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Donegà S, Rogalska ME, Pianigiani G, Igreja S, Amaral MD, Pagani F. Rescue of common exon-skipping mutations in cystic fibrosis with modified U1 snRNAs. Hum Mutat 2020; 41:2143-2154. [PMID: 32935393 DOI: 10.1002/humu.24116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
In cystic fibrosis (CF), the correction of splicing defects represents an interesting therapeutic approach to restore normal CFTR function. In this study, we focused on 10 common mutations/variants 711+3A>G/C, 711+5G>A, TG13T3, TG13T5, TG12T5, 1863C>T, 1898+3A>G, 2789+5G>A, and 3120G>A that induce skipping of the corresponding CFTR exons 5, 10, 13, 16, and 18. To rescue the splicing defects we tested, in a minigene assay, a panel of modified U1 small nuclear RNAs (snRNAs), named Exon Specific U1s (ExSpeU1s), that was engineered to bind to intronic sequences downstream of each defective exon. Using this approach, we show that all 10 splicing mutations analyzed are efficiently corrected by specific ExSpeU1s. Using complementary DNA-splicing competent minigenes, we also show that the ExspeU1-mediated splicing correction at the RNA level recovered the full-length CFTR protein for 1863C>T, 1898+3A>G, 2789+5G>A variants. In addition, detailed mutagenesis experiments performed on exon 13 led us to identify a novel intronic regulatory element involved in the ExSpeU1-mediated splicing rescue. These results provide a common strategy based on modified U1 snRNAs to correct exon skipping in a group of disease-causing CFTR mutations.
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Affiliation(s)
- Stefano Donegà
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Malgorzata Ewa Rogalska
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Pianigiani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Susana Igreja
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Margarida Duarte Amaral
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Franco Pagani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
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2
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Cabrini G. Innovative Therapies for Cystic Fibrosis: The Road from Treatment to Cure. Mol Diagn Ther 2019; 23:263-279. [PMID: 30478715 DOI: 10.1007/s40291-018-0372-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cystic fibrosis (CF), a life-threatening multiorgan genetic disease, is facing a new era of research and development using innovative gene-directed personalized therapies. The priority organ to cure is the lung, which suffers recurrent and chronic bacterial infection and inflammation since infancy, representing the main cause of morbidity and precocious mortality of these individuals. After the disappointing failure of gene-replacement approaches using gene therapy vectors, no single drug is presently available to repair all the CF gene defects. The impressive number of different CF gene mutations is now tackled with different chemical and biotechnological tools tailored to the specific molecular derangements, thanks to the extensive knowledge acquired over many years on the mechanisms of CF cell and organ pathology. This review provides an overview and recalls both the successes and limitations of the different experimental approaches, such as high-throughput screening on chemical libraries to discover CF gene correctors and potentiators, dual-acting compounds, read-through molecules, splicing defect repairing tools, cystic fibrosis transmembrane conductance regulator (CFTR) "amplifiers," CFTR interactome modulators and the first gene editing attempts.
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Affiliation(s)
- Giulio Cabrini
- Laboratory of Molecular Pathology, University Hospital, Verona, Italy. .,Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy.
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3
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Chen KG, Zhong P, Zheng W, Beekman JM. Pharmacological analysis of CFTR variants of cystic fibrosis using stem cell-derived organoids. Drug Discov Today 2019; 24:2126-2138. [PMID: 31173911 DOI: 10.1016/j.drudis.2019.05.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/09/2019] [Accepted: 05/30/2019] [Indexed: 12/29/2022]
Abstract
Cystic fibrosis (CF) is a life-shortening genetic disease caused by mutations of CFTR, the gene encoding cystic fibrosis transmembrane conductance regulator. Despite considerable progress in CF therapies, targeting specific CFTR genotypes based on small molecules has been hindered because of the substantial genetic heterogeneity of CFTR mutations in patients with CF, which is difficult to assess by animal models in vivo. There are broadly four classes (e.g., II, III, and IV) of CF genotypes that differentially respond to current CF drugs (e.g., VX-770 and VX-809). In this review, we shed light on the pharmacogenomics of diverse CFTR mutations and the emerging role of stem cell-based organoids in predicting the CF drug response. We discuss mechanisms that underlie differential CF drug responses both in organoid-based assays and in CF clinical trials, thereby facilitating the precision design of safer and more effective therapies for individual patients with CF.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbiology and Immunology, Georgetown University Medical Center, Washington DC, 20057, USA.
| | - Pingyu Zhong
- Singapore Immunology Network, Agency for Science, Technology and Research (A⁎STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
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Chen KG, Mallon BS, Park K, Robey PG, McKay RDG, Gottesman MM, Zheng W. Pluripotent Stem Cell Platforms for Drug Discovery. Trends Mol Med 2018; 24:805-820. [PMID: 30006147 DOI: 10.1016/j.molmed.2018.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 12/30/2022]
Abstract
Use of human pluripotent stem cells (hPSCs) and their differentiated derivatives have led to recent proof-of-principle drug discoveries, defining a pathway to the implementation of hPSC-based drug discovery (hPDD). Current hPDD strategies, however, have inevitable conceptual biases and technological limitations, including the dimensionality of cell-culture methods, cell maturity and functionality, experimental variability, and data reproducibility. In this review, we dissect representative hPDD systems via analysis of hPSC-based 2D-monolayers, 3D culture, and organoids. We discuss mechanisms of drug discovery and drug repurposing, and roles of membrane drug transporters in tissue maturation and hPDD using the example of drugs that target various mutations of CFTR, the cystic fibrosis transmembrane conductance regulator gene, in patients with cystic fibrosis.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Barbara S Mallon
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyeyoon Park
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela G Robey
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald D G McKay
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Michael M Gottesman
- The Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
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Abstract
Nucleic acid therapeutics are an established class of drugs that enable specific targeting of a gene of interest. This diverse family of drugs includes antisense oligonucleotides, siRNAs, and mRNA replacement therapies, which can elicit both gene repression and activation, primarily at the RNA level. Recent advances in medicinal chemistry have increased drug potency and enhanced delivery and distribution to a broad array of tissue and cell types. A key advantage of nucleic acid therapeutics is in their application to monogenic diseases. Cystic fibrosis (CF) is one such disease that affects ∼70,000 people globally. This severe disease is an excellent candidate for nucleic acid therapies, as it is due to a genetic defect in a single epithelial chloride channel. Although CF affects many tissues, the primary cause of patient mortality is lung disease. Here we review the various nucleic acid therapeutic modalities and their mechanisms of action, the opportunities and challenges associated with application of nucleic acid drugs to the lung pathology of CF, and the current state and prospects for nucleic acid drugs for the treatment of CF.
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Affiliation(s)
| | - Shuling Guo
- Ionis Pharmaceuticals, Inc. , Carlsbad, California
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Lee M, Roos P, Sharma N, Atalar M, Evans TA, Pellicore MJ, Davis E, Lam ATN, Stanley SE, Khalil SE, Solomon GM, Walker D, Raraigh KS, Vecchio-Pagan B, Armanios M, Cutting GR. Systematic Computational Identification of Variants That Activate Exonic and Intronic Cryptic Splice Sites. Am J Hum Genet 2017; 100:751-765. [PMID: 28475858 DOI: 10.1016/j.ajhg.2017.04.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/30/2017] [Indexed: 12/30/2022] Open
Abstract
We developed a variant-annotation method that combines sequence-based machine-learning classification with a context-dependent algorithm for selecting splice variants. Our approach is distinctive in that it compares the splice potential of a sequence bearing a variant with the splice potential of the reference sequence. After training, classification accurately identified 168 of 180 (93.3%) canonical splice sites of five genes. The combined method, CryptSplice, identified and correctly predicted the effect of 18 of 21 (86%) known splice-altering variants in CFTR, a well-studied gene whose loss-of-function variants cause cystic fibrosis (CF). Among 1,423 unannotated CFTR disease-associated variants, the method identified 32 potential exonic cryptic splice variants, two of which were experimentally evaluated and confirmed. After complete CFTR sequencing, the method found three cryptic intronic splice variants (one known and two experimentally verified) that completed the molecular diagnosis of CF in 6 of 14 individuals. CryptSplice interrogation of sequence data from six individuals with X-linked dyskeratosis congenita caused by an unknown disease-causing variant in DKC1 identified two splice-altering variants that were experimentally verified. To assess the extent to which disease-associated variants might activate cryptic splicing, we selected 458 pathogenic variants and 348 variants of uncertain significance (VUSs) classified as high confidence from ClinVar. Splice-site activation was predicted for 129 (28%) of the pathogenic variants and 75 (22%) of the VUSs. Our findings suggest that cryptic splice-site activation is more common than previously thought and should be routinely considered for all variants within the transcribed regions of genes.
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Affiliation(s)
- Melissa Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Melis Atalar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taylor A Evans
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Matthew J Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emily Davis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anh-Thu N Lam
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan E Stanley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sara E Khalil
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - George M Solomon
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - Doug Walker
- Pediatric Pulmonary Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen S Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Briana Vecchio-Pagan
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mary Armanios
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Functional Studies and In Silico Analyses to Evaluate Non-Coding Variants in Inherited Cardiomyopathies. Int J Mol Sci 2016; 17:ijms17111883. [PMID: 27834932 PMCID: PMC5133883 DOI: 10.3390/ijms17111883] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/19/2016] [Accepted: 10/27/2016] [Indexed: 12/18/2022] Open
Abstract
Point mutations are the most common cause of inherited diseases. Bioinformatics tools can help to predict the pathogenicity of mutations found during genetic screening, but they may work less well in determining the effect of point mutations in non-coding regions. In silico analysis of intronic variants can reveal their impact on the splicing process, but the consequence of a given substitution is generally not predictable. The aim of this study was to functionally test five intronic variants (MYBPC3-c.506-2A>C, MYBPC3-c.906-7G>T, MYBPC3-c.2308+3G>C, SCN5A-c.393-5C>A, and ACTC1-c.617-7T>C) found in five patients affected by inherited cardiomyopathies in the attempt to verify their pathogenic role. Analysis of the MYBPC3-c.506-2A>C mutation in mRNA from the peripheral blood of one of the patients affected by hypertrophic cardiac myopathy revealed the loss of the canonical splice site and the use of an alternative splicing site, which caused the loss of the first seven nucleotides of exon 5 (MYBPC3-G169AfsX14). In the other four patients, we generated minigene constructs and transfected them in HEK-293 cells. This minigene approach showed that MYBPC3-c.2308+3G>C and SCN5A-c.393-5C>A altered pre-mRNA processing, thus resulting in the skipping of one exon. No alterations were found in either MYBPC3-c.906-7G>T or ACTC1-c.617-7T>C. In conclusion, functional in vitro analysis of the effects of potential splicing mutations can confirm or otherwise the putative pathogenicity of non-coding mutations, and thus help to guide the patient's clinical management and improve genetic counseling in affected families.
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Di Resta C, Manzoni M, Berisso MZ, Siciliano G, Benedetti S, Ferrari M. Evaluation of damaging effects of splicing mutations: validation of an in vitro method for diagnostic laboratories. Clin Chim Acta 2014; 436:276-82. [PMID: 24915601 DOI: 10.1016/j.cca.2014.05.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND Pre-mRNA splicing defects may have an important impact on clinical phenotype in several diseases, but often their pathogenic role is difficult to demonstrate. The aim of this study was to validate an in vitro method to assess the effects of putative splicing variants. MATERIALS AND METHODS We studied three novel variants in vitro using a novel minigene approach and compared results with in silico and ex vivo strategies from patient samples. RESULTS For the c.1146C>T variant in the LMNA gene, in vitro and ex vivo studies were concordant with the prediction obtained by in silico tools, confirming the loss of 13 bp at the end of exon 6. In the second case (c.1140+1G>A, SCN5A gene), in vitro experiments identified the insertion of 94 intronic bp in exon 9 as well as exon 9 skipping, but these results were not correctly predicted by ex vivo data and in silico tools. In the third case (c.1608+1C>T, LMNA gene) in vitro and ex vivo studies suggested the recognition of an exonic cryptic site leading to the loss of 29 bp in exon 9, not predicted by in silico analysis. CONCLUSION Our results revealed how in silico tools are often unreliable requiring "wet" RNA analysis. Since ex vivo studies are not always feasible, the use of an in vitro construct represents an efficient and useful method for the evaluation of damaging effects of unknown splicing variants, especially in diagnostic laboratories.
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Affiliation(s)
| | | | - Massimo Zoni Berisso
- Department of Cardiology, Padre A. Micone Hospital, ASL 3 "Genovese," Genoa, Italy
| | - Gabriele Siciliano
- Neurological Clinics, Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - Sara Benedetti
- Clinical Molecular Biology and Cytogenetics Laboratory, IRCCS San Raffaele Hospital, Milan, Italy
| | - Maurizio Ferrari
- Vita-Salute San Raffaele University, Milan, Italy; Clinical Molecular Biology and Cytogenetics Laboratory, IRCCS San Raffaele Hospital, Milan, Italy.
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Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet 2013; 45:1160-7. [PMID: 23974870 PMCID: PMC3874936 DOI: 10.1038/ng.2745] [Citation(s) in RCA: 428] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 07/30/2013] [Indexed: 12/16/2022]
Abstract
Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation to clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 cystic fibrosis patients in registries and clinics in North America and Europe. Among these patients, 159 CFTR variants had an allele frequency of ≥0.01%. These variants were evaluated for both clinical severity and functional consequence with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of cystic fibrosis patients enabled assignment of 12 of the remaining 32 variants as neutral while the other 20 variants remained indeterminate. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically-relevant genomic variation.
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Scott A, Petrykowska HM, Hefferon T, Gotea V, Elnitski L. Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene. J Cyst Fibros 2012; 11:511-7. [PMID: 22591852 DOI: 10.1016/j.jcf.2012.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 04/10/2012] [Accepted: 04/16/2012] [Indexed: 11/17/2022]
Abstract
BACKGROUND Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Over 1800 CFTR mutations have been reported, and about 12% of mutations are believed to impair pre-mRNA splicing. Given that several synthetic, non-splice-junction synonymous substitutions have been reported to alter splicing in CFTR, we predicted that naturally occurring synonymous substitutions may be erroneously classified as functionally neutral. METHODS Computational tools were used to predict the effect of synonymous substitutions on CFTR pre-mRNA splicing. The functional consequences of selected substitutions were evaluated using a minigene splicing assay. RESULTS Two synonymous mutations were shown to have a dramatic effect on CFTR pre-mRNA splicing, and consequently could alter protein integrity and phenotypic outcome. CONCLUSIONS Traditional methods of mutation analysis overlook splicing defects that occur at internal positions in coding exons, especially synonymous substitutions. We show that bioinformatics tools and minigene splicing assays are a potent combination to prioritize and identify mutations that cause aberrant CFTR pre-mRNA splicing.
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Affiliation(s)
- Alexandra Scott
- DIR/GTB Genomic Functional Analysis Section, National Human Genome Research Institute, NIH Rockville, MD 20852, USA
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