1
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Engal E, Sharma A, Aviel U, Taqatqa N, Juster S, Jaffe-Herman S, Bentata M, Geminder O, Gershon A, Lewis R, Kay G, Hecht M, Epsztejn-Litman S, Gotkine M, Mouly V, Eiges R, Salton M, Drier Y. DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis. SCIENCE ADVANCES 2024; 10:eadn7732. [PMID: 38809976 PMCID: PMC11135424 DOI: 10.1126/sciadv.adn7732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is a noncanonical SMC protein and an epigenetic regulator. Mutations in SMCHD1 cause facioscapulohumeral muscular dystrophy (FSHD), by overexpressing DUX4 in muscle cells. Here, we demonstrate that SMCHD1 is a key regulator of alternative splicing in various cell types. We show how SMCHD1 loss causes splicing alterations of DNMT3B, which can lead to hypomethylation and DUX4 overexpression. Analyzing RNA sequencing data from muscle biopsies of patients with FSHD and Smchd1 knocked out cells, we found mis-splicing of hundreds of genes upon SMCHD1 loss. We conducted a high-throughput screen of splicing factors, revealing the involvement of the splicing factor RBM5 in the mis-splicing of DNMT3B. Subsequent RNA immunoprecipitation experiments confirmed that SMCHD1 is required for RBM5 recruitment. Last, we show that mis-splicing of DNMT3B leads to hypomethylation of the D4Z4 region and to DUX4 overexpression. These results suggest that DNMT3B mis-splicing due to SMCHD1 loss plays a major role in FSHD pathogenesis.
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Affiliation(s)
- Eden Engal
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Aveksha Sharma
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Uria Aviel
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Nadeen Taqatqa
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sarah Juster
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shiri Jaffe-Herman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Mercedes Bentata
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Adi Gershon
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Reyut Lewis
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Merav Hecht
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Silvina Epsztejn-Litman
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Marc Gotkine
- Department of Neurology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112002, Israel
| | - Vincent Mouly
- UPMC University Paris 06, Inserm UMRS974, CNRS FRE3617, Center for Research in Myology, Sorbonne University,75252 Paris, France
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yotam Drier
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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2
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Greene D, Thys C, Berry IR, Jarvis J, Ortibus E, Mumford AD, Freson K, Turro E. Mutations in the U4 snRNA gene RNU4-2 cause one of the most prevalent monogenic neurodevelopmental disorders. Nat Med 2024:10.1038/s41591-024-03085-5. [PMID: 38821540 DOI: 10.1038/s41591-024-03085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Most people with intellectual disability (ID) do not receive a molecular diagnosis following genetic testing. To identify new etiologies of ID, we performed a genetic association analysis comparing the burden of rare variants in 41,132 noncoding genes between 5,529 unrelated cases and 46,401 unrelated controls. RNU4-2, which encodes U4 small nuclear RNA, a critical component of the spliceosome, was the most strongly associated gene. We implicated de novo variants among 47 cases in two regions of RNU4-2 in the etiology of a syndrome characterized by ID, microcephaly, short stature, hypotonia, seizures and motor delay. We replicated this finding in three collections, bringing the number of unrelated cases to 73. Analysis of national genomic diagnostic data showed RNU4-2 to be a more common etiological gene for neurodevelopmental abnormality than any previously reported autosomal gene. Our findings add to the growing evidence of spliceosome dysfunction in the etiologies of neurological disorders.
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Affiliation(s)
- Daniel Greene
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chantal Thys
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Ian R Berry
- NHS South West Genomic Laboratory Hub, Southmead Hospital, Bristol, UK
- NHS South West Genomic Medicine Service Alliance, Bristol, UK
| | - Joanna Jarvis
- Clinical Genetics Unit, Birmingham Women's Hospital, Birmingham, UK
| | - Els Ortibus
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Paediatric Neurology Department, University Hospitals of KU Leuven, Leuven, Belgium
| | - Andrew D Mumford
- NHS South West Genomic Medicine Service Alliance, Bristol, UK
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Ernest Turro
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Griffin C, Saint-Jeannet JP. Human stem cell model of neural crest cell differentiation reveals a requirement of SF3B4 in survival, maintenance, and differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577202. [PMID: 38328054 PMCID: PMC10849718 DOI: 10.1101/2024.01.25.577202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In vitro modeling is a powerful approach to investigate the pathomechanisms driving human congenital conditions. Here we use human embryonic stem cells (hESCs) to model Nager and Rodriguez syndromes, two craniofacial conditions characterized by hypoplastic neural crest-derived craniofacial bones, caused by pathogenic variants of SF3B4, a core component of the spliceosome. We observed that siRNA-mediated knockdown of SF3B4 interferes with the production of hESC-derived neural crest cells, as seen by a marked reduction in neural crest gene expression. This phenotype is associated with an increase in neural crest cell apoptosis and premature neuronal differentiation. Altogether these results point at a role of SF3B4 in neural crest cell survival, maintenance, and differentiation. We propose that the dysregulation of these processes may contribute to Nager/Rodriguez syndrome associated craniofacial defects.
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Affiliation(s)
- Casey Griffin
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, USA
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4
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Yang WQ, Ge JY, Zhang X, Zhu WY, Lin L, Shi Y, Xu B, Liu RJ. THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration. Nucleic Acids Res 2024; 52:3291-3309. [PMID: 38165050 PMCID: PMC11014329 DOI: 10.1093/nar/gkad1243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
The mechanisms by which the relatively conserved spliceosome manages the enormously large number of splicing events that occur in humans (∼200 000 versus ∼300 in yeast) are poorly understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G) on the G72 of U6 snRNA (the catalytic center of the spliceosome) promotes efficient pre-mRNA splicing activity in human cells. This modification was identified to be conserved among vertebrates. Further, THUMPD2 was demonstrated as the methyltransferase responsible for U6 m2G72 by explicitly recognizing the U6-specific sequences and structural elements. The knock-out of THUMPD2 eliminated U6 m2G72 and impaired the pre-mRNA splicing activity, resulting in thousands of changed alternative splicing events of endogenous pre-mRNAs in human cells. Notably, the aberrantly spliced pre-mRNA population elicited the nonsense-mediated mRNA decay pathway. We further show that THUMPD2 was associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome regulates global pre-mRNA splicing and impacts physiology and disease.
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Affiliation(s)
- Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian-Yang Ge
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaofeng Zhang
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, China
| | - Wen-Yu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lin Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yigong Shi
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310064,Zhejiang Province, China
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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5
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Chen Y, Dawes R, Kim HC, Stenton SL, Walker S, Ljungdahl A, Lord J, Ganesh VS, Ma J, Martin-Geary AC, Lemire G, D’Souza EN, Dong S, Ellingford JM, Adams DR, Allan K, Bakshi M, Baldwin EE, Berger SI, Bernstein JA, Brown NJ, Burrage LC, Chapman K, Compton AG, Cunningham CA, D’Souza P, Délot EC, Dias KR, Elias ER, Evans CA, Ewans L, Ezell K, Fraser JL, Gallacher L, Genetti CA, Grant CL, Haack T, Kuechler A, Lalani SR, Leitão E, Fevre AL, Leventer RJ, Liebelt JE, Lockhart PJ, Ma AS, Macnamara EF, Maurer TM, Mendez HR, Montgomery SB, Nassogne MC, Neumann S, O’Leary M, Palmer EE, Phillips J, Pitsava G, Pysar R, Rehm HL, Reuter CM, Revencu N, Riess A, Rius R, Rodan L, Roscioli T, Rosenfeld JA, Sachdev R, Simons C, Sisodiya SM, Snell P, Clair L, Stark Z, Tan TY, Tan NB, Temple SEL, Thorburn DR, Tifft CJ, Uebergang E, VanNoy GE, Vilain E, Viskochil DH, Wedd L, Wheeler MT, White SM, Wojcik M, Wolfe LA, Wolfenson Z, Xiao C, Zocche D, Rubenstein JL, Markenscoff-Papadimitriou E, Fica SM, Baralle D, Depienne C, MacArthur DG, Howson JMM, Sanders SJ, O’Donnell-Luria A, Whiffin N. De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.07.24305438. [PMID: 38645094 PMCID: PMC11030480 DOI: 10.1101/2024.04.07.24305438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Increasingly, large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a novel syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 119 individuals with NDD. The vast majority of individuals (77.3%) have the same highly recurrent single base-pair insertion (n.64_65insT). We estimate that variants in this region explain 0.41% of individuals with NDD. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to its contiguous counterpart RNU4-1 and other U4 homologs, supporting RNU4-2's role as the primary U4 transcript in the brain. Overall, this work underscores the importance of non-coding genes in rare disorders. It will provide a diagnosis to thousands of individuals with NDD worldwide and pave the way for the development of effective treatments for these individuals.
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Affiliation(s)
- Yuyang Chen
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ruebena Dawes
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hyung Chul Kim
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah L Stenton
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alicia Ljungdahl
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | - Jenny Lord
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Vijay S Ganesh
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jialan Ma
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gabrielle Lemire
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elston N D’Souza
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Shan Dong
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | - Jamie M Ellingford
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - David R Adams
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Kirsten Allan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Madhura Bakshi
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | - Erin E Baldwin
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, USA
- Division of Genetics and Metabolism, Children’s National Hospital, Washington, DC, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kimberly Chapman
- Division of Genetics and Metabolism, Children’s National Hospital, Washington, DC, USA
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Chloe A Cunningham
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Precilla D’Souza
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Emmanuèle C Délot
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, USA
| | - Kerith-Rae Dias
- Neuroscience Research Australia, Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Ellen R Elias
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, CO, USA
- University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA
| | - Carey-Anne Evans
- Neuroscience Research Australia, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Kimberly Ezell
- Division of Medical Genetics & Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jamie L Fraser
- Center for Genetic Medicine Research, Children’s National Research Institute, Washington, DC, USA
- Division of Genetics and Metabolism, Children’s National Hospital, Washington, DC, USA
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Christina L Grant
- Division of Genetics and Metabolism, Children’s National Hospital, Washington, DC, USA
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anna Le Fevre
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Richard J Leventer
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Royal Children’s Hospital, Melbourne, VIC, Australia
| | - Jan E Liebelt
- Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women’s and Children’s Hospital, North Adelaide, SA, Australia
- Repromed, Dulwich, SA, Australia
| | - Paul J Lockhart
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Alan S Ma
- Department of Clinical Genetics, Sydney Children’s Hospitals Network Westmead, Sydney, NSW, Australia
- Specialty of Genomic Medicine, University of Sydney, Sydney, NSW, Australia
| | - Ellen F Macnamara
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Taylor M Maurer
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hector R Mendez
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Department of Genetics, Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Marie-Cécile Nassogne
- Service de Neurologie Pédiatrique, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium
- Institut des Maladies Rares, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium
| | - Serena Neumann
- Division of Medical Genetics & Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melanie O’Leary
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elizabeth E Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, NSW, Australia
| | - John Phillips
- Division of Medical Genetics & Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Georgia Pitsava
- Institute for Clinical and Translational Research, University of California, Irvine, CA, USA
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, NSW, Australia
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Westmead, NSW, Australia
| | - Heidi L Rehm
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole Revencu
- Center for Human Genetics, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Angelika Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rocio Rius
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Lance Rodan
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rani Sachdev
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, NSW, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
- UK and Chalfont Centre for Epilepsy, Bucks, UK
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Laura Clair
- Department of Clinical Genetics, Sydney Children’s Hospitals Network Westmead, Sydney, NSW, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Suzanna EL Temple
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia
- School of Women’s and Childrens’s Health, University of New South Wales, Sydney, NSW, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Cynthia J Tifft
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Eloise Uebergang
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - Grace E VanNoy
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, CA, USA
| | - David H Viskochil
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Laura Wedd
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Matthew T Wheeler
- GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Monica Wojcik
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynne A Wolfe
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Zoe Wolfenson
- Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA
| | - Changrui Xiao
- Department of Neurology, University of California, Irvine, CA, USA
| | - David Zocche
- North West Thames Regional Genetics Service, Northwick Park & St Mark’s Hospitals, London, UK
| | - John L Rubenstein
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | - Eirene Markenscoff-Papadimitriou
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | | | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton National Health Service (NHS) Foundation Trust, Southampton, UK
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Joanna MM Howson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre, Oxford, UK
| | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, USA
| | - Anne O’Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, Oxford, UK
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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6
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Griffin C, Coppenrath K, Khan D, Lin Z, Horb M, Saint-Jeannet JP. Sf3b4 mutation in Xenopus tropicalis causes RNA splicing defects followed by massive gene dysregulation that disrupt cranial neural crest development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578190. [PMID: 38352410 PMCID: PMC10862923 DOI: 10.1101/2024.01.31.578190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Nager syndrome is a rare craniofacial and limb disorder characterized by midface retrusion, micrognathia, absent thumbs, and radial hypoplasia. This disorder results from haploinsufficiency of SF3B4 (splicing factor 3b, subunit 4) a component of the pre-mRNA spliceosomal machinery. The spliceosome is a complex of RNA and proteins that function together to remove introns and join exons from transcribed pre-mRNA. While the spliceosome is present and functions in all cells of the body, most spliceosomopathies - including Nager syndrome - are cell/tissue-specific in their pathology. In Nager syndrome patients, it is the neural crest (NC)-derived craniofacial skeletal structures that are primarily affected. To understand the pathomechanism underlying this condition, we generated a Xenopus tropicalis sf3b4 mutant line using the CRISPR/Cas9 gene editing technology. Here we describe the sf3b4 mutant phenotype at neurula, tail bud, and tadpole stages, and performed temporal RNA-sequencing analysis to characterize the splicing events and transcriptional changes underlying this phenotype. Our data show that while loss of one copy of sf3b4 is largely inconsequential in Xenopus tropicalis, homozygous deletion of sf3b4 causes major splicing defects and massive gene dysregulation, which disrupt cranial NC cell migration and survival, thereby pointing at an essential role of Sf3b4 in craniofacial development.
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Affiliation(s)
- Casey Griffin
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, USA
| | - Kelsey Coppenrath
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Doha Khan
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, USA
| | - Ziyan Lin
- Applied Bioinformatics Laboratory, NYU Grossman School of Medicine, New York, NY, USA
| | - Marko Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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7
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Nian Q, Li Y, Li J, Zhao L, Rodrigues Lima F, Zeng J, Liu R, Ye Z. U2AF1 in various neoplastic diseases and relevant targeted therapies for malignant cancers with complex mutations (Review). Oncol Rep 2024; 51:5. [PMID: 37975232 PMCID: PMC10688450 DOI: 10.3892/or.2023.8664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
U2 small nuclear RNA auxiliary factor 1 (U2AF1) is a multifunctional protein that plays a crucial role in the regulation of RNA splicing during eukaryotic gene expression. U2AF1 belongs to the SR family of splicing factors and is involved in the removal of introns from mRNAs and exon-exon binding. Mutations in U2AF1 are frequently observed in myelodysplastic syndrome, primary myelofibrosis, chronic myelomonocytic leukaemia, hairy cell leukaemia and other solid tumours, particularly in lung, pancreatic, and ovarian carcinomas. Therefore, targeting U2AF1 for therapeutic interventions may be a viable strategy for treating malignant diseases. In the present review, the pathogenic mechanisms associated with U2AF1 in different malignant diseases were summarized, and the potential of related targeting agents was discussed. Additionally, the feasibility of natural product-based therapies directed against U2AF1 was explored.
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Affiliation(s)
- Qing Nian
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Yihui Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing 100730, P.R. China
| | - Jingwei Li
- Department of Transfusion, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Liyun Zhao
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, 75013 Paris, France
| | - Jinhao Zeng
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610000, P.R. China
| | - Rongxing Liu
- Department of Pharmacy, The Second Affiliated Hospital, Army Medical University, Chongqing 400000, P.R. China
| | - Zhijun Ye
- Department of Clinical Nutrition, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, P.R. China
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8
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Marszałek-Kruk BA, Myśliwiec A, Lipowicz A, Wolański W, Kulesa-Mrowiecka M, Dowgierd K. Children with Rare Nager Syndrome-Literature Review, Clinical and Physiotherapeutic Management. Genes (Basel) 2023; 15:29. [PMID: 38254920 PMCID: PMC10815867 DOI: 10.3390/genes15010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Nager syndrome is a rare human developmental disorder characterized by craniofacial defects including the downward slanting of the palpebral fissures, cleft palate, limb deformities, mandibular hypoplasia, hypoplasia or absence of thumbs, microretrognathia, and ankylosis of the temporomandibular joint. The prevalence is very rare and the literature describes only about a hundred cases of Nager syndrome. There is evidence of autosomal dominant and autosomal recessive inheritance for Nager syndrome, suggesting genetic heterogeneity. The majority of the described causes of Nager syndrome include pathogenic variants in the SF3B4 gene, which encodes a component of the spliceosome; therefore, the syndrome belongs to the spliceosomopathy group of diseases. The diagnosis is made on the basis of physical and radiological examination and detection of mutations in the SF3B4 gene. Due to the diversity of defects associated with Nager syndrome, patients require multidisciplinary, complex, and long-lasting treatment. Usually, it starts from birth until the age of twenty years. The surgical procedures vary over a patient's lifetime and are related to the needed function. First, breathing and feeding must be facilitated; then, oral and facial clefts should be addressed, followed by correcting eyelid deformities and cheekbone reconstruction. In later age, a surgery of the nose and external ear is performed. Speech and hearing disorders require specialized logopedic treatment. A defect of the thumb is treated by transplanting a tendon and muscle or transferring the position of the index finger. In addition to surgery, in order to maximize a patient's benefit and to reduce functional insufficiency, complementary treatments such as rehabilitation and physiotherapy are recommended. In our study, we describe eight patients of different ages with various cases of Nager syndrome. The aim of our work was to present the actual genetic knowledge on this disease and its treatment procedures.
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Affiliation(s)
| | - Andrzej Myśliwiec
- Laboratory of Physiotherapy and Physioprevention, Institute of Physiotherapy and Health Sciences, Academy of Physical Education in Katowice, 40-065 Katowice, Poland
| | - Anna Lipowicz
- Department of Anthropology, Faculty of Biology and Animal Science, Wroclaw University of Environmental and Life Sciences, 50-375 Wroclaw, Poland
| | - Wojciech Wolański
- Department of Biomechatronics, Faculty of Biomedical Engineering, Silesian University of Technology, 41-800 Zabrze, Poland
| | - Małgorzata Kulesa-Mrowiecka
- Department of Rehabilitation in Internal Diseases, Faculty of Health Sciences, Jagiellonian University Medical College, 31-126 Krakow, Poland
| | - Krzysztof Dowgierd
- Head and Neck Surgery Clinic for Children and Young Adults, Department of Clinical Pediatrics, Collegium Medicum, University of Warmia and Mazury, 10-561 Olsztyn, Poland
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9
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Engal E, Oja KT, Maroofian R, Geminder O, Le TL, Marzin P, Guimier A, Mor E, Zvi N, Elefant N, Zaki MS, Gleeson JG, Muru K, Pajusalu S, Wojcik MH, Pachat D, Elmaksoud MA, Chan Jeong W, Lee H, Bauer P, Zifarelli G, Houlden H, Daana M, Elpeleg O, Amiel J, Lyonnet S, Gordon CT, Harel T, Õunap K, Salton M, Mor-Shaked H. Bi-allelic loss-of-function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental syndrome. Am J Hum Genet 2023; 110:2112-2119. [PMID: 37963460 PMCID: PMC10716347 DOI: 10.1016/j.ajhg.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Over two dozen spliceosome proteins are involved in human diseases, also referred to as spliceosomopathies. WW domain-binding protein 4 (WBP4) is part of the early spliceosomal complex and has not been previously associated with human pathologies in the Online Mendelian Inheritance in Man (OMIM) database. Through GeneMatcher, we identified ten individuals from eight families with a severe neurodevelopmental syndrome featuring variable manifestations. Clinical manifestations included hypotonia, global developmental delay, severe intellectual disability, brain abnormalities, musculoskeletal, and gastrointestinal abnormalities. Genetic analysis revealed five different homozygous loss-of-function variants in WBP4. Immunoblotting on fibroblasts from two affected individuals with different genetic variants demonstrated a complete loss of protein, and RNA sequencing analysis uncovered shared abnormal splicing patterns, including in genes associated with abnormalities of the nervous system, potentially underlying the phenotypes of the probands. We conclude that bi-allelic variants in WBP4 cause a developmental disorder with variable presentations, adding to the growing list of human spliceosomopathies.
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Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Department of Military Medicine and "Tzameret," Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kaisa Teele Oja
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reza Maroofian
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Department of Military Medicine and "Tzameret," Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Thuy-Linh Le
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France
| | - Pauline Marzin
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France
| | - Anne Guimier
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France; Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France
| | - Evyatar Mor
- Department of Computer Science, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Naama Zvi
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Naama Elefant
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, Cairo, Egypt
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, USA; Rady Children's Institute for Genomic Medicine, San Diego, La Jolla, USA
| | - Kai Muru
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | | | - Divya Pachat
- Department of Medical Genetics, Aster MIMS (Malabar Institute of Medical Sciences)-Calicut, Kerala, India
| | - Marwa Abd Elmaksoud
- Neurology Unit, Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | | | | | - Peter Bauer
- CENTOGENE GmbH, Am Strande 7, 18055 Rostock, Germany
| | | | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Muhannad Daana
- Child Development Centers, Clalit Health Care Services, Jerusalem, Israel
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France; Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France; Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Katrin Õunap
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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10
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Harms FL, Dingemans AJM, Hempel M, Pfundt R, Bierhals T, Casar C, Müller C, Niermeijer JMF, Fischer J, Jahn A, Hübner C, Majore S, Agolini E, Novelli A, van der Smagt J, Ernst R, van Binsbergen E, Mancini GMS, van Slegtenhorst M, Barakat TS, Wakeling EL, Kamath A, Downie L, Pais L, White SM, de Vries BBA, Kutsche K. De novo PHF5A variants are associated with craniofacial abnormalities, developmental delay, and hypospadias. Genet Med 2023; 25:100927. [PMID: 37422718 DOI: 10.1016/j.gim.2023.100927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE The SF3B splicing complex is composed of SF3B1-6 and PHF5A. We report a developmental disorder caused by de novo variants in PHF5A. METHODS Clinical, genomic, and functional studies using subject-derived fibroblasts and a heterologous cellular system were performed. RESULTS We studied 9 subjects with congenital malformations, including preauricular tags and hypospadias, growth abnormalities, and developmental delay who had de novo heterozygous PHF5A variants, including 4 loss-of-function (LOF), 3 missense, 1 splice, and 1 start-loss variant. In subject-derived fibroblasts with PHF5A LOF variants, wild-type and variant PHF5A mRNAs had a 1:1 ratio, and PHF5A mRNA levels were normal. Transcriptome sequencing revealed alternative promoter use and downregulated genes involved in cell-cycle regulation. Subject and control fibroblasts had similar amounts of PHF5A with the predicted wild-type molecular weight and of SF3B1-3 and SF3B6. SF3B complex formation was unaffected in 2 subject cell lines. CONCLUSION Our data suggest the existence of feedback mechanisms in fibroblasts with PHF5A LOF variants to maintain normal levels of SF3B components. These compensatory mechanisms in subject fibroblasts with PHF5A or SF3B4 LOF variants suggest disturbed autoregulation of mutated splicing factor genes in specific cell types, that is, neural crest cells, during embryonic development rather than haploinsufficiency as pathomechanism.
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Affiliation(s)
- Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Casar
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Müller
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Jan Fischer
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Arne Jahn
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Christoph Hübner
- Department of Neuropaediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Silvia Majore
- Division of Medical Genetics, Department of Experimental Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Jasper van der Smagt
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Robert Ernst
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands; Discovery Unit, Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Emma L Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Arveen Kamath
- All Wales Medical Genomics Service/ Pennaeth Labordy Genomeg Cymru Gyfan, University Hospital of Wales, Heath Park, Cardiff, United Kingdom
| | - Lilian Downie
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, VIC; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lynn Pais
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Susan M White
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, VIC; Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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11
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Ulhaq ZS, Okamoto K, Ogino Y, Tse WKF. Dysregulation of Spliceosomes Complex Induces Retinitis Pigmentosa-Like Characteristics in sf3b4-Depleted Zebrafish. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1223-1233. [PMID: 37263342 DOI: 10.1016/j.ajpath.2023.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/03/2023]
Abstract
The SF3B4 gene encodes a highly conserved protein that plays a critical role in mRNA splicing. Mutations in this gene are known to cause Nager syndrome, a rare craniofacial disorder. Although SF3B4 expression is detected in the optic vesicle before it is detected in the limb and somite, the role of SF3B4 in the eye is not well understood. This study investigated the function of sf3b4 in the retina by performing transcriptome profiles, immunostaining, and behavioral analysis of sf3b4-/- mutant zebrafish. Results from this study suggest that dysregulation of the spliceosome complex affects not only craniofacial development but also retinogenesis. Zebrafish lacking functional sf3b4 displayed characteristics similar to retinitis pigmentosa (RP), marked by severe retinal pigment epithelium defects and rod degeneration. Pathway analysis revealed altered retinol metabolism and retinoic acid signaling in the sf3b4-/- mutants. Supplementation of retinoic acid rescued key cellular phenotypes observed in the sf3b4-/- mutants, offering potential therapeutic strategies for RP in the future. In conclusion, this study sheds light on the previously unknown role of SF3B4 in retinogenesis and provides insights into the underlying mechanisms of RP.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan; Research Center for Pre-clinical and Clinical Medicine, National Research and Innovation Agency, Republic of Indonesia, Cibinong, Indonesia.
| | - Keigo Okamoto
- Laboratory of Aquatic Molecular Developmental Biology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yukiko Ogino
- Laboratory of Aquatic Molecular Developmental Biology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.
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12
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Liu X, Jones WD, Quesnel-Vallières M, Devadiga SA, Lorent K, Valvezan AJ, Myers RL, Li N, Lengner CJ, Barash Y, Pack M, Klein PS. The Tumor Suppressor Adenomatous Polyposis Coli (apc) Is Required for Neural Crest-Dependent Craniofacial Development in Zebrafish. J Dev Biol 2023; 11:29. [PMID: 37489330 PMCID: PMC10366761 DOI: 10.3390/jdb11030029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 07/26/2023] Open
Abstract
Neural crest (NC) is a unique vertebrate cell type arising from the border of the neural plate and epidermis that gives rise to diverse tissues along the entire body axis. Roberto Mayor and colleagues have made major contributions to our understanding of NC induction, delamination, and migration. We report that a truncating mutation of the classical tumor suppressor Adenomatous Polyposis Coli (apc) disrupts craniofacial development in zebrafish larvae, with a marked reduction in the cranial neural crest (CNC) cells that contribute to mandibular and hyoid pharyngeal arches. While the mechanism is not yet clear, the altered expression of signaling molecules that guide CNC migration could underlie this phenotype. For example, apcmcr/mcr larvae express substantially higher levels of complement c3, which Mayor and colleagues showed impairs CNC cell migration when overexpressed. However, we also observe reduction in stroma-derived factor 1 (sdf1/cxcl12), which is required for CNC migration into the head. Consistent with our previous work showing that APC directly enhances the activity of glycogen synthase kinase 3 (GSK-3) and, independently, that GSK-3 phosphorylates multiple core mRNA splicing factors, we identify 340 mRNA splicing variations in apc mutant zebrafish, including a splice variant that deletes a conserved domain in semaphorin 3f (sema3f), an axonal guidance molecule and a known regulator of CNC migration. Here, we discuss potential roles for apc in CNC development in the context of some of the seminal findings of Mayor and colleagues.
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Affiliation(s)
- Xiaolei Liu
- Department of Medicine (Hematology-Oncology), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William D. Jones
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sudhish A. Devadiga
- Faculty of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristin Lorent
- Department of Medicine (Gastroenterology), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander J. Valvezan
- Department of Medicine (Hematology-Oncology), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rebecca L. Myers
- Department of Medicine (Hematology-Oncology), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ning Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher J. Lengner
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Pack
- Department of Medicine (Gastroenterology), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter S. Klein
- Department of Medicine (Hematology-Oncology), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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13
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Engal E, Oja KT, Maroofian R, Geminder O, Le TL, Mor E, Tzvi N, Elefant N, Zaki MS, Gleeson JG, Muru K, Pajusalu S, Wojcik MH, Pachat D, Elmaksoud MA, Jeong WC, Lee H, Bauer P, Zifarelli G, Houlden H, Elpeleg O, Gordon C, Harel T, Õunap K, Salton M, Mor-Shaked H. Biallelic loss of function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental delay syndrome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.19.23291425. [PMID: 37425688 PMCID: PMC10327195 DOI: 10.1101/2023.06.19.23291425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Over two dozen spliceosome proteins are involved in human diseases, also referred to as spliceosomopathies. WBP4 (WW Domain Binding Protein 4) is part of the early spliceosomal complex, and was not described before in the context of human pathologies. Ascertained through GeneMatcher we identified eleven patients from eight families, with a severe neurodevelopmental syndrome with variable manifestations. Clinical manifestations included hypotonia, global developmental delay, severe intellectual disability, brain abnormalities, musculoskeletal and gastrointestinal abnormalities. Genetic analysis revealed overall five different homozygous loss-of-function variants in WBP4. Immunoblotting on fibroblasts from two affected individuals with different genetic variants demonstrated complete loss of protein, and RNA sequencing analysis uncovered shared abnormal splicing patterns, including enrichment for abnormalities of the nervous system and musculoskeletal system genes, suggesting that the overlapping differentially spliced genes are related to the common phenotypes of the probands. We conclude that biallelic variants in WBP4 cause a spliceosomopathy. Further functional studies are called for better understanding of the mechanism of pathogenicity.
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Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kaisa Teele Oja
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reza Maroofian
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Evyatar Mor
- Department of computer science, Ben-Gurion University of the Negev
| | - Naama Tzvi
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Naama Elefant
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Maha S. Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, Cairo, Egypt
| | - Joseph G. Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, La Jolla, USA
| | - Kai Muru
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | | | | | - Marwa Abd Elmaksoud
- Neurology Unit, Alexandria University Children’s Hospital, Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | | | | | - Peter Bauer
- CENTOGENE N.V., Am Strande 7, 18055 Rostock, Germany
| | | | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Katrin Õunap
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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14
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Ayers KL, Eggers S, Rollo BN, Smith KR, Davidson NM, Siddall NA, Zhao L, Bowles J, Weiss K, Zanni G, Burglen L, Ben-Shachar S, Rosensaft J, Raas-Rothschild A, Jørgensen A, Schittenhelm RB, Huang C, Robevska G, van den Bergen J, Casagranda F, Cyza J, Pachernegg S, Wright DK, Bahlo M, Oshlack A, O'Brien TJ, Kwan P, Koopman P, Hime GR, Girard N, Hoffmann C, Shilon Y, Zung A, Bertini E, Milh M, Ben Rhouma B, Belguith N, Bashamboo A, McElreavey K, Banne E, Weintrob N, BenZeev B, Sinclair AH. Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nat Commun 2023; 14:3403. [PMID: 37296101 PMCID: PMC10256788 DOI: 10.1038/s41467-023-39040-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Squamous cell carcinoma antigen recognized by T cells 3 (SART3) is an RNA-binding protein with numerous biological functions including recycling small nuclear RNAs to the spliceosome. Here, we identify recessive variants in SART3 in nine individuals presenting with intellectual disability, global developmental delay and a subset of brain anomalies, together with gonadal dysgenesis in 46,XY individuals. Knockdown of the Drosophila orthologue of SART3 reveals a conserved role in testicular and neuronal development. Human induced pluripotent stem cells carrying patient variants in SART3 show disruption to multiple signalling pathways, upregulation of spliceosome components and demonstrate aberrant gonadal and neuronal differentiation in vitro. Collectively, these findings suggest that bi-allelic SART3 variants underlie a spliceosomopathy which we tentatively propose be termed INDYGON syndrome (Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY GONadal dysgenesis). Our findings will enable additional diagnoses and improved outcomes for individuals born with this condition.
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Affiliation(s)
- Katie L Ayers
- The Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Stefanie Eggers
- The Victorian Clinical Genetics Services, Melbourne, Australia
| | - Ben N Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Katherine R Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Nadia M Davidson
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- School of BioSciences, Faculty of Science, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Liang Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Institute of Technology, Haifa, Israel
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Et Laboratoire de Neurogénétique Moléculaire, Département de Génétique et Embryologie Médicale, APHP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Shay Ben-Shachar
- Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jenny Rosensaft
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Annick Raas-Rothschild
- Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anne Jørgensen
- Department of Growth and Reproduction, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | | | | | - Franca Casagranda
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Justyna Cyza
- The Murdoch Children's Research Institute, Melbourne, Australia
| | - Svenja Pachernegg
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - David K Wright
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Melanie Bahlo
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, Melbourne, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Terrence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Nadine Girard
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Chen Hoffmann
- Radiology Department, Sheba medical Centre, Tel Aviv, Israel
| | - Yuval Shilon
- Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Amnon Zung
- Pediatrics Department, Kaplan Medical Center, Rehovot, 76100, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School, Jerusalem, Israel
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mathieu Milh
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Bochra Ben Rhouma
- Higher Institute of Nursing Sciences of Gabes, University of Gabes, Gabes, Tunisia
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Anu Bashamboo
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Kenneth McElreavey
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Ehud Banne
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
- The Rina Mor Genetic Institute, Wolfson Medical Center, Holon, 58100, Israel
| | - Naomi Weintrob
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Endocrinology Unit, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
| | | | - Andrew H Sinclair
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
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15
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Cerulo L, Pezzella N, Caruso FP, Parente P, Remo A, Giordano G, Forte N, Busselez J, Boschi F, Galiè M, Franco B, Pancione M. Single-cell proteo-genomic reveals a comprehensive map of centrosome-associated spliceosome components. iScience 2023; 26:106602. [PMID: 37250316 PMCID: PMC10214398 DOI: 10.1016/j.isci.2023.106602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 01/16/2023] [Accepted: 03/29/2023] [Indexed: 05/31/2023] Open
Abstract
Ribonucleoprotein (RNP) condensates are crucial for controlling RNA metabolism and splicing events in animal cells. We used spatial proteomics and transcriptomic to elucidate RNP interaction networks at the centrosome, the main microtubule-organizing center in animal cells. We found a number of cell-type specific centrosome-associated spliceosome interactions localized in subcellular structures involved in nuclear division and ciliogenesis. A component of the nuclear spliceosome BUD31 was validated as an interactor of the centriolar satellite protein OFD1. Analysis of normal and disease cohorts identified the cholangiocarcinoma as target of centrosome-associated spliceosome alterations. Multiplexed single-cell fluorescent microscopy for the centriole linker CEP250 and spliceosome components including BCAS2, BUD31, SRSF2 and DHX35 recapitulated bioinformatic predictions on the centrosome-associated spliceosome components tissue-type specific composition. Collectively, centrosomes and cilia act as anchor for cell-type specific spliceosome components, and provide a helpful reference for explore cytoplasmic condensates functions in defining cell identity and in the origin of rare diseases.
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Affiliation(s)
- Luigi Cerulo
- Bioinformatics Laboratory, BIOGEM scrl, Ariano Irpino, Avellino, Italy
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Nunziana Pezzella
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, Pozzuoli, 80078 Naples, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, Naples, Italy
| | - Francesca Pia Caruso
- Bioinformatics Laboratory, BIOGEM scrl, Ariano Irpino, Avellino, Italy
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Paola Parente
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Andrea Remo
- Pathology Unit, Mater Salutis Hospital AULSS9, “Scaligera”, 37122 Verona, Italy
| | - Guido Giordano
- Unit of Medical Oncology and Biomolecular Therapy, Department of Medical and Surgical Sciences, University of Foggia, Policlinico Riuniti, 71122 Foggia, Italy
| | - Nicola Forte
- Department of Clinical Pathology, Fatebenefratelli Hospital, 82100 Benevento, Italy
| | - Johan Busselez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Federico Boschi
- Department of Computer Science, University of Verona, Strada Le Grazie 8, Verona, Italy
| | - Mirco Galiè
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, Pozzuoli, 80078 Naples, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, Naples, Italy
- Medical Genetics, Department of Translational Medicine, University of Naples “Federico II”, Via Sergio Pansini, 80131 Naples, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University Madrid, 28040 Madrid, Spain
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16
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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17
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Abdel-Salam GMH, Abdel-Hamid MS. A founder PPIL1 variant underlies a recognizable form of microlissencephaly with pontocerebellar hypoplasia. Clin Genet 2023. [PMID: 37190898 DOI: 10.1111/cge.14357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/17/2023]
Abstract
Biallelic variants in PPIL1 have been recently found to cause a very rare type of pontocerebellar hypoplasia and congenital microcephaly in which simplified gyral pattern was not observed in all of the patients. Here, we describe a series of nine patients from eight unrelated Egyptian families in whom whole exome sequencing detected a previously reported homozygous missense variant (c.295G>A, p.Ala99Thr) in PPIL1. Haplotype analysis confirmed that this variant has a founder effect in our population. All our patients displayed early onset drug-resistant epilepsy, profound developmental delay, and visual impairment. Remarkably, they presented with recognizable imaging findings showing profound microcephaly, hypoplastic frontal lobe and posteriorly predominant pachygyria, agenesis of corpus callosum with colpocephaly, and pontocerebellar hypoplasia. In addition, Dandy-Walker malformation was evident in three patients. Interestingly, four of our patients exhibited hematopoietic disorder (44% of cases). We compared the phenotype of our patients with other previously reported PPIL1 patients. Our results reinforce the hypothesis that the alterative splicing of PPIL1 causes a heterogeneous phenotype. Further, we affirm that hematopoietic disorder is a common feature of the condition and underscore the role of major spliceosomes in brain development.
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Affiliation(s)
- Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mohamed S Abdel-Hamid
- Medical Molecular Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
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18
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Garsetti DE, Sahay K, Wang Y, Rogers MB. Sex and the basal mRNA synthesis machinery. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1765. [PMID: 36195437 PMCID: PMC10070566 DOI: 10.1002/wrna.1765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022]
Abstract
Evolution and change generated an incredible diversity of organisms on this earth. Yet, some processes are so central to life that change is strongly selected against. Synthesis of the eukaryotic messenger RNA is one example. The assemblies that carry out transcription and processing (capping, polyadenylation, and splicing) are so conserved that most genes have recognizable orthologs in yeast and humans. Naturally, most would conclude transcription and processing are identical in both sexes. However, this is an assumption. Men and women vastly differ in their physiologies. The incidence of pathologies, symptom presentation, disease outcome, and therapeutic response in each sex vary enormously. Despite the harm ignorance causes women, biological research has been historically carried out without regard to sex. The male mouse was the default mammal. A cultured cell's sex was considered irrelevant. Attempts to fill this knowledge gap have revealed molecular dissimilarities. For example, the earliest embryonic male and female transcriptomes differ long before fetal sex hormones appear. We used public data to challenge the assumption of sameness by reviewing reports of sex-biased gene expression and gene targeting. We focused on 120 genes encoding nonregulatory proteins involved in mRNA synthesis. Remarkably, genes with recognizable orthologs in yeast and thus LEAST likely to differ, did differ between the sexes. The rapidly growing public databases can be used to compare the expression of any gene in male and female tissues. Appreciating the principles that drive sex differences will enrich our understanding of RNA biology in all humans-men and women. This article is categorized under: RNA in Disease and Development > RNA in Development RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Diane E Garsetti
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Khushboo Sahay
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Yue Wang
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
| | - Melissa B Rogers
- Rutgers-New Jersey Medical School (NJMS), Department of Microbiology, Biochemistry, and Molecular Genetics, Newark, New Jersey, USA
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19
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Sarafidou T, Galliopoulou E, Apostolopoulou D, Fragkiadakis GA, Moschonas NK. Reconstruction of a Comprehensive Interactome and Experimental Data Analysis of FRA10AC1 May Provide Insights into Its Biological Role in Health and Disease. Genes (Basel) 2023; 14:genes14030568. [PMID: 36980839 PMCID: PMC10048706 DOI: 10.3390/genes14030568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
FRA10AC1, the causative gene for the manifestation of the FRA10A fragile site, encodes a well-conserved nuclear protein characterized as a non-core spliceosomal component. Pre-mRNA splicing perturbations have been linked with neurodevelopmental diseases. FRA10AC1 variants have been, recently, causally linked with severe neuropathological and growth retardation phenotypes. To further elucidate the participation of FRA10AC1 in spliceosomal multiprotein complexes and its involvement in neurological phenotypes related to splicing, we exploited protein–protein interaction experimental data and explored network information and information deduced from transcriptomics. We confirmed the direct interaction of FRA10AC1with ESS2, a non-core spliceosomal protein, mapped their interacting domains, and documented their tissue co-localization and physical interaction at the level of intracellular protein stoichiometries. Although FRA10AC1 and SF3B2, a major core spliceosomal protein, were shown to interact under in vitro conditions, the endogenous proteins failed to co-immunoprecipitate. A reconstruction of a comprehensive, strictly binary, protein–protein interaction network of FRA10AC1 revealed dense interconnectivity with many disease-associated spliceosomal components and several non-spliceosomal regulatory proteins. The topological neighborhood of FRA10AC1 depicts an interactome associated with multiple severe monogenic and multifactorial neurodevelopmental diseases mainly referring to spliceosomopathies. Our results suggest that FRA10AC1 involvement in pre-mRNA processing might be strengthened by interconnecting splicing with transcription and mRNA export, and they propose the broader role(s) of FRA10AC1 in cell pathophysiology.
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Affiliation(s)
- Theologia Sarafidou
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece
- Correspondence: (T.S.); (N.K.M.)
| | - Eleni Galliopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece
| | | | - Georgios A. Fragkiadakis
- Department of Nutrition and Dietetics Sciences, Hellenic Mediterranean University, Tripitos, 72300 Siteia, Greece
| | - Nicholas K. Moschonas
- School of Medicine, University of Patras, 26500 Patras, Greece
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology Hellas (FORTH/ICE-HT), 26504 Patras, Greece
- Correspondence: (T.S.); (N.K.M.)
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20
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Amudhavalli SM, Paolillo V, Lawson C, Patterson M, Kussmann J, Nopper AJ, Lypka M, Saunders C. Novel blended SNRPE-related spliceosomopathy phenotype characterized by microcephaly and congenital atrichia. Am J Med Genet A 2023; 191:1425-1429. [PMID: 36814386 DOI: 10.1002/ajmg.a.63149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/14/2023] [Accepted: 01/20/2023] [Indexed: 02/24/2023]
Abstract
Variants in genes encoding core components of the spliceosomes are associated with craniofacial syndromes, collectively called craniofacial spliceosomopathies. SNRPE encodes a core component of pre-mRNA processing U-rich small nuclear ribonuclear proteins (UsnRNPs). Heterozygous variants in SNRPE have been reported in six families with isolated hypotrichosis simplex in addition to one case of isolated non syndromic congenital microcephaly. Here, we report a patient with a novel blended phenotype of microcephaly and congenital atrichia with multiple congenital anomalies due to a de novo intronic SNRPE deletion, c.82-28_82-16del, which results in exon skipping. As discussed within, this phenotype, which we propose be named SNRPE-related syndromic microcephaly and hypotrichosis, overlaps other craniofacial splicesosomopathies.
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Affiliation(s)
- Shivarajan M Amudhavalli
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - V Paolillo
- Clinical Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Caitlin Lawson
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,Clinical Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Melanie Patterson
- Clinical Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - J Kussmann
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - A J Nopper
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA.,Division of Dermatology, Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - M Lypka
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Carol Saunders
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA.,Clinical Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
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21
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Yassin SH, Henderson R, Lenberg J, Murillo V, Murdock DR, Friedman J, Jones MC, Wigby K, Borooah S. Further delineation of the CWC27-associated spliceosomeopathy: Case report and review of the literature. Am J Med Genet A 2023; 191:1378-1383. [PMID: 36718996 DOI: 10.1002/ajmg.a.63134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/16/2022] [Accepted: 01/18/2023] [Indexed: 02/01/2023]
Abstract
Pre-mRNA splicing factors are crucial in regulating transcript diversity, by removing introns from eukaryotic transcripts, an essential step in gene expression. Splicing of pre-mRNA is catalyzed by spliceosomes. CWC27 is a cyclophilin associated with spliceosome, in which genetic defects of its components have been linked to spliceosomopathies with clinical phenotypes including skeletal developmental defects, retinitis pigmentosa (RP), short stature, skeletal anomalies, and neurological disorders. We report two siblings (male and female) of Mexican descent with a novel homozygous frameshift variant in CWC27 and aim to highlight the cardinal features among the previously described 12 cases as well as expand the currently recognized phenotypic spectrum. Both siblings presented with a range of ocular and extraocular manifestations including novel features such as solitary kidney and tarsal coalition in the male sibling, together with gait abnormalities, and Hashimoto's thyroiditis in the female sibling. Finally, we highlight ectodermal involvement including sparse scalp hair, eyebrows and lashes, pigmentary differences, nail dysplasia, and dental anomalies as a core phenotype associated with the CWC27 spliceosomopathy.
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Affiliation(s)
- Shaden H Yassin
- Shiley Eye Institute, University of California, San Diego, California, USA
| | - Riley Henderson
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Viridiana Murillo
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - David R Murdock
- Invitae Clinical Genomics Group, Invitae Corporation, San Francisco, California, USA
| | - Jennifer Friedman
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Rady Children's Hospital-San Diego, Genetics and Dysmorphology Division, San Diego, California, USA.,Departments of Neurosciences and Pediatrics, University of California, San Diego, California, USA
| | - Marilyn C Jones
- Rady Children's Hospital-San Diego, Genetics and Dysmorphology Division, San Diego, California, USA.,Division of Genetics, Department of Pediatrics, University of California, San Diego, California, USA
| | - Kristen Wigby
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Rady Children's Hospital-San Diego, Genetics and Dysmorphology Division, San Diego, California, USA.,Division of Genetics, Department of Pediatrics, University of California, San Diego, California, USA
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California, San Diego, California, USA
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22
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Bykova M, Hou Y, Eng C, Cheng F. Quantitative trait locus (xQTL) approaches identify risk genes and drug targets from human non-coding genomes. Hum Mol Genet 2022; 31:R105-R113. [PMID: 36018824 PMCID: PMC9989738 DOI: 10.1093/hmg/ddac208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Advances and reduction of costs in various sequencing technologies allow for a closer look at variations present in the non-coding regions of the human genome. Correlating non-coding variants with large-scale multi-omic data holds the promise not only of a better understanding of likely causal connections between non-coding DNA and expression of traits but also identifying potential disease-modifying medicines. Genome-phenome association studies have created large datasets of DNA variants that are associated with multiple traits or diseases, such as Alzheimer's disease; yet, the functional consequences of variants, in particular of non-coding variants, remain largely unknown. Recent advances in functional genomics and computational approaches have led to the identification of potential roles of DNA variants, such as various quantitative trait locus (xQTL) techniques. Multi-omic assays and analytic approaches toward xQTL have identified links between genetic loci and human transcriptomic, epigenomic, proteomic and metabolomic data. In this review, we first discuss the recent development of xQTL from multi-omic findings. We then highlight multimodal analysis of xQTL and genetic data for identification of risk genes and drug targets using Alzheimer's disease as an example. We finally discuss challenges and future research directions (e.g. artificial intelligence) for annotation of non-coding variants in complex diseases.
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Affiliation(s)
- Marina Bykova
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
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23
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Olthof AM, White AK, Kanadia RN. The emerging significance of splicing in vertebrate development. Development 2022; 149:dev200373. [PMID: 36178052 PMCID: PMC9641660 DOI: 10.1242/dev.200373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Splicing is a crucial regulatory node of gene expression that has been leveraged to expand the proteome from a limited number of genes. Indeed, the vast increase in intron number that accompanied vertebrate emergence might have aided the evolution of developmental and organismal complexity. Here, we review how animal models for core spliceosome components have provided insights into the role of splicing in vertebrate development, with a specific focus on neuronal, neural crest and skeletal development. To this end, we also discuss relevant spliceosomopathies, which are developmental disorders linked to mutations in spliceosome subunits. Finally, we discuss potential mechanisms that could underlie the tissue-specific phenotypes often observed upon spliceosome inhibition and identify gaps in our knowledge that, we hope, will inspire further research.
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Affiliation(s)
- Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Alisa K. White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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24
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Huang W, Kew C, Fernandes SDA, Löhrke A, Han L, Demetriades C, Antebi A. Decreased spliceosome fidelity and egl-8 intron retention inhibit mTORC1 signaling to promote longevity. NATURE AGING 2022; 2:796-808. [PMID: 37118503 PMCID: PMC10154236 DOI: 10.1038/s43587-022-00275-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
AbstractChanges in splicing fidelity are associated with loss of homeostasis and aging, yet only a handful of splicing factors have been shown to be causally required to promote longevity, and the underlying mechanisms and downstream targets in these paradigms remain elusive. Surprisingly, we found a hypomorphic mutation within ribonucleoprotein RNP-6/poly(U)-binding factor 60 kDa (PUF60), a spliceosome component promoting weak 3′-splice site recognition, which causes aberrant splicing, elevates stress responses and enhances longevity in Caenorhabditis elegans. Through genetic suppressor screens, we identify a gain-of-function mutation within rbm-39, an RNP-6-interacting splicing factor, which increases nuclear speckle formation, alleviates splicing defects and curtails longevity caused by rnp-6 mutation. By leveraging the splicing changes induced by RNP-6/RBM-39 activities, we uncover intron retention in egl-8/phospholipase C β4 (PLCB4) as a key splicing target prolonging life. Genetic and biochemical evidence show that neuronal RNP-6/EGL-8 downregulates mammalian target of rapamycin complex 1 (mTORC1) signaling to control organismal lifespan. In mammalian cells, PUF60 downregulation also potently and specifically inhibits mTORC1 signaling. Altogether, our results reveal that splicing fidelity modulates lifespan through mTOR signaling.
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25
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Liang Y, Tan F, Sun X, Cui Z, Gu J, Mao S, Chan HF, Tang S, Chen J. Aberrant Retinal Pigment Epithelial Cells Derived from Induced Pluripotent Stem Cells of a Retinitis Pigmentosa Patient with the PRPF6 Mutation. Int J Mol Sci 2022; 23:ijms23169049. [PMID: 36012314 PMCID: PMC9409096 DOI: 10.3390/ijms23169049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
Pre-mRNA processing factors (PRPFs) are vital components of the spliceosome and are involved in the physiological process necessary for pre-mRNA splicing to mature mRNA. As an important member, PRPF6 mutation resulting in autosomal dominant retinitis pigmentosa (adRP) is not common. Recently, we reported the establishment of an induced pluripotent stem cells (iPSCs; CSUASOi004-A) model by reprogramming the peripheral blood mononuclear cells of a PRPF6-related adRP patient, which could recapitulate a consistent disease-specific genotype. In this study, a disease model of retinal pigment epithelial (RPE) cells was generated from the iPSCs of this patient to further investigate the underlying molecular and pathological mechanisms. The results showed the irregular morphology, disorganized apical microvilli and reduced expressions of RPE-specific genes in the patient’s iPSC-derived RPE cells. In addition, RPE cells carrying the PRPF6 mutation displayed a decrease in the phagocytosis of fluorescein isothiocyanate-labeled photoreceptor outer segments and exhibited impaired cell polarity and barrier function. This study will benefit the understanding of PRPF6-related RPE cells and future cell therapy.
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Affiliation(s)
- Yuqin Liang
- Aier School of Ophthalmology, Central South University, Changsha 410015, China
- Aier Eye Institute, Changsha 410015, China
| | - Feng Tan
- Aier School of Ophthalmology, Central South University, Changsha 410015, China
- Aier Eye Institute, Changsha 410015, China
| | - Xihao Sun
- Aier School of Ophthalmology, Central South University, Changsha 410015, China
- Aier Eye Institute, Changsha 410015, China
| | - Zekai Cui
- Aier School of Ophthalmology, Central South University, Changsha 410015, China
- Aier Eye Institute, Changsha 410015, China
| | - Jianing Gu
- Aier Eye Institute, Changsha 410015, China
| | | | - Hon Fai Chan
- Institute for Tissue Engineering and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Shibo Tang
- Aier School of Ophthalmology, Central South University, Changsha 410015, China
- Aier Eye Institute, Changsha 410015, China
- Correspondence: (S.T.); (J.C.); Tel.: +86-139-2510-0123 (S.T.); +86-186-7583-9029 (J.C.)
| | - Jiansu Chen
- Aier School of Ophthalmology, Central South University, Changsha 410015, China
- Aier Eye Institute, Changsha 410015, China
- Key Laboratory for Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou 510632, China
- Correspondence: (S.T.); (J.C.); Tel.: +86-139-2510-0123 (S.T.); +86-186-7583-9029 (J.C.)
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26
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The Core Splicing Factors EFTUD2, SNRPB and TXNL4A Are Essential for Neural Crest and Craniofacial Development. J Dev Biol 2022; 10:jdb10030029. [PMID: 35893124 PMCID: PMC9326569 DOI: 10.3390/jdb10030029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 12/11/2022] Open
Abstract
Mandibulofacial dysostosis (MFD) is a human congenital disorder characterized by hypoplastic neural-crest-derived craniofacial bones often associated with outer and middle ear defects. There is growing evidence that mutations in components of the spliceosome are a major cause for MFD. Genetic variants affecting the function of several core splicing factors, namely SF3B4, SF3B2, EFTUD2, SNRPB and TXNL4A, are responsible for MFD in five related but distinct syndromes known as Nager and Rodriguez syndromes (NRS), craniofacial microsomia (CFM), mandibulofacial dysostosis with microcephaly (MFDM), cerebro-costo-mandibular syndrome (CCMS) and Burn–McKeown syndrome (BMKS), respectively. Animal models of NRS and MFDM indicate that MFD results from an early depletion of neural crest progenitors through a mechanism that involves apoptosis. Here we characterize the knockdown phenotype of Eftud2, Snrpb and Txnl4a in Xenopus embryos at different stages of neural crest and craniofacial development. Our results point to defects in cranial neural crest cell formation as the likely culprit for MFD associated with EFTUD2, SNRPB and TXNL4A haploinsufficiency, and suggest a commonality in the etiology of these craniofacial spliceosomopathies.
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27
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Kornak U, Saha N, Keren B, Neumann A, Taylor Tavares AL, Piard J, Kopp J, Rodrigues Alves JG, Rodríguez de Los Santos M, El Choubassi N, Ehmke N, Jäger M, Spielmann M, Pantel JT, Lejeune E, Fauler B, Mielke T, Hecht J, Meierhofer D, Strom TM, Laugel V, Brice A, Mundlos S, Bertoli-Avella A, Bauer P, Heyd F, Boute O, Dupont J, Depienne C, Van Maldergem L, Fischer-Zirnsak B. Alternative splicing of BUD13 determines the severity of a developmental disorder with lipodystrophy and progeroid features. Genet Med 2022; 24:1927-1940. [PMID: 35670808 DOI: 10.1016/j.gim.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE In this study we aimed to identify the molecular genetic cause of a progressive multisystem disease with prominent lipodystrophy. METHODS In total, 5 affected individuals were investigated using exome sequencing. Dermal fibroblasts were characterized using RNA sequencing, proteomics, immunoblotting, immunostaining, and electron microscopy. Subcellular localization and rescue studies were performed. RESULTS We identified a lipodystrophy phenotype with a typical facial appearance, corneal clouding, achalasia, progressive hearing loss, and variable severity. Although 3 individuals showed stunted growth, intellectual disability, and died within the first decade of life (A1, A2, and A3), 2 are adults with normal intellectual development (A4 and A5). All individuals harbored an identical homozygous nonsense variant affecting the retention and splicing complex component BUD13. The nucleotide substitution caused alternative splicing of BUD13 leading to a stable truncated protein whose expression positively correlated with disease expression and life expectancy. In dermal fibroblasts, we found elevated intron retention, a global reduction of spliceosomal proteins, and nuclei with multiple invaginations, which were more pronounced in A1, A2, and A3. Overexpression of both BUD13 isoforms normalized the nuclear morphology. CONCLUSION Our results define a hitherto unknown syndrome and show that the alternative splice product converts a loss-of-function into a hypomorphic allele, thereby probably determining the severity of the disease and the survival of affected individuals.
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Affiliation(s)
- Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.
| | - Namrata Saha
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universtitätsmedizin Berlin, Germany; Max Planck International Research Network on Aging, Max Planck Society, Rostock, Germany
| | - Boris Keren
- Department of Genetics, DMU BioGem, Assistance Publique - Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
| | - Alexander Neumann
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Omiqa Bioinformatics, Berlin, Germany
| | - Ana Lisa Taylor Tavares
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Genomics England, London, United Kingdom
| | - Juliette Piard
- Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France.
| | - Johannes Kopp
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - João Guilherme Rodrigues Alves
- Serviço de Genética, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospital Universitário Lisboa Norte, Lisboa, Portugal
| | - Miguel Rodríguez de Los Santos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universtitätsmedizin Berlin, Germany
| | - Naji El Choubassi
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marten Jäger
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; BIH Genomics Core Unit, Berlin Institute of Health (BIH), Berlin, Germany
| | - Malte Spielmann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Jean Tori Pantel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elodie Lejeune
- Department of Genetics, DMU BioGem, Assistance Publique - Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
| | - Beatrix Fauler
- Microscopy and Cryo-electron Microscopy Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-electron Microscopy Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jochen Hecht
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - David Meierhofer
- Mass-Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tim M Strom
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Vincent Laugel
- Service de Pédiatrie 1, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, Faculté de Médecine de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Alexis Brice
- Department of Genetics, DMU BioGem, Assistance Publique - Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France; Institut du Cerveau - Paris Brain Institute - ICM, Inserm, Centre National de la Recherche Scientifique, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Peter Bauer
- CENTOGENE GmbH, Rostock, Germany; Department of Medicine Clinic III, Hematology, Oncology and Palliative Medicine, Rostock University Medical Center, Rostock, Germany
| | - Florian Heyd
- Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Odile Boute
- Génétique Clinique, Centre Hospitalier Universitaire de Lille, Hôpital Jeanne de Flandre, Lille, France.
| | - Juliette Dupont
- Serviço de Genética, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospital Universitário Lisboa Norte, Lisboa, Portugal.
| | - Christel Depienne
- Institut du Cerveau - Paris Brain Institute - ICM, Inserm, Centre National de la Recherche Scientifique, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France; Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Lionel Van Maldergem
- Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France; Center of Clinical investigation 1431, National Institute of Health and Medical Research (INSERM), CHU, Besancon, France
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Biallelic loss-of-function variants in the splicing regulator NSRP1 cause a severe neurodevelopmental disorder with spastic cerebral palsy and epilepsy. Genet Med 2021; 23:2455-2460. [PMID: 34385670 DOI: 10.1038/s41436-021-01291-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Alternative splicing plays a critical role in mouse neurodevelopment, regulating neurogenesis, cortical lamination, and synaptogenesis, yet few human neurodevelopmental disorders are known to result from pathogenic variation in splicing regulator genes. Nuclear Speckle Splicing Regulator Protein 1 (NSRP1) is a ubiquitously expressed splicing regulator not known to underlie a Mendelian disorder. METHODS Exome sequencing and rare variant family-based genomics was performed as a part of the Baylor-Hopkins Center for Mendelian Genomics Initiative. Additional families were identified via GeneMatcher. RESULTS We identified six patients from three unrelated families with homozygous loss-of-function variants in NSRP1. Clinical features include developmental delay, epilepsy, variable microcephaly (Z-scores -0.95 to -5.60), hypotonia, and spastic cerebral palsy. Brain abnormalities included simplified gyral pattern, underopercularization, and/or vermian hypoplasia. Molecular analysis identified three pathogenic NSRP1 predicted loss-of-function variant alleles: c.1359_1362delAAAG (p.Glu455AlafsTer20), c.1272dupG (p.Lys425GlufsTer5), and c.52C>T (p.Gln18Ter). The two frameshift variants result in a premature termination codon in the last exon, and the mutant transcripts are predicted to escape nonsense mediated decay and cause loss of a C-terminal nuclear localization signal required for NSRP1 function. CONCLUSION We establish NSRP1 as a gene for a severe autosomal recessive neurodevelopmental disease trait characterized by developmental delay, epilepsy, microcephaly, and spastic cerebral palsy.
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Maharana SK, Saint-Jeannet JP. Molecular mechanisms of hearing loss in Nager syndrome. Dev Biol 2021; 476:200-208. [PMID: 33864777 DOI: 10.1016/j.ydbio.2021.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023]
Abstract
Nager syndrome is a rare human developmental disorder characterized by hypoplastic neural crest-derived craniofacial bones and limb defects. Mutations in SF3B4 gene, which encodes a component of the spliceosome, are a major cause for Nager. A review of the literature indicates that 45% of confirmed cases are also affected by conductive, sensorineural or mixed hearing loss. Conductive hearing loss is due to defective middle ear ossicles, which are neural crest derived, while sensorineural hearing loss typically results from defective inner ear or vestibulocochlear nerve, which are both derived from the otic placode. Animal model of Nager syndrome indicates that upon Sf3b4 knockdown cranial neural crest progenitors are depleted, which may account for the conductive hearing loss in these patients. To determine whether Sf3b4 plays a role in otic placode formation we analyzed the impact of Sf3b4 knockdown on otic development. Sf3b4-depleted Xenopus embryos exhibited reduced expression of several pan-placodal genes six1, dmrta1 and foxi4.1. We confirmed the dependence of placode genes expression on Sf3b4 function in animal cap explants expressing noggin, a BMP antagonist critical to induce placode fate in the ectoderm. Later in development, Sf3b4 morphant embryos had reduced expression of pax8, tbx2, otx2, bmp4 and wnt3a at the otic vesicle stage, and altered otic vesicle development. We propose that in addition to the neural crest, Sf3b4 is required for otic development, which may account for sensorineural hearing loss in Nager syndrome.
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Affiliation(s)
- Santosh Kumar Maharana
- Department of Molecular Pathobiology, New York University, College of Dentistry, New York, USA
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Beauchamp MC, Djedid A, Bareke E, Merkuri F, Aber R, Tam AS, Lines MA, Boycott KM, Stirling PC, Fish JL, Majewski J, Jerome-Majewska LA. Mutation in Eftud2 causes craniofacial defects in mice via mis-splicing of Mdm2 and increased P53. Hum Mol Genet 2021; 30:739-757. [PMID: 33601405 DOI: 10.1093/hmg/ddab051] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 01/19/2023] Open
Abstract
EFTUD2 is mutated in patients with mandibulofacial dysostosis with microcephaly (MFDM). We generated a mutant mouse line with conditional mutation in Eftud2 and used Wnt1-Cre2 to delete it in neural crest cells. Homozygous deletion of Eftud2 causes brain and craniofacial malformations, affecting the same precursors as in MFDM patients. RNAseq analysis of embryonic heads revealed a significant increase in exon skipping and increased levels of an alternatively spliced Mdm2 transcript lacking exon 3. Exon skipping in Mdm2 was also increased in O9-1 mouse neural crest cells after siRNA knock-down of Eftud2 and in MFDM patient cells. Moreover, we found increased nuclear P53, higher expression of P53-target genes and increased cell death. Finally, overactivation of the P53 pathway in Eftud2 knockdown cells was attenuated by overexpression of non-spliced Mdm2, and craniofacial development was improved when Eftud2-mutant embryos were treated with Pifithrin-α, an inhibitor of P53. Thus, our work indicates that the P53-pathway can be targeted to prevent craniofacial abnormalities and shows a previously unknown role for alternative splicing of Mdm2 in the etiology of MFDM.
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Affiliation(s)
- Marie-Claude Beauchamp
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada
| | - Anissa Djedid
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Fjodor Merkuri
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Rachel Aber
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Matthew A Lines
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Loydie A Jerome-Majewska
- Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada.,Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
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Hooper JE, Jones KL, Smith FJ, Williams T, Li H. An Alternative Splicing Program for Mouse Craniofacial Development. Front Physiol 2020; 11:1099. [PMID: 33013468 PMCID: PMC7498679 DOI: 10.3389/fphys.2020.01099] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
Alternative splicing acts as a fundamental mechanism to increase the number of functional transcripts that can be derived from the genome - and its appropriate regulation is required to direct normal development, differentiation, and physiology, in many species. Recent studies have highlighted that mutation of splicing factors, resulting in the disruption of alternative splicing, can have profound consequences for mammalian craniofacial development. However, there has been no systematic analysis of the dynamics of differential splicing during the critical period of face formation with respect to age, tissue layer, or prominence. Here we used deep RNA sequencing to profile transcripts expressed in the developing mouse face for both ectodermal and mesenchymal tissues from the three facial prominences at critical ages for facial development, embryonic days 10.5, 11.5, and 12.5. We also derived separate expression data from the nasal pit relating to the differentiation of the olfactory epithelium for a total of 60 independent datasets. Analysis of these datasets reveals the differential expression of multiple genes, but we find a similar number of genes are regulated only via differential splicing, indicating that alternative splicing is a major source of transcript diversity during facial development. Notably, splicing changes between tissue layers and over time are more prevalent than between prominences, with exon skipping the most common event. We next examined how the variation in splicing correlated with the expression of RNA binding proteins across the various datasets. Further, we assessed how binding sites for splicing regulatory molecules mapped with respect to intron exon boundaries. Overall these studies help define an alternative splicing regulatory program that has important consequences for facial development.
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Affiliation(s)
- Joan E. Hooper
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kenneth L. Jones
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado School of Medicine, Aurora, CO, United States
| | - Francis J. Smith
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
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