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Tu Y, Yang Q, Tang M, Gao L, Wang Y, Wang J, Liu Z, Li X, Mao L, Jia RZ, Wang Y, Tang TS, Xu P, Liu Y, Dai L, Jia D. TBC1D23 mediates Golgi-specific LKB1 signaling. Nat Commun 2024; 15:1785. [PMID: 38413626 PMCID: PMC10899256 DOI: 10.1038/s41467-024-46166-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024] Open
Abstract
Liver kinase B1 (LKB1), an evolutionarily conserved serine/threonine kinase, is a master regulator of the AMPK subfamily and controls cellular events such as polarity, proliferation, and energy homeostasis. Functions and mechanisms of the LKB1-AMPK axis at specific subcellular compartments, such as lysosome and mitochondria, have been established. AMPK is known to be activated at the Golgi; however, functions and regulatory mechanisms of the LKB1-AMPK axis at the Golgi apparatus remain elusive. Here, we show that TBC1D23, a Golgi-localized protein that is frequently mutated in the neurodevelopment disorder pontocerebellar hypoplasia (PCH), is specifically required for the LKB1 signaling at the Golgi. TBC1D23 directly interacts with LKB1 and recruits LKB1 to Golgi, promoting Golgi-specific activation of AMPK upon energy stress. Notably, Golgi-targeted expression of LKB1 rescues TBC1D23 deficiency in zebrafish models. Furthermore, the loss of LKB1 causes neurodevelopmental abnormalities in zebrafish, which partially recapitulates defects in TBC1D23-deficient zebrafish, and LKB1 sustains normal neuronal development via TBC1D23 interaction. Our study uncovers a regulatory mechanism of the LKB1 signaling, and reveals that a disrupted Golgi-LKB1 signaling underlies the pathogenesis of PCH.
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Affiliation(s)
- Yingfeng Tu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Qin Yang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Min Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Li Gao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanhao Wang
- State Key Laboratory of Reproductive Medicine, Interdisciplinary InnoCenter for Organoids, Institute for Stem Cell and Neural Regeneration, School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Jiuqiang Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Binzhou Medical University, Yantai, 264003, China
| | - Zhe Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Xiaoyu Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Lejiao Mao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Rui Zhen Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Yuan Wang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pinglong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Yan Liu
- State Key Laboratory of Reproductive Medicine, Interdisciplinary InnoCenter for Organoids, Institute for Stem Cell and Neural Regeneration, School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Lunzhi Dai
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China.
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Matsuki T, Hamada N, Ito H, Sugawara R, Iwamoto I, Nakayama A, Nagata KI. Expression analysis of type I ARF small GTPases ARF1-3 during mouse brain development. Mol Biol Rep 2024; 51:106. [PMID: 38227057 DOI: 10.1007/s11033-023-09142-5] [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: 07/12/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND ARF (ADP-ribosylation factor) GTPases are major regulators of intracellular trafficking, and classified into 3 groups (Type I - III), among which the type I group members, ARF1 and 3, are responsible genes for neurodevelopmental disorders. METHODS In this study, we analysed the expression of Type I ARFs ARF1-3 during mouse brain development using biochemical and morphological methods. RESULTS Western blotting analyses revealed that ARF1-3 are weakly expressed in the mouse brain at embryonic day 13 and gradually increase until postnatal day 30. ARF1-3 appear to be abundantly expressed in various telencephalon regions. Biochemical fractionation studies detected ARF1-3 in the synaptosome fraction of cortical neurons containing both pre- and post-synapses, however ARF1-3 were not observed in post-synaptic compartments. In immunohistochemical analyses, ARF1-3 appeared to be distributed in the cytoplasm and dendrites of cortical and hippocampal neurons as well as in the cerebellar molecular layer including dendrites of Purkinje cells and granule cell axons. Immunofluorescence in primary cultured hippocampal neurons revealed that ARF1-3 are diffusely distributed in the cytoplasm and dendrites with partial colocalization with a pre-synaptic marker, synaptophysin. CONCLUSIONS Overall, our results support the notion that ARF1-3 could participate in vesicle trafficking both in the dendritic shaft (excluding spines) and axon terminals (pre-synaptic compartments).
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Affiliation(s)
- Tohru Matsuki
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Nanako Hamada
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Hidenori Ito
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Ryota Sugawara
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Ikuko Iwamoto
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
| | - Atsuo Nakayama
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan
- Department of Neurochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Nagoya, 466-8550, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, 480-0392, Japan.
- Department of Neurochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Nagoya, 466-8550, Japan.
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3
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Hirschenberger M, Lepelley A, Rupp U, Klute S, Hunszinger V, Koepke L, Merold V, Didry-Barca B, Wondany F, Bergner T, Moreau T, Rodero MP, Rösler R, Wiese S, Volpi S, Gattorno M, Papa R, Lynch SA, Haug MG, Houge G, Wigby KM, Sprague J, Lenberg J, Read C, Walther P, Michaelis J, Kirchhoff F, de Oliveira Mann CC, Crow YJ, Sparrer KMJ. ARF1 prevents aberrant type I interferon induction by regulating STING activation and recycling. Nat Commun 2023; 14:6770. [PMID: 37914730 PMCID: PMC10620153 DOI: 10.1038/s41467-023-42150-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
Type I interferon (IFN) signalling is tightly controlled. Upon recognition of DNA by cyclic GMP-AMP synthase (cGAS), stimulator of interferon genes (STING) translocates along the endoplasmic reticulum (ER)-Golgi axis to induce IFN signalling. Termination is achieved through autophagic degradation or recycling of STING by retrograde Golgi-to-ER transport. Here, we identify the GTPase ADP-ribosylation factor 1 (ARF1) as a crucial negative regulator of cGAS-STING signalling. Heterozygous ARF1 missense mutations cause a previously unrecognized type I interferonopathy associated with enhanced IFN-stimulated gene expression. Disease-associated, GTPase-defective ARF1 increases cGAS-STING dependent type I IFN signalling in cell lines and primary patient cells. Mechanistically, mutated ARF1 perturbs mitochondrial morphology, causing cGAS activation by aberrant mitochondrial DNA release, and leads to accumulation of active STING at the Golgi/ERGIC due to defective retrograde transport. Our data show an unexpected dual role of ARF1 in maintaining cGAS-STING homeostasis, through promotion of mitochondrial integrity and STING recycling.
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Affiliation(s)
| | - Alice Lepelley
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France
| | - Ulrich Rupp
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Susanne Klute
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Victoria Hunszinger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Veronika Merold
- Institute of Virology, Technical University of Munich, 81675, Munich, Germany
| | - Blaise Didry-Barca
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France
| | - Fanny Wondany
- Institute of Biophysics, Ulm University, 89081, Ulm, Germany
| | - Tim Bergner
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Tatiana Moreau
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France
| | - Mathieu P Rodero
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France
| | - Reinhild Rösler
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081, Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081, Ulm, Germany
| | - Stefano Volpi
- UOC Reumatologia e Malattie Autoinfiammatorie, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Università degli Studi di Genova, Genoa, Italy
| | - Marco Gattorno
- UOC Reumatologia e Malattie Autoinfiammatorie, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Riccardo Papa
- UOC Reumatologia e Malattie Autoinfiammatorie, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Sally-Ann Lynch
- Children's Health Ireland, Crumlin, Dublin, Eire
- University College Dublin, Dublin, Eire
| | - Marte G Haug
- Department of Medical Genetics, St. Olav's Hospital, Trondheim, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway
| | - Kristen M Wigby
- Division of Genomic Medicine, Department of Pediatrics, University of California, Davis in Sacramento, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jessica Sprague
- Division of Pediatric and Adolescent Dermatology, Rady Children's Hospital San Diego, San Diego, CA, USA
- Department of Dermatology, University of California San Diego School of Medicine, La Jolla, USA
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Clarissa Read
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081, Ulm, Germany
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, 89081, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Yanick J Crow
- Université Paris Cité, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, INSERM UMR1163, F-75015, Paris, France.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Gujar MR, Gao Y, Teng X, Deng Q, Lin KY, Tan YS, Toyama Y, Wang H. Golgi-dependent reactivation and regeneration of Drosophila quiescent neural stem cells. Dev Cell 2023; 58:1933-1949.e5. [PMID: 37567172 DOI: 10.1016/j.devcel.2023.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 04/26/2023] [Accepted: 07/17/2023] [Indexed: 08/13/2023]
Abstract
The ability of stem cells to switch between quiescent and proliferative states is crucial for maintaining tissue homeostasis and regeneration. In Drosophila, quiescent neural stem cells (qNSCs) extend a primary protrusion, a hallmark of qNSCs. Here, we have found that qNSC protrusions can be regenerated upon injury. This regeneration process relies on the Golgi apparatus that acts as the major acentrosomal microtubule-organizing center in qNSCs. A Golgi-resident GTPase Arf1 and its guanine nucleotide exchange factor Sec71 promote NSC reactivation and regeneration via the regulation of microtubule growth. Arf1 physically associates with its new effector mini spindles (Msps)/XMAP215, a microtubule polymerase. Finally, Arf1 functions upstream of Msps to target the cell adhesion molecule E-cadherin to NSC-neuropil contact sites during NSC reactivation. Our findings have established Drosophila qNSCs as a regeneration model and identified Arf1/Sec71-Msps pathway in the regulation of microtubule growth and NSC reactivation.
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Affiliation(s)
- Mahekta R Gujar
- Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Yang Gao
- Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Xiang Teng
- Mechanobiology Institute, Level 5, T-lab Building, 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Qiannan Deng
- Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Kun-Yang Lin
- Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Ye Sing Tan
- Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Yusuke Toyama
- Mechanobiology Institute, Level 5, T-lab Building, 5A Engineering Drive 1, Singapore 117411, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Hongyan Wang
- Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Integrative Sciences and Engineering Programme, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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5
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Polenghi M, Taverna E. Intracellular traffic and polarity in brain development. Front Neurosci 2023; 17:1172016. [PMID: 37859764 PMCID: PMC10583573 DOI: 10.3389/fnins.2023.1172016] [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: 02/22/2023] [Accepted: 07/31/2023] [Indexed: 10/21/2023] Open
Abstract
Neurons forming the human brain are generated during embryonic development by neural stem and progenitor cells via a process called neurogenesis. A crucial feature contributing to neural stem cell morphological and functional heterogeneity is cell polarity, defined as asymmetric distribution of cellular components. Cell polarity is built and maintained thanks to the interplay between polarity proteins and polarity-generating organelles, such as the endoplasmic reticulum (ER) and the Golgi apparatus (GA). ER and GA affect the distribution of membrane components and work as a hub where glycans are added to nascent proteins and lipids. In the last decades our knowledge on the role of polarity in neural stem and progenitor cells have increased tremendously. However, the role of traffic and associated glycosylation in neural stem and progenitor cells is still relatively underexplored. In this review, we discuss the link between cell polarity, architecture, identity and intracellular traffic, and highlight how studies on neurons have shaped our knowledge and conceptual framework on traffic and polarity. We will then conclude by discussing how a group of rare diseases, called congenital disorders of glycosylation (CDG) offers the unique opportunity to study the contribution of traffic and glycosylation in the context of neurodevelopment.
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de Sainte Agathe JM, Pode-Shakked B, Naudion S, Michaud V, Arveiler B, Fergelot P, Delmas J, Keren B, Poirsier C, Alkuraya FS, Tabarki B, Bend E, Davis K, Bebin M, Thompson ML, Bryant EM, Wagner M, Hannibal I, Lenberg J, Krenn M, Wigby KM, Friedman JR, Iascone M, Cereda A, Miao T, LeGuern E, Argilli E, Sherr E, Caluseriu O, Tidwell T, Bayrak-Toydemir P, Hagedorn C, Brugger M, Vill K, Morneau-Jacob FD, Chung W, Weaver KN, Owens JW, Husami A, Chaudhari BP, Stone BS, Burns K, Li R, de Lange IM, Biehler M, Ginglinger E, Gérard B, Stottmann RW, Trimouille A. ARF1-related disorder: phenotypic and molecular spectrum. J Med Genet 2023; 60:999-1005. [PMID: 37185208 PMCID: PMC10579487 DOI: 10.1136/jmg-2022-108803] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
PURPOSE ARF1 was previously implicated in periventricular nodular heterotopia (PVNH) in only five individuals and systematic clinical characterisation was not available. The aim of this study is to provide a comprehensive description of the phenotypic and genotypic spectrum of ARF1-related neurodevelopmental disorder. METHODS We collected detailed phenotypes of an international cohort of individuals (n=17) with ARF1 variants assembled through the GeneMatcher platform. Missense variants were structurally modelled, and the impact of several were functionally validated. RESULTS De novo variants (10 missense, 1 frameshift, 1 splice altering resulting in 9 residues insertion) in ARF1 were identified among 17 unrelated individuals. Detailed phenotypes included intellectual disability (ID), microcephaly, seizures and PVNH. No specific facial characteristics were consistent across all cases, however microretrognathia was common. Various hearing and visual defects were recurrent, and interestingly, some inflammatory features were reported. MRI of the brain frequently showed abnormalities consistent with a neuronal migration disorder. CONCLUSION We confirm the role of ARF1 in an autosomal dominant syndrome with a phenotypic spectrum including severe ID, microcephaly, seizures and PVNH due to impaired neuronal migration.
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Affiliation(s)
| | - Ben Pode-Shakked
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sophie Naudion
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Vincent Michaud
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Benoit Arveiler
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Patricia Fergelot
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
| | - Jean Delmas
- Pediatric and Prenatal Imaging Department, Centre Hospitalier Universitaire de Bordeaux Groupe hospitalier Pellegrin, Bordeaux, France
| | - Boris Keren
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
| | | | - Fowzan S Alkuraya
- Department of Translational Genomic, Center for Genomic Medicine, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Division of Pediatric Neurology, Department of Pediatrics, Prince Sultan Military and Medical City, Riyadh, Saudi Arabia
| | - Eric Bend
- PreventionGenetics LLC, Marshfield, Wisconsin, USA
| | - Kellie Davis
- Division of Medical Genetics, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Martina Bebin
- UAB Epilepsy Center, The University of Alabama at Birmingham Hospital, Birmingham, Alabama, USA
| | - Michelle L Thompson
- Greg Cooper's Laboratory, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Emily M Bryant
- Gillette Children's Specialty Healthcare, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Matias Wagner
- Institute of Human Genetics, Technische Universitat Munchen, Munchen, Germany
- Institute of Neurogenomics, Helmholtz Zentrum Munchen Deutsches Forschungszentrum fur Umwelt und Gesundheit, Neuherberg, Germany
| | - Iris Hannibal
- Department of Pediatrics, University Hospital Munich, Munchen, Germany
| | - Jerica Lenberg
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Martin Krenn
- Department of Neurology, Medizinische Universitat Wien, Wien, Austria
| | - Kristen M Wigby
- Rady Children's Hospital-San Diego, University of California, San Diego, California, USA
| | - Jennifer R Friedman
- Department of Neuroscience, Rady Children's Institute for Genomic Medicine, San Diego, California, USA
- Division of Neurology, Rady Children's Hospital San Diego, San Diego, California, USA
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Pediatric Department, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Térence Miao
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
- École d'ingénieurs biotechnologies Paris - SupBiotech, Sup'Biotech, Paris, France
| | - Eric LeGuern
- Department of Medical Genetics, Groupe Hospitalo-Universitaire Pitié-Salpêtrière, AP-HP.Sorbonne Université, Paris, France
- ICM, INSERM, Paris, France
| | - Emanuela Argilli
- Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Elliott Sherr
- Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta Hospital, Edmonton, Alberta, Canada
| | | | | | - Caroline Hagedorn
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munchen, Germany
| | - Katharina Vill
- Fachbereich Neuromuskuläre Erkrankungen und klinische Neurophysiologie, Dr. v. Hauner Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | | | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York City, New York, USA
| | - Kathryn N Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Joshua W Owens
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ammar Husami
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Bimal P Chaudhari
- Divisions of Neonatology, Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Brandon S Stone
- Divisions of Genetics and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Katie Burns
- Sanford Children's Specialty Clinic, Sioux Falls, South Dakota, USA
| | - Rachel Li
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
| | - Iris M de Lange
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Margaux Biehler
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals, Strasbourg, France
| | | | - Bénédicte Gérard
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals, Strasbourg, France
| | - Rolf W Stottmann
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Aurélien Trimouille
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- Maladies Rares : Génétique et Métabolisme (MRGM), U1211, INSERM, Bordeaux, France
- Service de Pathologie, University Hospital Centre Bordeaux Pellegrin Hospital Group, Bordeaux, France
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7
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Ishida M, Otero MG, Freeman C, Sánchez-Lara PA, Guardia CM, Pierson TM, Bonifacino JS. A neurodevelopmental disorder associated with an activating de novo missense variant in ARF1. Hum Mol Genet 2023; 32:1162-1174. [PMID: 36345169 PMCID: PMC10026249 DOI: 10.1093/hmg/ddac279] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
ADP-ribosylation factor 1 (ARF1) is a small GTPase that regulates membrane traffic at the Golgi apparatus and endosomes through recruitment of several coat proteins and lipid-modifying enzymes. Here, we report a pediatric patient with an ARF1-related disorder because of a monoallelic de novo missense variant (c.296 G > A; p.R99H) in the ARF1 gene, associated with developmental delay, hypotonia, intellectual disability and motor stereotypies. Neuroimaging revealed a hypoplastic corpus callosum and subcortical white matter abnormalities. Notably, this patient did not exhibit periventricular heterotopias previously observed in other patients with ARF1 variants (including p.R99H). Functional analysis of the R99H-ARF1 variant protein revealed that it was expressed at normal levels and properly localized to the Golgi apparatus; however, the expression of this variant caused swelling of the Golgi apparatus, increased the recruitment of coat proteins such as coat protein complex I, adaptor protein complex 1 and GGA3 and altered the morphology of recycling endosomes. In addition, we observed that the expression of R99H-ARF1 prevented dispersal of the Golgi apparatus by the ARF1-inhibitor brefeldin A. Finally, protein interaction analyses showed that R99H-ARF1 bound more tightly to the ARF1-effector GGA3 relative to wild-type ARF1. These properties were similar to those of the well-characterized constitutively active Q71L-ARF1 mutant, indicating that the pathogenetic mechanism of the R99H-ARF1 variant involves constitutive activation with resultant Golgi and endosomal alterations. The absence of periventricular nodular heterotopias in this R99H-ARF1 subject also indicates that this finding may not be a consistent phenotypic expression of all ARF1-related disorders.
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Affiliation(s)
- Morié Ishida
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - María G Otero
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christina Freeman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Pedro A Sánchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Carlos M Guardia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27703, USA
| | - Tyler Mark Pierson
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Pediatric Neurology, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shiver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Liu J, Hu J, Duan Y, Qin R, Guo C, Zhou H, Liu H, Liu C. Genetic analysis of periventricular nodular heterotopia 7 caused by a novel NEDD4L missense mutation: Case and literature summary. Mol Genet Genomic Med 2023:e2169. [PMID: 36934385 DOI: 10.1002/mgg3.2169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/01/2023] [Accepted: 03/01/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND Neurodevelopmental disorders associated with periventricular nodular heterotopia (PVNH) are characterized by phenotypic and genetic heterogeneity. NEDD4L mutation can lead to PVNH7. However, at present, only eight NEDD4L pathogenic variants have been identified across 15 cases of PVNH7 worldwide. Given this dearth of evidence, the precise correlations between genetic pathogenesis and phenotypes remain to be determined. METHODS This report discusses the case of a 19-month-old male child with cleft palate, seizures, psychomotor retardation, and hypotonia, for whom we verified the genetic etiology using Trio-whole-exome and Sanger sequencing to analyze the potential pathogenicity of the mutant protein structure. Mutant plasmids were constructed for in vitro analyses. After transfection into human 293 T cells, the mutant transcription process was analyzed using real-time PCR (RT-PCR), and levels of mutant protein expression were examined using western blotting (WB) and immunofluorescence (IF) experiments. RESULTS Genetic analyses revealed a novel missense mutation Gln900Arg, located in the homologous to E6-APC terminal (HECT) domain of NEDD4L and that the parents were wild-type, suggestive of a de novo mutation. The variant was predicted to be pathogenic by bioinformatics software, which also suggested alterations in the structural stability of the mutant protein. RT-PCR results indicated that the mutation did not affect mRNA expression, whereas WB and IF results indicated that the level of mutant protein was significantly reduced by 41.07%. CONCLUSION Functional experiments demonstrated that Gln900Arg probably did not lead to transcriptional abnormalities in this patient, instead leading to increased ubiquitination activity owing to the constitutive activation of the HECT domain, thereby promoting protein degradation. Extensive clinical reports should be generated for patients presenting with PVNH and/or polymicrogyria, developmental delay, syndactyly, and hypotonia to increase the pool of evidence related to NEDD4L.
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Affiliation(s)
- Juan Liu
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Jihong Hu
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Yaqing Duan
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Rong Qin
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Chunguang Guo
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Hongtao Zhou
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Hua Liu
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Chunlei Liu
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
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9
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Golgipathies reveal the critical role of the sorting machinery in brain and skeletal development. Nat Commun 2022; 13:7397. [PMID: 36456556 PMCID: PMC9715697 DOI: 10.1038/s41467-022-35101-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
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10
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Fasano G, Muto V, Radio FC, Venditti M, Mosaddeghzadeh N, Coppola S, Paradisi G, Zara E, Bazgir F, Ziegler A, Chillemi G, Bertuccini L, Tinari A, Vetro A, Pantaleoni F, Pizzi S, Conti LA, Petrini S, Bruselles A, Prandi IG, Mancini C, Chandramouli B, Barth M, Bris C, Milani D, Selicorni A, Macchiaiolo M, Gonfiantini MV, Bartuli A, Mariani R, Curry CJ, Guerrini R, Slavotinek A, Iascone M, Dallapiccola B, Ahmadian MR, Lauri A, Tartaglia M. Dominant ARF3 variants disrupt Golgi integrity and cause a neurodevelopmental disorder recapitulated in zebrafish. Nat Commun 2022; 13:6841. [PMID: 36369169 PMCID: PMC9652361 DOI: 10.1038/s41467-022-34354-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
Vesicle biogenesis, trafficking and signaling via Endoplasmic reticulum-Golgi network support essential developmental processes and their disruption lead to neurodevelopmental disorders and neurodegeneration. We report that de novo missense variants in ARF3, encoding a small GTPase regulating Golgi dynamics, cause a developmental disease in humans impairing nervous system and skeletal formation. Microcephaly-associated ARF3 variants affect residues within the guanine nucleotide binding pocket and variably perturb protein stability and GTP/GDP binding. Functional analysis demonstrates variably disruptive consequences of ARF3 variants on Golgi morphology, vesicles assembly and trafficking. Disease modeling in zebrafish validates further the dominant behavior of the mutants and their differential impact on brain and body plan formation, recapitulating the variable disease expression. In-depth in vivo analyses traces back impaired neural precursors' proliferation and planar cell polarity-dependent cell movements as the earliest detectable effects. Our findings document a key role of ARF3 in Golgi function and demonstrate its pleiotropic impact on development.
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Affiliation(s)
- Giulia Fasano
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Muto
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Clementina Radio
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Martina Venditti
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Niloufar Mosaddeghzadeh
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Simona Coppola
- grid.416651.10000 0000 9120 6856National Center for Rare Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Graziamaria Paradisi
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy ,grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Erika Zara
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy ,grid.7841.aDepartment of Biology and Biotechnology “Charles Darwin”, Università “Sapienza”, Rome, 00185 Italy
| | - Farhad Bazgir
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alban Ziegler
- grid.7252.20000 0001 2248 3363UFR Santé de l’Université d’Angers, INSERM U1083, CNRS UMR6015, MITOVASC, SFR ICAT, F-49000 Angers, France ,grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Giovanni Chillemi
- grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy ,grid.5326.20000 0001 1940 4177Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale delle Ricerche, 70126 Bari, Italy
| | - Lucia Bertuccini
- grid.416651.10000 0000 9120 6856Servizio grandi strumentazioni e core facilities, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonella Tinari
- grid.416651.10000 0000 9120 6856Centro di riferimento per la medicina di genere, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Annalisa Vetro
- grid.8404.80000 0004 1757 2304Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy
| | - Francesca Pantaleoni
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Libenzio Adrian Conti
- grid.414603.4Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- grid.414603.4Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Alessandro Bruselles
- grid.416651.10000 0000 9120 6856Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Ingrid Guarnetti Prandi
- grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Cecilia Mancini
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Balasubramanian Chandramouli
- grid.431603.30000 0004 1757 1950Super Computing Applications and Innovation, CINECA, 40033 Casalecchio di Reno, Italy
| | - Magalie Barth
- grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Céline Bris
- grid.7252.20000 0001 2248 3363UFR Santé de l’Université d’Angers, INSERM U1083, CNRS UMR6015, MITOVASC, SFR ICAT, F-49000 Angers, France ,grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Donatella Milani
- grid.414818.00000 0004 1757 8749Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Angelo Selicorni
- grid.512106.1Mariani Center for Fragile Children Pediatric Unit, Azienda Socio Sanitaria Territoriale Lariana, 22100 Como, Italy
| | - Marina Macchiaiolo
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michaela V. Gonfiantini
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Bartuli
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Riccardo Mariani
- grid.414603.4Department of Laboratories Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cynthia J. Curry
- grid.266102.10000 0001 2297 6811Genetic Medicine, Dept of Pediatrics, University of California San Francisco, Ca, Fresno, Ca, San Francisco, CA 94143 USA
| | - Renzo Guerrini
- grid.8404.80000 0004 1757 2304Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy
| | - Anne Slavotinek
- grid.266102.10000 0001 2297 6811Genetic Medicine, Dept of Pediatrics, University of California San Francisco, Ca, Fresno, Ca, San Francisco, CA 94143 USA
| | - Maria Iascone
- grid.460094.f0000 0004 1757 8431Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Bruno Dallapiccola
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Mohammad Reza Ahmadian
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Antonella Lauri
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marco Tartaglia
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
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11
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Penon-Portmann M, Eldomery MK, Potocki L, Marafi D, Posey JE, Coban-Akdemir Z, Harel T, Grochowski CM, Loucks H, Devine WP, Van Ziffle J, Doherty D, Lupski JR, Shieh JT. De novo heterozygous variants in SLC30A7 are a candidate cause for Joubert syndrome. Am J Med Genet A 2022; 188:2360-2366. [PMID: 35751429 PMCID: PMC9756141 DOI: 10.1002/ajmg.a.62872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 11/08/2022]
Abstract
Joubert syndrome (JS), a well-established ciliopathy, is characterized by the distinctive molar tooth sign on brain MRI, ataxia, and neurodevelopmental features. Other manifestations can include polydactyly, accessory frenula, renal, or liver disease. Here, we report individuals meeting criteria for JS with de novo heterozygous variants in SLC30A7 (Chr1p21.2). The first individual is a female with history of unilateral postaxial polydactyly, classic molar tooth sign on MRI, macrocephaly, ataxia, ocular motor apraxia, neurodevelopmental delay, and precocious puberty. Exome sequencing detected a de novo heterozygous missense variant in SLC30A7: NM_133496.5: c.407 T > C, (p.Val136Ala). The second individual had bilateral postaxial polydactyly, molar tooth sign, macrocephaly, developmental delay, and an extra oral frenulum. A de novo deletion-insertion variant in SLC30A7, c.490_491delinsAG (p.His164Ser) was found. Both de novo variants affect highly conserved residues. Variants were not identified in known Joubert genes for either case. SLC30A7 has not yet been associated with a human phenotype. The SLC30 family of zinc transporters, like SLC30A7, permit cellular efflux of zinc, and although it is expressed in the brain its functions remain unknown. Published data from proteomic studies support SLC30A7 interaction with TCTN3, another protein associated with JS. The potential involvement of such genes in primary cilia suggest a role in Sonic Hedgehog signaling. SLC30A7 is a candidate JS-associated gene. Future work could be directed toward further characterization of SLC30A7 variants and understanding its function.
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Affiliation(s)
- Monica Penon-Portmann
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Hailey Loucks
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Walter Patrick Devine
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
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12
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The GTPase Arf1 Is a Determinant of Yeast Vps13 Localization to the Golgi Apparatus. Int J Mol Sci 2021; 22:ijms222212274. [PMID: 34830155 PMCID: PMC8619211 DOI: 10.3390/ijms222212274] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
VPS13 proteins are evolutionarily conserved. Mutations in the four human genes (VPS13A-D) encoding VPS13A-D proteins are linked to developmental or neurodegenerative diseases. The relationship between the specific localization of individual VPS13 proteins, their molecular functions, and the pathology of these diseases is unknown. Here we used a yeast model to establish the determinants of Vps13's interaction with the membranes of Golgi apparatus. We analyzed the different phenotypes of the arf1-3 arf2Δ vps13∆ strain, with reduced activity of the Arf1 GTPase, the master regulator of Golgi function and entirely devoid of Vps13. Our analysis led us to propose that Vps13 and Arf1 proteins cooperate at the Golgi apparatus. We showed that Vps13 binds to the Arf1 GTPase through its C-terminal Pleckstrin homology (PH)-like domain. This domain also interacts with phosphoinositol 4,5-bisphosphate as it was bound to liposomes enriched with this lipid. The homologous domain of VPS13A exhibited the same behavior. Furthermore, a fusion of the PH-like domain of Vps13 to green fluorescent protein was localized to Golgi structures in an Arf1-dependent manner. These results suggest that the PH-like domains and Arf1 are determinants of the localization of VPS13 proteins to the Golgi apparatus in yeast and humans.
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13
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Vriend I, Oegema R. Genetic causes underlying grey matter heterotopia. Eur J Paediatr Neurol 2021; 35:82-92. [PMID: 34666232 DOI: 10.1016/j.ejpn.2021.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/21/2021] [Indexed: 11/15/2022]
Abstract
Grey matter heterotopia (GMH) can cause of seizures and are associated with a wide range of neurodevelopmental disorders and syndromes. They are caused by a failure of neuronal migration during fetal development, leading to clusters of neurons that have not reached their final destination in the cerebral cortex. We have performed an extensive literature search in Pubmed, OMIM, and Google scholar and provide an overview of known genetic associations with periventricular nodular heterotopia (PNVH), subcortical band heterotopia (SBH) and other subcortical heterotopia (SUBH). We classified the heterotopias as PVNH, SBH, SUBH or other and collected the genetic information, frequency, imaging features and salient features in tables for every subtype of heterotopia. This resulted in 105 PVNH, 16 SBH and 25 SUBH gene/locus associations, making a total of 146 genes and chromosomal loci. Our study emphasizes the extreme genetic heterogeneity underlying GMH. It will aid the clinician in establishing an differential diagnosis and eventually a molecular diagnosis in GMH patients. A diagnosis enables proper counseling of prognosis and recurrence risks, and enables individualized patient management.
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Affiliation(s)
- Ilona Vriend
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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14
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Wang G, Yin W, Shin H, Tian Q, Lu W, Hou SX. Neuronal accumulation of peroxidated lipids promotes demyelination and neurodegeneration through the activation of the microglial NLRP3 inflammasome. NATURE AGING 2021; 1:1024-1037. [PMID: 37118341 DOI: 10.1038/s43587-021-00130-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 09/27/2021] [Indexed: 04/30/2023]
Abstract
Peroxidated lipids accumulate in the presence of reactive oxygen species and are linked to neurodegenerative diseases. Here we find that neuronal ablation of ARF1, a small GTPase important for lipid homeostasis, promoted accumulation of peroxidated lipids, lipid droplets and ATP in the mouse brain and led to neuroinflammation, demyelination and neurodegeneration, mainly in the spinal cord and hindbrain. Ablation of ARF1 in cultured primary neurons led to an increase in peroxidated lipids in co-cultured microglia, activation of the microglial NLRP3 inflammasome and release of inflammatory cytokines in an Apolipoprotein E-dependent manner. Deleting the Nlrp3 gene rescued the neurodegenerative phenotypes in the neuronal Arf1-ablated mice. We also observed a reduction in ARF1 in human brain tissue from patients with amyotrophic lateral sclerosis and multiple sclerosis. Together, our results uncover a previously unrecognized role of peroxidated lipids released from damaged neurons in activation of a neurotoxic microglial NLRP3 pathway that may play a role in human neurodegeneration.
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Affiliation(s)
- Guohao Wang
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD, USA.
- Synapse and Neural Circuit Research Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Weiqin Yin
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD, USA
- Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hyunhee Shin
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD, USA
| | - Qingjun Tian
- Synapse and Neural Circuit Research Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Wei Lu
- Synapse and Neural Circuit Research Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Steven X Hou
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD, USA.
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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15
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Gana S, Casella A, Cociglio S, Tartara E, Rognone E, Giorgio E, Pichiecchio A, Orcesi S, Valente EM. ARF1 haploinsufficiency causes periventricular nodular heterotopia with variable clinical expressivity. J Med Genet 2021; 59:781-784. [PMID: 34353862 DOI: 10.1136/jmedgenet-2021-107783] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/23/2021] [Indexed: 11/03/2022]
Abstract
The primary anatomical defect leading to periventricular nodular heterotopia occurs within the neural progenitors along the neuroepithelial lining of the lateral ventricles and results from a defect in the initiation of neuronal migration, following disruption of the neuroependyma and impaired neuronal motility. Growing evidence indicates that the FLNA-dependent actin dynamics and regulation of vesicle formation and trafficking by activation of ADP-ribosylation factors (ARFs) can play an important role in this cortical malformation. We report the first inherited variant of ARF1 in a girl with intellectual disability and periventricular nodular heterotopia who inherited the variant from the father with previously undiagnosed single nodular heterotopia and mild clinical expression. Additionally, both patients presented some features suggestive of hypohidrotic ectodermal dysplasia. These clinical features showed similarities to those of three previously reported cases with ARF1 missense variants, confirming that haploinsufficiency of this gene causes a recognisable neurological disorder with abnormal neuronal migration and variable clinical expressivity.
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Affiliation(s)
- Simone Gana
- Medical Genetics Unit, Foundation National Neurological Institute C Mondino Institute for Hospitalization and Care Scientific, Pavia, Italy
| | - Antonella Casella
- Medical Genetics Unit, Foundation National Neurological Institute C Mondino Institute for Hospitalization and Care Scientific, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Sara Cociglio
- Department of Child Neurology and Psychiatry, Foundation National Neurological Institute C Mondino Institute for Hospitalization and Care Scientific, Pavia, Italy.,Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Elena Tartara
- Epilepsy Center, Foundation National Neurological Institute C Mondino Institute for Hospitalization and Care Scientific, Pavia, Italy
| | - Elisa Rognone
- Department of Neuroradiology, Foundation National Neurological Institute C Mondino Institute for Hospitalization and Care Scientific, Pavia, Italy
| | - Elisa Giorgio
- Medical Genetics Unit, Foundation National Neurological Institute C Mondino Institute for Hospitalization and Care Scientific, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Simona Orcesi
- Department of Child Neurology and Psychiatry, Foundation National Neurological Institute C Mondino Institute for Hospitalization and Care Scientific, Pavia, Italy
| | - Enza Maria Valente
- Medical Genetics Unit, Foundation National Neurological Institute C Mondino Institute for Hospitalization and Care Scientific, Pavia, Italy .,Department of Molecular Medicine, University of Pavia, Pavia, Italy
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16
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Sakamoto M, Sasaki K, Sugie A, Nitta Y, Kimura T, Gürsoy S, Cinleti T, Iai M, Sengoku T, Ogata K, Suzuki A, Okamoto N, Iwama K, Tsuchida N, Uchiyama Y, Koshimizu E, Fujita A, Hamanaka K, Miyatake S, Mizuguchi T, Taguri M, Ito S, Takahashi H, Miyake N, Matsumoto N. De novo ARF3 variants cause neurodevelopmental disorder with brain abnormality. Hum Mol Genet 2021; 31:69-81. [PMID: 34346499 DOI: 10.1093/hmg/ddab224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
An optimal Golgi transport system is important for mammalian cells. The adenosine diphosphate (ADP) ribosylation factors (ARF) are key proteins for regulating cargo sorting at the Golgi network. In this family, ARF3 mainly works at the trans-Golgi network (TGN), and no ARF3-related phenotypes have yet been described in humans. We here report the clinical and genetic evaluations of two unrelated children with de novo pathogenic variants in the ARF3 gene: c.200A > T (p.Asp67Val) and c.296G > T (p.Arg99Leu). Although the affected individuals presented commonly with developmental delay, epilepsy, and brain abnormalities, there were differences in severity, clinical course, and brain lesions. In vitro subcellular localization assays revealed that the p.Arg99Leu mutant localized to Golgi apparatus, similar to the wild-type, whereas the p.Asp67Val mutant tended to show a disperse cytosolic pattern together with abnormally dispersed Golgi localization, similar to that observed in a known dominant negative variant (p.Thr31Asn). Pull-down assays revealed that the p.Asp67Val had a loss-of-function effect and the p.Arg99Leu variant had increased binding of the adaptor protein, Golgi-localized, γ-adaptin ear-containing, ARF-binding protein 1 (GGA1), supporting the gain of function. Furthermore, in vivo studies revealed that p.Asp67Val transfection led to lethality in flies. In contrast, flies expressing p.Arg99Leu had abnormal rough eye, as observed in the gain-of-function variant p.Gln71Leu. These data indicate that two ARF3 variants, the possibly loss-of-function p.Asp67Val and the gain-of-function p.Arg99Leu, both impair the Golgi transport system. Therefore, it may not be unreasonable that they showed different clinical features like diffuse brain atrophy (p.Asp67Val) and cerebellar hypoplasia (p.Arg99Leu).
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Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazunori Sasaki
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Sugie
- Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Yohei Nitta
- Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Tetsuaki Kimura
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Semra Gürsoy
- Department of Pediatric Genetics, S.B.Ü. Dr. Behçet Uz Children's Education and Research Hospital, Izmir, 35210, Turkey
| | - Tayfun Cinleti
- Department of Pediatric Genetics, Dokuz Eylul University, Faculty of Medicine, Izumir, 35340, Turkey
| | - Mizue Iai
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, 232-8555, Japan
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Suzuki
- Molecular Cellular Biology Laboratory, Yokohama City University Graduate School of Medical Life Science, Yokohama, 230-0045, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, 594-1101, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Masataka Taguri
- Department of Data Science, Yokohama City University School of Data Science, Yokohama, 236-0027, Japan
| | - Shuuichi Ito
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
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17
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Lauri A, Fasano G, Venditti M, Dallapiccola B, Tartaglia M. In vivo Functional Genomics for Undiagnosed Patients: The Impact of Small GTPases Signaling Dysregulation at Pan-Embryo Developmental Scale. Front Cell Dev Biol 2021; 9:642235. [PMID: 34124035 PMCID: PMC8194860 DOI: 10.3389/fcell.2021.642235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/12/2021] [Indexed: 12/24/2022] Open
Abstract
While individually rare, disorders affecting development collectively represent a substantial clinical, psychological, and socioeconomic burden to patients, families, and society. Insights into the molecular mechanisms underlying these disorders are required to speed up diagnosis, improve counseling, and optimize management toward targeted therapies. Genome sequencing is now unveiling previously unexplored genetic variations in undiagnosed patients, which require functional validation and mechanistic understanding, particularly when dealing with novel nosologic entities. Functional perturbations of key regulators acting on signals' intersections of evolutionarily conserved pathways in these pathological conditions hinder the fine balance between various developmental inputs governing morphogenesis and homeostasis. However, the distinct mechanisms by which these hubs orchestrate pathways to ensure the developmental coordinates are poorly understood. Integrative functional genomics implementing quantitative in vivo models of embryogenesis with subcellular precision in whole organisms contribute to answering these questions. Here, we review the current knowledge on genes and mechanisms critically involved in developmental syndromes and pediatric cancers, revealed by genomic sequencing and in vivo models such as insects, worms and fish. We focus on the monomeric GTPases of the RAS superfamily and their influence on crucial developmental signals and processes. We next discuss the effectiveness of exponentially growing functional assays employing tractable models to identify regulatory crossroads. Unprecedented sophistications are now possible in zebrafish, i.e., genome editing with single-nucleotide precision, nanoimaging, highly resolved recording of multiple small molecules activity, and simultaneous monitoring of brain circuits and complex behavioral response. These assets permit accurate real-time reporting of dynamic small GTPases-controlled processes in entire organisms, owning the potential to tackle rare disease mechanisms.
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Affiliation(s)
- Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | | | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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18
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Hetts SW, Shieh JT, Ohliger MA, Conrad MB. Hereditary Hemorrhagic Telangiectasia: The Convergence of Genotype, Phenotype, and Imaging in Modern Diagnosis and Management of a Multisystem Disease. Radiology 2021; 300:17-30. [PMID: 33973836 DOI: 10.1148/radiol.2021203487] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant disease that manifests as vascular malformations in the brain, lung, liver, gastrointestinal tract, nasal mucosa, and skin. Diagnosis and management of HHT is guided in large part by imaging studies, making it a condition with which the radiology community needs familiarity. Proper screening and care lead to improved morbidity and mortality in patients with HHT. International guidelines were recently updated and form the basis for a detailed discussion of the role of imaging and image-guided therapy in HHT. © RSNA, 2021 Online supplemental material is available for this article.
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Affiliation(s)
- Steven W Hetts
- From the Department of Radiology and Biomedical Imaging (S.W.H., M.O., M.C.), HHT Center of Excellence (S.W.H., J.S., M.O., M.C.), and Department of -Pediatrics (J.S.), University of California San Francisco, 505 Parnassus Ave, L-351, San Francisco, CA 94143-0628
| | - Joseph T Shieh
- From the Department of Radiology and Biomedical Imaging (S.W.H., M.O., M.C.), HHT Center of Excellence (S.W.H., J.S., M.O., M.C.), and Department of -Pediatrics (J.S.), University of California San Francisco, 505 Parnassus Ave, L-351, San Francisco, CA 94143-0628
| | - Michael A Ohliger
- From the Department of Radiology and Biomedical Imaging (S.W.H., M.O., M.C.), HHT Center of Excellence (S.W.H., J.S., M.O., M.C.), and Department of -Pediatrics (J.S.), University of California San Francisco, 505 Parnassus Ave, L-351, San Francisco, CA 94143-0628
| | - Miles B Conrad
- From the Department of Radiology and Biomedical Imaging (S.W.H., M.O., M.C.), HHT Center of Excellence (S.W.H., J.S., M.O., M.C.), and Department of -Pediatrics (J.S.), University of California San Francisco, 505 Parnassus Ave, L-351, San Francisco, CA 94143-0628
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19
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De Angelis C, Byrne AB, Morrow R, Feng J, Ha T, Wang P, Schreiber AW, Babic M, Taranath A, Manton N, King-Smith SL, Schwarz Q, Arts P, Scott HS, Barnett C. Compound heterozygous variants in LAMC3 in association with posterior periventricular nodular heterotopia. BMC Med Genomics 2021; 14:64. [PMID: 33639934 PMCID: PMC7916305 DOI: 10.1186/s12920-021-00911-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 01/25/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Periventricular nodular heterotopia (PNH) is a malformation of cortical development characterized by nodules of abnormally migrated neurons. The cause of posteriorly placed PNH is not well characterised and we present a case that provides insights into the cause of posterior PNH. CASE PRESENTATION We report a fetus with extensive posterior PNH in association with biallelic variants in LAMC3. LAMC3 mutations have previously been shown to cause polymicrogyria and pachygyria in the occipital cortex, but not PNH. The occipital location of PNH in our case and the proposed function of LAMC3 in cortical development suggest that the identified LAMC3 variants may be causal of PNH in this fetus. CONCLUSION We hypothesise that this finding extends the cortical phenotype associated with LAMC3 and provides valuable insight into genetic cause of posterior PNH.
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Affiliation(s)
- Carla De Angelis
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Alicia B Byrne
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Rebecca Morrow
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Jinghua Feng
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Thuong Ha
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Paul Wang
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Andreas W Schreiber
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Milena Babic
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Ajay Taranath
- South Australian Medical Imaging, Women's and Children's Hospital, North Adelaide, SA, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Nick Manton
- Department of Surgical Pathology, Women's and Children's Hospital/SA Pathology, North Adelaide, SA, Australia
| | - Sarah L King-Smith
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomic Health Alliance, Melbourne, VIC, Australia
| | - Quenten Schwarz
- Neurovascular Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Peer Arts
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Hamish S Scott
- Genetics and Molecular Pathology Research Laboratory, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
- Australian Genomic Health Alliance, Melbourne, VIC, Australia
| | - Christopher Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, SA, Australia.
- School of Medicine, University of Adelaide, Adelaide, SA, Australia.
- SA Clinical Genetics Service, Women's and Children's Hospital, 72 King William Road, North Adelaide, SA, 5006, Australia.
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20
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Macken WL, Godwin A, Wheway G, Stals K, Nazlamova L, Ellard S, Alfares A, Aloraini T, AlSubaie L, Alfadhel M, Alajaji S, Wai HA, Self J, Douglas AGL, Kao AP, Guille M, Baralle D. Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly. Genome Med 2021; 13:34. [PMID: 33632302 PMCID: PMC7908744 DOI: 10.1186/s13073-021-00850-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as "coatopathies". METHODS Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1's splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2's missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2's mutation. RESULTS We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β'-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. CONCLUSIONS This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.
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Affiliation(s)
- William L Macken
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK
| | - Annie Godwin
- European Xenopus Resource Centre, University of Portsmouth School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Level 3 RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Liliya Nazlamova
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Level 3 RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- University of Exeter Medical School, RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Ahmed Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Lamia AlSubaie
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Sulaiman Alajaji
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Division of Allergy and Clinical Immunology, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Htoo A Wai
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Jay Self
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Alexander P Kao
- Zeiss Global Centre, School of Mechanical and Design Engineering, University of Portsmouth, Portsmouth, PO1 3DJ, UK
| | - Matthew Guille
- European Xenopus Resource Centre, University of Portsmouth School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK.
| | - Diana Baralle
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK.
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK.
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21
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Bellott DW, Page DC. Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals. Genome Res 2021; 31:198-210. [PMID: 33479023 PMCID: PMC7849413 DOI: 10.1101/gr.268516.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022]
Abstract
Different ancestral autosomes independently evolved into sex chromosomes in snakes, birds, and mammals. In snakes and birds, females are ZW and males are ZZ; in mammals, females are XX and males are XY. Although X and Z Chromosomes retain nearly all ancestral genes, sex-specific W and Y Chromosomes suffered extensive genetic decay. In both birds and mammals, the genes that survived on sex-specific chromosomes are enriched for broadly expressed, dosage-sensitive regulators of gene expression, subject to strong purifying selection. To gain deeper insight into the processes that govern survival on sex-specific chromosomes, we carried out a meta-analysis of survival across 41 species-three snakes, 24 birds, and 14 mammals-doubling the number of ancestral genes under investigation and increasing our power to detect enrichments among survivors relative to nonsurvivors. Of 2564 ancestral genes, representing an eighth of the ancestral amniote genome, only 324 survive on present-day sex-specific chromosomes. Survivors are enriched for dosage-sensitive developmental processes, particularly development of neural crest-derived structures, such as the face. However, there was no enrichment for expression in sex-specific tissues, involvement in sex determination or gonadogenesis pathways, or conserved sex-biased expression. Broad expression and dosage sensitivity contributed independently to gene survival, suggesting that pleiotropy imposes additional constraints on the evolution of dosage compensation. We propose that maintaining the viability of the heterogametic sex drove gene survival on amniote sex-specific chromosomes, and that subtle modulation of the expression of survivor genes and their autosomal orthologs has disproportionately large effects on development and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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22
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Tidwell T, Deshotel M, Palumbos J, Miller C, Bayrak-Toydemir P, Carey JC. Novel de novo ARCN1 intronic variant causes rhizomelic short stature with microretrognathia and developmental delay. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005728. [PMID: 33154040 PMCID: PMC7784487 DOI: 10.1101/mcs.a005728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022] Open
Abstract
The archain 1 (ARCN1) gene encodes the coatomer subunit delta protein and is a component of the COPI coatomer complex, which is involved in retrograde vesical trafficking from the Golgi complex to the endoplasmic reticulum. Variants in ARCN1 have recently been associated with rhizomelic short stature with microcephaly, microretrognathia, and developmental delay. Here we report a 3.5-yr-old boy with microcephaly, global developmental delay, and multiple congenital abnormalities and the ARCN1-related syndrome caused by a novel de novo intronic variant. Whole-exome sequencing of the proband and his parents was utilized to determine the genetic origin of the patient's disorder and identified a de novo variant, NM_001655.5:c.654-15A > G, in the ARCN1 gene. Follow-up functional characterization of mRNA from the patient demonstrated that this variant creates a splicing defect of the ARCN1 mRNA. ARCN1-related syndrome represents an emerging disorder of developmental delay, and this report represents the sixth described patient. Despite the few instances reported in literature, the phenotype is consistent between our patient and previously reported individuals.
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Affiliation(s)
| | | | - Janice Palumbos
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
| | - Chris Miller
- ARUP Laboratories, Salt Lake City, Utah 84108, USA
| | - Pinar Bayrak-Toydemir
- ARUP Laboratories, Salt Lake City, Utah 84108, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84113, USA
| | - John C Carey
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
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23
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Mendoza-Ferreira N, Karakaya M, Cengiz N, Beijer D, Brigatti KW, Gonzaga-Jauregui C, Fuhrmann N, Hölker I, Thelen MP, Zetzsche S, Rombo R, Puffenberger EG, De Jonghe P, Deconinck T, Zuchner S, Strauss KA, Carson V, Schrank B, Wunderlich G, Baets J, Wirth B. De Novo and Inherited Variants in GBF1 are Associated with Axonal Neuropathy Caused by Golgi Fragmentation. Am J Hum Genet 2020; 107:763-777. [PMID: 32937143 PMCID: PMC7491385 DOI: 10.1016/j.ajhg.2020.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/19/2020] [Indexed: 01/18/2023] Open
Abstract
Distal hereditary motor neuropathies (HMNs) and axonal Charcot-Marie-Tooth neuropathy (CMT2) are clinically and genetically heterogeneous diseases characterized primarily by motor neuron degeneration and distal weakness. The genetic cause for about half of the individuals affected by HMN/CMT2 remains unknown. Here, we report the identification of pathogenic variants in GBF1 (Golgi brefeldin A-resistant guanine nucleotide exchange factor 1) in four unrelated families with individuals affected by sporadic or dominant HMN/CMT2. Genomic sequencing analyses in seven affected individuals uncovered four distinct heterozygous GBF1 variants, two of which occurred de novo. Other known HMN/CMT2-implicated genes were excluded. Affected individuals show HMN/CMT2 with slowly progressive distal muscle weakness and musculoskeletal deformities. Electrophysiological studies confirmed axonal damage with chronic neurogenic changes. Three individuals had additional distal sensory loss. GBF1 encodes a guanine-nucleotide exchange factor that facilitates the activation of members of the ARF (ADP-ribosylation factor) family of small GTPases. GBF1 is mainly involved in the formation of coatomer protein complex (COPI) vesicles, maintenance and function of the Golgi apparatus, and mitochondria migration and positioning. We demonstrate that GBF1 is present in mouse spinal cord and muscle tissues and is particularly abundant in neuropathologically relevant sites, such as the motor neuron and the growth cone. Consistent with the described role of GBF1 in Golgi function and maintenance, we observed marked increase in Golgi fragmentation in primary fibroblasts derived from all affected individuals in this study. Our results not only reinforce the existing link between Golgi fragmentation and neurodegeneration but also demonstrate that pathogenic variants in GBF1 are associated with HMN/CMT2.
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Rasmussen ML, Robertson GL, Gama V. Break on Through: Golgi-Derived Vesicles Aid in Mitochondrial Fission. Cell Metab 2020; 31:1047-1049. [PMID: 32492390 PMCID: PMC8212386 DOI: 10.1016/j.cmet.2020.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mitochondrial fission is sustained through contact with several organelles, including the endoplasmic reticulum, lysosomes, and the actin cytoskeleton. Nagashima et al. (2020) now demonstrate that PI(4)P-containing Golgi-derived vesicles also modulate mitochondrial fission, driven by Arf1 and PI(4)KIIIβ activity, identifying a new organelle contact involved in maintaining mitochondrial homeostasis.
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Affiliation(s)
- Megan L Rasmussen
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Gabriella L Robertson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Vivian Gama
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.
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25
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Yarwood R, Hellicar J, Woodman PG, Lowe M. Membrane trafficking in health and disease. Dis Model Mech 2020; 13:13/4/dmm043448. [PMID: 32433026 PMCID: PMC7197876 DOI: 10.1242/dmm.043448] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Membrane trafficking pathways are essential for the viability and growth of cells, and play a major role in the interaction of cells with their environment. In this At a Glance article and accompanying poster, we outline the major cellular trafficking pathways and discuss how defects in the function of the molecular machinery that mediates this transport lead to various diseases in humans. We also briefly discuss possible therapeutic approaches that may be used in the future treatment of trafficking-based disorders. Summary: This At a Glance article and poster summarise the major intracellular membrane trafficking pathways and associated molecular machineries, and describe how defects in these give rise to disease in humans.
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Affiliation(s)
- Rebecca Yarwood
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - John Hellicar
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Philip G Woodman
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Martin Lowe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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26
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Pérez-Palma E, May P, Iqbal S, Niestroj LM, Du J, Heyne HO, Castrillon JA, O'Donnell-Luria A, Nürnberg P, Palotie A, Daly M, Lal D. Identification of pathogenic variant enriched regions across genes and gene families. Genome Res 2020; 30:62-71. [PMID: 31871067 PMCID: PMC6961572 DOI: 10.1101/gr.252601.119] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
Abstract
Missense variant interpretation is challenging. Essential regions for protein function are conserved among gene-family members, and genetic variants within these regions are potentially more likely to confer risk to disease. Here, we generated 2871 gene-family protein sequence alignments involving 9990 genes and performed missense variant burden analyses to identify novel essential protein regions. We mapped 2,219,811 variants from the general population into these alignments and compared their distribution with 76,153 missense variants from patients. With this gene-family approach, we identified 465 regions enriched for patient variants spanning 41,463 amino acids in 1252 genes. As a comparison, by testing the same genes individually, we identified fewer patient variant enriched regions, involving only 2639 amino acids and 215 genes. Next, we selected de novo variants from 6753 patients with neurodevelopmental disorders and 1911 unaffected siblings and observed an 8.33-fold enrichment of patient variants in our identified regions (95% C.I. = 3.90-Inf, P-value = 2.72 × 10-11). By using the complete ClinVar variant set, we found that missense variants inside the identified regions are 106-fold more likely to be classified as pathogenic in comparison to benign classification (OR = 106.15, 95% C.I = 70.66-Inf, P-value < 2.2 × 10-16). All pathogenic variant enriched regions (PERs) identified are available online through "PER viewer," a user-friendly online platform for interactive data mining, visualization, and download. In summary, our gene-family burden analysis approach identified novel PERs in protein sequences. This annotation can empower variant interpretation.
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Affiliation(s)
- Eduardo Pérez-Palma
- Cologne Center for Genomics, University of Cologne, Cologne, 50931 NRW, Germany
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University Luxembourg, L-4367 Esch-sur-Alzette, Luxembourg
| | - Sumaiya Iqbal
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Lisa-Marie Niestroj
- Cologne Center for Genomics, University of Cologne, Cologne, 50931 NRW, Germany
| | - Juanjiangmeng Du
- Cologne Center for Genomics, University of Cologne, Cologne, 50931 NRW, Germany
| | - Henrike O Heyne
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Anne O'Donnell-Luria
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02142, USA
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, 50931 NRW, Germany
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014 Helsinki, Finland
| | - Mark Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014 Helsinki, Finland
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, 50931 NRW, Germany
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
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27
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Abstract
Protein coats are supramolecular complexes that assemble on the cytosolic face of membranes to promote cargo sorting and transport carrier formation in the endomembrane system of eukaryotic cells. Several types of protein coats have been described, including COPI, COPII, AP-1, AP-2, AP-3, AP-4, AP-5, and retromer, which operate at different stages of the endomembrane system. Defects in these coats impair specific transport pathways, compromising the function and viability of the cells. In humans, mutations in subunits of these coats cause various congenital diseases that are collectively referred to as coatopathies. In this article, we review the fundamental properties of protein coats and the diseases that result from mutation of their constituent subunits.
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Affiliation(s)
- Esteban C Dell'Angelica
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Juan S Bonifacino
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland 20892, USA;
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28
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Wiel L, Baakman C, Gilissen D, Veltman JA, Vriend G, Gilissen C. MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum Mutat 2019; 40:1030-1038. [PMID: 31116477 PMCID: PMC6772141 DOI: 10.1002/humu.23798] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/21/2019] [Accepted: 05/15/2019] [Indexed: 01/19/2023]
Abstract
The growing availability of human genetic variation has given rise to novel methods of measuring genetic tolerance that better interpret variants of unknown significance. We recently developed a concept based on protein domain homology in the human genome to improve variant interpretation. For this purpose, we mapped population variation from the Exome Aggregation Consortium (ExAC) and pathogenic mutations from the Human Gene Mutation Database (HGMD) onto Pfam protein domains. The aggregation of these variation data across homologous domains into meta-domains allowed us to generate amino acid resolution of genetic intolerance profiles for human protein domains. Here, we developed MetaDome, a fast and easy-to-use web server that visualizes meta-domain information and gene-wide profiles of genetic tolerance. We updated the underlying data of MetaDome to contain information from 56,319 human transcripts, 71,419 protein domains, 12,164,292 genetic variants from gnomAD, and 34,076 pathogenic mutations from ClinVar. MetaDome allows researchers to easily investigate their variants of interest for the presence or absence of variation at corresponding positions within homologous domains. We illustrate the added value of MetaDome by an example that highlights how it may help in the interpretation of variants of unknown significance. The MetaDome web server is freely accessible at https://stuart.radboudumc.nl/metadome.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Coos Baakman
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Daan Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Bio‐informaticaHAN University of Applied SciencesNijmegenThe Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviourRadboud University Medical CenterNijmegenThe Netherlands
- Institute of Genetic Medicine, International Centre for LifeNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Gerrit Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
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29
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Diets IJ, van der Donk R, Baltrunaite K, Waanders E, Reijnders MRF, Dingemans AJM, Pfundt R, Vulto-van Silfhout AT, Wiel L, Gilissen C, Thevenon J, Perrin L, Afenjar A, Nava C, Keren B, Bartz S, Peri B, Beunders G, Verbeek N, van Gassen K, Thiffault I, Cadieux-Dion M, Huerta-Saenz L, Wagner M, Konstantopoulou V, Vodopiutz J, Griese M, Boel A, Callewaert B, Brunner HG, Kleefstra T, Hoogerbrugge N, de Vries BBA, Hwa V, Dauber A, Hehir-Kwa JY, Kuiper RP, Jongmans MCJ. De Novo and Inherited Pathogenic Variants in KDM3B Cause Intellectual Disability, Short Stature, and Facial Dysmorphism. Am J Hum Genet 2019; 104:758-766. [PMID: 30929739 PMCID: PMC6451728 DOI: 10.1016/j.ajhg.2019.02.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/21/2019] [Indexed: 01/17/2023] Open
Abstract
By using exome sequencing and a gene matching approach, we identified de novo and inherited pathogenic variants in KDM3B in 14 unrelated individuals and three affected parents with varying degrees of intellectual disability (ID) or developmental delay (DD) and short stature. The individuals share additional phenotypic features that include feeding difficulties in infancy, joint hypermobility, and characteristic facial features such as a wide mouth, a pointed chin, long ears, and a low columella. Notably, two individuals developed cancer, acute myeloid leukemia and Hodgkin lymphoma, in childhood. KDM3B encodes for a histone demethylase and is involved in H3K9 demethylation, a crucial part of chromatin modification required for transcriptional regulation. We identified missense and truncating variants, suggesting that KDM3B haploinsufficiency is the underlying mechanism for this syndrome. By using a hybrid facial-recognition model, we show that individuals with a pathogenic variant in KDM3B have a facial gestalt, and that they show significant facial similarity compared to control individuals with ID. In conclusion, pathogenic variants in KDM3B cause a syndrome characterized by ID, short stature, and facial dysmorphism.
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Affiliation(s)
- Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Roos van der Donk
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Kristina Baltrunaite
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, 6229HX Maastricht, the Netherlands
| | - Alexander J M Dingemans
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | | | - Laurens Wiel
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, 21079 Dijon, France; Equipe Génétique des Anomalies du Développement, Université de Bourgogne-France Comté, 21070 Dijon, France
| | - Laurence Perrin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, 21079 Dijon, France
| | - Alexandra Afenjar
- APHP, Département de Génétique et Embryologie Médicale, Centre de Référence Déficiences Intellectuelles de Causes Rares, GRC n°19, ConCer-LD, Hôpital Armand Trousseau, 75012 Paris, France
| | - Caroline Nava
- APHP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France; Sorbonne Universités, Institut du Cerveau et de la Moelle épinière, ICM, Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique UMR 7225, 75013, Paris, France
| | - Boris Keren
- APHP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Sarah Bartz
- Division of Endocrinology, Children's Hospital of Colorado, Aurora, CO 80045, USA
| | - Bethany Peri
- Division of Endocrinology, Children's Hospital of Colorado, Aurora, CO 80045, USA
| | - Gea Beunders
- Department of Clinical Genetics, VU University Medical Center, 1081HV Amsterdam, the Netherlands
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; University of Missouri, Kansas City School of Medicine, Kansas City, MO 66211, USA
| | - Maxime Cadieux-Dion
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA
| | - Lina Huerta-Saenz
- Children's Mercy Hospital, Kansas City, MO 66211, USA; Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, Penn State Hershey Children's Hospital, Hershey, PA 17033, USA
| | - Matias Wagner
- Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany; Institute for Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Vassiliki Konstantopoulou
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Julia Vodopiutz
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Matthias Griese
- Dr. von Hauner Children's Hospital, Division of Pediatric Pneumology, University Hospital Munich, German Center for Lung Research, 80333 Munich, Germany
| | - Annekatrien Boel
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202AZ Maastricht, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Vivian Hwa
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Andrew Dauber
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Endocrinology, Children's National Health System, Washington, DC 20010, USA
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Marjolijn C J Jongmans
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands.
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30
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Affiliation(s)
- Joseph T. C. Shieh
- Division of Medical Genetics, Department of Pediatrics, Institute for Human Genetics, University of California San Francisco, UCSF Benioff Children's Hospital, San Francisco, California, United States of America
- * E-mail:
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31
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Abstract
BACKGROUND Genetic data have the potential to impact patient care significantly. In primary care and in the ICU, patients are undergoing genetic testing. Genetics is also transforming cancer care and undiagnosed diseases. Optimal personalized medicine relies on the understanding of disease penetrance. In this article, I examine the complexity of penetrance. METHODS In this article, I assess how variable penetrance can be seen with many diseases, including those of different modes of inheritance, and how genomic testing is being applied effectively for many diseases. In this article, I also identify challenges in the field, including the interpretation of gene variants. RESULTS Using advancing bioinformatics and detailed phenotypic assessment, we can increase the yield of genomic testing, particularly for highly penetrant conditions. The technologies are useful and applicable to different medical situations. CONCLUSIONS There are now effective genome diagnostics for many diseases. However, the best personalized application of these data still requires skilled interpretation.
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Affiliation(s)
- Joseph T.C. Shieh
- Division of Medical Genetics, Department of Pediatrics, Institute for Human Genetics, University of California, San Francisco, San Francisco, California
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32
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Hiatt SM, Neu MB, Ramaker RC, Hardigan AA, Prokop JW, Hancarova M, Prchalova D, Havlovicova M, Prchal J, Stranecky V, Yim DKC, Powis Z, Keren B, Nava C, Mignot C, Rio M, Revah-Politi A, Hemati P, Stong N, Iglesias AD, Suchy SF, Willaert R, Wentzensen IM, Wheeler PG, Brick L, Kozenko M, Hurst ACE, Wheless JW, Lacassie Y, Myers RM, Barsh GS, Sedlacek Z, Cooper GM. De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay. PLoS Genet 2018; 14:e1007671. [PMID: 30500825 PMCID: PMC6291162 DOI: 10.1371/journal.pgen.1007671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/12/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations that alter signaling of RAS/MAPK-family proteins give rise to a group of Mendelian diseases known as RASopathies. However, among RASopathies, the matrix of genotype-phenotype relationships is still incomplete, in part because there are many RAS-related proteins and in part because the phenotypic consequences may be variable and/or pleiotropic. Here, we describe a cohort of ten cases, drawn from six clinical sites and over 16,000 sequenced probands, with de novo protein-altering variation in RALA, a RAS-like small GTPase. All probands present with speech and motor delays, and most have intellectual disability, low weight, short stature, and facial dysmorphism. The observed rate of de novo RALA variants in affected probands is significantly higher (p = 4.93 x 10−11) than expected from the estimated random mutation rate. Further, all de novo variants described here affect residues within the GTP/GDP-binding region of RALA; in fact, six alleles arose at only two codons, Val25 and Lys128. The affected residues are highly conserved across both RAL- and RAS-family genes, are devoid of variation in large human population datasets, and several are homologous to positions at which disease-associated variants have been observed in other GTPase genes. We directly assayed GTP hydrolysis and RALA effector-protein binding of the observed variants, and found that all but one tested variant significantly reduced both activities compared to wild-type. The one exception, S157A, reduced GTP hydrolysis but significantly increased RALA-effector binding, an observation similar to that seen for oncogenic RAS variants. These results show the power of data sharing for the interpretation and analysis of rare variation, expand the spectrum of molecular causes of developmental disability to include RALA, and provide additional insight into the pathogenesis of human disease caused by mutations in small GTPases. While many causes of developmental disabilities have been identified, a large number of affected children cannot be diagnosed despite extensive medical testing. Previously unknown genetic factors are likely to be the culprits in many of these cases. Using DNA sequencing, and by sharing information among many doctors and researchers, we have identified a set of individuals with developmental problems who all have changes to the same gene, RALA. The affected individuals all have similar symptoms, including intellectual disability, speech delay (or no speech), and problems with motor skills like walking. In nearly all of these cases (10 of 11), the genetic change found in the child was not inherited from either parent. The locations and biological properties of these changes suggest that they are likely to disrupt the normal functions of RALA. Functional experiments also show that the genetic changes found in these individuals alter two key functions of RALA. Together, we have provided evidence that genetic changes in RALA can cause developmental disabilities. These results will allow doctors and researchers to identify additional children with the same condition, providing a clinical diagnosis to these families and leading to new research opportunities.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Matthew B. Neu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Andrew A. Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, United States of America
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Darina Prchalova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Jan Prchal
- Laboratory of NMR Spectroscopy, University of Chemistry and Technology, Prague, Czech Republic
| | - Viktor Stranecky
- Department of Pediatrics and Adolescent Medicine, Diagnostic and Research Unit for Rare Diseases, Charles University 1st Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Dwight K. C. Yim
- Kaiser Permanente-Hawaii, Honolulu, HI, United States of America
| | - Zöe Powis
- Department of Emerging Genetic Medicine, Ambry Genetics, Aliso Viejo, CA, United States of America
| | - Boris Keren
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Nava
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cyril Mignot
- Department of Genetics, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Groupe de Recherche Clinique UPMC "Déficience Intellectuelle et Autisme", Paris, France
| | - Marlene Rio
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France
- Assistance Publique-Hôpitaux de Paris, service de Génétique, Hôpital Necker-Enfants-Malades, Paris, France
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Parisa Hemati
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Alejandro D. Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, United States of America
| | | | | | | | - Patricia G. Wheeler
- Arnold Palmer Hospital, Division of Genetics, Orlando, FL, United States of America
| | - Lauren Brick
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Mariya Kozenko
- Department of Genetics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - James W. Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Memphis, TN, United States of America
- Le Bonheur Children’s Hospital, Memphis, TN, United States of America
| | - Yves Lacassie
- Division of Clinical Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States of America
- Department of Genetics, Children's Hospital, New Orleans, LA, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- * E-mail:
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Penon M, Zahed H, Berger V, Su I, Shieh JT. Using exome sequencing to decipher family history in a healthy individual: Comparison of pathogenic and population MTM1 variants. Mol Genet Genomic Med 2018; 6:722-727. [PMID: 30047259 PMCID: PMC6160706 DOI: 10.1002/mgg3.405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/11/2018] [Accepted: 03/13/2018] [Indexed: 12/31/2022] Open
Abstract
Background When a family encounters the loss of a child early in life, extensive genetic testing of the affected neonate is sometimes not performed or not possible. However, the increasing availability of genomic sequencing may allow for direct application to families in cases where there is a condition inherited from parental gene(s). When neonatal testing is not possible, it is feasible to perform family testing as long as there is optimal interpretation of the genomic information. Here, we present an example of a healthy adult woman with a history of recurrent male neonatal losses due to severe respiratory distress who presented to Medical Genetics for evaluation. A family history of additional male neonatal loss was present, suggesting a potential inherited genetic etiology. Methods Although there was no DNA available from the neonates, by performing exome sequencing on the healthy adult woman, we found a missense variant in MTM1 as a potential candidate, which was deemed pathogenic based on multiple criteria including past report. Results By performing an analysis of all known MTM1‐disease associated mutations and control population variation, we can also better infer the effects of missense variations on MTM1, as not all variants are truncating. MTM1‐X‐linked myotubular myopathy is a condition that leads to male perinatal respiratory failure and a high risk for early mortality. Conclusions The application of genetic testing in the healthy population here highlights the broader utility of genomic sequencing in evaluating unexplained recurrent neonatal loss, especially when genetic testing is not available on the affected neonates.
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Affiliation(s)
- Monica Penon
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California
| | - Hengameh Zahed
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California
| | - Victoria Berger
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California.,Department of Obstetrics, Gynecology and Reproductive Science, University of California San Francisco, San Francisco, California
| | - Irene Su
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California
| | - Joseph T Shieh
- Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California.,Institute for Human Genetics, University of California San Francisco, San Francisco, California
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Abstract
The coat protein complex I (COPI) allows the precise sorting of lipids and proteins between Golgi cisternae and retrieval from the Golgi to the ER. This essential role maintains the identity of the early secretory pathway and impinges on key cellular processes, such as protein quality control. In this Cell Science at a Glance and accompanying poster, we illustrate the different stages of COPI-coated vesicle formation and revisit decades of research in the context of recent advances in the elucidation of COPI coat structure. By calling attention to an array of questions that have remained unresolved, this review attempts to refocus the perspectives of the field.
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Affiliation(s)
- Eric C Arakel
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany .,Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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35
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Slavotinek A, Risolino M, Losa M, Cho MT, Monaghan KG, Schneidman-Duhovny D, Parisotto S, Herkert JC, Stegmann APA, Miller K, Shur N, Chui J, Muller E, DeBrosse S, Szot JO, Chapman G, Pachter NS, Winlaw DS, Mendelsohn BA, Dalton J, Sarafoglou K, Karachunski PI, Lewis JM, Pedro H, Dunwoodie SL, Selleri L, Shieh J. De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects. Hum Mol Genet 2017; 26:4849-4860. [PMID: 29036646 PMCID: PMC6455034 DOI: 10.1093/hmg/ddx363] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/25/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
We present eight patients with de novo, deleterious sequence variants in the PBX1 gene. PBX1 encodes a three amino acid loop extension (TALE) homeodomain transcription factor that forms multimeric complexes with TALE and HOX proteins to regulate target gene transcription during development. As previously reported, Pbx1 homozygous mutant mice (Pbx1-/-) develop malformations and hypoplasia or aplasia of multiple organs, including the craniofacial skeleton, ear, branchial arches, heart, lungs, diaphragm, gut, kidneys, and gonads. Clinical findings similar to those in Pbx mutant mice were observed in all patients with varying expressivity and severity, including external ear anomalies, abnormal branchial arch derivatives, heart malformations, diaphragmatic hernia, renal hypoplasia and ambiguous genitalia. All patients but one had developmental delays. Previously reported patients with congenital anomalies affecting the kidney and urinary tract exhibited deletions and loss of function variants in PBX1. The sequence variants in our cases included missense substitutions adjacent to the PBX1 homeodomain (p.Arg184Pro, p.Met224Lys, and p.Arg227Pro) or within the homeodomain (p.Arg234Pro, and p.Arg235Gln), whereas p.Ser262Glnfs*2, and p.Arg288* yielded truncated PBX1 proteins. Functional studies on five PBX1 sequence variants revealed perturbation of intrinsic, PBX-dependent transactivation ability and altered nuclear translocation, suggesting abnormal interactions between mutant PBX1 proteins and wild-type TALE or HOX cofactors. It is likely that the mutations directly affect the transcription of PBX1 target genes to impact embryonic development. We conclude that deleterious sequence variants in PBX1 cause intellectual disability and pleiotropic malformations resembling those in Pbx1 mutant mice, arguing for strong conservation of gene function between these two species.
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Affiliation(s)
- Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Maurizio Risolino
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Marta Losa
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biochemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sarah Parisotto
- Division of Genetics, Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Johanna C Herkert
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Kathryn Miller
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Natasha Shur
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Jacqueline Chui
- Clinical Genetics, Stanford Children’s Health at CPMC, San Francisco, CA, USA
| | - Eric Muller
- Clinical Genetics, Stanford Children’s Health at CPMC, San Francisco, CA, USA
| | - Suzanne DeBrosse
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Justin O Szot
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Gavin Chapman
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - David S Winlaw
- University of Sydney, Medical School, Sydney, NSW, Australia
- Heart Centre for Children, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Bryce A Mendelsohn
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Joline Dalton
- Paul and Shelia Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
| | - Kyriakie Sarafoglou
- Department of Pediatrics, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | | | - Jane M Lewis
- Department of Urology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Helio Pedro
- Division of Genetics, Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Sally L Dunwoodie
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Licia Selleri
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
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36
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Lelieveld SH, Wiel L, Venselaar H, Pfundt R, Vriend G, Veltman JA, Brunner HG, Vissers LE, Gilissen C. Spatial Clustering of de Novo Missense Mutations Identifies Candidate Neurodevelopmental Disorder-Associated Genes. Am J Hum Genet 2017; 101:478-484. [PMID: 28867141 DOI: 10.1016/j.ajhg.2017.08.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022] Open
Abstract
Haploinsufficiency (HI) is the best characterized mechanism through which dominant mutations exert their effect and cause disease. Non-haploinsufficiency (NHI) mechanisms, such as gain-of-function and dominant-negative mechanisms, are often characterized by the spatial clustering of mutations, thereby affecting only particular regions or base pairs of a gene. Variants leading to haploinsufficency might occasionally cluster as well, for example in critical domains, but such clustering is on the whole less pronounced with mutations often spread throughout the gene. Here we exploit this property and develop a method to specifically identify genes with significant spatial clustering patterns of de novo mutations in large cohorts. We apply our method to a dataset of 4,061 de novo missense mutations from published exome studies of trios with intellectual disability and developmental disorders (ID/DD) and successfully identify 15 genes with clustering mutations, including 12 genes for which mutations are known to cause neurodevelopmental disorders. For 11 out of these 12, NHI mutation mechanisms have been reported. Additionally, we identify three candidate ID/DD-associated genes of which two have an established role in neuronal processes. We further observe a higher intolerance to normal genetic variation of the identified genes compared to known genes for which mutations lead to HI. Finally, 3D modeling of these mutations on their protein structures shows that 81% of the observed mutations are unlikely to affect the overall structural integrity and that they therefore most likely act through a mechanism other than HI.
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37
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Wiel L, Venselaar H, Veltman JA, Vriend G, Gilissen C. Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. Hum Mutat 2017; 38:1454-1463. [PMID: 28815929 PMCID: PMC5656839 DOI: 10.1002/humu.23313] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022]
Abstract
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population‐based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease‐causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 “meta‐domains.” These meta‐domains consist of 30,853 homologous Pfam protein domain instances that cover 36% of all human protein coding sequences. We find that genetic tolerance is consistent across protein domain homologues, and that patterns of genetic tolerance faithfully mimic patterns of evolutionary conservation. Furthermore, for a significant fraction (68%) of the meta‐domains high‐frequency population variation re‐occurs at the same positions across domain homologues more often than expected. In addition, we observe that the presence of pathogenic missense variants at an aligned homologous domain position is often paired with the absence of population variation and vice versa. The use of these meta‐domains can improve the interpretation of genetic variation.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
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