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Kong W, Cao X, Lu C. Clinical characteristics of BRAT1-related disease: a systematic literature review. Acta Neurol Belg 2024; 124:1281-1288. [PMID: 38607605 DOI: 10.1007/s13760-024-02507-y] [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: 01/04/2024] [Accepted: 02/08/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND BRAT1 (BRCA1-associated ataxia telangiectasia mutated activator 1) is involved in many important biological processes, including DNA damage response and maintenance of mitochondrial homeostasis. Dysfunctional BRAT1 causes variable clinical phenotypes, which hinders BRAT1-related disease from recognition and diagnosis. METHODS Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement was the guideline for this systematic review. MEDLINE was searched by terms ("BAAT1" and "BRAT1") from inception until June 21, 2022. RESULTS Twenty-eight studies, screened out of 49 records, were included for data extraction. The data from fifty patients with mutated BRAT1 were collected. There are 3 high relevant phenotypes, 4 medium relevant phenotypes and 3 low relevant phenotypes. Eye-related abnormal features were most frequently reported: 27 abnormal features were observed. Thirty-nine kinds of pathogenic nucleotide change in BRAT1 were reported. Top three common mutations of BRAT1 were c.638_639insA (16 cases), c.1395G > A (5 cases) and c.294dupA (4 cases). Homozygous mutations in BRAT1 presented a more severe phenotype than those who are compound heterozygotes. CONCLUSIONS This is the first comprehensive systematic review to present quantitative data about clinical characteristics of BRAT1-related disease, which helps doctors to recognize and diagnose it easier.
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Affiliation(s)
- Weijing Kong
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
| | - Xianying Cao
- Rehabilitation Department, Ju County Maternal and Child Health Hospital, Shandong, 276500, China
| | - Cheng Lu
- Beijing Hong Jian Medical Device Company, Beijing, 100176, China
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2
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Dokaneheifard S, Gomes Dos Santos H, Guiselle Valencia M, Arigela H, Edupuganti RR, Shiekhattar R. Neuronal differentiation requires BRAT1 complex to remove REST from chromatin. Proc Natl Acad Sci U S A 2024; 121:e2318740121. [PMID: 38805275 PMCID: PMC11161795 DOI: 10.1073/pnas.2318740121] [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: 10/26/2023] [Accepted: 04/17/2024] [Indexed: 05/30/2024] Open
Abstract
Repressor element-1 silencing transcription factor (REST) is required for the formation of mature neurons. REST dysregulation underlies a key mechanism of neurodegeneration associated with neurological disorders. However, the mechanisms leading to alterations of REST-mediated silencing of key neurogenesis genes are not known. Here, we show that BRCA1 Associated ATM Activator 1 (BRAT1), a gene linked to neurodegenerative diseases, is required for the activation of REST-responsive genes during neuronal differentiation. We find that INTS11 and INTS9 subunits of Integrator complex interact with BRAT1 as a distinct trimeric complex to activate critical neuronal genes during differentiation. BRAT1 depletion results in persistence of REST residence on critical neuronal genes disrupting the differentiation of NT2 cells into astrocytes and neuronal cells. We identified BRAT1 and INTS11 co-occupying the promoter region of these genes and pinpoint a role for BRAT1 in recruiting INTS11 to their promoters. Disease-causing mutations in BRAT1 diminish its association with INTS11/INTS9, linking the manifestation of disease phenotypes with a defect in transcriptional activation of key neuronal genes by BRAT1/INTS11/INTS9 complex. Finally, loss of Brat1 in mouse embryonic stem cells leads to a defect in neuronal differentiation assay. Importantly, while reconstitution with wild-type BRAT1 restores neuronal differentiation, the addition of a BRAT1 mutant is unable to associate with INTS11/INTS9 and fails to rescue the neuronal phenotype. Taken together, our study highlights the importance of BRAT1 association with INTS11 and INTS9 in the development of the nervous system.
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Affiliation(s)
- Sadat Dokaneheifard
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Helena Gomes Dos Santos
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Monica Guiselle Valencia
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Harikumar Arigela
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Raghu Ram Edupuganti
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
| | - Ramin Shiekhattar
- Department of Human Genetics, University of Miami, Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL33136
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3
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Engel C, Valence S, Delplancq G, Maroofian R, Accogli A, Agolini E, Alkuraya FS, Baglioni V, Bagnasco I, Becmeur-Lefebvre M, Bertini E, Borggraefe I, Brischoux-Boucher E, Bruel AL, Brusco A, Bubshait DK, Cabrol C, Cilio MR, Cornet MC, Coubes C, Danhaive O, Delague V, Denommé-Pichon AS, Di Giacomo MC, Doco-Fenzy M, Engels H, Cremer K, Gérard M, Gleeson JG, Heron D, Goffeney J, Guimier A, Harms FL, Houlden H, Iacomino M, Kaiyrzhanov R, Kamien B, Karimiani EG, Kraus D, Kuentz P, Kutsche K, Lederer D, Massingham L, Mignot C, Morris-Rosendahl D, Nagarajan L, Odent S, Ormières C, Partlow JN, Pasquier L, Penney L, Philippe C, Piccolo G, Poulton C, Putoux A, Rio M, Rougeot C, Salpietro V, Scheffer I, Schneider A, Srivastava S, Straussberg R, Striano P, Valente EM, Venot P, Villard L, Vitobello A, Wagner J, Wagner M, Zaki MS, Zara F, Lesca G, Yassaee VR, Miryounesi M, Hashemi-Gorji F, Beiraghi M, Ashrafzadeh F, Galehdari H, Walsh C, Novelli A, Tacke M, Sadykova D, Maidyrov Y, Koneev K, Shashkin C, Capra V, Zamani M, Van Maldergem L, Burglen L, Piard J. BRAT1-related disorders: phenotypic spectrum and phenotype-genotype correlations from 97 patients. Eur J Hum Genet 2023; 31:1023-1031. [PMID: 37344571 PMCID: PMC10474045 DOI: 10.1038/s41431-023-01410-z] [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: 12/22/2022] [Revised: 04/26/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
BRAT1 biallelic variants are associated with rigidity and multifocal seizure syndrome, lethal neonatal (RMFSL), and neurodevelopmental disorder associating cerebellar atrophy with or without seizures syndrome (NEDCAS). To date, forty individuals have been reported in the literature. We collected clinical and molecular data from 57 additional cases allowing us to study a large cohort of 97 individuals and draw phenotype-genotype correlations. Fifty-nine individuals presented with BRAT1-related RMFSL phenotype. Most of them had no psychomotor acquisition (100%), epilepsy (100%), microcephaly (91%), limb rigidity (93%), and died prematurely (93%). Thirty-eight individuals presented a non-lethal phenotype of BRAT1-related NEDCAS phenotype. Seventy-six percent of the patients in this group were able to walk and 68% were able to say at least a few words. Most of them had cerebellar ataxia (82%), axial hypotonia (79%) and cerebellar atrophy (100%). Genotype-phenotype correlations in our cohort revealed that biallelic nonsense, frameshift or inframe deletion/insertion variants result in the severe BRAT1-related RMFSL phenotype (46/46; 100%). In contrast, genotypes with at least one missense were more likely associated with NEDCAS (28/34; 82%). The phenotype of patients carrying splice variants was variable: 41% presented with RMFSL (7/17) and 59% with NEDCAS (10/17).
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Affiliation(s)
- Camille Engel
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France.
| | - Stéphanie Valence
- Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP Sorbonne Université, Paris, France
| | - Geoffroy Delplancq
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Reza Maroofian
- Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Valentina Baglioni
- Department of Human Neurosciences, Institute of Child and Adolescent Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Irene Bagnasco
- Division of Neuropsychiatry, Epilepsy Center for Children, Martini Hospital, 10141, Turin, Italy
| | | | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Ingo Borggraefe
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University of Munich, 80337, Munich, Germany
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Ange-Line Bruel
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126, Turin, Italy
| | - Dalal K Bubshait
- Department of Pediatrics, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Christelle Cabrol
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Maria Roberta Cilio
- Department of Pediatrics, Division of Pediatric Neurology Saint-Luc University Hospital, and Institute of Neuroscience (IoNS), Catholic University of Louvain, Brussels, Belgium
| | - Marie-Coralie Cornet
- Department of Pediatrics, Division of Neonatology, University of California San Francisco, San Francisco, CA, USA
| | - Christine Coubes
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Olivier Danhaive
- Division of Neonatology, Saint-Luc university Hospital, and Institut of Clinical and Experimental Research (IREC), Bruxelles, Belgium
| | - Valérie Delague
- Aix Marseille Univ, INSERM, Marseille Medical Genetics Center, MMG, Marseille, France
| | - Anne-Sophie Denommé-Pichon
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Marilena Carmela Di Giacomo
- Medical Genetics Service and Laboratory of Cytogenetics, SIC Anatomia Patologica, "San Carlo" Hospital, 85100, Potenza, Italy
| | - Martine Doco-Fenzy
- CHU Reims, Service de Génétique, Reims, France
- CHU de Nantes, service de génétique médicale, Nantes, France
- L'institut du thorax, INSERM, UNIV Nantes, Nantes, France
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Marion Gérard
- Clinical Genetics, Côte de Nacre University Hospital Center, Caen, France
| | - Joseph G Gleeson
- University of California San Diego, Department of Neurosciences, Rady Children's Institute for Genomic Medicine, San Diego, CA, 92037, USA
| | - Delphine Heron
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne University, Paris, France
| | - Joanna Goffeney
- Service de neuropédiatrie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Anne Guimier
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker Enfants Malades, Institut Imagine et Université Paris-Cité, Paris, France
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henry Houlden
- Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Instituto Giannina Gaslini, Genova, Italy
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Benjamin Kamien
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, 6008, Australia
| | - Ehsan Ghayoor Karimiani
- Department of Molecular Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Dror Kraus
- Department of Neurology, Schneider Children's Medical Center of Israel, Petah Tiqva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Paul Kuentz
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Damien Lederer
- Institute for Pathology and Genetics, 6040, Gosselies, Belgium
| | - Lauren Massingham
- Division of Medical Genetics, Department of Pediatrics, Hasbro Children's Hospital, Providence, RI, USA
| | - Cyril Mignot
- APHP, Sorbonne Université, Département de Génétique, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, GH Pitié-Salpêtrière/Hôpital Armand Trousseau, Paris, France
| | - Déborah Morris-Rosendahl
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, UK
- NHLI, Imperial College London, London, UK
| | - Lakshmi Nagarajan
- Department of Neurology, Perth Children's Hospital, Nedlands, WA, Australia
- University of Western Australia, Nedlands, WA, Australia
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Référence "Déficiences Intellectuelles de causes rares" (CRDI), Centre Référence Anomalies du développement (CLAD-Ouest), CHU Rennes, Univ Rennes, Rennes, France
| | - Clothilde Ormières
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker Enfants Malades, Institut Imagine et Université Paris-Cité, Paris, France
| | - Jennifer Neil Partlow
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre Référence "Déficiences Intellectuelles de causes rares" (CRDI), Centre Référence Anomalies du développement (CLAD-Ouest), CHU Rennes, Univ Rennes, Rennes, France
| | - Lynette Penney
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, NS, Canada
| | - Christophe Philippe
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Cathryn Poulton
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, 6008, Australia
| | - Audrey Putoux
- Hospices Civils de Lyon, Service de Génétique, Bron, France
- Équipe GENDEV, Centre de Recherche en Neurosciences de Lyon, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Marlène Rio
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker Enfants Malades, Institut Imagine et Université Paris-Cité, Paris, France
| | | | - Vincenzo Salpietro
- Department of Neuromuscular Diseases UCL Queen Square Institute of Neurology, University College London, London, UK
- IRCCS Giannina Gaslini Institute, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | - Ingrid Scheffer
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, Australia
- Royal Children's Hospital, Florey Institute and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amy Schneider
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, Australia
| | | | - Rachel Straussberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Pasquale Striano
- IRCCS Giannina Gaslini Institute, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Perrine Venot
- Neonatal Intensive Care Unit, Institut Alix de Champagne, Reims, France
| | - Laurent Villard
- Aix Marseille Univ, INSERM, Marseille Medical Genetics Center, MMG, Marseille, France
- Département de Génétique Médicale, AP-HM, Hôpital d'Enfants de La Timone, Marseille, France
| | - Antonio Vitobello
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Johanna Wagner
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University of Munich, 80337, Munich, Germany
| | - Matias Wagner
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University of Munich, 80337, Munich, Germany
- Institute for Neurogenomics, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Federizo Zara
- IRCCS Giannina Gaslini Institute, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | - Gaetan Lesca
- Hospices Civils de Lyon, Service de Génétique, Bron, France
- Pathophysiology and Genetics of Neuron and Muscle (PGNM, UCBL - CNRS UMR5261 - INSERM U1315), Université Claude Bernard Lyon 1, Lyon, France
| | - Vahid Reza Yassaee
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Miryounesi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hashemi-Gorji
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehran Beiraghi
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farah Ashrafzadeh
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Christopher Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Moritz Tacke
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University of Munich, 80337, Munich, Germany
| | | | - Yerdan Maidyrov
- S. D. Asfendiyarov Kazakh National Medical University Almaty, Almaty, Kazakhstan
| | - Kairgali Koneev
- Department of Neurology and Neurosurgery, Asfendiyarov Kazakh National Medical University, Almaty, 050000, Kazakhstan
| | - Chingiz Shashkin
- Department of Neurology, The International Institute of Postraduate Education, Almaty, Kazakhstan
| | - Valeria Capra
- Unit of Medical Genetics, IRCCS Instituto Giannina Gaslini, Genova, Italy
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Lionel Van Maldergem
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Département de Génétique, AP-HP, Sorbonne Université, Hôpital Trousseau, Paris, France
| | - Juliette Piard
- Centre de Génétique Humaine, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
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Dokaneheifard S, Gomes Dos Santos H, Valencia MG, Arigela H, Shiekhattar R. BRAT1 associates with INTS11/INTS9 heterodimer to regulate key neurodevelopmental genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552743. [PMID: 37609215 PMCID: PMC10441392 DOI: 10.1101/2023.08.10.552743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Integrator is a multi-subunits protein complex involved in regulation of gene expression. Several Integrator subunits have been found to be mutated in human neurodevelopmental disorders, suggesting a key role for the complex in the development of nervous system. BRAT1 is similarly linked with neurodegenerative diseases and neurodevelopmental disorders such as rigidity and multifocal-seizure syndrome. Here, we show that INTS11 and INTS9 subunits of Integrator complex interact with BRAT1 and form a trimeric complex in human HEK293T cells as well as in pluripotent human embryonal carcinoma cell line (NT2). We find that BRAT1 depletion disrupts the differentiation of NT2 cells into astrocytes and neural cells. Loss of BRAT1 results in inability to activate many neuronal genes that are targets of REST, a neuronal silencer. We identified BRAT1 and INTS11 co-occupying the promoter region of these genes and pinpoint a role for BRAT1 in recruiting INTS11 to their promoters. Disease-causing mutations in BRAT1 diminish its association with INTS11/INTS9, linking the manifestation of disease phenotypes with a defect in transcriptional activation of key neuronal genes by BRAT1/INTS11/INTS9 complex. Highlights Integrator subunits INTS9 and INTS11 tightly interact with BRAT1 Depletion of BRAT1 causes a dramatic delay in human neural differentiation BRAT1 and INTS11 module targets the promoters of neural marker genes and co-regulates their expression. The recruitment of INTS11 to these sites is BRAT1-dependent. Pathogenic E522K mutation in BRAT1 disrupts its interaction with INTS11/INTS9 heterodimer.
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5
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Tepe B, Macke EL, Niceta M, Weisz Hubshman M, Kanca O, Schultz-Rogers L, Zarate YA, Schaefer GB, Granadillo De Luque JL, Wegner DJ, Cogne B, Gilbert-Dussardier B, Le Guillou X, Wagner EJ, Pais LS, Neil JE, Mochida GH, Walsh CA, Magal N, Drasinover V, Shohat M, Schwab T, Schmitz C, Clark K, Fine A, Lanpher B, Gavrilova R, Blanc P, Burglen L, Afenjar A, Steel D, Kurian MA, Prabhakar P, Gößwein S, Di Donato N, Bertini ES, Wangler MF, Yamamoto S, Tartaglia M, Klee EW, Bellen HJ. Bi-allelic variants in INTS11 are associated with a complex neurological disorder. Am J Hum Genet 2023; 110:774-789. [PMID: 37054711 PMCID: PMC10183469 DOI: 10.1016/j.ajhg.2023.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/18/2023] [Indexed: 04/15/2023] Open
Abstract
The Integrator complex is a multi-subunit protein complex that regulates the processing of nascent RNAs transcribed by RNA polymerase II (RNAPII), including small nuclear RNAs, enhancer RNAs, telomeric RNAs, viral RNAs, and protein-coding mRNAs. Integrator subunit 11 (INTS11) is the catalytic subunit that cleaves nascent RNAs, but, to date, mutations in this subunit have not been linked to human disease. Here, we describe 15 individuals from 10 unrelated families with bi-allelic variants in INTS11 who present with global developmental and language delay, intellectual disability, impaired motor development, and brain atrophy. Consistent with human observations, we find that the fly ortholog of INTS11, dIntS11, is essential and expressed in the central nervous systems in a subset of neurons and most glia in larval and adult stages. Using Drosophila as a model, we investigated the effect of seven variants. We found that two (p.Arg17Leu and p.His414Tyr) fail to rescue the lethality of null mutants, indicating that they are strong loss-of-function variants. Furthermore, we found that five variants (p.Gly55Ser, p.Leu138Phe, p.Lys396Glu, p.Val517Met, and p.Ile553Glu) rescue lethality but cause a shortened lifespan and bang sensitivity and affect locomotor activity, indicating that they are partial loss-of-function variants. Altogether, our results provide compelling evidence that integrity of the Integrator RNA endonuclease is critical for brain development.
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Affiliation(s)
- Burak Tepe
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcello Niceta
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Monika Weisz Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Yuri A Zarate
- Division of Genetics and Metabolism, University of Kentucky, Lexington, KY, USA
| | - G Bradley Schaefer
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jorge Luis Granadillo De Luque
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel J Wegner
- Edward Mallinckrodt Department of Pediatrics, Washington University in St. Louis School of Medicine and St. Louis Children's Hospital, St. Louis, Missouri, USA
| | - Benjamin Cogne
- Laboratory of Molecular Genetics, CHU de Nantes, Nantes, France
| | | | | | - Eric J Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Lynn S Pais
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, and Howard Hughes Medical Institute, Boston Children's Hospital, and Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Nurit Magal
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Valerie Drasinover
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petach Tikva, Israel
| | - Mordechai Shohat
- Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel; Medical Genetics Institute of Maccabi HMO, Rechovot, Israel
| | - Tanya Schwab
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Chris Schmitz
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl Clark
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Anthony Fine
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Brendan Lanpher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ralitza Gavrilova
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Pierre Blanc
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, 75012 Paris, France
| | - Lydie Burglen
- APHP, Département de génétique, Sorbonne Université, GRC n°19, ConCer-LD, Centre de Référence déficiences intellectuelles de causes rares, Hôpital Armand Trousseau, 75012 Paris, France
| | - Alexandra Afenjar
- APHP. SU, Centre de Référence Malformations et maladies congénitales du cervelet, département de génétique et embryologie médicale, Hôpital Trousseau, 75012 Paris, France
| | - Dora Steel
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Prab Prabhakar
- Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Sophie Gößwein
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Enrico S Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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6
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Touhami R, Foddha H, Alix E, Jalloul A, Mougou-Zerelli S, Saad A, Sanlaville D, Haj Khelil A. Case report: 7p22.3 deletion and 8q24.3 duplication in a patient with epilepsy and psychomotor delay-Does both possibly act to modulate a candidate gene region for the patient's phenotype? Front Genet 2023; 13:1061539. [PMID: 36778913 PMCID: PMC9909830 DOI: 10.3389/fgene.2022.1061539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Background: Psychomotor delay, epilepsy and dysmorphic features are clinical signs which are described in multiple syndromes due to chromosomal imbalances or mutations involving key genes implicated in the stages of Early Embryonic Development. In this context, we report a 10 years old Tunisian patient with these three signs. Our objective is to determine the cause of developmental, behavioral and facial abnormalities in this patient. Methods: We used banding cytogenetics (karyotype) and Array Comparative Genomic Hybridization (Array CGH) to this purpose. Results: The karyotype was in favor of a derivative of chromosome 7 in the patient and Array CGH analysis revealed a loss of genetic material in 7p22.3-p22.1 (4,56 Mb) with a gain at 8q24.23-q24 (9.20 Mb) resulting from maternal 7/8 reciprocal translocation. An in silico analysis of the unbalanced region was carried out and showed that the 7p22.3-p22.1 deletion contains eight genes. Among them, BRAT1 gene, previously described in several neurodevelopmental diseases, may be a candidate gene which absence could be correlated to the patient's phenotype. However, the 8q24.23-q24 duplication could be involved in the phenotype of this patient. Conclusion: In this study, we report for the first time a 7p deletion/8q duplication in a patient with psychomoteur delay, epilepsy and facial dysmorphism. Our study showed that Array CGH still useful for delivering a conclusive genetic diagnosis for patients having neurodevelopmental abnormalities in the era of next-generation sequencing.
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Affiliation(s)
- Rahma Touhami
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia,Department of Cellular and Molecular Biology, Superior Institute of Biotechnology, University of Monastir, Monastir, Tunisia,Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Hajer Foddha
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Eudeline Alix
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Afef Jalloul
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Soumaya Mougou-Zerelli
- Laboratory of Cytogenetics, molecular genetics, and human reproduction biology, CHU Farhat Hached, Sousse, Tunisia
| | - Ali Saad
- Laboratory of Cytogenetics, molecular genetics, and human reproduction biology, CHU Farhat Hached, Sousse, Tunisia
| | - Damien Sanlaville
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Amel Haj Khelil
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia,Department of Cellular and Molecular Biology, Superior Institute of Biotechnology, University of Monastir, Monastir, Tunisia,*Correspondence: Amel Haj Khelil,
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7
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Li S, Yu S, Zhang Y, Wang Y, Jiang X, Wu C. Compound heterozygous loss-of-function variants in BRAT1 cause lethal neonatal rigidity and multifocal seizure syndrome. Mol Genet Genomic Med 2022; 11:e2092. [PMID: 36367347 PMCID: PMC9834191 DOI: 10.1002/mgg3.2092] [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: 05/10/2022] [Revised: 08/30/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Lethal neonatal rigidity and multifocal seizure syndrome (RMFSL, OMIM 614498) is a rare autosomal recessive disease characterized by the onset of rigidity and intractable seizures at or soon after birth. The BRAT1 has been identified to be the disease-causing gene for RMFSL. This study aimed to determine the underlying pathogenic mutations of a Chinese family with RMFSL and to confirm the effect of the splice-site mutation by reverse transcription analysis. METHODS Detailed family history and clinical data were recorded, and peripheral blood samples were collected from all available family members. Whole exome sequencing (WES), Sanger sequencing, and bioinformatics analysis were performed to investigate the causative variants. The impact of the intronic variant on splicing was subsequently analyzed by RT-PCR analysis. RESULTS We identified two compound heterozygous variants in the BRAT1, c.431-2A>G in intron 3 and c.1359_1361del(p.Leu454del) in exon 9 in the proband, one inherited from each parent. Furthermore, the 3'-splice site acceptor (c.431-2A>G) variant was found to activate a cryptic acceptor splice site, which resulted in the loss of 29 nucleotides and generation of a premature stop codon at code 180, producing a truncated BRAT1 (c.432_460del; p.Ala145Argfs*36). CONCLUSIONS This research identified two mutations in the BRAT1 of one Chinese family with RMFSL. These data can aid in developing clinical diagnoses as well as providing genetic counseling and prenatal interventions to the family. These findings also expand our knowledge of the spectrum of BRAT1 pathogenic variants in RMFSL syndrome.
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Affiliation(s)
- Shan Li
- Department of Molecular OrthopaedicsBeijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan HospitalBeijingChina
| | - Shunan Yu
- Department of Molecular OrthopaedicsBeijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan HospitalBeijingChina
| | - Yanzhuo Zhang
- Department of Molecular OrthopaedicsBeijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan HospitalBeijingChina
| | - Ying Wang
- Department of Molecular OrthopaedicsBeijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan HospitalBeijingChina
| | - Xu Jiang
- Department of Orthopaedics, Beijing Jishuitan HospitalThe Fourth Clinical Medical College of Peking UniversityBeijingChina
| | - Chengai Wu
- Department of Molecular OrthopaedicsBeijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan HospitalBeijingChina
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8
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BRAT1 links Integrator and defective RNA processing with neurodegeneration. Nat Commun 2022; 13:5026. [PMID: 36028512 PMCID: PMC9418311 DOI: 10.1038/s41467-022-32763-6] [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: 09/08/2021] [Accepted: 08/15/2022] [Indexed: 11/19/2022] Open
Abstract
Mutations in BRAT1, encoding BRCA1-associated ATM activator 1, have been associated with neurodevelopmental and neurodegenerative disorders characterized by heterogeneous phenotypes with varying levels of clinical severity. However, the underlying molecular mechanisms of disease pathology remain poorly understood. Here, we show that BRAT1 tightly interacts with INTS9/INTS11 subunits of the Integrator complex that processes 3' ends of various noncoding RNAs and pre-mRNAs. We find that Integrator functions are disrupted by BRAT1 deletion. In particular, defects in BRAT1 impede proper 3' end processing of UsnRNAs and snoRNAs, replication-dependent histone pre-mRNA processing, and alter the expression of protein-coding genes. Importantly, impairments in Integrator function are also evident in patient-derived cells from BRAT1 related neurological disease. Collectively, our data suggest that defects in BRAT1 interfere with proper Integrator functions, leading to incorrect expression of RNAs and proteins, resulting in neurodegeneration.
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9
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Qi Y, Ji X, Ding H, Liu L, Zhang Y, Yin A. Novel Biallelic Variant in the BRAT1 Gene Caused Nonprogressive Cerebellar Ataxia Syndrome. Front Genet 2022; 13:821587. [PMID: 35360849 PMCID: PMC8960271 DOI: 10.3389/fgene.2022.821587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/07/2022] [Indexed: 01/13/2023] Open
Abstract
Recessive mutations in BRAT1 cause lethal neonatal rigidity and multifocal seizure syndrome (RMFSL), a phenotype characterized by neonatal microcephaly, hypertonia, and refractory epilepsy with premature death. Recently, attenuated disease variants have been described, suggesting that a wider clinical spectrum of BRAT1-associated neurodegeneration exists than was previously thought. Here, we reported a 10-year-old girl with severe intellectual disability, rigidity, ataxia or dyspraxia, and cerebellar atrophy on brain MRI; two BRAT1 variants in the trans configuration [c.1014A > C (p.Pro338 = ); c.706delC (p.Leu236Cysfs*5)] were detected using whole-exome sequencing. RNA-seq confirmed significantly decreased BRAT1 transcript levels in the presence of the variant; further, it revealed an intron retention between exon 7 and exon 8 caused by the synonymous base substitute. Subsequent prenatal diagnosis for these two variants guided the parents to reproduce. We expand the phenotypic spectrum of BRAT1-associated disorders by first reporting the pathogenic synonymous variant of the BRAT1 gene, resulting in clinical severity that is mild compared to the severe phenotype seen in RMFSL. Making an accurate diagnosis and prognostic evaluation of BRAT1-associated neurodegeneration is important for reproductive consultation and disease management.
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Affiliation(s)
- Yiming Qi
- Prenatal Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, China,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xueqi Ji
- Prenatal Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, China,Clinical Medicine College, Guangzhou Medical University, Guangzhou, China
| | - Hongke Ding
- Prenatal Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, China,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
| | - Ling Liu
- Prenatal Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, China,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yan Zhang
- Prenatal Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, China,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
| | - Aihua Yin
- Prenatal Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, China,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China,Clinical Medicine College, Guangzhou Medical University, Guangzhou, China,*Correspondence: Aihua Yin,
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10
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Novel variant in BRAT1 with the lethal neonatal rigidity and multifocal seizure syndrome. Pediatr Res 2022; 91:565-571. [PMID: 33790413 DOI: 10.1038/s41390-021-01468-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/27/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND Lethal neonatal rigidity and multifocal seizure syndrome (RMFSL) is caused by variants in BRAT1 (BRCA1-associated protein required for ATM activation-1). However, the molecular mechanism of RMFSL is still unclear. METHODS An RMFSL infant was recruited and the peripheral blood samples from his trio-family were collected. The genomic DNA was extracted, and then the whole-exome sequencing was performed. The expression of BRAT1 was analyzed by Western blotting. The subcellular localization of BRAT1 and MitoSOX (mitochondrial superoxide level) was investigated by confocal microscopy. The RNA samples were obtained from transfected cells, and then the RNA sequencing was performed. RESULTS In this study, a novel homozygous BRAT1 variant c.233G > C with amino acid change of R with P at residue 78 (R78P) was identified. This variant altered the peptide structure and subcellular localization, as well as the expression in vitro. However, R78P did not alter the ability of BRAT1 to downregulate MitoSOX in mitochondria. Meanwhile, R78P BRAT1 was positively correlated with temporal lobe epilepsy, autosomal recessive primary microcephaly, defective/absent horizontal voluntary eye movements, and neuron apoptotic process as indicated by gene set enrichment analysis (GSEA). CONCLUSIONS The BRAT1 variant spectrum has been expanded, which will be helpful for genetic counseling. We also explored the molecular mechanism altered by R78P, which will provide a better understanding of the pathogenesis of RMFSL. IMPACT The detailed course of an infant with lethal neonatal RMFSL was depicted. A novel disease-causing variant R78P in BRAT1 for lethal neonatal RMFSL was identified. R78P led to reduced BRAT1 expression and nuclear localization in vitro. R78P did not alter the ability of BRAT1 to downregulate MitoSOX in the mitochondria. The variant R78P in BRAT1 was positively correlated with temporal lobe epilepsy, autosomal recessive primary microcephaly, defective/absent horizontal voluntary eye movements, and neuron apoptotic process as indicated by GSEA.
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11
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Chung EH, Frueh J, Lai A, Scheurer-Monaghan A. Whole Genome Sequencing: Early Diagnostic Tool in Newborns with Refractory Seizures. Neoreviews 2022; 23:e49-e55. [PMID: 34970664 DOI: 10.1542/neo.23-1-e49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Estefani Hee Chung
- Homer Stryker MD School of Medicine, Western Michigan University, Kalamazoo, MI
| | - Julia Frueh
- Homer Stryker MD School of Medicine, Western Michigan University, Kalamazoo, MI
| | - Angela Lai
- Southwest Michigan Neonatology, PC, Kalamazoo.,Bronson Children's Hospital, Kalamazoo, MI
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12
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A review of the clinical spectrum of BRAT1 disorders and case of developmental and epileptic encephalopathy surviving into adulthood. Epilepsy Behav Rep 2022; 19:100549. [PMID: 35620305 PMCID: PMC9126772 DOI: 10.1016/j.ebr.2022.100549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
We report a patient with a BRAT1 disorder who survived into adulthood. Infantile-onset developmental and epileptic encephalopathy rather than an ataxic presentation was the presenting feature. Compound heterozygous BRAT1 variants may be associated with later onset of seizures and longer survival reflecting a spectrum of clinical disease.
Pathogenic variants in BRAT1 are associated with a spectrum of clinical syndromes ranging from Lethal Neonatal Rigidity and Multifocal Seizure syndrome (RMFSL) to Neurodevelopmental Disorder with Cerebellar Atrophy and with or without Seizures (NEDCAS). RMFSL is characterized by early-onset multifocal seizures with microcephaly. Death occurs during infancy although a less severe course with later onset seizures and longer survival into childhood has been described. Here, we summarize published cases of BRAT1 disorders and present the case of a 20-year-old man with two heterozygous BRAT1 variants and a relatively later age of seizure onset with survival into adulthood. This case expands the spectrum of disease associated with BRAT1 variants and highlights the utility of genetic testing to identify the cause of developmental and epileptic encephalopathies where clinical heterogeneity within a spectrum of disease exists.
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13
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Nuovo S, Baglioni V, De Mori R, Tardivo S, Caputi C, Ginevrino M, Micalizzi A, Masuelli L, Federici G, Casella A, Lorefice E, Anello D, Tolve M, Farini D, Bertini E, Zanni G, Travaglini L, Vasco G, Sette C, Carducci C, Valente EM, Leuzzi V. Clinical variability at the mild end of BRAT1-related spectrum: Evidence from two families with genotype-phenotype discordance. Hum Mutat 2021; 43:67-73. [PMID: 34747546 DOI: 10.1002/humu.24293] [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: 12/30/2020] [Revised: 10/12/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022]
Abstract
Biallelic mutations in the BRAT1 gene, encoding BRCA1-associated ATM activator 1, result in variable phenotypes, from rigidity and multifocal seizure syndrome, lethal neonatal to neurodevelopmental disorder, and cerebellar atrophy with or without seizures, without obvious genotype-phenotype associations. We describe two families at the mildest end of the spectrum, differing in clinical presentation despite a common genotype at the BRAT1 locus. Two siblings displayed nonprogressive congenital ataxia and shrunken cerebellum on magnetic resonance imaging. A third unrelated patient showed normal neurodevelopment, adolescence-onset seizures, and ataxia, shrunken cerebellum, and ultrastructural abnormalities on skin biopsy, representing the mildest form of NEDCAS hitherto described. Exome sequencing identified the c.638dup and the novel c.1395G>A BRAT1 variants, the latter causing exon 10 skippings. The p53-MCL test revealed normal ATM kinase activity. Our findings broaden the allelic and clinical spectrum of BRAT1-related disease, which should be suspected in presence of nonprogressive cerebellar signs, even without a neurodevelopmental disorder.
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Affiliation(s)
- Sara Nuovo
- Department of Human Neuroscience, Sapienza University of Rome, Roma, Italy
| | - Valentina Baglioni
- Department of Human Neuroscience, Sapienza University of Rome, Roma, Italy
| | - Roberta De Mori
- Neurogenetics Unit, IRCCS Santa Lucia Foundation, Roma, Italy
| | - Silvia Tardivo
- Neurogenetics Unit, IRCCS Santa Lucia Foundation, Roma, Italy
| | - Caterina Caputi
- Department of Human Neuroscience, Sapienza University of Rome, Roma, Italy
| | - Monia Ginevrino
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Roma, Italy.,Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Roma, Italy
| | - Alessia Micalizzi
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Roma, Italy
| | - Laura Masuelli
- Department of Experimental Medicine, Sapienza University of Rome, Roma, Italy
| | - Giulia Federici
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS - Regina Elena National Cancer Institute, Roma, Italy
| | - Antonella Casella
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Elisa Lorefice
- Department of Molecular Medicine, Sapienza University of Rome, Roma, Italy
| | - Danila Anello
- Department of Medical and Surgery Sciences, Catholic University of the Sacred Heart, Roma, Italy
| | - Manuela Tolve
- Department of Experimental Medicine, Sapienza University of Rome, Roma, Italy
| | - Donatella Farini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Roma, Italy.,Laboratory of Neuroembryology, IRCCS Santa Lucia Foundation, Roma, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Gessica Vasco
- Neuroscience and Neurorehabilitation Department, MARlab, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Claudio Sette
- Laboratory of Neuroembryology, IRCCS Santa Lucia Foundation, Roma, Italy.,Section of Human Anatomy, Department of Neuroscience, Catholic University of the Sacred Heart, Roma, Italy
| | - Carla Carducci
- Department of Experimental Medicine, Sapienza University of Rome, Roma, Italy
| | - Enza M Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Sapienza University of Rome, Roma, Italy
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14
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Colak FK, Guleray N, Azapagasi E, Yazıcı MU, Aksoy E, Ceylan N. An intronic variant in BRAT1 creates a cryptic splice site, causing epileptic encephalopathy without prominent rigidity. Acta Neurol Belg 2020; 120:1425-1432. [PMID: 33040300 PMCID: PMC7547818 DOI: 10.1007/s13760-020-01513-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/28/2020] [Indexed: 12/31/2022]
Abstract
BRAT1-related neurodevelopmental disorders are characterized by heterogeneous phenotypes with varying levels of clinical severity. Since the discovery of BRAT1 variants as the molecular etiology of lethal neonatal rigidity and multifocal seizure syndrome (RMFSL, OMIM 614498), these variants have also been identified in patients with milder clinical forms including neurodevelopmental disorder with cerebellar atrophy and with or without seizures (NEDCAS, OMIM 618056), epilepsy of infancy with migrating focal seizures (EIMFS), and congenital ataxia (CA). This study aims to examine the consequences and pathogenicity of a novel homozygous splice site variant in BRAT1 in a patient presenting with migrating focal seizures since birth without prominent rigidity. The patient was born from a consanguineous marriage and has had seizures since the neonatal period. He presented with dysmorphic features, pontocerebellar hypoplasia, and migrating focal seizures. Despite supportive treatment, his symptoms rapidly progressed to intractable myoclonic seizures, bouts of apnea and bradycardia, and arrest of head growth, with no acquisition of developmental milestones. Clinical exome sequencing yielded a novel homozygous splice variant in BRAT1. Genetic analysis based on reverse transcription of the patient’s RNA followed by PCR amplifications performed on synthesized cDNA and Sanger sequencing was undertaken, and the functional effect of a BRAT1 variant on splicing machinery was demonstrated for the first time. The severe clinical presentation of migrating focal seizures and pontocerebellar hypoplasia in the absence of rigidity further expands the genotypic and phenotypic spectrum of BRAT1-related neurodevelopmental disorders.
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Affiliation(s)
- Fatma Kurt Colak
- Department of Medical Genetics, Dr. Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey.
| | - Naz Guleray
- Department of Medical Genetics, Dr. Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
| | - Ebru Azapagasi
- Division of Pediatric Intensive Care Unit, Dr. Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
| | - Mutlu Uysal Yazıcı
- Division of Pediatric Intensive Care Unit, Dr. Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
| | - Erhan Aksoy
- Department of Pediatric Neurology, Dr. Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
| | - Nesrin Ceylan
- Department of Pediatric Neurology, Dr. Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
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15
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Pourahmadiyan A, Heidari M, Shojaaldini Ardakani H, Noorian S, Savad S. A novel pathogenic variant of BRAT1 gene causes rigidity and multifocal seizure syndrome, lethal neonatal. Int J Neurosci 2020; 131:875-878. [PMID: 32345087 DOI: 10.1080/00207454.2020.1759589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Lethal neonatal rigidity and multifocal seizure syndrome (RMFSL) is a severe autosomal recessive epileptic encephalopathy characterized by microcephaly, rigidity, intractable focal seizures, apnea, and bradycardia at or soon after birth. RMFSL is related to BRCA1-associated ATM activator 1 (BRAT1) gene mutations. METHODS An Iranian couple with history of infant death due to RMFSL was referred to our genetics lab for specialized genetic counseling and testing. Whole Exome Sequencing (WES) was applied. Following WES, Sanger sequencing was performed to confirm the candidate variant. RESULT A novel nonsense variant (c.2041G > T, p. E681X) was identified in exon 14 of the BRAT1 gene. Based on the American College of Medical Genetics and Genomics guideline this variant was classified as a pathogenic variant. CONCLUSION This research expands the spectrum of BRAT1 pathogenic variants in RMFSL syndrome and demonstrates the utility of WES in genetic diagnostic.
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Affiliation(s)
- Azam Pourahmadiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | | | - Shahab Noorian
- Department of Pediatric Endocrinology Metabolism, Bahonar Hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Shahram Savad
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
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Mahjoub A, Cihlarova Z, Tétreault M, MacNeil L, Sondheimer N, Caldecott KW, Hanzlikova H, Yoon G. Homozygous pathogenic variant in BRAT1 associated with nonprogressive cerebellar ataxia. NEUROLOGY-GENETICS 2019; 5:e359. [PMID: 31742228 PMCID: PMC6773431 DOI: 10.1212/nxg.0000000000000359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/29/2019] [Indexed: 11/16/2022]
Abstract
Objective To investigate the pathogenicity of a novel homozygous BRAT1 variant in 2 siblings with nonprogressive cerebellar ataxia (NPCA) through functional studies on primary and immortalized patient cell lines. Methods BRAT1 protein levels and ataxia-telangiectasia mutated (ATM) kinase activity in patient-derived and control cell lines were assessed by Western blotting. The impact of the novel BRAT1 variants on mitochondrial function was also assessed, by comparing patient and control cell lines for rates of oxygen consumption and for phosphorylation (S293) of the E1⍺ subunit of pyruvate dehydrogenase (PDH). Results Two male siblings with NPCA, mild intellectual disability, and isolated cerebellar atrophy were found to be homozygous for a c.185T>A (p.Val62Glu) variant in BRAT1 by whole exome sequencing. Western blotting revealed markedly decreased BRAT1 protein levels in lymphocytes and/or fibroblast cells from both affected siblings compared to control cell lines. There were no differences between the patient and control cells in ATM kinase activation, following ionizing radiation. Mitochondrial studies were initially suggestive of a defect in regulation of PDH activity, but there was no evidence of increased phosphorylation of the E1⍺ subunit of the PDH complex. Measurement of oxygen consumption rates similarly failed to identify differences between patient and control cells. Conclusions Biallelic pathogenic variants in BRAT1 can be associated with NPCA, a phenotype considerably milder than previously reported. Surprisingly, despite the molecular role currently proposed for BRAT1 in ATM regulation, this disorder is unlikely to result from defective ATM kinase or mitochondrial dysfunction.
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Affiliation(s)
- Areej Mahjoub
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Zuzana Cihlarova
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Martine Tétreault
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Lauren MacNeil
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Neal Sondheimer
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Keith W Caldecott
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Hana Hanzlikova
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Grace Yoon
- Division of Neurology (A.M., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Canada; Department of Genome Dynamics (Z.C., K.W.C., H.H.), Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Science (Z.C.), Charles University in Prague, Czech Republic; Department of Neuroscience (M.T.), Université de Montréal, CHUM, Montréal, Québec, Canada; Department of Paediatric Laboratory Medicine (L.M.), Hospital for Sick Children; Department of Lab Medicine and Pathobiology (L.M.), University of Toronto, Ontario, Canada; Program in Genetics and Genome Biology (N.S.), SickKids Research Institute, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics (N.S., G.Y.), Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada; and Genome Damage and Stability Centre (K.W.C., H.H.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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Taylor J, Craft J, Blair E, Wordsworth S, Beeson D, Chandratre S, Cossins J, Lester T, Németh AH, Ormondroyd E, Patel SY, Pagnamenta AT, Taylor JC, Thomson KL, Watkins H, Wilkie AOM, Knight JC. Implementation of a genomic medicine multi-disciplinary team approach for rare disease in the clinical setting: a prospective exome sequencing case series. Genome Med 2019; 11:46. [PMID: 31345272 PMCID: PMC6659244 DOI: 10.1186/s13073-019-0651-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A multi-disciplinary approach to promote engagement, inform decision-making and support clinicians and patients is increasingly advocated to realise the potential of genome-scale sequencing in the clinic for patient benefit. Here we describe the results of establishing a genomic medicine multi-disciplinary team (GM-MDT) for case selection, processing, interpretation and return of results. METHODS We report a consecutive case series of 132 patients (involving 10 medical specialties with 43.2% cases having a neurological disorder) undergoing exome sequencing over a 10-month period following the establishment of the GM-MDT in a UK NHS tertiary referral hospital. The costs of running the MDT are also reported. RESULTS In total 76 cases underwent exome sequencing following triage by the GM-MDT with a clinically reportable molecular diagnosis in 24 (31.6%). GM-MDT composition, operation and rationale for whether to proceed to sequencing are described, together with the health economics (cost per case for the GM-MDT was £399.61), the utility and informativeness of exome sequencing for molecular diagnosis in a range of traits, the impact of choice of sequencing strategy on molecular diagnostic rates and challenge of defining pathogenic variants. In 5 cases (6.6%), an alternative clinical diagnosis was indicated by sequencing results. Examples were also found where findings from initial genetic testing were reconsidered in the light of exome sequencing including TP63 and PRKAG2 (detection of a partial exon deletion and a mosaic missense pathogenic variant respectively); together with tissue-specific mosaicism involving a cytogenetic abnormality following a normal prenatal array comparative genomic hybridization. CONCLUSIONS This consecutive case series describes the results and experience of a multidisciplinary team format that was found to promote engagement across specialties and facilitate return of results to the responsible clinicians.
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Affiliation(s)
- John Taylor
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jude Craft
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Wordsworth
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
| | - David Beeson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Saleel Chandratre
- Children’s Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Judith Cossins
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tracy Lester
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Andrea H. Németh
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Clinical Neurosciences, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
| | - Smita Y. Patel
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Department of Clinical Immunology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alistair T. Pagnamenta
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jenny C. Taylor
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kate L. Thomson
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew O. M. Wilkie
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
| | - Julian C. Knight
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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18
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Uncovering the Pharmacological Mechanism of Chaibei Zhixian Decoction on Epilepsy by Network Pharmacology Analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 2019:3104741. [PMID: 31214268 PMCID: PMC6535852 DOI: 10.1155/2019/3104741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/29/2019] [Accepted: 04/21/2019] [Indexed: 02/07/2023]
Abstract
Objective Epilepsy is a neuronal disorder that is characterized by epileptic seizures and linked with abnormal neural functioning in the brain. Traditional Chinese medicine (TCM) formula Chaibei Zhixian decoction (CZD) has been widely used for epilepsy in China while the pharmacological mechanisms are still unclear. In the present study, systematic and comprehensive network pharmacology was utilized for the first time to reveal the potential pharmacological mechanisms of CZD on epilepsy. Methods Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and analysis platform was utilized for the development of an ingredients-targets database. After identifying epileptic targets of CZD, their interaction with other proteins was estimated based on protein-protein interaction network created from STITCH and gene ontology (GO) enrichment analysis utilizing Cytoscape-ClueGO plugin. Results CZD formula was found to have 643 chemical ingredients, and the potential protein targets of these ingredients were 5230, as retrieved from TCMSP database. Twenty-six protein targets were found to be associated with epilepsy. Thirteen hub genes were regulated by CZD in epilepsy, including estradiol, ESR1, ESR2, SRC, CTNNB1, EP300, MAPK1, MAPK3, SP1, BRCA1, NCOA3, CHRM1, and GSK3B. The results of GO terms analysis showed that 8 GO terms were recovered in the form of 3 clusters, including negative regulation of protein kinase B signaling, positive regulation of interleukin-1 production, and microvillus assembly. Conclusions Network pharmacology approach provides better understanding of the underlying pharmacological mechanisms of CZD on epilepsy. Estradiol, ESR1, ESR2, CTNNB1, EP300, MAPK1, MAPK3, BRCA1, and GSK3B are likely to be important molecules regulated by CZD in treatment of epilepsy. Negative regulation of protein kinase B signaling may play vital roles in the treatment of epilepsy by CZD.
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Abstract
Although the majority of seizures in neonates are related to acute brain injury, a substantial minority are the first symptom of a neonatal-onset epilepsy often linked to a pathogenic genetic variant. Historically, studies on neonatal seizures including treatment response and long-term consequences have lumped all etiologies together. However, etiology has been consistently shown to be the most important determinant of outcome. In the past few years, an increasing number of monogenic disorders have been described and might explain up to a third of neonatal-onset epilepsy syndromes previously included under the umbrella of Ohtahara syndrome and early myoclonic encephalopathy. In this chapter, we define the concept of genetic epilepsy and review the classification. Then, we review the most relevant monogenic neonatal-onset epilepsies, detail their underlying pathophysiologic mechanisms, and present their electroclinical phenotypes. We highlight that, in some cases, such as neonates with KCNQ2 or KCNT1 gene mutations, the early recognition of the electroclinical phenotype can lead to targeted diagnostic testing and precision medicine treatment, enabling the possibility of improved outcome.
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20
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Van Ommeren RH, Gao AF, Blaser SI, Chitayat DA, Hazrati LN. BRAT1Mutation: The First Reported Case of Chinese Origin and Review of the Literature. J Neuropathol Exp Neurol 2018; 77:1071-1078. [DOI: 10.1093/jnen/nly093] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/12/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
| | | | | | - David A Chitayat
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada (DC)
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21
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Celik Y, Okuyaz C, Arslankoylu AE, Ceylaner S. Lethal neonatal rigidity and multifocal seizure syndrome with a new mutation in BRAT1. EPILEPSY & BEHAVIOR CASE REPORTS 2017; 8:31-32. [PMID: 28752061 PMCID: PMC5516089 DOI: 10.1016/j.ebcr.2017.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 05/17/2017] [Accepted: 05/22/2017] [Indexed: 11/08/2022]
Abstract
Rigidity and Multifocal Seizure Syndrome, Lethal Neonatal (RMFSL) (OMIM# 614498) is a rare and recently characterized epileptic encephalopathy that is related to variants in the BRAT1 gene (Breast Cancer 1-associated ataxia telangiectasia mutated activation-1 protein). In this report, an RMFSL case, who died in the 10th month of the life, with rigidity, drug-resistant myoclonic seizures in the face and extremities, with, significant motor delays is presented. The exon sequence was determined and a new homozygous variant (C.2230_2237dupAACATGC) was detected. This RMFSL case with a homozygous variant in the BRAT1 gene, is the fourth one in the literature and the first one being reported from a Turkish family.
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Affiliation(s)
- Yalcin Celik
- Mersin University School of Medicine, Department of Neonatology, 33343 Mersin, Turkey
| | - Cetin Okuyaz
- Mersin University School of Medicine, Department of Pediatric Neurology, 33343 Mersin, Turkey
| | - Ali Ertug Arslankoylu
- Mersin University School of Medicine, Department of Pediatric Intensive Care, 33343 Mersin, Turkey
| | - Serdar Ceylaner
- Intergen Genetic Diagnosis Center, Iran Caddesi, No:13/25, Cankaya, Ankara, Turkey
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Oatts JT, Duncan JL, Hoyt CS, Slavotinek AM, Moore AT. Inner retinal dystrophy in a patient with biallelic sequence variants in BRAT1. Ophthalmic Genet 2017. [DOI: 10.1080/13816810.2017.1290118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Julius T. Oatts
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, USA
| | - Jacque L. Duncan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, USA
| | - Creig S. Hoyt
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, USA
| | - Anne M. Slavotinek
- Department of Pediatrics, Division of Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Anthony T. Moore
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, USA
- UCL Institute of Ophthalmology, University College London, London, UK
- Inherited Eye Disease and Medical Retina Service, Moorfields Eye Hospital, London, UK
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23
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Smith NJ, Lipsett J, Dibbens LM, Heron SE. BRAT1-associated neurodegeneration: Intra-familial phenotypic differences in siblings. Am J Med Genet A 2016; 170:3033-3038. [DOI: 10.1002/ajmg.a.37853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/02/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Nicholas J. Smith
- Department of Neurology; Women's and Children's Health Network; Adelaide South Australia Australia
- School of Medicine; University of Adelaide; South Australia Australia
| | - Jill Lipsett
- Department of Anatomical Pathology; SA Pathology; Adelaide South Australia Australia
| | - Leanne M. Dibbens
- Epilepsy Research Program; School of Pharmacy and Medical Sciences; University of South Australia; Adelaide South Australia Australia
- Sansom Institute for Health Research; University of South Australia; Adelaide South Australia Australia
- Centre for Cancer Biology; University of South Australia; Adelaide South Australia Australia
| | - Sarah E. Heron
- Epilepsy Research Program; School of Pharmacy and Medical Sciences; University of South Australia; Adelaide South Australia Australia
- Sansom Institute for Health Research; University of South Australia; Adelaide South Australia Australia
- Centre for Cancer Biology; University of South Australia; Adelaide South Australia Australia
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Srivastava S, Olson HE, Cohen JS, Gubbels CS, Lincoln S, Davis BT, Shahmirzadi L, Gupta S, Picker J, Yu TW, Miller DT, Soul JS, Poretti A, Naidu S. BRAT1 mutations present with a spectrum of clinical severity. Am J Med Genet A 2016; 170:2265-73. [PMID: 27282546 DOI: 10.1002/ajmg.a.37783] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/23/2016] [Indexed: 01/22/2023]
Abstract
Mutations in BRAT1, encoding BRCA1-associated ATM activator 1, are associated with a severe phenotype known as rigidity and multifocal seizure syndrome, lethal neonatal (RMFSL; OMIM # 614498), characterized by intractable seizures, hypertonia, autonomic instability, and early death. We expand the phenotypic spectrum of BRAT1 related disorders by reporting on four individuals with various BRAT1 mutations resulting in clinical severity that is either mild or moderate compared to the severe phenotype seen in RMFSL. Representing mild severity are three individuals (Patients 1-3), who are girls (including two sisters, Patients 1-2) between 4 and 10 years old, with subtle dysmorphisms, intellectual disability, ataxia or dyspraxia, and cerebellar atrophy on brain MRI; additionally, Patient 3 has well-controlled epilepsy and microcephaly. Representing moderate severity is a 15-month-old boy (Patient 4) with severe global developmental delay, refractory epilepsy, microcephaly, spasticity, hyperkinetic movements, dysautonomia, and chronic lung disease. In contrast to RMFSL, his seizure onset occurred later at 4 months of age, and he is still alive. All four of the individuals have compound heterozygous BRAT1 mutations discovered via whole exome sequencing: c.638dupA (p.Val214Glyfs*189); c.803+1G>C (splice site mutation) in Patients 1-2; c.638dupA (p.Val214Glyfs*189); c.419T>C (p.Leu140Pro) in Patient 3; and c.171delG (p.Glu57Aspfs*7); c.419T>C (p.Leu140Pro) in Patient 4. Only the c.638dupA (p.Val214Glyfs*189) mutation has been previously reported in association with RMFSL. These patients illustrate that, compared with RMFSL, BRAT1 mutations can result in both moderately severe presentations evident by later-onset epilepsy and survival past infancy, as well as milder presentations that include intellectual disability, ataxia/dyspraxia, and cerebellar atrophy. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Siddharth Srivastava
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, Maryland.,Department of Neurology, The Johns Hopkins Hospital, Baltimore, Maryland.,Department of Pediatrics, The Johns Hopkins Hospital, Baltimore, Maryland
| | - Heather E Olson
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Julie S Cohen
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, Maryland
| | - Cynthia S Gubbels
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sharyn Lincoln
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Siddharth Gupta
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, Maryland
| | - Jonathan Picker
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Timothy W Yu
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.,Claritas Genomics, Cambridge, Massachusetts
| | - Janet S Soul
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrea Poretti
- Section of Pediatric Neuroradiology, Division of Pediatric Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins Hospital, Baltimore, Maryland
| | - SakkuBai Naidu
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, Maryland.,Department of Neurology, The Johns Hopkins Hospital, Baltimore, Maryland.,Department of Pediatrics, The Johns Hopkins Hospital, Baltimore, Maryland
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25
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Slavotinek A. Clinical care models in the era of next-generation sequencing. Mol Genet Genomic Med 2016; 4:239-42. [PMID: 27247951 PMCID: PMC4867557 DOI: 10.1002/mgg3.225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Anne Slavotinek
- UCSF Benioff Children's Hospital University of California, San Francisco Room 384D, Rock Hall, 1550 4th St San Francisco California 94143-2711
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