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Catasús N, Rosas I, Bonache S, Negro A, Torres-Martin M, Plana-Pla A, Salvador H, Serra E, Blanco I, Castellanos E. Antisense oligonucleotides targeting exon 11 are able to partially rescue the NF2-related schwannomatosis phenotype in vitro. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:493-505. [PMID: 36420221 PMCID: PMC9678674 DOI: 10.1016/j.omtn.2022.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
NF2-related schwannomatosis (NF2-related SWN) is an autosomal dominant condition caused by loss of function variants in the NF2 gene, which codes for the protein Merlin and is characterized by the development of multiple tumors of the nervous system. The clinical presentation of the disease is variable and related to the type of the inherited germline variant. Here, we tested if phosphorodiamidate morpholino oligomers (PMOs) could be used to correct the splice signaling caused by variants at ±13 within the intron-exon boundary region and showed that the PMOs designed for these variants do not constitute a therapeutic approach. Furthermore, we evaluated the use of PMOs to decrease the severity of the effects of NF2 truncating variants with the aim of generating milder hypomorphic isoforms in vitro through the induction of the in-frame deletion of the exon-carrying variant. We were able to specifically induce the skipping of exons 4, 8, and 11 maintaining the NF2 gene reading frame at cDNA level. Only the skipping of exon 11 produced a hypomorphic Merlin (Merlin-e11), which is able to partially rescue the observed phenotype in primary fibroblast cultures from NF2-related SWN patients, being encouraging for the treatment of patients harboring truncating variants located in exon 11.
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Affiliation(s)
- Núria Catasús
- Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
| | - Inma Rosas
- Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
- Clinical Genetics Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
| | - Sandra Bonache
- Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
- Clinical Genetics Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
| | - Alex Negro
- Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
- Clinical Genetics Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
| | - Miguel Torres-Martin
- Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
- Clinical Genetics Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
| | - Adrià Plana-Pla
- Dermatology Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Badalona, Barcelona 08916, Spain
| | - Hector Salvador
- Pediatric Oncology Unit, Hospital Sant Joan de Déu, Esplugues, Barcelona, Spain
| | - Eduard Serra
- Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP-PMPPC), Can Ruti Campus, Badalona, Barcelona 08916, Spain
| | - Ignacio Blanco
- Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
- Clinical Genetics Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
| | - Elisabeth Castellanos
- Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
- Clinical Genetics Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
| | - NF2-related SWN Spanish National Reference Centre HUGTP-ICO-IGTP
- Clinical Genomics Research Group, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
- Clinical Genetics Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Crta. Canyet, s/n. Badalona, Barcelona 08916, Spain
- Dermatology Department, Germans Trias i Pujol University Hospital (HUGTP), Can Ruti Campus, Badalona, Barcelona 08916, Spain
- Pediatric Oncology Unit, Hospital Sant Joan de Déu, Esplugues, Barcelona, Spain
- Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP-PMPPC), Can Ruti Campus, Badalona, Barcelona 08916, Spain
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2
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Amanat M, Nemeth CL, Fine AS, Leung DG, Fatemi A. Antisense Oligonucleotide Therapy for the Nervous System: From Bench to Bedside with Emphasis on Pediatric Neurology. Pharmaceutics 2022; 14:2389. [PMID: 36365206 PMCID: PMC9695718 DOI: 10.3390/pharmaceutics14112389] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 09/05/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are disease-modifying agents affecting protein-coding and noncoding ribonucleic acids. Depending on the chemical modification and the location of hybridization, ASOs are able to reduce the level of toxic proteins, increase the level of functional protein, or modify the structure of impaired protein to improve function. There are multiple challenges in delivering ASOs to their site of action. Chemical modifications in the phosphodiester bond, nucleotide sugar, and nucleobase can increase structural thermodynamic stability and prevent ASO degradation. Furthermore, different particles, including viral vectors, conjugated peptides, conjugated antibodies, and nanocarriers, may improve ASO delivery. To date, six ASOs have been approved by the US Food and Drug Administration (FDA) in three neurological disorders: spinal muscular atrophy, Duchenne muscular dystrophy, and polyneuropathy caused by hereditary transthyretin amyloidosis. Ongoing preclinical and clinical studies are assessing the safety and efficacy of ASOs in multiple genetic and acquired neurological conditions. The current review provides an update on underlying mechanisms, design, chemical modifications, and delivery of ASOs. The administration of FDA-approved ASOs in neurological disorders is described, and current evidence on the safety and efficacy of ASOs in other neurological conditions, including pediatric neurological disorders, is reviewed.
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Affiliation(s)
- Man Amanat
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christina L. Nemeth
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amena Smith Fine
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Doris G. Leung
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Genetic Muscle Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ali Fatemi
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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Piotrowski A, Koczkowska M, Poplawski AB, Bartoszewski R, Króliczewski J, Mieczkowska A, Gomes A, Crowley MR, Crossman DK, Chen Y, Lao P, Serra E, Llach MC, Castellanos E, Messiaen LM. Targeted massively parallel sequencing of candidate regions on chromosome 22q predisposing to multiple schwannomas: An analysis of 51 individuals in a single-center experience. Hum Mutat 2022; 43:74-84. [PMID: 34747535 DOI: 10.1002/humu.24294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023]
Abstract
Constitutional LZTR1 or SMARCB1 pathogenic variants (PVs) have been found in ∼86% of familial and ∼40% of sporadic schwannomatosis cases. Hence, we performed massively parallel sequencing of the entire LZTR1, SMARCB1, and NF2 genomic loci in 35 individuals with schwannomas negative for constitutional first-hit PVs in the LZTR1/SMARCB1/NF2 coding sequences; however, with 22q deletion and/or a different NF2 PV in each tumor, including six cases with only one tumor available. Furthermore, we verified whether any other LZTR1/SMARCB1/NF2 (likely) PVs could be found in 16 cases carrying a SMARCB1 constitutional variant in the 3'-untranslated region (3'-UTR) c.*17C>T, c.*70C>T, or c.*82C>T. As no additional variants were found, functional studies were performed to clarify the effect of these 3'-UTR variants on the transcript. The 3'-UTR variants c.*17C>T and c.*82C>T showed pathogenicity by negatively affecting the SMARCB1 transcript level. Two novel deep intronic SMARCB1 variants, c.500+883T>G and c.500+887G>A, resulting in out-of-frame missplicing of intron 4, were identified in two unrelated individuals. Further resequencing of the entire repeat-masked genomics sequences of chromosome 22q in individuals negative for PVs in the SMARCB1/LZTR1/NF2 coding- and noncoding regions revealed five potential schwannomatosis-predisposing candidate genes, that is, MYO18B, NEFH, SGSM1, SGSM3, and SBF1, pending further verification.
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Affiliation(s)
- Arkadiusz Piotrowski
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
- 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Koczkowska
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
- 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Andrzej B Poplawski
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Jarosław Króliczewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Alina Mieczkowska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Alicia Gomes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael R Crowley
- Genomic Core Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David K Crossman
- Genomic Core Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ping Lao
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eduard Serra
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Meritxell C Llach
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Elisabeth Castellanos
- Clinical Genomics Research Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Clinical Genomics Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Germans Trias i Pujol University Hospital (HUGTiP), Barcelona, Spain
| | - Ludwine M Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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5
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Catasús N, Garcia B, Galván-Femenía I, Plana A, Negro A, Rosas I, Ros A, Amilibia E, Becerra JL, Hostalot C, Rocaribas F, Bielsa I, Lazaro Garcia C, de Cid R, Serra E, Blanco I, Castellanos E. Revisiting the UK Genetic Severity Score for NF2: a proposal for the addition of a functional genetic component. J Med Genet 2021; 59:678-686. [PMID: 34348961 DOI: 10.1136/jmedgenet-2020-107548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/10/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Neurofibromatosis type 2 (NF2) is an autosomal dominant disorder characterised by the development of multiple schwannomas, especially on vestibular nerves, and meningiomas. The UK NF2 Genetic Severity Score (GSS) is useful to predict the progression of the disease from germline NF2 pathogenic variants, which allows the clinical follow-up and the genetic counselling offered to affected families to be optimised. METHODS 52 Spanish patients were classified using the GSS, and patients' clinical severity was measured and compared between GSS groups. The GSS was reviewed with the addition of phenotype quantification, genetic variant classification and functional assays of Merlin and its downstream pathways. Principal component analysis and regression models were used to evaluate the differences between severity and the effect of NF2 germline variants. RESULTS The GSS was validated in the Spanish NF2 cohort. However, for 25% of mosaic patients and patients harbouring variants associated with mild and moderate phenotypes, it did not perform as well for predicting clinical outcomes as it did for pathogenic variants associated with severe phenotypes. We studied the possibility of modifying the mutation classification in the GSS by adding the impact of pathogenic variants on the function of Merlin in 27 cases. This revision helped to reduce variability within NF2 mutation classes and moderately enhanced the correlation between patient phenotype and the different prognosis parameters analysed (R2=0.38 vs R2=0.32, p>0001). CONCLUSIONS We validated the UK NF2 GSS in a Spanish NF2 cohort, despite the significant phenotypic variability identified within it. The revision of the GSS, named Functional Genetic Severity Score, could add value for the classification of mosaic patients and patients showing mild and moderate phenotypes once it has been validated in other cohorts.
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Affiliation(s)
- Núria Catasús
- Clinical Genomics Research Unit, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP-PMPPC), Badalona, Spain
| | - Belen Garcia
- Clinical Genomics Research Unit, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP-PMPPC), Badalona, Spain.,Genetic Counseling Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Iván Galván-Femenía
- Genomes for Life-GCAT lab Group, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Spain
| | - Adrià Plana
- Dermatology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Alejandro Negro
- Clinical Genomics Research Unit, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP-PMPPC), Badalona, Spain.,Genetic Counseling Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Inma Rosas
- Clinical Genomics Research Unit, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP-PMPPC), Badalona, Spain.,Clinical Genomics Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Andrea Ros
- Clinical Genomics Research Unit, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP-PMPPC), Badalona, Spain.,Genetic Counseling Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Emilio Amilibia
- Otorhinolaryngology, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Juan Luis Becerra
- Neurology, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Cristina Hostalot
- Neurosurgery, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Francesc Rocaribas
- Otorhinolaryngology, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Isabel Bielsa
- Dermatology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Conxi Lazaro Garcia
- Hereditary Cancer Program, ICO-IDIBELL-CIBERONC, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rafael de Cid
- Genomes for Life-GCAT lab Group, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Spain
| | - Eduard Serra
- Hereditary Cancer Group, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP-PMPPC), Badalona, Spain
| | - Ignacio Blanco
- Clinical Genomics Research Unit, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP-PMPPC), Badalona, Spain.,Genetic Counseling Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Elisabeth Castellanos
- Clinical Genomics Research Unit, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP-PMPPC), Badalona, Spain .,Clinical Genomics Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Perez-Becerril C, Evans DG, Smith MJ. Pathogenic noncoding variants in the neurofibromatosis and schwannomatosis predisposition genes. Hum Mutat 2021; 42:1187-1207. [PMID: 34273915 DOI: 10.1002/humu.24261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/16/2021] [Accepted: 07/13/2021] [Indexed: 11/11/2022]
Abstract
Neurofibromatosis type 1 (NF1), type 2 (NF2), and schwannomatosis are a group of autosomal dominant disorders that predispose to the development of nerve sheath tumors. Pathogenic variants (PVs) that cause NF1 and NF2 are located in the NF1 and NF2 loci, respectively. To date, most variants associated with schwannomatosis have been identified in the SMARCB1 and LZTR1 genes, and a missense variant in the DGCR8 gene was recently reported to predispose to schwannomas. In spite of the high detection rate for PVs in NF1 and NF2 (over 90% of non-mosaic germline variants can be identified by routine genetic screening) underlying PVs for a proportion of clinical cases remain undetected. A higher proportion of non-NF2 schwannomatosis cases have no detected PV, with PVs currently only identified in around 70%-86% of familial cases and 30%-40% of non-NF2 sporadic schwannomatosis cases. A number of variants of uncertain significance have been observed for each disorder, many of them located in noncoding, regulatory, or intergenic regions. Here we summarize noncoding variants in this group of genes and discuss their established or potential role in the pathogenesis of NF1, NF2, and schwannomatosis.
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Affiliation(s)
- Cristina Perez-Becerril
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| | - D Gareth Evans
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Miriam J Smith
- Division of Evolution and Genomic Science, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, UK
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7
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Using antisense oligonucleotides for the physiological modulation of the alternative splicing of NF1 exon 23a during PC12 neuronal differentiation. Sci Rep 2021; 11:3661. [PMID: 33574490 PMCID: PMC7878752 DOI: 10.1038/s41598-021-83152-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 01/29/2021] [Indexed: 01/11/2023] Open
Abstract
Neurofibromatosis Type 1 (NF1) is a genetic condition affecting approximately 1:3500 persons worldwide. The NF1 gene codes for neurofibromin protein, a GTPase activating protein (GAP) and a negative regulator of RAS. The NF1 gene undergoes alternative splicing of exon 23a (E23a) that codes for 21 amino acids placed at the center of the GAP related domain (GRD). E23a-containing type II neurofibromin exhibits a weaker Ras-GAP activity compared to E23a-less type I isoform. Exon E23a has been related with the cognitive impairment present in NF1 individuals. We designed antisense Phosphorodiamidate Morpholino Oligomers (PMOs) to modulate E23a alternative splicing at physiological conditions of gene expression and tested their impact during PC12 cell line neuronal differentiation. Results show that any dynamic modification of the natural ratio between type I and type II isoforms disturbed neuronal differentiation, altering the proper formation of neurites and deregulating both the MAPK/ERK and cAMP/PKA signaling pathways. Our results suggest an opposite regulation of these pathways by neurofibromin and the possible existence of a feedback loop sensing neurofibromin-related signaling. The present work illustrates the utility of PMOs to study alternative splicing that could be applied to other alternatively spliced genes in vitro and in vivo.
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8
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Alvarez MEV, Chivers M, Borovska I, Monger S, Giannoulatou E, Kralovicova J, Vorechovsky I. Transposon clusters as substrates for aberrant splice-site activation. RNA Biol 2020; 18:354-367. [PMID: 32965162 PMCID: PMC7951965 DOI: 10.1080/15476286.2020.1805909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transposed elements (TEs) have dramatically shaped evolution of the exon-intron structure and significantly contributed to morbidity, but how recent TE invasions into older TEs cooperate in generating new coding sequences is poorly understood. Employing an updated repository of new exon-intron boundaries induced by pathogenic mutations, termed DBASS, here we identify novel TE clusters that facilitated exon selection. To explore the extent to which such TE exons maintain RNA secondary structure of their progenitors, we carried out structural studies with a composite exon that was derived from a long terminal repeat (LTR78) and AluJ and was activated by a C > T mutation optimizing the 5ʹ splice site. Using a combination of SHAPE, DMS and enzymatic probing, we show that the disease-causing mutation disrupted a conserved AluJ stem that evolved from helix 3.3 (or 5b) of 7SL RNA, liberating a primordial GC 5ʹ splice site from the paired conformation for interactions with the spliceosome. The mutation also reduced flexibility of conserved residues in adjacent exon-derived loops of the central Alu hairpin, revealing a cross-talk between traditional and auxilliary splicing motifs that evolved from opposite termini of 7SL RNA and were approximated by Watson-Crick base-pairing already in organisms without spliceosomal introns. We also identify existing Alu exons activated by the same RNA rearrangement. Collectively, these results provide valuable TE exon models for studying formation and kinetics of pre-mRNA building blocks required for splice-site selection and will be useful for fine-tuning auxilliary splicing motifs and exon and intron size constraints that govern aberrant splice-site activation.
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Affiliation(s)
| | - Martin Chivers
- School of Medicine, University of Southampton, Southampton, UK
| | - Ivana Borovska
- Slovak Academy of Sciences, Institute of Molecular Physiology and Genetics, Bratislava, Slovak Republic
| | - Steven Monger
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Eleni Giannoulatou
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Jana Kralovicova
- School of Medicine, University of Southampton, Southampton, UK.,Slovak Academy of Sciences, Institute of Molecular Physiology and Genetics, Bratislava, Slovak Republic
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Canson D, Glubb D, Spurdle AB. Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: Strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Hum Mutat 2020; 41:1705-1721. [PMID: 32623769 DOI: 10.1002/humu.24074] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
Abstract
It is possible to estimate the prior probability of pathogenicity for germline disease gene variants based on bioinformatic prediction of variant effect/s. However, routinely used approaches have likely led to the underestimation and underreporting of variants located outside donor and acceptor splice site motifs that affect messenger RNA (mRNA) processing. This review presents information about hereditary cancer gene germline variants, outside native splice sites, with experimentally validated splicing effects. We list 95 exonic variants that impact splicing regulatory elements (SREs) in BRCA1, BRCA2, MLH1, MSH2, MSH6, and PMS2. We utilized a pre-existing large-scale BRCA1 functional data set to map functional SREs, and assess the relative performance of different tools to predict effects of 283 variants on such elements. We also describe rare examples of intronic variants that impact branchpoint (BP) sites and create pseudoexons. We discuss the challenges in predicting variant effect on BP site usage and pseudoexonization, and suggest strategies to improve the bioinformatic prioritization of such variants for experimental validation. Importantly, our review and analysis highlights the value of considering impact of variants outside donor and acceptor motifs on mRNA splicing and disease causation.
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Affiliation(s)
- Daffodil Canson
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Dylan Glubb
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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10
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Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. ADVANCES IN GENETICS 2019; 103:39-90. [PMID: 30904096 DOI: 10.1016/bs.adgen.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.
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11
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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12
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Cunha KS, Oliveira NS, Fausto AK, de Souza CC, Gros A, Bandres T, Idrissi Y, Merlio JP, de Moura Neto RS, Silva R, Geller M, Cappellen D. Hybridization Capture-Based Next-Generation Sequencing to Evaluate Coding Sequence and Deep Intronic Mutations in the NF1 Gene. Genes (Basel) 2016; 7:genes7120133. [PMID: 27999334 PMCID: PMC5192509 DOI: 10.3390/genes7120133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 12/25/2022] Open
Abstract
Neurofibromatosis 1 (NF1) is one of the most common genetic disorders and is caused by mutations in the NF1 gene. NF1 gene mutational analysis presents a considerable challenge because of its large size, existence of highly homologous pseudogenes located throughout the human genome, absence of mutational hotspots, and diversity of mutations types, including deep intronic splicing mutations. We aimed to evaluate the use of hybridization capture-based next-generation sequencing to screen coding and noncoding NF1 regions. Hybridization capture-based next-generation sequencing, with genomic DNA as starting material, was used to sequence the whole NF1 gene (exons and introns) from 11 unrelated individuals and 1 relative, who all had NF1. All of them met the NF1 clinical diagnostic criteria. We showed a mutation detection rate of 91% (10 out of 11). We identified eight recurrent and two novel mutations, which were all confirmed by Sanger methodology. In the Sanger sequencing confirmation, we also included another three relatives with NF1. Splicing alterations accounted for 50% of the mutations. One of them was caused by a deep intronic mutation (c.1260 + 1604A > G). Frameshift truncation and missense mutations corresponded to 30% and 20% of the pathogenic variants, respectively. In conclusion, we show the use of a simple and fast approach to screen, at once, the entire NF1 gene (exons and introns) for different types of pathogenic variations, including the deep intronic splicing mutations.
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Affiliation(s)
- Karin Soares Cunha
- Graduate Program in Pathology, School of Medicine, Universidade Federal Fluminense, Niterói 24033-900, Brazil.
- Department of Pathology, School of Medicine, Universidade Federal Fluminense, Niterói 24033-900, Brazil.
- Neurofibromatosis National Center (Centro Nacional de Neurofibromatose), Rio de Janeiro 20011-330, Brazil.
| | - Nathalia Silva Oliveira
- Anatomy Pathology Service, Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Niterói 24033-900, Brazil.
| | - Anna Karoline Fausto
- Anatomy Pathology Service, Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Niterói 24033-900, Brazil.
| | | | - Audrey Gros
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France.
- Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France.
| | - Thomas Bandres
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France.
| | - Yamina Idrissi
- Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France.
| | - Jean-Philippe Merlio
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France.
- Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France.
| | | | - Rosane Silva
- Carlos Chagas Filho Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Mauro Geller
- Department of Immunology and Microbiology, School of Medicine, Centro Universitário Serra dos Órgãos, Teresópolis 25964-004, Brazil.
- Martagão Gesteira Child Care and Pediatrics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil.
| | - David Cappellen
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac F-33604, France.
- Inserm (Institut National de la Santé et de la Recherche Médicale) U1053, Bordeaux Research in Translational Oncology (BaRITON) and University of Bordeaux, Bordeaux F-33076, France.
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13
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Siva K, Covello G, Denti MA. Exon-skipping antisense oligonucleotides to correct missplicing in neurogenetic diseases. Nucleic Acid Ther 2014; 24:69-86. [PMID: 24506781 DOI: 10.1089/nat.2013.0461] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alternative splicing is an important regulator of the transcriptome. However, mutations may cause alteration of splicing patterns, which in turn leads to disease. During the past 10 years, exon skipping has been looked upon as a powerful tool for correction of missplicing in disease and progress has been made towards clinical trials. In this review, we discuss the use of antisense oligonucleotides to correct splicing defects through exon skipping, with a special focus on diseases affecting the nervous system, and the latest stage achieved in its progress.
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Affiliation(s)
- Kavitha Siva
- 1 Center for Integrative Biology (CIBIO), University of Trento , Trento, Italy
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Gossage L, Murtaza M, Slatter AF, Lichtenstein CP, Warren A, Haynes B, Marass F, Roberts I, Shanahan SJ, Claas A, Dunham A, May AP, Rosenfeld N, Forshew T, Eisen T. Clinical and pathological impact of VHL, PBRM1, BAP1, SETD2, KDM6A, and JARID1c in clear cell renal cell carcinoma. Genes Chromosomes Cancer 2014; 53:38-51. [PMID: 24166983 DOI: 10.1002/gcc.22116] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/16/2013] [Indexed: 12/21/2022] Open
Abstract
VHL is mutated in the majority of patients with clear cell renal cell carcinoma (ccRCC), with conflicting clinical relevance. Recent studies have identified recurrent mutations in histone modifying and chromatin remodeling genes, including BAP1, PBRM1, SETD2, KDM6A, and JARID1c. Current evidence suggests that BAP1 mutations are associated with aggressive disease. The clinical significance of the remaining genes is unknown. In this study, targeted sequencing of VHL and JARID1c (entire genes) and coding regions of BAP1, PBRM1, SETD2, and KDM6A was performed on 132 ccRCCs and matched normal tissues. Associations between mutations and clinical and pathological outcomes were interrogated. Inactivation of VHL (coding mutation or promoter methylation) was seen in 75% of ccRCCs. Somatic noncoding VHL alterations were identified in 29% of ccRCCs and may be associated with improved overall survival. BAP1 (11%), PBRM1 (33%), SETD2 (16%), JARID1c (4%), and KDM6A (3%) mutations were identified. BAP1-mutated tumors were associated with metastatic disease at presentation (P = 0.023), advanced clinical stage (P = 0.042) and a trend towards shorter recurrence free survival (P = 0.059) when compared with tumors exclusively mutated for PBRM1. Our results support those of recent publications pointing towards a role for BAP1 and PBRM1 mutations in risk stratifying ccRCCs. Further investigation of noncoding alterations in VHL is warranted.
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Affiliation(s)
- Lucy Gossage
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
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15
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Evans DGR, Wallace A, Newman W. Can manipulation of splicing offer gene therapy possibilities to those with tumour-prone disorders? Eur J Hum Genet 2012. [PMID: 23188050 DOI: 10.1038/ejhg.2012.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- D Gareth R Evans
- Genetic Medicine, Manchester Academic Health Science Centre Central Manchester University Hospitals, NHS Foundation Trust, Manchester Royal Infirmary, Manchester, UK.
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