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Han Y, Ge Y, Liu H, Liu L, Xie L, Chen X, Chen Q. A novel compound heterozygous mutation of UFC1 in a patient with neurodevelopmental disorder. Genes Genomics 2024; 46:1037-1043. [PMID: 39078589 DOI: 10.1007/s13258-024-01543-5] [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: 03/27/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) encompass a diverse group of disorders characterized by impaired cognition, behavior, and motor skills. Genetic factor is the leading cause in about 35% of NDDs patients. Mutations of UFC1, an E2 enzyme participating in the post-translational modification of proteins through attachment of ubiquitin-like proteins, were recently reported to be associated with NDDs. However, the UFC1 associated NDDs are rare and the data are scarce, thus making it difficult to identify this disease. OBJECTIVE This study reported a novel compound heterozygous mutation of UFC1 in a Chinese patient with NDD. METHODS Detailed clinical data were recorded. Whole exome sequencing (WES) was performed to determine the genetic cause of the patient. The candidate mutation was verified using Sanger sequencing. RESULTS WES analysis identified a novel compound heterozygous mutation of UFC1 (c.19 C > T, p.Arg7* and c.164G > A, p.Arg55Gln). The nonsense mutation c.19 C > T (p.Arg7*) led to a premature truncation of UFC1 and nonsense-mediated RNA decay. Arg55 is highly conserved among orthologues. Molecular modeling predicted that mutation c.164G > A (p.Arg55Gln) may influence the correct folding of UFC1. These two mutations were evaluated as likely pathogenic based on the ACMG guideline. Moreover, neurodevelopmental delay, microcephaly, and epilepsy were confirmed as major phenotypes of UFC1 mutation. CONCLUSION This study expands the mutational spectrum of NDDs. We reported the nonsense mutation of UFC1 for the first time. We also confirmed the major phenotypes that may guide clinical identification of UFC1 mutation. Ubiquitination mechanism is highlighted in NDDs pathogenesis.
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Affiliation(s)
- Ye Han
- Department of Neurology, The Affiliated Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Yangyang Ge
- Department of Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Haoran Liu
- Department of Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Liying Liu
- Department of Pediatrics, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Lina Xie
- Department of Neurology, The Affiliated Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Xiaoli Chen
- Department of Genetics, Capital Institute of Pediatrics, Beijing, China.
| | - Qian Chen
- Department of Neurology, The Affiliated Hospital of Capital Institute of Pediatrics, Beijing, China.
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2
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Banks E, Francis V, Lin SJ, Kharfallah F, Fonov V, Lévesque M, Han C, Kulasekaran G, Tuznik M, Bayati A, Al-Khater R, Alkuraya FS, Argyriou L, Babaei M, Bahlo M, Bakhshoodeh B, Barr E, Bartik L, Bassiony M, Bertrand M, Braun D, Buchert R, Budetta M, Cadieux-Dion M, Calame DG, Cope H, Cushing D, Efthymiou S, Elmaksoud MA, El Said HG, Froukh T, Gill HK, Gleeson JG, Gogoll L, Goh ESY, Gowda VK, Haack TB, Hashem MO, Hauser S, Hoffman TL, Hogue JS, Hosokawa A, Houlden H, Huang K, Huynh S, Karimiani EG, Kaulfuß S, Korenke GC, Kritzer A, Lee H, Lupski JR, Marco EJ, McWalter K, Minassian A, Minassian BA, Murphy D, Neira-Fresneda J, Northrup H, Nyaga DM, Oehl-Jaschkowitz B, Osmond M, Person R, Pehlivan D, Petree C, Sadleir LG, Saunders C, Schoels L, Shashi V, Spillmann RC, Srinivasan VM, Torbati PN, Tos T, Zaki MS, Zhou D, Zweier C, Trempe JF, Durcan TM, Gan-Or Z, Avoli M, Alves C, Varshney GK, Maroofian R, Rudko DA, McPherson PS. Loss of symmetric cell division of apical neural progenitors drives DENND5A-related developmental and epileptic encephalopathy. Nat Commun 2024; 15:7239. [PMID: 39174524 PMCID: PMC11341845 DOI: 10.1038/s41467-024-51310-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: 08/09/2023] [Accepted: 07/23/2024] [Indexed: 08/24/2024] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) feature altered brain development, developmental delay and seizures, with seizures exacerbating developmental delay. Here we identify a cohort with biallelic variants in DENND5A, encoding a membrane trafficking protein, and develop animal models with phenotypes like the human syndrome. We demonstrate that DENND5A interacts with Pals1/MUPP1, components of the Crumbs apical polarity complex required for symmetrical division of neural progenitor cells. Human induced pluripotent stem cells lacking DENND5A fail to undergo symmetric cell division with an inherent propensity to differentiate into neurons. These phenotypes result from misalignment of the mitotic spindle in apical neural progenitors. Cells lacking DENND5A orient away from the proliferative apical domain surrounding the ventricles, biasing daughter cells towards a more fate-committed state, ultimately shortening the period of neurogenesis. This study provides a mechanism for DENND5A-related DEE that may be generalizable to other developmental conditions and provides variant-specific clinical information for physicians and families.
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Affiliation(s)
- Emily Banks
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Vincent Francis
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Fares Kharfallah
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Vladimir Fonov
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Maxime Lévesque
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Chanshuai Han
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Gopinath Kulasekaran
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Marius Tuznik
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Armin Bayati
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | | | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Loukas Argyriou
- Institute of Human Genetics, University Medical Center, Göttingen, Germany
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Melanie Bahlo
- Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, Australia
| | | | - Eileen Barr
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Lauren Bartik
- University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
- Department of Pediatrics, Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Dominique Braun
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Mauro Budetta
- Paediatric and Child Neurology Unit, Cava de' Tirreni AOU S. Giovanni di Dio e Ruggiero d'Aragona Hospital, Salerno, Italy
| | - Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Daniel G Calame
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Donna Cushing
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON, Canada
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, University College London (UCL) Queen Square Institute of Neurology, London, UK
| | - Marwa Abd Elmaksoud
- Neurology Unit, Department of Pediatrics, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Huda G El Said
- Neurology Unit, Department of Pediatrics, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Harinder K Gill
- Provincial Medical Genetics Program at BC Women's Health Centre, Vancouver, BC, Canada
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Laura Gogoll
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Elaine S-Y Goh
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON, Canada
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Stefan Hauser
- German Center of Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Center for Neurology and Hertie Institute for Clinical Brain Research, University Tübingen, Tübingen, 72076, Germany
| | - Trevor L Hoffman
- Department of Regional Genetics, Southern California Kaiser Permanente Medical Group, Anaheim, CA, USA
| | | | - Akimoto Hosokawa
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London (UCL) Queen Square Institute of Neurology, London, UK
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Stephanie Huynh
- Provincial Medical Genetics Program at BC Women's Health Centre, Vancouver, BC, Canada
| | - Ehsan G Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Silke Kaulfuß
- Institute of Human Genetics, University Medical Center, Göttingen, Germany
| | - G Christoph Korenke
- Department of Neuropediatrics, University Children's Hospital, Klinikum Oldenburg, Oldenburg, Germany
| | - Amy Kritzer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Hane Lee
- 3billion Inc, Seoul, South Korea
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Arakel Minassian
- Centre for Applied Genomics, Genetics, and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Berge A Minassian
- Department of Pediatrics and Neurology, UT Southwestern Medical Center, Dallas, TX, USA
| | - David Murphy
- Department of Clinical and Movement Neurosciences, University College London (UCL) Queen Square Institute of Neurology, London, UK
| | | | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Denis M Nyaga
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | | | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - Davut Pehlivan
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | - Carol Saunders
- University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA
- Center for Pediatric Genomic Medicine Children's Mercy, Kansas City, MO, USA
| | - Ludger Schoels
- German Center of Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Center for Neurology and Hertie Institute for Clinical Brain Research, University Tübingen, Tübingen, 72076, Germany
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - Paria N Torbati
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Tulay Tos
- Department of Medical Genetics, University of Health Sciences, Zubeyde Hanim Research and Training Hospital of Women's Health and Diseases, Ankara, Turkey
| | - Maha S Zaki
- Human Genetics and Genome Research Institute, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Dihong Zhou
- University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
- Department of Pediatrics, Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Thomas M Durcan
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Ziv Gan-Or
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Massimo Avoli
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
| | - Cesar Alves
- Division of Neuroradiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London (UCL) Queen Square Institute of Neurology, London, UK
| | - David A Rudko
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada
- McConnell Brain Imaging Centre, the Neuro, Montréal, QC, Canada
- Department of Biomedical Engineering, McGill University, Montréal, QC, Canada
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, the Neuro, McGill University, Montréal, QC, Canada.
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3
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Zhou C, Zhu J, Tang P, Zhu J, Zhu X, Yang L, Bian W, Zhao W, Liu X. Compound heterozygous variants in SLC45A1 might cause syndromic intellectual disability by localization failure and activity attenuation in cells. Clin Genet 2024. [PMID: 39003656 DOI: 10.1111/cge.14588] [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: 04/04/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/15/2024]
Abstract
Intellectual disability (ID) is a kind of nervous developmental disorder and affects more than 1% of people worldwide. SLC45A1 as a transmembrane protein is implicated in the regulation of glucose homoeostasis. Through trio-based exome sequencing, the missense mutations of SLC45A1 c.103G>A (p.V35M) and c.1211T>G (p.F404C) were identified in the proband with syndromic ID. The distribution, expression and activity of SLC45A1 wild-type (WT) and variants were assayed in transfected COS7 cells. In SLC45A1 variants, the hydrogen bonds surrounding the 35th and 404th amino acid were changed, location on the cytomembrane was failed, their activity to transport glucose was also significantly decreased to contrast with SLC45A1-WT. No difference was observed at the mRNA and protein level. In conclusion, the compound heterozygous variants of SLC45A1 might be the genetic etiology for syndromic ID. These novel mutations probably attenuated its activity to transport glucose by the alteration of tertiary structure and failure of intracellular location.
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Affiliation(s)
- Chiyan Zhou
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Jianjun Zhu
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Ping Tang
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Jingkang Zhu
- Department of Critical Care Medicine, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xinyi Zhu
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Li Yang
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Wei Bian
- Department of Radiology, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Wei Zhao
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Xiaodan Liu
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
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4
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Garber A, Weingarten LS, Abreu NJ, Elloumi HZ, Haack T, Hildebrant C, Martínez-Gil N, Mathews J, Müller AJ, Valenzuela Palafoll I, Steigerwald C, Chung WK. Rare predicted deleterious FEZF2 variants are associated with a neurodevelopmental phenotype. Am J Med Genet A 2024; 194:e63578. [PMID: 38425142 PMCID: PMC11161304 DOI: 10.1002/ajmg.a.63578] [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: 12/13/2023] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
FEZF2 encodes a transcription factor critical to neurodevelopment that regulates other neurodevelopment genes. Rare variants in FEZF2 have previously been suggested to play a role in autism, and cases of 3p14 microdeletions that include FEZF2 share a neurodevelopmental phenotype including mild dysmorphic features and intellectual disability. We identified seven heterozygous predicted deleterious variants in FEZF2 (three frameshifts, one recurrent missense in two independent cases, one nonsense, and one complete gene deletion) in unrelated individuals with neurodevelopmental disorders including developmental delay/intellectual disability, autism, and/or attention-deficit/hyperactivity. Variants were confirmed to be de novo in five of seven cases and paternally inherited from an affected father in one. Predicted deleterious variants in FEZF2 may affect the expression of genes that are involved in fate choice pathways in developing neurons, and thus contribute to the neurodevelopmental phenotype. Future studies are needed to clarify the mechanism by which FEZF2 leads to this neurodevelopmental disorder.
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Affiliation(s)
- Alison Garber
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Lisa S Weingarten
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Nicolas J Abreu
- Department of Neurology, NYU Grossman School of Medicine, New York, New York, USA
| | | | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Clara Hildebrant
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Núria Martínez-Gil
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer Mathews
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Amelie Johanna Müller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Irene Valenzuela Palafoll
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Connolly Steigerwald
- Department of Neurology, NYU Grossman School of Medicine, New York, New York, USA
| | - Wendy K Chung
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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5
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Sandal S, Verma IC, Mahay SB, Dubey S, Sabharwal RK, Kulshrestha S, Saxena R, Suman P, Kumar P, Puri RD. Next-Generation Sequencing in Unexplained Intellectual Disability. Indian J Pediatr 2024; 91:682-695. [PMID: 37804371 DOI: 10.1007/s12098-023-04820-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/23/2023] [Indexed: 10/09/2023]
Abstract
OBJECTIVES To determine the diagnostic yield of next generation sequencing (NGS) in patients with moderate/severe/profound intellectual disability (ID) unexplained by conventional tests and to assess the impact of definitive diagnosis on the clinical management and genetic counselling of these families. METHODS This was a ambi-directional study conducted at Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. The study comprised 227 patients (prospective cohort - 126, retrospective cohort - 101) in whom NGS based tests were performed. RESULTS The mean age of study cohort was 4.5 ± 4.4 y (2.5 mo to 37.3 y). The male: female ratio was 1.6:1. The overall diagnostic yield of NGS was 53.3% (121/227) with causative variants identified in 84 known ID genes. Autosomal recessive intellectual disability (ARID) (23.3%, 53/227) was the most common followed by autosomal dominant intellectual disability (ADID) (20.7%, 47/227) and X-linked intellectual disability (XLID) (9.2%, 21/227). The diagnostic yield was notably higher for ID plus associated condition group (55.6% vs. 20%) (p = 0.0075, Fisher's exact test) compared to isolated ID group. The impact of diagnosis on active or long-term management was observed in 17/121 (14%) and on reproductive outcomes in 26/121 (21.4%) families. CONCLUSIONS There is paucity of data on molecular genetic spectrum of ID from India. The current study identifies extensive genetic heterogeneity and the impact of NGS in patients with ID unexplained by standard genetic tests. The study identified ARID as the most common cause of ID with additional implications for reproductive outcomes. It reiterates the importance of phenotype in genetic testing.
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Affiliation(s)
- Sapna Sandal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sudhisha Dubey
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - R K Sabharwal
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Suman
- Department of Developmental Pediatrics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Kumar
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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6
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Zhang J, Xu Y, Liu Y, Yue L, Jin H, Chen Y, Wang D, Wang M, Chen G, Yang L, Zhang G, Zhang X, Li S, Zhao H, Zhao Y, Niu G, Gao Y, Cai Z, Yang F, Zhu C, Zhu D. Genetic Testing for Global Developmental Delay in Early Childhood. JAMA Netw Open 2024; 7:e2415084. [PMID: 38837156 PMCID: PMC11154162 DOI: 10.1001/jamanetworkopen.2024.15084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/03/2024] [Indexed: 06/06/2024] Open
Abstract
Importance Global developmental delay (GDD) is characterized by a complex etiology, diverse phenotypes, and high individual heterogeneity, presenting challenges for early clinical etiologic diagnosis. Cognitive impairment is the core symptom, and despite the pivotal role of genetic factors in GDD development, the understanding of them remains limited. Objectives To assess the utility of genetic detection in patients with GDD and to examine the potential molecular pathogenesis of GDD to identify targets for early intervention. Design, Setting, and Participants This multicenter, prospective cohort study enrolled patients aged 12 to 60 months with GDD from 6 centers in China from July 4, 2020, to August 31, 2023. Participants underwent trio whole exome sequencing (trio-WES) coupled with copy number variation sequencing (CNV-seq). Bioinformatics analysis was used to unravel pathogenesis and identify therapeutic targets. Main Outcomes and Measures The main outcomes of this study involved enhancing the rate of positive genetic diagnosis for GDD, broadening the scope of genetic testing indications, and investigating the underlying pathogenesis. The classification of children into levels of cognitive impairment was based on the developmental quotient assessed using the Gesell scale. Results The study encompassed 434 patients with GDD (262 [60%] male; mean [SD] age, 25.75 [13.24] months) with diverse degrees of cognitive impairment: mild (98 [23%]), moderate (141 [32%]), severe (122 [28%]), and profound (73 [17%]). The combined use of trio-WES and CNV-seq resulted in a 61% positive detection rate. Craniofacial abnormalities (odds ratio [OR], 2.27; 95% CI, 1.45-3.56), moderate or severe cognitive impairment (OR, 1.69; 95% CI, 1.05-2.70), and age between 12 and 24 months (OR, 1.57; 95% CI, 1.05-2.35) were associated with a higher risk of carrying genetic variants. Additionally, bioinformatics analysis suggested that genetic variants may induce alterations in brain development and function, which may give rise to cognitive impairment. Moreover, an association was found between the dopaminergic pathway and cognitive impairment. Conclusions and Relevance In this cohort study of patients with GDD, combining trio-WES with CNV-seq was a demonstrable, instrumental strategy for advancing the diagnosis of GDD. The close association among genetic variations, brain development, and clinical phenotypes contributed valuable insights into the pathogenesis of GDD. Notably, the dopaminergic pathway emerged as a promising focal point for potential targets in future precision medical interventions for GDD.
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Affiliation(s)
- Jiamei Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yun Liu
- Kunming Children’s Hospital, Kunming, China
| | - Ling Yue
- Department of Neurological Rehabilitation, Children’s Hospital of Hebei Province, Shijiazhuang, China
| | - Hongfang Jin
- Qinghai Provincial Women and Children’s Hospital, Xining, China
| | | | - Dong Wang
- Department of Pediatric Neurology, Xi’an Children’s Hospital, Xi’an, China
| | - Mingmei Wang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gongxun Chen
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Yang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangyu Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Department of Pediatric Neurology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sansong Li
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huiling Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yunxia Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guohui Niu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongqiang Gao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhijun Cai
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Dengna Zhu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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7
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Chen Y, Long J, Wu S, Wei Y, Yan F, Li Q, Yan J, Zhang N, Xu W. Disruption of a DNA G-quadruplex causes a gain-of-function SCL45A1 variant relevant to developmental disorders. Acta Biochim Biophys Sin (Shanghai) 2024; 56:709-716. [PMID: 38655615 PMCID: PMC11177108 DOI: 10.3724/abbs.2024053] [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: 10/08/2023] [Accepted: 01/04/2024] [Indexed: 04/26/2024] Open
Abstract
SLC45A1 encodes a glucose transporter protein highly expressed in the brain. Mutations in SLC45A1 may lead to neurological diseases and developmental disorders, but its exact role is poorly understood. DNA G-quadruplexes (DNA G4s) are stable structures formed by four guanine bases and play a role in gene regulation and genomic stability. Changes in DNA G4s may affect brain development and function. The mechanism linking alterations in DNA G-quadruplex structures to SLC45A1 pathogenicity remains unknown. In this study, we identify a functional DNA G-quadruplex and its key binding site on SLC45A1 (NM_001080397.3: exon 2: c.449 G>A: p.R150K). This variant results in the upregulation of mRNA and protein expression, which may lead to intellectual developmental disorder with neuropsychiatric features. Mechanistically, the mutation is found to disrupt DNA G-quadruplex structures on SLC45A1, leading to transcriptional enhancement and a gain-of-function mutation, which further causes increased expression and function of the SLC45A1 protein. The identification of the functional DNA G-quadruplex and its effects on DNA G4s may provide new insights into the genetic basis of SLC45A1 pathogenicity and highlight the importance of DNA G4s of SLC45A1 in regulating gene expression and brain development.
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Affiliation(s)
- Yuxi Chen
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
- West China School of PharmacySichuan UniversityChengdu610041China
| | - Jiang Long
- The Mental Health Centre and the Psychiatric LaboratoryWest China HospitalSichuan UniversityChengdu610041China
| | - Sixian Wu
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Yazhen Wei
- West China School of PharmacySichuan UniversityChengdu610041China
| | - Fei Yan
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Qing Li
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Jierui Yan
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Nannan Zhang
- National Centre for Birth Defect MonitoringKey Laboratory of Birth Defects and Related Diseases of Women and ChildrenMinistry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
| | - Wenming Xu
- Joint Laboratory of Reproductive MedicineGynaecology and Paediatric Diseases and Birth Defects of Ministry of EducationWest China Second University HospitalSichuan UniversityChengdu610041China
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8
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Borgert L, Becker T, den Brave F. Conserved quality control mechanisms of mitochondrial protein import. J Inherit Metab Dis 2024. [PMID: 38790152 DOI: 10.1002/jimd.12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
Mitochondria carry out essential functions for the cell, including energy production, various biosynthesis pathways, formation of co-factors and cellular signalling in apoptosis and inflammation. The functionality of mitochondria requires the import of about 900-1300 proteins from the cytosol in baker's yeast Saccharomyces cerevisiae and human cells, respectively. The vast majority of these proteins pass the outer membrane in a largely unfolded state through the translocase of the outer mitochondrial membrane (TOM) complex. Subsequently, specific protein translocases sort the precursor proteins into the outer and inner membranes, the intermembrane space and matrix. Premature folding of mitochondrial precursor proteins, defects in the mitochondrial protein translocases or a reduction of the membrane potential across the inner mitochondrial membrane can cause stalling of precursors at the protein import apparatus. Consequently, the translocon is clogged and non-imported precursor proteins accumulate in the cell, which in turn leads to proteotoxic stress and eventually cell death. To prevent such stress situations, quality control mechanisms remove non-imported precursor proteins from the TOM channel. The highly conserved ubiquitin-proteasome system of the cytosol plays a critical role in this process. Thus, the surveillance of protein import via the TOM complex involves the coordinated activity of mitochondria-localized and cytosolic proteins to prevent proteotoxic stress in the cell.
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Affiliation(s)
- Lion Borgert
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Fabian den Brave
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
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9
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Wu R, Li X, Meng Z, Li P, He Z, Liang L. Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing. Orphanet J Rare Dis 2024; 19:205. [PMID: 38764027 PMCID: PMC11103872 DOI: 10.1186/s13023-024-03214-w] [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: 02/20/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Trio-based whole-exome sequencing (trio-WES) enables identification of pathogenic variants, including copy-number variants (CNVs), in children with unexplained neurodevelopmental delay (NDD) and neurodevelopmental comorbidities (NDCs), including autism spectrum disorder (ASD), epilepsy, and attention deficit hyperactivity disorder. Further phenotypic and genetic analysis on trio-WES-tested NDD-NDCs cases may help to identify key phenotypic factors related to higher diagnostic yield of using trio-WES and novel risk genes associated with NDCs in clinical settings. METHODS In this study, we retrospectively performed phenotypic analysis on 163 trio-WES-tested NDD-NDCs children to determine the phenotypic differences between genetically diagnosed and non-genetically diagnosed groups. Additionally, we conducted genetic analysis of ASD genes with the help of Simons Foundation for Autism Research Institute (SFARI) Gene database to identify novel possible ASD-risk genes underlying genetic NDD conditions. RESULTS Among these 163 patients, pathogenic variants were identified in 82 cases (82/163, 50.3%), including 20 cases with CNVs. By comparing phenotypic variables between genetically diagnosed group (82 cases) and non-genetically diagnosed group (81 cases) with multivariate binary logistic regression analysis, we revealed that NDD-NDCs cases presenting with severe-profound NDD [53/82 vs 17/81, adjusted-OR (95%CI): 4.865 (2.213 - 10.694), adjusted-P < 0.001] or having multiple NDCs [26/82 vs 8/81, adjusted-OR (95%CI): 3.731 (1.399 - 9.950), adjusted-P = 0.009] or accompanying ASD [64/82 vs 35/81, adjusted-OR (95%CI): 3.256 (1.479 - 7.168), adjusted-P = 0.003] and head circumference abnormality [33/82 vs 11/81, adjusted-OR (95%CI): 2.788 (1.148 - 6.774), adjusted-P = 0.024] were more likely to have a genetic diagnosis using trio-WES. Moreover, 37 genes with monogenetic variants were identified in 48 patients genetically diagnosed with NDD-ASD, and 15 dosage-sensitive genes were identified in 16 individuals with NDD-ASD carrying CNVs. Most of those genes had been proven to be ASD-related genes. However, some of them (9 genes) were not proven sufficiently to correlate with ASD. By literature review and constructing protein-protein interaction networks among these 9 candidate ASD-risk genes and 102 established ASD genes obtained from the SFARI Gene database, we identified CUL4B, KCNH1, and PLA2G6 as novel possible ASD-risk genes underlying genetic NDD conditions. CONCLUSIONS Trio-WES testing is recommended for patients with unexplained NDD-NDCs that have severe-profound NDD or multiple NDCs, particularly those with accompanying ASD and head circumference abnormality, as these independent factors may increase the likelihood of genetic diagnosis using trio-WES. Moreover, NDD patients with pathogenic variants in CUL4B, KCNH1 and PLA2G6 should be aware of potential risks of developing ASD during their disease courses.
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Affiliation(s)
- Ruohao Wu
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Xiaojuan Li
- Department of Research and Molecular Diagnostics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Zhe Meng
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Pinggan Li
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Zhanwen He
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
| | - Liyang Liang
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
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10
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Panda PK, Mandal S, Gupta D, Elwadhi A, Sharawat IK. Intellectual Developmental Disorder with Speech Delay and Axonal Peripheral Neuropathy (IDDSAPN): A Mixed Phenotype. Ann Indian Acad Neurol 2024; 27:338-340. [PMID: 38819420 PMCID: PMC11232835 DOI: 10.4103/aian.aian_1017_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 04/02/2024] [Accepted: 04/27/2024] [Indexed: 06/01/2024] Open
Affiliation(s)
- Prateek Kumar Panda
- Pediatric Neurology Division, Department of Pediatrics, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
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11
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Donoghue S, Wright J, Voss AK, Lockhart PJ, Amor DJ. The Mendelian disorders of chromatin machinery: Harnessing metabolic pathways and therapies for treatment. Mol Genet Metab 2024; 142:108360. [PMID: 38428378 DOI: 10.1016/j.ymgme.2024.108360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
The Mendelian disorders of chromatin machinery (MDCMs) represent a distinct subgroup of disorders that present with neurodevelopmental disability. The chromatin machinery regulates gene expression by a range of mechanisms, including by post-translational modification of histones, responding to histone marks, and remodelling nucleosomes. Some of the MDCMs that impact on histone modification may have potential therapeutic interventions. Two potential treatment strategies are to enhance the intracellular pool of metabolites that can act as substrates for histone modifiers and the use of medications that may inhibit or promote the modification of histone residues to influence gene expression. In this article we discuss the influence and potential treatments of histone modifications involving histone acetylation and histone methylation. Genomic technologies are facilitating earlier diagnosis of many Mendelian disorders, providing potential opportunities for early treatment from infancy. This has parallels with how inborn errors of metabolism have been afforded early treatment with newborn screening. Before this promise can be fulfilled, we require greater understanding of the biochemical fingerprint of these conditions, which may provide opportunities to supplement metabolites that can act as substrates for chromatin modifying enzymes. Importantly, understanding the metabolomic profile of affected individuals may also provide disorder-specific biomarkers that will be critical for demonstrating efficacy of treatment, as treatment response may not be able to be accurately assessed by clinical measures.
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Affiliation(s)
- Sarah Donoghue
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Biochemical Genetics, Victorian Clinical Genetics Services, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia.
| | - Jordan Wright
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville 3052, Australia
| | - Paul J Lockhart
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
| | - David J Amor
- Murdoch Children's Research Institute, Parkville 3052, Australia; Department of Paediatrics, The University of Melbourne, Parkville 3052, Australia
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12
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Ma H, Zhu L, Yang X, Ao M, Zhang S, Guo M, Dai X, Ma X, Zhang X. Genetic and phenotypic analysis of 225 Chinese children with developmental delay and/or intellectual disability using whole-exome sequencing. BMC Genomics 2024; 25:391. [PMID: 38649797 PMCID: PMC11034079 DOI: 10.1186/s12864-024-10279-1] [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: 10/17/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1-2% of children worldwide, which have diverse genetic causes that should be identified. Genetic studies can elucidate the pathogenesis underlying DD/ID. In this study, whole-exome sequencing (WES) was performed on 225 Chinese DD/ID children (208 cases were sequenced as proband-parent trio) who were classified into seven phenotype subgroups. The phenotype and genomic data of patients with DD/ID were further retrospectively analyzed. There were 96/225 (42.67%; 95% confidence interval [CI] 36.15-49.18%) patients were found to have causative single nucleotide variants (SNVs) and small insertions/deletions (Indels) associated with DD/ID based on WES data. The diagnostic yields among the seven subgroups ranged from 31.25 to 71.43%. Three specific clinical features, hearing loss, visual loss, and facial dysmorphism, can significantly increase the diagnostic yield of WES in patients with DD/ID (P = 0.005, P = 0.005, and P = 0.039, respectively). Of note, hearing loss (odds ratio [OR] = 1.86%; 95% CI = 1.00-3.46, P = 0.046) or abnormal brainstem auditory evoked potential (BAEP) (OR = 1.91, 95% CI = 1.02-3.50, P = 0.042) was independently associated with causative genetic variants in DD/ID children. Our findings enrich the variation spectrums of SNVs/Indels associated with DD/ID, highlight the value genetic testing for DD/ID children, stress the importance of BAEP screen in DD/ID children, and help to facilitate early diagnose, clinical management and reproductive decisions, improve therapeutic response to medical treatment.
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Affiliation(s)
- Heqian Ma
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Lina Zhu
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Xiao Yang
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Meng Ao
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Shunxiang Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Meizhen Guo
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xuelin Dai
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xiuwei Ma
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China.
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China.
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China.
| | - Xiaoying Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- The Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
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13
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Husain RA, Jiao X, Hennings JC, Giesecke J, Palsule G, Beck-Wödl S, Osmanović D, Bjørgo K, Mir A, Ilyas M, Abbasi SM, Efthymiou S, Dominik N, Maroofian R, Houlden H, Rankin J, Pagnamenta AT, Nashabat M, Altwaijri W, Alfadhel M, Umair M, Khouj E, Reardon W, El-Hattab AW, Mekki M, Houge G, Beetz C, Bauer P, Putoux A, Lesca G, Sanlaville D, Alkuraya FS, Taylor RW, Mentzel HJ, Hübner CA, Huppke P, Hart RP, Haack TB, Kiledjian M, Rubio I. Biallelic NUDT2 variants defective in mRNA decapping cause a neurodevelopmental disease. Brain 2024; 147:1197-1205. [PMID: 38141063 PMCID: PMC10994549 DOI: 10.1093/brain/awad434] [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: 07/12/2023] [Revised: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Dysfunctional RNA processing caused by genetic defects in RNA processing enzymes has a profound impact on the nervous system, resulting in neurodevelopmental conditions. We characterized a recessive neurological disorder in 18 children and young adults from 10 independent families typified by intellectual disability, motor developmental delay and gait disturbance. In some patients peripheral neuropathy, corpus callosum abnormalities and progressive basal ganglia deposits were present. The disorder is associated with rare variants in NUDT2, a mRNA decapping and Ap4A hydrolysing enzyme, including novel missense and in-frame deletion variants. We show that these NUDT2 variants lead to a marked loss of enzymatic activity, strongly implicating loss of NUDT2 function as the cause of the disorder. NUDT2-deficient patient fibroblasts exhibit a markedly altered transcriptome, accompanied by changes in mRNA half-life and stability. Amongst the most up-regulated mRNAs in NUDT2-deficient cells, we identified host response and interferon-responsive genes. Importantly, add-back experiments using an Ap4A hydrolase defective in mRNA decapping highlighted loss of NUDT2 decapping as the activity implicated in altered mRNA homeostasis. Our results confirm that reduction or loss of NUDT2 hydrolase activity is associated with a neurological disease, highlighting the importance of a physiologically balanced mRNA processing machinery for neuronal development and homeostasis.
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Affiliation(s)
- Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Xinfu Jiao
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Jan Giesecke
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
| | - Geeta Palsule
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Stefanie Beck-Wödl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Dina Osmanović
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Kathrine Bjørgo
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Asif Mir
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Muhammad Ilyas
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Saad M Abbasi
- Department of Biological Sciences, Faculty of Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Hospital, Exeter, EX1 2ED, UK
| | - Alistair T Pagnamenta
- Oxford NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Marwan Nashabat
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Waleed Altwaijri
- Department of Pediatrics, Neurology Division, King Abdullah Specialist Children’s Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | | | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, 27272, Sharjah, United Arab Emirates
- Department of Pediatrics, University Hospital Sharjah, 72772, Sharjah, United Arab Emirates
| | - Mohammed Mekki
- Department of Pediatrics, University Hospital Sharjah, 72772, Sharjah, United Arab Emirates
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | | | | | - Audrey Putoux
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Équipe GENDEV, Centre de Recherche en Neurosciences de Lyon, Univ Lyon, Univ Lyon 1, INSERM U1028 CNRS UMR5292, 69008 Lyon, France
| | - Gaetan Lesca
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Physiopathologie et Génétique du Neurone et du Muscle, Univ Lyon, Univ Lyon 1, CNRS, INSERM, UMR5261, U1315, Institut NeuroMyoGène, 69008 Lyon, France
| | - Damien Sanlaville
- Groupement Hospitalier Est, Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, 69677 Bron Cedex, France
- Physiopathologie et Génétique du Neurone et du Muscle, Univ Lyon, Univ Lyon 1, CNRS, INSERM, UMR5261, U1315, Institut NeuroMyoGène, 69008 Lyon, France
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Hans-Joachim Mentzel
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
- Section of Pediatric Radiology, Department of Radiology, Jena University Hospital, 07747 Jena, Germany
| | - Christian A Hübner
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Peter Huppke
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Ignacio Rubio
- Department of Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
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14
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Werren EA, LaForce GR, Srivastava A, Perillo DR, Li S, Johnson K, Baris S, Berger B, Regan SL, Pfennig CD, de Munnik S, Pfundt R, Hebbar M, Jimenez-Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles EJ, Louie RJ, Lebel RR, Le TL, Amiel J, Gordon CT, Boztug K, Girisha KM, Shukla A, Bielas SL, Schaffer AE. TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome. Nat Commun 2024; 15:1640. [PMID: 38388531 PMCID: PMC10884030 DOI: 10.1038/s41467-024-45948-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: 10/02/2022] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members, implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together, these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Delia R Perillo
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Shaokun Li
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Katherine Johnson
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Brandon Berger
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christian D Pfennig
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 98195, Seattle, WA, USA
| | - Raúl Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Jasmin Dmytrus
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Ken Corning
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - E J Prijoles
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | | | - Robert Roger Lebel
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
| | - Jeanne Amiel
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, 75015, France
| | | | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, 1090, Austria
- St. Anna Children's Hospital and Children's Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, Vienna, 1090, Austria
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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15
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Chaves TF, Ocampos M, Barbato IT, de Camargo Pinto LL, de Luca GR, Barbato Filho JH, Bernardi P, Costa Netto Muniz Y, Francesca Maris A. A cohort study of neurodevelopmental disorders and/or congenital anomalies using high resolution chromosomal microarrays in southern Brazil highlighting the significance of ASD. Sci Rep 2024; 14:3762. [PMID: 38355898 PMCID: PMC10867078 DOI: 10.1038/s41598-024-54385-2] [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: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 02/16/2024] Open
Abstract
Chromosomal microarray (CMA) is the reference in evaluation of copy number variations (CNVs) in individuals with neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and/or autism spectrum disorder (ASD), which affect around 3-4% of the world's population. Modern platforms for CMA, also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH). These regions result from complete or segmental chromosomal homozygosis and may be indicative of uniparental disomy (UPD), inbreeding, population characteristics, as well as replicative DNA repair events. In this retrospective study, we analyzed CMA reading files requested by geneticists and neurologists for diagnostic purposes along with available clinical data. Our objectives were interpreting CNVs and assess the frequencies and implications of LCSH detected by Affymetrix CytoScan HD (41%) or 750K (59%) platforms in 1012 patients from the south of Brazil. The patients were mainly children with NDDs and/or congenital anomalies (CAs). A total of 206 CNVs, comprising 132 deletions and 74 duplications, interpreted as pathogenic, were found in 17% of the patients in the cohort and across all chromosomes. Additionally, 12% presented rare variants of uncertain clinical significance, including LPCNVs, as the only clinically relevant CNV. Within the realm of NDDs, ASD carries a particular importance, owing to its escalating prevalence and its growing repercussions for individuals, families, and communities. ASD was one clinical phenotype, if not the main reason for referral to testing, for about one-third of the cohort, and these patients were further analyzed as a sub-cohort. Considering only the patients with ASD, the diagnostic rate was 10%, within the range reported in the literature (8-21%). It was higher (16%) when associated with dysmorphic features and lower (7%) for "isolated" ASD (without ID and without dysmorphic features). In 953 CMAs of the whole cohort, LCSH (≥ 3 Mbp) were analyzed not only for their potential pathogenic significance but were also explored to identify common LCSH in the South Brazilians population. CMA revealed at least one LCSH in 91% of the patients. For about 11.5% of patients, the LCSH suggested consanguinity from the first to the fifth degree, with a greater probability of clinical impact, and in 2.8%, they revealed a putative UPD. LCSH found at a frequency of 5% or more were considered common LCSH in the general population, allowing us to delineate 10 regions as potentially representing ancestral haplotypes of neglectable clinical significance. The main referrals for CMA were developmental delay (56%), ID (33%), ASD (33%) and syndromic features (56%). Some phenotypes in this population may be predictive of a higher probability of indicating a carrier of a pathogenic CNV. Here, we present the largest report of CMA data in a cohort with NDDs and/or CAs from the South of Brazil. We characterize the rare CNVs found along with the main phenotypes presented by each patient and show the importance and usefulness of LCSH interpretation in CMA results that incorporate SNPs, as well as we illustrate the value of CMA to investigate CNV in ASD.
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Affiliation(s)
- Tiago Fernando Chaves
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Maristela Ocampos
- Laboratory Neurogene (former), Florianopolis, SC, Brazil
- Mercolab Diagnóstica (actual), Florianopolis, SC, Brazil
| | | | | | | | | | - Priscila Bernardi
- University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
| | - Yara Costa Netto Muniz
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Angelica Francesca Maris
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Children's Hospital Joana de Gusmão, Florianópolis, SC, Brazil.
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16
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Banks E, Francis V, Lin SJ, Kharfallah F, Fonov V, Levesque M, Han C, Kulasekaran G, Tuznik M, Bayati A, Al-Khater R, Alkuraya FS, Argyriou L, Babaei M, Bahlo M, Bakhshoodeh B, Barr E, Bartik L, Bassiony M, Bertrand M, Braun D, Buchert R, Budetta M, Cadieux-Dion M, Calame D, Cope H, Cushing D, Efthymiou S, Elmaksoud MA, El Said HG, Froukh T, Gill HK, Gleeson JG, Gogoll L, Goh ESY, Gowda VK, Haack TB, Hashem MO, Hauser S, Hoffman TL, Hogue JS, Hosokawa A, Houlden H, Huang K, Huynh S, Karimiani EG, Kaulfuß S, Korenke GC, Kritzer A, Lee H, Lupski JR, Marco EJ, McWalter K, Minassian A, Minassian BA, Murphy D, Neira-Fresneda J, Northrup H, Nyaga D, Oehl-Jaschkowitz B, Osmond M, Person R, Pehlivan D, Petree C, Sadleir LG, Saunders C, Schoels L, Shashi V, Spillman RC, Srinivasan VM, Torbati PN, Tos T, Zaki MS, Zhou D, Zweier C, Trempe JF, Durcan TM, Gan-Or Z, Avoli M, Alves C, Varshney GK, Maroofian R, Rudko DA, McPherson PS. Loss of symmetric cell division of apical neural progenitors drives DENND5A-related developmental and epileptic encephalopathy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2022.08.23.22278845. [PMID: 38352438 PMCID: PMC10863025 DOI: 10.1101/2022.08.23.22278845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Developmental and epileptic encephalopathies (DEEs) are a heterogenous group of epilepsies in which altered brain development leads to developmental delay and seizures, with the epileptic activity further negatively impacting neurodevelopment. Identifying the underlying cause of DEEs is essential for progress toward precision therapies. Here we describe a group of individuals with biallelic variants in DENND5A and determine that variant type is correlated with disease severity. We demonstrate that DENND5A interacts with MUPP1 and PALS1, components of the Crumbs apical polarity complex, which is required for both neural progenitor cell identity and the ability of these stem cells to divide symmetrically. Induced pluripotent stem cells lacking DENND5A fail to undergo symmetric cell division during neural induction and have an inherent propensity to differentiate into neurons, and transgenic DENND5A mice, with phenotypes like the human syndrome, have an increased number of neurons in the adult subventricular zone. Disruption of symmetric cell division following loss of DENND5A results from misalignment of the mitotic spindle in apical neural progenitors. A subset of DENND5A is localized to centrosomes, which define the spindle poles during mitosis. Cells lacking DENND5A orient away from the proliferative apical domain surrounding the ventricles, biasing daughter cells towards a more fate-committed state and ultimately shortening the period of neurogenesis. This study provides a mechanism behind DENND5A-related DEE that may be generalizable to other developmental conditions and provides variant-specific clinical information for physicians and families.
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Affiliation(s)
- Emily Banks
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Vincent Francis
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Fares Kharfallah
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Vladimir Fonov
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Maxime Levesque
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Chanshuai Han
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Gopinath Kulasekaran
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Marius Tuznik
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Armin Bayati
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Reem Al-Khater
- Johns Hopkins Aramco Healthcare, Dhahran 34465, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Loukas Argyriou
- Institute of Human Genetics, University Medical Center, Göttingen 37073, Germany
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Melanie Bahlo
- Walter and Eliza Hall Institute for Medical Research, Parkville Victoria 3052, Australia
| | | | - Eileen Barr
- Emory University, Department of Human Genetics, Atlanta, GA 30322, USA
| | - Lauren Bartik
- University of Missouri-Kansas City, School of Medicine, Kansas City, MO 64108, USA
- Department of Pediatrics, Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | | | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
| | - Dominique Braun
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
| | - Mauro Budetta
- Paediatric and Child Neurology Unit, Cava de' Tirreni AOU S. Giovanni di Dio e Ruggiero d'Aragona Hospital, Salerno, Italy
| | - Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Daniel Calame
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Donna Cushing
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON L5B 1B8, Canada
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Marwa A Elmaksoud
- Neurology Unit, Department of Pediatrics, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Huda G El Said
- Department of Family Health, High Institute of Public Health, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman 19392, Jordan
| | - Harinder K Gill
- Provincial Medical Genetics Program at BC Women's Health Centre, Vancouver, BC V6H 3N1, Canada
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Laura Gogoll
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Elaine S-Y Goh
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, ON L5B 1B8, Canada
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Stefan Hauser
- Center for Neurology and Hertie Institute for Clinical Brain Research, University Tübingen, Tübingen 72076, Germany
- German Center of Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Trevor L Hoffman
- Southern California Kaiser Permanente Medical Group, Department of Regional Genetics, Anaheim, CA 92806, USA
| | | | - Akimoto Hosokawa
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Stephanie Huynh
- Provincial Medical Genetics Program at BC Women's Health Centre, Vancouver, BC V6H 3N1, Canada
| | - Ehsan G Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London SW17 0RE, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Silke Kaulfuß
- Institute of Human Genetics, University Medical Center, Göttingen 37073, Germany
| | - G Christoph Korenke
- Department of Neuropediatrics, University Children's Hospital, Klinikum Oldenburg, Oldenburg 26133, Germany
| | - Amy Kritzer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Hane Lee
- 3billion, Inc, Seoul, South Korea
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Arakel Minassian
- Centre for Applied Genomics, Genetics, and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Berge A Minassian
- UT Southwestern Medical Center, Departments of Pediatrics and Neurology, Dallas, TX 75390, USA
| | - David Murphy
- Department of Neuromuscular Diseases, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | | | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Denis Nyaga
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | | | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa K1H 8L1, Canada
| | | | - Davut Pehlivan
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Carol Saunders
- University of Missouri-Kansas City, School of Medicine, Kansas City, MO 64108, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
- Center for Pediatric Genomic Medicine Children's Mercy - Kansas City, Missouri, USA
| | - Ludger Schoels
- Center for Neurology and Hertie Institute for Clinical Brain Research, University Tübingen, Tübingen 72076, Germany
- German Center of Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Rebecca C Spillman
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Paria N Torbati
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Tulay Tos
- University of Health Sciences, Zubeyde Hanim Research and Training Hospital of Women's Health and Diseases, Department of Medical Genetics, Ankara 06080, Turkey
| | - Maha S Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Dihong Zhou
- University of Missouri-Kansas City, School of Medicine, Kansas City, MO 64108, USA
- Department of Pediatrics, Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Thomas M Durcan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Ziv Gan-Or
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 2B4, Canada
| | - Massimo Avoli
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Cesar Alves
- Division of Neuroradiology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Guarav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London (UCL) Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - David A Rudko
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
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17
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Bi B, Chen X, Huang S, Peng M, Gu W, Zhu H, Ming Y. The first case of intellectual disability caused by novel compound heterozygosity for NUDT2 variants. BMC Pediatr 2024; 24:60. [PMID: 38243213 PMCID: PMC10797960 DOI: 10.1186/s12887-024-04542-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024] Open
Abstract
NUDT2 is an enzyme important for maintaining the intracellular level of the diadenosine tetraphosphate (Ap4A). Bi-allelic loss of function variants in NUDT2 has recently been reported as a rare cause of intellectual disability (ID). Herein, we describe a Chinese girl with ID, attention deficit hyperactivity disorder (ADHD), and motor delays with abnormal walking posture and difficulty climbing stairs, who bears compound heterozygous variants c.34 C > T (p.R12*) and c.194T > G (p.I65R) in NUDT2. Homozygous variants c.34 C > T (p.R12*) or c.186del (p.A63Qfs*3) in NUDT2 were previously reported to cause ID. This is the first patient with ID due to compound heterozygous variants in NUDT2 and p.I65R is a novel missense variant. This study enriched the genotype and phenotype of NUDT2-related ID and supported the critical developmental involvement of NUDT2.
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Affiliation(s)
- Bo Bi
- Department of Rehabilitation, Wuhan Children's Hospital, Tongji Medical Colllege, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaohong Chen
- Department of Rehabilitation, Wuhan Children's Hospital, Tongji Medical Colllege, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shan Huang
- Department of Rehabilitation, Wuhan Children's Hospital, Tongji Medical Colllege, Huazhong University of Science and Technology, Wuhan, Hubei, China
- School of Medicine, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Min Peng
- Chigene (Beijing) Translational Medical Research Center Co., Ltd, Beijing, China
| | - Weiyue Gu
- Chigene (Beijing) Translational Medical Research Center Co., Ltd, Beijing, China
| | - Hongmin Zhu
- Department of Rehabilitation, Wuhan Children's Hospital, Tongji Medical Colllege, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Yangcan Ming
- Department of Pediatrics, Traditional Chinese and Western Medicine Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan No. 1 Hospital, Wuhan, Hubei, China.
- College of Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, Hubei, China.
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18
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Alagar Boopathy LR, Beadle E, Garcia-Bueno Rico A, Vera M. Proteostasis regulation through ribosome quality control and no-go-decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1809. [PMID: 37488089 DOI: 10.1002/wrna.1809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/14/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023]
Abstract
Cell functionality relies on the existing pool of proteins and their folding into functional conformations. This is achieved through the regulation of protein synthesis, which requires error-free mRNAs and ribosomes. Ribosomes are quality control hubs for mRNAs and proteins. Problems during translation elongation slow down the decoding rate, leading to ribosome halting and the eventual collision with the next ribosome. Collided ribosomes form a specific disome structure recognized and solved by ribosome quality control (RQC) mechanisms. RQC pathways orchestrate the degradation of the problematic mRNA by no-go decay and the truncated nascent peptide, the repression of translation initiation, and the recycling of the stalled ribosomes. All these events maintain protein homeostasis and return valuable ribosomes to translation. As such, cell homeostasis and function are maintained at the mRNA level by preventing the production of aberrant or unnecessary proteins. It is becoming evident that the crosstalk between RQC and the protein homeostasis network is vital for cell function, as the absence of RQC components leads to the activation of stress response and neurodegenerative diseases. Here, we review the molecular events of RQC discovered through well-designed stalling reporters. Given the impact of RQC in proteostasis, we discuss the relevance of identifying endogenous mRNA regulated by RQC and their preservation in stress conditions. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms Translation > Regulation.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Canada
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19
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Bartolomaeus T, Hentschel J, Jamra RA, Popp B. Re-evaluation and re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 18. Eur J Hum Genet 2023; 31:1154-1164. [PMID: 37460657 PMCID: PMC10545662 DOI: 10.1038/s41431-023-01425-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
Iterative re-analysis of NGS results is not well investigated for published research cohorts of rare diseases. We revisited a cohort of 152 consanguineous families with developmental disorders (NDD) reported five years ago. We re-evaluated all reported variants according to diagnostic classification guidelines or our candidate gene scoring system (AutoCaSc) and systematically scored the validity of gene-disease associations (GDA). Sequencing data was re-processed using an up-to-date pipeline for case-level re-analysis. In 28/152 (18%) families, we identified a clinically relevant change. Ten previously reported (likely) pathogenic variants were re-classified as VUS/benign. In one case, the GDA (TSEN15) validity was judged as limited, and in five cases GDAs are meanwhile established. We identified 12 new disease causing variants. Two previously reported variants were missed by our updated pipeline due to alignment or reference issues. Our results support the need to re-evaluate screening studies, not only the negative cases but including supposedly solved ones. This also applies in a diagnostic setting. We highlight that the complexity of computational re-analysis for old data should be weighed against the decreasing re-testing costs. Since extensive re-analysis per case is beyond the resources of most institutions, we recommend a screening procedure that would quickly identify the majority (83%) of new variants.
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Affiliation(s)
- Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Functional Genomics, Hessische Straße 4A, 10115, Berlin, Germany.
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20
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Mattioli F, Worpenberg L, Li CT, Ibrahim N, Naz S, Sharif S, Firouzabadi SG, Vosoogh S, Saraeva-Lamri R, Raymond L, Trujillo C, Guex N, Antonarakis SE, Ansar M, Darvish H, Liu RJ, Roignant JY, Reymond A. Biallelic variants in NSUN6 cause an autosomal recessive neurodevelopmental disorder. Genet Med 2023; 25:100900. [PMID: 37226891 DOI: 10.1016/j.gim.2023.100900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023] Open
Abstract
PURPOSE 5-methylcytosine RNA modifications are driven by NSUN methyltransferases. Although variants in NSUN2 and NSUN3 were associated with neurodevelopmental diseases, the physiological role of NSUN6 modifications on transfer RNAs and messenger RNAs remained elusive. METHODS We combined exome sequencing of consanguineous families with functional characterization to identify a new neurodevelopmental disorder gene. RESULTS We identified 3 unrelated consanguineous families with deleterious homozygous variants in NSUN6. Two of these variants are predicted to be loss-of-function. One maps to the first exon and is predicted to lead to the absence of NSUN6 via nonsense-mediated decay, whereas we showed that the other maps to the last exon and encodes a protein that does not fold correctly. Likewise, we demonstrated that the missense variant identified in the third family has lost its enzymatic activity and is unable to bind the methyl donor S-adenosyl-L-methionine. The affected individuals present with developmental delay, intellectual disability, motor delay, and behavioral anomalies. Homozygous ablation of the NSUN6 ortholog in Drosophila led to locomotion and learning impairment. CONCLUSION Our data provide evidence that biallelic pathogenic variants in NSUN6 cause one form of autosomal recessive intellectual disability, establishing another link between RNA modification and cognition.
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Affiliation(s)
- Francesca Mattioli
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Lina Worpenberg
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Nazia Ibrahim
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Zoology, Lahore College for Women University, Jail Road Lahore, Pakistan
| | - Shagufta Naz
- Department of Zoology, Lahore College for Women University, Jail Road Lahore, Pakistan
| | - Saima Sharif
- Department of Zoology, Lahore College for Women University, Jail Road Lahore, Pakistan
| | - Saghar G Firouzabadi
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran; Nikagene Genetic Diagnostic Laboratory, Gorgan, Golestan, Iran
| | - Shohreh Vosoogh
- Clinical Research Development Unit (CRDU), Sayad Shirazi Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | - Carlos Trujillo
- Facultad de Medicina, Departmento de Genetica, Universidad CES, Medellin, Colombia; Genome Unit, KFMRC, Jeddah, Saudi Arabia
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, Switzerland; Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Muhammad Ansar
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jean-Yves Roignant
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany.
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
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21
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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22
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Oliveras-Cañellas N, Castells-Nobau A, de la Vega-Correa L, Latorre-Luque J, Motger-Albertí A, Arnoriaga-Rodriguez M, Garre-Olmo J, Zapata-Tona C, Coll-Martínez C, Ramió-Torrentà L, Moreno-Navarrete JM, Puig J, Villarroya F, Ramos R, Casadó-Anguera V, Martín-García E, Maldonado R, Mayneris-Perxachs J, Fernández-Real JM. Adipose tissue coregulates cognitive function. SCIENCE ADVANCES 2023; 9:eadg4017. [PMID: 37566655 PMCID: PMC10421051 DOI: 10.1126/sciadv.adg4017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/10/2023] [Indexed: 08/13/2023]
Abstract
Obesity is associated with cognitive decline. Recent observations in mice propose an adipose tissue (AT)-brain axis. We identified 188 genes from RNA sequencing of AT in three cohorts that were associated with performance in different cognitive domains. These genes were mostly involved in synaptic function, phosphatidylinositol metabolism, the complement cascade, anti-inflammatory signaling, and vitamin metabolism. These findings were translated into the plasma metabolome. The circulating blood expression levels of most of these genes were also associated with several cognitive domains in a cohort of 816 participants. Targeted misexpression of candidate gene ortholog in the Drosophila fat body significantly altered flies memory and learning. Among them, down-regulation of the neurotransmitter release cycle-associated gene SLC18A2 improved cognitive abilities in Drosophila and in mice. Up-regulation of RIMS1 in Drosophila fat body enhanced cognitive abilities. Current results show previously unidentified connections between AT transcriptome and brain function in humans, providing unprecedented diagnostic/therapeutic targets in AT.
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Affiliation(s)
- Núria Oliveras-Cañellas
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Lisset de la Vega-Correa
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Jessica Latorre-Luque
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Anna Motger-Albertí
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Arnoriaga-Rodriguez
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Garre-Olmo
- Department of Nursing (Serra-Hunter Professor), University of Girona, Girona, Spain
| | - Cristina Zapata-Tona
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Clàudia Coll-Martínez
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Lluís Ramió-Torrentà
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
- Girona Neurodegeneration and Neuroinflammation Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - José Maria Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Puig
- Department of Radiology (IDI), Girona Biomedical Research Institute (IdIBGi), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Francesc Villarroya
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biology, University of Barcelona, Barcelona. Spain
| | - Rafel Ramos
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Vascular Health Research Group of Girona (ISV-Girona), Jordi Gol Institute for Primary Care Research (Institut Universitari per a la Recerca en Atenció Primària Jordi Gol I Gorina -IDIAPJGol), Girona, Spain
| | - Verònica Casadó-Anguera
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain
| | - Elena Martín-García
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology-Neurophar, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Catalonia, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
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23
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Bashiri FA, AlSheikh R, Hamad MH, Alsheikh H, Alsheikh RA, Kentab A, AlTheeb N, Alghamdi M. Genotype-Phenotype Analysis of Children with Epilepsy Referred for Whole-Exome Sequencing at a Tertiary Care University Hospital. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1334. [PMID: 37628333 PMCID: PMC10453392 DOI: 10.3390/children10081334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Despite the high consanguinity rates, data on genetic epilepsy in Saudi Arabia is limited. The objective of the current study was to characterize genetic mutations associated with epilepsy in pediatric patients and describe their phenotypic presentations. METHODS A retrospective chart review was conducted among children presented with epilepsy in one center in Saudi Arabia between 2015 and 2018. Only those who had undergone genetic testing were included. RESULTS A total of 45 patients had positive whole-exome sequencing (WES) genetic testing with 37 mutations. Six mutations (SCN1A, DENND5A, KCNQ2, ACY1, SCN2A, and PCDH19) were repeated in 15 patients, with largely heterogeneous phenotypic presentations in patients with the same mutation. Several mutations are reported for the first time in Saudi Arabia. The median age at epilepsy onset was four months. Consanguineous parents and family history of epilepsy were frequent (31.8% and 33.3%, respectively). Developmental delay (44.4%), cognitive delay (42.2%), language delay (40.0%), behavioral features (28.9%), and microcephaly (20.0%) were frequent presentations. At initial diagnosis, 68.9% of EEG and 48.9% of brain MRI were abnormal. The most currently used antiseizure medications (ASMs) were levetiracetam (48.9%), topiramate (28.9%), and valproic acid (20.0%). Approximately 60% of the patients were controlled with (47.6%) or without (11.9%) ASMs, and three (7.1%) patients died. CONCLUSIONS Multiple mutations among children with epilepsy are reported in one hospital in Saudi Arabia, with the majority reported for the first time. The current findings highlight the importance of doing genetic testing for the evaluation of childhood epilepsy.
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Affiliation(s)
- Fahad A. Bashiri
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (A.K.); (M.A.)
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia; (M.H.H.); (H.A.)
| | - Rawan AlSheikh
- Division of Pediatric Neurology, Department of Pediatrics, King Saud Medical City, Riyadh 11461, Saudi Arabia; (R.A.); (R.A.A.)
| | - Muddathir H. Hamad
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia; (M.H.H.); (H.A.)
| | - Hamad Alsheikh
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia; (M.H.H.); (H.A.)
| | - Rana Abdullah Alsheikh
- Division of Pediatric Neurology, Department of Pediatrics, King Saud Medical City, Riyadh 11461, Saudi Arabia; (R.A.); (R.A.A.)
| | - Amal Kentab
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (A.K.); (M.A.)
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia; (M.H.H.); (H.A.)
| | - Najd AlTheeb
- College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Malak Alghamdi
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (A.K.); (M.A.)
- Division of Medical Genetics, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
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24
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Gracia-Diaz C, Zhou Y, Yang Q, Maroofian R, Espana-Bonilla P, Lee CH, Zhang S, Padilla N, Fueyo R, Waxman EA, Lei S, Otrimski G, Li D, Sheppard SE, Mark P, Harr MH, Hakonarson H, Rodan L, Jackson A, Vasudevan P, Powel C, Mohammed S, Maddirevula S, Alzaidan H, Faqeih EA, Efthymiou S, Turchetti V, Rahman F, Maqbool S, Salpietro V, Ibrahim SH, di Rosa G, Houlden H, Alharbi MN, Al-Sannaa NA, Bauer P, Zifarelli G, Estaras C, Hurst ACE, Thompson ML, Chassevent A, Smith-Hicks CL, de la Cruz X, Holtz AM, Elloumi HZ, Hajianpour MJ, Rieubland C, Braun D, Banka S, French DL, Heller EA, Saade M, Song H, Ming GL, Alkuraya FS, Agrawal PB, Reinberg D, Bhoj EJ, Martínez-Balbás MA, Akizu N. Gain and loss of function variants in EZH1 disrupt neurogenesis and cause dominant and recessive neurodevelopmental disorders. Nat Commun 2023; 14:4109. [PMID: 37433783 PMCID: PMC10336078 DOI: 10.1038/s41467-023-39645-5] [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: 07/14/2022] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Genetic variants in chromatin regulators are frequently found in neurodevelopmental disorders, but their effect in disease etiology is rarely determined. Here, we uncover and functionally define pathogenic variants in the chromatin modifier EZH1 as the cause of dominant and recessive neurodevelopmental disorders in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 methyltransferases of the PRC2 complex. Unlike the other PRC2 subunits, which are involved in cancers and developmental syndromes, the implication of EZH1 in human development and disease is largely unknown. Using cellular and biochemical studies, we demonstrate that recessive variants impair EZH1 expression causing loss of function effects, while dominant variants are missense mutations that affect evolutionarily conserved aminoacids, likely impacting EZH1 structure or function. Accordingly, we found increased methyltransferase activity leading to gain of function of two EZH1 missense variants. Furthermore, we show that EZH1 is necessary and sufficient for differentiation of neural progenitor cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell-derived neural cultures and forebrain organoids, we demonstrate that EZH1 variants perturb cortical neuron differentiation. Overall, our work reveals a critical role of EZH1 in neurogenesis regulation and provides molecular diagnosis for previously undefined neurodevelopmental disorders.
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Affiliation(s)
- Carolina Gracia-Diaz
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yijing Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qian Yang
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Paula Espana-Bonilla
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Chul-Hwan Lee
- Department of Biomedical Sciences and Pharmacology, Seoul National University, College of Medicine, Seoul, South Korea
| | - Shuo Zhang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Natàlia Padilla
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Raquel Fueyo
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Elisa A Waxman
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sunyimeng Lei
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Garrett Otrimski
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah E Sheppard
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul Mark
- Department of Pediatrics, Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Margaret H Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lance Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Pradeep Vasudevan
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK
| | - Corrina Powel
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK
| | | | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hamad Alzaidan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Valentina Turchetti
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Fatima Rahman
- Developmental and Behavioral Pediatrics, University of Child Health Sciences & The Children's Hospital, Lahore, Pakistan
| | - Shazia Maqbool
- Developmental and Behavioral Pediatrics, University of Child Health Sciences & The Children's Hospital, Lahore, Pakistan
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Shahnaz H Ibrahim
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Gabriella di Rosa
- Child Neuropsychiatry Unit, Department of Pediatrics, University of Messina, Messina, 98100, Italy
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Maha Nasser Alharbi
- Maternity and Children Hospital Buraidah, Qassim Health Cluster, Buraydah, Saudi Arabia
| | | | | | | | - Conchi Estaras
- Center for Translational Medicine, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA, USA
| | - Anna C E Hurst
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Anna Chassevent
- Department of Neurogenetics, Neurology and Developmental Medicine Kennedy Krieger Institute, Baltimore, MD, USA
| | - Constance L Smith-Hicks
- Department of Neurogenetics, Neurology and Developmental Medicine Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alexander M Holtz
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - M J Hajianpour
- Division of Medical Genetics and Genomics, Department of Pediatrics, Albany Medical College, Albany, NY, USA
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Dominique Braun
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Deborah L French
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Murielle Saade
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Pankaj B Agrawal
- Division of Genetics & Genomics, Boston Children's Hospital, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
- Division of Neonatology, Department of Pediatrics, University of Miami School of Medicine and Holtz Children's Hospital, Jackson Heath System, Miami, FL, USA
| | | | - Elizabeth J Bhoj
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marian A Martínez-Balbás
- Department of Structural and Molecular Biology, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Kim MJ, Kim SY, Lee JS, Kang S, Park LJ, Choi W, Jung JY, Kim T, Park SS, Ko JM, Seong MW, Chae JH. Rapid Targeted Sequencing Using Dried Blood Spot Samples for Patients With Suspected Actionable Genetic Diseases. Ann Lab Med 2023; 43:280-289. [PMID: 36544340 PMCID: PMC9791005 DOI: 10.3343/alm.2023.43.3.280] [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: 03/18/2022] [Revised: 07/09/2022] [Accepted: 11/16/2022] [Indexed: 12/24/2022] Open
Abstract
Background New genome sequencing technologies with enhanced diagnostic efficiency have emerged. Rapid and timely diagnosis of treatable rare genetic diseases can alter their medical management and clinical course. However, multiple factors, including ethical issues, must be considered. We designed a targeted sequencing platform to avoid ethical issues and reduce the turnaround time. Methods We designed an automated sequencing platform using dried blood spot samples and a NEOseq_ACTION panel comprising 254 genes associated with Mendelian diseases having curable or manageable treatment options. Retrospective validation was performed using data from 24 genetically and biochemically confirmed patients. Prospective validation was performed using data from 111 patients with suspected actionable genetic diseases. Results In prospective clinical validation, 13.5% patients presented with medically actionable diseases, including short- or medium-chain acyl-CoA dehydrogenase deficiencies (N=6), hyperphenylalaninemia (N=2), mucopolysaccharidosis type IVA (N=1), alpha thalassemia (N=1), 3-methylcrotonyl-CoA carboxylase 2 deficiency (N=1), propionic acidemia (N=1), glycogen storage disease, type IX(a) (N=1), congenital myasthenic syndrome (N=1), and citrullinemia, type II (N=1). Using the automated analytic pipeline, the turnaround time from blood collection to result reporting was <4 days. Conclusions This pilot study evaluated the possibility of rapid and timely diagnosis of treatable rare genetic diseases using a panel designed by a multidisciplinary team. The automated analytic pipeline maximized the clinical utility of rapid targeted sequencing for medically actionable genes, providing a strategy for appropriate and timely treatment of rare genetic diseases.
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Affiliation(s)
- Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea,Rare Disease Center, Seoul National University Hospital, Seoul, Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea,Rare Disease Center, Seoul National University Hospital, Seoul, Korea
| | - Jin Sook Lee
- Department of Pediatrics, Department of Genome Medicine and Science, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | | | - Lae-Jeong Park
- Department of Electrical Engineering, Gangneung-Wonju National University, Gangneung, Korea
| | | | | | | | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Min Ko
- Rare Disease Center, Seoul National University Hospital, Seoul, Korea,Department of Pediatrics, Department of Genome Medicine and Science, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea,Corresponding author: Moon-Woo Seong, M.D., Ph.D. Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea Tel: +82-2-2072-4180 Fax: +82-2-747-0359 E-mail: ;
| | - Jong Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea,Rare Disease Center, Seoul National University Hospital, Seoul, Korea,Department of Pediatrics, Seoul National University Children’s Hospital, Seoul National University College of Medicine, Seoul, Korea,Co-corresponding author: Jong Hee Chae, M.D., Ph.D. Department of Genomic Medicine, Seoul National University Hospital, Department of Pediatrics, Seoul National University Children’s Hospital, Seoul National University College of Medicine, Rare Disease Center, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea Tel: +82-2-2072-3622 Fax: +82-2-2072-3917 E-mail:
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Rasool IG, Zahoor MY, Ahmed I, Iqbal M, Shafqat S, Anjum AA, Shehzad W. Description of novel variants in consanguineous Pakistani families affected with intellectual disability. Genes Genomics 2023; 45:457-465. [PMID: 35150401 DOI: 10.1007/s13258-022-01219-y] [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: 08/21/2021] [Accepted: 01/16/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Intellectual disability (ID) is a neurodevelopmental condition, affecting 1-3% of the population. Genetic factors play a key role causing the limitation in intellectual functioning and adaptive behavior. The heterogeneity of ID makes it more difficult for genetic and clinical diagnosis. Mapping of variants through next generation DNA sequencing in consanguineous families would help to understand the molecular parthenogenesis of ID. OBJECTIVE The aim of this study was to describe the genetic variants of ID in consanguineous Pakistani families. METHODS We analyzed four unrelated consanguineous Pakistani families having an intellectual disability through whole exome sequencing (WES). Data was analyzed using different bioinformatics tools and software. RESULTS We mapped four novel variants in different ID genes. Each variant is found in different family, co-segregating with a recessive pattern of inheritance. The variants found are; c.1437delG:p.Asn480Thrfs*10, mapped in FKRP, c.2041 C>A:p.Leu681Met in HIRA, c.382 C>T:p.Arg128Cys in BDH1 and c.267+1G>A:p.? identified in TRAPPC6B. CONCLUSIONS These variants help in demonstration of status and molecular basis of intellectual disability in Pakistani population leading to provision of genetic counseling services and a contribution in disease variant database.
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Affiliation(s)
- Iqra Ghulam Rasool
- Molecular Biology and Biotechnology Section, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Yasir Zahoor
- Molecular Biology and Biotechnology Section, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Irfan Ahmed
- Molecular Biology and Biotechnology Section, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Iqbal
- Department of Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Shehla Shafqat
- Department of Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Aftab Ahmad Anjum
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Molecular Biology and Biotechnology Section, Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
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Zare Ashrafi F, Akhtarkhavari T, Fattahi Z, Asadnezhad M, Beheshtian M, Arzhangi S, Najmabadi H, Kahrizi K. Emerging Epidemiological Data on Rare Intellectual Disability Syndromes from Analyzing the Data of a Large Iranian Cohort. ARCHIVES OF IRANIAN MEDICINE 2023; 26:186-197. [PMID: 38301078 PMCID: PMC10685746 DOI: 10.34172/aim.2023.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/25/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Intellectual disability (ID) is a genetically heterogeneous condition, and so far, 1679 human genes have been identified for this phenotype. Countries with a high rate of parental consanguinity, such as Iran, provide an excellent opportunity to identify the remaining novel ID genes, especially those with an autosomal recessive (AR) mode of inheritance. This study aimed to investigate the most prevalent ID genes identified via next-generation sequencing (NGS) in a large ID cohort at the Genetics Research Center (GRC) of the University of Social Welfare and Rehabilitation Sciences. METHODS First, we surveyed the epidemiological data of 619 of 1295 families in our ID cohort, who referred to the Genetics Research Center from all over the country between 2004 and 2021 for genetic investigation via the NGS pipeline. We then compared our data with those of several prominent studies conducted in consanguineous countries. Data analysis, including cohort data extraction, categorization, and comparison, was performed using the R program version 4.1.2. RESULTS We categorized the most common ID genes that were mutated in more than two families into 17 categories. The most common syndromic ID in our cohort was AP4 deficiency syndrome, and the most common non-syndromic autosomal recessive intellectual disability (ARID) gene was ASPM. We identified two unrelated families for the 36 ID genes. We found 14 genes in common between our cohort and the Arab and Pakistani groups, of which three genes (AP4M1, AP4S1, and ADGRG1) were repeated more than once. CONCLUSION To date, there has been no comprehensive targeted NGS platform for the detection of ID genes in our country. Due to the large sample size of our study, our data may provide the initial step toward designing an indigenously targeted NGS platform for the diagnosis of ID, especially common ARID in our population.
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Affiliation(s)
- Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Asadnezhad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Tantry MSA, Santhakumar K. Insights on the Role of α- and β-Tubulin Isotypes in Early Brain Development. Mol Neurobiol 2023; 60:3803-3823. [PMID: 36943622 DOI: 10.1007/s12035-023-03302-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
Tubulins are the highly conserved subunit of microtubules which involve in various fundamental functions including brain development. Microtubules help in neuronal proliferation, migration, differentiation, cargo transport along the axons, synapse formation, and many more. Tubulin gene family consisting of multiple isotypes, their differential expression and varied post translational modifications create a whole new level of complexity and diversity in accomplishing manifold neuronal functions. The studies on the relation between tubulin genes and brain development opened a new avenue to understand the role of each tubulin isotype in neurodevelopment. Mutations in tubulin genes are reported to cause brain development defects especially cortical malformations, referred as tubulinopathies. There is an increased need to understand the molecular correlation between various tubulin mutations and the associated brain pathology. Recently, mutations in tubulin isotypes (TUBA1A, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB3, and TUBG1) have been linked to cause various neurodevelopmental defects like lissencephaly, microcephaly, cortical dysplasia, polymicrogyria, schizencephaly, subcortical band heterotopia, periventricular heterotopia, corpus callosum agenesis, and cerebellar hypoplasia. This review summarizes on the microtubule dynamics, their role in neurodevelopment, tubulin isotypes, post translational modifications, and the role of tubulin mutations in causing specific neurodevelopmental defects. A comprehensive list containing all the reported tubulin pathogenic variants associated with brain developmental defects has been prepared to give a bird's eye view on the broad range of tubulin functions.
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Affiliation(s)
- M S Ananthakrishna Tantry
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603203, India
| | - Kirankumar Santhakumar
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603203, India.
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Stojkovic M, Ortuño Guzmán FM, Han D, Stojkovic P, Dopazo J, Stankovic KM. Polystyrene nanoplastics affect transcriptomic and epigenomic signatures of human fibroblasts and derived induced pluripotent stem cells: Implications for human health. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 320:120849. [PMID: 36509347 DOI: 10.1016/j.envpol.2022.120849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Plastic pollution is increasing at an alarming rate yet the impact of this pollution on human health is poorly understood. Because human induced pluripotent stem cells (hiPSC) are frequently derived from dermal fibroblasts, these cells offer a powerful platform for the identification of molecular biomarkers of environmental pollution in human cells. Here, we describe a novel proof-of-concept for deriving hiPSC from human dermal fibroblasts deliberately exposed to polystyrene (PS) nanoplastic particles; unexposed hiPSC served as controls. In parallel, unexposed hiPSC were exposed to low and high concentrations of PS nanoparticles. Transcriptomic and epigenomic signatures of all fibroblasts and hiPSCs were defined using RNA-seq and whole genome methyl-seq, respectively. Both PS-treated fibroblasts and derived hiPSC showed alterations in expression of ESRRB and HNF1A genes and circuits involved in the pluripotency of stem cells, as well as in pathways involved in cancer, inflammatory disorders, gluconeogenesis, carbohydrate metabolism, innate immunity, and dopaminergic synapse. Similarly, the expression levels of identified key transcriptional and DNA methylation changes (DNMT3A, ESSRB, FAM133CP, HNF1A, SEPTIN7P8, and TTC34) were significantly affected in both PS-exposed fibroblasts and hiPSC. This study illustrates the power of human cellular models of environmental pollution to narrow down and prioritize the list of candidate molecular biomarkers of environmental pollution. This knowledge will facilitate the deciphering of the origins of environmental diseases.
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Affiliation(s)
| | | | - Dongjun Han
- Otolaryngology - Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Joaquin Dopazo
- Bioinformatics Area, Andalusian Public Foundation Progress and Health-FPS, Sevilla, 41013, Spain; Bioinformatics in Rare Diseases (BiER), Centro de Investigaciones Biomédicas en Reden Enfermedades Raras (CIBERER), Seville, Spain; Computational Systems Medicine Group, Institute of Biomedicine of Seville (IBIS), Hospital Virgen Del Rocío, Seville, Spain
| | - Konstantina M Stankovic
- Otolaryngology - Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA, USA.
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Evaluation of Individuals with Non-Syndromic Global Developmental Delay and Intellectual Disability. CHILDREN 2023; 10:children10030414. [PMID: 36979972 PMCID: PMC10047567 DOI: 10.3390/children10030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Global Developmental Delay (GDD) and Intellectual Disability (ID) are two of the most common presentations encountered by physicians taking care of children. GDD/ID is classified into non-syndromic GDD/ID, where GDD/ID is the sole evident clinical feature, or syndromic GDD/ID, where there are additional clinical features or co-morbidities present. Careful evaluation of children with GDD and ID, starting with detailed history followed by a thorough examination, remain the cornerstone for etiologic diagnosis. However, when initial history and examination fail to identify a probable underlying etiology, further genetic testing is warranted. In recent years, genetic testing has been shown to be the single most important diagnostic modality for clinicians evaluating children with non-syndromic GDD/ID. In this review, we discuss different genetic testing currently available, review common underlying copy-number variants and molecular pathways, explore the recent evidence and recommendations for genetic evaluation and discuss an approach to the diagnosis and management of children with non-syndromic GDD and ID.
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Kocaaga A, Yimenicioglu S. Identification of Novel Gene Variants in Children With Drug-Resistant Epilepsy: Expanding the Genetic Spectrum. Pediatr Neurol 2023; 139:7-12. [PMID: 36493596 DOI: 10.1016/j.pediatrneurol.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/09/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Resistance to antiseizure drugs is an important problem in the treatment of individuals with epilepsy. Identifying the molecular etiology of drug-resistant epilepsy (DRE) is crucial for better management of epilepsy. Here, we explore the utility of whole exome sequencing (WES) in identifying causative gene variants in children with DRE. METHODS Forty-five children with DRE who underwent WES tests were included. Genetic examination of all patients included chromosomal analysis and clinical chromosomal microarray followed by WES. The identified variants by WES analysis were classified for pathogenicity based on the American College of Medical Genetics and Genomics guidelines and in silico protein prediction tools. RESULTS The overall diagnostic yield was 55.5% (25 of 45). A total of 26 variants spanning 22 genes were identified in 25 patients. Of note, only 19 of these genes were examined as novel. Ten patients (22.2%) had a pathogenic or likely pathogenic variant. There was a trend associated with a diagnostic genetic test result in girls compared with boys in DRE (P = 0.028). CONCLUSION Our findings expand the mutational spectrum of genes related to DRE. To form disease-specific treatment in children with DRE, the WES analysis should be included in the diagnostic algorithm because of its high diagnostic efficiency.
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Affiliation(s)
- Ayca Kocaaga
- Department of Medical Genetics, Eskisehir City Hospital, Eskişehir, Turkey.
| | - Sevgi Yimenicioglu
- Department of Pediatric Neurology, Eskisehir City Hospital, Eskişehir, Turkey
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Abstract
Macroautophagy and microautophagy are highly conserved eukaryotic cellular processes that degrade cytoplasmic material in lysosomes. Both pathways involve characteristic membrane dynamics regulated by autophagy-related proteins and other molecules, some of which are shared between the two pathways. Over the past few years, the application of new technologies, such as cryo-electron microscopy, coevolution-based structural prediction and in vitro reconstitution, has revealed the functions of individual autophagy gene products, especially in autophagy induction, membrane reorganization and cargo recognition. Concomitantly, mutations in autophagy genes have been linked to human disorders, particularly neurodegenerative diseases, emphasizing the potential pathogenic implications of autophagy defects. Accumulating genome data have also illuminated the evolution of autophagy genes within eukaryotes as well as their transition from possible ancestral elements in prokaryotes.
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Affiliation(s)
- Hayashi Yamamoto
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan ,grid.410821.e0000 0001 2173 8328Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Sidi Zhang
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Streață I, Caramizaru A, Riza AL, Șerban-Sosoi S, Pîrvu A, Cara ML, Cucu MG, Dobrescu AM, Shelby ES, Albeanu A, Burada F, Ioana M. Pathogenic Copy Number Variations Involved in the Genetic Etiology of Syndromic and Non-Syndromic Intellectual Disability-Data from a Romanian Cohort. Diagnostics (Basel) 2022; 12:diagnostics12123137. [PMID: 36553144 PMCID: PMC9777762 DOI: 10.3390/diagnostics12123137] [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: 11/08/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
The investigation of unexplained global developmental delay (GDD)/intellectual disability (ID) is challenging. In low resource settings, patients may not follow a standardized diagnostic process that makes use of the benefits of advanced technologies. Our study aims to explore the contribution of chromosome microarray analysis (CMA) in identifying the genetic etiology of GDD/ID. A total of 371 Romanian patients with syndromic or non-syndromic GDD/ID, without epilepsy, were routinely evaluated in tertiary clinics. A total of 234 males (63.07%) and 137 (36.93%) females, with ages ranging from 6 months to 40 years (median age of 5.5 years), were referred for genetic diagnosis between 2015 and 2022; testing options included CMA and/or karyotyping. Agilent Technologies and Oxford Gene Technology CMA workflows were used. Pathogenic/likely pathogenic copy number variations (pCNVs) were identified in 79 patients (21.29%). Diagnosis yield was comparable between mild ID (17.05%, 22/129) and moderate/severe ID 23.55% (57/242). Higher rates were found in cases where facial dysmorphism (22.97%, 71/309), autism spectrum disorder (ASD) (19.11%, 26/136) and finger anomalies (20%, 27/96) were associated with GDD/ID. GDD/ID plus multiple congenital anomalies (MCA) account for the highest detection rates at 27.42% (17/62). pCNVs represent a significant proportion of the genetic causes of GDD/ID. Our study confirms the utility of CMA in assessing GDD/ID with an uncertain etiology, especially in patients with associated comorbidities.
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Affiliation(s)
- Ioana Streață
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Alexandru Caramizaru
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Anca-Lelia Riza
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Simona Șerban-Sosoi
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Andrei Pîrvu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Monica-Laura Cara
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Department of Public Health, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Mihai-Gabriel Cucu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Amelia Mihaela Dobrescu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Ro-NMCA-ID Group
- The Ro-NMCA-ID (RoNetwork Multiple Congenital Abnormalities with ID) Member of European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA) [EU Framework Partnership Agreement ID: 3HP-HP-FPA ERN-01-2016/739516], 400011 Timisoara, Romania
| | | | | | - Elena-Silvia Shelby
- National University Center for Children’s Neurorehabilitation “Dr. Nicolae Robănescu”, 44 Dumitru Mincă Street, District 4, 041408 Bucharest, Romania
| | - Adriana Albeanu
- Department of Pediatric Neurology, Clinical Emergency Children Hospital Brasov, Nicopole Street No. 45, 500063 Brasov, Romania
| | - Florin Burada
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Mihai Ioana
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
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Syx D, Delbaere S, Bui C, De Clercq A, Larson G, Mizumoto S, Kosho T, Fournel-Gigleux S, Malfait F. Alterations in glycosaminoglycan biosynthesis associated with the Ehlers-Danlos syndromes. Am J Physiol Cell Physiol 2022; 323:C1843-C1859. [PMID: 35993517 DOI: 10.1152/ajpcell.00127.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteoglycans consist of a core protein substituted with one or more glycosaminoglycan (GAG) chains and execute versatile functions during many physiological and pathological processes. The biosynthesis of GAG chains is a complex process that depends on the concerted action of a variety of enzymes. Central to the biosynthesis of heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (CS/DS) GAG chains is the formation of a tetrasaccharide linker region followed by biosynthesis of HS or CS/DS-specific repeating disaccharide units, which then undergo modifications and epimerization. The importance of these biosynthetic enzymes is illustrated by several severe pleiotropic disorders that arise upon their deficiency. The Ehlers-Danlos syndromes (EDS) constitute a special group among these disorders. Although most EDS types are caused by defects in fibrillar types I, III, or V collagen, or their modifying enzymes, a few rare EDS types have recently been linked to defects in GAG biosynthesis. Spondylodysplastic EDS (spEDS) is caused by defective formation of the tetrasaccharide linker region, either due to β4GalT7 or β3GalT6 deficiency, whereas musculocontractural EDS (mcEDS) results from deficiency of D4ST1 or DS-epi1, impairing DS formation. This narrative review highlights the consequences of GAG deficiency in these specific EDS types, summarizes the associated phenotypic features and the molecular spectrum of reported pathogenic variants, and defines the current knowledge on the underlying pathophysiological mechanisms based on studies in patient-derived material, in vitro analyses, and animal models.
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Affiliation(s)
- Delfien Syx
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Sarah Delbaere
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | - Adelbert De Clercq
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Ostend, Belgium
| | - Göran Larson
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Tomoki Kosho
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan.,Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | | | - Fransiska Malfait
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
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Kentab AY. Gamma-Aminobutyric Acid Transaminase (GABA-T) Deficiency in a Consanguineous Saudi Family: A Case Report and Literature Review. JOURNAL OF PEDIATRIC EPILEPSY 2022. [DOI: 10.1055/s-0042-1757447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractGamma-aminobutyric acid transaminase (GABA-T) deficiency is a rare, autosomal recessive disorder caused by mutations in the 4-aminobutyrate aminotransferase (ABAT) gene, which encodes an enzyme involved in GABA catabolism. It is characterized by severe psychomotor retardation, early-onset epileptic encephalopathy, intractable seizures, hypotonia, hyperreflexia, movement disorder, hypersomnolence, and early childhood mortality. It is associated with elevated free GABA in cerebrospinal fluid (CSF), GABA-T deficiency in cultured lymphoblasts, hypomyelination on brain magnetic resonance imaging (MRI), and elevated GABA level in the basal ganglia on proton magnetic resonance spectroscopy (MRS). Only 14 cases have been published in the literature. A rare case of infantile epileptic encephalopathy caused by GABA-T deficiency resulting from a previously unreported homozygous missense mutation in the ABAT gene is described. Our findings add to the phenotypic, neuroradiological, and genetic spectrum of ABAT mutations.
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Affiliation(s)
- Amal Y. Kentab
- Department of Paediatrics, Neurology Division, College of Medicine, King Saud University, King Saud University Medical City, Riyadh, Saudi Arabia
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Dilber C, Yücel G, Şahin Y. Novel homozygous AP3B2 mutations in four individuals with developmental and epileptic encephalopathy: A rare clinical entity. Clin Neurol Neurosurg 2022; 223:107509. [PMID: 36356440 DOI: 10.1016/j.clineuro.2022.107509] [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: 08/18/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Developmental and epileptic encephalopathies (DEEs) are heterogeneous severe neurodevelopmental disorders characterized by recurrent clinical seizures that begin in the neonatal period and early childhood and regression or delay in cognitive, sensory and motor skills in the context of accompanying epileptiform abnormalities. Adaptor-related protein complex 3 beta-2 subunit (AP3B2) gene variants are thought to cause disruption of neuron-specific neurotransmitter release. METHODS In this case report, whole exome sequencing (WES) was performed on two of the four pediatric patients who came from two unrelated families and were affected by DEE. As a result of WES, previously unreported variants, that is, p.Ala149Serfs* 34 and p.Pro993Argfs* 5, were detected in the AP3B2 gene. These variants were studied using Sanger sequencing in the siblings affected by DEE of the said pediatric patients and in their healthy parents. RESULTS Autosomal recessive variants of the AP3B2 are associated with the development of DEE. To date, only 14 cases of AP3B2 mutations have been reported in the literature. Consequentially, DEE phenotype involving severe global developmental delay emerged, which is characterized by early-onset infantile epileptic encephalopathy, severe hypotonia, postnatal microcephaly, poor eye contact, speech retardation, abnormal involuntary movements, stereotypical hand movements, progressive intellectual disability, and behavioral and neuropsychiatric findings. CONCLUSION Given the limited number of patients reported in the literature, detailed studies of the specific clinical and molecular features of AP3B2 gene variants, will shed light on the genotype-phenotype correlation.
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Affiliation(s)
- Cengiz Dilber
- Department of Pediatric Neurology, Sütçü İmam Universty Faculty of Medicine, Kahramanmaraş, Turkey.
| | - Gül Yücel
- Department of Pediatric Neurology, Konya City Hospital, Konya, Turkey.
| | - Yavuz Şahin
- Department of Medical Genetics, Genoks Genetic Diseases Diagnosis Center, Gaziantep, Turkey.
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The diagnostic yield, candidate genes, and pitfalls for a genetic study of intellectual disability in 118 middle eastern families. Sci Rep 2022; 12:18862. [PMID: 36344539 PMCID: PMC9640568 DOI: 10.1038/s41598-022-22036-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
Abstract
Global Developmental Delay/Intellectual disability (ID) is the term used to describe various disorders caused by abnormal brain development and characterized by impairments in cognition, communication, behavior, or motor skills. In the past few years, whole-exome sequencing (WES) has been proven to be a powerful, robust, and scalable approach for candidate gene discoveries in consanguineous populations. In this study, we recruited 215 patients affected with ID from 118 Middle Eastern families. Whole-exome sequencing was completed for 188 individuals. The average age at which WES was completed was 8.5 years. Pathogenic or likely pathogenic variants were detected in 32/118 families (27%). Variants of uncertain significance were seen in 33/118 families (28%). The candidate genes with a possible association with ID were detected in 32/118 (27%) with a total number of 64 affected individuals. These genes are novel, were previously reported in a single family, or cause strikingly different phenotypes with a different mode of inheritance. These genes included: AATK, AP1G2, CAMSAP1, CCDC9B, CNTROB, DNAH14, DNAJB4, DRG1, DTNBP1, EDRF1, EEF1D, EXOC8, EXOSC4, FARSB, FBXO22, FILIP1, INPP4A, P2RX7, PRDM13, PTRHD1, SCN10A, SCYL2, SMG8, SUPV3L1, TACC2, THUMPD1, XPR1, ZFYVE28. During the 5 years of the study and through gene matching databases, several of these genes have now been confirmed as causative of ID. In conclusion, understanding the causes of ID will help understand biological mechanisms, provide precise counseling for affected families, and aid in primary prevention.
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Almannai M, Marafi D, El-Hattab AW. WIPI proteins: Biological functions and related syndromes. Front Mol Neurosci 2022; 15:1011918. [PMID: 36157071 PMCID: PMC9500159 DOI: 10.3389/fnmol.2022.1011918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
WIPI (WD-repeat protein Interacting with PhosphoInositides) are important effectors in autophagy. These proteins bind phosphoinositides and recruit autophagy proteins. In mammals, there are four WIPI proteins: WIPI1, WIPI2, WIPI3 (WDR45B), and WIPI4 (WDR45). These proteins consist of a seven-bladed β-propeller structure. Recently, pathogenic variants in genes encoding these proteins have been recognized to cause human diseases with a predominant neurological phenotype. Defects in WIPI2 cause a disease characterized mainly by intellectual disability and variable other features while pathogenic variants in WDR45B and WDR45 have been recently reported to cause El-Hattab-Alkuraya syndrome and beta-propeller protein-associated neurodegeneration (BPAN), respectively. Whereas, there is no disease linked to WIPI1 yet, one study linked it neural tube defects (NTD). In this review, the role of WIPI proteins in autophagy is discussed first, then syndromes related to these proteins are summarized.
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Affiliation(s)
- Mohammed Almannai
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- *Correspondence: Mohammed Almannai
| | - Dana Marafi
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Ayman W. El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Department of Pediatrics, University Hospital Sharjah, Sharjah, United Arab Emirates
- Genetics and Metabolic Department, KidsHeart Medical Center, Abu Dhabi, United Arab Emirates
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Alhasan KA, Alshuaibi W, Hamad MH, Salim S, Jamjoom DZ, Alhashim AH, AlGhamdi MA, Kentab AY, Bashiri FA. Hypermanganesemia with Dystonia Type 2: A Potentially Treatable Neurodegenerative Disorder: A Case Series in a Tertiary University Hospital. CHILDREN 2022; 9:children9091335. [PMID: 36138644 PMCID: PMC9497897 DOI: 10.3390/children9091335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/25/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022]
Abstract
Importance: Hypermanganesemia with dystonia type 2 is a rare autosomal recessive neurodegenerative disorder characterized by the loss of previously acquired milestones, dystonia, parkinsonian features, a high serum manganese level, and characteristic neuroimaging findings such as bilateral and symmetrically increased T1 and decreased T2/fluid-attenuated inversion recovery signal intensity in the basal ganglia. This condition is secondary to a mutation in the SLC39A14 gene. Objective: To present a series of three cases of hypermanganesemia with dystonia type 2, which was genetically confirmed secondary to a mutation in the SLC39A14 gene, and to describe the treatment and clinical course in these cases. Design: A retrospective case series. Setting: University, Tertiary hospital. Participants: Three unrelated pediatric patients with hypermanganesemia with dystonia type 2, genetically confirmed to be secondary to a mutation in the SLC39A14 gene. Exposures: Chelation therapy using calcium disodium edetate. Main outcome(s) and measure(s): The response to chelation therapy based on clinical improvements in motor and cognition developments. Results: All three patients were started on chelation therapy using calcium disodium edetate, and two of them showed an improvement in their clinical course. The chelation therapy could alter the course of the disease and prevent deterioration in the clinical setting. Conclusions and Relevance: Early diagnosis and intervention with chelating agents, such as calcium disodium edetate, will help change the outcome in patients with hypermanganesemia with dystonia type 2. This finding highlights the importance of early diagnosis and treatment in improving the outcomes of patients with treatable neurodegenerative disorders.
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Affiliation(s)
- Khalid A. Alhasan
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
- Division of Pediatric Nephrology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
| | - Walaa Alshuaibi
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
- Division of Medical Genetics, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
| | - Muddathir H. Hamad
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
| | - Suha Salim
- Division of Pediatric Nephrology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
| | - Dima Z. Jamjoom
- Department of Radiology and Medical Imaging, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Aqeela H. Alhashim
- Pediatric Neurology Department, King Fahad Medical City, Riyadh 11525, Saudi Arabia
| | - Malak Ali AlGhamdi
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
- Division of Medical Genetics, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
| | - Amal Y. Kentab
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
| | - Fahad A. Bashiri
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
- Division of Pediatric Neurology, Department of Pediatrics, King Saud University Medical City, Riyadh 11461, Saudi Arabia
- Correspondence: ; Tel.: +966-118066331
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Zhang J, Lu Y, Tian X, Men X, Zhang Y, Yan H, Yang F, Yang Z, Wang X. A homozygous variant of WDR45B results in global developmental delay: Additional case and literature review. Mol Genet Genomic Med 2022; 10:e2036. [PMID: 35962600 PMCID: PMC9544213 DOI: 10.1002/mgg3.2036] [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: 02/22/2022] [Revised: 07/25/2022] [Accepted: 08/02/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Global developmental delay (GDD) has a heterogeneous clinical profile among patients, accounting for approximately 1%-3% of cases in children. An increasing number of gene defects have been demonstrated to be associated with GDD; up to now, only limited studies have reported developmental disorders driven by WDR45B. METHODS Trio-whole exome sequencing (Trio-WES) was performed for the patient and her family. All variants with a minor allele frequency <0.01 were selected for further interpretation according to the ACMG guidelines. Candidate pathogenic variants were validated by Sanger sequencing in her family. RESULTS A homozygous nonsynonymous variant in WDR45B [NM_019613.4: c.677G>C (p. Arg226Thr)] was identified from the proband. The variant was absent in published databases such as gnomAD and Exome Aggregation Consortium (ExAC). The variant was predicted to be damaging for proteins and classified as VUS according to the ACMG guidelines. We reviewed the literature, and the development delay level in our case was less severe than the other reported cases. CONCLUSION We reported another case with a novel homozygous variant of WDR45B and showed the heterogeneity of clinical features.
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Affiliation(s)
- Jinhong Zhang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yan Lu
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaoyu Tian
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xinyi Men
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yange Zhang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Huifang Yan
- Department of Pediatrics, Hengshui people's Hospital, Hengshui, Hebei, China
| | | | | | - Xiuxia Wang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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Doamekpor SK, Sharma S, Kiledjian M, Tong L. Recent insights into noncanonical 5' capping and decapping of RNA. J Biol Chem 2022; 298:102171. [PMID: 35750211 PMCID: PMC9283932 DOI: 10.1016/j.jbc.2022.102171] [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: 04/26/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022] Open
Abstract
The 5' N7-methylguanosine cap is a critical modification for mRNAs and many other RNAs in eukaryotic cells. Recent studies have uncovered an RNA 5' capping quality surveillance mechanism, with DXO/Rai1 decapping enzymes removing incomplete caps and enabling the degradation of the RNAs, in a process we also refer to as "no-cap decay." It has also been discovered recently that RNAs in eukaryotes, bacteria, and archaea can have noncanonical caps (NCCs), which are mostly derived from metabolites and cofactors such as NAD, FAD, dephospho-CoA, UDP-glucose, UDP-N-acetylglucosamine, and dinucleotide polyphosphates. These NCCs can affect RNA stability, mitochondrial functions, and possibly mRNA translation. The DXO/Rai1 enzymes and selected Nudix (nucleotide diphosphate linked to X) hydrolases have been shown to remove NCCs from RNAs through their deNADding, deFADding, deCoAping, and related activities, permitting the degradation of the RNAs. In this review, we summarize the recent discoveries made in this exciting new area of RNA biology.
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Affiliation(s)
- Selom K. Doamekpor
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Sunny Sharma
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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Al-Jawahiri R, Foroutan A, Kerkhof J, McConkey H, Levy M, Haghshenas S, Rooney K, Turner J, Shears D, Holder M, Lefroy H, Castle B, Reis LM, Semina EV, Lachlan K, Chandler K, Wright T, Clayton-Smith J, Hug FP, Pitteloud N, Bartoloni L, Hoffjan S, Park SM, Thankamony A, Lees M, Wakeling E, Naik S, Hanker B, Girisha KM, Agolini E, Giuseppe Z, Alban Z, Tessarech M, Keren B, Afenjar A, Zweier C, Reis A, Smol T, Tsurusaki Y, Nobuhiko O, Sekiguchi F, Tsuchida N, Matsumoto N, Kou I, Yonezawa Y, Ikegawa S, Callewaert B, Freeth M, Kleinendorst L, Donaldson A, Alders M, De Paepe A, Sadikovic B, McNeill A. SOX11 variants cause a neurodevelopmental disorder with infrequent ocular malformations and hypogonadotropic hypogonadism and with distinct DNA methylation profile. Genet Med 2022; 24:1261-1273. [PMID: 35341651 PMCID: PMC9245088 DOI: 10.1016/j.gim.2022.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/28/2022] Open
Abstract
PURPOSE This study aimed to undertake a multidisciplinary characterization of the phenotype associated with SOX11 variants. METHODS Individuals with protein altering variants in SOX11 were identified through exome and genome sequencing and international data sharing. Deep clinical phenotyping was undertaken by referring clinicians. Blood DNA methylation was assessed using Infinium MethylationEPIC array. The expression pattern of SOX11 in developing human brain was defined using RNAscope. RESULTS We reported 38 new patients with SOX11 variants. Idiopathic hypogonadotropic hypogonadism was confirmed as a feature of SOX11 syndrome. A distinctive pattern of blood DNA methylation was identified in SOX11 syndrome, separating SOX11 syndrome from other BAFopathies. CONCLUSION SOX11 syndrome is a distinct clinical entity with characteristic clinical features and episignature differentiating it from BAFopathies.
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Affiliation(s)
- Reem Al-Jawahiri
- Department of Psychology, The University of Sheffield, Sheffield, United Kingdom
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Michael Levy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Jasmin Turner
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Debbie Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Muriel Holder
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Henrietta Lefroy
- Peninsula Clinical Genetics Service, RD&E Heavitree Hospital, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Bruce Castle
- Peninsula Clinical Genetics Service, RD&E Heavitree Hospital, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Children's Wisconsin, Milwaukee, WI
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Children's Wisconsin, Milwaukee, WI
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Thomas Wright
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Franziska Phan Hug
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Nelly Pitteloud
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Lucia Bartoloni
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Sabine Hoffjan
- Ruhr-Universitat Bochum, Abteilung für Humangenetik, Bochum, Germany
| | - Soo-Mi Park
- Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ajay Thankamony
- Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Melissa Lees
- Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Emma Wakeling
- Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Swati Naik
- West Midlands Regional Clinical Genetics Centre and Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Britta Hanker
- Ambulanzzentrum UKSH, Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Emanuele Agolini
- Medical Genetics Laboratory, Bambino Gesu Children's Hospital, Rome, Italy
| | - Zampino Giuseppe
- Paediatric Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | | | | | - Boris Keren
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Afenjar
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andre Reis
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas Smol
- EA7364 RADEME, Institute of Medical Genetics, Lille University Hospital, Lille University, Lille, France
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Okamoto Nobuhiko
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Ikuyo Kou
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Yoshiro Yonezawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan; Department of Orthopedic Surgery, Keio University School of Medicine, Keio University, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Megan Freeth
- Department of Psychology, The University of Sheffield, Sheffield, United Kingdom
| | - Lotte Kleinendorst
- Centrum voor Medische Genetica - UZ Gent, Ghent University Hospital, Gent, Belgium
| | - Alan Donaldson
- Department of Clinical Genetics Service, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anne De Paepe
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - Alisdair McNeill
- Department of Neuroscience, The Medical School, The University of Sheffield, Sheffield, United Kingdom; Department of Clinical Genetics, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, United Kingdom.
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Višnjar T, Maver A, Writzl K, Maloku O, Bergant G, Jaklič H, Neubauer D, Fogolari F, Pečarič Meglič N, Peterlin B. Biallelic ATOH1 Gene Variant in Siblings With Pontocerebellar Hypoplasia, Developmental Delay, and Hearing Loss. Neurol Genet 2022; 8:e677. [PMID: 35518571 PMCID: PMC9067583 DOI: 10.1212/nxg.0000000000000677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/04/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives To report on the novel association of biallelic variant in atonal basic helix-loop-helix transcription factor 1 (ATOH1) gene and pontocerebellar hypoplasia (PCH), severe global developmental delay, intellectual disability, and hearing loss in a family with 2 affected siblings. Methods A detailed clinical assessment and exome sequencing of peripheral blood sample were performed. Segregation analysis with Sanger sequencing and structural modeling of the variant was performed to support the pathogenicity of the variant. Results A homozygous missense variant (NM_005172.1:c.481C>G) in the ATOH1 gene was identified in the proband and his affected sister. The segregation analysis subsequently confirmed its segregation with an apparently recessive PCH in this family. ATOH1 encodes for the atonal basic helix-loop-helix (bHLH) transcription factor 1, a core transcription factor in the developing cerebellum, brainstem, and dorsal spinal cord, and in the ear. The identified variant results in the p.(Arg161Gly) amino acid substitution in the evolutionarily conserved DNA-binding bHLH domain of the ATOH1 protein. Biallelic missense variants in this domain were previously reported to result in disordered cerebellar development and hearing loss in animal models. In silico homology modeling revealed that p.Arg161Gly in ATOH1 protein probably disrupts a salt bridge with DNA backbone phosphate and increases the flexibility of the bHLH helix-both of which together affect the binding capability of the bHLH domain to the DNA. Discussion Based on the sequencing results and evidence from structural modeling of the identified variant, as well as with previous reports of ATOH1 gene disruption, we conclude that ATOH1 may represent a novel candidate gene associated with the phenotype of PCH, global developmental delay, and hearing loss in humans.
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Affiliation(s)
- Tanja Višnjar
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Aleš Maver
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Karin Writzl
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Ornela Maloku
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Gaber Bergant
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - David Neubauer
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Federico Fogolari
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Nuška Pečarič Meglič
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine (T.V., A.M., K.W., G.B., H.J., B.P.), University Medical Centre Ljubljana, Slovenia; Medical Faculty (K.W., D.N.), University of Ljubljana, Slovenia; Division of Paediatrics (D.N.), Department of Child, Adolescent & Developmental Neurology, University Medical Centre Ljubljana, Slovenia; Clinical Institute of Radiology (N.P.M.), University Medical Centre Ljubljana, Slovenia; and Department of Mathematics (O.M., F.F.), Informatics and Physics, University of Udine, Italy
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Almannai M, Marafi D, Abdel-Salam GMH, Zaki MS, Duan R, Calame D, Herman I, Levesque FSHA, Elbendary HM, Hegazy I, Chung WK, Kavus H, Saeidi K, Maroofian R, AlHashim A, Al-Otaibi A, Madhi AA, Aboalseood HM, Alasmari A, Houlden H, Gleeson JG, Hunter JV, Posey JE, Lupski JR, El-Hattab AW. El-Hattab-Alkuraya syndrome caused by biallelic WDR45B pathogenic variants: further delineation of the phenotype and genotype. Clin Genet 2022; 101:530-540. [PMID: 35322404 PMCID: PMC9359317 DOI: 10.1111/cge.14132] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/30/2022]
Abstract
Homozygous pathogenic variants in WDR45B were first identified in six subjects from three unrelated families with global development delay, refractory seizures, spastic quadriplegia, and brain malformations. Since the initial report in 2018, no further cases have been described. In this report, we present 12 additional individuals from seven unrelated families and their clinical, radiological, and molecular findings. Six different variants in WDR45B were identified, five of which are novel. Microcephaly and global developmental delay were observed in all subjects, and seizures and spastic quadriplegia in most. Common findings on brain imaging include cerebral atrophy, ex-vacuo ventricular dilatation, brainstem volume loss, and symmetric under-opercularization. El-Hattab-Alkuraya syndrome is associated with a consistent phenotype characterized by early onset cerebral atrophy resulting in microcephaly, developmental delay, spastic quadriplegia, and seizures. The phenotype appears to be more severe among individuals with loss-of-function variants whereas those with missense variants were less severely affected suggesting a potential genotype-phenotype correlation in this disorder. A brain imaging pattern emerges which is consistent among individuals with loss-of-function variants and could potentially alert the neuroradiologists or clinician to consider WDR45B-related El-Hattab-Alkuraya syndrome. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mohammed Almannai
- Genetics and Precision Medicine department (GPM), King Abdullah Specialized Children's Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Institute National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute National Research Centre, Cairo, Egypt.,Genetics Department, Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Isabella Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Felix S H A Levesque
- Division of medical genetics and metabolic, Department of Paediatrics, Jim Pattison Children's Hospital, University of Saskatchewan, Saskatoon, Canada
| | - Hasnaa M Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Institute National Research Centre, Cairo, Egypt
| | - Ibrahim Hegazy
- Clinical Genetics Department, Human Genetics and Genome Research Institute National Research Centre, Cairo, Egypt
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Haluk Kavus
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Kolsoum Saeidi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Maroofian
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Aqeela AlHashim
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Al-Otaibi
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Asma Al Madhi
- Department of Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hager M Aboalseood
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Alasmari
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Henry Houlden
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Jill V Hunter
- Texas Children's Hospital, Houston, Texas, USA.,Department of Radiology, Baylor College of Medicine, Houston, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Genetics Clinics, University Hospital Sharjah, Sharjah, United Arab Emirates
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45
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Kouchi Z, Kojima M. Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis. Sci Rep 2022; 12:4325. [PMID: 35279680 PMCID: PMC8918327 DOI: 10.1038/s41598-022-08147-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 03/02/2022] [Indexed: 11/21/2022] Open
Abstract
Recent investigations of neurological developmental disorders have revealed the Rho-family modulators such as Syde and its interactors as the candidate genes. Although the mammalian Syde proteins are reported to possess GTPase-accelerating activity for RhoA-family proteins, diverse species-specific substrate selectivities and binding partners have been described, presumably based on their evolutionary variance in the molecular organization. A comprehensive in silico analysis of Syde family proteins was performed to elucidate their molecular functions and neurodevelopmental networks. Predicted structural modeling of the RhoGAP domain may account for the molecular constraints to substrate specificity among Rho-family proteins. Deducing conserved binding motifs can extend the Syde interaction network and highlight diverse but Syde isoform-specific signaling pathways in neuronal homeostasis, differentiation, and synaptic plasticity from novel aspects of post-translational modification and proteolysis.
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46
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Glassford MR, Purcell RH, Pass S, Murphy MM, Bassell GJ, Mulle JG. Caregiver Perspectives on a Child's Diagnosis of 3q29 Deletion: "We Can't Just Wish This Thing Away". J Dev Behav Pediatr 2022; 43:e94-e102. [PMID: 34320535 PMCID: PMC8792091 DOI: 10.1097/dbp.0000000000000977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/15/2021] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Genetic diagnoses are increasingly common in cases of intellectual disability and developmental delay. Although ascertainment of a relatively common, well-studied variant may provide guidance related to treatments and developmental expectations, it is less clear how the diagnosis of a rare variant affects caregivers, especially when the phenotype may include later-onset manifestations such as psychosis. In this study, we sought to identify caregiver concerns in the first qualitative study to assess the psychosocial impact of diagnosis on caregivers of individuals with 3q29 deletion syndrome (3q29Del), which is associated with a 40-fold increase in risk for psychosis. METHODS Participants were recruited from the national 3q29Del registry housed at Emory University (3q29deletion.org). Fifteen participants completed a semistructured phone interview during which they were asked about their experiences before, during, and after their child received a diagnosis of 3q29Del. Interview responses were analyzed using the general inductive approach, and overarching themes were identified. RESULTS We identified the following overarching themes: difficult "diagnostic odyssey," mixed feelings about diagnosis, frustration with degree of uncertainty, and importance of resources. Importantly, our data suggest that future risk for psychosis is often not disclosed by medical professionals, consistent with the experience of individuals with 22q11.2 deletion syndrome. CONCLUSIONS These results highlight potential gaps in how caregivers are informed of risk for adult-onset conditions and indicate key caregiver concerns for consideration in the diagnosis of 3q29Del.
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Affiliation(s)
- Megan R Glassford
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA; Ms. Glassford is now with the Department of Pediatric Genetics, University of Michigan, Ann Arbor, MI; Ms. Pass is now with the Anderson Cancer Center, University of Texas, Houston, TX
| | - Ryan H Purcell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA
| | - Sarah Pass
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA; Ms. Glassford is now with the Department of Pediatric Genetics, University of Michigan, Ann Arbor, MI; Ms. Pass is now with the Anderson Cancer Center, University of Texas, Houston, TX
| | - Melissa M Murphy
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA; Ms. Glassford is now with the Department of Pediatric Genetics, University of Michigan, Ann Arbor, MI; Ms. Pass is now with the Anderson Cancer Center, University of Texas, Houston, TX
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA; Ms. Glassford is now with the Department of Pediatric Genetics, University of Michigan, Ann Arbor, MI; Ms. Pass is now with the Anderson Cancer Center, University of Texas, Houston, TX
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta GA
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47
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Romero R, de la Fuente L, Del Pozo-Valero M, Riveiro-Álvarez R, Trujillo-Tiebas MJ, Martín-Mérida I, Ávila-Fernández A, Iancu IF, Perea-Romero I, Núñez-Moreno G, Damián A, Rodilla C, Almoguera B, Cortón M, Ayuso C, Mínguez P. An evaluation of pipelines for DNA variant detection can guide a reanalysis protocol to increase the diagnostic ratio of genetic diseases. NPJ Genom Med 2022; 7:7. [PMID: 35087072 PMCID: PMC8795168 DOI: 10.1038/s41525-021-00278-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/09/2021] [Indexed: 01/01/2023] Open
Abstract
Clinical exome (CE) sequencing has become a first-tier diagnostic test for hereditary diseases; however, its diagnostic rate is around 30-50%. In this study, we aimed to increase the diagnostic yield of CE using a custom reanalysis algorithm. Sequencing data were available for three cohorts using two commercial protocols applied as part of the diagnostic process. Using these cohorts, we compared the performance of general and clinically relevant variant calling and the efficacy of an in-house bioinformatic protocol (FJD-pipeline) in detecting causal variants as compared to commercial protocols. On the whole, the FJD-pipeline detected 99.74% of the causal variants identified by the commercial protocol in previously solved cases. In the unsolved cases, FJD-pipeline detects more INDELs and non-exonic variants, and is able to increase the diagnostic yield in 2.5% and 3.2% in the re-analysis of 78 cancer and 62 cardiovascular cases. These results were considered to design a reanalysis, filtering and prioritization algorithm that was tested by reassessing 68 inconclusive cases of monoallelic autosomal recessive retinal dystrophies increasing the diagnosis by 4.4%. In conclusion, a guided NGS reanalysis of unsolved cases increases the diagnostic yield in genetic disorders, making it a useful diagnostic tool in medical genetics.
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Affiliation(s)
- Raquel Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Bioinformatics Unit, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Riveiro-Álvarez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - María José Trujillo-Tiebas
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada Martín-Mérida
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Almudena Ávila-Fernández
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ionut-Florin Iancu
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gonzalo Núñez-Moreno
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Bioinformatics Unit, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Alejandra Damián
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Rodilla
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Berta Almoguera
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Cortón
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
| | - Pablo Mínguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Bioinformatics Unit, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.
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48
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Beshlawy AE, Zekri AER, Ramadan MS, Selim YMM, Abdel-Salam A, Hegazy MT, Ragab L, Gaggiano C, Cantarini L, Ragab G. Genotype-phenotype associations in familial Mediterranean fever: a study of 500 Egyptian pediatric patients. Clin Rheumatol 2022; 41:1511-1521. [PMID: 34988684 DOI: 10.1007/s10067-021-06006-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/03/2022]
Abstract
INTRODUCTION Familial Mediterranean fever (FMF) is the most prevalent monogenic autoinflammatory disease, caused by recessively inherited MEFV gene mutations. The most frequent MEFV mutations differ in penetrance and disease severity. We investigated the genotype-phenotype associations of the three most frequent MEFV gene mutations (M680I, M694V, and V726A) in Egyptian FMF children, regarding clinical features, severity, and colchicine response. METHODS We conducted a retrospective analysis of the medical registries of 500 FMF pediatric patients from Metropolitan Cairo between 2010 and 2015. The diagnosis was based on the Tel-Hashomer clinical diagnostic criteria. Clinical data and baseline investigations were collected. Mutation analysis was performed by the amplification-refractory mutation system (ARMS)-PCR method. RESULTS Males represented 54% and ages ranged from 2 to 18 years. The most frequent symptoms were abdominal pain, fever, and arthralgia. Clinical features mostly associated with M694V mutation either homozygous or heterozygous whether simple, double, or triple. Of the patients, 94.6% completely responded to colchicine. Among patients benefiting from colchicine, 42.5% had M694V/V726A, 21.6% had M694V/V726A/M680I, and 21.1% had M694V genotype. Simple heterozygous M694V or V726A mutations conveyed a moderate phenotype in 57.1% and 50% of cases, respectively. Homozygous M694V mutation showed moderate and severe phenotypes in 21.7% and 65.2% of cases, respectively. Compound M694V/V726A mutation associated with moderate or severe disease in 48.3% and 33.8% of cases, respectively. CONCLUSION This study encompasses the largest group of Egyptian pediatric FMF up to date to explore their genotype-phenotype associations. Our results support the notion that the genotype influences the phenotype as regards clinical manifestations, disease severity, and colchicine response. KEY POINTS • This study encompasses the largest group of Egyptian pediatric patients affected by FMF up to date to explore their genotype-phenotype associations. • Our results support the notion that the genotype influences the phenotype as regards the clinical manifestations, the disease severity, and the response to colchicine treatment.
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Affiliation(s)
- Amal El Beshlawy
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Abd El Rahman Zekri
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Manal S Ramadan
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Yasmeen M M Selim
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Amina Abdel-Salam
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Tharwat Hegazy
- Internal Medicine Department, Rheumatology and Clinical Immunology Unit, Faculty of Medicine, Cairo University, Cairo, Egypt.,Newgiza University (NGU), Giza, Egypt
| | | | - Carla Gaggiano
- Department of Medical Sciences, Surgery, and Neurosciences, Rheumatology Unit, University of Siena, Policlinico "Le Scotte", Siena, Italy
| | - Luca Cantarini
- Department of Medical Sciences, Surgery, and Neurosciences, Rheumatology Unit, University of Siena, Policlinico "Le Scotte", Siena, Italy
| | - Gaafar Ragab
- Internal Medicine Department, Rheumatology and Clinical Immunology Unit, Faculty of Medicine, Cairo University, Cairo, Egypt. .,Newgiza University (NGU), Giza, Egypt.
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Yang M, Johnsson P, Bräutigam L, Yang XR, Thrane K, Gao J, Tobin NP, Zhou Y, Yu R, Nagy N, Engström PG, Tuominen R, Eriksson H, Lundeberg J, Tucker MA, Goldstein AM, Egyhazi-Brage S, Zhao J, Cao Y, Höiom V. Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma. Genet Med 2022; 24:157-169. [PMID: 34906508 PMCID: PMC10617683 DOI: 10.1016/j.gim.2021.09.003] [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: 05/05/2021] [Revised: 08/05/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022] Open
Abstract
PURPOSE More than half of the familial cutaneous melanomas have unknown genetic predisposition. This study aims at characterizing a novel melanoma susceptibility gene. METHODS We performed exome and targeted sequencing in melanoma-prone families without any known melanoma susceptibility genes. We analyzed the expression of candidate gene DENND5A in melanoma samples in relation to pigmentation and UV signature. Functional studies were carried out using microscopic approaches and zebrafish model. RESULTS We identified a novel DENND5A truncating variant that segregated with melanoma in a Swedish family and 2 additional rare DENND5A variants, 1 of which segregated with the disease in an American family. We found that DENND5A is significantly enriched in pigmented melanoma tissue. Our functional studies show that loss of DENND5A function leads to decrease in melanin content in vitro and pigmentation defects in vivo. Mechanistically, harboring the truncating variant or being suppressed leads to DENND5A losing its interaction with SNX1 and its ability to transport the SNX1-associated vesicles from melanosomes. Consequently, untethered SNX1-premelanosome protein and redundant tyrosinase are redirected to lysosomal degradation by default, causing decrease in melanin content. CONCLUSION Our findings provide evidence of a physiological role of DENND5A in the skin context and link its variants to melanoma susceptibility.
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Affiliation(s)
- Muyi Yang
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Per Johnsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - Lars Bräutigam
- Comparative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD
| | - Kim Thrane
- Department of Gene Technology, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jiwei Gao
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas P Tobin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Yitian Zhou
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Rong Yu
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Noemi Nagy
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pär G Engström
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Rainer Tuominen
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Hanna Eriksson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Joakim Lundeberg
- Department of Gene Technology, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD
| | | | - Jian Zhao
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Yihai Cao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Veronica Höiom
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden.
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50
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Mir A, Almudhry M, Alghamdi F, Albaradie R, Ibrahim M, Aldurayhim F, Alhedaithy A, Alamr M, Bawazir M, Mohammad S, Abdelhay S, Bashir S, Housawi Y. SLC gene mutations and pediatric neurological disorders: diverse clinical phenotypes in a Saudi Arabian population. Hum Genet 2021; 141:81-99. [PMID: 34797406 DOI: 10.1007/s00439-021-02404-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022]
Abstract
The uptake and efflux of solutes across a plasma membrane is controlled by transporters. There are two main superfamilies of transporters, adenosine 5'-triphosphate (ATP) binding cassettes (ABCs) and solute carriers (SLCs). In the brain, SLC transporters are involved in transporting various solutes across the blood-brain barrier, blood-cerebrospinal fluid barrier, astrocytes, neurons, and other brain cell types including oligodendrocytes and microglial cells. SLCs play an important role in maintaining normal brain function. Hence, mutations in the genes that encode SLC transporters can cause a variety of neurological disorders. We identified the following SLC gene variants in 25 patients in our cohort: SLC1A2, SLC2A1, SLC5A1, SLC6A3, SLC6A5, SLC6A8, SLC9A6, SLC9A9, SLC12A6, SLC13A5, SLC16A1, SLC17A5, SLC19A3, SLC25A12, SLC25A15, SLC27A4, SLC45A1, SLC46A1, and SLC52A3. Eight patients harbored pathogenic or likely pathogenic mutations (SLC5A1, SLC9A6, SLC12A6, SLC16A1, SLC19A3, and SLC52A3), and 12 patients were found to have variants of unknown clinical significance (VOUS); these variants occurred in 11 genes (SLC1A2, SLC2A1, SLC6A3, SLC6A5, SLC6A8, SLC9A6, SLC9A9, SLC13A5, SLC25A12, SLC27A4, and SLC45A1). Five patients were excluded as they were carriers. In the remaining 20 patients with SLC gene variants, we identified 16 possible distinct neurological disorders. Based on the clinical presentation, we categorized them into genes causing intellectual delay (ID) or autism spectrum disorder (ASD), those causing epilepsy, those causing vitamin-related disorders, and those causing other neurological diseases. Several variants were detected that indicated possible personalized therapies: SLC2A1 led to dystonia or epilepsy, which can be treated with a ketogenic diet; SLC6A3 led to infantile parkinsonism-dystonia 1, which can be treated with levodopa; SLC6A5 led to hyperekplexia 3, for which unnecessary treatment with antiepileptic drugs should be avoided; SLC6A8 led to creatine deficiency syndrome type 1, which can be treated with creatine monohydrate; SLC16A1 led to monocarboxylate transporter 1 deficiency, which causes seizures that should not be treated with a ketogenic diet; SLC19A3 led to biotin-thiamine-responsive basal ganglia disease, which can be treated with biotin and thiamine; and SLC52A3 led to Brown-Vialetto-Van-Laere syndrome 1, which can be treated with riboflavin. The present study examines the prevalence of SLC gene mutations in our cohort of children with epilepsy and other neurological disorders. It highlights the diverse phenotypes associated with mutations in this large family of SLC transporter proteins, and an opportunity for personalized genomics and personalized therapeutics.
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Affiliation(s)
- Ali Mir
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia.
| | - Montaha Almudhry
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Fouad Alghamdi
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Raidah Albaradie
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Mona Ibrahim
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Fatimah Aldurayhim
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Abdullah Alhedaithy
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Mushari Alamr
- Genetic and Metabolic Department, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
| | - Maryam Bawazir
- Genetic and Metabolic Department, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
| | - Sahar Mohammad
- Department of Pediatric, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
| | - Salma Abdelhay
- Department of Pediatric, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
| | - Shahid Bashir
- Department of Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Ammar Bin Thabit Street, Dammam, 31444, Kingdom of Saudi Arabia
| | - Yousef Housawi
- Genetic and Metabolic Department, King Fahad Specialist Hospital, Dammam, Kingdom of Saudi Arabia
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