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Sen D, Sarkar S, Mukhopadhyay P. Prime Editing: An Emerging Tool in Cancer Treatment. Mol Biotechnol 2023; 65:509-520. [PMID: 36251123 PMCID: PMC9574179 DOI: 10.1007/s12033-022-00580-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022]
Abstract
Prime Editing is a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) based genome editing technique having promising potential in terms of reducing off target activity. It introduces fragments of DNA sequences into the target site using a guide RNA (gRNA) molecule, composed of both the sequence that is to be inserted into the target site along with an inactive Cas9 nickase and a reverse transcriptase. Prime Editing can cause insertions, deletions, and various point mutations for reverting the phenetic characteristics of a disease specially tested in human adult stem cells and cancer cell lines. The main aim of our review is to explore how Prime Editing and its various forms are being utilized as an emerging tool to cure deleterious diseases like cancer, also as a delivery strategy of the tool into cells. There are almost five generations of Prime Editors (PE) with increasing levels of efficiency from one level to another that have huge clinical potential in correcting mutations; however, the necessity for a pegRNA design is extremely significant. But besides having such advantages, the limitations of this technology particularly include generation of double nicks while optimizing the efficiency of PE3. So, it is important to consider all such consequences and customize PE as per requirements.
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Affiliation(s)
- Debmitra Sen
- Department of Microbiology, Barrackpore Rastraguru Surendranath College, Kolkata, West Bengal 700120 India ,Department of Microbiology, University of Kalyani, Nadia, 741235 India
| | - Sutripta Sarkar
- Department of Food and Nutrition, Barrackpore Rastraguru Surendranath College, Kolkata, West Bengal 700120 India
| | - Poulami Mukhopadhyay
- Department of Microbiology, Barrackpore Rastraguru Surendranath College, Kolkata, West Bengal, 700120, India.
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2
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Fajardo-Ortiz D, Hornbostel S, Montenegro de Wit M, Shattuck A. Funding CRISPR: Understanding the role of government and philanthropic institutions in supporting academic research within the CRISPR innovation system. QUANTITATIVE SCIENCE STUDIES 2022. [DOI: 10.1162/qss_a_00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Abstract
CRISPR/Cas has the potential to revolutionize medicine, agriculture, and biology. Understanding the trajectory of CRISPR research, how it is influenced and who pays for it, is an essential research policy question. We use a combination of methods to map, via quantitative content analysis of CRISPR papers, the research funding profile of major government agencies and organizations philanthropic, and the networks involved in supporting key stages of high-influence research, namely basic biological research and technological development. The results of the content analysis show how the research supported by the main US government agencies focus both on the study of CRISPR as a biological phenomenon and on its technological development and use as a biomedical research tool. US philanthropic organizations with the exception of HHMI, tend, by contrast, to specialize in funding CRISPR as a genome editing technology. We present a model of co-funding networks at the two most prominent institutions for CRISPR/Cas research, the University of California and the Harvard/MIT/Broad Institute, to illuminate how philanthropic organizations have articulated with government agencies to co-finance the discovery and development of CRISPR/Cas. Our results raise fundamental questions about the role of the state and the influence of philanthropy over the trajectory of transformative technologies.
Peer Review
https://publons.com/publon/10.1162/qss_a_00187
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Affiliation(s)
- David Fajardo-Ortiz
- Research System and Science Dynamics Research Area, Deutsche Zentrum für Hochschul-und Wissenschaftsforschung (DZHW), Berlin, Germany
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Stefan Hornbostel
- Institut für Sozialwissenschaften, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Maywa Montenegro de Wit
- Environmental Studies Department, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Annie Shattuck
- Department of Geography, Indiana University, Bloomington, Indiana, United States of America
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3
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Landmesser U, Poller W, Tsimikas S, Most P, Paneni F, Lüscher TF. From traditional pharmacological towards nucleic acid-based therapies for cardiovascular diseases. Eur Heart J 2021; 41:3884-3899. [PMID: 32350510 DOI: 10.1093/eurheartj/ehaa229] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/17/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleic acid-based therapeutics are currently developed at large scale for prevention and management of cardiovascular diseases (CVDs), since: (i) genetic studies have highlighted novel therapeutic targets suggested to be causal for CVD; (ii) there is a substantial recent progress in delivery, efficacy, and safety of nucleic acid-based therapies; (iii) they enable effective modulation of therapeutic targets that cannot be sufficiently or optimally addressed using traditional small molecule drugs or antibodies. Nucleic acid-based therapeutics include (i) RNA-targeted therapeutics for gene silencing; (ii) microRNA-modulating and epigenetic therapies; (iii) gene therapies; and (iv) genome-editing approaches (e.g. CRISPR-Cas-based): (i) RNA-targeted therapeutics: several large-scale clinical development programmes, using antisense oligonucleotides (ASO) or short interfering RNA (siRNA) therapeutics for prevention and management of CVD have been initiated. These include ASO and/or siRNA molecules to lower apolipoprotein (a) [apo(a)], proprotein convertase subtilisin/kexin type 9 (PCSK9), apoCIII, ANGPTL3, or transthyretin (TTR) for prevention and treatment of patients with atherosclerotic CVD or TTR amyloidosis. (ii) MicroRNA-modulating and epigenetic therapies: novel potential therapeutic targets are continually arising from human non-coding genome and epigenetic research. First microRNA-based therapeutics or therapies targeting epigenetic regulatory pathways are in clinical studies. (iii) Gene therapies: EMA/FDA have approved gene therapies for non-cardiac monogenic diseases and LDL receptor gene therapy is currently being examined in patients with homozygous hypercholesterolaemia. In experimental studies, gene therapy has significantly improved cardiac function in heart failure animal models. (iv) Genome editing approaches: these technologies, such as using CRISPR-Cas, have proven powerful in stem cells, however, important challenges are remaining, e.g. low rates of homology-directed repair in somatic cells such as cardiomyocytes. In summary, RNA-targeted therapies (e.g. apo(a)-ASO and PCSK9-siRNA) are now in large-scale clinical outcome trials and will most likely become a novel effective and safe therapeutic option for CVD in the near future. MicroRNA-modulating, epigenetic, and gene therapies are tested in early clinical studies for CVD. CRISPR-Cas-mediated genome editing is highly effective in stem cells, but major challenges are remaining in somatic cells, however, this field is rapidly advancing.
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Affiliation(s)
- Ulf Landmesser
- Department of Cardiology, Campus Benjamin Franklin, CC11 (Cardiovascular Medicine), Charite-Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany.,Berlin Institute of Health, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, CC11 (Cardiovascular Medicine), Charite-Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Sotirios Tsimikas
- Division of Cardiovascular Medicine, Sulpizio Cardiovascular Center, University of California San Diego, 9500 Gilman Drive, BSB 1080, La Jolla, CA 92093-0682, USA
| | - Patrick Most
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany.,Center for Translational Medicine, Jefferson Medical College, 1020 Locust Street, Philadelphia, PA 19107, USA.,Molecular and Translational Cardiology, Department of Medicine III, Heidelberg University Hospital, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Department of Cardiology, University Heart Center, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Rämistrasse 100, MOU2, 8091 Zurich, Switzerland
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Research, Education and Development, Royal Brompton and Harefield Hospital Trust and Imperial College London, National Heart and Lung Institute, Guy Scadding Building, Dovehouse Street, London SW3 6LY, UK
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4
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Emmerich CH, Gamboa LM, Hofmann MCJ, Bonin-Andresen M, Arbach O, Schendel P, Gerlach B, Hempel K, Bespalov A, Dirnagl U, Parnham MJ. Improving target assessment in biomedical research: the GOT-IT recommendations. Nat Rev Drug Discov 2021; 20:64-81. [PMID: 33199880 PMCID: PMC7667479 DOI: 10.1038/s41573-020-0087-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Academic research plays a key role in identifying new drug targets, including understanding target biology and links between targets and disease states. To lead to new drugs, however, research must progress from purely academic exploration to the initiation of efforts to identify and test a drug candidate in clinical trials, which are typically conducted by the biopharma industry. This transition can be facilitated by a timely focus on target assessment aspects such as target-related safety issues, druggability and assayability, as well as the potential for target modulation to achieve differentiation from established therapies. Here, we present recommendations from the GOT-IT working group, which have been designed to support academic scientists and funders of translational research in identifying and prioritizing target assessment activities and in defining a critical path to reach scientific goals as well as goals related to licensing, partnering with industry or initiating clinical development programmes. Based on sets of guiding questions for different areas of target assessment, the GOT-IT framework is intended to stimulate academic scientists' awareness of factors that make translational research more robust and efficient, and to facilitate academia-industry collaboration.
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Affiliation(s)
| | - Lorena Martinez Gamboa
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Martine C J Hofmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
| | - Marc Bonin-Andresen
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Arbach
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- SPARK-Validation Fund, Berlin Institute of Health, Berlin, Germany
| | - Pascal Schendel
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Katja Hempel
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Anton Bespalov
- PAASP GmbH, Heidelberg, Germany
- Valdman Institute of Pharmacology, Pavlov Medical University, St. Petersburg, Russia
| | - Ulrich Dirnagl
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
- Faculty of Biochemistry, Chemistry & Pharmacy, J.W. Goethe University Frankfurt, Frankfurt am Main, Germany
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5
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Martufi M, Good RB, Rapiteanu R, Schmidt T, Patili E, Tvermosegaard K, New M, Nanthakumar CB, Betts J, Blanchard AD, Maratou K. Single-Step, High-Efficiency CRISPR-Cas9 Genome Editing in Primary Human Disease-Derived Fibroblasts. CRISPR J 2020; 2:31-40. [PMID: 31021235 PMCID: PMC6636881 DOI: 10.1089/crispr.2018.0047] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genome editing is a tool that has many applications, including the validation of potential drug targets. However, performing genome editing in low-passage primary human cells with the greatest physiological relevance is notoriously difficult. High editing efficiency is desired because it enables gene knockouts (KO) to be generated in bulk cellular populations and circumvents the problem of having to generate clonal cell isolates. Here, we describe a single-step workflow enabling >90% KO generation in primary human lung fibroblasts via CRISPR ribonucleoprotein delivery in the absence of antibiotic selection or clonal expansion. As proof of concept, we edited two SMAD family members and demonstrated that in response to transforming growth factor beta, SMAD3, but not SMAD2, is critical for deposition of type I collagen in the fibrotic response. The optimization of this workflow can be readily transferred to other primary cell types.
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Affiliation(s)
- Matteo Martufi
- 1 Target Sciences Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Robert B Good
- 2 Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Radu Rapiteanu
- 1 Target Sciences Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Tobias Schmidt
- 1 Target Sciences Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Eleni Patili
- 1 Target Sciences Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Ketil Tvermosegaard
- 1 Target Sciences Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Maria New
- 1 Target Sciences Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Carmel B Nanthakumar
- 2 Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Joanna Betts
- 1 Target Sciences Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Andy D Blanchard
- 2 Fibrosis Discovery Performance Unit, Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
| | - Klio Maratou
- 1 Target Sciences Respiratory Therapy Area, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, United Kingdom
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Development of conventional and real time PCR assays for rapid species authentication of mammalian cell lines commonly used in veterinary diagnostic laboratories. Res Vet Sci 2019; 126:170-177. [PMID: 31505453 DOI: 10.1016/j.rvsc.2019.08.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 12/19/2022]
Abstract
Mammalian cell lines are valuable tools in biomedical fields, with applications ranging from disease diagnosis to the production of biological reagents and vaccines. Here we report the development of new conventional (cPCR) and real time PCR (qPCR) assays for species identification of several mammalian kidney cell lines originated from swine, green monkey, hamster and bovine tissues that are extensively used in veterinary diagnostic laboratories. The PCR primers and probes were selected from highly conserved mitochondrial genes and analyzed in silico by nucleotide BLAST in the National Center for Biotechnology Information (NCBI) website to ensure target specificity. The assays were highly species-specific and had no cross-reactivity against other tested cell lines originated from different mammalian species. Assay sensitivity (limit of detection; LOD) was determined using serial dilutions of cell line DNA as template. The estimated LODs were between 2.95 and 48 pg (picogram) DNA/assay for cPCR, and between 1.5 × 10-3 and 4.8 × 10-2 pg DNA/assay for qPCR. Multiplex qPCR assays were developed for simultaneous detection of up to three species in a single assay. The multiplex qPCR assays exhibited the same sensitivity as the corresponding singleplex assays with the exception of the green monkey species that demonstrated a 10-100 fold decline in the sensitivity. Contamination of swine cells was detected in one of the rabbit cell lines. The contamination was further confirmed by Sanger and Next-Generation sequencing.
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7
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Cardiac macrotissues-on-a-plate models for phenotypic drug screens. Adv Drug Deliv Rev 2019; 140:93-100. [PMID: 30902615 DOI: 10.1016/j.addr.2019.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/11/2019] [Accepted: 03/13/2019] [Indexed: 12/17/2022]
Abstract
Facilitated by the introduction of human induced pluripotent stem cells and protocols for their efficient directed differentiation at high quantity and quality, innovative human heart muscle models are being developed for applications in drug screens. Employed models range from the microscopic cardiomyocytes-on-a-chip scale to the cardiac macrotissues-on-a-plate scale. Whilst cardiomyocyte-on-a-chip models can be readily adapted to high-throughput primary screening, they are limited as to the deep phenotyping of contractility, and here in particular contractile force development. In lower throughput cardiac macrotissue-on-a-plate platforms, organotypic function, including anisotropic electrical spread of excitation and contractility, can be recapitulated at the macroscopic scale. This review serves as an overview of cardiac macrotissue-on-a-plate technologies with a focus on their application in the investigation of drug effects on heart muscle contractility and disease modeling.
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8
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Kimberland ML, Hou W, Alfonso-Pecchio A, Wilson S, Rao Y, Zhang S, Lu Q. Strategies for controlling CRISPR/Cas9 off-target effects and biological variations in mammalian genome editing experiments. J Biotechnol 2018; 284:91-101. [DOI: 10.1016/j.jbiotec.2018.08.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/06/2018] [Accepted: 08/20/2018] [Indexed: 12/26/2022]
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9
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Dangi AK, Sinha R, Dwivedi S, Gupta SK, Shukla P. Cell Line Techniques and Gene Editing Tools for Antibody Production: A Review. Front Pharmacol 2018; 9:630. [PMID: 29946262 PMCID: PMC6006397 DOI: 10.3389/fphar.2018.00630] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/16/2022] Open
Abstract
The present day modern formulation practices for drugs are based on newer tools and techniques toward effective utilization. The methods of antibody formulations are to be revolutionized based on techniques of cell engineering and gene editing. In the present review, we have discussed innovations in cell engineering toward production of novel antibodies for therapeutic applications. Moreover, this review deciphers the use of RNAi, ribozyme engineering, CRISPR-Cas-based techniques for better strategies for antibody production. Overall, this review describes the multidisciplinary aspects of the production of therapeutic proteins that has gained more attention due to its increasing demand.
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Affiliation(s)
- Arun K. Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | | | - Shailja Dwivedi
- Advanced Biotech Lab, Ipca Laboratories Limited, Mumbai, India
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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Abstract
Exciting new technologies are often self-limiting in their rollout, as access to state-of-the-art instrumentation or the need for years of hands-on experience, for better or worse, ensures slow adoption by the community. CRISPR technology, however, presents the opposite dilemma, where the simplicity of the system enabled the parallel development of many applications, improvements and derivatives, and new users are now presented with an almost paralyzing abundance of choices. This Review intends to guide users through the process of applying CRISPR technology to their biological problems of interest, especially in the context of discovering gene function at scale.
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Affiliation(s)
- John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA
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