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1
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Babushkina NP, Kucher AN. Regulatory Potential of SNP Markers in Genes of DNA Repair Systems. Mol Biol 2023. [DOI: 10.1134/s002689332301003x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Micronuclei Formation upon Radioiodine Therapy for Well-Differentiated Thyroid Cancer: The Influence of DNA Repair Genes Variants. Genes (Basel) 2020; 11:genes11091083. [PMID: 32957448 PMCID: PMC7565468 DOI: 10.3390/genes11091083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/07/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
Radioiodine therapy with 131I remains the mainstay of standard treatment for well-differentiated thyroid cancer (DTC). Prognosis is good but concern exists that 131I-emitted ionizing radiation may induce double-strand breaks in extra-thyroidal tissues, increasing the risk of secondary malignancies. We, therefore, sought to evaluate the induction and 2-year persistence of micronuclei (MN) in lymphocytes from 26 131I-treated DTC patients and the potential impact of nine homologous recombination (HR), non-homologous end-joining (NHEJ), and mismatch repair (MMR) polymorphisms on MN levels. MN frequency was determined by the cytokinesis-blocked micronucleus assay while genotyping was performed through pre-designed TaqMan® Assays or conventional PCR-restriction fragment length polymorphism (RFLP). MN levels increased significantly one month after therapy and remained persistently higher than baseline for 2 years. A marked reduction in lymphocyte proliferation capacity was also apparent 2 years after therapy. MLH1 rs1799977 was associated with MN frequency (absolute or net variation) one month after therapy, in two independent groups. Significant associations were also observed for MSH3 rs26279, MSH4 rs5745325, NBN rs1805794, and tumor histotype. Overall, our results suggest that 131I therapy may pose a long-term challenge to cells other than thyrocytes and that the individual genetic profile may influence 131I sensitivity, hence its risk-benefit ratio. Further studies are warranted to confirm the potential utility of these single nucleotide polymorphisms (SNPs) as radiogenomic biomarkers in the personalization of radioiodine therapy.
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Tang L, Xu M. Candidate polymorphisms and susceptibility to inflammatory bowel disease: A systematic review and meta-analysis. Gene X 2020; 753:144814. [DOI: 10.1016/j.gene.2020.144814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022] Open
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Hodel KP, de Borja R, Henninger EE, Campbell BB, Ungerleider N, Light N, Wu T, LeCompte KG, Goksenin AY, Bunnell BA, Tabori U, Shlien A, Pursell ZF. Explosive mutation accumulation triggered by heterozygous human Pol ε proofreading-deficiency is driven by suppression of mismatch repair. eLife 2018; 7:32692. [PMID: 29488881 PMCID: PMC5829921 DOI: 10.7554/elife.32692] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/04/2018] [Indexed: 12/14/2022] Open
Abstract
Tumors defective for DNA polymerase (Pol) ε proofreading have the highest tumor mutation burden identified. A major unanswered question is whether loss of Pol ε proofreading by itself is sufficient to drive this mutagenesis, or whether additional factors are necessary. To address this, we used a combination of next generation sequencing and in vitro biochemistry on human cell lines engineered to have defects in Pol ε proofreading and mismatch repair. Absent mismatch repair, monoallelic Pol ε proofreading deficiency caused a rapid increase in a unique mutation signature, similar to that observed in tumors from patients with biallelic mismatch repair deficiency and heterozygous Pol ε mutations. Restoring mismatch repair was sufficient to suppress the explosive mutation accumulation. These results strongly suggest that concomitant suppression of mismatch repair, a hallmark of colorectal and other aggressive cancers, is a critical force for driving the explosive mutagenesis seen in tumors expressing exonuclease-deficient Pol ε.
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Affiliation(s)
- Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
| | - Richard de Borja
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Erin E Henninger
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
| | - Brittany B Campbell
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, New Orleans, United States
| | - Nicholas Light
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Tong Wu
- Department of Pathology, Tulane University School of Medicine, New Orleans, United States
| | - Kimberly G LeCompte
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
| | - A Yasemin Goksenin
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States
| | - Bruce A Bunnell
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, United States.,Tulane Center for Stem Cell Research and Regenerative Medicine, Tulane University School of Medicine, New Orleans, United States
| | - Uri Tabori
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada.,Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, United States.,Tulane Cancer Center, Tulane University School of Medicine, New Orleans, United States
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Dominguez-Valentin M, Wernhoff P, Cajal AR, Kalfayan PG, Piñero TA, Gonzalez ML, Ferro A, Sammartino I, Causada Calo NS, Vaccaro CA. MLH1 Ile219Val Polymorphism in Argentinean Families with Suspected Lynch Syndrome. Front Oncol 2016; 6:189. [PMID: 27606285 PMCID: PMC4996012 DOI: 10.3389/fonc.2016.00189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/08/2016] [Indexed: 12/20/2022] Open
Affiliation(s)
- Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital , Oslo , Norway
| | - Patrik Wernhoff
- Unit of Muscle Biology, Lund Transgenic Core Facility/Reproductive Immunology, Department of Experimental Medical Science, Lund University , Lund , Sweden
| | - Andrea R Cajal
- Institute of Basic Sciences and Experimental Medicine (ICBME), Instituto Universitario Hospital Italiano , Buenos Aires , Argentina
| | - Pablo G Kalfayan
- Programa de Cancer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires , Buenos Aires , Argentina
| | - Tamara A Piñero
- Programa de Cancer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires , Buenos Aires , Argentina
| | - Maria L Gonzalez
- Programa de Cancer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires , Buenos Aires , Argentina
| | - Alejandra Ferro
- Programa de Cancer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires , Buenos Aires , Argentina
| | - Ines Sammartino
- Programa de Cancer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires , Buenos Aires , Argentina
| | - Natalia S Causada Calo
- Programa de Cancer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires , Buenos Aires , Argentina
| | - Carlos A Vaccaro
- Programa de Cancer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires , Buenos Aires , Argentina
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Kuehn F, Klar E, Bliemeister A, Linnebacher M. Reactivity against microsatellite instability-induced frameshift mutations in patients with inflammatory bowel disease. World J Gastroenterol 2015; 21:221-228. [PMID: 25574094 PMCID: PMC4284338 DOI: 10.3748/wjg.v21.i1.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/20/2014] [Accepted: 08/13/2014] [Indexed: 02/06/2023] Open
Abstract
AIM To analyze the cellular immune response towards microsatellite-instability (MSI)-induced frameshift-peptides (FSPs) in patients suffering from inflammatory bowel disease (IBD) with and without thiopurine-based immunosuppressive treatment. METHODS Frequencies of peripheral blood T cell responses of IBD patients (n = 75) against FSPs derived from 14 microsatellite-containing candidate genes were quantified by interferon-γ enzyme-linked immunospot. T cells derived from 20 healthy individuals served as controls. RESULTS Significant T cell reactivities against MSI-induced FSPs were observed in 59 of 75 IBD patients (78.7%). This was significantly more as we could observe in 20 healthy controls (P = 0.001). Overall, the reactivity was significantly influenced by thiopurine treatment (P = 0.032) and duration of disease (P = 0.002) but not by duration or cumulative amount of thiopurine therapy (P = 0.476). Unexpected, 15 of 24 (62.5%) IBD patients without prior thiopurine treatment also showed increased FSP-specific immune responses (P = 0.001). CONCLUSION These findings propose FSPs as potential novel class of inflammation-associated antigens and this in turn may have implications for screening, diagnosis as well as clinical management of patients suffering from IBD and other inflammatory conditions.
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Farrell MP, Hughes DJ, Drost M, Wallace AJ, Cummins RJ, Fletcher TA, Meany MA, Kay EW, de Wind N, Power DG, Andrews EJ, Green AJ, Gallagher DJ. Multivariate analysis of MLH1 c.1664T>C (p.Leu555Pro) mismatch repair gene variant demonstrates its pathogenicity. Fam Cancer 2013; 12:741-7. [PMID: 23712482 DOI: 10.1007/s10689-013-9652-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Genetic testing of an Irish kindred identified an exonic nucleotide substitution c.1664T>C (p.Leu555Pro) in the MLH1 mismatch repair (MMR) gene. This previously unreported variant is classified as a "variant of uncertain significance" (VUS). Immunohistochemical (IHC) analysis and microsatellite instability (MSI) studies, genetic testing, a literature and online MMR mutation database review, in silico phenotype prediction tools, and an in vitro MMR activity assay were used to study the clinical significance of this variant. The MLH1 c.1664T>C (p.Leu555Pro) VUS co-segregated with three cases of classic Lynch syndrome-associated malignancies over two generations, with consistent loss of MLH1 and PMS2 protein expression on IHC, and evidence of the MSI-High mutator phenotype. The leucine at position 555 is well conserved across a number of species, and this novel variant has not been reported as a normal polymorphism in the general population. In silico and in vitro analyses suggest that this variant may have a deleterious effect on the MLH1 protein and abrogate MMR activity. Evidence from clinical, histological, immunohistochemical, and molecular genetic data suggests that MLH1 c.1664T>C (p.Leu555Pro) is likely to be the pathogenic cause of Lynch syndrome in this family.
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Affiliation(s)
- M P Farrell
- Cancer Genetics Department, Mater Private Hospital, 73 Eccles St, Dublin 7, Ireland,
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Borràs E, Pineda M, Brieger A, Hinrichsen I, Gómez C, Navarro M, Balmaña J, Ramón y Cajal T, Torres A, Brunet J, Blanco I, Plotz G, Lázaro C, Capellá G. Comprehensive functional assessment of MLH1 variants of unknown significance. Hum Mutat 2012; 33:1576-88. [PMID: 22736432 DOI: 10.1002/humu.22142] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 12/15/2022]
Abstract
Lynch syndrome is associated with germline mutations in DNA mismatch repair (MMR) genes. Up to 30% of DNA changes found are variants of unknown significance (VUS). Our aim was to assess the pathogenicity of eight MLH1 VUS identified in patients suspected of Lynch syndrome. All of them are novel or not previously characterized. For their classification, we followed a strategy that integrates family history, tumor pathology, and control frequency data with a variety of in silico and in vitro analyses at RNA and protein level, such as MMR assay, MLH1 and PMS2 expression, and subcellular localization. Five MLH1 VUS were classified as pathogenic: c.[248G>T(;)306G>C], c.[780C>G;788A>C], and c.791-7T>A affected mRNA processing, whereas c.218T>C (p.L73P) and c.244A>G [corrected] (p.T82A) impaired MMR activity. Two other VUS were considered likely neutral: the silent c.702G>A variant did not affect mRNA processing or stability, and c.974G>A (p.R325Q) did not influence MMR function. In contrast, variant c.25C>T (p.R9W) could not be classified, as it associated with intermediate levels of MMR activity. Comprehensive functional assessment of MLH1 variants was useful in their classification and became relevant in the diagnosis and genetic counseling of carrier families.
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Affiliation(s)
- Ester Borràs
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Spain
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Drost M, Zonneveld JEBM, van Dijk L, Morreau H, Tops CM, Vasen HFA, Wijnen JT, de Wind N. A cell-free assay for the functional analysis of variants of the mismatch repair protein MLH1. Hum Mutat 2010; 31:247-53. [PMID: 20020535 DOI: 10.1002/humu.21180] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The hereditary colon and endometrium cancer predisposition Lynch Syndrome (also called HNPCC) is caused by a germ-line mutation in one of the DNA mismatch repair (MMR) genes. A significant fraction of the gene alterations detected in suspected Lynch Syndrome patients is comprised of amino acid substitutions. The relevance for cancer risk of these variants is difficult to assess, as currently no time- and cost-effective, validated, and widely applicable functional assays for the measurement of MMR activity are available. Here we describe a rapid, cell-free, and easily quantifiable MMR activity assay for the diagnostic assessment of variants of the MLH1 MMR protein. This assay allows the parallel generation and functional analysis of a series of variants of the MLH1 protein in vitro using readily available, or preprepared, reagents. Using this assay we have tested 26 MLH1 variants and of these, 15 had lost activity. These results are in concordance with those obtained from first-generation assays and with in silico and pathology data. After its multifocal technical and clinical validation this assay could have great impact for the diagnosis and counseling of carriers of an MLH1 variant and their relatives.
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Affiliation(s)
- Mark Drost
- Departments of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
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Vietri MT, Riegler G, De Paola M, Simeone S, Boggia M, Improta A, Parisi M, Molinari AM, Cioffi M. I219V polymorphism in hMLH1 gene in patients affected with ulcerative colitis. Genet Test Mol Biomarkers 2009; 13:193-7. [PMID: 19371218 DOI: 10.1089/gtmb.2008.0088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
INTRODUCTION hMLH1 gene, lying on chromosome 3p21-23, is a key factor of the mismatch repair (MMR) complex, which amends DNA replication errors. MMR alterations are involved in the development of both hereditary and sporadic forms of colorectal carcinoma related to ulcerative colitis (UC). I219V Polymorphism is located on exon 8 of hMLH1 and provides an aminoacidic substitution of isoleucine to valine, on the protein codon 219. This may affect the speed and fidelity of protein synthesis because of a tRNA paucity or changes in the mRNA secondary structure. Most of the hereditary nonpolyposis colon cancer-associated missense mutations of hMLH1 cause structural changes of the amino- or carboxy-terminal regions, involving the domains that interact with ATP and hPMS2. AIMS AND METHODS In this study, we analyzed the hMLH1 I219V polymorphism frequency in colectomized patients with UC. Venous blood from 100 ulcerative patients and 97 apparently healthy subjects has been collected. Out of 100 patients affected with UC, 75 noncolectomized showed an alternating course of disease, while 25 did not respond to the common drugs, and underwent colectomy. Genotyping was performed by polymerase chain reaction and following enzymatic digestion by BccI. RESULTS No significant differences were found between patients with UC and controls both for genotype and allele frequencies. However, our data show a significant association when colectomized and noncolectomized patients are compared. The frequencies of G homozygosity were 28% in colectomized and 10.7% in noncolectomized patients (p < 0.05, chi(2) = 4.4, Odds ratio = 3.3). The allele frequencies of allele A were 52% in colectomized and 68% in noncolectomized patients; while those of allele G were 48% and 32%, respectively. CONCLUSIONS I219V polymorphism in hMLH1 could influence the clinical course of the disease and lead to resistance to therapy.
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Affiliation(s)
- Maria Teresa Vietri
- Dipartimento di Patologia generale, Cattedra di Patologia clinica, Seconda Università degli studi Napoli, Naples, Italy
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Tanaka Y, Zaman MS, Majid S, Liu J, Kawakami K, Shiina H, Tokizane T, Dahiya AV, Sen S, Nakajima K. Polymorphisms of MLH1 in benign prostatic hyperplasia and sporadic prostate cancer. Biochem Biophys Res Commun 2009; 383:440-4. [PMID: 19364498 DOI: 10.1016/j.bbrc.2009.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 04/08/2009] [Indexed: 10/20/2022]
Abstract
Mismatch repair is one of several DNA repair pathways of which defects may lead to cancer. We hypothesize that polymorphisms of the MLH1 gene can be a risk factor for benign prostatic hyperplasia (BPH) and prostate cancer. The genetic distribution of MLH1 polymorphisms that lead to amino acid changes at codons 132, 219, 384, and 723 were analyzed in BPH and sporadic prostate cancer patients, and compared to healthy controls from an Asian population. These experiments demonstrate a protective role for the codon 384 variant allele against prostate cancer (P=0.031) but not BPH when compared to normal controls and furthermore, an inverse association was observed with stage (P=0.074) and grade (P=0.056) of cancer. This is the first report that demonstrates a protective effect for the race-related MLH1 polymorphism at codon 384 against prostate cancer and these results are important in understanding their role in this disease.
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Affiliation(s)
- Yuichiro Tanaka
- Department of Surgery/Urology (112F), Veterans Affairs Medical Center, University of California, 4150 Clement St., San Francisco, CA 94121, USA.
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Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P. The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol 2008; 382:610-27. [PMID: 18619468 DOI: 10.1016/j.jmb.2008.06.056] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 06/13/2008] [Accepted: 06/23/2008] [Indexed: 12/22/2022]
Abstract
DNA mismatch repair (MMR) is responsible for correcting replication errors. MutLalpha, one of the main players in MMR, has been recently shown to harbor an endonuclease/metal-binding activity, which is important for its function in vivo. This endonuclease activity has been confined to the C-terminal domain of the hPMS2 subunit of the MutLalpha heterodimer. In this work, we identify a striking sequence-structure similarity of hPMS2 to the metal-binding/dimerization domain of the iron-dependent repressor protein family and present a structural model of the metal-binding domain of MutLalpha. According to our model, this domain of MutLalpha comprises at least three highly conserved sequence motifs, which are also present in most MutL homologs from bacteria that do not rely on the endonuclease activity of MutH for strand discrimination. Furthermore, based on our structural model, we predict that MutLalpha is a zinc ion binding protein and confirm this prediction by way of biochemical analysis of zinc ion binding using the full-length and C-terminal domain of MutLalpha. Finally, we demonstrate that the conserved residues of the metal ion binding domain are crucial for MMR activity of MutLalpha in vitro.
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Affiliation(s)
- Jan Kosinski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
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