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Subedi A, Tiwari A, Etemad AF, Huang Y, Chatterjee B, McLeod SL, Lu Y, Gonzalez D, Ghosh K, Singh SK, Ruiz Echartea ME, Grimm SL, Coarfa C, Pan HL, Majumder S. Nerve injury inhibits Oprd1 and Cnr1 transcription through REST in primary sensory neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.17.579842. [PMID: 38585789 PMCID: PMC10996832 DOI: 10.1101/2024.02.17.579842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The transcription repressor REST in the dorsal root ganglion (DRG) is upregulated by peripheral nerve injury and promotes the development of chronic pain. However, the genes targeted by REST in neuropathic pain development remain unclear. The expression levels of 4 opioid receptor (Oprm1, Oprd1, Oprl1, Oprk1) and the cannabinoid CB1 receptor (Cnr1) genes in the DRG regulate nociception. In this study, we determined the role of REST in the control of their expression in the DRG induced by spared nerve injury (SNI) in both male and female mice. Transcriptomic analyses of male mouse DRGs followed by quantitative reverse transcription polymerase chain reaction analyses of both male and female mouse DRGs showed that SNI upregulated expression of Rest and downregulated mRNA levels of all 4 opioid receptor and Cnr1 genes, but Oprm1 was upregulated in female mice. Analysis of publicly available bioinformatic data suggested that REST binds to the promoter regions of Oprm1 and Cnr1. Chromatin immunoprecipitation analyses indicated differing levels of REST at these promoters in male and female mice. Full-length Rest conditional knockout in primary sensory neurons reduced SNI-induced pain hypersensitivity and rescued the SNI-induced reduction in the expression of Oprd1 and Cnr1 in the DRG in both male and female mice. Our results suggest that nerve injury represses the transcription of Oprd1 and Cnr1 via REST in primary sensory neurons and that REST is a potential therapeutic target for neuropathic pain.
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Zengel J, Wang YX, Seo JW, Ning K, Hamilton JN, Wu B, Raie M, Holbrook C, Su S, Clements DR, Pillay S, Puschnik AS, Winslow MM, Idoyaga J, Nagamine CM, Sun Y, Mahajan VB, Ferrara KW, Blau HM, Carette JE. Hardwiring tissue-specific AAV transduction in mice through engineered receptor expression. Nat Methods 2023; 20:1070-1081. [PMID: 37291262 PMCID: PMC10333121 DOI: 10.1038/s41592-023-01896-x] [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: 05/23/2022] [Accepted: 04/25/2023] [Indexed: 06/10/2023]
Abstract
The development of transgenic mouse models that express genes of interest in specific cell types has transformed our understanding of basic biology and disease. However, generating these models is time- and resource-intensive. Here we describe a model system, SELective Expression and Controlled Transduction In Vivo (SELECTIV), that enables efficient and specific expression of transgenes by coupling adeno-associated virus (AAV) vectors with Cre-inducible overexpression of the multi-serotype AAV receptor, AAVR. We demonstrate that transgenic AAVR overexpression greatly increases the efficiency of transduction of many diverse cell types, including muscle stem cells, which are normally refractory to AAV transduction. Superior specificity is achieved by combining Cre-mediated AAVR overexpression with whole-body knockout of endogenous Aavr, which is demonstrated in heart cardiomyocytes, liver hepatocytes and cholinergic neurons. The enhanced efficacy and exquisite specificity of SELECTIV has broad utility in development of new mouse model systems and expands the use of AAV for gene delivery in vivo.
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Affiliation(s)
- James Zengel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Genetic Disorders and Aging, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jai Woong Seo
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ke Ning
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
| | - James N Hamilton
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bo Wu
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marina Raie
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Colin Holbrook
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shiqi Su
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Derek R Clements
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Sirika Pillay
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andreas S Puschnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Juliana Idoyaga
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Claude M Nagamine
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Sun
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
- Palo Alto Veterans Administration, Palo Alto, CA, USA
| | - Vinit B Mahajan
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, USA
- Palo Alto Veterans Administration, Palo Alto, CA, USA
| | - Katherine W Ferrara
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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Kim KS, Koo HY, Bok J. Alternative splicing in shaping the molecular landscape of the cochlea. Front Cell Dev Biol 2023; 11:1143428. [PMID: 36936679 PMCID: PMC10018040 DOI: 10.3389/fcell.2023.1143428] [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] [Received: 01/13/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
The cochlea is a complex organ comprising diverse cell types with highly specialized morphology and function. Until now, the molecular underpinnings of its specializations have mostly been studied from a transcriptional perspective, but accumulating evidence points to post-transcriptional regulation as a major source of molecular diversity. Alternative splicing is one of the most prevalent and well-characterized post-transcriptional regulatory mechanisms. Many molecules important for hearing, such as cadherin 23 or harmonin, undergo alternative splicing to produce functionally distinct isoforms. Some isoforms are expressed specifically in the cochlea, while some show differential expression across the various cochlear cell types and anatomical regions. Clinical phenotypes that arise from mutations affecting specific splice variants testify to the functional relevance of these isoforms. All these clues point to an essential role for alternative splicing in shaping the unique molecular landscape of the cochlea. Although the regulatory mechanisms controlling alternative splicing in the cochlea are poorly characterized, there are animal models with defective splicing regulators that demonstrate the importance of RNA-binding proteins in maintaining cochlear function and cell survival. Recent technological breakthroughs offer exciting prospects for overcoming some of the long-standing hurdles that have complicated the analysis of alternative splicing in the cochlea. Efforts toward this end will help clarify how the remarkable diversity of the cochlear transcriptome is both established and maintained.
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Affiliation(s)
- Kwan Soo Kim
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hei Yeun Koo
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
- *Correspondence: Jinwoong Bok,
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Liu X, Yan J, Liu F, Zhou P, Lv X, Cheng N, Liu L. Overexpression of REST Causes Neuronal Injury and Decreases Cofilin Phosphorylation in Mice. J Alzheimers Dis 2022; 87:873-886. [DOI: 10.3233/jad-210285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: RE1-silencing transcription factor (REST) is known to silence target genes involved in synaptic plasticity and neuronal differentiation. Although previous studies implicate REST in neurodegenerative diseases, its function in the progression of Alzheimer’s disease (AD) is uncertain. Objective: The aim of the present work was to explore the mechanisms of AD and determine whether and how REST was involved in the pathogenesis of AD. Methods: We investigated the differentially expressed genes and key transcription factors in AD using bioinformatics analysis. In addition, we assessed the expression of REST under the influence of AD-related factors. Mice overexpressing REST were generated and analyzed by proteomics analysis. We used transmission electron microscopy, Golgi-cox staining, immunohistochemistry, and western blotting to examine the impact of REST on neurons. Results: The results of bioinformatics analysis revealed REST as a hub transcriptional regulator in AD. We demonstrate that the mRNA expression of REST was significantly upregulated compared with that in the control groups, not only in AD patients but also in APP/PS1 transgenic mice, lipopolysaccharide-induced neuroinflammatory mice, and oxidative and glutamate stressed neurons. Using proteomics analysis, we showed that the upregulation of REST increased the expression of genes involved in apoptotic and mitochondrial pathways. Long-term overexpression of REST significantly reduced the number of dendritic spines and increased the mitochondrial defect and apoptosis. Reduction of the cofilin phosphorylation may be one of its mechanisms, and cofilin activity could be affected through the P38 MAPK/CREB signaling pathway. Conclusion: These results demonstrated the possible mechanism underlying AD and indicated REST as a potential therapeutic target for AD.
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Affiliation(s)
- Xiang Liu
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, PR China
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Jie Yan
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Fangbo Liu
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Peipei Zhou
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Xinyue Lv
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
| | - Nengneng Cheng
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, PR China
| | - Li Liu
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, PR China
- Shanghai Professional and Technical Service Center for Biological Material Drug-ability Evaluation, Shanghai, PR China
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Butler-Ryan R, Wood IC. The functions of repressor element 1-silencing transcription factor in models of epileptogenesis and post-ischemia. Metab Brain Dis 2021; 36:1135-1150. [PMID: 33813634 PMCID: PMC8272694 DOI: 10.1007/s11011-021-00719-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/17/2021] [Indexed: 12/14/2022]
Abstract
Epilepsy is a debilitating neurological disorder characterised by recurrent seizures for which 30% of patients are refractory to current treatments. The genetic and molecular aetiologies behind epilepsy are under investigation with the goal of developing new epilepsy medications. The transcriptional repressor REST (Repressor Element 1-Silencing Transcription factor) is a focus of interest as it is consistently upregulated in epilepsy patients and following brain insult in animal models of epilepsy and ischemia. This review analyses data from different epilepsy models and discusses the contribution of REST to epileptogenesis. We propose that in healthy brains REST acts in a protective manner to homeostatically downregulate increases in excitability, to protect against seizure through downregulation of BDNF (Brain-Derived Neurotrophic Factor) and its receptor, TrkB (Tropomyosin receptor kinase B). However, in epilepsy patients and post-seizure, REST may increase to a larger degree, which allows downregulation of the glutamate receptor subunit GluR2. This leads to AMPA glutamate receptors lacking GluR2 subunits, which have increased permeability to Ca2+, causing excitotoxicity, cell death and seizure. This concept highlights therapeutic potential of REST modulation through gene therapy in epilepsy patients.
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Affiliation(s)
- Ruth Butler-Ryan
- School of Biomedical Sciences, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT UK
| | - Ian C. Wood
- School of Biomedical Sciences, Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT UK
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Marisetty AL, Lu L, Veo BL, Liu B, Coarfa C, Kamal MM, Kassem DH, Irshad K, Lu Y, Gumin J, Henry V, Paulucci-Holthauzen A, Rao G, Baladandayuthapani V, Lang FF, Fuller GN, Majumder S. REST-DRD2 mechanism impacts glioblastoma stem cell-mediated tumorigenesis. Neuro Oncol 2020; 21:775-785. [PMID: 30953587 DOI: 10.1093/neuonc/noz030] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) is a lethal, heterogeneous human brain tumor, with regulatory mechanisms that have yet to be fully characterized. Previous studies have indicated that the transcriptional repressor REST (repressor element-1 silencing transcription factor) regulates the oncogenic potential of GBM stem cells (GSCs) based on level of expression. However, how REST performs its regulatory role is not well understood. METHODS We examined 2 independent high REST (HR) GSC lines using genome-wide assays, biochemical validations, gene knockdown analysis, and mouse tumor models. We analyzed in-house patient tumors and patient data present in The Cancer Genome Atlas (TCGA). RESULTS Genome-wide transcriptome and DNA-binding analyses suggested the dopamine receptor D2 (DRD2) gene, a dominant regulator of neurotransmitter signaling, as a direct target of REST. Biochemical analyses and mouse intracranial tumor models using knockdown of REST and double knockdown of REST and DRD2 validated this target and suggested that DRD2 is a downstream target of REST regulating tumorigenesis, at least in part, through controlling invasion and apoptosis. Further, TCGA GBM data support the presence of the REST-DRD2 axis and reveal that high REST/low DRD2 (HRLD) and low REST/high DRD2 (LRHD) tumors are specific subtypes, are molecularly different from the known GBM subtypes, and represent functional groups with distinctive patterns of enrichment of gene sets and biological pathways. The inverse HRLD/LRHD expression pattern is also seen in in-house GBM tumors. CONCLUSIONS These findings suggest that REST regulates neurotransmitter signaling pathways through DRD2 in HR-GSCs to impact tumorigenesis. They further suggest that the REST-DRD2 mechanism forms distinct subtypes of GBM.
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Affiliation(s)
- Anantha L Marisetty
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Lu
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bethany L Veo
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bin Liu
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Mohamed Mostafa Kamal
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dina Hamada Kassem
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Khushboo Irshad
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yungang Lu
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joy Gumin
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Verlene Henry
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Ganesh Rao
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Frederick F Lang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory N Fuller
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sadhan Majumder
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
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7
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Poiana G, Gioia R, Sineri S, Cardarelli S, Lupo G, Cacci E. Transcriptional regulation of adult neural stem/progenitor cells: tales from the subventricular zone. Neural Regen Res 2020; 15:1773-1783. [PMID: 32246617 PMCID: PMC7513981 DOI: 10.4103/1673-5374.280301] [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] [Indexed: 01/06/2023] Open
Abstract
In rodents, well characterized neurogenic niches of the adult brain, such as the subventricular zone of the lateral ventricles and the subgranular zone of the hippocampus, support the maintenance of neural/stem progenitor cells (NSPCs) and the production of new neurons throughout the lifespan. The adult neurogenic process is dependent on the intrinsic gene expression signatures of NSPCs that make them competent for self-renewal and neuronal differentiation. At the same time, it is receptive to regulation by various extracellular signals that allow the modulation of neuronal production and integration into brain circuitries by various physiological stimuli. A drawback of this plasticity is the sensitivity of adult neurogenesis to alterations of the niche environment that can occur due to aging, injury or disease. At the core of the molecular mechanisms regulating neurogenesis, several transcription factors have been identified that maintain NSPC identity and mediate NSPC response to extrinsic cues. Here, we focus on REST, Egr1 and Dbx2 and their roles in adult neurogenesis, especially in the subventricular zone. We review recent work from our and other laboratories implicating these transcription factors in the control of NSPC proliferation and differentiation and in the response of NSPCs to extrinsic influences from the niche. We also discuss how their altered regulation may affect the neurogenic process in the aged and in the diseased brain. Finally, we highlight key open questions that need to be addressed to foster our understanding of the transcriptional mechanisms controlling adult neurogenesis.
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Affiliation(s)
- Giancarlo Poiana
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Roberta Gioia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Serena Sineri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Silvia Cardarelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Giuseppe Lupo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Emanuele Cacci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
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