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Abstract
Pre-mRNA splicing is performed by the spliceosome, a dynamic macromolecular complex consisting of five small uridine-rich ribonucleoprotein complexes (the U1, U2, U4, U5, and U6 snRNPs) and numerous auxiliary splicing factors. A plethora of human disorders are caused by genetic variants affecting the function and/or expression of splicing factors, including the core snRNP proteins. Variants in the genes encoding proteins of the U5 snRNP cause two distinct and tissue-specific human disease phenotypes – variants in PRPF6, PRPF8, and SNRP200 are associated with retinitis pigmentosa (RP), while variants in EFTUD2 and TXNL4A cause the craniofacial disorders mandibulofacial dysostosis Guion-Almeida type (MFDGA) and Burn-McKeown syndrome (BMKS), respectively. Furthermore, recurrent somatic mutations or changes in the expression levels of a number of U5 snRNP proteins (PRPF6, PRPF8, EFTUD2, DDX23, and SNRNP40) have been associated with human cancers. How and why variants in ubiquitously expressed spliceosome proteins required for pre-mRNA splicing in all human cells result in tissue-restricted disease phenotypes is not clear. Additionally, why variants in different, yet interacting, proteins making up the same core spliceosome snRNP result in completely distinct disease outcomes – RP, craniofacial defects or cancer – is unclear. In this review, we define the roles of different U5 snRNP proteins in RP, craniofacial disorders and cancer, including how disease-associated genetic variants affect pre-mRNA splicing and the proposed disease mechanisms. We then propose potential hypotheses for how U5 snRNP variants cause tissue specificity resulting in the restricted and distinct human disorders.
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Affiliation(s)
- Katherine A Wood
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Megan A Eadsforth
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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Thomas HB, Wood KA, Buczek WA, Gordon CT, Pingault V, Attié-Bitach T, Hentges KE, Varghese VC, Amiel J, Newman WG, O'Keefe RT. EFTUD2 missense variants disrupt protein function and splicing in mandibulofacial dysostosis Guion-Almeida type. Hum Mutat 2020; 41:1372-1382. [PMID: 32333448 DOI: 10.1002/humu.24027] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/26/2020] [Accepted: 04/19/2020] [Indexed: 12/20/2022]
Abstract
Pathogenic variants in the core spliceosome U5 small nuclear ribonucleoprotein gene EFTUD2/SNU114 cause the craniofacial disorder mandibulofacial dysostosis Guion-Almeida type (MFDGA). MFDGA-associated variants in EFTUD2 comprise large deletions encompassing EFTUD2, intragenic deletions and single nucleotide truncating or missense variants. These variants are predicted to result in haploinsufficiency by loss-of-function of the variant allele. While the contribution of deletions within EFTUD2 to allele loss-of-function are self-evident, the mechanisms by which missense variants are disease-causing have not been characterized functionally. Combining bioinformatics software prediction, yeast functional growth assays, and a minigene (MG) splicing assay, we have characterized how MFDGA missense variants result in EFTUD2 loss-of-function. Only four of 19 assessed missense variants cause EFTUD2 loss-of-function through altered protein function when modeled in yeast. Of the remaining 15 missense variants, five altered the normal splicing pattern of EFTUD2 pre-messenger RNA predominantly through exon skipping or cryptic splice site activation, leading to the introduction of a premature termination codon. Comparison of bioinformatic predictors for each missense variant revealed a disparity amongst different software packages and, in many cases, an inability to correctly predict changes in splicing subsequently determined by MG interrogation. This study highlights the need for laboratory-based validation of bioinformatic predictions for EFTUD2 missense variants.
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Affiliation(s)
- Huw B Thomas
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Katherine A Wood
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Weronika A Buczek
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Véronique Pingault
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Tania Attié-Bitach
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France.,INSERM UMR 1163, Institut Imagine, Paris, France
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformation, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Center for Genomic Medicine, St. Mary's Hospital, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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3
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Huang L, Vanstone MR, Hartley T, Osmond M, Barrowman N, Allanson J, Baker L, Dabir TA, Dipple KM, Dobyns WB, Estrella J, Faghfoury H, Favaro FP, Goel H, Gregersen PA, Gripp KW, Grix A, Guion-Almeida ML, Harr MH, Hudson C, Hunter AGW, Johnson J, Joss SK, Kimball A, Kini U, Kline AD, Lauzon J, Lildballe DL, López-González V, Martinezmoles J, Meldrum C, Mirzaa GM, Morel CF, Morton JEV, Pyle LC, Quintero-Rivera F, Richer J, Scheuerle AE, Schönewolf-Greulich B, Shears DJ, Silver J, Smith AC, Temple IK, van de Kamp JM, van Dijk FS, Vandersteen AM, White SM, Zackai EH, Zou R, Bulman DE, Boycott KM, Lines MA. Mandibulofacial Dysostosis with Microcephaly: Mutation and Database Update. Hum Mutat 2015; 37:148-54. [PMID: 26507355 DOI: 10.1002/humu.22924] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/12/2015] [Indexed: 11/08/2022]
Abstract
Mandibulofacial dysostosis with microcephaly (MFDM) is a multiple malformation syndrome comprising microcephaly, craniofacial anomalies, hearing loss, dysmorphic features, and, in some cases, esophageal atresia. Haploinsufficiency of a spliceosomal GTPase, U5-116 kDa/EFTUD2, is responsible. Here, we review the molecular basis of MFDM in the 69 individuals described to date, and report mutations in 38 new individuals, bringing the total number of reported individuals to 107 individuals from 94 kindreds. Pathogenic EFTUD2 variants comprise 76 distinct mutations and seven microdeletions. Among point mutations, missense substitutions are infrequent (14 out of 76; 18%) relative to stop-gain (29 out of 76; 38%), and splicing (33 out of 76; 43%) mutations. Where known, mutation origin was de novo in 48 out of 64 individuals (75%), dominantly inherited in 12 out of 64 (19%), and due to proven germline mosaicism in four out of 64 (6%). Highly penetrant clinical features include, microcephaly, first and second arch craniofacial malformations, and hearing loss; esophageal atresia is present in an estimated ∼27%. Microcephaly is virtually universal in childhood, with some adults exhibiting late "catch-up" growth and normocephaly at maturity. Occasionally reported anomalies, include vestibular and ossicular malformations, reduced mouth opening, atrophy of cerebral white matter, structural brain malformations, and epibulbar dermoid. All reported EFTUD2 mutations can be found in the EFTUD2 mutation database (http://databases.lovd.nl/shared/genes/EFTUD2).
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Affiliation(s)
- Lijia Huang
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Megan R Vanstone
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Matthew Osmond
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Nick Barrowman
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Judith Allanson
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, The Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Laura Baker
- Division of Medical Genetics, A. I. duPont Hospital for Children, Wilmington, Delaware
| | - Tabib A Dabir
- Clinical Genetics Department, Belfast City Hospital, Belfast, UK
| | - Katrina M Dipple
- Department of Pediatrics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - William B Dobyns
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Jane Estrella
- Department of Medical Genetics, Westmead Hospital, Sydney, Australia
| | - Hanna Faghfoury
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Francine P Favaro
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil
| | - Himanshu Goel
- Hunter Genetics, Newcastle, Waratah, Australia.,University of Newcastle, Newcastle - School of Medicine and Public Health, Faculty of Health, Callaghan, Australia
| | | | - Karen W Gripp
- Division of Medical Genetics, A. I. duPont Hospital for Children, Wilmington, Delaware
| | - Art Grix
- Department of Genetics, Permanente Medical Group, Roseville, California
| | - Maria-Leine Guion-Almeida
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil
| | - Margaret H Harr
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - John Johnson
- Shodair Children's Hospital, Helena, Montana.,Clinical Genetics and Metabolism, Floating Hospital for Children, Tufts Medical Center, Boston, Massachusetts
| | - Shelagh K Joss
- West of Scotland Clinical Genetics Service, South Glasgow University Hospital, Glasgow, UK
| | - Amy Kimball
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, Maryland
| | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, Maryland
| | - Julie Lauzon
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Dorte L Lildballe
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Vanesa López-González
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain.,Grupo Clínico Vinculado al Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | | | | | - Ghayda M Mirzaa
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Chantal F Morel
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Jenny E V Morton
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - Louise C Pyle
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Julie Richer
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, The Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Angela E Scheuerle
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Bitten Schönewolf-Greulich
- Genetic Counselling Clinic Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Deborah J Shears
- Oxford Regional Genetics Service, The Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Josh Silver
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Amanda C Smith
- Department of Genetics, The Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - I Karen Temple
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | | | - Fleur S van Dijk
- Department of Clinical Genetics, VU Medical Center, Amsterdam, The Netherlands
| | | | - Sue M White
- Victoria Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Elaine H Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ruobing Zou
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Dennis E Bulman
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Newborn Screening Ontario, The Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Kym M Boycott
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Genetics, The Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Matthew A Lines
- The Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada.,Metabolics and Newborn Screening, Department of Pediatrics, The Children's Hospital of Eastern Ontario, Ottawa, Canada
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