inducible extracellular interactions that are capable of modulating animal behavior, extracellular tyrosine phosphorylation of EphBs may represent a previously unknown class of mechanism mediating protein interaction and function. The activity of proteins can be finely and reversibly tuned by post-translational modifications. The attachment of phosphate groups to tyrosine residues is one of such modifications. While the existence of extracellular phosphoproteins has been known, the functional significance of extracellular phosphorylation is poorly understood. Here we describe a single extracellular tyrosine whose inducible phosphorylation may represent an archetype for a new class of mechanism mediating protein—protein interaction and regulating protein function. We show that the interaction between EphB2—which occurs upon receptor activation by its ligand ephrin-B—and the N-methyl-D-aspartate receptor (NMDAR) depends on extracellular phosphorylation of EphB2. This interaction regulates the localization of the NMDA receptor to synaptic sites in neurons. In vivo, EphB2 is phosphorylated in response to injury, and the subsequent up-regulation of the interaction between EphB2 and NMDA receptors enhances injury-induced pain behavior and mechanical hypersensitivity in mice. Importantly, our study defines a specific extracellular phosphorylation event as a mechanism driving protein interaction and suggests that extracellular phosphorylation of proteins is an underappreciated mechanism contributing to the development and function of the nervous system and synapse.
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Affiliation(s)
- Kenji Hanamura
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
- Department of Neurobiology and Behavior, Gunma University Graduate School of Medicine, Maebashi City, Gunma, Japan
| | - Halley R. Washburn
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Sean I. Sheffler-Collins
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
- Neuroscience Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Nan L. Xia
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Nathan Henderson
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Dipti V. Tillu
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Shayne Hassler
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Daniel S. Spellman
- Department of Cell Biology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York, United States of America
| | - Guoan Zhang
- Department of Cell Biology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York, United States of America
| | - Thomas A. Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York, United States of America
| | - Theodore J. Price
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Matthew B. Dalva
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Acevedo-Jake AM, Ngo DH, Hartgerink JD. Control of Collagen Triple Helix Stability by Phosphorylation. Biomacromolecules 2017; 18:1157-1161. [PMID: 28282118 DOI: 10.1021/acs.biomac.6b01814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The phosphorylation of the collagen triple helix plays an important role in collagen synthesis, assembly, signaling, and immune response, although no reports detailing the effect this modification has on the structure and stability of the triple helix exist. Here we investigate the changes in stability and structure resulting from the phosphorylation of collagen. Additionally, the formation of pairwise interactions between phosphorylated residues and lysine is examined. In all tested cases, phosphorylation increases helix stability. When charged-pair interactions are possible, stabilization via phosphorylation can play a very large role, resulting inasmuch as a 13.0 °C increase in triple helix stability. Two-dimensional NMR and molecular modeling are used to study the local structure of the triple helix. Our results suggest a mechanism of action for phosphorylation in the regulation of collagen and also expand upon our understanding of pairwise amino acid stabilization of the collagen triple helix.
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Affiliation(s)
- Amanda M Acevedo-Jake
- Department of Chemistry, Rice University 6100 Main Street, Houston, Texas 77005, United States
| | - Daniel H Ngo
- Department of Chemistry, Rice University 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey D Hartgerink
- Department of Chemistry, Rice University 6100 Main Street, Houston, Texas 77005, United States
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WHSC1L1-mediated EGFR mono-methylation enhances the cytoplasmic and nuclear oncogenic activity of EGFR in head and neck cancer. Sci Rep 2017; 7:40664. [PMID: 28102297 PMCID: PMC5244396 DOI: 10.1038/srep40664] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/09/2016] [Indexed: 12/18/2022] Open
Abstract
While multiple post-translational modifications have been reported to regulate the function of epidermal growth factor receptor (EGFR), the effect of protein methylation on its function has not been well characterized. In this study, we show that WHSC1L1 mono-methylates lysine 721 in the tyrosine kinase domain of EGFR, and that this methylation leads to enhanced activation of its downstream ERK cascade without EGF stimulation. We also show that EGFR K721 mono-methylation not only affects the function of cytoplasmic EGFR, but also that of nuclear EGFR. WHSC1L1-mediated methylation of EGFR in the nucleus enhanced its interaction with PCNA in squamous cell carcinoma of the head and neck (SCCHN) cells and resulted in enhanced DNA synthesis and cell cycle progression. Overall, our study demonstrates the multifaceted oncogenic function of the protein lysine methyltransferase WHSC1L1 in SCCHN, which is mediated through direct non-histone methylation of the EGFR protein with effects both in its cytoplasmic and nuclear functions.
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Giorgianni F, Beranova-Giorgianni S. Phosphoproteome Discovery in Human Biological Fluids. Proteomes 2016; 4:proteomes4040037. [PMID: 28248247 PMCID: PMC5260970 DOI: 10.3390/proteomes4040037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/11/2016] [Accepted: 11/23/2016] [Indexed: 01/07/2023] Open
Abstract
Phosphorylation plays a critical role in regulating protein function and thus influences a vast spectrum of cellular processes. With the advent of modern bioanalytical technologies, examination of protein phosphorylation on a global scale has become one of the major research areas. Phosphoproteins are found in biological fluids and interrogation of the phosphoproteome in biological fluids presents an exciting opportunity for discoveries that hold great potential for novel mechanistic insights into protein function in health and disease, and for translation to improved diagnostic and therapeutic approaches for the clinical setting. This review focuses on phosphoproteome discovery in selected human biological fluids: serum/plasma, urine, cerebrospinal fluid, saliva, and bronchoalveolar lavage fluid. Bioanalytical workflows pertinent to phosphoproteomics of biological fluids are discussed with emphasis on mass spectrometry-based approaches, and summaries of studies on phosphoproteome discovery in major fluids are presented.
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Affiliation(s)
- Francesco Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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Zhou J, Du X, Berciu C, He H, Shi J, Nicastro D, Xu B. Enzyme-Instructed Self-Assembly for Spatiotemporal Profiling of the Activities of Alkaline Phosphatases on Live Cells. Chem 2016; 1:246-263. [PMID: 28393126 DOI: 10.1016/j.chempr.2016.07.003] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Alkaline phosphatase (ALP), an ectoenzyme, plays important roles in biology. But there is no activity probes for imaging ALPs in live cell environment due to the diffusion and cytotoxicity of current probes. Here we report the profiling of the activities of ALPs on live cells by enzyme-instructed self-assembly (EISA) of a D-peptidic derivative that forms fluorescent, non-diffusive nanofibrils. Our study reveals the significantly higher activities of ALP on cancer cells than on stromal cells in their co-culture and shows an inherent and dynamic difference in ALP activities between drug sensitive and resistant cancer cells or between cancer cells with and without hormonal stimulation. Being complementary to genomic profiling of cells, EISA, as a reaction-diffusion controlled process, achieves high spatiotemporal resolution for profiling activities of ALPs of live cells at single cell level. The activity probes of ALP contribute to understanding the reversible phosphorylation/dephosphorylation in the extracellular domains that is an emerging frontier in biomedicine.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
| | - Xuewen Du
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
| | - Cristina Berciu
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
| | | | - Bing Xu
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
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Trost B, Maleki F, Kusalik A, Napper S. DAPPLE 2: a Tool for the Homology-Based Prediction of Post-Translational Modification Sites. J Proteome Res 2016; 15:2760-7. [PMID: 27367363 DOI: 10.1021/acs.jproteome.6b00304] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The post-translational modification of proteins is critical for regulating their function. Although many post-translational modification sites have been experimentally determined, particularly in certain model organisms, experimental knowledge of these sites is severely lacking for many species. Thus, it is important to be able to predict sites of post-translational modification in such species. Previously, we described DAPPLE, a tool that facilitates the homology-based prediction of one particular post-translational modification, phosphorylation, in an organism of interest using known phosphorylation sites from other organisms. Here, we describe DAPPLE 2, which expands and improves upon DAPPLE in three major ways. First, it predicts sites for many post-translational modifications (20 different types) using data from several sources (15 online databases). Second, it has the ability to make predictions approximately 2-7 times faster than DAPPLE depending on the database size and the organism of interest. Third, it simplifies and accelerates the process of selecting predicted sites of interest by categorizing them based on gene ontology terms, keywords, and signaling pathways. We show that DAPPLE 2 can successfully predict known human post-translational modification sites using, as input, known sites from species that are either closely (e.g., mouse) or distantly (e.g., yeast) related to humans. DAPPLE 2 can be accessed at http://saphire.usask.ca/saphire/dapple2 .
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Affiliation(s)
- Brett Trost
- Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada
| | - Farhad Maleki
- Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada
| | - Anthony Kusalik
- Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization, ‡Department of Computer Science, and §Department of Biochemistry, University of Saskatchewan , Saskatoon, SK S7N 5A2, Canada
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38
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Beekmann K, de Haan LHJ, Actis-Goretta L, van Bladeren PJ, Rietjens IMCM. Effect of Glucuronidation on the Potential of Kaempferol to Inhibit Serine/Threonine Protein Kinases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:1256-1263. [PMID: 26808477 DOI: 10.1021/acs.jafc.5b05456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To study the effect of metabolic conjugation of flavonoids on the potential to inhibit protein kinase activity, the inhibitory effects of the dietary flavonol kaempferol and its major plasma conjugate kaempferol-3-O-glucuronide on protein kinases were studied. To this end, the inhibition of the phosphorylation activity of recombinant protein kinase A (PKA) and of cell lysate from the hepatocellular carcinoma cell line HepG2 on 141 putative serine/threonine phosphorylation sites derived from human proteins was assessed. Glucuronidation reduced the inhibitory potency of kaempferol on the phosphorylation activity of PKA and HepG2 lysate on average about 16 and 3.5 times, respectively, but did not appear to affect the target selectivity for kinases present in the lysate. The data demonstrate that, upon glucuronidation, kaempferol retains part of its intrinsic kinase inhibition potential, which implies that K3G does not necessarily need to be deconjugated to the aglycone for a potential inhibitory effect on protein kinases.
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Affiliation(s)
- Karsten Beekmann
- Division of Toxicology, Wageningen University , Postbus 8000, 6700EA, Wageningen, The Netherlands
| | - Laura H J de Haan
- Division of Toxicology, Wageningen University , Postbus 8000, 6700EA, Wageningen, The Netherlands
| | - Lucas Actis-Goretta
- Nestlé Research Center, Nestec Ltd., Vers-chez-les-Blanc, Case Postale 44, 1000 Lausanne 26, Switzerland
| | - Peter J van Bladeren
- Division of Toxicology, Wageningen University , Postbus 8000, 6700EA, Wageningen, The Netherlands
- Nestlé Research Center, Nestec Ltd., Vers-chez-les-Blanc, Case Postale 44, 1000 Lausanne 26, Switzerland
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University , Postbus 8000, 6700EA, Wageningen, The Netherlands
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Abstract
Members of the four-jointed and VLK families of secretory pathway kinases appear to be responsible for the phosphorylation of secreted proteins and proteoglycans. These enzymes have been implicated in many biological processes and mutations in several of these kinases cause human diseases. Here, we describe methods to purify and assay two members of the four-jointed family of secretory kinases: the Fam20C protein kinase and the Fam20B proteoglycan kinase.
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Affiliation(s)
- Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75390-9148, USA.
| | - Jianzhong Wen
- Discovery Bioanalytics, Merck and Co, Rahway, NJ, USA
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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40
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Liao HW, Hsu JM, Xia W, Wang HL, Wang YN, Chang WC, Arold ST, Chou CK, Tsou PH, Yamaguchi H, Fang YF, Lee HJ, Lee HH, Tai SK, Yang MH, Morelli MP, Sen M, Ladbury JE, Chen CH, Grandis JR, Kopetz S, Hung MC. PRMT1-mediated methylation of the EGF receptor regulates signaling and cetuximab response. J Clin Invest 2015; 125:4529-43. [PMID: 26571401 DOI: 10.1172/jci82826] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/17/2015] [Indexed: 01/08/2023] Open
Abstract
Posttranslational modifications to the intracellular domain of the EGFR are known to regulate EGFR functions; however, modifications to the extracellular domain and their effects remain relatively unexplored. Here, we determined that methylation at R198 and R200 of the EGFR extracellular domain by protein arginine methyltransferase 1 (PRMT1) enhances binding to EGF and subsequent receptor dimerization and signaling activation. In a mouse orthotopic colorectal cancer xenograft model, expression of a methylation-defective EGFR reduced tumor growth. Moreover, increased EGFR methylation sustained signaling activation and cell proliferation in the presence of the therapeutic EGFR monoclonal antibody cetuximab. In colorectal cancer patients, EGFR methylation level also correlated with a higher recurrence rate after cetuximab treatment and reduced overall survival. Together, these data indicate that R198/R200 methylation of the EGFR plays an important role in regulating EGFR functionality and resistance to cetuximab treatment.
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Couto N, Schooling SR, Dutcher JR, Barber J. Proteome Profiles of Outer Membrane Vesicles and Extracellular Matrix of Pseudomonas aeruginosa Biofilms. J Proteome Res 2015; 14:4207-22. [PMID: 26303878 DOI: 10.1021/acs.jproteome.5b00312] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present work, two different proteomic platforms, gel-based and gel-free, were used to map the matrix and outer membrane vesicle exoproteomes of Pseudomonas aeruginosa PAO1 biofilms. These two proteomic strategies allowed us a confident identification of 207 and 327 proteins from enriched outer membrane vesicles and whole matrix isolated from biofilms. Because of the physicochemical characteristics of these subproteomes, the two strategies showed complementarity, and thus, the most comprehensive analysis of P. aeruginosa exoproteome to date was achieved. Under our conditions, outer membrane vesicles contribute approximately 20% of the whole matrix proteome, demonstrating that membrane vesicles are an important component of the matrix. The proteomic profiles were analyzed in terms of their biological context, namely, a biofilm. Accordingly relevant metabolic processes involved in cellular adaptation to the biofilm lifestyle as well as those related to P. aeruginosa virulence capabilities were a key feature of the analyses. The diversity of the matrix proteome corroborates the idea of high heterogeneity within the biofilm; cells can display different levels of metabolism and can adapt to local microenvironments making this proteomic analysis challenging. In addition to analyzing our own primary data, we extend the analysis to published data by other groups in order to deepen our understanding of the complexity inherent within biofilm populations.
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Affiliation(s)
- Narciso Couto
- Michael Barber Centre for Mass Spectrometry, Manchester Institute for Biotechnology, University of Manchester , Princess Road, Manchester, M1 7DN, U.K
| | - Sarah R Schooling
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph , Guelph, ON N1G 2W1, Canada.,Department of Physics, University of Guelph , Guelph, ON N1G 2W1, Canada
| | - John R Dutcher
- Department of Physics, University of Guelph , Guelph, ON N1G 2W1, Canada
| | - Jill Barber
- Michael Barber Centre for Mass Spectrometry, Manchester Institute for Biotechnology, University of Manchester , Princess Road, Manchester, M1 7DN, U.K.,Manchester Pharmacy School, University of Manchester , Stopford Building, Oxford Road, Manchester, M13 9PT, U.K
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Design, validation and efficacy of bisubstrate inhibitors specifically affecting ecto-CK2 kinase activity. Biochem J 2015; 471:415-30. [PMID: 26349539 DOI: 10.1042/bj20141127] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 09/08/2015] [Indexed: 11/17/2022]
Abstract
By derivatizing the purely competitive CK2 inhibitor N1-(4,5,6,7-tetrabromo-1H-benzimidazol-2-yl)-propane-1,3-diamine (K137) at its 3-amino position with a peptidic fragment composed of three or four glutamic or aspartic acid residues, a new family of bisubstrate inhibitors has been generated whose ability to simultaneously interact with both the ATP and the phosphoacceptor substrate-binding sites has been probed by running mixed competition kinetics and by mutational mapping of the kinase residues implicated in substrate recognition. The most effective bisubstrate inhibitor, K137-E4, interacts with three functional regions of the kinase: the hydrophobic pocket close to the ATP-binding site, the basic residues of the p+1 loop that recognizes the acidic determinant at position n+1 and the basic residues of α-helixC that recognize the acidic determinant at position n+3. Compared with the parent inhibitor (K137), K137-E4 is severalfold more potent (IC50 25 compared with 130 nM) and more selective, failing to inhibit any other kinase as drastically as CK2 out of 140 enzymes, whereas 35 kinases are inhibited more potently than CK2 by K137. K137-E4 is unable to penetrate the cell and to inhibit endogenous CK2, its pro-apoptotic efficacy being negligible compared with cell-permeant inhibitors; however, it readily inhibits ecto-CK2 on the outer cell surface, reducing the phosphorylation of several external phosphoproteins. Inhibition of ecto-CK2 by K137-E4 is accompanied by a slower migration of cancer cells as judged by wound healing assays. On the basis of the cellular responses to K137-E4, we conclude that ecto-CK2 is implicated in cell motility, whereas its contribution to the pro-survival role of CK2 is negligible.
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Yalak G, Olsen BR. Proteomic database mining opens up avenues utilizing extracellular protein phosphorylation for novel therapeutic applications. J Transl Med 2015; 13:125. [PMID: 25927841 PMCID: PMC4427915 DOI: 10.1186/s12967-015-0482-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/07/2015] [Indexed: 02/07/2023] Open
Abstract
Recent advances in extracellular signaling suggest that extracellular protein phosphorylation is a regulatory mechanism outside the cell. The list of reported active extracellular protein kinases and phosphatases is growing, and phosphorylation of an increasing number of extracellular matrix molecules and extracellular domains of trans-membrane proteins is being documented. Here, we use public proteomic databases, collagens – the major components of the extracellular matrix, extracellular signaling molecules and proteolytic enzymes as examples to assess what the roles of extracellular protein phosphorylation may be in health and disease. We propose that novel tools be developed to help assess the role of extracellular protein phosphorylation and translate the findings for biomedical applications. Furthermore, we suggest that the phosphorylation state of extracellular matrix components as well as the presence of extracellular kinases be taken into account when designing translational medical applications.
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Affiliation(s)
- Garif Yalak
- Department of Developmental Biology, Harvard Medical School/Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA.
| | - Bjorn R Olsen
- Department of Developmental Biology, Harvard Medical School/Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA.
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Bordoli MR, Yum J, Breitkopf SB, Thon JN, Italiano JE, Xiao J, Worby C, Wong SK, Lin G, Edenius M, Keller TL, Asara JM, Dixon JE, Yeo CY, Whitman M. A secreted tyrosine kinase acts in the extracellular environment. Cell 2015; 158:1033-1044. [PMID: 25171405 DOI: 10.1016/j.cell.2014.06.048] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/06/2014] [Accepted: 06/20/2014] [Indexed: 11/17/2022]
Abstract
Although tyrosine phosphorylation of extracellular proteins has been reported to occur extensively in vivo, no secreted protein tyrosine kinase has been identified. As a result, investigation of the potential role of extracellular tyrosine phosphorylation in physiological and pathological tissue regulation has not been possible. Here, we show that VLK, a putative protein kinase previously shown to be essential in embryonic development, is a secreted protein kinase, with preference for tyrosine, that phosphorylates a broad range of secreted and ER-resident substrate proteins. We find that VLK is rapidly and quantitatively secreted from platelets in response to stimuli and can tyrosine phosphorylate coreleased proteins utilizing endogenous as well as exogenous ATP sources. We propose that discovery of VLK activity provides an explanation for the extensive and conserved pattern of extracellular tyrosine phosphophorylation seen in vivo, and extends the importance of regulated tyrosine phosphorylation into the extracellular environment.
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Affiliation(s)
- Mattia R Bordoli
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Jina Yum
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA; Department of Life Science and Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan N Thon
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Joseph E Italiano
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Vascular Biology Program, Department of Surgery, Children's Hospital, Boston, MA 02115, USA
| | - Junyu Xiao
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Carolyn Worby
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Swee-Kee Wong
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Grace Lin
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Maja Edenius
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Tracy L Keller
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Chang-Yeol Yeo
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA; Department of Life Science and Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA.
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45
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Sanjoh M, Iizuka D, Matsumoto A, Miyahara Y. Boronate based metal-free platform for diphosphate-specific molecular recognitions. Org Lett 2015; 17:588-91. [PMID: 25594134 DOI: 10.1021/ol5036003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A reversible boronate-diol interaction provides a versatile synthetic platform for molecular recognitions whose binding specificity can be molecularly tailored. We found that boronate derivatives with relatively strong acidity generally undergo a diphosphate-specific recognition among other phosphates under weakly acidic pH conditions, a feature relevant to DNA sequencing. (11)B and (31)P NMR studies identified "tetrahedral boronate and divalent diphosphate" as a pair responsible for forming a 1:1 stoichiometric complex, which manifests as a unique pH-dependent stability.
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Affiliation(s)
- Mai Sanjoh
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University , Kanda-surugadai 2-3-10, Chiyoda-ku, Tokyo 101-0062, Japan
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46
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Yalak G, Vogel V. Ectokinases as novel cancer markers and drug targets in cancer therapy. Cancer Med 2014; 4:404-14. [PMID: 25504773 PMCID: PMC4380966 DOI: 10.1002/cam4.368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 01/13/2023] Open
Abstract
While small-molecule kinase inhibitors became the most prominent anticancer drugs, novel combinatorial strategies need to be developed as the fight against cancer is not yet won. We review emerging literature showing that the release of several ectokinases is significantly upregulated in body fluids from cancer patients and that they leave behind their unique signatures on extracellular matrix (ECM) proteins. Our analysis of proteomic data reveals that fibronectin is heavily phosphorylated in cancer tissues particularly within its growth factor binding sites and on domains that regulate fibrillogenesis. We are thus making the case that cancer is not only a disease of cells but also of the ECM. Targeting extracellular kinases or the extracellular signatures they leave behind might thus create novel opportunities in cancer diagnosis as well as new avenues to interfere with cancer progression and malignancy.
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Affiliation(s)
- Garif Yalak
- Harvard Medical School/Harvard School of Dental Medicine, Department of Developmental Biology, Harvard University, Boston, Massachusetts, 02115; Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Switzerland
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Amtul Z, Rahman AU. Neural Plasticity and Memory: Is Memory Encoded in Hydrogen Bonding Patterns? Neuroscientist 2014; 22:9-18. [PMID: 25168338 DOI: 10.1177/1073858414547934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Current models of memory storage recognize posttranslational modification vital for short-term and mRNA translation for long-lasting information storage. However, at the molecular level things are quite vague. A comprehensive review of the molecular basis of short and long-lasting synaptic plasticity literature leads us to propose that the hydrogen bonding pattern at the molecular level may be a permissive, vital step of memory storage. Therefore, we propose that the pattern of hydrogen bonding network of biomolecules (glycoproteins and/or DNA template, for instance) at the synapse is the critical edifying mechanism essential for short- and long-term memories. A novel aspect of this model is that nonrandom impulsive (or unplanned) synaptic activity functions as a synchronized positive-feedback rehearsal mechanism by revising the configurations of the hydrogen bonding network by tweaking the earlier tailored hydrogen bonds. This process may also maintain the elasticity of the related synapses involved in memory storage, a characteristic needed for such networks to alter intricacy and revise endlessly. The primary purpose of this review is to stimulate the efforts to elaborate the mechanism of neuronal connectivity both at molecular and chemical levels.
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Affiliation(s)
- Zareen Amtul
- Department of Psychiatry, University of Western Ontario, London, Ontario, Canada H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Atta-Ur Rahman
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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48
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Masson JF, Breault-Turcot J, Faid R, Poirier-Richard HP, Yockell-Lelièvre H, Lussier F, Spatz JP. Plasmonic Nanopipette Biosensor. Anal Chem 2014; 86:8998-9005. [DOI: 10.1021/ac501473c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jean-Francois Masson
- Department
of Chemistry, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montreal, QC, Canada, H3C 3J7
- Department
of New Materials and Biosystems, Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
- Centre for Self-Assembled
Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada, H3A 2K6
| | - Julien Breault-Turcot
- Department
of Chemistry, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montreal, QC, Canada, H3C 3J7
- Department
of New Materials and Biosystems, Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
| | - Rita Faid
- Department
of Chemistry, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montreal, QC, Canada, H3C 3J7
| | - Hugo-Pierre Poirier-Richard
- Department
of Chemistry, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montreal, QC, Canada, H3C 3J7
| | - Hélène Yockell-Lelièvre
- Department
of Chemistry, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montreal, QC, Canada, H3C 3J7
| | - Félix Lussier
- Department
of Chemistry, Université de Montréal, C.P. 6128 Succ. Centre-Ville, Montreal, QC, Canada, H3C 3J7
| | - Joachim P. Spatz
- Department
of New Materials and Biosystems, Max Planck Institute for Intelligent Systems, Heisenbergstr. 3, 70569 Stuttgart, Germany
- Department
of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer
Feld 253, 69120 Heidelberg, Germany
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49
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Sadeqzadeh E, de Bock CE, O'Donnell MR, Timofeeva A, Burns GF, Thorne RF. FAT1 cadherin is multiply phosphorylated on its ectodomain but phosphorylation is not catalysed by the four-jointed homologue. FEBS Lett 2014; 588:3511-7. [PMID: 25150169 DOI: 10.1016/j.febslet.2014.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/11/2014] [Indexed: 01/15/2023]
Abstract
The interaction between the Drosophila cadherins fat and dachsous is regulated by phosphorylation of their respective ectodomains, a process catalysed by the atypical kinase four-jointed. Given that many signalling functions are conserved between Drosophila and vertebrate Fat cadherins, we sought to determine whether ectodomain phosphorylation is conserved in FAT1 cadherin, and also whether FJX1, the vertebrate orthologue of four-jointed, was involved in such phosphorylation events. Potential Fj consensus phosphorylation motifs were identified in FAT1 and biochemical experiments revealed the presence of phosphoserine and phosphothreonine residues in its extracellular domain. However, silencing FJX1 did not influence the levels of FAT1 ectodomain phosphorylation, indicating that other mechanisms are likely responsible.
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Affiliation(s)
- Elham Sadeqzadeh
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Charles E de Bock
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Maureen R O'Donnell
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Anna Timofeeva
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Gordon F Burns
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Rick F Thorne
- Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia; School of Environmental & Life Sciences, University of Newcastle, Ourimbah, NSW 2258, Australia.
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50
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Yalak G, Ehrlich YH, Olsen BR. Ecto-protein kinases and phosphatases: an emerging field for translational medicine. J Transl Med 2014; 12:165. [PMID: 24923278 PMCID: PMC4071215 DOI: 10.1186/1479-5876-12-165] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 05/29/2014] [Indexed: 12/30/2022] Open
Abstract
Progress in translational research has led to effective new treatments of a large number of diseases. Despite this progress, diseases including cancer and cardiovascular disorders still are at the top in death statistics and disorders such as osteoporosis and osteoarthritis represent an increasing disease burden in the aging population. Novel strategies in research are needed more than ever to overcome such diseases. The growing field of extracellular protein phosphorylation provides excellent opportunities to make major discoveries of disease mechanisms that can lead to novel therapies. Reversible phosphorylation/dephosphorylation of sites in the extracellular domains of matrix, cell-surface and trans-membrane proteins is emerging as a critical regulatory mechanism in health and disease. Moreover, a new concept is emerging from studies of extracellular protein phosphorylation: in cells where ATP is stored within secretory vesicles and released by exocytosis upon cell-stimulation, phosphorylation of extracellular proteins can operate as a messenger operating uniquely in signaling pathways responsible for long-term cellular adaptation. Here, we highlight new concepts that arise from this research, and discuss translation of the findings into clinical applications such as development of diagnostic disease markers and next-generation drugs.
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Affiliation(s)
| | | | - Bjorn R Olsen
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA 02115, USA.
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