1
|
Chen JM, Lin JH, Masson E, Liao Z, Férec C, Cooper DN, Hayden M. The Experimentally Obtained Functional Impact Assessments of 5' Splice Site GT'GC Variants Differ Markedly from Those Predicted. Curr Genomics 2020; 21:56-66. [PMID: 32655299 PMCID: PMC7324893 DOI: 10.2174/1389202921666200210141701] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/26/2023] Open
Abstract
Introduction: 5' splice site GT>GC or +2T>C variants have been frequently reported to cause human genetic disease and are routinely scored as pathogenic splicing mutations. However, we have recently demonstrated that such variants in human disease genes may not invariably be pathogenic. Moreover, we found that no splicing prediction tools appear to be capable of reliably distinguishing those +2T>C variants that generate wild-type transcripts from those that do not. Methodology Herein, we evaluated the performance of a novel deep learning-based tool, SpliceAI, in the context of three datasets of +2T>C variants, all of which had been characterized functionally in terms of their impact on pre-mRNA splicing. The first two datasets refer to our recently described “in vivo” dataset of 45 known disease-causing +2T>C variants and the “in vitro” dataset of 103 +2T>C substitutions subjected to full-length gene splicing assay. The third dataset comprised 12 BRCA1 +2T>C variants that were recently analyzed by saturation genome editing. Results Comparison of the SpliceAI-predicted and experimentally obtained functional impact assessments of these variants (and smaller datasets of +2T>A and +2T>G variants) revealed that although SpliceAI performed rather better than other prediction tools, it was still far from perfect. A key issue was that the impact of those +2T>C (and +2T>A) variants that generated wild-type transcripts represents a quantitative change that can vary from barely detectable to an almost full expression of wild-type transcripts, with wild-type transcripts often co-existing with aberrantly spliced transcripts. Conclusion Our findings highlight the challenges that we still face in attempting to accurately identify splice-altering variants.
Collapse
Affiliation(s)
- Jian-Min Chen
- 1EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200Brest, France; 2Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China; 3Shanghai Institute of Pancreatic Diseases, Shanghai, China; 4CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France; 5Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Jin-Huan Lin
- 1EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200Brest, France; 2Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China; 3Shanghai Institute of Pancreatic Diseases, Shanghai, China; 4CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France; 5Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Emmanuelle Masson
- 1EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200Brest, France; 2Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China; 3Shanghai Institute of Pancreatic Diseases, Shanghai, China; 4CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France; 5Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Zhuan Liao
- 1EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200Brest, France; 2Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China; 3Shanghai Institute of Pancreatic Diseases, Shanghai, China; 4CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France; 5Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Claude Férec
- 1EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200Brest, France; 2Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China; 3Shanghai Institute of Pancreatic Diseases, Shanghai, China; 4CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France; 5Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - David N Cooper
- 1EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200Brest, France; 2Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China; 3Shanghai Institute of Pancreatic Diseases, Shanghai, China; 4CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France; 5Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Matthew Hayden
- 1EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200Brest, France; 2Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China; 3Shanghai Institute of Pancreatic Diseases, Shanghai, China; 4CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France; 5Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| |
Collapse
|
2
|
Lin JH, Tang XY, Boulling A, Zou WB, Masson E, Fichou Y, Raud L, Le Tertre M, Deng SJ, Berlivet I, Ka C, Mort M, Hayden M, Leman R, Houdayer C, Le Gac G, Cooper DN, Li ZS, Férec C, Liao Z, Chen JM. First estimate of the scale of canonical 5' splice site GT>GC variants capable of generating wild-type transcripts. Hum Mutat 2019; 40:1856-1873. [PMID: 31131953 DOI: 10.1002/humu.23821] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/10/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022]
Abstract
It has long been known that canonical 5' splice site (5'SS) GT>GC variants may be compatible with normal splicing. However, to date, the actual scale of canonical 5'SSs capable of generating wild-type transcripts in the case of GT>GC substitutions remains unknown. Herein, combining data derived from a meta-analysis of 45 human disease-causing 5'SS GT>GC variants and a cell culture-based full-length gene splicing assay of 103 5'SS GT>GC substitutions, we estimate that ~15-18% of canonical GT 5'SSs retain their capacity to generate between 1% and 84% normal transcripts when GT is substituted by GC. We further demonstrate that the canonical 5'SSs in which substitution of GT by GC-generated normal transcripts exhibit stronger complementarity to the 5' end of U1 snRNA than those sites whose substitutions of GT by GC did not lead to the generation of normal transcripts. We also observed a correlation between the generation of wild-type transcripts and a milder than expected clinical phenotype but found that none of the available splicing prediction tools were capable of reliably distinguishing 5'SS GT>GC variants that generated wild-type transcripts from those that did not. Our findings imply that 5'SS GT>GC variants in human disease genes may not invariably be pathogenic.
Collapse
Affiliation(s)
- Jin-Huan Lin
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Xin-Ying Tang
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Arnaud Boulling
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France
| | - Yann Fichou
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Loann Raud
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | | | - Shun-Jiang Deng
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | | | - Chandran Ka
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Matthew Hayden
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Raphaël Leman
- Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse, Caen, France.,Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - Claude Houdayer
- Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - Gerald Le Gac
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Claude Férec
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| |
Collapse
|
3
|
Laššuthová P, Žaliová M, Inoue K, Haberlová J, Sixtová K, Sakmaryová I, Paděrová K, Mazanec R, Zámečník J, Šišková D, Garbern J, Seeman P. Three new PLP1 splicing mutations demonstrate pathogenic and phenotypic diversity of Pelizaeus-Merzbacher disease. J Child Neurol 2014; 29:924-31. [PMID: 23771846 DOI: 10.1177/0883073813492387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/09/2013] [Indexed: 11/16/2022]
Abstract
Pelizaeus-Merzbacher disease is a severe X-linked disorder of central myelination caused by mutations affecting the proteolipid protein gene. We describe 3 new PLP1 splicing mutations, their effect on splicing and associated phenotypes. Mutation c.453_453+6del7insA affects the exon 3B donor splice site and disrupts the PLP1-transcript without affecting the DM20, was found in a patient with severe Pelizaeus-Merzbacher disease and in his female cousin with early-onset spastic paraparesis. Mutation c.191+1G>A causes exon 2 skipping with a frame shift, is expected to result in a functionally null allele, and was found in a patient with mild Pelizaeus-Merzbacher disease and in his aunt with late-onset spastic paraparesis. Mutation c.696+1G>A utilizes a cryptic splice site in exon 5, causes partial exon 5 skipping and in-frame deletion, and was found in an isolated patient with a severe classical Pelizaeus-Merzbacher. PLP1 splice-site mutations express a variety of disease phenotypes mediated by different molecular pathogenic mechanisms.
Collapse
Affiliation(s)
- Petra Laššuthová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Markéta Žaliová
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Jana Haberlová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Klára Sixtová
- Department of Paediatric Neurology, Thomayer's Hospital, Prague, Czech Republic
| | - Iva Sakmaryová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Kateřina Paděrová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Radim Mazanec
- Department of Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Josef Zámečník
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| | - Dana Šišková
- Department of Paediatric Neurology, Thomayer's Hospital, Prague, Czech Republic
| | - Jim Garbern
- Department of Neurology and Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Pavel Seeman
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Czech Republic
| |
Collapse
|