1
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Li Y, Cacciottolo TM, Yin N, He Y, Liu H, Liu H, Yang Y, Henning E, Keogh JM, Lawler K, Mendes de Oliveira E, Gardner EJ, Kentistou KA, Laouris P, Bounds R, Ong KK, Perry JRB, Barroso I, Tu L, Bean JC, Yu M, Conde KM, Wang M, Ginnard O, Fang X, Tong L, Han J, Darwich T, Williams KW, Yang Y, Wang C, Joss S, Firth HV, Xu Y, Farooqi IS. Loss of transient receptor potential channel 5 causes obesity and postpartum depression. Cell 2024; 187:4176-4192.e17. [PMID: 38959890 DOI: 10.1016/j.cell.2024.06.001] [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: 12/25/2023] [Revised: 03/24/2024] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
Hypothalamic neural circuits regulate instinctive behaviors such as food seeking, the fight/flight response, socialization, and maternal care. Here, we identified microdeletions on chromosome Xq23 disrupting the brain-expressed transient receptor potential (TRP) channel 5 (TRPC5). This family of channels detects sensory stimuli and converts them into electrical signals interpretable by the brain. Male TRPC5 deletion carriers exhibited food seeking, obesity, anxiety, and autism, which were recapitulated in knockin male mice harboring a human loss-of-function TRPC5 mutation. Women carrying TRPC5 deletions had severe postpartum depression. As mothers, female knockin mice exhibited anhedonia and depression-like behavior with impaired care of offspring. Deletion of Trpc5 from oxytocin neurons in the hypothalamic paraventricular nucleus caused obesity in both sexes and postpartum depressive behavior in females, while Trpc5 overexpression in oxytocin neurons in knock-in mice reversed these phenotypes. We demonstrate that TRPC5 plays a pivotal role in mediating innate human behaviors fundamental to survival, including food seeking and maternal care.
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Affiliation(s)
- Yongxiang Li
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Tessa M Cacciottolo
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Na Yin
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yang He
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Hesong Liu
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Hailan Liu
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yuxue Yang
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Taizhou People's Hospital, Medical School of Yangzhou University, Taizhou, Jiangsu, China
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Julia M Keogh
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Katherine Lawler
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Edson Mendes de Oliveira
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Eugene J Gardner
- MRC Epidemiology Unit, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Katherine A Kentistou
- MRC Epidemiology Unit, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Panayiotis Laouris
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Rebecca Bounds
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - John R B Perry
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK; MRC Epidemiology Unit, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Inês Barroso
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, Exeter, UK
| | - Longlong Tu
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan C Bean
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Meng Yu
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kristine M Conde
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Mengjie Wang
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Olivia Ginnard
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Xing Fang
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Lydia Tong
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Junying Han
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Tia Darwich
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kevin W Williams
- Center for Hypothalamic Research, Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9077, USA
| | - Yongjie Yang
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Chunmei Wang
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Shelagh Joss
- West of Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow, UK
| | - Helen V Firth
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust & Wellcome Sanger Institute, Cambridge, UK
| | - Yong Xu
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
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2
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Kharrat M, Issa AB, Tlili A, Jallouli O, Alila-Fersi O, Maalej M, Chouchen J, Ghouylia Y, Kamoun F, Triki C, Fakhfakh F. A Novel Mutation in the MAP7D3 Gene in Two Siblings with Severe Intellectual Disability and Autistic Traits: Concurrent Assessment of BDNF Functional Polymorphism, X-Inactivation and Oxidative Stress to Explain Disease Severity. J Mol Neurosci 2023; 73:853-864. [PMID: 37817054 DOI: 10.1007/s12031-023-02163-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023]
Abstract
Intellectual disabilities (ID) and autism spectrum disorders (ASD) are characterized by extreme genetic and phenotypic heterogeneity. However, understanding this heterogeneity is difficult due to the intricate interplay among multiple interconnected genes, epigenetic factors, oxidative stress, and environmental factors. Employing next-generation sequencing (NGS), we revealed the genetic cause of ID and autistic traits in two patients from a consanguineous family followed by segregation analysis. Furthermore, in silico prediction methods and 3D modeling were conducted to predict the effect of the variants. To establish genotype-phenotype correlation, X-chromosome inactivation using Methylation-specific PCR and oxidative stress markers were also investigated. By analyzing the NGS data of the two patients, we identified a novel frameshift mutation c.2174_2177del (p.Thr725MetfsTer2) in the MAP7D3 gene inherited from their mother along with the functional BDNF Val66Met polymorphism inherited from their father. The 3D modeling demonstrated that the p.Thr725MetfsTer2 variant led to the loss of the C-terminal tail of the MAP7D3 protein. This change could destabilize its structure and impact kinesin-1's binding to microtubules via an allosteric effect. Moreover, the analysis of oxidative stress biomarkers revealed an elevated oxidative stress in the two patients compared to the controls. To the best of our knowledge, this is the first report describing severe ID and autistic traits in familial cases with novel frameshift mutation c.2174_2177del in the MAP7D3 gene co-occurring with the functional polymorphism Val66M in the BDNF gene. Besides, our study underlines the importance of investigating combined genetic variations, X-chromosome inactivation (XCI) patterns, and oxidative stress markers for a better understanding of ID and autism etiology.
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Affiliation(s)
- Marwa Kharrat
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax University, Sfax, Tunisia.
| | - Abir Ben Issa
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Olfa Jallouli
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Olfa Alila-Fersi
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax University, Sfax, Tunisia
| | - Marwa Maalej
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax University, Sfax, Tunisia
| | - Jihen Chouchen
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Yosra Ghouylia
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Fatma Kamoun
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Chahnez Triki
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax University, Sfax, Tunisia.
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3
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Timms RT, Mena EL, Leng Y, Li MZ, Tchasovnikarova IA, Koren I, Elledge SJ. Defining E3 ligase-substrate relationships through multiplex CRISPR screening. Nat Cell Biol 2023; 25:1535-1545. [PMID: 37735597 PMCID: PMC10567573 DOI: 10.1038/s41556-023-01229-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 08/11/2023] [Indexed: 09/23/2023]
Abstract
Specificity within the ubiquitin-proteasome system is primarily achieved through E3 ubiquitin ligases, but for many E3s their substrates-and in particular the molecular features (degrons) that they recognize-remain largely unknown. Current approaches for assigning E3s to their cognate substrates are tedious and low throughput. Here we developed a multiplex CRISPR screening platform to assign E3 ligases to their cognate substrates at scale. A proof-of-principle multiplex screen successfully performed ~100 CRISPR screens in a single experiment, refining known C-degron pathways and identifying an additional pathway through which Cul2FEM1B targets C-terminal proline. Further, by identifying substrates for Cul1FBXO38, Cul2APPBP2, Cul3GAN, Cul3KLHL8, Cul3KLHL9/13 and Cul3KLHL15, we demonstrate that the approach is compatible with pools of full-length protein substrates of varying stabilities and, when combined with site-saturation mutagenesis, can assign E3 ligases to their cognate degron motifs. Thus, multiplex CRISPR screening will accelerate our understanding of how specificity is achieved within the ubiquitin-proteasome system.
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Affiliation(s)
- Richard T Timms
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Elijah L Mena
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Mamie Z Li
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Iva A Tchasovnikarova
- Wellcome/CRUK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA.
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4
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Hershberger CE, Louis S, Busch RM, Vegh D, Najm I, Bazeley P, Eng C, Jehi L, Rotroff DM. Molecular subtypes of epilepsy associated with post-surgical seizure recurrence. Brain Commun 2023; 5:fcad251. [PMID: 37881482 PMCID: PMC10597540 DOI: 10.1093/braincomms/fcad251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/07/2023] [Accepted: 09/29/2023] [Indexed: 10/27/2023] Open
Abstract
Approximately 50% of individuals who undergo resective epilepsy surgery experience seizure recurrence. The heterogenous post-operative outcomes are not fully explained by clinical, imaging and electrophysiological variables. We hypothesized that molecular features may be useful in understanding surgical response, and that individuals with epilepsy can be classified into molecular subtypes that are associated with seizure freedom or recurrence after surgical resection. Pre-operative blood samples, brain tissue and post-operative seizure outcomes were collected from a cohort of 40 individuals with temporal lobe epilepsy, 23 of whom experienced post-operative seizure recurrence. Messenger RNA and microRNA extracted from the blood and tissue samples were sequenced. The messenger RNA and microRNA expression levels from the blood and brain were each subjected to a novel clustering approach combined with multiple logistic regression to separate individuals into genetic clusters that identify novel subtypes associated with post-operative seizure outcomes. We then compared the microRNAs and messenger RNAs from patient blood and brain tissue that were significantly associated with each subtype to identify signatures that are similarly over- or under-represented for an outcome and more likely to represent endophenotypes with common molecular aetiology. These target microRNAs and messenger RNAs were further characterized by pathway analysis to assess their functional role in epilepsy. Using blood-derived microRNA and messenger RNA expression levels, we identified two subtypes of epilepsy that were significantly associated with seizure recurrence (clusters A1 and B4) (adjusted P < 0.20). A total of 551 microRNAs and 2486 messenger RNAs were associated with clusters A1 and B4, respectively (adjusted P < 0.05). Clustering of brain-tissue messenger RNA expression levels revealed an additional subtype (C2) associated with seizure recurrence that had high overlap of dysregulated messenger RNA transcripts with cluster B4. Clusters A1, B4 and C2 also shared significant overlap of subjects, which altogether suggests a coordinated mechanism by which microRNA and messenger RNA transcripts may be related to seizure recurrence. Epileptic subtypes A1, B4 and C2 reveal both known and novel microRNA and messenger RNA targets in seizure recurrence. Furthermore, targets identified in A1 and B4 are quantifiable in pre-operative blood samples and could potentially serve as biomarkers for surgical resection outcomes.
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Affiliation(s)
- Courtney E Hershberger
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shreya Louis
- Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Robyn M Busch
- Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Deborah Vegh
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Imad Najm
- Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Charis Eng
- Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Personalized Genetic Healthcare, Community Care and Population Health, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44195, USA
| | - Lara Jehi
- Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Daniel M Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
- Endocrinology and Metabolism Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Center for Quantitative Metabolic Research, Cleveland Clinic, Cleveland, OH 44195, USA
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5
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Kido J, Egami K, Misumi Y, Sugawara K, Tsuchida N, Matsumoto N, Ueda M, Nakamura K. X-linked intellectual disability related to a novel variant of KLHL15. Hum Genome Var 2023; 10:21. [PMID: 37452054 PMCID: PMC10349042 DOI: 10.1038/s41439-023-00248-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 07/18/2023] Open
Abstract
Kelch-like (KLHL) 15, localized on chromosome Xp22.11, was recently identified as an X-linked intellectual disability gene. Herein, we report a case of a male patient with a novel nonsense variant, c.736 C > T p.(Arg246*), in KLHL15, who presented with impaired intelligence, short stature, frequent hypoglycemia, and periodic fever. Patients with nonsense variants in KLHL15 may develop intellectual disabilities, minor skeletal anomalies, and facial dysmorphisms.
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Affiliation(s)
- Jun Kido
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan.
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
| | | | - Yohei Misumi
- Department of Neurology, Kumamoto University Hospital, Kumamoto, Japan
| | - Keishin Sugawara
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Kumamoto University Hospital, Kumamoto, Japan
| | - Kimitoshi Nakamura
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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6
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Caswell RC, Baptista J, Cairns LM, Wilson K, Stewart H. Clinical findings and structural analysis involving a patient with a novel KLHL15 variant. Eur J Med Genet 2023; 66:104768. [PMID: 37059329 DOI: 10.1016/j.ejmg.2023.104768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/16/2023]
Abstract
A de novo novel variant of uncertain significance p. (Arg532del) in the KLHL15 gene was identified by trio exome analysis in a child with global developmental delay, coarse facial features, repetitive behaviour, increased fatigability, poor feeding and gastro-oesophageal reflux. Comparative modelling and structural analysis were performed to gain insight into the effects of the variant on KLHL15 protein structure and function, with a view to aiding variant classification. The p. (Arg532del) variant affects a highly conserved residue within one of the Kelch repeats of the KLHL15 protein. This residue contributes to the stability of loop regions at the substrate binding surface of the protein; comparative modelling of the variant protein predicts altered topology at this surface, including at residue Tyr552, which is known to be important for substrate binding. We propose that it is highly probable that the p. (Arg532del) variant has a deleterious impact on KLHL15 structure, leading to a reduced level of protein function in vivo.
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Affiliation(s)
- Richard C Caswell
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, EX2 5DW, UK
| | - Julia Baptista
- Peninsula Medical School, Faculty of Health, University of Plymouth, UK
| | - Lauren M Cairns
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7HE, UK; Royal Berkshire Hospital, Royal Berkshire NHS Foundation Trust, Reading, RG1 5AN, UK
| | - Kate Wilson
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7HE, UK; Genes Australia, 298 Gilchrist Ave, Herston QLD, 4006, Australia
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7HE, UK.
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7
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Systematic analysis and prediction of genes associated with monogenic disorders on human chromosome X. Nat Commun 2022; 13:6570. [PMID: 36323681 PMCID: PMC9630267 DOI: 10.1038/s41467-022-34264-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Disease gene discovery on chromosome (chr) X is challenging owing to its unique modes of inheritance. We undertook a systematic analysis of human chrX genes. We observe a higher proportion of disorder-associated genes and an enrichment of genes involved in cognition, language, and seizures on chrX compared to autosomes. We analyze gene constraints, exon and promoter conservation, expression, and paralogues, and report 127 genes sharing one or more attributes with known chrX disorder genes. Using machine learning classifiers trained to distinguish disease-associated from dispensable genes, we classify 247 genes, including 115 of the 127, as having high probability of being disease-associated. We provide evidence of an excess of variants in predicted genes in existing databases. Finally, we report damaging variants in CDK16 and TRPC5 in patients with intellectual disability or autism spectrum disorders. This study predicts large-scale gene-disease associations that could be used for prioritization of X-linked pathogenic variants.
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8
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Mitani T, Isikay S, Gezdirici A, Gulec EY, Punetha J, Fatih JM, Herman I, Akay G, Du H, Calame DG, Ayaz A, Tos T, Yesil G, Aydin H, Geckinli B, Elcioglu N, Candan S, Sezer O, Erdem HB, Gul D, Demiral E, Elmas M, Yesilbas O, Kilic B, Gungor S, Ceylan AC, Bozdogan S, Ozalp O, Cicek S, Aslan H, Yalcintepe S, Topcu V, Bayram Y, Grochowski CM, Jolly A, Dawood M, Duan R, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Marafi D, Akdemir ZC, Karaca E, Carvalho CMB, Gibbs RA, Posey JE, Lupski JR, Pehlivan D. High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population. Am J Hum Genet 2021; 108:1981-2005. [PMID: 34582790 PMCID: PMC8546040 DOI: 10.1016/j.ajhg.2021.08.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
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Affiliation(s)
- Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, University of Gaziantep, Gaziantep 27310, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303 Istanbul, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Isabella Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Akif Ayaz
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey; Departments of Medical Genetics, School of Medicine, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Tulay Tos
- University of Health Sciences Zubeyde Hanim Research and Training Hospital of Women's Health and Diseases, Department of Medical Genetics, Ankara 06080, Turkey
| | - Gozde Yesil
- Istanbul Faculty of Medicine, Department of Medical Genetics, Istanbul University, Istanbul 34093, Turkey
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Private Reyap Istanbul Hospital, Istanbul 34515, Turkey
| | - Bilgen Geckinli
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Department of Medical Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey; Eastern Mediterranean University Medical School, Magosa, Mersin 10, Turkey
| | - Sukru Candan
- Medical Genetics Section, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Ozlem Sezer
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun 55100, Turkey
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Emine Demiral
- Department of Medical Genetics, School of Medicine, University of Inonu, Malatya 44280, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Bezmialem Foundation University, Istanbul 34093, Turkey; Department of Pediatrics, Division of Pediatric Critical Care Medicine, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Betul Kilic
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Serdal Gungor
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Ahmet C Ceylan
- Department of Medical Genetics, University of Health Sciences, Ankara Training and Research Hospital, Ankara 06110, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Cukurova University Faculty of Medicine, Adana 01330, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Salih Cicek
- Department of Medical Genetics, Konya Training and Research Hospital, Konya 42250, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, School of Medicine, Trakya University, Edirne 22130, Turkey
| | - Vehap Topcu
- Department of Medical Genetics, Ankara City Hospital, Ankara 06800, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
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9
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Ebstein F, Küry S, Papendorf JJ, Krüger E. Neurodevelopmental Disorders (NDD) Caused by Genomic Alterations of the Ubiquitin-Proteasome System (UPS): the Possible Contribution of Immune Dysregulation to Disease Pathogenesis. Front Mol Neurosci 2021; 14:733012. [PMID: 34566579 PMCID: PMC8455891 DOI: 10.3389/fnmol.2021.733012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
Over thirty years have passed since the first description of ubiquitin-positive structures in the brain of patients suffering from Alzheimer’s disease. Meanwhile, the intracellular accumulation of ubiquitin-modified insoluble protein aggregates has become an indisputable hallmark of neurodegeneration. However, the role of ubiquitin and a fortiori the ubiquitin-proteasome system (UPS) in the pathogenesis of neurodevelopmental disorders (NDD) is much less described. In this article, we review all reported monogenic forms of NDD caused by lesions in genes coding for any component of the UPS including ubiquitin-activating (E1), -conjugating (E2) enzymes, ubiquitin ligases (E3), ubiquitin hydrolases, and ubiquitin-like modifiers as well as proteasome subunits. Strikingly, our analysis revealed that a vast majority of these proteins have a described function in the negative regulation of the innate immune response. In this work, we hypothesize a possible involvement of autoinflammation in NDD pathogenesis. Herein, we discuss the parallels between immune dysregulation and neurodevelopment with the aim at improving our understanding the biology of NDD and providing knowledge required for the design of novel therapeutic strategies.
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Affiliation(s)
- Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'Institut du Thorax, CNRS, INSERM, CHU Nantes, Université de Nantes, Nantes, France
| | - Jonas Johannes Papendorf
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
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10
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Rasheed M, Khan V, Harripaul R, Siddiqui M, Malik MA, Ullah Z, Zahid M, Vincent JB, Ansar M. Exome sequencing identifies novel and known mutations in families with intellectual disability. BMC Med Genomics 2021; 14:211. [PMID: 34452636 PMCID: PMC8399827 DOI: 10.1186/s12920-021-01066-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/25/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Intellectual disability (ID) is a phenotypically and genetically heterogeneous disorder. METHODS In this study, genome wide SNP microarray and whole exome sequencing are used for the variant identification in eight Pakistani families with ID. Beside ID, most of the affected individuals had speech delay, facial dysmorphism and impaired cognitive abilities. Repetitive behavior was observed in MRID143, while seizures were reported in affected individuals belonging to MRID137 and MRID175. RESULTS In two families (MRID137b and MRID175), we identified variants in the genes CCS and ELFN1, which have not previously been reported to cause ID. In four families, variants were identified in ARX, C5orf42, GNE and METTL4. A copy number variation (CNV) was identified in IL1RAPL1 gene in MRID165. CONCLUSION These findings expand the existing knowledge of variants and genes implicated in autosomal recessive and X linked ID.
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Affiliation(s)
- Memoona Rasheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Valeed Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Maimoona Siddiqui
- Division of Neurology, Shifa College of Medicine, H-8/1, Islamabad, Pakistan
| | - Madiha Amin Malik
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Zahid Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
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11
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Jiang E, Fitzgerald MP, Helbig KL, Goldberg EM. IL1RAPL1 Gene Deletion in a Female Patient with Developmental Delay and Continuous Spike-Wave during Sleep. JOURNAL OF PEDIATRIC EPILEPSY 2021. [DOI: 10.1055/s-0041-1731816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractInterleukin-1 receptor accessory protein-like 1 (IL1RAPL1) encodes a protein that is highly expressed in neurons and has been shown to regulate neurite outgrowth as well as synapse formation and synaptic transmission. Clinically, mutations in or deletions of IL1RAPL1 have been associated with a spectrum of neurological dysfunction including autism spectrum disorder and nonsyndromic X-linked developmental delay/intellectual disability of varying severity. Nearly all reported cases are in males; in the few reported cases involving females, the clinical presentation was mild or the deletion was identified in phenotypically normal carriers in accordance with X-linked inheritance. Using genome-wide microarray analysis, we identified a novel de novo 373 kb interstitial deletion of the X chromosome (Xp21.1-p21.2) that includes exons 4 to 6 of the IL1RAPL1 gene in an 8-year-old girl with severe intellectual disability and behavioral disorder with a history of developmental regression. Overnight continuous video electroencephalography revealed electrical status epilepticus in sleep (ESES). This case expands the clinical genetic spectrum of IL1RAPL1-related neurodevelopmental disorders and highlights a new genetic association of ESES.
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Affiliation(s)
- Evan Jiang
- College of Arts and Sciences, The University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Mark P. Fitzgerald
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
- The Epilepsy NeuroGenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Katherine L. Helbig
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
- The Epilepsy NeuroGenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Ethan M. Goldberg
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
- The Epilepsy NeuroGenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
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12
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Brand BA, Blesson AE, Smith-Hicks CL. The Impact of X-Chromosome Inactivation on Phenotypic Expression of X-Linked Neurodevelopmental Disorders. Brain Sci 2021; 11:brainsci11070904. [PMID: 34356138 PMCID: PMC8305405 DOI: 10.3390/brainsci11070904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/16/2021] [Accepted: 06/20/2021] [Indexed: 12/20/2022] Open
Abstract
Nearly 20% of genes located on the X chromosome are associated with neurodevelopmental disorders (NDD) due to their expression and role in brain functioning. Given their location, several of these genes are either subject to or can escape X-chromosome inactivation (XCI). The degree to which genes are subject to XCI can influence the NDD phenotype between males and females. We provide a general review of X-linked NDD genes in the context of XCI and detailed discussion of the sex-based differences related to MECP2 and FMR1, two common X-linked causes of NDD that are subject to XCI. Understanding the effects of XCI on phenotypic expression of NDD genes may guide the development of stratification biomarkers in X-linked disorders.
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Affiliation(s)
- Boudewien A Brand
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA; (B.A.B.); (A.E.B.)
| | - Alyssa E Blesson
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA; (B.A.B.); (A.E.B.)
| | - Constance L. Smith-Hicks
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Correspondence:
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13
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Kokkonen H, Siren A, Määttä T, Kamila Kadlubowska M, Acharya A, Nouel-Saied LM, Leal SM, Järvelä I, Schrauwen I. Identification of microduplications at Xp21.2 and Xq13.1 in neurodevelopmental disorders. Mol Genet Genomic Med 2021; 9:e1703. [PMID: 33982443 PMCID: PMC8683627 DOI: 10.1002/mgg3.1703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/05/2021] [Accepted: 04/20/2021] [Indexed: 11/21/2022] Open
Abstract
Background Microduplications are a rare cause of disease in X‐linked neurodevelopmental disorders but likely have been under reported due challenges in detection and interpretation. Methods We performed exome sequencing and subsequent microarray analysis in two families with a neurodevelopmental disorder. Results Here, we report on two families each with unique inherited microduplications at Xp21.2 and Xq13.1, respectively. In the first family, a 562.8‐kb duplication at Xq13.1 covering DLG3, TEX11, SLC7A3, GDPD2, and part KIF4A was identified in a boy whose phenotype was characterized by delayed speech development, mild intellectual disability (ID), mild dysmorphic facial features, a heart defect, and neuropsychiatric symptoms. By interrogating all reported Xq13.1 duplications in individuals affected with a neurodevelopmental disorder, we provide evidence that this genomic region and particularly DLG3 might be sensitive to an increased dosage. In the second family with four affected males, we found a noncontinuous 223‐ and 204‐kb duplication at Xp21.2, of which the first duplication covers exon 6 of IL1RAPL1. The phenotype of the male patients was characterized by delayed speech development, mild to moderate ID, strabismus, and neurobehavioral symptoms. The carrier daughter and her mother had learning difficulties. IL1RAPL1 shows nonrecurrent causal structural variation and is located at a common fragile site (FRAXC), prone to re‐arrangement. Conclusion In conclusion, we show that comprehensive clinical and genetic examination of microduplications on the X‐chromosome can be helpful in undiagnosed cases of neurodevelopmental disease.
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Affiliation(s)
- Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab and Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Auli Siren
- Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Tuomo Määttä
- Disability Services, Joint Authority for Kainuu, Kajaani, Finland
| | - Magda Kamila Kadlubowska
- Center for Statistical Genetics, Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York, NY, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Department of Neurology, Columbia University Medical Center, New York, NY, USA
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14
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Song J, Merrill RA, Usachev AY, Strack S. The X-linked intellectual disability gene product and E3 ubiquitin ligase KLHL15 degrades doublecortin proteins to constrain neuronal dendritogenesis. J Biol Chem 2020; 296:100082. [PMID: 33199366 PMCID: PMC7948412 DOI: 10.1074/jbc.ra120.016210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/27/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022] Open
Abstract
Proper brain development and function requires finely controlled mechanisms for protein turnover, and disruption of genes involved in proteostasis is a common cause of neurodevelopmental disorders. Kelch-like 15 (KLHL15) is a substrate adaptor for cullin3-containing E3 ubiquitin ligases, and KLHL15 gene mutations were recently described as a cause of severe X-linked intellectual disability. Here, we used a bioinformatics approach to identify a family of neuronal microtubule-associated proteins as KLHL15 substrates, which are themselves critical for early brain development. We biochemically validated doublecortin (DCX), also an X-linked disease protein, and doublecortin-like kinase 1 and 2 as bona fide KLHL15 interactors and mapped KLHL15 interaction regions to their tandem DCX domains. Shared with two previously identified KLHL15 substrates, a FRY tripeptide at the C-terminal edge of the second DCX domain is necessary for KLHL15-mediated ubiquitination of DCX and doublecortin-like kinase 1 and 2 and subsequent proteasomal degradation. Conversely, silencing endogenous KLHL15 markedly stabilizes these DCX domain-containing proteins and prolongs their half-life. Functionally, overexpression of KLHL15 in the presence of WT DCX reduces dendritic complexity of cultured hippocampal neurons, whereas neurons expressing FRY-mutant DCX are resistant to KLHL15. Collectively, our findings highlight the critical importance of the E3 ubiquitin ligase adaptor KLHL15 in proteostasis of neuronal microtubule-associated proteins and identify a regulatory network important for development of the mammalian nervous system.
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Affiliation(s)
- Jianing Song
- Department of Neuroscience and Pharmacology and the Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA
| | - Ronald A Merrill
- Department of Neuroscience and Pharmacology and the Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA
| | - Andrew Y Usachev
- Department of Neuroscience and Pharmacology and the Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA
| | - Stefan Strack
- Department of Neuroscience and Pharmacology and the Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, USA.
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15
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Lescouzères L, Bomont P. E3 Ubiquitin Ligases in Neurological Diseases: Focus on Gigaxonin and Autophagy. Front Physiol 2020; 11:1022. [PMID: 33192535 PMCID: PMC7642974 DOI: 10.3389/fphys.2020.01022] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a dynamic post-translational modification that regulates the fate of proteins and therefore modulates a myriad of cellular functions. At the last step of this sophisticated enzymatic cascade, E3 ubiquitin ligases selectively direct ubiquitin attachment to specific substrates. Altogether, the ∼800 distinct E3 ligases, combined to the exquisite variety of ubiquitin chains and types that can be formed at multiple sites on thousands of different substrates confer to ubiquitination versatility and infinite possibilities to control biological functions. E3 ubiquitin ligases have been shown to regulate behaviors of proteins, from their activation, trafficking, subcellular distribution, interaction with other proteins, to their final degradation. Largely known for tagging proteins for their degradation by the proteasome, E3 ligases also direct ubiquitinated proteins and more largely cellular content (organelles, ribosomes, etc.) to destruction by autophagy. This multi-step machinery involves the creation of double membrane autophagosomes in which engulfed material is degraded after fusion with lysosomes. Cooperating in sustaining homeostasis, actors of ubiquitination, proteasome and autophagy pathways are impaired or mutated in wide range of human diseases. From initial discovery of pathogenic mutations in the E3 ligase encoding for E6-AP in Angelman syndrome and Parkin in juvenile forms of Parkinson disease, the number of E3 ligases identified as causal gene for neurological diseases has considerably increased within the last years. In this review, we provide an overview of these diseases, by classifying the E3 ubiquitin ligase types and categorizing the neurological signs. We focus on the Gigaxonin-E3 ligase, mutated in giant axonal neuropathy and present a comprehensive analysis of the spectrum of mutations and the recent biological models that permitted to uncover novel mechanisms of action. Then, we discuss the common functions shared by Gigaxonin and the other E3 ligases in cytoskeleton architecture, cell signaling and autophagy. In particular, we emphasize their pivotal roles in controlling multiple steps of the autophagy pathway. In light of the various targets and extending functions sustained by a single E3 ligase, we finally discuss the challenge in understanding the complex pathological cascade underlying disease and in designing therapeutic approaches that can apprehend this complexity.
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Affiliation(s)
- Léa Lescouzères
- ATIP-Avenir Team, INM, INSERM, University of Montpellier, Montpellier, France
| | - Pascale Bomont
- ATIP-Avenir Team, INM, INSERM, University of Montpellier, Montpellier, France
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16
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Trpc5 deficiency causes hypoprolactinemia and altered function of oscillatory dopamine neurons in the arcuate nucleus. Proc Natl Acad Sci U S A 2019; 116:15236-15243. [PMID: 31285329 DOI: 10.1073/pnas.1905705116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Dopamine neurons of the hypothalamic arcuate nucleus (ARC) tonically inhibit the release of the protein hormone prolactin from lactotropic cells in the anterior pituitary gland and thus play a central role in prolactin homeostasis of the body. Prolactin, in turn, orchestrates numerous important biological functions such as maternal behavior, reproduction, and sexual arousal. Here, we identify the canonical transient receptor potential channel Trpc5 as an essential requirement for normal function of dopamine ARC neurons and prolactin homeostasis. By analyzing female mice carrying targeted mutations in the Trpc5 gene including a conditional Trpc5 deletion, we show that Trpc5 is required for maintaining highly stereotyped infraslow membrane potential oscillations of dopamine ARC neurons. Trpc5 is also required for eliciting prolactin-evoked tonic plateau potentials in these neurons that are part of a regulatory feedback circuit. Trpc5 mutant females show severe prolactin deficiency or hypoprolactinemia that is associated with irregular reproductive cyclicity, gonadotropin imbalance, and impaired reproductive capabilities. These results reveal a previously unknown role for the cation channel Trpc5 in prolactin homeostasis of female mice and provide strategies to explore the genetic basis of reproductive disorders and other malfunctions associated with defective prolactin regulation in humans.
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17
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Neri G, Schwartz CE, Lubs HA, Stevenson RE. X-linked intellectual disability update 2017. Am J Med Genet A 2018; 176:1375-1388. [PMID: 29696803 DOI: 10.1002/ajmg.a.38710] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/23/2018] [Accepted: 03/23/2018] [Indexed: 12/28/2022]
Abstract
The X-chromosome comprises only about 5% of the human genome but accounts for about 15% of the genes currently known to be associated with intellectual disability. The early progress in identifying the X-linked intellectual disability (XLID)-associated genes through linkage analysis and candidate gene sequencing has been accelerated with the use of high-throughput technologies. In the 10 years since the last update, the number of genes associated with XLID has increased by 96% from 72 to 141 and duplications of all 141 XLID genes have been described, primarily through the application of high-resolution microarrays and next generation sequencing. The progress in identifying genetic and genomic alterations associated with XLID has not been matched with insights that improve the clinician's ability to form differential diagnoses, that bring into view the possibility of curative therapies for patients, or that inform scientists of the impact of the genetic alterations on cell organization and function.
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Affiliation(s)
- Giovanni Neri
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina.,Istituto di Medicina Genomica, Università Cattolica del S. Cuore, Rome, Italy
| | - Charles E Schwartz
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Herbert A Lubs
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Roger E Stevenson
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
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18
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Moortgat S, Lederer D, Deprez M, Buzatu M, Clapuyt P, Boulanger S, Benoit V, Mary S, Guichet A, Ziegler A, Colin E, Bonneau D, Maystadt I. Expanding the phenotypic spectrum associated with OPHN1 mutations: Report of 17 individuals with intellectual disability but no cerebellar hypoplasia. Eur J Med Genet 2018; 61:442-450. [PMID: 29510240 DOI: 10.1016/j.ejmg.2018.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 01/20/2023]
Abstract
Mutations in the oligophrenin 1 gene (OPHN1) have been identified in patients with X-linked intellectual disability (XLID) associated with cerebellar hypoplasia and ventriculomegaly, suggesting it could be a recognizable syndromic intellectual disability (ID). Affected individuals share additional clinical features including speech delay, seizures, strabismus, behavioral difficulties, and slight facial dysmorphism. OPHN1 is located in Xq12 and encodes a Rho-GTPase-activating protein involved in the regulation of the G-protein cycle. Rho protein members play an important role in dendritic growth and in plasticity of excitatory synapses. Here we report on 17 individuals from four unrelated families affected by mild to severe intellectual disability due to OPHN1 mutations without cerebellar anomaly on brain MRI. We describe clinical, genetic and neuroimaging data of affected patients. Among the identified OPHN1 mutations, we report for the first time a missense mutation occurring in a mosaic state. We discuss the intrafamilial clinical variability of the disease and compare our patients with those previously reported. We emphasize the power of next generation techniques (X-exome sequencing, whole-exome sequencing and targeted multi-gene panel) to expand the phenotypic and mutational spectrum of OPHN1-related ID.
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Affiliation(s)
- Stéphanie Moortgat
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Charleroi, Gosselies, Belgium.
| | - Damien Lederer
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Charleroi, Gosselies, Belgium
| | - Marie Deprez
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Charleroi, Gosselies, Belgium; Département de Neuro-pédiatrie, Clinique Sainte-Elisabeth, Namur, Belgium
| | - Marga Buzatu
- Département de Neuro-pédiatrie, Hôpital Civil Marie Curie, Charleroi, Belgium
| | - Philippe Clapuyt
- Department of Radiology, Pediatric Imaging Unit, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Sébastien Boulanger
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Charleroi, Gosselies, Belgium
| | - Valérie Benoit
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Charleroi, Gosselies, Belgium
| | - Sandrine Mary
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Charleroi, Gosselies, Belgium
| | - Agnès Guichet
- Department of Biochemistry and Genetics, Angers University Hospital, and UMR INSERM 1083, CNRS 6015, Angers, France
| | - Alban Ziegler
- Department of Biochemistry and Genetics, Angers University Hospital, and UMR INSERM 1083, CNRS 6015, Angers, France
| | - Estelle Colin
- Department of Biochemistry and Genetics, Angers University Hospital, and UMR INSERM 1083, CNRS 6015, Angers, France
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, Angers University Hospital, and UMR INSERM 1083, CNRS 6015, Angers, France
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Charleroi, Gosselies, Belgium
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19
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Griesi-Oliveira K, Suzuki AM, Muotri AR. TRPC Channels and Mental Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 976:137-148. [PMID: 28508319 DOI: 10.1007/978-94-024-1088-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transient receptor potential canonical (TRPC) channels mediate the influx of different types of cations through the cell membrane and are involved in many functions of the organism. Evidences of involvement of TRPC channels in neuronal development suggest that this family of proteins might play a role in certain neurological disorders. As reported, knockout mice for different TRPC channels show alterations in neuronal morphological and functional parameters, with behavioral abnormalities, such as in exploratory and social behaviors. Although mutations in TRPC channels could be related to mental/neurological disorders, there are only a few cases reported in literature, indicating that this correlation should be further explored. Nonetheless, other functional evidences support the implication of these channels in neurological diseases. In this chapter, we summarize the main findings relating TRPC channels to neurological disorders, such as autism spectrum disorders, bipolar disorder, and intellectual disability among others.
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Affiliation(s)
| | - Angela May Suzuki
- Department of Genetics and Evolutionary Biology, Bioscience Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Alysson Renato Muotri
- Department of Pediatrics and Department of Cellular & Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA. .,Rady Children's Hospital San Diego, San Diego, CA, USA. .,UCSD Stem Cell Program, Institute for Genomic Medicine, New York, NY, USA.
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20
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Laino L, Bottillo I, Piedimonte C, Bernardini L, Torres B, Grammatico B, Bargiacchi S, Mulargia C, Calvani M, Cardona F, Castori M, Grammatico P. Clinical and molecular characterization of a boy with intellectual disability, facial dysmorphism, minor digital anomalies and a complex IL1RAPL1 intragenic rearrangement. Eur J Paediatr Neurol 2016; 20:971-976. [PMID: 27470653 DOI: 10.1016/j.ejpn.2016.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/22/2016] [Accepted: 07/02/2016] [Indexed: 01/16/2023]
Abstract
X-linked intellectual disability accounts for 10-12% of cases of cognitive impairment in males. Mutations in IL1RAPL1 are an emerging form of apparently non-syndromic X-linked intellectual disability. We report a 8-year-old intellectually disabled boy with speech delay, and unusual facial and digital anomalies who showed a novel and complex IL1RAPL1 rearrangement. It was defined by two intragenic non-contiguous duplications inherited from the unaffected mother. Chromosome X inactivation study on the mother's blood leukocytes, urinary sediment and buccal swab did not show a significant skewed inactivation. Comparison with previously described patients with IL1RAPL1 disruption was carried. Although data on craniofacial features were scanty in many papers, subtle facial dysmorphism with a thin upper lip seemed a quietly represented picture without any other genotype-phenotype correlations. Our study expands the molecular repertoire of IL1RAPL1 mutations in intellectual disability and points out the need of more accurate clinical descriptions to better define the related phenotype.
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Affiliation(s)
- Luigi Laino
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy.
| | - Irene Bottillo
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Caterina Piedimonte
- Department of Pediatrics and Child Neuropsychiatry, Sapienza University, Policlinico Umberto I University Hospital, Rome, Italy
| | - Laura Bernardini
- Unit of Cytogenetics, Mendel Laboratory, Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, FG, Italy
| | - Barbara Torres
- Unit of Cytogenetics, Mendel Laboratory, Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, FG, Italy
| | - Barbara Grammatico
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Simone Bargiacchi
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Claudia Mulargia
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Mauro Calvani
- Division of Pediatrics, San Camillo-Forlanini Hospital, Rome, Italy
| | - Francesco Cardona
- Department of Pediatrics and Child Neuropsychiatry, Sapienza University, Policlinico Umberto I University Hospital, Rome, Italy
| | - Marco Castori
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Paola Grammatico
- Laboratory of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
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21
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Schumann M, Hofmann A, Krutzke SK, Hilger AC, Marsch F, Stienen D, Gembruch U, Ludwig M, Merz WM, Reutter H. Array-based molecular karyotyping in fetuses with isolated brain malformations identifies disease-causing CNVs. J Neurodev Disord 2016; 8:11. [PMID: 27087860 PMCID: PMC4832534 DOI: 10.1186/s11689-016-9144-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/15/2016] [Indexed: 11/21/2022] Open
Abstract
Background The overall birth prevalence for congenital malformations of the central nervous system (CNS) among Europeans may be as high as 1 in 100 live births. The etiological factors remain largely unknown. The aim of this study was to detect causative copy number variations (CNVs) in fetuses of terminated pregnancies with prenatally detected isolated brain malformations. Methods Array-based molecular karyotyping was performed in a cohort of 35 terminated fetuses with isolated CNS malformations. Identified putative disease-causing CNVs were confirmed using quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification. Results Based on their de novo occurrence and/or their established association with congenital brain malformations, we detected five disease-causing CNVs in four fetuses involving chromosomal regions 6p25.1-6p25.3 (FOXC1), 6q27, 16p12.3, Xp22.2-Xp22.32 (MID1), and Xp22.32-Xp22.33. Furthermore, we detected a probably disease-causing CNV involving chromosomal region 3p26.3 in one fetus, and in addition, we detected 12 CNVs in nine fetuses of unknown clinical significance. All CNVs except for two were absent in 1307 healthy in-house controls (frequency <0.0008). Each of the two CNVs present in in-house controls was present only once (frequency = 0.0008). Furthermore, our data suggests the involvement of CNTN6 and KLHL15 in the etiology of agenesis of the corpus callosum, the involvement of RASD1 and PTPRD in Dandy-Walker malformation, and the involvement of ERMARD in ventriculomegaly. Conclusions Our study suggests that CNVs play an important role in the etiology of isolated brain malformations.
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Affiliation(s)
- Madita Schumann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany ; Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | | | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Florian Marsch
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University of Bonn Medical School, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Waltraut M Merz
- Department of Obstetrics and Prenatal Medicine, University of Bonn Medical School, Bonn, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany ; Department of Neonatology and Pediatric Intensive Care & Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
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22
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Hu H, Haas SA, Chelly J, Van Esch H, Raynaud M, de Brouwer APM, Weinert S, Froyen G, Frints SGM, Laumonnier F, Zemojtel T, Love MI, Richard H, Emde AK, Bienek M, Jensen C, Hambrock M, Fischer U, Langnick C, Feldkamp M, Wissink-Lindhout W, Lebrun N, Castelnau L, Rucci J, Montjean R, Dorseuil O, Billuart P, Stuhlmann T, Shaw M, Corbett MA, Gardner A, Willis-Owen S, Tan C, Friend KL, Belet S, van Roozendaal KEP, Jimenez-Pocquet M, Moizard MP, Ronce N, Sun R, O'Keeffe S, Chenna R, van Bömmel A, Göke J, Hackett A, Field M, Christie L, Boyle J, Haan E, Nelson J, Turner G, Baynam G, Gillessen-Kaesbach G, Müller U, Steinberger D, Budny B, Badura-Stronka M, Latos-Bieleńska A, Ousager LB, Wieacker P, Rodríguez Criado G, Bondeson ML, Annerén G, Dufke A, Cohen M, Van Maldergem L, Vincent-Delorme C, Echenne B, Simon-Bouy B, Kleefstra T, Willemsen M, Fryns JP, Devriendt K, Ullmann R, Vingron M, Wrogemann K, Wienker TF, Tzschach A, van Bokhoven H, Gecz J, Jentsch TJ, Chen W, Ropers HH, Kalscheuer VM. X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Mol Psychiatry 2016; 21:133-48. [PMID: 25644381 PMCID: PMC5414091 DOI: 10.1038/mp.2014.193] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/17/2014] [Accepted: 12/08/2014] [Indexed: 12/27/2022]
Abstract
X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.
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Affiliation(s)
- H Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - S A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - J Chelly
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - H Van Esch
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - M Raynaud
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - A P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - S Weinert
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - G Froyen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium,Human Genome Laboratory, Department of Human Genetics, K.U. Leuven, Leuven, Belgium
| | - S G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center, azM, Maastricht, The Netherlands,School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - F Laumonnier
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France
| | - T Zemojtel
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M I Love
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - H Richard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A-K Emde
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Bienek
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - C Jensen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Hambrock
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - U Fischer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - C Langnick
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - M Feldkamp
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - W Wissink-Lindhout
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - N Lebrun
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - L Castelnau
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - J Rucci
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - R Montjean
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - O Dorseuil
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - P Billuart
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - T Stuhlmann
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - M Shaw
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - M A Corbett
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - A Gardner
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - S Willis-Owen
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,National Heart and Lung Institute, Imperial College London, London, UK
| | - C Tan
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
| | - K L Friend
- SA Pathology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - S Belet
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium,Human Genome Laboratory, Department of Human Genetics, K.U. Leuven, Leuven, Belgium
| | - K E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center, azM, Maastricht, The Netherlands,School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - M Jimenez-Pocquet
- Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - M-P Moizard
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - N Ronce
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - R Sun
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - S O'Keeffe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - R Chenna
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A van Bömmel
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - J Göke
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A Hackett
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - M Field
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - L Christie
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - J Boyle
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - E Haan
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,SA Pathology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - J Nelson
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
| | - G Turner
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - G Baynam
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia,Telethon Kids Institute, Perth, WA, Australia
| | | | - U Müller
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany,bio.logis Center for Human Genetics, Frankfurt a. M., Germany
| | - D Steinberger
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany,bio.logis Center for Human Genetics, Frankfurt a. M., Germany
| | - B Budny
- Chair and Department of Endocrinology, Metabolism and Internal Diseases, Ponzan University of Medical Sciences, Poznan, Poland
| | - M Badura-Stronka
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - A Latos-Bieleńska
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - L B Ousager
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - P Wieacker
- Institut für Humangenetik, Universitätsklinikum Münster, Muenster, Germany
| | | | - M-L Bondeson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - G Annerén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - A Dufke
- Institut für Medizinische Genetik und Angewandte Genomik, Tübingen, Germany
| | - M Cohen
- Kinderzentrum München, München, Germany
| | - L Van Maldergem
- Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France
| | - C Vincent-Delorme
- Service de Génétique, Hôpital Jeanne de Flandre CHRU de Lilles, Lille, France
| | - B Echenne
- Service de Neuro-Pédiatrie, CHU Montpellier, Montpellier, France
| | - B Simon-Bouy
- Laboratoire SESEP, Centre hospitalier de Versailles, Le Chesnay, France
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - M Willemsen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - J-P Fryns
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - K Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - R Ullmann
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - K Wrogemann
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - T F Wienker
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A Tzschach
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - H van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - J Gecz
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - T J Jentsch
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - W Chen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - H-H Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - V M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany. E-mail:
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23
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Kim J, Moon SH, Shin YC, Jeon JH, Park KJ, Lee KP, So I. Intracellular spermine blocks TRPC4 channel via electrostatic interaction with C-terminal negative amino acids. Pflugers Arch 2015; 468:551-61. [PMID: 26631167 DOI: 10.1007/s00424-015-1753-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 01/09/2023]
Abstract
Transient receptor potential canonical (TRPC) 4 channels are calcium-permeable, nonselective cation channels and are widely expressed in mammalian tissue, especially in the GI tract and brain. TRPC4 channels are known to be involved in neurogenic contraction of ileal smooth muscle cells via generating cationic current after muscarinic stimulation (muscarinic cationic current (mIcat)). Polyamines exist in numerous tissues and are believed to be involved in cell proliferation, differentiation, scar formation, wound healing, and carcinogenesis. Besides, physiological polyamines are essential to maintain inward rectification of cardiac potassium channels (Kir2.1). At membrane potentials more positive than equilibrium potential, intracellular polyamines plug the cytosolic surface of the Kir2.1 so that potassium ions cannot pass through the pore. Recently, it was reported that polyamines inhibit not only cardiac potassium channels but also nonselective cation channels that mediate the generation of mIcat. Here, we report that TRPC4, a definite mIcat mediator, is inhibited by intracellular spermine with great extent. The inhibition was specific to TRPC4 and TRPC5 channels but was not effective to TRPC1/4, TRPC1/5, and TRPC3 channels. For this inhibition to occur, we found that glutamates at 728th and 729th position of TRPC4 channels are essential whereby we conclude that spermine blocks the TRPC4 channel with electrostatic interaction between negative amino acids at the C-terminus of the channel.
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Affiliation(s)
- Jinsung Kim
- College of Medicine, Catholic University of Korea, Seoul, 137-701, Republic of Korea.,Department of Physiology, College of Medicine, Seoul National University, Seoul, 110-799, Republic of Korea
| | - Sang Hui Moon
- Department of Surgery, College of Medicine, Seoul National University, Seoul, 110-799, Republic of Korea
| | - Young-Cheul Shin
- Department of Physiology, College of Medicine, Seoul National University, Seoul, 110-799, Republic of Korea
| | - Ju-Hong Jeon
- Department of Physiology, College of Medicine, Seoul National University, Seoul, 110-799, Republic of Korea
| | - Kyu Joo Park
- Department of Surgery, College of Medicine, Seoul National University, Seoul, 110-799, Republic of Korea
| | - Kyu Pil Lee
- Department of Physiology, College of Veterinary Medicine, Chungnam National University, Daejeon, 305-764, Republic of Korea.
| | - Insuk So
- Department of Physiology, College of Medicine, Seoul National University, Seoul, 110-799, Republic of Korea.
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Ramos-Brossier M, Montani C, Lebrun N, Gritti L, Martin C, Seminatore-Nole C, Toussaint A, Moreno S, Poirier K, Dorseuil O, Chelly J, Hackett A, Gecz J, Bieth E, Faudet A, Heron D, Frank Kooy R, Loeys B, Humeau Y, Sala C, Billuart P. Novel IL1RAPL1 mutations associated with intellectual disability impair synaptogenesis. Hum Mol Genet 2014; 24:1106-18. [PMID: 25305082 DOI: 10.1093/hmg/ddu523] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mutations in interleukin-1 receptor accessory protein like 1 (IL1RAPL1) gene have been associated with non-syndromic intellectual disability (ID) and autism spectrum disorder. This protein interacts with synaptic partners like PSD-95 and PTPδ, regulating the formation and function of excitatory synapses. The aim of this work was to characterize the synaptic consequences of three IL1RAPL1 mutations, two novel causing the deletion of exon 6 (Δex6) and one point mutation (C31R), identified in patients with ID. Using immunofluorescence and electrophysiological recordings, we examined the effects of IL1RAPL1 mutant over-expression on synapse formation and function in cultured rodent hippocampal neurons. Δex6 but not C31R mutation leads to IL1RAPL1 protein instability and mislocalization within dendrites. Analysis of different markers of excitatory synapses and sEPSC recording revealed that both mutants fail to induce pre- and post-synaptic differentiation, contrary to WT IL1RAPL1 protein. Cell aggregation and immunoprecipitation assays in HEK293 cells showed a reduction of the interaction between IL1RAPL1 mutants and PTPδ that could explain the observed synaptogenic defect in neurons. However, these mutants do not affect all cellular signaling because their over-expression still activates JNK pathway. We conclude that both mutations described in this study lead to a partial loss of function of the IL1RAPL1 protein through different mechanisms. Our work highlights the important function of the trans-synaptic PTPδ/IL1RAPL1 interaction in synaptogenesis and as such in ID in the patients.
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Affiliation(s)
- Mariana Ramos-Brossier
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris 75014, France
| | - Caterina Montani
- CNR Neuroscience Institute and Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan 20129, Italy
| | - Nicolas Lebrun
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris 75014, France
| | - Laura Gritti
- CNR Neuroscience Institute and Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan 20129, Italy
| | | | | | - Aurelie Toussaint
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Biochimie et Génétique Moléculaire, Hôpital Cochin, APHP, Paris 75014, France
| | - Sarah Moreno
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris 75014, France
| | - Karine Poirier
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris 75014, France
| | - Olivier Dorseuil
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris 75014, France
| | - Jamel Chelly
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris 75014, France
| | - Anna Hackett
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Jozef Gecz
- School of Paediatrics and Reproductive Health, Robinson Institute, The University of Adelaide, Adelaide, SA 5006, Australia
| | - Eric Bieth
- Service de Génétique Médicale, Hôpital Purpan, Toulouse 31059, France
| | - Anne Faudet
- Genetics and Cytogenetics Department, GRC-UPMC, Pitié-Salpetrière CHU, Paris 75013, France and
| | - Delphine Heron
- Genetics and Cytogenetics Department, GRC-UPMC, Pitié-Salpetrière CHU, Paris 75013, France and
| | - R Frank Kooy
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University and University Hospital Antwerp, Antwerp 2610, Belgium
| | - Bart Loeys
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University and University Hospital Antwerp, Antwerp 2610, Belgium
| | - Yann Humeau
- IINS, CNRS UMR5297, Université de Bordeaux, Bordeaux 33000, France
| | - Carlo Sala
- CNR Neuroscience Institute and Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan 20129, Italy
| | - Pierre Billuart
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris 75014, France,
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