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Martinello C, Panza E, Orlacchio A. Hereditary spastic paraplegias proteome: common pathways and pathogenetic mechanisms. Expert Rev Proteomics 2023; 20:171-188. [PMID: 37788157 DOI: 10.1080/14789450.2023.2260952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023]
Abstract
INTRODUCTION Hereditary spastic paraplegias (HSPs) are a group of inherited neurodegenerative disorders characterized by progressive spasticity and weakness of the lower limbs. These conditions are caused by lesions in the neuronal pyramidal tract and exhibit clinical and genetic variability. Ongoing research focuses on understanding the underlying mechanisms of HSP onset, which ultimately lead to neuronal degeneration. Key molecular mechanisms involved include axonal transport, cytoskeleton dynamics, myelination abnormalities, membrane trafficking, organelle morphogenesis, ER homeostasis, mitochondrial dysfunction, and autophagy deregulation. AREAS COVERED This review aims to provide an overview of the shared pathogenetic mechanisms in various forms of HSPs. By examining disease-causing gene products and their associated functional pathways, this understanding could lead to the discovery of new therapeutic targets and the development of treatments to modify the progression of the disease. EXPERT OPINION Investigating gene functionality is crucial for identifying shared pathogenetic pathways underlying different HSP subtypes. Categorizing protein function and identifying pathways aids in finding biomarkers, predicting early onset, and guiding treatment for a better quality of life. Targeting shared mechanisms enables efficient and cost-effective therapies. Prospects involve identifying new disease-causing genes, refining molecular processes, and implementing findings in diagnosis, key for advancing HSP understanding and developing effective treatments.
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Affiliation(s)
- Chiara Martinello
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Emanuele Panza
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- Unità di Genetica Medica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Antonio Orlacchio
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy
- Dipartimento di Medicina e Chirurgia, Università di Perugia, Perugia, Italy
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Nanayakkara R, Gurung R, Rodgers SJ, Eramo MJ, Ramm G, Mitchell CA, McGrath MJ. Autophagic lysosome reformation in health and disease. Autophagy 2022:1-18. [DOI: 10.1080/15548627.2022.2128019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Randini Nanayakkara
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Rajendra Gurung
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Samuel J. Rodgers
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Matthew J. Eramo
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Georg Ramm
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Monash Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Christina A. Mitchell
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Meagan J. McGrath
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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Spastic paraplegia 51: phenotypic spectrum related to novel homozygous AP4E1 mutation. J Genet 2022. [DOI: 10.1007/s12041-022-01385-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Mahungu AC, Monnakgotla N, Nel M, Heckmann JM. A review of the genetic spectrum of hereditary spastic paraplegias, inherited neuropathies and spinal muscular atrophies in Africans. Orphanet J Rare Dis 2022; 17:133. [PMID: 35331287 PMCID: PMC8944057 DOI: 10.1186/s13023-022-02280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genetic investigations of inherited neuromuscular disorders in Africans, have been neglected. We aimed to summarise the published data and comment on the genetic evidence related to inherited neuropathies (Charcot-Marie-Tooth disease (CMT)), hereditary spastic paraplegias (HSP) and spinal muscular atrophy (SMA) in Africans. Methods PubMed was searched for relevant articles and manual checking of references and review publications were performed for African-ancestry participants with relevant phenotypes and identified genetic variants. For each case report we extracted phenotype information, inheritance pattern, variant segregation and variant frequency in population controls (including up to date frequencies from the gnomAD database). Results For HSP, 23 reports were found spanning the years 2000–2019 of which 19 related to North Africans, with high consanguinity, and six included sub-Saharan Africans. For CMT, 19 reports spanning years 2002–2021, of which 16 related to North Africans and 3 to sub-Saharan Africans. Most genetic variants had not been previously reported. There were 12 reports spanning years 1999–2020 related to SMN1-SMA caused by homozygous exon 7 ± 8 deletion. Interestingly, the population frequency of heterozygous SMN1-exon 7 deletion mutations appeared 2 × lower in Africans compared to Europeans, in addition to differences in the architecture of the SMN2 locus which may impact SMN1-SMA prognosis. Conclusions Overall, genetic data on inherited neuromuscular diseases in sub-Saharan Africa, are sparse. If African patients with rare neuromuscular diseases are to benefit from the expansion in genomics capabilities and therapeutic advancements, then it is critical to document the mutational spectrum of inherited neuromuscular disease in Africa. Highlights Review of genetic variants reported in hereditary spastic paraplegia in Africans Review of genetic variants reported in genetic neuropathies in Africans Review of genetic underpinnings of spinal muscular atrophies in Africans Assessment of pathogenic evidence for candidate variants
Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02280-2.
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Affiliation(s)
- Amokelani C Mahungu
- Neurology Research Group, University of Cape Town Neuroscience Institute, Cape Town, South Africa
| | | | - Melissa Nel
- Neurology Research Group, University of Cape Town Neuroscience Institute, Cape Town, South Africa
| | - Jeannine M Heckmann
- E8-74 Neurology, Department of Medicine, Groote Schuur Hospital and the University of Cape Town Neuroscience Institute, University of Cape Town, Cape Town, South Africa.
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Shin J, Nile A, Oh JW. Role of adaptin protein complexes in intracellular trafficking and their impact on diseases. Bioengineered 2021; 12:8259-8278. [PMID: 34565296 PMCID: PMC8806629 DOI: 10.1080/21655979.2021.1982846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Adaptin proteins (APs) play a crucial role in intracellular cell trafficking. The 'classical' role of APs is carried out by AP1‒3, which bind to clathrin, cargo, and accessory proteins. Accordingly, AP1-3 are crucial for both vesicle formation and sorting. All APs consist of four subunits that are indispensable for their functions. In fact, based on studies using cells, model organism knockdown/knock-out, and human variants, each subunit plays crucial roles and contributes to the specificity of each AP. These studies also revealed that the sorting and intracellular trafficking function of AP can exert varying effects on pathology by controlling features such as cell development, signal transduction related to the apoptosis and proliferation pathways in cancer cells, organelle integrity, receptor presentation, and viral infection. Although the roles and functions of AP1‒3 are relatively well studied, the functions of the less abundant and more recently identified APs, AP4 and AP5, are still to be investigated. Further studies on these APs may enable a better understanding and targeting of specific diseases.APs known or suggested locations and functions.
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Affiliation(s)
- Juhyun Shin
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Arti Nile
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
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Toupenet Marchesi L, Leblanc M, Stevanin G. Current Knowledge of Endolysosomal and Autophagy Defects in Hereditary Spastic Paraplegia. Cells 2021; 10:cells10071678. [PMID: 34359848 PMCID: PMC8307360 DOI: 10.3390/cells10071678] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 12/25/2022] Open
Abstract
Hereditary spastic paraplegia (HSP) refers to a group of neurological disorders involving the degeneration of motor neurons. Due to their clinical and genetic heterogeneity, finding common effective therapeutics is difficult. Therefore, a better understanding of the common pathological mechanisms is necessary. The role of several HSP genes/proteins is linked to the endolysosomal and autophagic pathways, suggesting a functional convergence. Furthermore, impairment of these pathways is particularly interesting since it has been linked to other neurodegenerative diseases, which would suggest that the nervous system is particularly sensitive to the disruption of the endolysosomal and autophagic systems. In this review, we will summarize the involvement of HSP proteins in the endolysosomal and autophagic pathways in order to clarify their functioning and decipher some of the pathological mechanisms leading to HSP.
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Affiliation(s)
- Liriopé Toupenet Marchesi
- Institut du Cerveau—Paris Brain Institute—ICM, INSERM, CNRS, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 75013 Paris, France; (L.T.M.); (M.L.)
- Neurogenetics Team, EPHE, Paris Sciences Lettres Research University, 75000 Paris, France
| | - Marion Leblanc
- Institut du Cerveau—Paris Brain Institute—ICM, INSERM, CNRS, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 75013 Paris, France; (L.T.M.); (M.L.)
- Neurogenetics Team, EPHE, Paris Sciences Lettres Research University, 75000 Paris, France
| | - Giovanni Stevanin
- Institut du Cerveau—Paris Brain Institute—ICM, INSERM, CNRS, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, 75013 Paris, France; (L.T.M.); (M.L.)
- Neurogenetics Team, EPHE, Paris Sciences Lettres Research University, 75000 Paris, France
- Correspondence:
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The role of AP-4 in cargo export from the trans-Golgi network and hereditary spastic paraplegia. Biochem Soc Trans 2020; 48:1877-1888. [PMID: 33084855 DOI: 10.1042/bst20190664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/02/2023]
Abstract
Heterotetrameric adaptor protein (AP) complexes play key roles in protein sorting and transport vesicle formation in the endomembrane system of eukaryotic cells. One of these complexes, AP-4, was identified over 20 years ago but, up until recently, its function remained unclear. AP-4 associates with the trans-Golgi network (TGN) through interaction with small GTPases of the ARF family and recognizes transmembrane proteins (i.e. cargos) having specific sorting signals in their cytosolic domains. Recent studies identified accessory proteins (tepsin, RUSC2 and the FHF complex) that co-operate with AP-4, and cargos (amyloid precursor protein, ATG9A and SERINC3/5) that are exported from the TGN in an AP-4-dependent manner. Defective export of ATG9A from the TGN in AP-4-deficient cells was shown to reduce ATG9A delivery to pre-autophagosomal structures, impairing autophagosome formation and/or maturation. In addition, mutations in AP-4-subunit genes were found to cause neurological dysfunction in mice and a form of complicated hereditary spastic paraplegia referred to as 'AP-4-deficiency syndrome' in humans. These findings demonstrated that mammalian AP-4 is required for the development and function of the central nervous system, possibly through its role in the sorting of ATG9A for the maintenance of autophagic homeostasis. In this article, we review the properties and functions of AP-4, and discuss how they might explain the clinical features of AP-4 deficiency.
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Ebrahimi-Fakhari D, Teinert J, Behne R, Wimmer M, D'Amore A, Eberhardt K, Brechmann B, Ziegler M, Jensen DM, Nagabhyrava P, Geisel G, Carmody E, Shamshad U, Dies KA, Yuskaitis CJ, Salussolia CL, Ebrahimi-Fakhari D, Pearson TS, Saffari A, Ziegler A, Kölker S, Volkmann J, Wiesener A, Bearden DR, Lakhani S, Segal D, Udwadia-Hegde A, Martinuzzi A, Hirst J, Perlman S, Takiyama Y, Xiromerisiou G, Vill K, Walker WO, Shukla A, Dubey Gupta R, Dahl N, Aksoy A, Verhelst H, Delgado MR, Kremlikova Pourova R, Sadek AA, Elkhateeb NM, Blumkin L, Brea-Fernández AJ, Dacruz-Álvarez D, Smol T, Ghoumid J, Miguel D, Heine C, Schlump JU, Langen H, Baets J, Bulk S, Darvish H, Bakhtiari S, Kruer MC, Lim-Melia E, Aydinli N, Alanay Y, El-Rashidy O, Nampoothiri S, Patel C, Beetz C, Bauer P, Yoon G, Guillot M, Miller SP, Bourinaris T, Houlden H, Robelin L, Anheim M, Alamri AS, Mahmoud AAH, Inaloo S, Habibzadeh P, Faghihi MA, Jansen AC, Brock S, Roubertie A, Darras BT, Agrawal PB, Santorelli FM, Gleeson J, Zaki MS, Sheikh SI, Bennett JT, Sahin M. Defining the clinical, molecular and imaging spectrum of adaptor protein complex 4-associated hereditary spastic paraplegia. Brain 2020; 143:2929-2944. [PMID: 32979048 PMCID: PMC7780481 DOI: 10.1093/brain/awz307] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/25/2019] [Accepted: 08/16/2019] [Indexed: 12/21/2022] Open
Abstract
Bi-allelic loss-of-function variants in genes that encode subunits of the adaptor protein complex 4 (AP-4) lead to prototypical yet poorly understood forms of childhood-onset and complex hereditary spastic paraplegia: SPG47 (AP4B1), SPG50 (AP4M1), SPG51 (AP4E1) and SPG52 (AP4S1). Here, we report a detailed cross-sectional analysis of clinical, imaging and molecular data of 156 patients from 101 families. Enrolled patients were of diverse ethnic backgrounds and covered a wide age range (1.0-49.3 years). While the mean age at symptom onset was 0.8 ± 0.6 years [standard deviation (SD), range 0.2-5.0], the mean age at diagnosis was 10.2 ± 8.5 years (SD, range 0.1-46.3). We define a set of core features: early-onset developmental delay with delayed motor milestones and significant speech delay (50% non-verbal); intellectual disability in the moderate to severe range; mild hypotonia in infancy followed by spastic diplegia (mean age: 8.4 ± 5.1 years, SD) and later tetraplegia (mean age: 16.1 ± 9.8 years, SD); postnatal microcephaly (83%); foot deformities (69%); and epilepsy (66%) that is intractable in a subset. At last follow-up, 36% ambulated with assistance (mean age: 8.9 ± 6.4 years, SD) and 54% were wheelchair-dependent (mean age: 13.4 ± 9.8 years, SD). Episodes of stereotypic laughing, possibly consistent with a pseudobulbar affect, were found in 56% of patients. Key features on neuroimaging include a thin corpus callosum (90%), ventriculomegaly (65%) often with colpocephaly, and periventricular white-matter signal abnormalities (68%). Iron deposition and polymicrogyria were found in a subset of patients. AP4B1-associated SPG47 and AP4M1-associated SPG50 accounted for the majority of cases. About two-thirds of patients were born to consanguineous parents, and 82% carried homozygous variants. Over 70 unique variants were present, the majority of which are frameshift or nonsense mutations. To track disease progression across the age spectrum, we defined the relationship between disease severity as measured by several rating scales and disease duration. We found that the presence of epilepsy, which manifested before the age of 3 years in the majority of patients, was associated with worse motor outcomes. Exploring genotype-phenotype correlations, we found that disease severity and major phenotypes were equally distributed among the four subtypes, establishing that SPG47, SPG50, SPG51 and SPG52 share a common phenotype, an 'AP-4 deficiency syndrome'. By delineating the core clinical, imaging, and molecular features of AP-4-associated hereditary spastic paraplegia across the age spectrum our results will facilitate early diagnosis, enable counselling and anticipatory guidance of affected families and help define endpoints for future interventional trials.
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Affiliation(s)
- Darius Ebrahimi-Fakhari
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julian Teinert
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Child Neurology and Metabolic Medicine, Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Robert Behne
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| | - Miriam Wimmer
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Angelica D'Amore
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Kathrin Eberhardt
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Barbara Brechmann
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marvin Ziegler
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dana M Jensen
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Premsai Nagabhyrava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gregory Geisel
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Erin Carmody
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Uzma Shamshad
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kira A Dies
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher J Yuskaitis
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Catherine L Salussolia
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel Ebrahimi-Fakhari
- Pediatric Neurology, Saarland University Medical Center, Homburg/Saar, Germany
- Department of General Pediatrics, University Children's Hospital Muenster, Muenster, Germany
| | - Toni S Pearson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Afshin Saffari
- Division of Child Neurology and Metabolic Medicine, Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Ziegler
- Division of Child Neurology and Metabolic Medicine, Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Kölker
- Division of Child Neurology and Metabolic Medicine, Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Jens Volkmann
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany
| | - Antje Wiesener
- Institute of Human Genetics, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - David R Bearden
- Child Neurology, University of Rochester School of Medicine, Rochester, NY, USA
| | - Shenela Lakhani
- Center for Neurogenetics, Weill Cornell Medical College, New York, NY, USA
| | - Devorah Segal
- Center for Neurogenetics, Weill Cornell Medical College, New York, NY, USA
- Division of Child Neurology, Weill Cornell Medicine, New York City, NY, USA
| | - Anaita Udwadia-Hegde
- Department of Pediatric Neurology, Jaslok Hospital and Research Centre, Mumbai, India
| | - Andrea Martinuzzi
- Scientific Institute, IRCCS E. Medea, Unità Operativa Conegliano, Treviso, Italy
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Seth Perlman
- Division of Neurology, Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | | | - Katharina Vill
- Pediatric Neurology and Developmental Medicine, Dr. v. Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - William O Walker
- Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | | | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ayse Aksoy
- Pediatric Neurology, Dr. Sami Ulus Hospital, Ankara, Turkey
| | - Helene Verhelst
- Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | - Mauricio R Delgado
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Radka Kremlikova Pourova
- Department of Biology and Medical Genetics, Second Medical Faculty, Charles University and UH Motol, Prague, Czech Republic
| | - Abdelrahim A Sadek
- Pediatric Neurology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | | | - Lubov Blumkin
- Movement Disorders Clinic, Pediatric Neurology Unit, Wolfson Medical Center, Holon, Sackler School of Medicine, Tel-Aviv University, Israel
| | | | - David Dacruz-Álvarez
- Neurología Pediátrica, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Thomas Smol
- CHU Lille, Institut de Génétique Médicale, RADEME, Lille, France
| | - Jamal Ghoumid
- CHU Lille, Institut de Génétique Médicale, RADEME, Lille, France
| | - Diego Miguel
- Serviço de Genética Médica, Universidade Federal da Bahia, Salvador, Brazil
| | - Constanze Heine
- Institute of Human Genetics, University Hospital Leipzig, Leipzig, Germany
| | | | | | - Jonathan Baets
- Neurogenetics Group and Neuromuscular Reference Center, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Saskia Bulk
- Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Hossein Darvish
- Cancer Research Center and Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Elizabeth Lim-Melia
- Pediatric Medical Genetics, Maria Fareri Children's Hospital, Valhalla, NY, USA
| | - Nur Aydinli
- Pediatric Genetics, Department of Pediatrics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Yasemin Alanay
- Pediatric Neurology, Istanbul Medical Faculty, Istanbul, Turkey
| | | | | | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | | | | | - Grace Yoon
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Mireille Guillot
- Department of Paediatrics, The Hospital for Sick Children and The University of Toronto, Toronto, Canada
| | - Steven P Miller
- Department of Paediatrics, The Hospital for Sick Children and The University of Toronto, Toronto, Canada
| | - Thomas Bourinaris
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Laura Robelin
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Mathieu Anheim
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Abdullah S Alamri
- Pediatric Neurology, National Neuroscience Institute, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Adel A H Mahmoud
- Pediatrics, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Soroor Inaloo
- Neonatal Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parham Habibzadeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Anna C Jansen
- Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium
| | - Stefanie Brock
- Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium
| | | | - Basil T Darras
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine and Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Joseph Gleeson
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Maha S Zaki
- Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | | | - James T Bennett
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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Chow HM, Garnett EO, Li H, Etchell A, Sepulcre J, Drayna D, Chugani D, Chang SE. Linking Lysosomal Enzyme Targeting Genes and Energy Metabolism with Altered Gray Matter Volume in Children with Persistent Stuttering. NEUROBIOLOGY OF LANGUAGE (CAMBRIDGE, MASS.) 2020; 1:365-380. [PMID: 34041495 PMCID: PMC8138901 DOI: 10.1162/nol_a_00017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 05/13/2020] [Indexed: 04/12/2023]
Abstract
Developmental stuttering is a childhood onset neurodevelopmental disorder with an unclear etiology. Subtle changes in brain structure and function are present in both children and adults who stutter. It is a highly heritable disorder, and 12-20% of stuttering cases may carry a mutation in one of four genes involved in intracellular trafficking. To better understand the relationship between genetics and neuroanatomical changes, we used gene expression data from the Allen Institute for Brain Science and voxel-based morphometry to investigate the spatial correspondence between gene expression patterns and differences in gray matter volume between children with persistent stuttering (n = 26, and 87 scans) and their fluent peers (n = 44, and 139 scans). We found that the expression patterns of two stuttering-related genes (GNPTG and NAGPA) from the Allen Institute data exhibited a strong positive spatial correlation with the magnitude of between-group gray matter volume differences. Additional gene set enrichment analyses revealed that genes whose expression was highly correlated with the gray matter volume differences were enriched for glycolysis and oxidative metabolism in mitochondria. Because our current study did not examine the participants' genomes, these results cannot establish the direct association between genetic mutations and gray matter volume differences in stuttering. However, our results support further study of the involvement of lysosomal enzyme targeting genes, as well as energy metabolism in stuttering. Future studies assessing variations of these genes in the participants' genomes may lead to increased understanding of the biological mechanisms of the observed spatial relationship between gene expression and gray matter volume.
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Affiliation(s)
- Ho Ming Chow
- Department of Communication Sciences and Disorders, University of Delaware, Newark, DE
- Katzin Diagnostic & Research PET/MRI Center, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE
- Department of Psychiatry, University of Michigan, Ann Arbor, MI
- * Corresponding Author:
| | | | - Hua Li
- Katzin Diagnostic & Research PET/MRI Center, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE
| | - Andrew Etchell
- Department of Psychiatry, University of Michigan, Ann Arbor, MI
| | - Jorge Sepulcre
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Dennis Drayna
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD
| | - Diane Chugani
- Department of Communication Sciences and Disorders, University of Delaware, Newark, DE
| | - Soo-Eun Chang
- Department of Psychiatry, University of Michigan, Ann Arbor, MI
- Cognitive Imaging Research Center, Department of Radiology, Michigan State University, East Lansing, MI
- Department of Communicative Sciences and Disorders, Michigan State University, East Lansing, MI
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10
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van Eyk CL, Corbett MA, Frank MSB, Webber DL, Newman M, Berry JG, Harper K, Haines BP, McMichael G, Woenig JA, MacLennan AH, Gecz J. Targeted resequencing identifies genes with recurrent variation in cerebral palsy. NPJ Genom Med 2019; 4:27. [PMID: 31700678 PMCID: PMC6828700 DOI: 10.1038/s41525-019-0101-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/17/2019] [Indexed: 01/13/2023] Open
Abstract
A growing body of evidence points to a considerable and heterogeneous genetic aetiology of cerebral palsy (CP). To identify recurrently variant CP genes, we designed a custom gene panel of 112 candidate genes. We tested 366 clinically unselected singleton cases with CP, including 271 cases not previously examined using next-generation sequencing technologies. Overall, 5.2% of the naïve cases (14/271) harboured a genetic variant of clinical significance in a known disease gene, with a further 4.8% of individuals (13/271) having a variant in a candidate gene classified as intolerant to variation. In the aggregate cohort of individuals from this study and our previous genomic investigations, six recurrently hit genes contributed at least 4% of disease burden to CP: COL4A1, TUBA1A, AGAP1, L1CAM, MAOB and KIF1A. Significance of Rare VAriants (SORVA) burden analysis identified four genes with a genome-wide significant burden of variants, AGAP1, ERLIN1, ZDHHC9 and PROC, of which we functionally assessed AGAP1 using a zebrafish model. Our investigations reinforce that CP is a heterogeneous neurodevelopmental disorder with known as well as novel genetic determinants.
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Affiliation(s)
- C L van Eyk
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - M A Corbett
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - M S B Frank
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - D L Webber
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - M Newman
- 3Alzheimer's Disease Genetics Laboratory, Centre for Molecular Pathology, School of Biological Sciences, University of Adelaide, Adelaide, SA Australia
| | - J G Berry
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - K Harper
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - B P Haines
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - G McMichael
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - J A Woenig
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - A H MacLennan
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia
| | - J Gecz
- 1Robinson Research Institute, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,2Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA Australia.,4South Australian Health and Medical Research Institute, Adelaide, SA Australia
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11
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Bandres-Ciga S, Saez-Atienzar S, Bonet-Ponce L, Billingsley K, Vitale D, Blauwendraat C, Gibbs JR, Pihlstrøm L, Gan-Or Z, Cookson MR, Nalls MA, Singleton AB. The endocytic membrane trafficking pathway plays a major role in the risk of Parkinson's disease. Mov Disord 2019; 34:460-468. [PMID: 30675927 DOI: 10.1002/mds.27614] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/05/2018] [Accepted: 12/23/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND PD is a complex polygenic disorder. In recent years, several genes from the endocytic membrane-trafficking pathway have been suggested to contribute to disease etiology. However, a systematic analysis of pathway-specific genetic risk factors is yet to be performed. OBJECTIVES To comprehensively study the role of the endocytic membrane-trafficking pathway in the risk of PD. METHODS Linkage disequilibrium score regression was used to estimate PD heritability explained by 252 genes involved in the endocytic membrane-trafficking pathway including genome-wide association studies data from 18,869 cases and 22,452 controls. We used pathway-specific single-nucleotide polymorphisms to construct a polygenic risk score reflecting the cumulative risk of common variants. To prioritize genes for follow-up functional studies, summary-data based Mendelian randomization analyses were applied to explore possible functional genomic associations with expression or methylation quantitative trait loci. RESULTS The heritability estimate attributed to endocytic membrane-trafficking pathway was 3.58% (standard error = 1.17). Excluding previously nominated PD endocytic membrane-trafficking pathway genes, the missing heritability was 2.21% (standard error = 0.42). Random heritability simulations were estimated to be 1.44% (standard deviation = 0.54), indicating that the unbiased total heritability explained by the endocytic membrane-trafficking pathway was 2.14%. Polygenic risk score based on endocytic membrane-trafficking pathway showed a 1.25 times increase of PD risk per standard deviation of genetic risk. Finally, Mendelian randomization identified 11 endocytic membrane-trafficking pathway genes showing functional consequence associated to PD risk. CONCLUSIONS We provide compelling genetic evidence that the endocytic membrane-trafficking pathway plays a relevant role in disease etiology. Further research on this pathway is warranted given that critical effort should be made to identify potential avenues within this biological process suitable for therapeutic interventions. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Sara Saez-Atienzar
- Transgenics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Luis Bonet-Ponce
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.,Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Dan Vitale
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Jesse Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Ziv Gan-Or
- Department of Neurology and Neurosurgery, Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | | | - Mark R Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Mike A Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Data Tecnica International, Glen Echo, Maryland, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
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12
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Davies AK, Itzhak DN, Edgar JR, Archuleta TL, Hirst J, Jackson LP, Robinson MS, Borner GHH. AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A. Nat Commun 2018; 9:3958. [PMID: 30262884 PMCID: PMC6160451 DOI: 10.1038/s41467-018-06172-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/17/2018] [Indexed: 12/03/2022] Open
Abstract
Adaptor protein 4 (AP-4) is an ancient membrane trafficking complex, whose function has largely remained elusive. In humans, AP-4 deficiency causes a severe neurological disorder of unknown aetiology. We apply unbiased proteomic methods, including 'Dynamic Organellar Maps', to find proteins whose subcellular localisation depends on AP-4. We identify three transmembrane cargo proteins, ATG9A, SERINC1 and SERINC3, and two AP-4 accessory proteins, RUSC1 and RUSC2. We demonstrate that AP-4 deficiency causes missorting of ATG9A in diverse cell types, including patient-derived cells, as well as dysregulation of autophagy. RUSC2 facilitates the transport of AP-4-derived, ATG9A-positive vesicles from the trans-Golgi network to the cell periphery. These vesicles cluster in close association with autophagosomes, suggesting they are the "ATG9A reservoir" required for autophagosome biogenesis. Our study uncovers ATG9A trafficking as a ubiquitous function of the AP-4 pathway. Furthermore, it provides a potential molecular pathomechanism of AP-4 deficiency, through dysregulated spatial control of autophagy.
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Affiliation(s)
- Alexandra K Davies
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Daniel N Itzhak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Tara L Archuleta
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.
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13
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Kong XF, Martinez-Barricarte R, Kennedy J, Mele F, Lazarov T, Deenick EK, Ma CS, Breton G, Lucero KB, Langlais D, Bousfiha A, Aytekin C, Markle J, Trouillet C, Jabot-Hanin F, Arlehamn CSL, Rao G, Picard C, Lasseau T, Latorre D, Hambleton S, Deswarte C, Itan Y, Abarca K, Moraes-Vasconcelos D, Ailal F, Ikinciogullari A, Dogu F, Benhsaien I, Sette A, Abel L, Boisson-Dupuis S, Schröder B, Nussenzweig MC, Liu K, Geissmann F, Tangye SG, Gros P, Sallusto F, Bustamante J, Casanova JL. Disruption of an antimycobacterial circuit between dendritic and helper T cells in human SPPL2a deficiency. Nat Immunol 2018; 19:973-985. [PMID: 30127434 PMCID: PMC6130844 DOI: 10.1038/s41590-018-0178-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 07/02/2018] [Indexed: 12/21/2022]
Abstract
Human inborn errors of IFN-γ immunity underlie mycobacterial diseases. We describe patients with Mycobacterium bovis (BCG) disease who are homozygous for loss-of-function mutations of SPPL2A. This gene encodes a transmembrane protease that degrades the N-terminal fragment (NTF) of CD74 (HLA invariant chain) in antigen-presenting cells. The CD74 NTF therefore accumulates in the HLA class II+ myeloid and lymphoid cells of SPPL2a-deficient patients. This toxic fragment selectively depletes IL-12- and IL-23-producing CD1c+ conventional dendritic cells (cDC2s) and their circulating progenitors. Moreover, SPPL2a-deficient memory TH1* cells selectively fail to produce IFN-γ when stimulated with mycobacterial antigens in vitro. Finally, Sppl2a-/- mice lack cDC2s, have CD4+ T cells that produce small amounts of IFN-γ after BCG infection, and are highly susceptible to infection with BCG or Mycobacterium tuberculosis. These findings suggest that inherited SPPL2a deficiency in humans underlies mycobacterial disease by decreasing the numbers of cDC2s and impairing IFN-γ production by mycobacterium-specific memory TH1* cells.
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Affiliation(s)
- Xiao-Fei Kong
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA
| | - Ruben Martinez-Barricarte
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA
| | - James Kennedy
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Federico Mele
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland, Bellinzona, Switzerland
| | - Tomi Lazarov
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York , NY, USA
| | - Elissa K Deenick
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales, Australia
| | - Cindy S Ma
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales, Australia
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York , NY, USA
| | - Kimberly B Lucero
- Department of Microbiology and Immunology, Columbia University Medical Center, New York , NY, USA
| | - David Langlais
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, Casablanca, Morocco
- Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, Casablanca, Morocco
| | - Caner Aytekin
- Department of Pediatric Immunology, Dr. Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Janet Markle
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA
| | - Céline Trouillet
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York , NY, USA
| | - Fabienne Jabot-Hanin
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | | | - Geetha Rao
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales, Australia
| | - Capucine Picard
- Paris Descartes University, Imagine Institute, Paris, France
- Study Center for Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Théo Lasseau
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA
| | - Daniela Latorre
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland, Bellinzona, Switzerland
| | - Sophie Hambleton
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA
| | - Katia Abarca
- Department of Pediatric Infectious Diseases and Immunology, Millennium Institute of Immunology and Immunotherapy, School of Medicine, Pontifical Catholic University of Chile, Santiago, Chile
| | - Dewton Moraes-Vasconcelos
- Laboratory of Investigation in Dermatology and Immunodeficiencies, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Fatima Ailal
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, Casablanca, Morocco
- Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, Casablanca, Morocco
| | - Aydan Ikinciogullari
- Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, Ankara, Turkey
| | - Figen Dogu
- Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, Ankara, Turkey
| | - Ibtihal Benhsaien
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, Casablanca, Morocco
- Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, Casablanca, Morocco
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Bernd Schröder
- Biochemical Institute, Christian Albrechts University of Kiel, Kiel, Germany
- Institute of Physiological Chemistry, Technical University Dresden, Dresden, Germany
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York , NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Kang Liu
- Department of Microbiology and Immunology, Columbia University Medical Center, New York , NY, USA
| | - Frédéric Geissmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York , NY, USA
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales, Australia
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Federica Sallusto
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zürich, Switzerland
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
- Study Center for Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York , NY, USA.
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.
- Paris Descartes University, Imagine Institute, Paris, France.
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France.
- Howard Hughes Medical Institute, New York, NY, USA.
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14
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Analysis of 182 cerebral palsy transcriptomes points to dysregulation of trophic signalling pathways and overlap with autism. Transl Psychiatry 2018; 8:88. [PMID: 29681622 PMCID: PMC5911435 DOI: 10.1038/s41398-018-0136-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 02/18/2018] [Indexed: 12/01/2022] Open
Abstract
Cerebral palsy (CP) is the most common motor disability of childhood. It is characterised by permanent, non-progressive but not unchanging problems with movement, posture and motor function, with a highly heterogeneous clinical spectrum and frequent neurodevelopmental comorbidities. The aetiology of CP is poorly understood, despite recent reports of a genetic contribution in some cases. Here we demonstrate transcriptional dysregulation of trophic signalling pathways in patient-derived cell lines from an unselected cohort of 182 CP-affected individuals using both differential expression analysis and weighted gene co-expression network analysis (WGCNA). We also show that genes differentially expressed in CP, as well as network modules significantly correlated with CP status, are enriched for genes associated with ASD. Combining transcriptome and whole exome sequencing (WES) data for this CP cohort likely resolves an additional 5% of cases separated to the 14% we have previously reported as resolved by WES. Collectively, these results support a convergent molecular abnormality in CP and ASD.
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15
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Accogli A, Hamdan FF, Poulin C, Nassif C, Rouleau GA, Michaud JL, Srour M. A novel homozygous AP4B1 mutation in two brothers with AP-4 deficiency syndrome and ocular anomalies. Am J Med Genet A 2018; 176:985-991. [PMID: 29430868 DOI: 10.1002/ajmg.a.38628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 01/09/2023]
Abstract
Adaptor protein complex-4 (AP-4) is a heterotetrameric protein complex which plays a key role in vesicle trafficking in neurons. Mutations in genes affecting different subunits of AP-4, including AP4B1, AP4E1, AP4S1, and AP4M1, have been recently associated with an autosomal recessive phenotype, consisting of spastic tetraplegia, and intellectual disability (ID). The overlapping clinical picture among individuals carrying mutations in any of these genes has prompted the terms "AP-4 deficiency syndrome" for this clinically recognizable phenotype. Using whole-exome sequencing, we identified a novel homozygous mutation (c.991C>T, p.Q331*, NM_006594.4) in AP4B1 in two siblings from a consanguineous Pakistani couple, who presented with severe ID, progressive spastic tetraplegia, epilepsy, and microcephaly. Sanger sequencing confirmed the mutation was homozygous in the siblings and heterozygous in the parents. Similar to previously reported individuals with AP4B1 mutations, brain MRI revealed ventriculomegaly and white matter loss. Interestingly, in addition to the typical facial gestalt reported in other AP-4 deficiency cases, the older brother presented with congenital left Horner syndrome, bilateral optic nerve atrophy and cataract, which have not been previously reported in this condition. In summary, we report a novel AP4B1 homozygous mutation in two siblings and review the phenotype of AP-4 deficiency, speculating on a possible role of AP-4 complex in eye development.
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Affiliation(s)
- Andrea Accogli
- Department of Pediatrics, McGill University, Montreal, Canada.,Istituto Giannina Gaslini, Genova, Italy
| | - Fadi F Hamdan
- CHU Sainte-Justine Research Center, Montréal, Canada
| | - Chantal Poulin
- Department of Pediatrics, McGill University, Montreal, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | | | - Guy A Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Jacques L Michaud
- CHU Sainte-Justine Research Center, Montréal, Canada.,Departments of Pediatrics and Neurosciences, Université de Montréal, Montreal, Canada
| | - Myriam Srour
- Department of Pediatrics, McGill University, Montreal, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
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16
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Frigerio-Domingues C, Drayna D. Genetic contributions to stuttering: the current evidence. Mol Genet Genomic Med 2017; 5:95-102. [PMID: 28361094 PMCID: PMC5370225 DOI: 10.1002/mgg3.276] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Evidence for genetic factors in persistent developmental stuttering has accumulated over the past four decades, and the genes that underlie this disorder are starting to be identified. The genes identified to date, all point to deficits in intracellular trafficking in this disorder.
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Affiliation(s)
- Carlos Frigerio-Domingues
- National Institute on Deafness and Other Communication Disorders Porter Neuroscience Research Center National Institutes of Health
| | - Dennis Drayna
- National Institute on Deafness and Other Communication Disorders Porter Neuroscience Research Center National Institutes of Health
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Informed consent for next-generation nucleotide sequencing studies: Aiding communication between participants and investigators. J Clin Transl Sci 2017. [PMID: 28649453 PMCID: PMC5471895 DOI: 10.1017/cts.2016.21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Obtaining informed consent from prospective participants for research studies that include next-generation nucleotide sequencing (NGS) presents significant challenges because of the need to explain all the potential implications of participating, including the possible return of "incidental" findings, in easy-to-understand language. METHODS AND RESULTS After reviewing the consent processes at other institutions, we decided to supplement the protocol-specific informed consent form with the following: (1) a short pamphlet for the prospective participant that includes a series of questions that she or he is encouraged to ask the investigator, and (2) a more detailed companion guide for investigators to help them develop simple-language answers to the questions. Both documents are available to use or modify. CONCLUSIONS We propose an approach to obtaining informed consent for NGS studies that encourages discussion of key issues without creating a complex, comprehensive document for participants; it also maximizes investigator flexibility. We also suggest mechanisms to return restricted information to participants.
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Assoum M, Philippe C, Isidor B, Perrin L, Makrythanasis P, Sondheimer N, Paris C, Douglas J, Lesca G, Antonarakis S, Hamamy H, Jouan T, Duffourd Y, Auvin S, Saunier A, Begtrup A, Nowak C, Chatron N, Ville D, Mireskandari K, Milani P, Jonveaux P, Lemeur G, Milh M, Amamoto M, Kato M, Nakashima M, Miyake N, Matsumoto N, Masri A, Thauvin-Robinet C, Rivière JB, Faivre L, Thevenon J. Autosomal-Recessive Mutations in AP3B2, Adaptor-Related Protein Complex 3 Beta 2 Subunit, Cause an Early-Onset Epileptic Encephalopathy with Optic Atrophy. Am J Hum Genet 2016; 99:1368-1376. [PMID: 27889060 DOI: 10.1016/j.ajhg.2016.10.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/14/2016] [Accepted: 10/14/2016] [Indexed: 11/30/2022] Open
Abstract
Early-onset epileptic encephalopathy (EOEE) represents a heterogeneous group of severe disorders characterized by seizures, interictal epileptiform activity with a disorganized electroencephalography background, developmental regression or retardation, and onset before 1 year of age. Among a cohort of 57 individuals with epileptic encephalopathy, we ascertained two unrelated affected individuals with EOEE associated with developmental impairment and autosomal-recessive variants in AP3B2 by means of whole-exome sequencing. The targeted sequencing of AP3B2 in 86 unrelated individuals with EOEE led to the identification of an additional family. We gathered five additional families with eight affected individuals through the Matchmaker Exchange initiative by matching autosomal-recessive mutations in AP3B2. Reverse phenotyping of 12 affected individuals from eight families revealed a homogeneous EOEE phenotype characterized by severe developmental delay, poor visual contact with optic atrophy, and postnatal microcephaly. No spasticity, albinism, or hematological symptoms were reported. AP3B2 encodes the neuron-specific subunit of the AP-3 complex. Autosomal-recessive variations of AP3B1, the ubiquitous isoform, cause Hermansky-Pudlak syndrome type 2. The only isoform for the δ subunit of the AP-3 complex is encoded by AP3D1. Autosomal-recessive mutations in AP3D1 cause a severe disorder cumulating the symptoms of the AP3B1 and AP3B2 defects.
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Affiliation(s)
- Mirna Assoum
- Equipe d'Accueil 4271, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France
| | - Christophe Philippe
- Laboratoire de Génétique Médicale, INSERM U954 (Nutrition-Genetics-Environmental Risk Exposure), Centre Hospitalier Universaire Hôpitaux de Brabois, 54511 Vandoeuvre les Nancy, France
| | - Bertrand Isidor
- Service de Génétique Médicale, Centre Hospitalier Universaire de Nantes, 44093 Nantes, France; INSERM UMR_S957, 44093 Nantes, France
| | - Laurence Perrin
- Département de Génétique, Centre Hospitalier Universaire Paris - Hôpital Robert Debré, Assistance Publique - Hôpitaux de Paris, 75019 Paris, France
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva 4, Switzerland
| | - Neal Sondheimer
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
| | - Caroline Paris
- Centre Hospitalier Régional Universitaire, Hôpital Jean Minjoz, 25030 Besançon, France
| | - Jessica Douglas
- Boston Children's Hospital, Feingold Center, Boston, MA 02115, USA
| | - Gaetan Lesca
- Department of Medical Genetics, Groupement Hospitalier Est, Hospices Civils de Lyon, 69677 Bron, France; Université de Lyon, 69100 Villeurbanne, France; Centre Nationnal de la Recherche Scientifique UMR 5292, INSERM U1028, Centre de Recherche en Neurosciences de Lyon, bâtiment l'Institut Multidisciplinaire de Biochimie des Lipides, 69621 Villeurbanne, France
| | - Stylianos Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva, University of Geneva, 1211 Geneva 4, Switzerland
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, University of Geneva, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Thibaud Jouan
- Equipe d'Accueil 4271, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France
| | - Yannis Duffourd
- Equipe d'Accueil 4271, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France; Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, Centre Hospitalier Universitaire Dijon, 21079 Dijon, France
| | - Stéphane Auvin
- INSERM 1141, Service de Neurologie Pédiatrique, Hôpital Robert Debré, 75019 Paris, France
| | - Aline Saunier
- Laboratoire de Génétique Médicale, INSERM U954 (Nutrition-Genetics-Environmental Risk Exposure), Centre Hospitalier Universaire Hôpitaux de Brabois, 54511 Vandoeuvre les Nancy, France
| | - Amber Begtrup
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Catherine Nowak
- Boston Children's Hospital, Feingold Center, Boston, MA 02115, USA
| | - Nicolas Chatron
- Department of Medical Genetics, Groupement Hospitalier Est, Hospices Civils de Lyon, 69677 Bron, France; Université de Lyon, 69100 Villeurbanne, France; Centre Nationnal de la Recherche Scientifique UMR 5292, INSERM U1028, Centre de Recherche en Neurosciences de Lyon, bâtiment l'Institut Multidisciplinaire de Biochimie des Lipides, 69621 Villeurbanne, France
| | - Dorothée Ville
- Department of Pediatric Neurology, Groupement Hospitalier Est, Hospices Civils de Lyon, 69677 Bron, France
| | - Kamiar Mireskandari
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
| | - Paolo Milani
- Service de Physiologie Clinique et Explorations Fonctionnelles, Hôpital Lariboisière, Assistance Publique - Hôpitaux de Paris, 75475 Paris, France
| | - Philippe Jonveaux
- Laboratoire de Génétique Médicale, INSERM U954 (Nutrition-Genetics-Environmental Risk Exposure), Centre Hospitalier Universaire Hôpitaux de Brabois, 54511 Vandoeuvre les Nancy, France
| | - Guylène Lemeur
- Service d'Ophtalmologie, Centre Hospitalo-Universitaire de Nantes, 44093 Nantes, France
| | - Mathieu Milh
- Service de Neurologie Pédiatrique, Hôpital de la Timone, Assistance Publique des Hôpitaux de Marseille, 13005 Marseille, France; INSERM UMR_S910, Aix-Marseille Université, 13005 Marseille, France
| | - Masano Amamoto
- Pediatrics Emergency Center, Kitakyushu Municipal Yahata Hospitals, Kitakyushu 803-8501, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo 142-8555, Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Amira Masri
- Department of Paediatrics, Faculty of Medicine, Jordan University, Amman 11942, Jordan
| | - Christel Thauvin-Robinet
- Equipe d'Accueil 4271, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France; INSERM 1141, Service de Neurologie Pédiatrique, Hôpital Robert Debré, 75019 Paris, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, 21079 Dijon, France
| | - Jean-Baptiste Rivière
- Equipe d'Accueil 4271, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France; INSERM 1141, Service de Neurologie Pédiatrique, Hôpital Robert Debré, 75019 Paris, France
| | - Laurence Faivre
- Equipe d'Accueil 4271, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France; INSERM 1141, Service de Neurologie Pédiatrique, Hôpital Robert Debré, 75019 Paris, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, 21079 Dijon, France
| | - Julien Thevenon
- Equipe d'Accueil 4271, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France; INSERM 1141, Service de Neurologie Pédiatrique, Hôpital Robert Debré, 75019 Paris, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, 21079 Dijon, France.
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Duncan C, Jamieson F, Mehaffy C. Preliminary evaluation of exome sequencing to identify genetic markers of susceptibility to tuberculosis disease. BMC Res Notes 2015; 8:750. [PMID: 26643661 PMCID: PMC4672511 DOI: 10.1186/s13104-015-1740-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/25/2015] [Indexed: 12/11/2022] Open
Abstract
Background Recent studies have shown that certain human genetic polymorphisms could be associated with susceptibility to tuberculosis (TB) infection and disease. Advances in next generation sequencing include the ability to rapidly sequence the entire human exome. These new technologies can be exploited to identify new associations of human genetic polymorphisms and TB infection and disease. In this preliminary study we compared two different strategies for sequencing of the human exome in a small sample set consisting of three individuals with a history of TB disease and two individuals with latent TB infection. Findings Sequencing of the entire exome of the five participants using Agilent SureSelect kit resulted in the identification of 1611 single nucleotide polymorphisms (SNPs) that were only present in the individuals with a history of active TB but not in the latent TB cases. Alternatively, sequencing of 4000 target genes available in the TruSight kit resulted in identification of 182 SNPs only present in the active TB cases and not in the latent TB participants. The overlap of the two kits was 112 SNPs. Conclusions Even though this pilot study was restricted to a small number of participants, we demonstrated the feasibility of using exome sequencing technologies to mine potential genetic associations of susceptibility to TB disease and presented a number of potential targets that can be further explore in larger research trials. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1740-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Frances Jamieson
- Public Health Ontario, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | - Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, Colorado State University, 1619 Campus Delivery, Fort Collins, CO, 80523-1601, USA.
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Raza MH, Mattera R, Morell R, Sainz E, Rahn R, Gutierrez J, Paris E, Root J, Solomon B, Brewer C, Basra MAR, Khan S, Riazuddin S, Braun A, Bonifacino JS, Drayna D. Association between Rare Variants in AP4E1, a Component of Intracellular Trafficking, and Persistent Stuttering. Am J Hum Genet 2015; 97:715-25. [PMID: 26544806 PMCID: PMC4667129 DOI: 10.1016/j.ajhg.2015.10.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/13/2015] [Indexed: 12/28/2022] Open
Abstract
Stuttering is a common, highly heritable neurodevelopmental disorder characterized by deficits in the volitional control of speech. Whole-exome sequencing identified two heterozygous AP4E1 coding variants, c.1549G>A (p.Val517Ile) and c.2401G>A (p.Glu801Lys), that co-segregate with persistent developmental stuttering in a large Cameroonian family, and we observed the same two variants in unrelated Cameroonians with persistent stuttering. We found 23 other rare variants, including predicted loss-of-function variants, in AP4E1 in unrelated stuttering individuals in Cameroon, Pakistan, and North America. The rate of rare variants in AP4E1 was significantly higher in unrelated Pakistani and Cameroonian stuttering individuals than in population-matched control individuals, and coding variants in this gene are exceptionally rare in the general sub-Saharan West African, South Asian, and North American populations. Clinical examination of the Cameroonian family members failed to identify any symptoms previously reported in rare individuals carrying homozygous loss-of-function mutations in this gene. AP4E1 encodes the ε subunit of the heterotetrameric (ε-β4-μ4-σ4) AP-4 complex, involved in protein sorting at the trans-Golgi network. We found that the μ4 subunit of AP-4 interacts with NAGPA, an enzyme involved in the synthesis of the mannose 6-phosphate signal that targets acid hydrolases to the lysosome and the product of a gene previously associated with stuttering. These findings implicate deficits in intracellular trafficking in persistent stuttering.
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Affiliation(s)
- M Hashim Raza
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Rafael Mattera
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Robert Morell
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Eduardo Sainz
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Rachel Rahn
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Joanne Gutierrez
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Emily Paris
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Jessica Root
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Beth Solomon
- Clinical Center Speech Language Pathology Service, NIH, Bethesda, MD 20892, USA
| | - Carmen Brewer
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - M Asim Raza Basra
- Institute of Chemistry, University of the Punjab, Lahore 54590, Pakistan
| | - Shaheen Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | | | - Allen Braun
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Juan S Bonifacino
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Dennis Drayna
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA.
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Langouët M, Siquier-Pernet K, Sanquer S, Bole-Feysot C, Nitschke P, Boddaert N, Munnich A, Mancini GMS, Barouki R, Amiel J, Colleaux L. Contiguous mutation syndrome in the era of high-throughput sequencing. Mol Genet Genomic Med 2015; 3:215-20. [PMID: 26029708 PMCID: PMC4444163 DOI: 10.1002/mgg3.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 01/27/2023] Open
Abstract
We investigated two siblings, born to consanguineous parents, with neurological features reminiscent of adaptor protein complex 4 (AP4) deficiency, an autosomal recessive neurodevelopmental disorder characterized by neonatal hypotonia that progresses to hypertonia and spasticity, severe intellectual disability speech delay, microcephaly, and growth retardation. Yet, both children also presented with early onset obesity. Whole-exome sequencing identified two homozygous substitutions in two genes 170 kb apart on 7q22.1: a c.1137+1G>T splice mutation in AP4M1 previously described in a familial case of AP4-deficiency syndrome and the AZGP1 c.595A>T missense variant. Haplotyping analysis indicated a founder effect of the AP4M1 mutation, whereas the AZGP1 mutation arose more recently in our family. AZGP1 encodes an adipokine that stimulate lipolysis in adipocytes and regulates body weight in mice. We propose that the siblings' phenotype results from the combined effects of mutations in both AP4M1 and AZGP1 that account for the neurological signs and the morbid obesity of early onset, respectively. Contiguous gene syndromes are the consequence of loss of two or more adjacent genes sensible to gene dosage and the phenotype reflects a combination of endophenotypes. We propose to broaden this concept to phenotypes resulting from independent mutations in two genetically linked genes causing a contiguous mutation syndrome.
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Affiliation(s)
- Maéva Langouët
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital 75015, Paris, France
| | - Karine Siquier-Pernet
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital 75015, Paris, France
| | - Sylvia Sanquer
- Metabolic and Proteomic Biochemistry Service, Necker-Enfants Malades Hospital, AP-HP 75015, Paris, France
| | - Christine Bole-Feysot
- Genomic Platform, INSERM UMR 1163, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute 75015, Paris, France
| | - Patrick Nitschke
- Bioinformatic Platform, INSERM UMR 1163, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute 75015, Paris, France
| | - Nathalie Boddaert
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital 75015, Paris, France ; Service de Radiologie Pédiatrique, Hôpital Necker-Enfants Malades, AP-HP 75015, Paris, France
| | - Arnold Munnich
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital 75015, Paris, France
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center 3015 CN, Rotterdam, The Netherlands
| | - Robert Barouki
- Metabolic and Proteomic Biochemistry Service, Necker-Enfants Malades Hospital, AP-HP 75015, Paris, France
| | - Jeanne Amiel
- Service de Génétique, Hôpital Necker-Enfants Malades, AP-HP 75015, Paris, France
| | - Laurence Colleaux
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Necker-Enfants Malades Hospital 75015, Paris, France
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Hardies K, May P, Djémié T, Tarta-Arsene O, Deconinck T, Craiu D, Helbig I, Suls A, Balling R, Weckhuysen S, De Jonghe P, Hirst J. Recessive loss-of-function mutations in AP4S1 cause mild fever-sensitive seizures, developmental delay and spastic paraplegia through loss of AP-4 complex assembly. Hum Mol Genet 2014; 24:2218-27. [PMID: 25552650 DOI: 10.1093/hmg/ddu740] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report two siblings with infantile onset seizures, severe developmental delay and spastic paraplegia, in whom whole-genome sequencing revealed compound heterozygous mutations in the AP4S1 gene, encoding the σ subunit of the adaptor protein complex 4 (AP-4). The effect of the predicted loss-of-function variants (p.Gln46Profs*9 and p.Arg97*) was further investigated in a patient's fibroblast cell line. We show that the premature stop mutations in AP4S1 result in a reduction of all AP-4 subunits and loss of AP-4 complex assembly. Recruitment of the AP-4 accessory protein tepsin, to the membrane was also abolished. In retrospect, the clinical phenotype in the family is consistent with previous reports of the AP-4 deficiency syndrome. Our study reports the second family with mutations in AP4S1 and describes the first two patients with loss of AP4S1 and seizures. We further discuss seizure phenotypes in reported patients, highlighting that seizures are part of the clinical manifestation of the AP-4 deficiency syndrome. We also hypothesize that endosomal trafficking is a common theme between heritable spastic paraplegia and some inherited epilepsies.
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Affiliation(s)
- Katia Hardies
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg, Institute for Systems Biology, Seattle, USA
| | - Tania Djémié
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Oana Tarta-Arsene
- Pediatric Neurology Clinic, Al Obregia Hospital, Bucharest, Romania, Department of Neurology, Pediatric Neurology, Psychiatry, Child and Adolescent Psychiatry, and Neurosurgery, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Tine Deconinck
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Dana Craiu
- Pediatric Neurology Clinic, Al Obregia Hospital, Bucharest, Romania, Department of Neurology, Pediatric Neurology, Psychiatry, Child and Adolescent Psychiatry, and Neurosurgery, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | | | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian Albrechts University, Kiel, Germany, Division of Neurology, The Children's Hospital of Philadelphia, Philadephia, USA
| | - Arvid Suls
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Rudy Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sarah Weckhuysen
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Peter De Jonghe
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium, Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium, Division of Neurology, Antwerp University Hospital, Antwerp, Belgium and
| | - Jennifer Hirst
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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Bustamante J, Boisson-Dupuis S, Abel L, Casanova JL. Mendelian susceptibility to mycobacterial disease: genetic, immunological, and clinical features of inborn errors of IFN-γ immunity. Semin Immunol 2014; 26:454-70. [PMID: 25453225 DOI: 10.1016/j.smim.2014.09.008] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 09/28/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022]
Abstract
Mendelian susceptibility to mycobacterial disease (MSMD) is a rare condition characterized by predisposition to clinical disease caused by weakly virulent mycobacteria, such as BCG vaccines and environmental mycobacteria, in otherwise healthy individuals with no overt abnormalities in routine hematological and immunological tests. MSMD designation does not recapitulate all the clinical features, as patients are also prone to salmonellosis, candidiasis and tuberculosis, and more rarely to infections with other intramacrophagic bacteria, fungi, or parasites, and even, perhaps, a few viruses. Since 1996, nine MSMD-causing genes, including seven autosomal (IFNGR1, IFNGR2, STAT1, IL12B, IL12RB1, ISG15, and IRF8) and two X-linked (NEMO, and CYBB) genes have been discovered. The high level of allelic heterogeneity has already led to the definition of 18 different disorders. The nine gene products are physiologically related, as all are involved in IFN-γ-dependent immunity. These disorders impair the production of (IL12B, IL12RB1, IRF8, ISG15, NEMO) or the response to (IFNGR1, IFNGR2, STAT1, IRF8, CYBB) IFN-γ. These defects account for only about half the known MSMD cases. Patients with MSMD-causing genetic defects may display other infectious diseases, or even remain asymptomatic. Most of these inborn errors do not show complete clinical penetrance for the case-definition phenotype of MSMD. We review here the genetic, immunological, and clinical features of patients with inborn errors of IFN-γ-dependent immunity.
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Affiliation(s)
- Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, INSERM-U1163, Paris, France, EU; Paris Descartes University, Imagine Institute, Paris, France, EU; Center for the Study of Primary Immunodeficiencies, Assistance Publique-Hôpitaux de Paris AP-HP, Necker-Enfants Malades Hospital, Paris, France, EU.
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, INSERM-U1163, Paris, France, EU; Paris Descartes University, Imagine Institute, Paris, France, EU; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, INSERM-U1163, Paris, France, EU; Paris Descartes University, Imagine Institute, Paris, France, EU; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, INSERM-U1163, Paris, France, EU; Paris Descartes University, Imagine Institute, Paris, France, EU; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, NY, USA; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France, EU
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An AP4B1 frameshift mutation in siblings with intellectual disability and spastic tetraplegia further delineates the AP-4 deficiency syndrome. Eur J Hum Genet 2014; 23:256-9. [PMID: 24781758 DOI: 10.1038/ejhg.2014.73] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/04/2014] [Accepted: 03/07/2014] [Indexed: 01/28/2023] Open
Abstract
The recently proposed adaptor protein 4 (AP-4) deficiency syndrome comprises a group of congenital neurological disorders characterized by severe intellectual disability (ID), delayed or absent speech, hereditary spastic paraplegia, and growth retardation. AP-4 is a heterotetrameric protein complex with important functions in vesicle trafficking. Mutations in genes affecting different subunits of AP-4, including AP4B1, AP4E1, AP4S1, and AP4M1, have been reported in patients with the AP-4 deficiency phenotype. We describe two siblings from a non-consanguineous couple who presented with severe ID, absent speech, microcephaly, growth retardation, and progressive spastic tetraplegia. Whole-exome sequencing in the two patients identified the novel homozygous 2-bp deletion c.1160_1161delCA (p.(Thr387Argfs*30)) in AP4B1. Sanger sequencing confirmed the mutation in the siblings and revealed it in the heterozygous state in both parents. The AP4B1-associated phenotype has previously been assigned to spastic paraplegia-47. Identification of a novel AP4B1 alteration in two patients with clinical manifestations highly similar to other individuals with mutations affecting one of the four AP-4 subunits further supports the observation that loss of AP-4 assembly or functionality underlies the common clinical features in these patients and underscores the existence of the clinically recognizable AP-4 deficiency syndrome.
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Srivastava AK, Schwartz CE. Intellectual disability and autism spectrum disorders: causal genes and molecular mechanisms. Neurosci Biobehav Rev 2014; 46 Pt 2:161-74. [PMID: 24709068 DOI: 10.1016/j.neubiorev.2014.02.015] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/30/2014] [Accepted: 02/12/2014] [Indexed: 12/19/2022]
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are the most common developmental disorders present in humans. Combined, they affect between 3 and 5% of the population. Additionally, they can be found together in the same individual thereby complicating treatment. The causative factors (genes, epigenetic and environmental) are quite varied and likely interact so as to further complicate the assessment of an individual patient. Nonetheless, much valuable information has been gained by identifying candidate genes for ID or ASD. Understanding the etiology of either ID or ASD is of utmost importance for families. It allows a determination of the risk of recurrence, the possibility of other comorbidity medical problems, the molecular and cellular nature of the pathobiology and hopefully potential therapeutic approaches.
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Affiliation(s)
- Anand K Srivastava
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - Charles E Schwartz
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA.
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26
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Pérez de Diego R, Mulvey C, Casanova JL, Godovac-Zimmermann J. Proteomics in immunity and herpes simplex encephalitis. Expert Rev Proteomics 2013; 11:21-9. [PMID: 24351021 DOI: 10.1586/14789450.2014.864954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The genetic theory of infectious diseases has proposed that susceptibility to life-threatening infectious diseases in childhood, occurring in the course of primary infection, results mostly from individually rare but collectively diverse single-gene variants. Recent evidence of an ever-expanding spectrum of genes involved in susceptibility to infectious disease indicates that the paradigm has important implications for diagnosis and treatment. One such pathology is childhood herpes simplex encephalitis, which shows a pattern of rare but diverse disease-disposing genetic variants. The present report shows how proteomics can help to understand susceptibility to childhood herpes simplex encephalitis and other viral infections, suggests that proteomics may have a particularly important role to play, emphasizes that variation over the population is a critical issue for proteomics and notes some new challenges for proteomics and related bioinformatics tools in the context of rare but diverse genetic defects.
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Affiliation(s)
- Rebeca Pérez de Diego
- Immunology Unit, IdiPAZ Institute for Health Research, La Paz University Hospital, 261 Pº Castellana, Madrid 28046, Spain
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27
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Chung RH, Shih CC. SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies. BMC Bioinformatics 2013; 14:199. [PMID: 23782512 PMCID: PMC3693898 DOI: 10.1186/1471-2105-14-199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/14/2013] [Indexed: 11/22/2022] Open
Abstract
Background Association studies based on next-generation sequencing (NGS) technology have become popular, and statistical association tests for NGS data have been developed rapidly. A flexible tool for simulating sequence data in either unrelated case–control or family samples with different disease and quantitative trait models would be useful for evaluating the statistical power for planning a study design and for comparing power among statistical methods based on NGS data. Results We developed a simulation tool, SeqSIMLA, which can simulate sequence data with user-specified disease and quantitative trait models. We implemented two disease models, in which the user can flexibly specify the number of disease loci, effect sizes or population attributable risk, disease prevalence, and risk or protective loci. We also implemented a quantitative trait model, in which the user can specify the number of quantitative trait loci (QTL), proportions of variance explained by the QTL, and genetic models. We compiled recombination rates from the HapMap project so that genomic structures similar to the real data can be simulated. Conclusions SeqSIMLA can efficiently simulate sequence data with disease or quantitative trait models specified by the user. SeqSIMLA will be very useful for evaluating statistical properties for new study designs and new statistical methods using NGS. SeqSIMLA can be downloaded for free at http://seqsimla.sourceforge.net.
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Affiliation(s)
- Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, Taiwan.
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