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Functional Assays Combined with Pre-mRNA-Splicing Analysis Improve Variant Classification and Diagnostics for Individuals with Neurofibromatosis Type 1 and Legius Syndrome. Hum Mutat 2023. [DOI: 10.1155/2023/9628049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Neurofibromatosis type 1 (NF1) and Legius syndrome (LS) are caused by inactivating variants in NF1 and SPRED1. NF1 encodes neurofibromin (NF), a GTPase-activating protein (GAP) for RAS that interacts with the SPRED1 product, Sprouty-related protein with an EVH (Ena/Vasp homology) domain 1 (SPRED1). Obtaining a clinical and molecular diagnosis of NF1 or LS can be challenging due to the phenotypic diversity, the size and complexity of the NF1 and SPRED1 loci, and uncertainty over the effects of some NF1 and SPRED1 variants on pre-mRNA splicing and/or protein expression and function. To improve NF1 and SPRED1 variant classification and establish pathogenicity for NF1 and SPRED1 variants identified in individuals with NF1 or LS, we analyzed patient RNA by RT-PCR and performed in vitro exon trap experiments and estimated NF and SPRED1 protein expression, RAS GAP activity, and interaction. We obtained evidence to support pathogenicity according to American College of Medical Genetics guidelines for 73/114 variants tested, demonstrating the utility of functional approaches for NF1 and SPRED1 variant classification and NF and LS diagnostics.
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2
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Douben HCW, Nellist M, van Unen L, Elfferich P, Kasteleijn E, Hoogeveen-Westerveld M, Louwen J, van Veghel-Plandsoen M, de Valk W, Saris JJ, Hendriks F, Korpershoek E, Hoefsloot LH, van Vliet M, van Bever Y, van de Laar I, Aten E, Lachmeijer AMA, Taal W, van den Bersselaar L, Schuurmans J, Oostenbrink R, van Minkelen R, van Ierland Y, van Ham TJ. High-yield identification of pathogenic NF1 variants by skin fibroblast transcriptome screening after apparently normal diagnostic DNA testing. Hum Mutat 2022; 43:2130-2140. [PMID: 36251260 PMCID: PMC10099955 DOI: 10.1002/humu.24487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023]
Abstract
Neurofibromatosis type 1 (NF1) is caused by inactivating mutations in NF1. Due to the size, complexity, and high mutation rate at the NF1 locus, the identification of causative variants can be challenging. To obtain a molecular diagnosis in 15 individuals meeting diagnostic criteria for NF1, we performed transcriptome analysis (RNA-seq) on RNA obtained from cultured skin fibroblasts. In each case, routine molecular DNA diagnostics had failed to identify a disease-causing variant in NF1. A pathogenic variant or abnormal mRNA splicing was identified in 13 cases: 6 deep intronic variants and 2 transposon insertions causing noncanonical splicing, 3 postzygotic changes, 1 branch point mutation and, in 1 case, abnormal splicing for which the responsible DNA change remains to be identified. These findings helped resolve the molecular findings for an additional 17 individuals in multiple families with NF1, demonstrating the utility of skin-fibroblast-based transcriptome analysis for molecular diagnostics. RNA-seq improves mutation detection in NF1 and provides a powerful complementary approach to DNA-based methods. Importantly, our approach is applicable to other genetic disorders, particularly those caused by a wide variety of variants in a limited number of genes and specifically for individuals in whom routine molecular DNA diagnostics did not identify the causative variant.
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Affiliation(s)
- Hannie C W Douben
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leontine van Unen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter Elfferich
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esmee Kasteleijn
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Jesse Louwen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Walter de Valk
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Femke Hendriks
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esther Korpershoek
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Margreethe van Vliet
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ingrid van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Augusta M A Lachmeijer
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Walter Taal
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.,Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lisa van den Bersselaar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juliette Schuurmans
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rianne Oostenbrink
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.,Department of General Pediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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3
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Comparison of In Silico Tools for Splice-Altering Variant Prediction Using Established Spliceogenic Variants: An End-User’s Point of View. Int J Genomics 2022; 2022:5265686. [PMID: 36275637 PMCID: PMC9584665 DOI: 10.1155/2022/5265686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/18/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022] Open
Abstract
Assessing the impact of variants of unknown significance on splicing has become a critical issue and a bottleneck, especially with the widespread implementation of whole-genome or exome sequencing. Although multiple in silico tools are available, the interpretation and application of these tools are difficult and practical guidelines are still lacking. A streamlined decision-making process can facilitate the downstream RNA analysis in a more efficient manner. Therefore, we evaluated the performance of 8 in silico tools (Splice Site Finder, MaxEntScan, Splice-site prediction by neural network, GeneSplicer, Human Splicing Finder, SpliceAI, Splicing Predictions in Consensus Elements, and SpliceRover) using 114 NF1 spliceogenic variants, experimentally validated at the mRNA level. The change in the predicted score incurred by the variant of the nearest wild-type splice site was analyzed, and for type II, III, and IV splice variants, the change in the prediction score of de novo or cryptic splice site was also analyzed. SpliceAI and SpliceRover, tools based on deep learning, outperformed all other tools, with AUCs of 0.972 and 0.924, respectively. For de novo and cryptic splice sites, SpliceAI outperformed all other tools and showed a sensitivity of 95.7% at an optimal cut-off of 0.02 score change. Our results show that deep learning algorithms, especially those of SpliceAI, are validated at a significantly higher rate than other in silico tools for clinically relevant NF1 variants. This suggests that deep learning algorithms outperform traditional probabilistic approaches and classical machine learning tools in predicting the de novo and cryptic splice sites.
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Geysels RC, Bernal Barquero CE, Martín M, Peyret V, Nocent M, Sobrero G, Muñoz L, Signorino M, Testa G, Castro RB, Masini-Repiso AM, Miras MB, Nicola JP. Silent but Not Harmless: A Synonymous SLC5A5 Gene Variant Leading to Dyshormonogenic Congenital Hypothyroidism. Front Endocrinol (Lausanne) 2022; 13:868891. [PMID: 35600585 PMCID: PMC9114739 DOI: 10.3389/fendo.2022.868891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/23/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Congenital iodide transport defect (ITD) is an uncommon cause of dyshormonogenic congenital hypothyroidism characterized by the absence of active iodide accumulation in the thyroid gland. ITD is an autosomal recessive disorder caused by loss-of-function variants in the sodium/iodide symporter (NIS)-coding SLC5A5 gene. OBJECTIVE We aimed to identify, and if so to functionally characterize, novel ITD-causing SLC5A5 gene variants in a cohort of five unrelated pediatric patients diagnosed with dyshormonogenic congenital hypothyroidism with minimal to absent 99mTc-pertechnetate accumulation in the thyroid gland. METHODS The coding region of the SLC5A5 gene was sequenced using Sanger sequencing. In silico analysis and functional in vitro characterization of a novel synonymous variant were performed. RESULTS Sanger sequencing revealed a novel homozygous synonymous SLC5A5 gene variant (c.1326A>C in exon 11). In silico analysis revealed that the c.1326A>C variant is potentially deleterious for NIS pre-mRNA splicing. The c.1326A>C variant was predicted to lie within a putative exonic splicing enhancer reducing the binding of splicing regulatory trans-acting protein SRSF5. Splicing minigene reporter assay revealed that c.1326A>C causes exon 11 or exon 11 and 12 skipping during NIS pre-mRNA splicing leading to the NIS pathogenic variants p.G415_P443del and p.G415Lfs*32, respectively. Significantly, the frameshift variant p.G415Lfs*32 is predicted to be subjected to degradation by nonsense-mediated decay. CONCLUSIONS We identified the first exonic synonymous SLC5A5 gene variant causing aberrant NIS pre-mRNA splicing, thus expanding the mutational landscape of the SLC5A5 gene leading to dyshormonogenic congenital hypothyroidism.
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Affiliation(s)
- Romina Celeste Geysels
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología - Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
| | - Carlos Eduardo Bernal Barquero
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología - Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
| | - Mariano Martín
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología - Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
| | - Victoria Peyret
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología - Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
| | - Martina Nocent
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología - Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
| | - Gabriela Sobrero
- Programa Provincial de Pesquisa Neonatal, Servicio de Endocrinología, Hospital de Niños de la Santísima Trinidad de Córdoba, Córdoba, Argentina
| | - Liliana Muñoz
- Programa Provincial de Pesquisa Neonatal, Servicio de Endocrinología, Hospital de Niños de la Santísima Trinidad de Córdoba, Córdoba, Argentina
| | - Malvina Signorino
- Programa Provincial de Pesquisa Neonatal, Servicio de Endocrinología, Hospital de Niños de la Santísima Trinidad de Córdoba, Córdoba, Argentina
| | - Graciela Testa
- Programa Provincial de Pesquisa Neonatal, Servicio de Endocrinología, Hospital de Niños de la Santísima Trinidad de Córdoba, Córdoba, Argentina
| | | | - Ana María Masini-Repiso
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología - Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
| | - Mirta Beatriz Miras
- Programa Provincial de Pesquisa Neonatal, Servicio de Endocrinología, Hospital de Niños de la Santísima Trinidad de Córdoba, Córdoba, Argentina
| | - Juan Pablo Nicola
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología - Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
- *Correspondence: Juan Pablo Nicola,
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5
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Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq. NPJ Genom Med 2021; 6:95. [PMID: 34782607 PMCID: PMC8593033 DOI: 10.1038/s41525-021-00258-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/15/2021] [Indexed: 11/08/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is caused by loss-of-function variants in the NF1 gene. Approximately 10% of these variants affect RNA splicing and are either missed by conventional DNA diagnostics or are misinterpreted by in silico splicing predictions. Therefore, a targeted RNAseq-based approach was designed to detect pathogenic RNA splicing and associated pathogenic DNA variants. For this method RNA was extracted from lymphocytes, followed by targeted RNAseq. Next, an in-house developed tool (QURNAs) was used to calculate the enrichment score (ERS) for each splicing event. This method was thoroughly tested using two different patient cohorts with known pathogenic splice-variants in NF1. In both cohorts all 56 normal reference transcript exon splice junctions, 24 previously described and 45 novel non-reference splicing events were detected. Additionally, all expected pathogenic splice-variants were detected. Eleven patients with NF1 symptoms were subsequently tested, three of which have a known NF1 DNA variant with a putative effect on RNA splicing. This effect could be confirmed for all 3. The other eight patients were previously without any molecular confirmation of their NF1-diagnosis. A deep-intronic pathogenic splice variant could now be identified for two of them (25%). These results suggest that targeted RNAseq can be successfully used to detect pathogenic RNA splicing variants in NF1.
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6
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Abrahams L, Savisaar R, Mordstein C, Young B, Kudla G, Hurst LD. Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption. Nucleic Acids Res 2021; 49:9665-9685. [PMID: 34469537 PMCID: PMC8464065 DOI: 10.1093/nar/gkab750] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
Transcripts containing premature termination codons (PTCs) can be subject to nonsense-associated alternative splicing (NAS). Two models have been evoked to explain this, scanning and splice motif disruption. The latter postulates that exonic cis motifs, such as exonic splice enhancers (ESEs), are disrupted by nonsense mutations. We employ genome-wide transcriptomic and k-mer enrichment methods to scrutinize this model. First, we show that ESEs are prone to disruptive nonsense mutations owing to their purine richness and paucity of TGA, TAA and TAG. The motif model correctly predicts that NAS rates should be low (we estimate 5–30%) and approximately in line with estimates for the rate at which random point mutations disrupt splicing (8–20%). Further, we find that, as expected, NAS-associated PTCs are predictable from nucleotide-based machine learning approaches to predict splice disruption and, at least for pathogenic variants, are enriched in ESEs. Finally, we find that both in and out of frame mutations to TAA, TGA or TAG are associated with exon skipping. While a higher relative frequency of such skip-inducing mutations in-frame than out of frame lends some credence to the scanning model, these results reinforce the importance of considering splice motif modulation to understand the etiology of PTC-associated disease.
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Affiliation(s)
- Liam Abrahams
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.,Aarhus University, Department of Molecular Biology and Genetics, C F Møllers Allé 3, 8000 Aarhus, Denmark
| | - Bethan Young
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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7
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Rosen SM, Joshi M, Hitt T, Beggs AH, Agrawal PB. Knockin mouse model of the human CFL2 p.A35T mutation results in a unique splicing defect and severe myopathy phenotype. Hum Mol Genet 2021; 29:1996-2003. [PMID: 32160286 DOI: 10.1093/hmg/ddaa035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 11/13/2022] Open
Abstract
Cofilin-2 is an actin-binding protein that is predominantly expressed in skeletal and cardiac muscles and belongs to the AC group of proteins, which includes cofilin-1 and destrin. In humans, cofilin-2 (CFL2) mutations have been associated with congenital myopathies that include nemaline and myofibrillar myopathy. To understand the pathogenicity of the human CFL2 mutation, p.A35T, that first linked cofilin-2 with the human disease, we created a knock-in mouse model. The Cfl2A35T/A35T (KI) mice were indistinguishable from their wild-type littermates at birth, but they rapidly worsened and died by postnatal day 9. The phenotypic, histopathologic and molecular findings mimicked the constitutive Cfl2-knockout (KO) mice described previously, including sarcomeric disruption and actin accumulations in skeletal muscles and negligible amounts of cofilin-2 protein. In addition, KI mice demonstrated a marked reduction in Cfl2 mRNA levels in various tissues including skeletal muscles. Further investigation revealed evidence of alternative splicing with the presence of two alternate transcripts of smaller size. These alternate transcripts were expressed at very low levels in the wild-type mice and were significantly upregulated in the mutant mice, indicating that pre-translational splicing defects may be a critical component of the disease mechanism associated with the mutation. Evidence of reduced expression of the full-length CFL2 transcript was also observed in the muscle biopsy sample of the patient with p.A35T mutation.
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Affiliation(s)
- Samantha M Rosen
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mugdha Joshi
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Talia Hitt
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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8
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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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9
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Morbidoni V, Baschiera E, Forzan M, Fumini V, Ali DS, Giorgi G, Buson L, Desbats MA, Cassina M, Clementi M, Salviati L, Trevisson E. Hybrid Minigene Assay: An Efficient Tool to Characterize mRNA Splicing Profiles of NF1 Variants. Cancers (Basel) 2021; 13:cancers13050999. [PMID: 33673681 PMCID: PMC7957615 DOI: 10.3390/cancers13050999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/08/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is caused by heterozygous loss of function mutations in the NF1 gene. Although patients are diagnosed according to clinical criteria and few genotype-phenotype correlations are known, molecular analysis remains important. NF1 displays allelic heterogeneity, with a high proportion of variants affecting splicing, including deep intronic alleles and changes outside the canonical splice sites, making validation problematic. Next Generation Sequencing (NGS) technologies integrated with multiplex ligation-dependent probe amplification (MLPA) have largely overcome RNA-based techniques but do not detect splicing defects. A rapid minigene-based system was set up to test the effects of NF1 variants on splicing. We investigated 29 intronic and exonic NF1 variants identified in patients during the diagnostic process. The minigene assay showed the coexistence of multiple mechanisms of splicing alterations for seven variants. A leaky effect on splicing was documented in one de novo substitution detected in a sporadic patient with a specific phenotype without neurofibromas. Our splicing assay proved to be a reliable and fast method to validate novel NF1 variants potentially affecting splicing and to detect hypomorphic effects that might have phenotypic consequences, avoiding the requirement of patient's RNA.
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Affiliation(s)
- Valeria Morbidoni
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Elisa Baschiera
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Monica Forzan
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Valentina Fumini
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Dario Seif Ali
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Gianpietro Giorgi
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Lisa Buson
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Maria Andrea Desbats
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
- Correspondence: ; Tel.: + 39-(04)-9821-1402
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10
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Evaluation of clinical findings and neurofibromatosis type 1 bright objects on brain magnetic resonance images of 60 Turkish patients with NF1 gene variants. Neurol Sci 2021; 42:2045-2057. [PMID: 33443663 DOI: 10.1007/s10072-020-04988-0] [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] [Received: 07/24/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022]
Abstract
Neurofibromatosis type 1 (NF1) is caused by mutations in the NF1 gene. This retrospective study aims to evaluate the clinical manifestations and brain magnetic resonance images (MRI) analysis in 60 genetically confirmed NF1 patients. The results of next-generation sequencing (NGS), Sanger sequencing, and MLPA of NF1 gene were evaluated. A total of 54 different variants were identified. Fourteen out of them were novel variants (25.9%). Patients who complied with NIH criteria had most frequently frameshift variants (11/32 patients), and those with only CALMs had missense variants (9/28 patients). Neurofibromatosis type 1 bright objects (NBOs) on T2-weighted MRI were detected in 42 patients (42/56; 75%). These brain lesions were detected mostly in basal ganglia and in cerebellar vermis. NBOs were detected more in the patients who complied with NIH criteria (80.6%) compared to those who were only CALMs (68%). While frameshift variants (33.3%) were the most common type variants in the patients who had NBOs, the most common variants were splicing (35.7%) and missense (35.7%) variants in the patients whose MRIs were normal. Frameshift variants (11/28 patients; 39.3%) were the most common in the patients with more than one brain locus involvement. Therefore, we consider that frameshift variants may be associated with increased incidence of NBOs and involvement of more than one brain locus. In addition, NBOs may occur less frequently in the patients with splicing variants. To our knowledge, this is the first study evaluated the relationship between NF1 gene variants and NBOs. Future studies may help us understand the etiology of NBOs.
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11
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Rowlands CF, Baralle D, Ellingford JM. Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing. Cells 2019; 8:E1513. [PMID: 31779139 PMCID: PMC6953098 DOI: 10.3390/cells8121513] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022] Open
Abstract
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient's variant landscape, the ability to characterize variants causing splicing defects has not progressed with the same speed. To address this, recent years have seen a sharp spike in the number of splice prediction tools leveraging machine learning approaches, leaving clinical geneticists with a plethora of choices for in silico analysis. In this review, some basic principles of machine learning are introduced in the context of genomics and splicing analysis. A critical comparative approach is then used to describe seven recent machine learning-based splice prediction tools, revealing highly diverse approaches and common caveats. We find that, although great progress has been made in producing specific and sensitive tools, there is still much scope for personalized approaches to prediction of variant impact on splicing. Such approaches may increase diagnostic yields and underpin improvements to patient care.
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Affiliation(s)
- Charlie F Rowlands
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, MP808, Tremona Road, Southampton SO16 6YD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
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12
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CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation. Nat Commun 2019; 10:4056. [PMID: 31492834 PMCID: PMC6731291 DOI: 10.1038/s41467-019-12028-5] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
The introduction of insertion-deletions (INDELs) by non-homologous end-joining (NHEJ) pathway underlies the mechanistic basis of CRISPR-Cas9-directed genome editing. Selective gene ablation using CRISPR-Cas9 is achieved by installation of a premature termination codon (PTC) from a frameshift-inducing INDEL that elicits nonsense-mediated decay (NMD) of the mutant mRNA. Here, by examining the mRNA and protein products of CRISPR targeted genes in a cell line panel with presumed gene knockouts, we detect the production of foreign mRNAs or proteins in ~50% of the cell lines. We demonstrate that these aberrant protein products stem from the introduction of INDELs that promote internal ribosomal entry, convert pseudo-mRNAs (alternatively spliced mRNAs with a PTC) into protein encoding molecules, or induce exon skipping by disruption of exon splicing enhancers (ESEs). Our results reveal challenges to manipulating gene expression outcomes using INDEL-based mutagenesis and strategies useful in mitigating their impact on intended genome-editing outcomes.
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13
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Setrajcic Dragos V, Blatnik A, Klancar G, Stegel V, Krajc M, Blatnik O, Novakovic S. Two Novel NF1 Pathogenic Variants Causing the Creation of a New Splice Site in Patients With Neurofibromatosis Type I. Front Genet 2019; 10:762. [PMID: 31507634 PMCID: PMC6714493 DOI: 10.3389/fgene.2019.00762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/17/2019] [Indexed: 01/12/2023] Open
Abstract
Neurofibromatosis type I (NF1) is one of the most common autosomal dominant disorders, since the estimated incidence is one in 3,500 births. In this study, we present bioinformatical and functional characterization of two novel splicing NF1 variants, detected in NF1 patients. Patient 1, carrying NF1:c.122A>T, which introduces a new exonic 5’ donor splice site, was diagnosed with hormone-positive, Her-2-negative breast cancer at the age of 47. She had an atypical presentation of NF1, with few café-au-lait spots and no Lisch nodules. Patient developed a hemothorax due to subclavian artery rupture, which has previously been described as an extremely rare complication of NF1. Patient 2, carrying NF1:c.7395-17T>G that creates a new intronic 3’ acceptor splice site, had quite a typical clinical presentation of NF1: formations on her tongue in the region of her left metacarpal bones and on her left foot, plexiform neurofibroma in her pelvis, several café-au-lait spots, and axillary freckling. She was also diagnosed with cognitive impairment. In the report, we are presenting two novel variants which were successfully classified based on NGS and mRNA analysis. Based on results of mRNA analysis, both variants were classified as likely pathogenic according to ACMG guidelines applying evidence categories PS3, PM2, PP3, and PP1 supporting. By characterizing those two novel NF1 splicing variants, we have confirmed the neurofibromatosis type I phenotype in the two probands.
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Affiliation(s)
- Vita Setrajcic Dragos
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Ana Blatnik
- Cancer Genetics Clinic, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Gasper Klancar
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Vida Stegel
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Mateja Krajc
- Cancer Genetics Clinic, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Olga Blatnik
- Department of Pathology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Srdjan Novakovic
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
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14
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Frankiw L, Baltimore D, Li G. Alternative mRNA splicing in cancer immunotherapy. Nat Rev Immunol 2019; 19:675-687. [PMID: 31363190 DOI: 10.1038/s41577-019-0195-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2019] [Indexed: 12/12/2022]
Abstract
Immunotherapies are yielding effective treatments for several previously untreatable cancers. Still, the identification of suitable antigens specific to the tumour that can be targets for cancer vaccines and T cell therapies is a challenge. Alternative processing of mRNA, a phenomenon that has been shown to alter the proteomic diversity of many cancers, may offer the potential of a broadened target space. Here, we discuss the promise of analysing mRNA processing events in cancer cells, with an emphasis on mRNA splicing, for the identification of potential new targets for cancer immunotherapy. Further, we highlight the challenges that must be overcome for this new avenue to have clinical applicability.
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Affiliation(s)
- Luke Frankiw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Guideng Li
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. .,Suzhou Institute of Systems Medicine, Suzhou, China.
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15
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Connahs H, Tlili S, van Creij J, Loo TYJ, Banerjee TD, Saunders TE, Monteiro A. Activation of butterfly eyespots by Distal-less is consistent with a reaction-diffusion process. Development 2019; 146:dev169367. [PMID: 30992277 PMCID: PMC6526720 DOI: 10.1242/dev.169367] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 04/05/2019] [Indexed: 01/08/2023]
Abstract
Eyespots on the wings of nymphalid butterflies represent colorful examples of pattern formation, yet the developmental origins and mechanisms underlying eyespot center differentiation are still poorly understood. Using CRISPR-Cas9 we re-examine the function of Distal-less (Dll) as an activator or repressor of eyespots, a topic that remains controversial. We show that the phenotypic outcome of CRISPR mutations depends upon which specific exon is targeted. In Bicyclus anynana, exon 2 mutations are associated with both missing and ectopic eyespots, and also exon skipping. Exon 3 mutations, which do not lead to exon skipping, produce only null phenotypes, including missing eyespots, lighter wing coloration and loss of scales. Reaction-diffusion modeling of Dll function, using Wnt and Dpp as candidate morphogens, accurately replicates these complex crispant phenotypes. These results provide new insight into the function of Dll as a potential activator of eyespot development, scale growth and melanization, and suggest that the tuning of Dll expression levels can generate a diversity of eyespot phenotypes, including their appearance on the wing.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Heidi Connahs
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Sham Tlili
- Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Jelle van Creij
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Tricia Y J Loo
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Tirtha Das Banerjee
- Department of Biological Sciences, National University of Singapore, Singapore 117558
| | - Timothy E Saunders
- Department of Biological Sciences, National University of Singapore, Singapore 117558
- Mechanobiology Institute, National University of Singapore, Singapore 117411
- Institute of Molecular and Cell Biology, A*Star, Proteos, Singapore 138673
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117558
- Yale-NUS College, Singapore 138527
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16
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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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17
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Azimi A, Nejati P, Tahmasebi S, Alimoradi S, Alibakhshi R. Characterization of the IVS-II-821 (A>C) ( HBB: c.316-30A>C) Mutation in a β-Thalassemia Phenotype in Iran. Hemoglobin 2019; 43:23-26. [DOI: 10.1080/03630269.2019.1592760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Azam Azimi
- Medical Genetics Laboratory, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parham Nejati
- Medical Genetics Laboratory, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Soosan Tahmasebi
- Medical Genetics Laboratory, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sasan Alimoradi
- Medical Genetics Laboratory, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Alibakhshi
- Department of Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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18
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Lassaunière R, Paximadis M, Ebrahim O, Chaisson RE, Martinson NA, Tiemessen CT. The FCGR2C allele that modulated the risk of HIV-1 infection in the Thai RV144 vaccine trial is implicated in HIV-1 disease progression. Genes Immun 2018; 20:651-659. [PMID: 30563969 PMCID: PMC6881233 DOI: 10.1038/s41435-018-0053-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 11/10/2022]
Abstract
In the HIV-1 Thai RV144 vaccine trial—the only trial to demonstrate any
vaccine efficacy to date—a three-variant haplotype within the Fc gamma receptor 2C
gene (FCGR2C) modified the risk of HIV-1
acquisition. A similar vaccine regimen is currently being evaluated in South Africa
in the HVTN702 trial, where the predominant population is polymorphic for only a
single variant in the haplotype, c.134-96C>T. To investigate the significance of
c.134-96C>T in HIV-specific immunity in South Africans, this study assessed its
role in HIV-1 disease progression. In a cohort of HIV-1-infected South African
controllers (n = 71) and progressors (n = 73), the c.134-96C>T minor allele significantly
associated with increased odds of HIV-1 disease progression (odds ratio 3.80, 95%
confidence interval 1.90–7.62; P = 2.0 × 10–4, PBonf = 2.4 × 10–3).
It is unlikely that the underlying mechanism involves wild-type FcγRIIc function,
since only a single study participant was predicted to express wild-type FcγRIIc as
determined by the FCGR2C c.798+1A>G
splice-site variant. Conversely, in silico analysis revealed a potential role for
c.134-96C> T in modulating mRNA transcription. In conclusion, these data provide
additional evidence towards a role for FCGR2C
c.134-96C>T in the context of HIV-1 and underscore the need to investigate its
significance in the HVTN702 efficacy trial in South Africa.
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Affiliation(s)
- Ria Lassaunière
- National Institute for Communicable Diseases, Centre for HIV and STI's, Johannesburg, South Africa.,University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.,Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Maria Paximadis
- National Institute for Communicable Diseases, Centre for HIV and STI's, Johannesburg, South Africa.,University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa
| | - Osman Ebrahim
- University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.,Brenthurst Clinic, Johannesburg, South Africa
| | | | - Neil A Martinson
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa.,MRC Soweto Matlosana Centre for HIV/AIDS and TB Research, Johannesburg, South Africa
| | - Caroline T Tiemessen
- National Institute for Communicable Diseases, Centre for HIV and STI's, Johannesburg, South Africa. .,University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa.
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19
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Suerink M, Ripperger T, Messiaen L, Menko FH, Bourdeaut F, Colas C, Jongmans M, Goldberg Y, Nielsen M, Muleris M, van Kouwen M, Slavc I, Kratz C, Vasen HF, Brugiѐres L, Legius E, Wimmer K. Constitutional mismatch repair deficiency as a differential diagnosis of neurofibromatosis type 1: consensus guidelines for testing a child without malignancy. J Med Genet 2018; 56:53-62. [PMID: 30415209 DOI: 10.1136/jmedgenet-2018-105664] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022]
Abstract
Constitutional mismatch repair deficiency (CMMRD) is a rare childhood cancer predisposition syndrome caused by biallelic germline mutations in one of four mismatch-repair genes. Besides very high tumour risks, CMMRD phenotypes are often characterised by the presence of signs reminiscent of neurofibromatosis type 1 (NF1). Because NF1 signs may be present prior to tumour onset, CMMRD is a legitimate differential diagnosis in an otherwise healthy child suspected to have NF1/Legius syndrome without a detectable underlying NF1/SPRED1 germline mutation. However, no guidelines indicate when to counsel and test for CMMRD in this setting. Assuming that CMMRD is rare in these patients and that expected benefits of identifying CMMRD prior to tumour onset should outweigh potential harms associated with CMMRD counselling and testing in this setting, we aimed at elaborating a strategy to preselect, among children suspected to have NF1/Legius syndrome without a causative NF1/SPRED1 mutation and no overt malignancy, those children who have a higher probability of having CMMRD. At an interdisciplinary workshop, we discussed estimations of the frequency of CMMRD as a differential diagnosis of NF1 and potential benefits and harms of CMMRD counselling and testing in a healthy child with no malignancy. Preselection criteria and strategies for counselling and testing were developed and reviewed in two rounds of critical revisions. Existing diagnostic CMMRD criteria were adapted to serve as a guideline as to when to consider CMMRD as differential diagnosis of NF1/Legius syndrome. In addition, counselling and testing strategies are suggested to minimise potential harms.
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Affiliation(s)
- Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ludwine Messiaen
- Department of Genetics, University of Alabama, Birmingham, Alabama, USA
| | - Fred H Menko
- Family Cancer Clinic, Antoni van Leeuwenhoek Hospital and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Franck Bourdeaut
- Département d'Oncologie Pédiatrique et d'Adolescents Jeunes Adultes, Institut Curie, Paris, France
| | - Chrystelle Colas
- Department of Genetics, Institut Curie, Paris Sciences Lettres Research University, Paris, France.,Centre de Recherche Saint-Antoine, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Paris, France
| | - Marjolijn Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Yael Goldberg
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Martine Muleris
- Centre de Recherche Saint-Antoine, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Paris, France
| | - Mariëtte van Kouwen
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Irene Slavc
- Department of Pediatrics, Medical University Vienna, Vienna, Austria
| | - Christian Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Hans F Vasen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Laurence Brugiѐres
- Children and Adolescent Oncology Department, Gustave Roussy Cancer Institute, Villejuif, France
| | - Eric Legius
- Department of Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
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20
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Clinical characteristics and NF1 gene mutation analysis of three successive generations in three different Indian families with neurofibromatosis type 1 and peripheral nerve sheath tumours. J Clin Neurosci 2018; 53:62-68. [PMID: 29680440 DOI: 10.1016/j.jocn.2018.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/05/2018] [Accepted: 04/02/2018] [Indexed: 11/21/2022]
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21
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ArulJothi KN, Suruthi Abirami B, Devi A. Genetic spectrum of low density lipoprotein receptor gene variations in South Indian population. Clin Chim Acta 2017; 478:28-36. [PMID: 29269200 DOI: 10.1016/j.cca.2017.12.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/14/2017] [Accepted: 12/17/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Low density lipoprotein receptor (LDLR) is a membrane bound receptor maintaining cholesterol homeostasis along with Apolipoprotein B (APOB), Proprotein Convertase Subtilisin/Kexin type 9 (PCSK9) and other genes of lipid metabolism. Any pathogenic variation in these genes alters the function of the receptor and leads to Familial Hypercholesterolemia (FH) and other cardiovascular diseases. OBJECTIVE This study was aimed at screening the LDLR, APOB and PCSK9 genes in Hypercholesterolemic patients to define the genetic spectrum of FH in Indian population. METHODS Familial Hypercholesterolemia patients (n=78) of South Indian Tamil population with LDL cholesterol and Total cholesterol levels above 4.9mmol/l and 7.5mmol/l with family history of Myocardial infarction were involved. DNA was isolated by organic extraction method from blood samples and LDLR, APOB and PCSK9 gene exons were amplified using primers that cover exon-intron boundaries. The amplicons were screened using High Resolution Melt (HRM) Analysis and the screened samples were sequenced after purification. RESULTS This study reports 20 variations in South Indian population for the first time. In this set of variations 9 are novel variations which are reported for the first time, 11 were reported in other studies also. The in silico analysis for all the variations detected in this study were done to predict the probabilistic effect in pathogenicity of FH. CONCLUSION This study adds 9 novel variations and 11 recurrent variations to the spectrum of LDLR gene mutations in Indian population. All these variations are reported for the first time in Indian population. This spectrum of variations was different from the variations of previous Indian reports.
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Affiliation(s)
- K N ArulJothi
- Cardiovascular Genetics Group, Department of Genetic Genetic Engineering, SRM University, India
| | - B Suruthi Abirami
- Cardiovascular Genetics Group, Department of Genetic Genetic Engineering, SRM University, India
| | - Arikketh Devi
- Cardiovascular Genetics Group, Department of Genetic Genetic Engineering, SRM University, India.
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22
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RNA splicing in human disease and in the clinic. Clin Sci (Lond) 2017; 131:355-368. [PMID: 28202748 DOI: 10.1042/cs20160211] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 12/15/2016] [Indexed: 01/12/2023]
Abstract
Defects at the level of the pre-mRNA splicing process represent a major cause of human disease. Approximately 15-50% of all human disease mutations have been shown to alter functioning of basic and auxiliary splicing elements. These elements are required to ensure proper processing of pre-mRNA splicing molecules, with their disruption leading to misprocessing of the pre-mRNA molecule and disease. The splicing process is a complex process, with much still to be uncovered before we are able to accurately predict whether a reported genomic sequence variant (GV) represents a splicing-associated disease mutation or a harmless polymorphism. Furthermore, even when a mutation is correctly identified as affecting the splicing process, there still remains the difficulty of providing an exact evaluation of the potential impact on disease onset, severity and duration. In this review, we provide a brief overview of splicing diagnostic methodologies, from in silico bioinformatics approaches to wet lab in vitro and in vivo systems to evaluate splicing efficiencies. In particular, we provide an overview of how the latest developments in high-throughput sequencing can be applied to the clinic, and are already changing clinical approaches.
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Prykhozhij SV, Steele SL, Razaghi B, Berman JN. A rapid and effective method for screening, sequencing and reporter verification of engineered frameshift mutations in zebrafish. Dis Model Mech 2017; 10:811-822. [PMID: 28280001 PMCID: PMC5483001 DOI: 10.1242/dmm.026765] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 03/03/2017] [Indexed: 12/30/2022] Open
Abstract
Clustered regularly interspaced palindromic repeats (CRISPR)/Cas-based adaptive immunity against pathogens in bacteria has been adapted for genome editing and applied in zebrafish (Danio rerio) to generate frameshift mutations in protein-coding genes. Although there are methods to detect, quantify and sequence CRISPR/Cas9-induced mutations, identifying mutations in F1 heterozygous fish remains challenging. Additionally, sequencing a mutation and assuming that it causes a frameshift does not prove causality because of possible alternative translation start sites and potential effects of mutations on splicing. This problem is compounded by the relatively few antibodies available for zebrafish proteins, limiting validation at the protein level. To address these issues, we developed a detailed protocol to screen F1 mutation carriers, and clone and sequence identified mutations. In order to verify that mutations actually cause frameshifts, we created a fluorescent reporter system that can detect frameshift efficiency based on the cloning of wild-type and mutant cDNA fragments and their expression levels. As proof of principle, we applied this strategy to three CRISPR/Cas9-induced mutations in pycr1a, chd7 and hace1 genes. An insertion of seven nucleotides in pycr1a resulted in the first reported observation of exon skipping by CRISPR/Cas9-induced mutations in zebrafish. However, of these three mutant genes, the fluorescent reporter revealed effective frameshifting exclusively in the case of a two-nucleotide deletion in chd7, suggesting activity of alternative translation sites in the other two mutants even though pycr1a exon-skipping deletion is likely to be deleterious. This article provides a protocol for characterizing frameshift mutations in zebrafish, and highlights the importance of checking mutations at the mRNA level and verifying their effects on translation by fluorescent reporters when antibody detection of protein loss is not possible.
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Affiliation(s)
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8
| | - Babak Razaghi
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8 .,Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada B3H 4R2.,Department of Pathology, Dalhousie University, Halifax, NS, Canada B3H4R2
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24
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ArulJothi K, Whitthall R, Futema M, Humphries S, George M, Elangovan S, Nair DR, Devi A. Molecular analysis of the LDLR gene in coronary artery disease patients from the Indian population. Clin Biochem 2016; 49:669-674. [DOI: 10.1016/j.clinbiochem.2016.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/22/2016] [Accepted: 02/24/2016] [Indexed: 02/07/2023]
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25
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Gonzalez-Paredes FJ, Ramos-Trujillo E, Claverie-Martin F. Three exonic mutations in polycystic kidney disease-2 gene (PKD2) alter splicing of its pre-mRNA in a minigene system. Gene 2016; 578:117-23. [DOI: 10.1016/j.gene.2015.12.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/05/2015] [Accepted: 12/07/2015] [Indexed: 11/25/2022]
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26
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Functional Analysis of Mutations in Exon 9 of NF1 Reveals the Presence of Several Elements Regulating Splicing. PLoS One 2015; 10:e0141735. [PMID: 26509978 PMCID: PMC4624989 DOI: 10.1371/journal.pone.0141735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/11/2015] [Indexed: 11/19/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is one of the most common human hereditary disorders, predisposing individuals to the development of benign and malignant tumors in the nervous system, as well as other clinical manifestations. NF1 is caused by heterozygous mutations in the NF1 gene and around 25% of the pathogenic changes affect pre-mRNA splicing. Since the molecular mechanisms affected by these mutations are poorly understood, we have analyzed the splicing mutations identified in exon 9 of NF1, which is particularly prone to such changes, to better define the possible splicing regulatory elements. Using a minigene approach, we studied the effect of five splicing mutations in this exon described in patients. These highlighted three regulatory motifs within the exon. An in vivo splicing analysis of an extensive collection of changes generated in the minigene demonstrated that the CG motif at c.910-911 is critical for the recognition of exon 9. We also found that the GC motif at c.945-946 is involved in exon recognition through SRSF2 and that this motif is part of a Composite Exon Splicing Regulatory Element made up of physically overlapping enhancer and silencer elements. Finally, through an in vivo splicing analysis and in vitro binding assays, we demonstrated that the c.1007G>A mutation creates an Exonic Splicing Silencer element that binds the hnRNPA1 protein. The complexity of the splicing regulatory elements present in exon 9 is most likely responsible for the fact that mutations in this region represent 25% of all exonic changes that affect splicing in the NF1 gene.
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27
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Caminsky NG, Mucaki EJ, Rogan PK. Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis. F1000Res 2015. [DOI: 10.12688/f1000research.5654.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.
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28
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Caminsky N, Mucaki EJ, Rogan PK. Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis. F1000Res 2014; 3:282. [PMID: 25717368 PMCID: PMC4329672 DOI: 10.12688/f1000research.5654.1] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2014] [Indexed: 12/14/2022] Open
Abstract
The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.
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Affiliation(s)
- Natasha Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Peter K Rogan
- Departments of Biochemistry and Computer Science, Western University, London, ON, N6A 2C1, Canada
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Absence of an intron splicing silencer in porcine Smn1 intron 7 confers immunity to the exon skipping mutation in human SMN2. PLoS One 2014; 9:e98841. [PMID: 24892836 PMCID: PMC4043917 DOI: 10.1371/journal.pone.0098841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 05/08/2014] [Indexed: 11/19/2022] Open
Abstract
Spinal Muscular Atrophy is caused by homozygous loss of SMN1. All patients retain at least one copy of SMN2 which produces an identical protein but at lower levels due to a silent mutation in exon 7 which results in predominant exclusion of the exon. Therapies targeting the splicing of SMN2 exon 7 have been in development for several years, and their efficacy has been measured using either in vitro cellular assays or in vivo small animal models such as mice. In this study we evaluated the potential for constructing a mini-pig animal model by introducing minimal changes in the endogenous porcine Smn1 gene to maintain the native genomic structure and regulation. We found that while a Smn2-like mutation can be introduced in the porcine Smn1 gene and can diminish the function of the ESE, it would not recapitulate the splicing pattern seen in human SMN2 due to absence of a functional ISS immediately downstream of exon 7. We investigated the ISS region and show here that the porcine ISS is inactive due to disruption of a proximal hnRNP A1 binding site, while a distal hnRNP A1 binding site remains functional but is unable to maintain the functionality of the ISS as a whole.
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30
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Xu W, Yang X, Hu X, Li S. Fifty-four novel mutations in the NF1 gene and integrated analyses of the mutations that modulate splicing. Int J Mol Med 2014; 34:53-60. [PMID: 24789688 PMCID: PMC4072343 DOI: 10.3892/ijmm.2014.1756] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 03/14/2014] [Indexed: 12/12/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a common autosomal dominant genetic disorder caused by mutations in the NF1 gene. One of the hallmarks of NF1 is the high mutation rate in this gene. In this study, we present 127 different NF1 mutations and 54 novel mutations detected at both the genomic DNA and mRNA level using a retrospective case series review. We found that 25.2% of these different mutations induced aberrant splicing. Of note, 40.6% of these splicing errors were caused by exonic variants. In addition, one mutation produced mosaicism in the post-transcriptional profile. However, studies investigating these splicing aberrations are limited. In order to better understand the pathogenicity of NF1 and to provide a more accurate interpretation in molecular diagnostic testing, combined computational analyses were employed to elucidate the underlying mechanisms of the variants modulating NF1 gene splicing.
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Affiliation(s)
- Weihong Xu
- Genetics Laboratory, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, USA
| | - Xiao Yang
- Genetics Laboratory, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, USA
| | - Xiaoxia Hu
- Genetics Laboratory, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, USA
| | - Shibo Li
- Genetics Laboratory, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73117, USA
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31
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Nemethova M, Bolcekova A, Ilencikova D, Durovcikova D, Hlinkova K, Hlavata A, Kovacs L, Kadasi L, Zatkova A. Thirty-nine novel neurofibromatosis 1 (NF1) gene mutations identified in Slovak patients. Ann Hum Genet 2013; 77:364-79. [PMID: 23758643 DOI: 10.1111/ahg.12026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 04/22/2013] [Indexed: 01/20/2023]
Abstract
We performed a complex analysis of the neurofibromatosis type 1 (NF1) gene in Slovakia based on direct cDNA sequencing supplemented by multiple ligation dependent probe amplification (MLPA) analysis. All 108 patients had café-au-lait spots, 85% had axilary and/or inguinal freckling, 61% neurofibromas, 36% Lisch nodules of the iris and 31% optic pathway glioma, 5% suffered from typical skeletal disorders, and 51% of patients had family members with NF1. In 78 of the 86 (90.7%) index patients our analysis revealed the presence of NF1 mutations, 68 of which were small changes (87.2%), including 39 (50%) novel. Among the identified mutations the most prevalent were small deletions and insertions causing frameshift (42.3%), followed by nonsense (14.1%), missense (12.8%), and typical splicing (11.5%) mutations. Type 1 NF1 deletions and intragenic deletions/duplication were identified in five cases each (6.4%). Interestingly, in five other cases nontypical splicing variants were found, whose real effect on NF1 transcript would have remained undetected if using a DNA-based method alone, thus underlying the advantage of using the cDNA-based sequencing. We show that Slovak NF1 patients have a similar repertoire of NF1 germline mutations compared to other populations, with some prevalence of small deletions/insertions and a decreased proportion of nonsense mutations.
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Affiliation(s)
- Martina Nemethova
- Laboratory of Genetics, Institute of Molecular Physiology and Genetics, Bratislava, Slovakia
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32
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Juan-Mateu J, González-Quereda L, Rodríguez MJ, Verdura E, Lázaro K, Jou C, Nascimento A, Jiménez-Mallebrera C, Colomer J, Monges S, Lubieniecki F, Foncuberta ME, Pascual-Pascual SI, Molano J, Baiget M, Gallano P. Interplay between DMD point mutations and splicing signals in Dystrophinopathy phenotypes. PLoS One 2013; 8:e59916. [PMID: 23536893 PMCID: PMC3607557 DOI: 10.1371/journal.pone.0059916] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/19/2013] [Indexed: 12/12/2022] Open
Abstract
DMD nonsense and frameshift mutations lead to severe Duchenne muscular dystrophy while in-frame mutations lead to milder Becker muscular dystrophy. Exceptions are found in 10% of cases and the production of alternatively spliced transcripts is considered a key modifier of disease severity. Several exonic mutations have been shown to induce exon-skipping, while splice site mutations result in exon-skipping or activation of cryptic splice sites. However, factors determining the splicing pathway are still unclear. Point mutations provide valuable information regarding the regulation of pre-mRNA splicing and elements defining exon identity in the DMD gene. Here we provide a comprehensive analysis of 98 point mutations related to clinical phenotype and their effect on muscle mRNA and dystrophin expression. Aberrant splicing was found in 27 mutations due to alteration of splice sites or splicing regulatory elements. Bioinformatics analysis was performed to test the ability of the available algorithms to predict consequences on mRNA and to investigate the major factors that determine the splicing pathway in mutations affecting splicing signals. Our findings suggest that the splicing pathway is highly dependent on the interplay between splice site strength and density of regulatory elements.
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Affiliation(s)
- Jonàs Juan-Mateu
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Lidia González-Quereda
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Maria José Rodríguez
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Edgard Verdura
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Kira Lázaro
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Cristina Jou
- Servei d'Anatomia Patològica Hospital Sant Joan de Déu, Barcelona, Spain
| | - Andrés Nascimento
- Unitat de Patologia Neuromuscular, Servei de Neurologia, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Jaume Colomer
- Unitat de Patologia Neuromuscular, Servei de Neurologia, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Soledad Monges
- Servicio de Neuropediatría, Hospital Nacional Pediátrico Garrahan, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Servicio de Patología, Hospital Nacional Pediátrico Garrahan, Buenos Aires, Argentina
| | | | | | - Jesús Molano
- Unidad de Genética Molecular and CIBERER U753, Hospital Universitario Materno Infantil La Paz, Madrid, Spain
| | - Montserrat Baiget
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
| | - Pia Gallano
- Servei de Genètica, Hospital de la Santa Creu i Sant Pau and CIBERER U705, Barcelona, Spain
- * E-mail:
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Wappenschmidt B, Becker AA, Hauke J, Weber U, Engert S, Köhler J, Kast K, Arnold N, Rhiem K, Hahnen E, Meindl A, Schmutzler RK. Analysis of 30 putative BRCA1 splicing mutations in hereditary breast and ovarian cancer families identifies exonic splice site mutations that escape in silico prediction. PLoS One 2012; 7:e50800. [PMID: 23239986 PMCID: PMC3519833 DOI: 10.1371/journal.pone.0050800] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/25/2012] [Indexed: 12/12/2022] Open
Abstract
Screening for pathogenic mutations in breast and ovarian cancer genes such as BRCA1/2, CHEK2 and RAD51C is common practice for individuals from high-risk families. However, test results may be ambiguous due to the presence of unclassified variants (UCV) in the concurrent absence of clearly cancer-predisposing mutations. Especially the presence of intronic or exonic variants within these genes that possibly affect proper pre-mRNA processing poses a challenge as their functional implications are not immediately apparent. Therefore, it appears necessary to characterize potential splicing UCV and to develop appropriate classification tools. We investigated 30 distinct BRCA1 variants, both intronic and exonic, regarding their spliceogenic potential by commonly used in silico prediction algorithms (HSF, MaxEntScan) along with in vitro transcript analyses. A total of 25 variants were identified spliceogenic, either causing/enhancing exon skipping or activation of cryptic splice sites, or both. Except from a single intronic variant causing minor effects on BRCA1 pre-mRNA processing in our analyses, 23 out of 24 intronic variants were correctly predicted by MaxEntScan, while HSF was less accurate in this cohort. Among the 6 exonic variants analyzed, 4 severely impair correct pre-mRNA processing, while the remaining two have partial effects. In contrast to the intronic alterations investigated, only half of the spliceogenic exonic variants were correctly predicted by HSF and/or MaxEntScan. These data support the idea that exonic splicing mutations are commonly disease-causing and concurrently prone to escape in silico prediction, hence necessitating experimental in vitro splicing analysis.
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Affiliation(s)
- Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Alexandra A. Becker
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Jan Hauke
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Ute Weber
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Stefanie Engert
- Department of Gynaecology and Obstetrics, Klinikum rechts der Isar at the Technical University, Munich, Germany
| | - Juliane Köhler
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Karin Kast
- Department of Gynecology and Obstetrics, Technical University of Dresden, Dresden, Germany
| | - Norbert Arnold
- Division of Oncology, Department of Gynaecology and Obstetrics, University Hospital Schleswig-Holstein, Christian-Albrechts-University, Kiel, Germany
| | - Kerstin Rhiem
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Eric Hahnen
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Alfons Meindl
- Department of Gynaecology and Obstetrics, Klinikum rechts der Isar at the Technical University, Munich, Germany
| | - Rita K. Schmutzler
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- * E-mail:
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34
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Jin P, Cai R, Zhou X, Li-Ling J, Ma F. Features of missense/nonsense mutations in exonic splicing enhancer sequences from cancer-related human genes. Mutat Res 2012; 740:6-12. [PMID: 23123687 DOI: 10.1016/j.mrfmmm.2012.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Revised: 08/31/2012] [Accepted: 10/19/2012] [Indexed: 11/18/2022]
Affiliation(s)
- Ping Jin
- College of Life Science, Nanjing Normal University, Nanjing, China
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35
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Buratti E, Baralle M, Baralle FE. From single splicing events to thousands: the ambiguous step forward in splicing research. Brief Funct Genomics 2012; 12:3-12. [DOI: 10.1093/bfgp/els048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Hernández-Imaz E, Campos B, Rodríguez-Álvarez FJ, Abad O, Melean G, Gardenyes J, Martín Y, Hernández-Chico C. Characterization ofNF1allele containing two nonsense mutations in exon 37 that segregates with neurofibromatosis type 1. Clin Genet 2012; 83:462-6. [DOI: 10.1111/j.1399-0004.2012.01952.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 07/31/2012] [Accepted: 08/07/2012] [Indexed: 12/14/2022]
Affiliation(s)
- E Hernández-Imaz
- Unidad de Genética Molecular; Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS); Madrid; Spain
| | - B Campos
- Centre de Diagnòstic Genètic Molecular (CDGM); Institut d'Investigació Biomèdica de Bellvitge (IDIBELL); Barcelona; Spain
| | - FJ Rodríguez-Álvarez
- Unidad de Genética Molecular; Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS); Madrid; Spain
| | - O Abad
- Centre de Diagnòstic Genètic Molecular (CDGM); Institut d'Investigació Biomèdica de Bellvitge (IDIBELL); Barcelona; Spain
| | - G Melean
- Unidad de Genética Molecular; Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS); Madrid; Spain
| | - J Gardenyes
- Centre de Diagnòstic Genètic Molecular (CDGM); Institut d'Investigació Biomèdica de Bellvitge (IDIBELL); Barcelona; Spain
| | - Y Martín
- Unidad de Genética Molecular; Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS); Madrid; Spain
| | - C Hernández-Chico
- Unidad de Genética Molecular; Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS); Madrid; Spain
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37
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Flanigan KM, Dunn DM, von Niederhausern A, Soltanzadeh P, Howard MT, Sampson JB, Swoboda KJ, Bromberg MB, Mendell JR, Taylor LE, Anderson CB, Pestronk A, Florence JM, Connolly AM, Mathews KD, Wong B, Finkel RS, Bonnemann CG, Day JW, McDonald C, Weiss RB. Nonsense mutation-associated Becker muscular dystrophy: interplay between exon definition and splicing regulatory elements within the DMD gene. Hum Mutat 2012; 32:299-308. [PMID: 21972111 DOI: 10.1002/humu.21426] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nonsense mutations are usually predicted to function as null alleles due to premature termination of protein translation. However, nonsense mutations in the DMD gene, encoding the dystrophin protein, have been associated with both the severe Duchenne Muscular Dystrophy (DMD) and milder Becker Muscular Dystrophy (BMD) phenotypes. In a large survey, we identified 243 unique nonsense mutations in the DMD gene, and for 210 of these we could establish definitive phenotypes. We analyzed the reading frame predicted by exons flanking those in which nonsense mutations were found, and present evidence that nonsense mutations resulting in BMD likely do so by inducing exon skipping, confirming that exonic point mutations affecting exon definition have played a significant role in determining phenotype. We present a new model based on the combination of exon definition and intronic splicing regulatory elements for the selective association of BMD nonsense mutations with a subset of DMD exons prone to mutation-induced exon skipping.
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Affiliation(s)
- Kevin M Flanigan
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA.
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Tripathi S, Schultz I, Becker E, Montag J, Borchert B, Francino A, Navarro-Lopez F, Perrot A, Özcelik C, Osterziel KJ, McKenna WJ, Brenner B, Kraft T. Unequal allelic expression of wild-type and mutated β-myosin in familial hypertrophic cardiomyopathy. Basic Res Cardiol 2011; 106:1041-55. [PMID: 21769673 PMCID: PMC3228959 DOI: 10.1007/s00395-011-0205-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 06/29/2011] [Accepted: 07/07/2011] [Indexed: 11/29/2022]
Abstract
Familial hypertrophic cardiomyopathy (FHC) is an autosomal dominant disease, which in about 30% of the patients is caused by missense mutations in one allele of the β-myosin heavy chain (β-MHC) gene (MYH7). To address potential molecular mechanisms underlying the family-specific prognosis, we determined the relative expression of mutant versus wild-type MYH7-mRNA. We found a hitherto unknown mutation-dependent unequal expression of mutant to wild-type MYH7-mRNA, which is paralleled by similar unequal expression of β-MHC at the protein level. Relative abundance of mutated versus wild-type MYH7-mRNA was determined by a specific restriction digest approach and by real-time PCR (RT-qPCR). Fourteen samples from M. soleus and myocardium of 12 genotyped and clinically well-characterized FHC patients were analyzed. The fraction of mutated MYH7-mRNA in five patients with mutation R723G averaged to 66 and 68% of total MYH7-mRNA in soleus and myocardium, respectively. For mutations I736T, R719W and V606M, fractions of mutated MYH7-mRNA in M. soleus were 39, 57 and 29%, respectively. For all mutations, unequal abundance was similar at the protein level. Importantly, fractions of mutated transcripts were comparable among siblings, in younger relatives and unrelated carriers of the same mutation. Hence, the extent of unequal expression of mutated versus wild-type transcript and protein is characteristic for each mutation, implying cis-acting regulatory mechanisms. Bioinformatics suggest mRNA stability or splicing effectors to be affected by certain mutations. Intriguingly, we observed a correlation between disease expression and fraction of mutated mRNA and protein. This strongly suggests that mutation-specific allelic imbalance represents a new pathogenic factor for FHC.
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Affiliation(s)
- Snigdha Tripathi
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Imke Schultz
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl Neuberg Str. 1, 30625 Hannover, Germany
- Present Address: Niederwiesenring 4, 63110 Rodgau, Germany
| | - Edgar Becker
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Judith Montag
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Bianca Borchert
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl Neuberg Str. 1, 30625 Hannover, Germany
- Present Address: Department of Cardiac, Thoracic, Transplantation and Vascular Surgery, Hannover Medical School, Carl-Neuberg Str. 1, 30625 Hannover, Germany
| | - Antonio Francino
- Hospital Clinic/IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | | | - Andreas Perrot
- Charité-Unversitätsmedizin Berlin, Experimental and Clinical Research Center (ECRC) am Max-Delbrück-Centrum für Molekulare Medizin, Kardio-Genetisches Labor, 13125 Berlin, Germany
| | - Cemil Özcelik
- Charité-Unversitätsmedizin Berlin, Experimental and Clinical Research Center (ECRC) am Max-Delbrück-Centrum für Molekulare Medizin, Kardio-Genetisches Labor, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, Kardiologie am Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Karl-Josef Osterziel
- Charité-Universitätsmedizin Berlin, Kardiologie am Campus Virchow-Klinikum, 13353 Berlin, Germany
- Present Address: Kardiologische Gemeinschaftspraxis, Marienstraße 9, 92224 Amberg, Germany
| | - William J. McKenna
- Institute of Cardiovascular Science, University College London, London, WC1E 6BT United Kingdom
| | - Bernhard Brenner
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Theresia Kraft
- Institute of Molecular and Cell Physiology, Hannover Medical School, Carl Neuberg Str. 1, 30625 Hannover, Germany
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Sterne-Weiler T, Howard J, Mort M, Cooper DN, Sanford JR. Loss of exon identity is a common mechanism of human inherited disease. Genome Res 2011; 21:1563-71. [PMID: 21750108 DOI: 10.1101/gr.118638.110] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
It is widely accepted that at least 10% of all mutations causing human inherited disease disrupt splice-site consensus sequences. In contrast to splice-site mutations, the role of auxiliary cis-acting elements such as exonic splicing enhancers (ESE) and exonic splicing silencers (ESS) in human inherited disease is still poorly understood. Here we use a top-down approach to determine rates of loss or gain of known human exonic splicing regulatory (ESR) sequences associated with either disease-causing mutations or putatively neutral single nucleotide polymorphisms (SNPs). We observe significant enrichment toward loss of ESEs and gain of ESSs among inherited disease-causing variants relative to neutral polymorphisms, indicating that exon skipping may play a prominent role in aberrant gene regulation. Both computational and biochemical approaches underscore the relevance of exonic splicing enhancer loss and silencer gain in inherited disease. Additionally, we provide direct evidence that both SRp20 (SRSF3) and possibly PTB (PTBP1) are involved in the function of a splicing silencer that is created de novo by a total of 83 different inherited disease mutations in 67 different disease genes. Taken together, we find that ~25% (7154/27,681) of known mis-sense and nonsense disease-causing mutations alter functional splicing signals within exons, suggesting a much more widespread role for aberrant mRNA processing in causing human inherited disease than has hitherto been appreciated.
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Affiliation(s)
- Timothy Sterne-Weiler
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
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Assessing the RNA effect of 26 DNA variants in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat 2011; 132:979-92. [PMID: 21735045 DOI: 10.1007/s10549-011-1661-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 06/24/2011] [Indexed: 12/17/2022]
Abstract
Comprehensive genetic testing of the breast cancer susceptibility genes BRCA1 and BRCA2 identified approximately 16% of variants of unknown significance (VUS), a significant proportion of which could affect the correct splicing of the genes. Our aim is to establish a workflow for classifying VUS in these complex genes, the first stage of which is splicing analysis. We used a combined approach consisting of five in silico splicing prediction programs and RT-PCR analysis for a set of 26 variants not previously studied at the mRNA level and six variants that had already been studied, four of which were used as positive controls as they were found to affect the splicing of these genes and the other two were used as negative controls. We identified a splicing defect in 8 of the 26 newly studied variants and ruled out splicing alteration in the remaining 18 variants. The results for the four positive and the two negative control variants were consistent with results presented in the literature. Our results strongly suggest that the combination of RNA analysis and in silico programs is an important step towards the classification of VUS. The results revealed a very high correlation between experimental data and in silico programs when using tools for predicting acceptor/donor sites but a lower correlation in the case of tools for identifying ESE elements.
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Doktor TK, Schroeder LD, Vested A, Palmfeldt J, Andersen HS, Gregersen N, Andresen BS. SMN2 exon 7 splicing is inhibited by binding of hnRNP A1 to a common ESS motif that spans the 3' splice site. Hum Mutat 2011; 32:220-30. [PMID: 21120954 DOI: 10.1002/humu.21419] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 11/02/2010] [Indexed: 11/05/2022]
Abstract
Spinal Muscular Atrophy is caused by homozygous loss of SMN1 with phenotypic modulation by SMN2. SMN2 expresses only limited amounts of full-length transcript due to skipping of exon 7 caused by disruption of an SF2/ASF binding ESE. Additionally, hnRNP A1 has been reported to inhibit inclusion of SMN2 exon 7. We previously reported high similarity between the sequence spanning the 3' ss of SMN1 and SMN2 exon 7 and an hnRNP A1 binding ESS, which regulates MCAD exon 5 splicing. We show here that this 3' ss motif indeed functions as a crucial hnRNP A1 binding ESS, which inhibits inclusion of SMN1/2 exon 7 and is antagonized by the SMN1 ESE, but not by the inactive SMN2 sequence. Pull-down experiments revealed a specific interaction between hnRNP A1 and the 3' ss AG-dinucleotide, which could be disrupted by mutations shown to improve splicing in reporter minigenes. Genomic analyses revealed that in the human genome, 3' ss matching the SMN1/2 ESS motif region are much less abundant than 3' ss with a disrupted ESS motif. This indicates that this ESS may be a general splicing inhibitory motif, which binds hnRNP A1 and inhibits exon inclusion by binding to 3' ss harboring this ESS motif.
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Affiliation(s)
- Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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Abstract
It appears that all types of genomic nucleotide variations can be deleterious by affecting normal pre-mRNA splicing via disruption/creation of splice site consensus sequences. As it is neither pertinent nor realistic to perform functional testing for all of these variants, it is important to identify those that could lead to a splice defect in order to restrict experimental transcript analyses to the most appropriate cases. In silico tools designed to provide this type of prediction are available. In this chapter, we present in silico splice tools integrated in the Alamut (Interactive Biosoftware) application and detail their use in routine diagnostic applications. At this time, in silico predictions are useful for variants that decrease the strength of wild-type splice sites or create a cryptic splice site. Importantly, in silico predictions are not sufficient to classify variants as neutral or deleterious: they should be used as part of the decision-making process to detect potential candidates for splicing anomalies, prompting molecular geneticists to carry out transcript analyses in a limited and pertinent number of cases which could be managed in routine settings.
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Affiliation(s)
- Claude Houdayer
- Faculty of Pharmacy, Institut Curie, Paris Descartes University, Paris, France.
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43
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Talkowski ME, McCann KL, Chen M, McClain L, Bamne M, Wood J, Chowdari KV, Watson A, Prasad KM, Kirov G, Georgieva L, Toncheva D, Mansour H, Lewis DA, Owen M, O’Donovan M, Papasaikas P, Sullivan P, Ruderfer D, Yao JK, Leonard S, Thomas P, Miyajima F, Quinn J, Lopez AJ, Nimgaonkar VL. Fine-mapping reveals novel alternative splicing of the dopamine transporter. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:1434-47. [PMID: 20957647 PMCID: PMC4575812 DOI: 10.1002/ajmg.b.31125] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 08/04/2010] [Indexed: 01/14/2023]
Abstract
The dopamine transporter gene (SLC6A3, DAT) has been implicated in the pathogenesis of numerous psychiatric and neurodevelopmental disorders, including schizophrenia (SZ). We previously detected association between SZ and intronic SLC6A3 variants that replicated in two independent Caucasian samples, but had no obvious function. In follow-up analyses, we sequenced the coding and intronic regions of SLC6A3 to identify complete linkage disequilibrium patterns of common variations. We genotyped 78 polymorphisms, narrowing the potentially causal region to two correlated clusters of associated SNPs localized predominantly to introns 3 and 4. Our computational analysis of these intronic regions predicted a novel cassette exon within intron 3, designated E3b, which is conserved among primates. We confirmed alternative splicing of E3b in post-mortem human substantia nigra (SN). As E3b introduces multiple in-frame stop codons, the SLC6A3 open reading frame is truncated and the spliced product may undergo nonsense mediated decay. Thus, factors that increase E3b splicing could reduce the amount of unspliced product available for translation. Observations consistent with this prediction were made using cellular assays and in post-mortem human SN. In mini-gene constructs, the extent of splicing is also influenced by at least two common haplotypes, so the alternative splicing was evaluated in relation to SZ risk. Meta-analyses across genome-wide association studies did not support the initial associations and further post-mortem studies did not suggest case-control differences in splicing. These studies do not provide a compelling link to schizophrenia. However, the impact of the alternative splicing on other neuropsychiatric disorders should be investigated. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Michael E. Talkowski
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Kathleen L. McCann
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Michael Chen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Lora McClain
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Mikhil Bamne
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joel Wood
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kodavali V. Chowdari
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Annie Watson
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Konasale M. Prasad
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
| | - Lyudmilla Georgieva
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Hader Mansour
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David A. Lewis
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Michael Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael O’Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
| | - Panagiotis Papasaikas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Patrick Sullivan
- Department of Genetics & Carolina Center for Genome Science, University of North Carolina, Chapel Hill, North Carolina
| | - Douglas Ruderfer
- Center for Human Genetic Research, Massachusetts General Hospital and Broad Institute, Boston, Massachusetts
| | - Jeffrey K Yao
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania,VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | - Sherry Leonard
- Department of Psychiatry, University of Colorado at Denver, Aurora, Colorado
| | - Pramod Thomas
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Fabio Miyajima
- Division of Human Anatomy and Cell Biology School of Biomedical Sciences, University of Liverpool, Liverpool, UK
| | - John Quinn
- Division of Human Anatomy and Cell Biology School of Biomedical Sciences, University of Liverpool, Liverpool, UK
| | - A. Javier Lopez
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Vishwajit L. Nimgaonkar
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania,Correspondence: Vishwajit L. Nimgaonkar, Department of Psychiatry and Human Genetics, University of Pittsburgh School of Medicine and Graduate School of Public Health, WPIC, Room 441, 3811 O’Hara St, Pittsburgh, PA 15213
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Hölzel M, Huang S, Koster J, Ora I, Lakeman A, Caron H, Nijkamp W, Xie J, Callens T, Asgharzadeh S, Seeger RC, Messiaen L, Versteeg R, Bernards R. NF1 is a tumor suppressor in neuroblastoma that determines retinoic acid response and disease outcome. Cell 2010; 142:218-29. [PMID: 20655465 DOI: 10.1016/j.cell.2010.06.004] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/04/2010] [Accepted: 05/26/2010] [Indexed: 11/26/2022]
Abstract
Retinoic acid (RA) induces differentiation of neuroblastoma cells in vitro and is used with variable success to treat aggressive forms of this disease. This variability in clinical response to RA is enigmatic, as no mutations in components of the RA signaling cascade have been found. Using a large-scale RNAi genetic screen, we identify crosstalk between the tumor suppressor NF1 and retinoic acid-induced differentiation in neuroblastoma. Loss of NF1 activates RAS-MEK signaling, which in turn represses ZNF423, a critical transcriptional coactivator of the retinoic acid receptors. Neuroblastomas with low levels of both NF1 and ZNF423 have extremely poor outcome. We find NF1 mutations in neuroblastoma cell lines and in primary tumors. Inhibition of MEK signaling downstream of NF1 restores responsiveness to RA, suggesting a therapeutic strategy to overcome RA resistance in NF1-deficient neuroblastomas.
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Affiliation(s)
- Michael Hölzel
- Divisions of Molecular Carcinogenesis and Molecular Genetics, Center for Biomedical Genetics and Cancer Genomics Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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45
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Dobrowolski SF, Andersen HS, Doktor TK, Andresen BS. The phenylalanine hydroxylase c.30C>G synonymous variation (p.G10G) creates a common exonic splicing silencer. Mol Genet Metab 2010; 100:316-23. [PMID: 20457534 DOI: 10.1016/j.ymgme.2010.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/07/2010] [Indexed: 11/30/2022]
Abstract
PKU is caused by mutations in PAH. A c.30C>G synonymous variation in exon 1, previously reported as neutral, was observed in two patients. The variation creates a GGG triplet, which is part of several exonic splicing silencer (ESS) motifs. Because the 5'-splice site of PAH exon 1 is intrinsically weak and therefore could be responsive to a new flanking ESS, we hypothesized that c.30C>G could cause aberrant mRNA splicing. We demonstrate that c.30C>G causes aberrant mRNA splicing in two different reporter minigenes, and that this is abolished if a preexisting flanking GGG triplet is disrupted. GGG triplets are part of the consensus motif bound by splicing-inhibitory hnRNPH proteins and we observed a dramatic increase in hnRNPH binding to c.30C>G PAH RNA. We conclude that c.30C>G creates a hnRNPH-binding ESS, which can disrupt mRNA splicing. A disease-causing mutation in HEXB, which has previously been associated with exon skipping in patients also creates a GGG triplet. We show that the mutant HEXB motif causes exon skipping of a reporter minigene and that this is also influenced by a flanking GGG triplet. We suggest that aberrant splicing caused by creation/abolishment of GGG triplets located together with a preexisting flanking GGG triplet, may be an underreported cause of human disease. It is important to recognize that exonic sequence changes may disrupt mRNA splicing. This is particularly important in PAH, since PKU patients harboring such mutations are unlikely to respond to therapy with 6R-tetrahydrobiopterin (BH(4)), despite the fact that the genetic code indicates otherwise.
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Affiliation(s)
- Steven F Dobrowolski
- Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT, USA
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46
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Levit A, Nutman D, Osher E, Kamhi E, Navon R. Two novel exonic point mutations in HEXA identified in a juvenile Tay-Sachs patient: role of alternative splicing and nonsense-mediated mRNA decay. Mol Genet Metab 2010; 100:176-83. [PMID: 20363167 DOI: 10.1016/j.ymgme.2010.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/13/2010] [Accepted: 03/14/2010] [Indexed: 11/30/2022]
Abstract
We have identified three mutations in the beta-hexoseaminidase A (HEXA) gene in a juvenile Tay-Sachs disease (TSD) patient, which exhibited a reduced level of HEXA mRNA. Two mutations are novel, c.814G>A (p.Gly272Arg) and c.1305C>T (p.=), located in exon 8 and in exon 11, respectively. The third mutation, c.1195A>G (p.Asn399Asp) in exon 11, has been previously characterized as a common polymorphism in African-Americans. Hex A activity measured in TSD Glial cells, transfected with HEXA cDNA constructs bearing these mutations, was unaltered from the activity level measured in normal HEXA cDNA. Analysis of RT-PCR products revealed three aberrant transcripts in the patient, one where exon 8 was absent, one where exon 11 was absent and a third lacking both exons 10 and 11. All three novel transcripts contain frameshifts resulting in premature termination codons (PTCs). Transfection of mini-gene constructs carrying the c.814G>A and c.1305C>T mutations proved that the two mutations result in exon skipping. mRNAs that harbor a PTC are detected and degraded by the nonsense-mediated mRNA decay (NMD) pathway to prevent synthesis of abnormal proteins. However, although NMD is functional in the patient's fibroblasts, aberrant transcripts are still present. We suggest that the level of correctly spliced transcripts as well as the efficiency in which NMD degrade the PTC-containing transcripts, apparently plays an important role in the phenotype severity of the unique patient and thus should be considered as a potential target for drug therapy.
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Affiliation(s)
- A Levit
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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47
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Whiley PJ, Pettigrew CA, Brewster BL, Walker LC, Spurdle AB, Brown MA. Effect of BRCA2 sequence variants predicted to disrupt exonic splice enhancers on BRCA2 transcripts. BMC MEDICAL GENETICS 2010; 11:80. [PMID: 20507642 PMCID: PMC2897790 DOI: 10.1186/1471-2350-11-80] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 05/28/2010] [Indexed: 12/02/2022]
Abstract
Background Genetic screening of breast cancer patients and their families have identified a number of variants of unknown clinical significance in the breast cancer susceptibility genes, BRCA1 and BRCA2. Evaluation of such unclassified variants may be assisted by web-based bioinformatic prediction tools, although accurate prediction of aberrant splicing by unclassified variants affecting exonic splice enhancers (ESEs) remains a challenge. Methods This study used a combination of RT-PCR analysis and splicing reporter minigene assays to assess five unclassified variants in the BRCA2 gene that we had previously predicted to disrupt an ESE using bioinformatic approaches. Results Analysis of BRCA2 c.8308 G > A (p.Ala2770Thr) by mRNA analysis, and BRCA2 c.8962A > G (p.Ser2988Gly), BRCA2 c.8972G > A (p.Arg2991His), BRCA2 c.9172A > G (p.Ser3058Gly), and BRCA2 c.9213G > T (p.Glu3071Asp) by a minigene assay, revealed no evidence for aberrant splicing. Conclusions These results illustrate the need for improved methods for predicting functional ESEs and the potential consequences of sequence variants contained therein.
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Affiliation(s)
- Phillip J Whiley
- School of Chemistry and Molecular Biosciences, The University of Queensland, Australia
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48
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Woolfe A, Mullikin JC, Elnitski L. Genomic features defining exonic variants that modulate splicing. Genome Biol 2010; 11:R20. [PMID: 20158892 PMCID: PMC2872880 DOI: 10.1186/gb-2010-11-2-r20] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 02/03/2010] [Accepted: 02/16/2010] [Indexed: 12/21/2022] Open
Abstract
A comparative analysis of SNPs and their exonic and intronic environments identifies the features predictive of splice affecting variants. Background Single point mutations at both synonymous and non-synonymous positions within exons can have severe effects on gene function through disruption of splicing. Predicting these mutations in silico purely from the genomic sequence is difficult due to an incomplete understanding of the multiple factors that may be responsible. In addition, little is known about which computational prediction approaches, such as those involving exonic splicing enhancers and exonic splicing silencers, are most informative. Results We assessed the features of single-nucleotide genomic variants verified to cause exon skipping and compared them to a large set of coding SNPs common in the human population, which are likely to have no effect on splicing. Our findings implicate a number of features important for their ability to discriminate splice-affecting variants, including the naturally occurring density of exonic splicing enhancers and exonic splicing silencers of the exon and intronic environment, extensive changes in the number of predicted exonic splicing enhancers and exonic splicing silencers, proximity to the splice junctions and evolutionary constraint of the region surrounding the variant. By extending this approach to additional datasets, we also identified relevant features of variants that cause increased exon inclusion and ectopic splice site activation. Conclusions We identified a number of features that have statistically significant representation among exonic variants that modulate splicing. These analyses highlight putative mechanisms responsible for splicing outcome and emphasize the role of features important for exon definition. We developed a web-tool, Skippy, to score coding variants for these relevant splice-modulating features.
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Affiliation(s)
- Adam Woolfe
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20892, USA.
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Musante L, Kunde SA, Sulistio TO, Fischer U, Grimme A, Frints SG, Schwartz CE, MartÃnez F, Romano C, Ropers HH, Kalscheuer VM. Common pathological mutations inPQBP1induce nonsense-mediated mRNA decay and enhance exclusion of the mutant exon. Hum Mutat 2010; 31:90-8. [DOI: 10.1002/humu.21146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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50
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Vorechovsky I. Transposable elements in disease-associated cryptic exons. Hum Genet 2009; 127:135-54. [PMID: 19823873 DOI: 10.1007/s00439-009-0752-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/27/2009] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) make up a half of the human genome, but the extent of their contribution to cryptic exon activation that results in genetic disease is unknown. Here, a comprehensive survey of 78 mutation-induced cryptic exons previously identified in 51 disease genes revealed the presence of TEs in 40 cases (51%). Most TE-containing exons were derived from short interspersed nuclear elements (SINEs), with Alus and mammalian interspersed repeats (MIRs) covering >18 and >16% of the exonized sequences, respectively. The majority of SINE-derived cryptic exons had splice sites at the same positions of the Alu/MIR consensus as existing SINE exons and their inclusion in the mRNA was facilitated by phylogenetically conserved changes that improved both traditional and auxiliary splicing signals, thus marking intronic TEs amenable for pathogenic exonization. The overrepresentation of MIRs among TE exons is likely to result from their high average exon inclusion levels, which reflect their strong splice sites, a lack of splicing silencers and a high density of enhancers, particularly (G)AA(G) motifs. These elements were markedly depleted in antisense Alu exons, had the most prominent position on the exon-intron gradient scale and are proposed to promote exon definition through enhanced tertiary RNA interactions involving unpaired (di)adenosines. The identification of common mechanisms by which the most dynamic parts of the genome contribute both to new exon creation and genetic disease will facilitate detection of intronic mutations and the development of computational tools that predict TE hot-spots of cryptic exon activation.
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Affiliation(s)
- Igor Vorechovsky
- Division of Human Genetics, University of Southampton School of Medicine, MP808, Tremona Road, Southampton SO16 6YD, UK.
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