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He F, Zhang F, Liao Y, Tang MS, Wu XR. Structural or functional defects of PTEN in urothelial cells lacking P53 drive basal/squamous-subtype muscle-invasive bladder cancer. Cancer Lett 2022; 550:215924. [PMID: 36195293 PMCID: PMC9813857 DOI: 10.1016/j.canlet.2022.215924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/10/2022] [Accepted: 09/19/2022] [Indexed: 01/07/2023]
Abstract
Muscle-invasive bladder cancer (MIBC) exhibits strong inter- and intra-tumor heterogeneity that affects biological behaviors, therapeutic responses, and prognoses. Mutations that activate RTK-RAS-PI3K and inactivate P19-P53-P21 coexist in 60-70% of MIBC. By time-controlled ablation of Tp53 and Pten, singly or combined, in adult mouse urothelium, we found that Tp53 loss alone produced no abnormality. While Pten loss elicited hyperplasia, it synergized with Tp53 loss to trigger 100% penetrant MIBC that exhibited basal/squamous features that resembled its human counterpart. Furthermore, PTEN was inactivated in human MIBC cell lines and specimens primarily by hyperphosphorylation of the C-terminus. Mutated or tailless PTEN incapable of C-terminal phosphorylation demonstrated increased inhibition of proliferation and invasion than full-length PTEN in cultured MIBC cells. In xenograft and transgenic mice, tailless PTEN, but not full-length PTEN, prevented further growth in established tumors. Collectively, deficiencies of both PTEN and P53 drive basal/squamous subtype MIBC. PTEN is inactivated by C-terminal hyperphosphorylation, and this modification may serve as a biomarker for subtyping MIBC and predicting tumor progression. Tailless PTEN is a potential molecular therapeutic for tumors, such as bladder cancer (BC), that can be readily accessed.
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Affiliation(s)
- Feng He
- Department of Urology, New York University School of Medicine, New York, NY, 10016, USA; Veterans Affairs New York Harbor Healthcare System, Manhattan Campus, New York, NY, 10010, USA
| | - Fenglin Zhang
- Department of Urology, New York University School of Medicine, New York, NY, 10016, USA
| | - Yi Liao
- Department of Urology, New York University School of Medicine, New York, NY, 10016, USA
| | - Moon-Shong Tang
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, 10010, USA
| | - Xue-Ru Wu
- Department of Urology, New York University School of Medicine, New York, NY, 10016, USA; Department of Pathology, New York University School of Medicine, New York, NY, 10016, USA; Veterans Affairs New York Harbor Healthcare System, Manhattan Campus, New York, NY, 10010, USA.
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2
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Wu Y, Ma Y, Li J, Zhou XL, Li L, Xu PX, Li XR, Xue M. The bioinformatics and metabolomics research on anti-hypoxic molecular mechanisms of Salidroside via regulating the PTEN mediated PI3K/Akt/NF-κB signaling pathway. Chin J Nat Med 2021; 19:442-453. [PMID: 34092295 DOI: 10.1016/s1875-5364(21)60043-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Indexed: 12/08/2022]
Abstract
Salidroside (SAL), a major bioactive compound of Rhodiola crenulata, has significant anti-hypoxia effect, however, its underlying molecular mechanism has not been elucidated. In order to explore the protective mechanism of SAL, the lactate dehydrogenase (LDH), reactive oxygen species (ROS), superoxide dismutase (SOD) and hypoxia-induced factor 1α (HIF-1α) were measured to establish the PC12 cell hypoxic model. Cell staining and cell viability analyses were performed to evaluate the protective effects of SAL. The metabolomics and bioinformatics methods were used to explore the protective effects of salidroside under hypoxia condition. The metabolite-protein interaction networks were further established and the protein expression level was examined by Western blotting. The results showed that 59 endogenous metabolites changed and the expression of the hub proteins of CK2, p-PTEN/PTEN, PI3K, p-Akt/Akt, NF-κB p65 and Bcl-2 were increased, suggesting that SAL could increase the expression of CK2, which induced the phosphorylation and inactivation of PTEN, reduced the inhibitory effect on PI3K signaling pathways and activated the PI3K/Akt/NF-κB survival signaling pathway. Our study provided an important insight to reveal the protective molecular mechanism of SAL as a novel drug candidate.
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Affiliation(s)
- Yi Wu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Yi Ma
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jing Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xue-Lin Zhou
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China; Beijing Engineering Research Center for Nerve System Drugs, Beijing 100053, China
| | - Lei Li
- Central Laboratory, Capital Medical University, Beijing 100069, China
| | - Ping-Xiang Xu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China; Beijing Engineering Research Center for Nerve System Drugs, Beijing 100053, China
| | - Xiao-Rong Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China; Beijing Engineering Research Center for Nerve System Drugs, Beijing 100053, China.
| | - Ming Xue
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China; Beijing Engineering Research Center for Nerve System Drugs, Beijing 100053, China.
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3
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Huang B, Liu Y, Yao H, Zhao Y. NMR-based investigation into protein phosphorylation. Int J Biol Macromol 2020; 145:53-63. [DOI: 10.1016/j.ijbiomac.2019.12.171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
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Abstract
Phosphorylation is a ubiquitous posttranslational modification that is essential for the regulation of many cellular processes. The human genome consists of more than 200,000 phosphorylation sites, whose phosphorylation is tightly controlled by ≥500 kinases and ~200 phosphatases. Given the large number of phosphorylation sites and the key role phosphorylation plays in regulating cellular processes, it is essential to characterize the impact of phosphorylation on substrate structure, dynamics, and function. However, a major challenge is the large-scale production of phosphorylated proteins in vitro for these structural, functional, and dynamic studies. Here, we describe an efficient protocol used routinely in our laboratory for the production of phosphorylated proteins. We also describe the methods used for identifying, characterizing, and separating the resulting phosphorylated proteins for subsequent studies.
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Affiliation(s)
- Ganesan Senthil Kumar
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States.
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5
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Cox N, Kuemmerle R, Millard P, Cahoreau E, François JM, Parrou JL, Lippens G. Integrated pH Measurement during Reaction Monitoring with Dual-Reception 1H- 31P NMR Spectroscopy. Anal Chem 2019; 91:3959-3963. [PMID: 30767511 DOI: 10.1021/acs.analchem.8b05147] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simultaneous detection of 1H and 31P NMR signals through a dual-detection scheme with two receivers allows monitoring of both the signals of a molecule and the pH of the solution through the resonance of the inorganic phosphate. We evaluate here the method in terms of sensitivity and ease of implementation and show that the additional information obtained without any loss of information or increase in measuring time can be of practical importance in a number of biochemical systems.
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Affiliation(s)
- Neil Cox
- LISBP , Université de Toulouse, CNRS, INRA, INSA , 135 avenue de Rangueil , 31077 Toulouse CEDEX 04, France
| | - Rainer Kuemmerle
- Bruker Biospin AG , Industriestrasse 26 , 8117 Faellanden , Switzerland
| | - Pierre Millard
- LISBP , Université de Toulouse, CNRS, INRA, INSA , 135 avenue de Rangueil , 31077 Toulouse CEDEX 04, France
| | - Edern Cahoreau
- LISBP , Université de Toulouse, CNRS, INRA, INSA , 135 avenue de Rangueil , 31077 Toulouse CEDEX 04, France
| | - Jean-Marie François
- LISBP , Université de Toulouse, CNRS, INRA, INSA , 135 avenue de Rangueil , 31077 Toulouse CEDEX 04, France
| | - Jean-Luc Parrou
- LISBP , Université de Toulouse, CNRS, INRA, INSA , 135 avenue de Rangueil , 31077 Toulouse CEDEX 04, France
| | - Guy Lippens
- LISBP , Université de Toulouse, CNRS, INRA, INSA , 135 avenue de Rangueil , 31077 Toulouse CEDEX 04, France
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Gibbs EB, Lu F, Portz B, Fisher MJ, Medellin BP, Laremore TN, Zhang YJ, Gilmour DS, Showalter SA. Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain. Nat Commun 2017; 8:15233. [PMID: 28497798 PMCID: PMC5437310 DOI: 10.1038/ncomms15233] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/09/2017] [Indexed: 01/25/2023] Open
Abstract
The carboxy-terminal domain (CTD) of the RNA polymerase II (Pol II) large subunit cycles through phosphorylation states that correlate with progression through the transcription cycle and regulate nascent mRNA processing. Structural analyses of yeast and mammalian CTD are hampered by their repetitive sequences. Here we identify a region of the Drosophila melanogaster CTD that is essential for Pol II function in vivo and capitalize on natural sequence variations within it to facilitate structural analysis. Mass spectrometry and NMR spectroscopy reveal that hyper-Ser5 phosphorylation transforms the local structure of this region via proline isomerization. The sequence context of this switch tunes the activity of the phosphatase Ssu72, leading to the preferential de-phosphorylation of specific heptads. Together, context-dependent conformational switches and biased dephosphorylation suggest a mechanism for the selective recruitment of cis-proline-specific regulatory factors and region-specific modulation of the CTD code that may augment gene regulation in developmentally complex organisms.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Feiyue Lu
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Bede Portz
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael J Fisher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Brenda P Medellin
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Tatiana N Laremore
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - David S Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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7
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Gibbs EB, Cook EC, Showalter SA. Application of NMR to studies of intrinsically disordered proteins. Arch Biochem Biophys 2017; 628:57-70. [PMID: 28502465 DOI: 10.1016/j.abb.2017.05.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/20/2022]
Abstract
The prevalence of intrinsically disordered protein regions, particularly in eukaryotic proteins, and their clear functional advantages for signaling and gene regulation have created an imperative for high-resolution structural and mechanistic studies. NMR spectroscopy has played a central role in enhancing not only our understanding of the intrinsically disordered native state, but also how that state contributes to biological function. While pathological functions associated with protein aggregation are well established, it has recently become clear that disordered regions also mediate functionally advantageous assembly into high-order structures that promote the formation of membrane-less sub-cellular compartments and even hydrogels. Across the range of functional assembly states accessed by disordered regions, post-translational modifications and regulatory macromolecular interactions, which can also be investigated by NMR spectroscopy, feature prominently. Here we will explore the many ways in which NMR has advanced our understanding of the physical-chemical phase space occupied by disordered protein regions and provide prospectus for the future role of NMR in this emerging and exciting field.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik C Cook
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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Danis C, Despres C, Bessa LM, Malki I, Merzougui H, Huvent I, Qi H, Lippens G, Cantrelle FX, Schneider R, Hanoulle X, Smet-Nocca C, Landrieu I. Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins. J Vis Exp 2016. [PMID: 28060278 DOI: 10.3791/55001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aggregates of the neuronal Tau protein are found inside neurons of Alzheimer's disease patients. Development of the disease is accompanied by increased, abnormal phosphorylation of Tau. In the course of the molecular investigation of Tau functions and dysfunctions in the disease, nuclear magnetic resonance (NMR) spectroscopy is used to identify the multiple phosphorylations of Tau. We present here detailed protocols of recombinant production of Tau in bacteria, with isotopic enrichment for NMR studies. Purification steps that take advantage of Tau's heat stability and high isoelectric point are described. The protocol for in vitro phosphorylation of Tau by recombinant activated ERK2 allows for generating multiple phosphorylations. The protein sample is ready for data acquisition at the issue of these steps. The parameter setup to start recording on the spectrometer is considered next. Finally, the strategy to identify phosphorylation sites of modified Tau, based on NMR data, is explained. The benefit of this methodology compared to other techniques used to identify phosphorylation sites, such as immuno-detection or mass spectrometry (MS), is discussed.
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Affiliation(s)
- Clément Danis
- UMR8576, CNRS, Lille University; UMR-S1172, INSERM CNRS, Lille University
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Abstract
Discovered in 1997, PTEN remains one of the most studied tumor suppressors. In this issue of Methods in Molecular Biology, we assembled a series of papers describing various clinical and experimental approaches to studying PTEN function. Due to its broad expression, regulated subcellular localization, and intriguing phosphatase activity, methodologies aimed at PTEN study have often been developed in the context of mutations affecting various aspects of its regulation, found in patients burdened with PTEN loss-driven tumors. PTEN's extensive posttranslational modifications and dynamic localization pose unique challenges for studying PTEN features in isolation and necessitate considerable development of experimental systems to enable controlled characterization. Nevertheless, ongoing efforts towards the development of PTEN knockout and knock-in animals and cell lines, antibodies, and enzymatic assays have facilitated a huge body of work, which continues to unravel the fascinating biology of PTEN.
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10
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Chia YCJ, Catimel B, Lio DSS, Ang CS, Peng B, Wu H, Zhu HJ, Cheng HC. The C-terminal tail inhibitory phosphorylation sites of PTEN regulate its intrinsic catalytic activity and the kinetics of its binding to phosphatidylinositol-4,5-bisphosphate. Arch Biochem Biophys 2015; 587:48-60. [PMID: 26471078 DOI: 10.1016/j.abb.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/04/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
Dephosphorylation of four major C-terminal tail sites and occupancy of the phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]-binding site of PTEN cooperate to activate its phospholipid phosphatase activity and facilitate its recruitment to plasma membrane. Our investigation of the mechanism by which phosphorylation of these C-terminal sites controls the PI(4,5)P2-binding affinity and catalytic activity of PTEN resulted in the following findings. First, dephosphorylation of all four sites leads to full activation; and phosphorylation of any one site significantly reduces the intrinsic catalytic activity of PTEN. These findings suggest that coordinated inhibition of the upstream protein kinases and activation of the protein phosphatases targeting the four sites are needed to fully activate PTEN phosphatase activity. Second, PI(4,5)P2 cannot activate the phosphopeptide phosphatase activity of PTEN, suggesting that PI(4,5)P2 can only activate the phospholipid phosphatase activity but not the phosphoprotein phosphatase activity of PTEN. Third, dephosphorylation of all four sites significantly decreases the affinity of PTEN for PI(4,5)P2. Since PI(4,5)P2 is a major phospholipid co-localizing with the phospholipid- and phosphoprotein-substrates in plasma membrane, we hypothesise that the reduced affinity facilitates PTEN to "hop" on the plasma membrane to dephosphorylate these substrates.
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Affiliation(s)
- Yeong-Chit Joel Chia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bruno Catimel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Daisy Sio Seng Lio
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ching-Seng Ang
- Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Benjamin Peng
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hong Wu
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hong-Jian Zhu
- Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria 3052, Australia
| | - Heung-Chin Cheng
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria 3010, Australia.
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Pulido R. A rapid guide to PTEN function. Methods 2015; 77-78:1-2. [PMID: 25843296 DOI: 10.1016/j.ymeth.2015.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Rafael Pulido
- Biocruces Health Research Institute, Barakaldo, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
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