1
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Kantner DS, Megill E, Bostwick A, Yang V, Bekeova C, Van Scoyk A, Seifert EL, Deininger MW, Snyder NW. Comparison of colorimetric, fluorometric, and liquid chromatography-mass spectrometry assays for acetyl-coenzyme A. Anal Biochem 2024; 685:115405. [PMID: 38016493 PMCID: PMC10955768 DOI: 10.1016/j.ab.2023.115405] [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: 08/18/2023] [Revised: 11/08/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Acetyl-Coenzyme A is a central metabolite in catabolic and anabolic pathways as well as the acyl donor for acetylation reactions. Multiple quantitative measurement techniques for acetyl-CoA have been reported, including commercially available kits. Comparisons between techniques for acetyl-CoA measurement have not been reported. This lack of comparability between assays makes context-specific assay selection and interpretation of results reporting changes in acetyl-CoA metabolism difficult. We compared commercially available colorimetric ELISA and fluorometric enzymatic-based kits to liquid chromatography-mass spectrometry-based assays using tandem mass spectrometry (LC-MS/MS) and high-resolution mass spectrometry (LC-HRMS). The colorimetric ELISA kit did not produce interpretable results even with commercially available pure standards. The fluorometric enzymatic kit produced comparable results to the LC-MS-based assays depending on matrix and extraction. LC-MS/MS and LC-HRMS assays produced well-aligned results, especially when incorporating stable isotope-labeled internal standards. In addition, we demonstrated the multiplexing capability of the LC-HRMS assay by measuring a suite of short-chain acyl-CoAs in a variety of acute myeloid leukemia cell lines and patient cells.
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Affiliation(s)
- Daniel S Kantner
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA
| | - Emily Megill
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA
| | - Anna Bostwick
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA
| | - Vicky Yang
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA
| | - Carmen Bekeova
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | | | - Erin L Seifert
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Michael W Deininger
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Nathaniel W Snyder
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA.
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2
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Azouaoui D, Choinière MR, Khan M, Sayfi S, Jaffer S, Yousef S, Patten DA, Green AE, Menzies KJ. Meta-analysis of NAD(P)(H) quantification results exhibits variability across mammalian tissues. Sci Rep 2023; 13:2464. [PMID: 36774401 PMCID: PMC9922293 DOI: 10.1038/s41598-023-29607-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/07/2023] [Indexed: 02/13/2023] Open
Abstract
Nicotinamide Adenine Dinucleotide (NAD+) plays an important role in energy metabolism and signaling pathways controlling crucial cellular functions. The increased interest in NAD+ metabolism and NAD+-boosting therapies has reinforced the necessity for accurate NAD+ quantification. To examine the published NAD(P)(H) measures across mammalian tissues, we performed a meta-analysis of the existing data. An Ovid MEDLINE database search identified articles with NAD(P)(H) quantification results obtained from mammalian tissues published between 1961 and 2021. We screened 4890 records and extracted quantitative data, as well as the quantification methods, pre-analytical conditions, and subject characteristics. The extracted physiological NAD(P)(H) concentrations in various tissues from mice, rats, and humans, revealed an important inter- and intra-method variability that extended to recent publications. This highlights the relatively poor potential for cross-experimental analyses for NAD(P)(H) quantitative data and the importance of standardization for NAD(P)(H) quantification methods and pre-analytical procedures for future preclinical and clinical studies.
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Affiliation(s)
- Dassine Azouaoui
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Michael René Choinière
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Momtafin Khan
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Shahab Sayfi
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Simran Jaffer
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Selvia Yousef
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - David A Patten
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Alexander E Green
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Keir J Menzies
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada.
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3
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Trefely S, Huber K, Liu J, Noji M, Stransky S, Singh J, Doan MT, Lovell CD, von Krusenstiern E, Jiang H, Bostwick A, Pepper HL, Izzo L, Zhao S, Xu JP, Bedi KC, Rame JE, Bogner-Strauss JG, Mesaros C, Sidoli S, Wellen KE, Snyder NW. Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation. Mol Cell 2022; 82:447-462.e6. [PMID: 34856123 PMCID: PMC8950487 DOI: 10.1016/j.molcel.2021.11.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 11/03/2021] [Indexed: 01/22/2023]
Abstract
Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.
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Affiliation(s)
- Sophie Trefely
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katharina Huber
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Biochemistry, Graz University of Technology, Graz 8010, Austria
| | - Joyce Liu
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Noji
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jay Singh
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Mary T Doan
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Claudia D Lovell
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eliana von Krusenstiern
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Helen Jiang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Anna Bostwick
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Hannah L Pepper
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Luke Izzo
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven Zhao
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jimmy P Xu
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth C Bedi
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Eduardo Rame
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Clementina Mesaros
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
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4
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Fields AM, Welle K, Ho ES, Mesaros C, Susiarjo M. Vitamin B6 deficiency disrupts serotonin signaling in pancreatic islets and induces gestational diabetes in mice. Commun Biol 2021; 4:421. [PMID: 33772108 PMCID: PMC7998034 DOI: 10.1038/s42003-021-01900-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 02/17/2021] [Indexed: 12/11/2022] Open
Abstract
In pancreatic islets, catabolism of tryptophan into serotonin and serotonin receptor 2B (HTR2B) activation is crucial for β-cell proliferation and maternal glucose regulation during pregnancy. Factors that reduce serotonin synthesis and perturb HTR2B signaling are associated with decreased β-cell number, impaired insulin secretion, and gestational glucose intolerance in mice. Albeit the tryptophan-serotonin pathway is dependent on vitamin B6 bioavailability, how vitamin B6 deficiency impacts β-cell proliferation during pregnancy has not been investigated. In this study, we created a vitamin B6 deficient mouse model and investigated how gestational deficiency influences maternal glucose tolerance. Our studies show that gestational vitamin B6 deficiency decreases serotonin levels in maternal pancreatic islets and reduces β-cell proliferation in an HTR2B-dependent manner. These changes were associated with glucose intolerance and insulin resistance, however insulin secretion remained intact. Our findings suggest that vitamin B6 deficiency-induced gestational glucose intolerance involves additional mechanisms that are complex and insulin independent. Fields et al. investigate the impact of vitamin B6 deficiency on islet β-cell proliferation during pregnancy, using vitamin B6-deficient mice. They find that gestational vitamin B6 deficiency decreases serotonin levels in pancreatic islets and reduces β-cell proliferation, showing that vitamin B6 deficiency regulates maternal glucose tolerance in a serotonin-dependent manner.
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Affiliation(s)
- Ashley M Fields
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Kevin Welle
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, NY, USA
| | - Elaine S Ho
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Clementina Mesaros
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Martha Susiarjo
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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5
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Yu X, Willmann MR, Vandivier LE, Trefely S, Kramer MC, Shapiro J, Guo R, Lyons E, Snyder NW, Gregory BD. Messenger RNA 5' NAD + Capping Is a Dynamic Regulatory Epitranscriptome Mark That Is Required for Proper Response to Abscisic Acid in Arabidopsis. Dev Cell 2020; 56:125-140.e6. [PMID: 33290723 DOI: 10.1016/j.devcel.2020.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/02/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
Although eukaryotic messenger RNAs (mRNAs) normally possess a 5' end N7-methyl guanosine (m7G) cap, a non-canonical 5' nicotinamide adenine dinucleotide (NAD+) cap can tag certain transcripts for degradation mediated by the NAD+ decapping enzyme DXO1. Despite this importance, whether NAD+ capping dynamically responds to specific stimuli to regulate eukaryotic transcriptomes remains unknown. Here, we reveal a link between NAD+ capping and tissue- and hormone response-specific mRNA stability. In the absence of DXO1 function, transcripts displaying a high proportion of NAD+ capping are instead processed into RNA-dependent RNA polymerase 6-dependent small RNAs, resulting in their continued turnover likely to free the NAD+ molecules. Additionally, the NAD+-capped transcriptome is significantly remodeled in response to the essential plant hormone abscisic acid in a mechanism that is primarily independent of DXO1. Overall, our findings reveal a previously uncharacterized and essential role of NAD+ capping in dynamically regulating transcript stability during specific physiological responses.
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Affiliation(s)
- Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Willmann
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Lee E Vandivier
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sophie Trefely
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Marianne C Kramer
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffrey Shapiro
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rong Guo
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; CyVerse, University of Arizona, Tucson, AZ 85721, USA
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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Verhagen KJA, van Gulik WM, Wahl SA. Dynamics in redox metabolism, from stoichiometry towards kinetics. Curr Opin Biotechnol 2020; 64:116-123. [DOI: 10.1016/j.copbio.2020.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/05/2020] [Accepted: 01/06/2020] [Indexed: 12/12/2022]
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7
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Cao W, Xia T, Cui Y, Yu Y, Qian G. Lanthanide metal–organic frameworks with nitrogen functional sites for the highly selective and sensitive detection of NADPH. Chem Commun (Camb) 2020; 56:10851-10854. [DOI: 10.1039/d0cc04152a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A series of isostructural fluorescent Ln-MOF [Ln(BPDC-xN)] (Ln = Eu/Tb, x = 0, 1, 2] probes was prepared using a nitrogen modification strategy to achieve the improved selective detection of NADPH.
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Affiliation(s)
- Wenqian Cao
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Tifeng Xia
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Yuanjing Cui
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Yang Yu
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Guodong Qian
- State Key Laboratory of Silicon Materials
- Cyrus Tang Center for Sensor Materials and Applications
- School of Materials Science and Engineering
- Zhejiang University
- Hangzhou 310027
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Analytical Methods for Mass Spectrometry-Based Metabolomics Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:635-647. [DOI: 10.1007/978-3-030-15950-4_38] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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