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Zhang H, Xin M, Lin L, Chen C, Balestra D, Ding Q. Pleiotropic effects of different exonic nucleotide changes at the same position contribute to hemophilia B phenotypic variation. J Thromb Haemost 2024; 22:975-989. [PMID: 38184202 DOI: 10.1016/j.jtha.2023.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND The disease-causing effects of genetic variations often depend on their location within a gene. Exonic changes generally lead to alterations in protein production, secretion, activity, or clearance. However, owing to the overlap between proteins and splicing codes, missense variants can also affect messenger RNA splicing, thus adding a layer of complexity and influencing disease phenotypes. OBJECTIVES To extensively characterize a panel of 13 exonic variants in the F9 gene occurring at 6 different factor IX positions and associated with varying severities of hemophilia B (HB). METHODS Computational predictions, splicing analysis, and recombinant factor IX assays were exploited to characterize F9 variants. RESULTS We demonstrated that 5 (38%) of 13 selected F9 exonic variants have pleiotropic effects. Although bioinformatic approaches accurately classified effects, extensive experimental assays were required to elucidate and deepen the molecular mechanisms underlying the pleiotropic effects. Importantly, their characterization was instrumental in developing tailored RNA therapeutics based on engineered U7 small nuclear RNA to mask cryptic splice sites and compensatory U1 small nuclear RNA to enhance exon definition. CONCLUSION Overall, albeit a multitool bioinformatic approach suggested the molecular effects of multiple HB variants, the deep investigation of molecular mechanisms revealed insights into the HB phenotype-genotype relationship, enabling accurate classification of HB variants. Importantly, knowledge of molecular mechanisms allowed the development of tailored RNA therapeutics, which can also be translated to other genetic diseases.
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Affiliation(s)
- Huayang Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Min Xin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Liya Lin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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2
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Todaro AM, Radu CM, Ciccone M, Toffanin S, Serino ML, Campello E, Bulato C, Lunghi B, Gemmati D, Cuneo A, Hackeng TM, Simioni P, Bernardi F, Castoldi E. In vitro and ex vivo rescue of a nonsense mutation responsible for severe coagulation factor V deficiency. J Thromb Haemost 2024; 22:410-422. [PMID: 37866515 DOI: 10.1016/j.jtha.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND Coagulation factor V (FV) deficiency is a rare bleeding disorder that is usually managed with fresh-frozen plasma. Patients with nonsense mutations may respond to treatment with readthrough agents. OBJECTIVES To investigate whether the F5 p.Arg1161Ter mutation, causing severe FV deficiency in several patients, would be amenable to readthrough therapy. METHODS F5 mRNA and protein expression were evaluated in a F5 p.Arg1161Ter-homozygous patient. Five readthrough agents with different mechanisms of action, i.e. G418, ELX-02, PTC-124, 2,6-diaminopurine (2,6-DAP), and Amlexanox, were tested in in vitro and ex vivo models of the mutation. RESULTS The F5 p.Arg1161Ter-homozygous patient showed residual F5 mRNA and functional platelet FV, indicating detectable levels of natural readthrough. COS-1 cells transfected with the FV-Arg1161Ter cDNA expressed 0.7% FV activity compared to wild-type. Treatment with 0-500 μM G418, ELX-02, and 2,6-DAP dose-dependently increased FV activity up to 7.0-fold, 3.1-fold, and 10.8-fold, respectively, whereas PTC-124 and Amlexanox (alone or in combination) were ineffective. These findings were confirmed by thrombin generation assays in FV-depleted plasma reconstituted with conditioned media of treated cells. All compounds except ELX-02 showed some degree of cytotoxicity. Ex vivo differentiated megakaryocytes of the F5 p.Arg1161Ter-homozygous patient, which were negative at FV immunostaining, turned positive after treatment with all 5 readthrough agents. Notably, they were also able to internalize mutant FV rescued with G418 or 2,6-DAP, which would be required to maintain the crucial platelet FV pool in vivo. CONCLUSION These findings provide in vitro and ex vivo proof-of-principle for readthrough-mediated rescue of the F5 p.Arg1161Ter mutation.
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Affiliation(s)
- Alice M Todaro
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Claudia M Radu
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Maria Ciccone
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Serena Toffanin
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - M Luisa Serino
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Elena Campello
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Cristiana Bulato
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Barbara Lunghi
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Donato Gemmati
- Department of Translational Medicine, Haemostasis & Thrombosis Centre, Ferrara University, Ferrara, Italy
| | - Antonio Cuneo
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Tilman M Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Paolo Simioni
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Elisabetta Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands.
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3
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Mashima R, Takada S, Miyamoto Y. RNA-Based Therapeutic Technology. Int J Mol Sci 2023; 24:15230. [PMID: 37894911 PMCID: PMC10607345 DOI: 10.3390/ijms242015230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/09/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
RNA-based therapy has been an expanding area of clinical research since the COVID-19 outbreak. Often, its comparison has been made to DNA-based gene therapy, such as adeno-associated virus- and lentivirus-mediated therapy. These DNA-based therapies show persistent expression, with maximized therapeutic efficacy. However, accumulating data indicate that proper control of gene expression is occasionally required. For example, in cancer immunotherapy, cytokine response syndrome is detrimental for host animals, while excess activation of the immune system induces supraphysiological cytokines. RNA-based therapy seems to be a rather mild therapy, and it has room to fit unmet medical needs, whereas current DNA-based therapy has unclear issues. This review focused on RNA-based therapy for cancer immunotherapy, hematopoietic disorders, and inherited disorders, which have received attention for possible clinical applications.
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Affiliation(s)
- Ryuichi Mashima
- Department of Clinical Laboratory Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Yoshitaka Miyamoto
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
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4
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Antisense-Mediated Down-Regulation of Factor V-Short Splicing in a Liver Cell Line Model. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11209621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Coagulation factor V (FV) is a liver-derived protein encoded by the F5 gene. Alternative splicing of F5 exon 13 produces a low-abundance splicing isoform, known as FV-short, which binds the anticoagulant protein tissue factor pathway inhibitor (TFPIα) with high affinity, stabilising it in the circulation and potently enhancing its anticoagulant activity. Accordingly, rare F5 gene mutations that up-regulate FV-short splicing are associated with bleeding. In this study we have explored the possibility of decreasing FV-short splicing by antisense-based splicing modulation. To this end, we have designed morpholino antisense oligonucleotides (MAOs) targeting the FV-short-specific donor and acceptor splice sites and tested their efficacy in a liver cell line (HepG2) that naturally expresses full-length FV and FV-short. Cells were treated with 0–20 µM MAO, and full-length FV and FV-short mRNA expression was analysed by RT-(q)PCR. Both MAOs, alone or in combination, decreased the FV-short/full-length FV mRNA ratio down to ~50% of its original value in a specific and dose-dependent manner. This pilot study provides proof-of-principle for the possibility to decrease FV-short expression by antisense-mediated splicing modulation. In turn, this may form the basis for novel therapeutic approaches to bleeding disorders caused by FV-short over-expression and/or elevated TFPIα (activity) levels.
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Lesman D, Rodriguez Y, Rajakumar D, Wein N. U7 snRNA, a Small RNA with a Big Impact in Gene Therapy. Hum Gene Ther 2021; 32:1317-1329. [PMID: 34139889 DOI: 10.1089/hum.2021.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The uridine-rich 7 (U7) small nuclear RNA (snRNA) is a component of a small nuclear ribonucleoprotein (snRNP) complex. U7 snRNA naturally contains an antisense sequence that identifies histone premessenger RNAs (pre-mRNAs) and is involved in their 3' end processing. By altering this antisense sequence, researchers have turned U7 snRNA into a versatile tool for targeting pre-mRNAs and modifying splicing. Encapsulating a modified U7 snRNA into a viral vector such as adeno-associated virus (also referred as vectorized exon skipping/inclusion, or VES/VEI) enables the delivery of this highly efficacious splicing modulator into a range of cell lines, primary cells, and tissues. In addition, and in contrast to antisense oligonucleotides, viral delivery of U7 snRNA enables long-term expression of antisense sequences in the nucleus as part of a stable snRNP complex. As a result, VES/VEI has emerged as a promising therapeutic platform for treating a large variety of human diseases caused by errors in pre-mRNA splicing or its regulation. Here we provide an overview of U7 snRNA's natural function and its applications in gene therapy.
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Affiliation(s)
- Daniel Lesman
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Yacidzohara Rodriguez
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Dhanarajan Rajakumar
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Nicolas Wein
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatric, The Ohio State University, Columbus, Ohio, USA
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Zhou X, Xu H, Cai X, Tang B, Liu X, Shi Y, Zheng J, Liao W, Yu L. Differences in SCN1A intronic variants result in diverse aberrant splicing patterns and are related to the phenotypes of epilepsy with febrile seizures. Epilepsy Res 2021; 176:106711. [PMID: 34293681 DOI: 10.1016/j.eplepsyres.2021.106711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/05/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE Intronic variants of the SCN1A gene are detected in patients with epilepsy with febrile seizures (EFS), which includes a series of phenotypes with different severities. However, the pathogenicity of intronic variants and their genotype-phenotype correlation remain under characterized. The purpose of this study was to determine the changes in mRNA splicing caused by SCN1A intronic variants associated with EFS and their association with phenotypes. METHODS Five SCN1A intronic variants detected in patients with focal epilepsy with antecedent febrile seizures plus (FEFS+) and Dravet syndrome (DS) were molecularly cloned. Through an in vitro minigene splicing assay, their influence on mRNA splicing was qualitatively and quantitatively compared and analyzed using reverse-transcription polymerase chain reaction (RT-PCR) and fluorescence quantitative PCR (Q-PCR). RESULTS The severe phenotype of DS-associated variants c.602 + 1G > A and c.4853-1G > C, which occurred in canonical splice sites of introns, caused exon skipping and little retention of full-length mRNA, while the milder phenotype of FEFS+-associated variants c.473 + 5G > A, c.473 + 5G > C and c.4853-25T > A, which occurred in potential splice sites or in deep intronic regions, presented partial exon skipping or intronic insertion and significantly higher retention of full-length mRNA at different levels. Full-length mRNA retention was negatively correlated with the location of intronic variants and phenotype severity. CONCLUSION The different aberrant splicing patterns resulting from SCN1A intronic variants with different positions represent a potential molecular mechanism for phenotypic differences in EFS. This research provides valuable clues for functional studies on the pathogenicity of intronic variants and for the evaluation of genotype-phenotype correlations.
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Affiliation(s)
- Xijing Zhou
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
| | - Haiqing Xu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Xiuqu Cai
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Bin Tang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Xiaorong Liu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Yiwu Shi
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Jinou Zheng
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
| | - Weiping Liao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China.
| | - Lu Yu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, GX, China.
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Li M, Lu X, Dong J, Yao Z, Wu Y, Rao H, Huang X, Chen X, Huang Y, Wu Y. A synonymous mutation in exon 39 of FBN1 causes exon skipping leading to Marfan syndrome. Genomics 2020; 112:3856-3861. [PMID: 32562828 DOI: 10.1016/j.ygeno.2020.06.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 11/15/2022]
Abstract
Marfan syndrome is a heritable autosomal-dominant connective tissue disorder and it was typically caused by mutations in FBN1. However, the synonymous mutation was seldom recorded to be related to Marfan syndrome. Hereon, Multiplex ligation-dependent probe amplification failed to detect a copy number variant involving FBN1 but a synonymous mutation c.4773A > G (p.Gly1591Gly) was identified by NGS in exon 39. RNA was extracted from patient's aortic tissue and reverse polymerase chain reaction demonstrated the presence of a shortened mRNA transcript. Results of minigene models indicated that c.4773A > G was bona fide responsibility for the aberrant splicing pattern, and artificial mutations of c.4773A > C and c.4773A > T also gave rise to fragments with exon 39 entire skipped. Together, the novel synonymous mutations in c.4773 position (A > G, C, T), middle of exon 39 of FBN1 gene, was found to be associated with Marfan syndrome by altering the splicing pattern of pre-mRNA.
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Affiliation(s)
- Mingjie Li
- Department of Clinical Laboratory, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Xinxin Lu
- Department of Clinical Laboratory, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Jian Dong
- Department of Clinical Laboratory, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Zuwu Yao
- Department of Cardiovascular Surgery, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Yinlong Wu
- Department of Clinical Laboratory, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Huiying Rao
- Department of Ophthalmology, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Xiaoli Huang
- Department of Clinical Laboratory, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Xijun Chen
- Department of Clinical Laboratory, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Yi Huang
- Department of Clinical Laboratory, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou 350001, China
| | - Yan'an Wu
- Department of Clinical Laboratory, Fujian Provincial Hospital, Shengli Clinical Medical College, Fujian Medical University, Fuzhou 350001, China.
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8
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Ferraresi P, Balestra D, Guittard C, Buthiau D, Pan-Petesh B, Maestri I, Farah R, Pinotti M, Giansily-Blaizot M. Next-generation sequencing and recombinant expression characterized aberrant splicing mechanisms and provided correction strategies in factor VII deficiency. Haematologica 2019; 105:829-837. [PMID: 31273093 PMCID: PMC7049351 DOI: 10.3324/haematol.2019.217539] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/02/2019] [Indexed: 01/22/2023] Open
Abstract
Despite the exhaustive screening of F7 gene exons and exon-intron boundaries and promoter region, a significant proportion of mutated alleles remains unidentified in patients with coagulation factor VII deficiency. Here, we applied next-generation sequencing to 13 FVII-deficient patients displaying genotype-phenotype discrepancies upon conventional sequencing, and identified six rare intronic variants. Computational analysis predicted splicing effects for three of them, which would strengthen (c.571+78G>A; c.806-329G>A) or create (c.572-392C>G) intronic 5′ splice sites (5′ss). In F7 minigene assays, the c.806-329G>A was ineffective while the c.571+78G>A change led to usage of the +79 cryptic 5′ss with only trace levels of correct transcripts (3% of wild-type), in accordance with factor VII activity levels in homozygotes (1-3% of normal). The c.572-392C>G change led to pseudo-exonization and frame-shift, but also substantial levels of correct transcripts (approx. 70%). However, this variant was associated with the common F7 polymorphic haplotype, predicted to further decrease factor VII levels; this provided some kind of explanation for the 10% factor VII levels in the homozygous patient. Intriguingly, the effect of the c.571+78G>A and c.572-392C>G changes, and particularly of the former (the most severe and well-represented in our cohort), was counteracted by antisense U7snRNA variants targeting the intronic 5′ss, thus demonstrating their pathogenic role. In conclusion, the combination of next-generation sequencing of the entire F7 gene with the minigene expression studies elucidated the molecular bases of factor VII deficiency in 10 of 13 patients, thus improving diagnosis and genetic counseling. It also provided a potential therapeutic approach based on antisense molecules that has been successfully exploited in other disorders.
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Affiliation(s)
- Paolo Ferraresi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Caroline Guittard
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
| | - Delphine Buthiau
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
| | | | - Iva Maestri
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Roula Farah
- Department of Pediatrics, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Muriel Giansily-Blaizot
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
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Balestra D, Branchini A. Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies. Int J Mol Sci 2019; 20:ijms20123036. [PMID: 31234407 PMCID: PMC6627357 DOI: 10.3390/ijms20123036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/07/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular strategies tailored to promote/correct the expression and/or processing of defective coagulation factors would represent innovative therapeutic approaches beyond standard substitutive therapy. Here, we focus on the molecular mechanisms and determinants underlying innovative approaches acting at DNA, mRNA and protein levels in inherited coagulation factor deficiencies, and in particular on: (i) gene editing approaches, which have permitted intervention at the DNA level through the specific recognition, cleavage, repair/correction or activation of target sequences, even in mutated gene contexts; (ii) the rescue of altered pre-mRNA processing through the engineering of key spliceosome components able to promote correct exon recognition and, in turn, the synthesis and secretion of functional factors, as well as the effects on the splicing of missense changes affecting exonic splicing elements; this section includes antisense oligonucleotide- or siRNA-mediated approaches to down-regulate target genes; (iii) the rescue of protein synthesis/function through the induction of ribosome readthrough targeting nonsense variants or the correction of folding defects caused by amino acid substitutions. Overall, these approaches have shown the ability to rescue the expression and/or function of potentially therapeutic levels of coagulation factors in different disease models, thus supporting further studies in the future aimed at evaluating the clinical translatability of these new strategies.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
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10
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A series of 10 Polish patients with thromboembolic events and antithrombin deficiency: two new c.1154-1 G>C and c.1219-534 A>G SERPINC1 gene splicing mutations. Blood Coagul Fibrinolysis 2019; 30:193-198. [PMID: 31157679 DOI: 10.1097/mbc.0000000000000816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
: Inherited antithrombin (AT) deficiency, with prevalence in the general population ranging 0.02-0.17%, is an autosomal dominant disorder associated with a high risk of venous thromboembolism. In most cases, deficiency is caused by mutations in the AT-coding gene (SERPINC1). Only 24 splicing defects have been described causing AT deficiency, all affecting exon flanking regions. The aim of the current study was to characterize the mutations underlying AT deficiency in 10 venous thromboembolism Polish patients aged 42.9 (14-63) years. Whole SERPINC1 gene sequencing was done by next generation sequencing methods. Eight cases had mutations previously described. However, we identified two new intronic mutations that might affect the correct splicing of exon 6 according to in-silico predictions: c.1154-1 G>C, which strongly disturbs the acceptor sequence and c.1219-534 A>G, a deep intronic mutation that might generate a cryptic donor sequence; both might compete with the wild-type donor sequence and explain the associated moderate AT deficiency of carriers. In conclusion, we show the molecular base of AT deficiency in 10 new Polish patients, including two novel SERPINC1 gene mutations potentially affecting splicing.
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11
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Donadon I, Pinotti M, Rajkowska K, Pianigiani G, Barbon E, Morini E, Motaln H, Rogelj B, Mingozzi F, Slaugenhaupt SA, Pagani F. Exon-specific U1 snRNAs improve ELP1 exon 20 definition and rescue ELP1 protein expression in a familial dysautonomia mouse model. Hum Mol Genet 2018; 27:2466-2476. [PMID: 29701768 PMCID: PMC6030917 DOI: 10.1093/hmg/ddy151] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/30/2022] Open
Abstract
Familial dysautonomia (FD) is a rare genetic disease with no treatment, caused by an intronic point mutation (c.2204+6T>C) that negatively affects the definition of exon 20 in the elongator complex protein 1 gene (ELP1 also known as IKBKAP). This substitution modifies the 5' splice site and, in combination with regulatory splicing factors, induces different levels of exon 20 skipping, in various tissues. Here, we evaluated the therapeutic potential of a novel class of U1 snRNA molecules, exon-specific U1s (ExSpeU1s), in correcting ELP1 exon 20 recognition. Lentivirus-mediated expression of ELP1-ExSpeU1 in FD fibroblasts improved ELP1 splicing and protein levels. We next focused on a transgenic mouse model that recapitulates the same tissue-specific mis-splicing seen in FD patients. Intraperitoneal delivery of ELP1-ExSpeU1s-adeno-associated virus particles successfully increased the production of full-length human ELP1 transcript and protein. This splice-switching class of molecules is the first to specifically correct the ELP1 exon 20 splicing defect. Our data provide proof of principle of ExSpeU1s-adeno-associated virus particles as a novel therapeutic strategy for FD.
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Affiliation(s)
- Irving Donadon
- Human Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Katarzyna Rajkowska
- Human Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Pianigiani
- Human Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Elisabetta Morini
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Helena Motaln
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
- Biomedical Research Institute BRIS, Ljubljana, Slovenia
| | - Federico Mingozzi
- Genethon and INSERM U951, Evry, France
- University Pierre and Marie Curie and INSERM U974, Paris, France
| | - Susan A Slaugenhaupt
- Center for Genomic Medicine, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Franco Pagani
- Human Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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de la Morena‐Barrio ME, López‐Gálvez R, Martínez‐Martínez I, Asenjo S, Sevivas TS, López MF, Wypasek E, Entrena L, Vicente V, Corral J. Defects of splicing in antithrombin deficiency. Res Pract Thromb Haemost 2017; 1:216-222. [PMID: 30046692 PMCID: PMC6058262 DOI: 10.1002/rth2.12025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/13/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND There is increasing evidence supporting the relevance of aberrant splicing in multiple disorders. In antithrombin deficiency only 22 intronic mutations affecting splicing sites (7% of SERPINC1 mutations) are considered as splicing mutations. METHODS SERPINC1 was analyzed by Sanger sequencing and MLPA in 141 unrelated cases with antithrombin deficiency. Plasma antithrombin was studied by functional and western blot assays, purified by FPLC and characterized by proteomic analysis. In silico predictions on splicing was done with the Human Splicing Finder software. RESULTS We detected 89 different SERPINC1 defects, 13 with potential effect on splicing. Ten cases presented 9 mutations disturbing splicing sites, 5 new. Three gross or small gene defects also disturbed a correct splicing. Interestingly, the first duplication of a single exon ever described (c.1154-13_1218+115dup), caused mild deficiency (75%). A deeper intronic mutation (c.1154-14G>A), identified in three unrelated patients with traces of disulphide dimers of antithrombin in plasma, created a cryptic splicing site that might generate a variant with 4 additional in frame residues according to in silico predictions. This aberrant splicing was confirmed by proteomic analysis of the dimer purified from plasma. CONCLUSIONS A high proportion of cases with antithrombin deficiency (up to 13%) may be explained by an aberrant splicing. Up to 15% of mutations in SERPINC1: splicing site variations, gross gene defects and deep intronic mutations, may affect a correct splicing with three potential consequences type I, type II, and even moderate antithrombin deficiency.
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Affiliation(s)
- María E. de la Morena‐Barrio
- Servicio de Hematología y Oncología MédicaHospital Universitario Morales MeseguerCentro Regional de HemodonaciónUniversidad de MurciaIMIB‐ArrixacaMurciaSpain
- CIBERERMadridSpain
| | - Raquel López‐Gálvez
- Servicio de Hematología y Oncología MédicaHospital Universitario Morales MeseguerCentro Regional de HemodonaciónUniversidad de MurciaIMIB‐ArrixacaMurciaSpain
| | - Irene Martínez‐Martínez
- Servicio de Hematología y Oncología MédicaHospital Universitario Morales MeseguerCentro Regional de HemodonaciónUniversidad de MurciaIMIB‐ArrixacaMurciaSpain
- CIBERERMadridSpain
| | - Susana Asenjo
- Servicio de HematologíaHospital Clínico San CarlosMadridSpain
| | - Teresa S. Sevivas
- Serviço de Hematologia do Centro Hospitalar e Universitário de CoimbraCoimbraPortugal
| | - María F. López
- Servicio de Hematología Hospital Juan CanalejoA CoruñaSpain
| | - Ewa Wypasek
- The John Paul II HospitalKrakówPoland
- Institute of CardiologyJagiellonian University Medical CollegeKrakówPoland
| | - Laura Entrena
- Servicio de HematologíaHospital Virgen de las NievesGranadaSpain
| | - Vicente Vicente
- Servicio de Hematología y Oncología MédicaHospital Universitario Morales MeseguerCentro Regional de HemodonaciónUniversidad de MurciaIMIB‐ArrixacaMurciaSpain
- CIBERERMadridSpain
| | - Javier Corral
- Servicio de Hematología y Oncología MédicaHospital Universitario Morales MeseguerCentro Regional de HemodonaciónUniversidad de MurciaIMIB‐ArrixacaMurciaSpain
- CIBERERMadridSpain
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Radu CM, Spiezia L, Bulato C, Gavasso S, Campello E, Sartorello F, Castoldi E, Simioni P. Endocytosis of exogenous factor V by ex-vivo differentiated megakaryocytes from patients with severe parahaemophilia. Br J Haematol 2016; 175:517-524. [PMID: 27443583 DOI: 10.1111/bjh.14262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/07/2016] [Indexed: 11/29/2022]
Abstract
Although human megakaryocytes can synthesize factor V (FV), platelet FV derives largely from endocytosis of plasma FV. Recently, it has been shown that plasma transfusions can replenish the platelet FV pool in parahaemophilic patients. Here we corroborate this finding by showing FV endocytosis by ex vivo differentiated megakaryocytes derived from patients with inherited parahaemophilia. Mononuclear stem cells isolated from peripheral blood of healthy subjects and of three patients with severe parahaemophilia were cultured in the presence of thrombopoietin and interleukin-3 and differentiated into CD41-positive polynucleated megakaryocytes. Exogenous purified FV was added to the culture medium to evaluate FV endocytosis. Immunofluorescence staining revealed abundant FV expression in megakaryocytes derived from healthy donors, but no FV expression in those derived from patients with severe parahaemophilia. However, after the addition of purified FV to the culture medium, megakaryocytes from parahaemophilia patients became positive upon FV immunostaining, suggesting endocytosis of exogenous FV. Endocytosed FV retained factor Xa-co-factor activity as assessed by a prothrombin time-based functional test in megakaryocyte lysates. Addition of exogenous FV to culture medium can restore the FV content of megakaryocytes derived from patients with severe FV defects. This rescue mechanism can have important clinical implications in the management of parahaemophilia patients.
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Affiliation(s)
- Claudia M Radu
- Department of Medicine - DIMED, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Haemophilia and Thrombophilia Centre, University of Padua Medical School, Padua, Italy
| | - Luca Spiezia
- Department of Medicine - DIMED, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Haemophilia and Thrombophilia Centre, University of Padua Medical School, Padua, Italy
| | - Cristiana Bulato
- Department of Medicine - DIMED, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Haemophilia and Thrombophilia Centre, University of Padua Medical School, Padua, Italy
| | - Sabrina Gavasso
- Department of Medicine - DIMED, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Haemophilia and Thrombophilia Centre, University of Padua Medical School, Padua, Italy
| | - Elena Campello
- Department of Medicine - DIMED, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Haemophilia and Thrombophilia Centre, University of Padua Medical School, Padua, Italy
| | - Francesca Sartorello
- Department of Medicine - DIMED, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Haemophilia and Thrombophilia Centre, University of Padua Medical School, Padua, Italy
| | - Elisabetta Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Paolo Simioni
- Department of Medicine - DIMED, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Haemophilia and Thrombophilia Centre, University of Padua Medical School, Padua, Italy.
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14
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Nuzzo F, Beshlawi I, Wali Y, Castoldi E. High incidence of intracranial bleeding in factor V-deficient patients with homozygous F5 splicing mutations. Br J Haematol 2016; 179:163-166. [PMID: 27351627 DOI: 10.1111/bjh.14195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Francesca Nuzzo
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Ismail Beshlawi
- Child Health Department, Sultan Qaboos University Hospital, Muscat, Sultanate of Oman.,Queen's Medical Centre, Nottingham University Hospitals' NHS Trust, Nottingham, UK
| | - Yasser Wali
- Child Health Department, Sultan Qaboos University Hospital, Muscat, Sultanate of Oman.,Alexandria University Children's Hospital, Alexandria, Egypt
| | - Elisabetta Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
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15
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Casini A, de Moerloose P. Factor concentrates for rare congenital coagulation disorders: where are we now? Expert Opin Orphan Drugs 2015. [DOI: 10.1517/21678707.2016.1108188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Bonini J, Varilh J, Raynal C, Thèze C, Beyne E, Audrezet MP, Ferec C, Bienvenu T, Girodon E, Tuffery-Giraud S, Des Georges M, Claustres M, Taulan-Cadars M. Small-scale high-throughput sequencing-based identification of new therapeutic tools in cystic fibrosis. Genet Med 2015; 17:796-806. [PMID: 25569440 DOI: 10.1038/gim.2014.194] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/24/2014] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Although 97-99% of CFTR mutations have been identified, great efforts must be made to detect yet-unidentified mutations. METHODS We developed a small-scale next-generation sequencing approach for reliably and quickly scanning the entire gene, including noncoding regions, to identify new mutations. We applied this approach to 18 samples from patients suffering from cystic fibrosis (CF) in whom only one mutation had hitherto been identified. RESULTS Using an in-house bioinformatics pipeline, we could rapidly identify a second disease-causing CFTR mutation for 16 of 18 samples. Of them, c.1680-883A>G was found in three unrelated CF patients. Analysis of minigenes and patients' transcripts showed that this mutation results in aberrantly spliced transcripts because of the inclusion of a pseudoexon. It is located only three base pairs from the c.1680-886A>G mutation (1811+1.6kbA>G), the fourth most frequent mutation in southwestern Europe. We next tested the effect of antisense oligonucleotides targeting splice sites on these two mutations on pseudoexon skipping. Oligonucleotide transfection resulted in the restoration of the full-length, in-frame CFTR transcript, demonstrating the effect of antisense oligonucleotide-induced pseudoexon skipping in CF. CONCLUSION Our data confirm the importance of analyzing noncoding regions to find unidentified mutations, which is essential to designing targeted therapeutic approaches.
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Affiliation(s)
- Jennifer Bonini
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Université Montpellier I, UFR de Médecine, Montpellier, France
| | - Jessica Varilh
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Caroline Raynal
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Corinne Thèze
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Emmanuelle Beyne
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | | | - Claude Ferec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU, Brest, France
| | - Thierry Bienvenu
- AP-HP, Service de Biochimie et Génétique Moléculaires, Groupe Hospitalier Cochin Broca Hôtel Dieu, Paris, France
| | - Emmanuelle Girodon
- AP-HP, Service de Biochimie et Génétique Moléculaires, Groupe Hospitalier Cochin Broca Hôtel Dieu, Paris, France
| | - Sylvie Tuffery-Giraud
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Université Montpellier I, UFR de Médecine, Montpellier, France
| | - Marie Des Georges
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Mireille Claustres
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Université Montpellier I, UFR de Médecine, Montpellier, France
| | - Magali Taulan-Cadars
- INSERM U827, Laboratoire de Génétique de Maladies Rares, Montpellier, France.,Université Montpellier I, UFR de Médecine, Montpellier, France
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Nuzzo F, Bulato C, Nielsen BI, Lee K, Wielders SJ, Simioni P, Key NS, Castoldi E. Characterization of an apparently synonymous F5 mutation causing aberrant splicing and factor V deficiency. Haemophilia 2014; 21:241-248. [PMID: 25470420 DOI: 10.1111/hae.12554] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2014] [Indexed: 01/07/2023]
Abstract
Coagulation factor V (FV) deficiency is a rare autosomal recessive bleeding disorder. We investigated a patient with severe FV deficiency (FV:C < 3%) and moderate bleeding symptoms. Thrombin generation experiments showed residual FV expression in the patient's plasma, which was quantified as 0.7 ± 0.3% by a sensitive prothrombinase-based assay. F5 gene sequencing identified a novel missense mutation in exon 4 (c.578G>C, p.Cys193Ser), predicting the abolition of a conserved disulphide bridge, and an apparently synonymous variant in exon 8 (c.1281C>G). The observation that half of the patient's F5 mRNA lacked the last 18 nucleotides of exon 8 prompted us to re-evaluate the c.1281C>G variant for its possible effects on splicing. Bioinformatics sequence analysis predicted that this transversion would activate a cryptic donor splice site and abolish an exonic splicing enhancer. Characterization in a F5 minigene model confirmed that the c.1281C>G variant was responsible for the patient's splicing defect, which could be partially corrected by a mutation-specific morpholino antisense oligonucleotide. The aberrantly spliced F5 mRNA, whose stability was similar to that of the normal mRNA, encoded a putative FV mutant lacking amino acids 427-432. Expression in COS-1 cells indicated that the mutant protein is poorly secreted and not functional. In conclusion, the c.1281C>G mutation, which was predicted to be translationally silent and hence neutral, causes FV deficiency by impairing pre-mRNA splicing. This finding underscores the importance of cDNA analysis for the correct assessment of exonic mutations.
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Affiliation(s)
- F Nuzzo
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
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