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Shinohara F, Oashi T, Harumoto T, Nishikawa T, Takayama Y, Miyagi H, Takahashi Y, Nakajima T, Sawada T, Koda Y, Makino A, Sato A, Hamaguchi K, Suzuki M, Yamamoto J, Tomari Y, Saito JI. siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand. RNA 2021; 27:163-173. [PMID: 33177188 PMCID: PMC7812868 DOI: 10.1261/rna.073783.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 11/05/2020] [Indexed: 05/03/2023]
Abstract
Small interfering RNAs (siRNAs) can be utilized not only as functional biological research tools but also as therapeutic agents. For the clinical use of siRNA as drugs, various chemical modifications have been used to improve the activity of siRNA drugs, and further chemical modifications are expected to improve the utility of siRNA therapeutics. As the 5' nucleobase of the guide strand affects the interaction between an siRNA and AGO2 and target cleavage activity, structural optimization of this specific position may be a useful strategy for improving siRNA activity. Here, using the in silico model of the complex between human AGO2 MID domain and nucleoside monophosphates, we screened and synthesized an original adenine-derived analog, 6-(3-(2-carboxyethyl)phenyl)purine (6-mCEPh-purine), that fits better than the natural nucleotide bases into the MID domain of AGO2. Introduction of the 6-mCEPh-purine analog at the 5'-end of the siRNA guide strand significantly enhanced target knockdown activity in both cultured cell lines and in vivo animal models. Our findings can help expand strategies for rationally optimizing siRNA activity via chemical modifications of nucleotide bases.
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Affiliation(s)
- Fumikazu Shinohara
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Taiji Oashi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Toshimasa Harumoto
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Tomoyuki Nishikawa
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yuki Takayama
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Hikaru Miyagi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yuichi Takahashi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takahiro Nakajima
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takashi Sawada
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yasuo Koda
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Asana Makino
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Atsuko Sato
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Kaori Hamaguchi
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Michihiko Suzuki
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Junichiro Yamamoto
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Jun-Ichi Saito
- Research Function Unit, R&D Division, Kyowa Kirin Co. Ltd., Chiyoda-ku, Tokyo 100-0004, Japan
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Duschmalé J, Hansen HF, Duschmalé M, Koller E, Albaek N, Møller MR, Jensen K, Koch T, Wengel J, Bleicher K. In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3' and 5' thiophosphate linkages. Nucleic Acids Res 2020; 48:63-74. [PMID: 31754711 PMCID: PMC6943131 DOI: 10.1093/nar/gkz1099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022] Open
Abstract
The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.
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Affiliation(s)
- Jörg Duschmalé
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
- To whom correspondence should be addressed. Tel: +41 61 68 86081; Fax: +41 61 68 88714;
| | - Henrik Frydenlund Hansen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Erich Koller
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Nanna Albaek
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Marianne Ravn Møller
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Klaus Jensen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Troels Koch
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Konrad Bleicher
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
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Schaefer EAK, Meixiong J, Mark C, Deik A, Motola DL, Fusco D, Yang A, Brisac C, Salloum S, Lin W, Clish CB, Peng LF, Chung RT. Apolipoprotein B100 is required for hepatitis C infectivity and Mipomersen inhibits hepatitis C. World J Gastroenterol 2016; 22:9954-9965. [PMID: 28018102 PMCID: PMC5143762 DOI: 10.3748/wjg.v22.i45.9954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/01/2016] [Accepted: 10/27/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To characterize the role of apolipoprotein B100 (apoB100) in hepatitis C viral (HCV) infection.
METHODS In this study, we utilize a gene editing tool, transcription activator-like effector nucleases (TALENs), to generate human hepatoma cells with a stable genetic deletion of APOB to assess of apoB in HCV. Using infectious cell culture-competent HCV, viral pseudoparticles, replicon models, and lipidomic analysis we determined the contribution of apoB to each step of the viral lifecycle. We further studied the effect of mipomersen, an FDA-approved antisense inhibitor of apoB100, on HCV using in vitro cell-culture competent HCV and determined its impact on viral infectivity with the TCID50 method.
RESULTS We found that apoB100 is indispensable for HCV infection. Using the JFH-1 fully infectious cell-culture competent virus in Huh 7 hepatoma cells with TALEN-mediated gene deletion of apoB (APOB KO), we found a significant reduction in HCV RNA and protein levels following infection. Pseudoparticle and replicon models demonstrated that apoB did not play a role in HCV entry or replication. However, the virus produced by APOB KO cells had significantly diminished infectivity as measured by the TCID-50 method compared to wild-type virus. Lipidomic analysis demonstrated that these virions have a fundamentally altered lipidome, with complete depletion of cholesterol esters. We further demonstrate that inhibition of apoB using mipomersen, an FDA-approved anti-sense oligonucleotide, results in a potent anti-HCV effect and significantly reduces the infectivity of the virus.
CONCLUSION ApoB is required for the generation of fully infectious HCV virions, and inhibition of apoB with mipomersen blocks HCV. Targeting lipid metabolic pathways to impair viral infectivity represents a novel host targeted strategy to inhibit HCV.
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Abstract
The aim of the study was to verify whether post-menopausal hormone replacement therapy (HRT) modifies autoantibody titers against oxidized low-density lipoprotein (LDL) (anti-LDLoxi), against epitopes of oxidized apolipoprotein B100 and common carotid intima-media thickness (IMT) in these women. Sixty-eight women in pre-menopause (PMW) and 216 in post-menopause (POMW) were recruited; eighty-three had undergone HRT for at least 12 months, where 48 received conjugated estrogens alone (EHRT) and 35 received conjugated estrogen and medroxyprogesterone acetate (CHRT). ELISA was used to determine autoantibodies. Lipoprotein lipase (LPL), hepatic lipase (HL), cholesterol ester transfer protein (CETP) and phospholipid transfer protein (PLTP) activities were assayed by radiometric methods. IMT was measured using Doppler ultrasound. Anti-oxidized LDL and anti-D antibodies increased by 40% (p ≤ 0.003) and 42% (p ≤ 0.006), respectively, with menopause. There was a surprising and significant 7% reduction in anti-D2 antibody titers with HRT (p ≤ 0.050), indicating a positive effect of treatment on the immune response to oxidized LDL. Combined HRT decreased activities of HL and LPL. HRT did not change common carotid IMT, which was increased by 32% as expected after menopause (p ≤ 0.030). This study describes, for the first time, the protective effect of HRT on decreasing autoantibody titers against oxidized apolipoprotein B in LDL.
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Affiliation(s)
- Vera Sylvia Castanho
- Clinical Pathology Department, Faculty of Medical Sciences, /FCM/University of Campinas, São Paulo, Brazil
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Abstract
Genzyme Corporation and Isis Pharmaceuticals have a worldwide licensing and collaboration agreement for the development of subcutaneous mipomersen (ISIS 147764; ISIS 301012; ISIS301012; mipomersen-sodium). Mipomersen, an oligonucleotide antisense inhibitor directed against apolipoprotein B-100 (apoB-100) mRNA, is in phase III clinical evaluation for the treatment of familial hypercholesterolemia, a form of type IIa hyperlipoproteinemia, and hypercholesterolemia in patients with severely high cholesterol levels or at high risk for coronary heart disease in the US, European Union, Brazil, Canada, South Africa, and South East Asia. This review discusses the development history and scientific profile of this new compound.
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Raal FJ, Santos RD, Blom DJ, Marais AD, Charng MJ, Cromwell WC, Lachmann RH, Gaudet D, Tan JL, Chasan-Taber S, Tribble DL, Flaim JD, Crooke ST. Mipomersen, an apolipoprotein B synthesis inhibitor, for lowering of LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia: a randomised, double-blind, placebo-controlled trial. Lancet 2010; 375:998-1006. [PMID: 20227758 DOI: 10.1016/s0140-6736(10)60284-x] [Citation(s) in RCA: 674] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Homozygous familial hypercholesterolaemia is a rare genetic disorder in which both LDL-receptor alleles are defective, resulting in very high concentrations of LDL cholesterol in plasma and premature coronary artery disease. This study investigated whether an antisense inhibitor of apolipoprotein B synthesis, mipomersen, is effective and safe as an adjunctive agent to lower LDL cholesterol concentrations in patients with this disease. METHODS This randomised, double-blind, placebo-controlled, phase 3 study was undertaken in nine lipid clinics in seven countries. Patients aged 12 years and older with clinical diagnosis or genetic confirmation of homozygous familial hypercholesterolaemia, who were already receiving the maximum tolerated dose of a lipid-lowering drug, were randomly assigned to mipomersen 200 mg subcutaneously every week or placebo for 26 weeks. Randomisation was computer generated and stratified by weight (<50 kg vs >/=50 kg) in a centralised blocked randomisation, implemented with a computerised interactive voice response system. All clinical, medical, and pharmacy personnel, and patients were masked to treatment allocation. The primary endpoint was percentage change in LDL cholesterol concentration from baseline. Analysis was by intention to treat. This trial is registered with ClinicalTrials.gov, number NCT00607373. FINDINGS 34 patients were assigned to mipomersen and 17 to placebo; data for all patients were analysed. 45 patients completed the 26-week treatment period (28 mipomersen, 17 placebo). Mean concentrations of LDL cholesterol at baseline were 11.4 mmol/L (SD 3.6) in the mipomersen group and 10.4 mmol/L (3.7) in the placebo group. The mean percentage change in LDL cholesterol concentration was significantly greater with mipomersen (-24.7%, 95% CI -31.6 to -17.7) than with placebo (-3.3%, -12.1 to 5.5; p=0.0003). The most common adverse events were injection-site reactions (26 [76%] patients in mipomersen group vs four [24%] in placebo group). Four (12%) patients in the mipomersen group but none in the placebo group had increases in concentrations of alanine aminotransferase of three times or more the upper limit of normal. INTERPRETATION Inhibition of apolipoprotein B synthesis by mipomersen represents a novel, effective therapy to reduce LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia who are already receiving lipid-lowering drugs, including high-dose statins. FUNDING ISIS Pharmaceuticals and Genzyme Corporation.
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Affiliation(s)
- Frederick J Raal
- Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa.
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Affiliation(s)
- R Dermot G Neely
- Clinical Biochemistry Department, Royal Victoria Infirmary, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP, UK.
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Abstract
OBJECTIVE To present an overview of antisense technology and to review and assess available literature on the chemistry, pharmacology, pharmacokinetics, drug interactions, preclinical and clinical studies, dosing, and adverse events of ISIS 301012 in the treatment of hyperlipidemia. DATA SOURCES PubMed database searches were conducted from 1966 to May 2007 using the search terms ISIS 301012, antisense, oligonucleotide, hypercholesterolemia, hyperlipidemia, and apolipoprotein B. Bibliographies of relevant review articles and information from the manufacturer were reviewed for additional references. STUDY SELECTION AND DATA EXTRACTION Available English-language literature, including abstracts, preclinical, and clinical trials, review articles, and scientific presentations were examined. DATA SYNTHESIS Apolipoprotein B is an important structural protein on the surface of atherogenic lipoproteins such as remnant very-low-density lipoprotein and low-density lipoprotein and facilitates the clearance of these particles from the circulation by binding to the low-density lipoprotein receptor. Overproduction of apolipoprotein B or reduced receptor-mediated clearance of lipoproteins leads to elevated serum cholesterol levels and premature atherosclerosis. ISIS 301012 is an antisense oligonucleotide that inhibits apolipoprotein B production by binding directly to and reducing the expression of apolipoprotein B messenger RNA. In a clinical trial, ISIS 301012 50-400 mg administered weekly via subcutaneous injection for 4 weeks reduced apolipoprotein B by 14.3-47.4% and low-density lipoprotein cholesterol by 5.9-40% at 55 days. The most frequent adverse event was injection-site erythema that resolved spontaneously. Studies are ongoing to further define the safety, efficacy, and pharmacokinetics of ISIS 301012 as add-on therapy in patients with heterozygous and homozygous familial hypercholesterolemia. No pharmacokinetic interactions have been demonstrated with ezetimibe and simvastatin. CONCLUSIONS ISIS 301012 is the first agent to enter clinical trials utilizing an antisense mechanism for reducing the production of apolipoprotein B. Further studies are needed to verify its safety, efficacy, and position of therapy in the dyslipidemic patient.
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Affiliation(s)
- Matthew K Ito
- College of Pharmacy, Oregon State University/Oregon Health & Science University, Portland Campus at OHSU, 3303 SW Bond Ave., Portland, OR 97239, USA.
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Dashti N, Manchekar M, Liu Y, Sun Z, Segrest JP. Microsomal triglyceride transfer protein activity is not required for the initiation of apolipoprotein B-containing lipoprotein assembly in McA-RH7777 cells. J Biol Chem 2007; 282:28597-28608. [PMID: 17690102 DOI: 10.1074/jbc.m700229200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously demonstrated that the N-terminal 1000 amino acid residues of human apolipoprotein (apo) B (designated apoB:1000) are competent to fold into a three-sided lipovitellin-like lipid binding cavity to form the apoB "lipid pocket" without a structural requirement for microsomal triglyceride transfer protein (MTP). Our results established that this primordial apoB-containing particle is phospholipid-rich (Manchekar, M., Richardson, P. E., Forte, T. M., Datta, G., Segrest, J. P., and Dashti, N. (2004) J. Biol. Chem. 279, 39757-39766). In this study we have investigated the putative functional role of MTP in the initial lipidation of apoB:1000 in stable transformants of McA-RH7777 cells. Inhibition of MTP lipid transfer activity by 0.1 microm BMS-197636 and 5, 10, and 20 microm of BMS-200150 had no detectable effect on the synthesis, lipidation, and secretion of apoB:1000-containing particles. Under identical experimental conditions, the synthesis, lipidation, and secretion of endogenous apoB100-containing particles in HepG2 and parental untransfected McA-RH7777 cells were inhibited by 86-94%. BMS-200150 at 40 microm nearly abolished the secretion of endogenous apoB100-containing particles in HepG2 and parental McA-RH cells but caused only 15-20% inhibition in the secretion of apoB: 1000-containing particles. This modest decrease was attributable to the nonspecific effect of a high concentration of this compound on hepatic protein synthesis, as reflected in a similar (20-25%) reduction in albumin secretion. Suppression of MTP gene expression in stable transformants of McA-RH7777 cells by micro-interfering RNA led to 60-70% decrease in MTP mRNA and protein levels, but it had no detectable effect on the secretion of apoB:1000. Our results provide a compelling argument that the initial addition of phospholipids to apoB:1000 and initiation of apoB-containing lipoprotein assembly occur independently of MTP lipid transfer activity.
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Affiliation(s)
- Nassrin Dashti
- Department of Medicine, Basic Sciences Section, Atherosclerosis Research Unit, University of Alabama at Birmingham Medical Center, Birmingham, Alabama 35294; Department of Cell Biology, University of Alabama at Birmingham Medical Center, Birmingham, Alabama 35294.
| | - Medha Manchekar
- Department of Medicine, Basic Sciences Section, Atherosclerosis Research Unit, University of Alabama at Birmingham Medical Center, Birmingham, Alabama 35294
| | - Yanwen Liu
- Department of Medicine, Basic Sciences Section, Atherosclerosis Research Unit, University of Alabama at Birmingham Medical Center, Birmingham, Alabama 35294
| | - Zhihuan Sun
- Department of Medicine, Basic Sciences Section, Atherosclerosis Research Unit, University of Alabama at Birmingham Medical Center, Birmingham, Alabama 35294
| | - Jere P Segrest
- Department of Medicine, Basic Sciences Section, Atherosclerosis Research Unit, University of Alabama at Birmingham Medical Center, Birmingham, Alabama 35294; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham Medical Center, Birmingham, Alabama 35294
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