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K SSNSP, Vagha K, Varma A, Javvaji CK, Bhanushali K, Malik A, Handargule A. Beyond the Norm: A Report of a Rare Case of Sodium Channel 8 Alpha (SCN8A) Gene-Related Epilepsy Unveiled in a Nine-Year-Old Child. Cureus 2024; 16:e59775. [PMID: 38846250 PMCID: PMC11154020 DOI: 10.7759/cureus.59775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
Sodium channel 8 alpha (SCN8A) mutations encompass a spectrum of epilepsy phenotypes with diverse clinical manifestations, posing diagnostic challenges. We present a case of a nine-year-old male with SCN8A gene-associated developmental and epileptic encephalopathies (DEEs), characterized by generalized tonic-clonic seizures (GTCS) since infancy. Despite treatment with multiple antiepileptic drugs (AEDs), including phenytoin, valproate, levetiracetam, carbamazepine, and clobazam, seizure control remained elusive, prompting genetic testing. Whole exome sequencing confirmed a heterozygous mutation (p.Phe210Ser) in SCN8A exon 6, indicative of DEE-13. Functional studies revealed a gain-of-function mechanism in SCN8A variants, resulting in heightened ion channel activity and altered voltage dependence of activation. Despite treatment adjustments, the patient's seizures persisted until topiramate was introduced, offering partial relief. SCN8A, encoding Nav1.6 sodium channels, modulates neuronal excitability, with mutations leading to increased persistent currents and hyperexcitability. Early seizure onset and developmental delays are hallmarks of SCN8A-related DEE. This case highlights the significance of genetic testing in refractory epilepsy management, guiding personalized treatment strategies. Sodium channel blockers like phenytoin and carbamazepine are often first-line therapies, while topiramate presents as a potential adjunctive option in SCN8A-related DEE. Overall, this case underscores the diagnostic and therapeutic complexities of managing SCN8A-related epileptic encephalopathy, emphasizing the importance of long-term monitoring and personalized treatment approaches for optimizing outcomes in refractory epilepsy.
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Affiliation(s)
- Sri Sita Naga Sai Priya K
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Keta Vagha
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Ashish Varma
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Chaitanya Kumar Javvaji
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Krupa Bhanushali
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Aashita Malik
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Anuja Handargule
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Mao M, Mattei C, Rollo B, Byars S, Cuddy C, Berecki G, Heighway J, Pachernegg S, Menheniott T, Apted D, Jia L, Dalby K, Nemiroff A, Mullen S, Reid CA, Maljevic S, Petrou S. Distinctive In Vitro Phenotypes in iPSC-Derived Neurons From Patients With Gain- and Loss-of-Function SCN2A Developmental and Epileptic Encephalopathy. J Neurosci 2024; 44:e0692232023. [PMID: 38148154 PMCID: PMC10883610 DOI: 10.1523/jneurosci.0692-23.2023] [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: 04/17/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 12/28/2023] Open
Abstract
SCN2A encodes NaV1.2, an excitatory neuron voltage-gated sodium channel and a major monogenic cause of neurodevelopmental disorders, including developmental and epileptic encephalopathies (DEE) and autism. Clinical presentation and pharmocosensitivity vary with the nature of SCN2A variant dysfunction and can be divided into gain-of-function (GoF) cases with pre- or peri-natal seizures and loss-of-function (LoF) patients typically having infantile spasms after 6 months of age. We established and assessed patient induced pluripotent stem cell (iPSC) - derived neuronal models for two recurrent SCN2A DEE variants with GoF R1882Q and LoF R853Q associated with early- and late-onset DEE, respectively. Two male patient-derived iPSC isogenic pairs were differentiated using Neurogenin-2 overexpression yielding populations of cortical-like glutamatergic neurons. Functional properties were assessed using patch clamp and multielectrode array recordings and transcriptomic profiles obtained with total mRNA sequencing after 2-4 weeks in culture. At 3 weeks of differentiation, increased neuronal activity at cellular and network levels was observed for R1882Q iPSC-derived neurons. In contrast, R853Q neurons showed only subtle changes in excitability after 4 weeks and an overall reduced network activity after 7 weeks in vitro. Consistent with the reported efficacy in some GoF SCN2A patients, phenytoin (sodium channel blocker) reduced the excitability of neurons to the control levels in R1882Q neuronal cultures. Transcriptomic alterations in neurons were detected for each variant and convergent pathways suggested potential shared mechanisms underlying SCN2A DEE. In summary, patient iPSC-derived neuronal models of SCN2A GoF and LoF pathogenic variants causing DEE show specific functional and transcriptomic in vitro phenotypes.
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Affiliation(s)
- Miaomiao Mao
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Cristiana Mattei
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Ben Rollo
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria 3800, Australia
| | - Sean Byars
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Claire Cuddy
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Geza Berecki
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Jacqueline Heighway
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Svenja Pachernegg
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
| | - Trevelyan Menheniott
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
| | - Danielle Apted
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Linghan Jia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Kelley Dalby
- Rogcon Biosciences, Cambridge, MA 02142
- Praxis Precision Medicines, Inc., Cambridge, MA 02142
| | - Alex Nemiroff
- Rogcon Biosciences, Cambridge, MA 02142
- Praxis Precision Medicines, Inc., Cambridge, MA 02142
| | - Saul Mullen
- Austin Health, University of Melbourne, Melbourne, Victoria 3084, Australia
| | - Christopher A Reid
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Snezana Maljevic
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Steven Petrou
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3052, Australia
- Praxis Precision Medicines, Inc., Cambridge, MA 02142
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Thompson AC, Aizenman CD. Characterization of Na + currents regulating intrinsic excitability of optic tectal neurons. Life Sci Alliance 2024; 7:e202302232. [PMID: 37918964 PMCID: PMC10622587 DOI: 10.26508/lsa.202302232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
Developing neurons adapt their intrinsic excitability to maintain stable output despite changing synaptic input. The mechanisms behind this process remain unclear. In this study, we examined Xenopus optic tectal neurons and found that the expressions of Nav1.1 and Nav1.6 voltage-gated Na+ channels are regulated during changes in intrinsic excitability, both during development and becsuse of changes in visual experience. Using whole-cell electrophysiology, we demonstrate the existence of distinct, fast, persistent, and resurgent Na+ currents in the tectum, and show that these Na+ currents are co-regulated with changes in Nav channel expression. Using antisense RNA to suppress the expression of specific Nav subunits, we found that up-regulation of Nav1.6 expression, but not Nav1.1, was necessary for experience-dependent increases in Na+ currents and intrinsic excitability. Furthermore, this regulation was also necessary for normal development of sensory guided behaviors. These data suggest that the regulation of Na+ currents through the modulation of Nav1.6 expression, and to a lesser extent Nav1.1, plays a crucial role in controlling the intrinsic excitability of tectal neurons and guiding normal development of the tectal circuitry.
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Affiliation(s)
- Adrian C Thompson
- https://ror.org/05gq02987 Department of Neuroscience, Brown University, Providence, RI, USA
| | - Carlos D Aizenman
- https://ror.org/05gq02987 Department of Neuroscience, Brown University, Providence, RI, USA
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He L, Guo H, Wang H, Zhu K, Li D, Zhang C, Ai Y, Yang JJ. Rbfox1 regulates alternative splicing of Nrcam in primary sensory neurons to mediate peripheral nerve injury-induced neuropathic pain. Neurotherapeutics 2024; 21:e00309. [PMID: 38241164 PMCID: PMC10903086 DOI: 10.1016/j.neurot.2023.e00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024] Open
Abstract
The primary sensory neurons of the dorsal root ganglia (DRG) are subject to transcriptional alterations following peripheral nerve injury. These alterations are believed to play a pivotal role in the genesis of neuropathic pain. Alternative RNA splicing is a process that generates multiple transcript variants from a single gene, significantly contributing to the complexity of the transcriptome. However, little is known about the functional significance and control of alternative RNA splicing in injured DRG after spinal nerve ligation (SNL). In our study, we conducted a comprehensive transcriptome profiling and bioinformatic analysis to approach and identified a neuron-specific isoform of an RNA splicing regulator, RNA-binding Fox1 (Rbfox1, also known as A2BP1), as a crucial regulator of alternative RNA splicing in injured DRG after SNL. Notably, Rbfox1 expression is markedly reduced in injured DRG following peripheral nerve injury. Restoring this reduction effectively mitigates nociceptive hypersensitivity. Conversely, mimicking the downregulation of Rbfox1 expression generates neuropathic pain symptoms. Mechanistically, we uncovered that Rbfox1 may be a key factor influencing alternative RNA splicing of neuron-glial related cell adhesion molecule (NrCAM), a key neuronal cell adhesion molecule. In injured DRG after SNL, the downregulation of Rbfox1amplifies the insertion of exon 10 in Nrcam transcripts, leading to an increase in long Nrcam variants (L-Nrcam) and a corresponding decrease in short Nrcam variants (S-Nrcam) within injured DRG. In summary, our study supports the essential role of Rbfox1 in neuropathic pain within DRG, probably via the regulation of Nrcam splicing. These findings suggest that Rbfox1 could be a potential target for neuropathic pain therapy.
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Affiliation(s)
- Long He
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Haoyu Guo
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China; Department of Laboratory Animal Resources, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Hongwei Wang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Kuicheng Zhu
- Department of Laboratory Animal Resources, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Da Li
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Chaofan Zhang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Yanqiu Ai
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
| | - Jian-Jun Yang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
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5
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Mukherjee A, Nongthomba U. To RNA-binding and beyond: Emerging facets of the role of Rbfox proteins in development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1813. [PMID: 37661850 DOI: 10.1002/wrna.1813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 09/05/2023]
Abstract
The RNA-binding Fox-1 homologue (Rbfox) proteins represent an ancient family of splicing factors, conserved through evolution. All members share an RNA recognition motif (RRM), and a particular affinity for the GCAUG signature in target RNA molecules. The role of Rbfox, as a splice factor, deciding the tissue-specific inclusion/exclusion of an exon, depending on its binding position on the flanking introns, is well known. Rbfox often acts in concert with other splicing factors, and forms splicing regulatory networks. Apart from this canonical role, recent studies show that Rbfox can also function as a transcription co-factor, and affects mRNA stability and translation. The repertoire of Rbfox targets is vast, including genes involved in the development of tissue lineages, such as neurogenesis, myogenesis, and erythropoeiesis, and molecular processes, including cytoskeletal dynamics, and calcium handling. A second layer of complexity is added by the fact that Rbfox expression itself is regulated by multiple mechanisms, and, in vertebrates, exhibits tissue-specific expression. The optimum dosage of Rbfox is critical, and its misexpression is etiological to various disease conditions. In this review, we discuss the contextual roles played by Rbfox as a tissue-specific regulator for the expression of many important genes with diverse functions, through the lens of the emerging data which highlights its involvement in many human diseases. Furthermore, we explore the mechanistic details provided by studies in model organisms, with emphasis on the work with Drosophila. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Amartya Mukherjee
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Upendra Nongthomba
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
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6
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Felker SA, Lawlor JMJ, Hiatt SM, Thompson ML, Latner DR, Finnila CR, Bowling KM, Bonnstetter ZT, Bonini KE, Kelly NR, Kelley WV, Hurst ACE, Rashid S, Kelly MA, Nakouzi G, Hendon LG, Bebin EM, Kenny EE, Cooper GM. Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. Genet Med 2023; 25:100884. [PMID: 37161864 PMCID: PMC10524927 DOI: 10.1016/j.gim.2023.100884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023] Open
Abstract
PURPOSE Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains below 50%, suggesting that clinically relevant variants may be missed by standard analyses. Here, we analyze "poison exons" (PEs), which are evolutionarily conserved alternative exons often absent from standard gene annotations. Variants that alter PE inclusion can lead to loss of function and may be highly penetrant contributors to disease. METHODS We curated published RNA sequencing data from developing mouse cortex to define 1937 conserved PE regions potentially relevant to NDDs, and we analyzed variants found by genome sequencing in multiple NDD cohorts. RESULTS Across 2999 probands, we found 6 novel clinically relevant variants in PE regions. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family (SCN1A, SCN2A, and SCN8A), which is associated with epilepsies. One variant is in SNRPB, associated with cerebrocostomandibular syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and in genes with gene-phenotype associations consistent with each probands reported features. CONCLUSION With a very minimal increase in variant analysis burden (average of 0.77 variants per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.
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Affiliation(s)
| | | | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | | | | | | | | | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Division of Pediatric Genetic Medicine, Department of Pediatrics, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | | | | | | | | | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
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7
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Happ HC, Schneider PN, Hong JH, Goes E, Bandouil M, Biar CG, Ramamurthy A, Reese F, Engel K, Weckhuysen S, Scheffer IE, Mefford HC, Calhoun JD, Carvill GL. Long-read sequencing and profiling of RNA-binding proteins reveals the pathogenic mechanism of aberrant splicing of an SCN1A poison exon in epilepsy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.538282. [PMID: 37205386 PMCID: PMC10187291 DOI: 10.1101/2023.05.04.538282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Pathogenic loss-of-function SCN1A variants cause a spectrum of seizure disorders. We previously identified variants in individuals with SCN1A -related epilepsy that fall in or near a poison exon (PE) in SCN1A intron 20 (20N). We hypothesized these variants lead to increased PE inclusion, which introduces a premature stop codon, and, therefore, reduced abundance of the full-length SCN1A transcript and Na v 1.1 protein. We used a splicing reporter assay to interrogate PE inclusion in HEK293T cells. In addition, we used patient-specific induced pluripotent stem cells (iPSCs) differentiated into neurons to quantify 20N inclusion by long and short-read sequencing and Na v 1.1 abundance by western blot. We performed RNA-antisense purification with mass spectrometry to identify RNA-binding proteins (RBPs) that could account for the aberrant PE splicing. We demonstrate that variants in/near 20N lead to increased 20N inclusion by long-read sequencing or splicing reporter assay and decreased Na v 1.1 abundance. We also identified 28 RBPs that differentially interact with variant constructs compared to wild-type, including SRSF1 and HNRNPL. We propose a model whereby 20N variants disrupt RBP binding to splicing enhancers (SRSF1) and suppressors (HNRNPL), to favor PE inclusion. Overall, we demonstrate that SCN1A 20N variants cause haploinsufficiency and SCN1A -related epilepsies. This work provides insights into the complex control of RBP-mediated PE alternative splicing, with broader implications for PE discovery and identification of pathogenic PE variants in other genetic conditions.
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Maassen J, Guenther R, Hondrich TJJ, Cepkenovic B, Brinkmann D, Maybeck V, Offenhäusser A, Dittrich B, Müller A, Skazik-Voogt C, Kosel M, Baum C, Gutermuth A. In Vitro Simulated Neuronal Environmental Conditions Qualify Umbilical Cord Derived Highly Potent Stem Cells for Neuronal Differentiation. Stem Cell Rev Rep 2023:10.1007/s12015-023-10538-w. [PMID: 37093520 PMCID: PMC10390376 DOI: 10.1007/s12015-023-10538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2023] [Indexed: 04/25/2023]
Abstract
The healing of neuronal injuries is still an unachieved goal. Medicine-based therapies can only extend the survival of patients, but not finally lead to a healing process. Currently, a variety of stem cell-based tissue engineering developments are the subject of many research projects to bridge this gap. As yet, neuronal differentiation of induced pluripotent stem cells (iPS), embryonic cell lines, or neuronal stem cells could be accomplished and produce functional neuronally differentiated cells. However, clinical application of cells from these sources is hampered by ethical considerations. To overcome these hurdles numerous studies investigated the potential of adult mesenchymal stem cells (MSCs) as a potential stem cell source. Adult MSCs have been approved as cellular therapeutical products due to their regenerative potential and immunomodulatory properties. Only a few of these studies could demonstrate the capacity to differentiate MSCs into active firing neuron like cells. With this study we investigated the potential of Wharton's Jelly (WJ) derived stem cells and focused on the intrinsic pluripotent stem cell pool and their potential to differentiate into active neurons. With a comprehensive neuronal differentiation protocol comprised of mechanical and biochemical inductive cues, we investigated the capacity of spontaneously forming stem cell spheroids (SCS) from cultured WJ stromal cells in regard to their neuronal differentiation potential and compared them to undifferentiated spheroids or adherent MSCs. Spontaneously formed SCSs show pluripotent and neuroectodermal lineage markers, meeting the pre-condition for neuronal differentiation and contain a higher amount of cells which can be differentiated into cells whose functional phenotypes in calcium and voltage responsive electrical activity are similar to neurons. In conclusion we show that up-concentration of stem cells from WJ with pluripotent characteristics is a tool to generate neuronal cell replacement.
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Affiliation(s)
- Jessika Maassen
- Department for Applied Cell Biology, Fraunhofer Institute for Production Technology, Steinbachstr. 17, 52074, Aachen, Germany
| | - Rebecca Guenther
- Department for Applied Cell Biology, Fraunhofer Institute for Production Technology, Steinbachstr. 17, 52074, Aachen, Germany
| | - Timm J J Hondrich
- Institute for Biological Information Processing, IBI-3, Forschungszentrum Jülich GmbH, Leo Brandtstrasse Station 71, 52425, Jülich, Germany
| | - Bogdana Cepkenovic
- Institute for Biological Information Processing, IBI-3, Forschungszentrum Jülich GmbH, Leo Brandtstrasse Station 71, 52425, Jülich, Germany
- Department of Biology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Dominik Brinkmann
- Institute for Biological Information Processing, IBI-3, Forschungszentrum Jülich GmbH, Leo Brandtstrasse Station 71, 52425, Jülich, Germany
| | - Vanessa Maybeck
- Institute for Biological Information Processing, IBI-3, Forschungszentrum Jülich GmbH, Leo Brandtstrasse Station 71, 52425, Jülich, Germany
| | - Andreas Offenhäusser
- Institute for Biological Information Processing, IBI-3, Forschungszentrum Jülich GmbH, Leo Brandtstrasse Station 71, 52425, Jülich, Germany
| | - Barbara Dittrich
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstrasse 50, 52074, Aachen, Germany
| | - Anna Müller
- Department for Applied Cell Biology, Fraunhofer Institute for Production Technology, Steinbachstr. 17, 52074, Aachen, Germany
| | - Claudia Skazik-Voogt
- Department for Applied Cell Biology, Fraunhofer Institute for Production Technology, Steinbachstr. 17, 52074, Aachen, Germany
| | - Maximilian Kosel
- Department for Applied Cell Biology, Fraunhofer Institute for Production Technology, Steinbachstr. 17, 52074, Aachen, Germany
| | - Christoph Baum
- Department for Applied Cell Biology, Fraunhofer Institute for Production Technology, Steinbachstr. 17, 52074, Aachen, Germany
| | - Angela Gutermuth
- Department for Applied Cell Biology, Fraunhofer Institute for Production Technology, Steinbachstr. 17, 52074, Aachen, Germany.
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9
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Felker SA, Lawlor JMJ, Hiatt SM, Thompson ML, Latner DR, Finnila CR, Bowling KM, Bonnstetter ZT, Bonini KE, Kelly NR, Kelley WV, Hurst ACE, Kelly MA, Nakouzi G, Hendon LG, Bebin EM, Kenny EE, Cooper GM. Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523654. [PMID: 36711854 PMCID: PMC9882217 DOI: 10.1101/2023.01.12.523654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Purpose Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains around 50%, suggesting some clinically relevant rare variants may be missed by standard analyses. Here we analyze "poison exons" (PEs) which, while often absent from standard gene annotations, are alternative exons whose inclusion results in a premature termination codon. Variants that alter PE inclusion can lead to loss-of-function and may be highly penetrant contributors to disease. Methods We curated published RNA-seq data from developing mouse cortex to define 1,937 PE regions conserved between humans and mice and potentially relevant to NDDs. We then analyzed variants found by genome sequencing in multiple NDD cohorts. Results Across 2,999 probands, we found six clinically relevant variants in PE regions that were previously overlooked. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family ( SCN1A, SCN2A , and SCN8A ), associated with epilepsies. One variant is in SNRPB , associated with Cerebrocostomandibular Syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and were observed in probands with features consistent with those reported for the associated gene. Conclusion With only a minimal increase in variant analysis burden (most probands had zero or one candidate PE variants in a known NDD gene, with an average of 0.77 per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.
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Affiliation(s)
| | - James MJ Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | | | - Donald R Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | | | - Kevin M Bowling
- Washington University School of Medicine, Saint Louis, MO, USA 63110
| | | | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai. New York, NY, USA 10029
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA 10467
| | - Whitley V Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
| | - Anna CE Hurst
- University of Alabama in Birmingham, Birmingham, AL, USA 35294
| | | | | | - Laura G Hendon
- University of Mississippi Medical Center, Jackson, MS, 39216
| | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA 35294
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai. New York, NY, USA 10029
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA 10029
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA 35806
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10
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Thompson JA, Miralles RM, Wengert ER, Wagley PK, Yu W, Wenker IC, Patel MK. Astrocyte reactivity in a mouse model of SCN8A epileptic encephalopathy. Epilepsia Open 2022; 7:280-292. [PMID: 34826216 PMCID: PMC9159254 DOI: 10.1002/epi4.12564] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/15/2021] [Accepted: 11/23/2021] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE SCN8A epileptic encephalopathy is caused predominantly by de novo gain-of-function mutations in the voltage-gated sodium channel Nav 1.6. The disorder is characterized by early onset of seizures and developmental delay. Most patients with SCN8A epileptic encephalopathy are refractory to current anti-seizure medications. Previous studies determining the mechanisms of this disease have focused on neuronal dysfunction as Nav 1.6 is expressed by neurons and plays a critical role in controlling neuronal excitability. However, glial dysfunction has been implicated in epilepsy and alterations in glial physiology could contribute to the pathology of SCN8A encephalopathy. In the current study, we examined alterations in astrocyte and microglia physiology in the development of seizures in a mouse model of SCN8A epileptic encephalopathy. METHODS Using immunohistochemistry, we assessed microglia and astrocyte reactivity before and after the onset of spontaneous seizures. Expression of glutamine synthetase and Nav 1.6, and Kir 4.1 channel currents were assessed in astrocytes in wild-type (WT) mice and mice carrying the N1768D SCN8A mutation (D/+). RESULTS Astrocytes in spontaneously seizing D/+ mice become reactive and increase expression of glial fibrillary acidic protein (GFAP), a marker of astrocyte reactivity. These same astrocytes exhibited reduced barium-sensitive Kir 4.1 currents compared to age-matched WT mice and decreased expression of glutamine synthetase. These alterations were only observed in spontaneously seizing mice and not before the onset of seizures. In contrast, microglial morphology remained unchanged before and after the onset of seizures. SIGNIFICANCE Astrocytes, but not microglia, become reactive only after the onset of spontaneous seizures in a mouse model of SCN8A encephalopathy. Reactive astrocytes have reduced Kir 4.1-mediated currents, which would impair their ability to buffer potassium. Reduced expression of glutamine synthetase would modulate the availability of neurotransmitters to excitatory and inhibitory neurons. These deficits in potassium and glutamate handling by astrocytes could exacerbate seizures in SCN8A epileptic encephalopathy. Targeting astrocytes may provide a new therapeutic approach to seizure suppression.
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Affiliation(s)
- Jeremy A. Thompson
- Department of AnesthesiologyUniversity of Virginia Health SystemCharlottesvilleVAUSA
- Neuroscience Graduate ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Raquel M. Miralles
- Department of AnesthesiologyUniversity of Virginia Health SystemCharlottesvilleVAUSA
- Neuroscience Graduate ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Eric R. Wengert
- Department of AnesthesiologyUniversity of Virginia Health SystemCharlottesvilleVAUSA
- Neuroscience Graduate ProgramUniversity of VirginiaCharlottesvilleVAUSA
| | - Pravin K. Wagley
- Department of AnesthesiologyUniversity of Virginia Health SystemCharlottesvilleVAUSA
| | - Wenxi Yu
- Department of Human GeneticsUniversity of MichiganAnn ArborMIUSA
| | - Ian C. Wenker
- Department of AnesthesiologyUniversity of Virginia Health SystemCharlottesvilleVAUSA
| | - Manoj K. Patel
- Department of AnesthesiologyUniversity of Virginia Health SystemCharlottesvilleVAUSA
- Neuroscience Graduate ProgramUniversity of VirginiaCharlottesvilleVAUSA
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11
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Sodium channel expression and transcript variation in the developing brain of human, Rhesus monkey, and mouse. Neurobiol Dis 2022; 164:105622. [PMID: 35031483 DOI: 10.1016/j.nbd.2022.105622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/16/2022] Open
Abstract
Genetic variation in voltage-gated sodium (NaV) channels is a significant contributor to neurodevelopmental disorders. NaV channel alpha subunits are encoded by the SCNxA family and four are predominately expressed in the brain: SCN1A, SCN2A, SCN3A, and SCN8A. Gene expression is developmentally regulated, and they are known to express functionally distinct transcript variants. Precision therapies targeting these genes and their transcript variants are currently in preclinical development, yet the developmental expression of these transcripts in the human brain is yet to be fully understood. Additionally, the functional consequences of some mutations differ depending on the studied channel isoform, suggesting differential transcript variant expression can affect disease prognoses. We characterise the expression of the four SCNxAs and their transcript variants in human, Rhesus monkey and mouse brain using publicly available RNA-sequencing data and analysis tools, demonstrating that this approach can be used to answer important biological questions of gene and transcript developmental regulation. We find that gene expression and transcript variant regulation are conserved across species at similar developmental stages and determine the developmental milestones for transcript variant expression. Our study provides a guide to researchers testing therapies and clinicians advising prognoses based on the expression of channel isoforms.
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12
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Liang L, Fazel Darbandi S, Pochareddy S, Gulden FO, Gilson MC, Sheppard BK, Sahagun A, An JY, Werling DM, Rubenstein JLR, Sestan N, Bender KJ, Sanders SJ. Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain. Genome Med 2021; 13:135. [PMID: 34425903 PMCID: PMC8383430 DOI: 10.1186/s13073-021-00949-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes vary across development in the rodent brain, including mutually exclusive copies of the fifth protein-coding exon detected in the neonate (5N) and adult (5A). A second pair of mutually exclusive exons is reported in SCN8A only (18N and 18A). We aimed to quantify the expression of individual exons in the developing human brain. METHODS RNA-seq data from 783 human brain samples across development were analyzed to estimate exon-level expression. Developmental changes in exon utilization were validated by assessing intron splicing. Exon expression was also estimated in RNA-seq data from 58 developing mouse neocortical samples. RESULTS In the mature human neocortex, exon 5A is consistently expressed at least 4-fold higher than exon 5N in all four genes. For SCN2A, SCN3A, and SCN8A, a brain-wide synchronized 5N to 5A transition occurs between 24 post-conceptual weeks (2nd trimester) and 6 years of age. In mice, the equivalent 5N to 5A transition begins at or before embryonic day 15.5. In SCN8A, over 90% of transcripts in the mature human cortex include exon 18A. Early in fetal development, most transcripts include 18N or skip both 18N and 18A, with a transition to 18A inclusion occurring from 13 post-conceptual weeks to 6 months of age. No other protein-coding exons showed comparably dynamic developmental trajectories. CONCLUSIONS Exon usage in SCN1A, SCN2A, SCN3A, and SCN8A changes dramatically during human brain development. These splice isoforms, which alter the biophysical properties of the encoded channels, may account for some of the observed phenotypic differences across development and between specific variants. Manipulation of the proportion of splicing isoforms at appropriate stages of development may act as a therapeutic strategy for specific mutations or even epilepsy in general.
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Affiliation(s)
- Lindsay Liang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Siavash Fazel Darbandi
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Sirisha Pochareddy
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Forrest O Gulden
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Michael C Gilson
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Brooke K Sheppard
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Atehsa Sahagun
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Donna M Werling
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John L R Rubenstein
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
- Department of Comparative Medicine, Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Kevin J Bender
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, 94158, USA.
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13
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Yu W, Smolen CE, Hill SF, Meisler MH. Spontaneous seizures and elevated seizure susceptibility in response to somatic mutation of sodium channel Scn8a in the mouse. Hum Mol Genet 2021; 30:902-907. [PMID: 33822038 PMCID: PMC8165645 DOI: 10.1093/hmg/ddab092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 02/05/2023] Open
Abstract
De novo mutations of neuronal sodium channels are responsible for ~5% of developmental and epileptic encephalopathies, but the role of somatic mutation of these genes in adult-onset epilepsy is not known. We evaluated the role of post-zygotic somatic mutation by adult activation of a conditional allele of the pathogenic variant Scn8aR1872W in the mouse. After activation of CAG-Cre-ER by tamoxifen, the mutant transcript was expressed throughout the brain at a level proportional to tamoxifen dose. The threshold for generation of spontaneous seizures was reached when the proportion of mutant transcript reached 8% of total Scn8a transcript, equivalent to expression of the epileptogenic variant in 16% of heterozygous neurons. Expression below this level did not result in spontaneous seizures, but did increase susceptibility to seizure induction by kainate or auditory stimulation. The relatively high threshold for spontaneous seizures indicates that somatic mutation of sodium channels is unlikely to contribute to the elevated incidence of epilepsy in the elderly population. However, somatic mutation could increase susceptibility to other seizure stimuli.
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Affiliation(s)
- Wenxi Yu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Corrine E Smolen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Sophie F Hill
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
| | - Miriam H Meisler
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109 USA
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14
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Praticò A, Gulizia C, Gangi G, Oliva C, Romano C, Marino S, Polizzi A, Ruggieri M, Falsaperla R. SCN8A and Its Related Epileptic Phenotypes. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1729142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractSodium channelopathies are among the most common single-gene causes of epilepsy and have been considered model disorders for the study of genetic epilepsies. Epilepsies due to SCN8A pathogenic variants can present with a broad range of phenotypes varying from a severe epileptic encephalopathy with multiple types of drug-resistant seizure to neurodevelopmental delay, mental retardation, and electroencephalogram (EEG) findings of multifocal spike and waves (mostly in the temporal/parietal/occipital areas). In rare cases, benign familial infantile seizures and developmental delay with/without ataxia have been reported. A first-level, specific SCN8A Sanger's sequencing, although available, is rarely performed because the clinical phenotype is not strictly characteristic and several overlaps with other genetic epilepsies may occur. Given its indistinctive phenotype, diagnosis is usually performed through a specific gene panel for epileptic encephalopathies, early epilepsies, or genetic epilepsy in general, or through whole exome sequencing (WES) and more rarely through whole genome sequencing (WGS). Mutations in SCN8A occur as an autosomal dominant trait. The great majority of individuals diagnosed with SCN8A epilepsy do not have an affected parent, because usually SCN8A patients do not reproduce, and mutations are inherited as a “de novo” trait. In rare cases, SCN8A mutations may be inherited in the setting of parental germline mosaicism. SCN8A-related epilepsies have not shown a clear genotype–phenotype correlation, the same variants have been described with different clinical expressivity and this could be due to other genetic factors or to interacting environmental factors. There is no standardized treatment for SCN8A-related epilepsy because of the rarity of the disease and the unavailability of specific, targeted drugs. Treatment is based mainly on antiepileptic drugs which include classic wide-spectrum drugs such as valproic acid, levetiracetam, and lamotrigine. Sodium-channel blockers (phenytoin, carbamazepine, oxcarbazepine, and lamotrigine) have shown appreciable results in terms of seizure reduction, in particular, in patients presenting gain-of-function mutations. Nowadays, new potentially transformative gene therapy treatment approaches are currently being explored, allowing in the next future, a precision-based treatment directed against the gene defect and protein alterations.
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Affiliation(s)
- Andrea Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Carmela Gulizia
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Gloria Gangi
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Claudia Oliva
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | - Simona Marino
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Agata Polizzi
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
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15
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Aziz MC, Schneider PN, Carvill GL. Targeting Poison Exons to Treat Developmental and Epileptic Encephalopathy. Dev Neurosci 2021; 43:241-246. [PMID: 33971653 DOI: 10.1159/000516143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/16/2021] [Indexed: 11/19/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) describe a subset of neurodevelopmental disorders categorized by refractory epilepsy that is often associated with intellectual disability and autism spectrum disorder. The majority of DEEs are now known to have a genetic basis with de novo coding variants accounting for the majority of cases. More recently, a small number of individuals have been identified with intronic SCN1A variants that result in alternative splicing events that lead to ectopic inclusion of poison exons (PEs). PEs are short highly conserved exons that contain a premature truncation codon, and when spliced into the transcript, lead to premature truncation and subsequent degradation by nonsense-mediated decay. The reason for the inclusion/exclusion of these PEs is not entirely clear, but research suggests an autoregulatory role in gene expression and protein abundance. This is seen in proteins such as RNA-binding proteins and serine/arginine-rich proteins. Recent studies have focused on targeting these PEs as a method for therapeutic intervention. Targeting PEs using antisense oligonucleotides (ASOs) has shown to be effective in modulating alternative splicing events by decreasing the amount of transcripts harboring PEs, thus increasing the abundance of full-length transcripts and thereby the amount of protein in haploinsufficient genes implicated in DEE. In the age of personalized medicine, cellular and animal models of the genetic epilepsies have become essential in developing and testing novel precision therapeutics, including PE-targeting ASOs in a subset of DEEs.
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Affiliation(s)
- Miriam C Aziz
- Ken and Ruth Davee Department of Neurology, Northwestern University School of Medicine, Chicago, Illinois, USA
| | - Patricia N Schneider
- Ken and Ruth Davee Department of Neurology, Northwestern University School of Medicine, Chicago, Illinois, USA.,Instituto de Ciencias Biologicas, Universidade Federal do Para, Belem, Brazil
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University School of Medicine, Chicago, Illinois, USA.,Department of Pharmacology and Pediatrics, Northwestern University School of Medicine, Chicago, Illinois, USA
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16
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Abstract
The voltage-gated sodium channel α-subunit genes comprise a highly conserved gene family. Mutations of three of these genes, SCN1A, SCN2A and SCN8A, are responsible for a significant burden of neurological disease. Recent progress in identification and functional characterization of patient variants is generating new insights and novel approaches to therapy for these devastating disorders. Here we review the basic elements of sodium channel function that are used to characterize patient variants. We summarize a large body of work using global and conditional mouse mutants to characterize the in vivo roles of these channels. We provide an overview of the neurological disorders associated with mutations of the human genes and examples of the effects of patient mutations on channel function. Finally, we highlight therapeutic interventions that are emerging from new insights into mechanisms of sodium channelopathies.
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17
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Voskobiynyk Y, Battu G, Felker SA, Cochran JN, Newton MP, Lambert LJ, Kesterson RA, Myers RM, Cooper GM, Roberson ED, Barsh GS. Aberrant regulation of a poison exon caused by a non-coding variant in a mouse model of Scn1a-associated epileptic encephalopathy. PLoS Genet 2021; 17:e1009195. [PMID: 33411788 PMCID: PMC7790302 DOI: 10.1371/journal.pgen.1009195] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Dravet syndrome (DS) is a developmental and epileptic encephalopathy that results from mutations in the Nav1.1 sodium channel encoded by SCN1A. Most known DS-causing mutations are in coding regions of SCN1A, but we recently identified several disease-associated SCN1A mutations in intron 20 that are within or near to a cryptic and evolutionarily conserved "poison" exon, 20N, whose inclusion is predicted to lead to transcript degradation. However, it is not clear how these intron 20 variants alter SCN1A expression or DS pathophysiology in an organismal context, nor is it clear how exon 20N is regulated in a tissue-specific and developmental context. We address those questions here by generating an animal model of our index case, NM_006920.4(SCN1A):c.3969+2451G>C, using gene editing to create the orthologous mutation in laboratory mice. Scn1a heterozygous knock-in (+/KI) mice exhibited an ~50% reduction in brain Scn1a mRNA and Nav1.1 protein levels, together with characteristics observed in other DS mouse models, including premature mortality, seizures, and hyperactivity. In brain tissue from adult Scn1a +/+ animals, quantitative RT-PCR assays indicated that ~1% of Scn1a mRNA included exon 20N, while brain tissue from Scn1a +/KI mice exhibited an ~5-fold increase in the extent of exon 20N inclusion. We investigated the extent of exon 20N inclusion in brain during normal fetal development in RNA-seq data and discovered that levels of inclusion were ~70% at E14.5, declining progressively to ~10% postnatally. A similar pattern exists for the homologous sodium channel Nav1.6, encoded by Scn8a. For both genes, there is an inverse relationship between the level of functional transcript and the extent of poison exon inclusion. Taken together, our findings suggest that poison exon usage by Scn1a and Scn8a is a strategy to regulate channel expression during normal brain development, and that mutations recapitulating a fetal-like pattern of splicing cause reduced channel expression and epileptic encephalopathy.
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Affiliation(s)
- Yuliya Voskobiynyk
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer’s Disease Center, and Evelyn F. McKnight Brain Institute, Departments, of Neurology and Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Gopal Battu
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Stephanie A. Felker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- Department of Department of Biotechnology Science and Engineering, University of Alabama in Huntsville, Hunstville, AL, United States AL, United States of America
| | - J. Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Megan P. Newton
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Laura J. Lambert
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Robert A. Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Gregory M. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Erik D. Roberson
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer’s Disease Center, and Evelyn F. McKnight Brain Institute, Departments, of Neurology and Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
- * E-mail: (GSB); (EDR)
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
- * E-mail: (GSB); (EDR)
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18
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Iijima T, Yoshimura T. A Perspective on the Role of Dynamic Alternative RNA Splicing in the Development, Specification, and Function of Axon Initial Segment. Front Mol Neurosci 2019; 12:295. [PMID: 31866821 PMCID: PMC6906172 DOI: 10.3389/fnmol.2019.00295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is a powerful mechanism for molecular and functional diversification. In neurons, alternative splicing extensively controls various developmental steps as well as the plasticity and remodeling of neuronal activity in the adult brain. The axon initial segment (AIS) is the specialized compartment of proximal axons that initiates action potential (AP). At the AIS, the ion channels and cell adhesion molecules (CAMs) required for AP initiation are densely clustered via the scaffolding and cytoskeletal proteins. Notably, recent studies have elucidated that multiple AIS proteins are controlled by extensive alternative splicing in developing and adult brains. Here, we argue the potential role of dynamic regulation of alternative splicing in the development, specification, and functions of the AIS. In particular, we propose the novel concept that alternative splicing potentially modulates the structural and functional plasticity at the AIS.
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Affiliation(s)
- Takatoshi Iijima
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Takeshi Yoshimura
- Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, Japan
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19
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Ma F, Dong Z, Berberoglu MA. Expression of RNA-binding protein Rbfox1l demarcates a restricted population of dorsal telencephalic neurons within the adult zebrafish brain. Gene Expr Patterns 2019; 31:32-41. [PMID: 30634066 DOI: 10.1016/j.gep.2019.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/22/2018] [Accepted: 01/04/2019] [Indexed: 01/16/2023]
Abstract
Rbfox RNA-binding proteins are expressed in the adult mammalian brain and are required for proper brain development and function. Studies in mice and humans have implicated Rbfox1/RBFOX1 in autism, neuronal excitation and epilepsy, and Rbfox2/RBFOX2 in cerebellar development. The zebrafish has emerged as a prominent model system for brain study, possessing neuroanatomical conservation with mammals and an extensive capacity for adult neurogenesis and plasticity. In this study, we characterize Rbfox1l and Rbfox2 expression in the adult zebrafish brain. While Rbfox2 is expressed broadly, Rbfox1l is expressed in restricted populations of neurons in the dorsal telencephalon and cerebellum. In the dorsal telencephalon, Rbfox1l is expressed in a specific population of neurons spanning Dm and Dc regions. In the cerebellum, Rbfox1l and Rbfox2 are expressed in the Purkinje cell layer, reminiscent of Rbfox1 and Rbfox2 expression in the mammalian cerebellum. Our findings motivate future studies of Rbfox function in the zebrafish brain.
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Affiliation(s)
- Fengjun Ma
- Bio-Medical Center, College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhiqiang Dong
- Bio-Medical Center, College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Michael A Berberoglu
- Bio-Medical Center, College of Life Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University, Nationwide Children's Hospital, Columbus, OH, 43210, USA.
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20
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Carvill GL, Engel KL, Ramamurthy A, Cochran JN, Roovers J, Stamberger H, Lim N, Schneider AL, Hollingsworth G, Holder DH, Regan BM, Lawlor J, Lagae L, Ceulemans B, Bebin EM, Nguyen J, Barsh GS, Weckhuysen S, Meisler M, Berkovic SF, De Jonghe P, Scheffer IE, Myers RM, Cooper GM, Mefford HC, Striano P, Zara F, Helbig I, Møller RS, von Spiczak S, Muhle H, Caglayan H, Sterbova K, Craiu D, Hoffman D, Lehesjoki AE, Selmer K, Depienne C, Lemke J, Marini C, Guerrini R, Neubauer B, Talvik T, Leguern E, de Jonghe P, Weckhuysen S. Aberrant Inclusion of a Poison Exon Causes Dravet Syndrome and Related SCN1A-Associated Genetic Epilepsies. Am J Hum Genet 2018; 103:1022-1029. [PMID: 30526861 DOI: 10.1016/j.ajhg.2018.10.023] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are a group of severe epilepsies characterized by refractory seizures and developmental impairment. Sequencing approaches have identified causal genetic variants in only about 50% of individuals with DEEs.1-3 This suggests that unknown genetic etiologies exist, potentially in the ∼98% of human genomes not covered by exome sequencing (ES). Here we describe seven likely pathogenic variants in regions outside of the annotated coding exons of the most frequently implicated epilepsy gene, SCN1A, encoding the alpha-1 sodium channel subunit. We provide evidence that five of these variants promote inclusion of a "poison" exon that leads to reduced amounts of full-length SCN1A protein. This mechanism is likely to be broadly relevant to human disease; transcriptome studies have revealed hundreds of poison exons,4,5 including some present within genes encoding other sodium channels and in genes involved in neurodevelopment more broadly.6 Future research on the mechanisms that govern neuronal-specific splicing behavior might allow researchers to co-opt this system for RNA therapeutics.
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21
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Stress-dependent miR-980 regulation of Rbfox1/A2bp1 promotes ribonucleoprotein granule formation and cell survival. Nat Commun 2018; 9:312. [PMID: 29358748 PMCID: PMC5778076 DOI: 10.1038/s41467-017-02757-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 12/21/2017] [Indexed: 12/22/2022] Open
Abstract
Upon stress, profound post-transcriptional adjustments of gene expression occur in spatially restricted, subcellular, membraneless compartments, or ribonucleoprotein (RNP) granules, which are formed by liquid phase separation of RNA-binding proteins with low complexity sequence domains (LCDs). Here, we show that Rbfox1 is an LCD-containing protein that aggregates into liquid droplets and amyloid-like fibers and promiscuously joins different nuclear and cytoplasmic RNP granules. Using Drosophila oogenesis as an in vivo system for stress response, we demonstrate a mechanism by which Rbfox1 promotes cell survival. The stress-dependent miRNA miR-980 acts to buffer Rbfox1 levels, since it targets only those Rbfox1 transcripts that contain extended 3′UTRs. Reduced miR-980 expression during stress leads to increased Rbfox1 levels, widespread formation of various RNP granules, and increased cell viability. We show that human RBFOX proteins also contain multiple LCDs and form membraneless compartments, suggesting that the RNP granule-linked control of cellular adaptive responses may contribute to a wide range of RBFOX-associated pathologies in humans. Rbfox1, a pro-survival RNA-binding protein, is expressed in a complex manner and mediates diverse developmental processes. Here, the authors observe alternative splicing of Rbfox1 and stress-dependent regulation by miR-980 in Drosophila ovaries and Rbfox1 localisation in ribonucleoprotein granules in human cells.
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22
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Berberoglu MA, Gallagher TL, Morrow ZT, Talbot JC, Hromowyk KJ, Tenente IM, Langenau DM, Amacher SL. Satellite-like cells contribute to pax7-dependent skeletal muscle repair in adult zebrafish. Dev Biol 2017; 424:162-180. [PMID: 28279710 DOI: 10.1016/j.ydbio.2017.03.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/02/2017] [Accepted: 03/05/2017] [Indexed: 12/24/2022]
Abstract
Satellite cells, also known as muscle stem cells, are responsible for skeletal muscle growth and repair in mammals. Pax7 and Pax3 transcription factors are established satellite cell markers required for muscle development and regeneration, and there is great interest in identifying additional factors that regulate satellite cell proliferation, differentiation, and/or skeletal muscle regeneration. Due to the powerful regenerative capacity of many zebrafish tissues, even in adults, we are exploring the regenerative potential of adult zebrafish skeletal muscle. Here, we show that adult zebrafish skeletal muscle contains cells similar to mammalian satellite cells. Adult zebrafish satellite-like cells have dense heterochromatin, express Pax7 and Pax3, proliferate in response to injury, and show peak myogenic responses 4-5 days post-injury (dpi). Furthermore, using a pax7a-driven GFP reporter, we present evidence implicating satellite-like cells as a possible source of new muscle. In lieu of central nucleation, which distinguishes regenerating myofibers in mammals, we describe several characteristics that robustly identify newly-forming myofibers from surrounding fibers in injured adult zebrafish muscle. These characteristics include partially overlapping expression in satellite-like cells and regenerating myofibers of two RNA-binding proteins Rbfox2 and Rbfoxl1, known to regulate embryonic muscle development and function. Finally, by analyzing pax7a; pax7b double mutant zebrafish, we show that Pax7 is required for adult skeletal muscle repair, as it is in the mouse.
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Affiliation(s)
- Michael A Berberoglu
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Thomas L Gallagher
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Zachary T Morrow
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Jared C Talbot
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Kimberly J Hromowyk
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Inês M Tenente
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Molecular Pathology and Regenerative Medicine, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David M Langenau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Molecular Pathology and Regenerative Medicine, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sharon L Amacher
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA.
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23
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Shukla JP, Deshpande G, Shashidhara LS. Ataxin 2-binding protein 1 is a context-specific positive regulator of Notch signaling during neurogenesis in Drosophila melanogaster. Development 2017; 144:905-915. [PMID: 28174239 DOI: 10.1242/dev.140657] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 01/18/2017] [Indexed: 12/28/2022]
Abstract
The role of the Notch pathway during the lateral inhibition that underlies binary cell fate choice is extensively studied, but the context specificity that generates diverse outcomes is less well understood. In the peripheral nervous system of Drosophila melanogaster, differential Notch signaling between cells of the proneural cluster orchestrates sensory organ specification. Here we report functional analysis of Drosophila Ataxin 2-binding protein 1 (A2BP1) during this process. Its human ortholog is linked to type 2 spinocerebellar ataxia and other complex neuronal disorders. Downregulation of Drosophila A2BP1 in the proneural cluster increases adult sensory bristle number, whereas its overexpression results in loss of bristles. We show that A2BP1 regulates sensory organ specification by potentiating Notch signaling. Supporting its direct involvement, biochemical analysis shows that A2BP1 is part of the Suppressor of Hairless [Su(H)] complex in the presence and absence of Notch. However, in the absence of Notch signaling, the A2BP1 interacting fraction of Su(H) does not associate with the repressor proteins Groucho and CtBP. We propose a model explaining the requirement of A2BP1 as a positive regulator of context-specific Notch activity.
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Affiliation(s)
- Jay Prakash Shukla
- Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Girish Deshpande
- Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India.,Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - L S Shashidhara
- Indian Institute of Science Education and Research Pune, Dr Homi Bhabha Road, Pune, Maharashtra 411008, India
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24
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Abstract
Alternative precursor-mRNA splicing is a key mechanism for regulating gene expression in mammals and is controlled by specialized RNA-binding proteins. The misregulation of splicing is implicated in multiple neurological disorders. We describe recent mouse genetic studies of alternative splicing that reveal its critical role in both neuronal development and the function of mature neurons. We discuss the challenges in understanding the extensive genetic programmes controlled by proteins that regulate splicing, both during development and in the adult brain.
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Affiliation(s)
- Celine K Vuong
- Molecular Biology Interdepartmental Graduate Program, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Sika Zheng
- Division of Biomedical Sciences, University of California at Riverside, Riverside, California 92521, USA
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25
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Hamada N, Ito H, Nishijo T, Iwamoto I, Morishita R, Tabata H, Momiyama T, Nagata KI. Essential role of the nuclear isoform of RBFOX1, a candidate gene for autism spectrum disorders, in the brain development. Sci Rep 2016; 6:30805. [PMID: 27481563 PMCID: PMC4969621 DOI: 10.1038/srep30805] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/07/2016] [Indexed: 01/10/2023] Open
Abstract
Gene abnormalities in RBFOX1, encoding an mRNA-splicing factor, have been shown to cause autism spectrum disorder and other neurodevelopmental disorders. Since pathophysiological significance of the dominant nuclear isoform in neurons, RBFOX1-isoform1 (iso1), remains to be elucidated, we performed comprehensive analyses of Rbfox1-iso1 during mouse corticogenesis. Knockdown of Rbfox1-iso1 by in utero electroporation caused abnormal neuronal positioning during corticogenesis, which was attributed to impaired migration. The defects were found to occur during radial migration and terminal translocation, perhaps due to impaired nucleokinesis. Axon extension and dendritic arborization were also suppressed in vivo in Rbfox1-iso1-deficient cortical neurons. In addition, electrophysiology experiments revealed significant defects in the membrane and synaptic properties of the deficient neurons. Aberrant morphology was further confirmed by in vitro analyses; Rbfox1-iso1-konckdown in hippocampal neurons resulted in the reduction of primary axon length, total length of dendrites, spine density and mature spine number. Taken together, this study shows that Rbfox1-iso1 plays an important role in neuronal migration and synapse network formation during corticogenesis. Defects in these critical processes may induce structural and functional defects in cortical neurons, and consequently contribute to the pathophysiology of neurodevelopmental disorders with RBFOX1 abnormalities.
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Affiliation(s)
- Nanako Hamada
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan.,Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hidenori Ito
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Takuma Nishijo
- Department of Pharmacology, Jikei University School of Medicine, Tokyo, Japan
| | - Ikuko Iwamoto
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Rika Morishita
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Hidenori Tabata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan
| | - Toshihiko Momiyama
- Department of Pharmacology, Jikei University School of Medicine, Tokyo, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan.,Department of Neurochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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26
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Meisler MH, Helman G, Hammer MF, Fureman BE, Gaillard WD, Goldin AL, Hirose S, Ishii A, Kroner BL, Lossin C, Mefford HC, Parent JM, Patel M, Schreiber J, Stewart R, Whittemore V, Wilcox K, Wagnon JL, Pearl PL, Vanderver A, Scheffer IE. SCN8A encephalopathy: Research progress and prospects. Epilepsia 2016; 57:1027-35. [PMID: 27270488 PMCID: PMC5495462 DOI: 10.1111/epi.13422] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2016] [Indexed: 01/15/2023]
Abstract
On April 21, 2015, the first SCN8A Encephalopathy Research Group convened in Washington, DC, to assess current research into clinical and pathogenic features of the disorder and prepare an agenda for future research collaborations. The group comprised clinical and basic scientists and representatives of patient advocacy groups. SCN8A encephalopathy is a rare disorder caused by de novo missense mutations of the sodium channel gene SCN8A, which encodes the neuronal sodium channel Nav 1.6. Since the initial description in 2012, approximately 140 affected individuals have been reported in publications or by SCN8A family groups. As a result, an understanding of the severe impact of SCN8A mutations is beginning to emerge. Defining a genetic epilepsy syndrome goes beyond identification of molecular etiology. Topics discussed at this meeting included (1) comparison between mutations of SCN8A and the SCN1A mutations in Dravet syndrome, (2) biophysical properties of the Nav 1.6 channel, (3) electrophysiologic effects of patient mutations on channel properties, (4) cell and animal models of SCN8A encephalopathy, (5) drug screening strategies, (6) the phenotypic spectrum of SCN8A encephalopathy, and (7) efforts to develop a bioregistry. A panel discussion of gaps in bioregistry, biobanking, and clinical outcomes data was followed by a planning session for improved integration of clinical and basic science research. Although SCN8A encephalopathy was identified only recently, there has been rapid progress in functional analysis and phenotypic classification. The focus is now shifting from identification of the underlying molecular cause to the development of strategies for drug screening and prioritized patient care.
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Affiliation(s)
- Miriam H. Meisler
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, U.S.A
| | - Guy Helman
- Department of Neurology, Children’s National Health System, Washington, District of Columbia, U.S.A
- Center for Genetic Medicine Research, Children’s National Health System, Washington, District of Columbia, U.S.A
| | - Michael F. Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, U.S.A
| | - Brandy E. Fureman
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - William D. Gaillard
- Department of Neurology, Children’s National Health System, Washington, District of Columbia, U.S.A
- Center for Neuroscience Research, Children’s National Health System, Washington, District of Columbia, U.S.A
| | - Alan L. Goldin
- Microbiology & Molecular Genetics and Anatomy & Neurobiology, University of California, Irvine, California, U.S.A
| | - Shinichi Hirose
- Department of Pediatrics, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Atsushi Ishii
- Department of Pediatrics, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Barbara L. Kroner
- Biostatistics and Epidemiology, RTI International, Rockville, Maryland, U.S.A
| | - Christoph Lossin
- Department of Neurology, School of Medicine, University of California Davis, Sacramento, California, U.S.A
| | - Heather C. Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, U.S.A
| | - Jack M. Parent
- Department of Neurology, University of Michigan Medical Center and VA Ann Arbor Healthcare System, Ann Arbor, Michigan, U.S.A
| | - Manoj Patel
- Department of Anesthesiology, University of Virginia Health System, Charlottesville, Virginia, U.S.A
| | - John Schreiber
- Department of Neurology, Children’s National Health System, Washington, District of Columbia, U.S.A
| | - Randall Stewart
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Vicky Whittemore
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Karen Wilcox
- Anticonvulsant Drug Development Program, Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, U.S.A
| | - Jacy L Wagnon
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, U.S.A
| | - Phillip L. Pearl
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Adeline Vanderver
- Department of Neurology, Children’s National Health System, Washington, District of Columbia, U.S.A
- Center for Genetic Medicine Research, Children’s National Health System, Washington, District of Columbia, U.S.A
- Department of Integrated Systems Biology and Pediatrics, George Washington University, Washington, District of Columbia, U.S.A
| | - Ingrid E. Scheffer
- Department of Neurology, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Florey Institute of Neurosciences and Mental Health, Melbourne, Victoria, Australia
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27
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Lipscombe D, Pan JQ, Schorge S. Tracks through the genome to physiological events. Exp Physiol 2015; 100:1429-40. [PMID: 26053180 PMCID: PMC5008151 DOI: 10.1113/ep085129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022]
Abstract
New Findings What is the topic of this review? We discuss tools available to access genome‐wide data sets that harbour cell‐specific, brain region‐specific and tissue‐specific information on exon usage for several species, including humans. In this Review, we demonstrate how to access this information in genome databases and its enormous value to physiology. What advances does it highlight? The sheer scale of protein diversity that is possible from complex genes, including those that encode voltage‐gated ion channels, is vast. But this choice is critical for a complete understanding of protein function in the most physiologically relevant context.
Many proteins of great interest to physiologists and neuroscientists are structurally complex and located in specialized subcellular domains, such as neuronal synapses and transverse tubules of muscle. Genes that encode these critical signalling molecules (receptors, ion channels, transporters, enzymes, cell adhesion molecules, cell–cell interaction proteins and cytoskeletal proteins) are similarly complex. Typically, these genes are large; human Dystrophin (DMD) encodes a cytoskeletal protein of muscle and it is the largest naturally occurring gene at a staggering 2.3 Mb. Large genes contain many non‐coding introns and coding exons; human Titin (TTN), which encodes a protein essential for the assembly and functioning of vertebrate striated muscles, has over 350 exons and consequently has an enormous capacity to generate different forms of Titin mRNAs that have unique exon combinations. Functional and pharmacological differences among protein isoforms originating from the same gene may be subtle but nonetheless of critical physiological significance. Standard functional, immunological and pharmacological approaches, so useful for characterizing proteins encoded by different genes, typically fail to discriminate among splice isoforms of individual genes. Tools are now available to access genome‐wide data sets that harbour cell‐specific, brain region‐specific and tissue‐specific information on exon usage for several species, including humans. In this Review, we demonstrate how to access this information in genome databases and its enormous value to physiology.
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Affiliation(s)
- Diane Lipscombe
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
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28
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Sposito T, Preza E, Mahoney CJ, Setó-Salvia N, Ryan NS, Morris HR, Arber C, Devine MJ, Houlden H, Warner TT, Bushell TJ, Zagnoni M, Kunath T, Livesey FJ, Fox NC, Rossor MN, Hardy J, Wray S. Developmental regulation of tau splicing is disrupted in stem cell-derived neurons from frontotemporal dementia patients with the 10 + 16 splice-site mutation in MAPT. Hum Mol Genet 2015; 24:5260-9. [PMID: 26136155 PMCID: PMC4550814 DOI: 10.1093/hmg/ddv246] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 06/23/2015] [Indexed: 12/13/2022] Open
Abstract
The alternative splicing of the tau gene, MAPT, generates six protein isoforms in the adult human central nervous system (CNS). Tau splicing is developmentally regulated and dysregulated in disease. Mutations in MAPT that alter tau splicing cause frontotemporal dementia (FTD) with tau pathology, providing evidence for a causal link between altered tau splicing and disease. The use of induced pluripotent stem cell (iPSC)-derived neurons has revolutionized the way we model neurological disease in vitro. However, as most tau mutations are located within or around the alternatively spliced exon 10, it is important that iPSC–neurons splice tau appropriately in order to be used as disease models. To address this issue, we analyzed the expression and splicing of tau in iPSC-derived cortical neurons from control patients and FTD patients with the 10 + 16 intronic mutation in MAPT. We show that control neurons only express the fetal tau isoform (0N3R), even at extended time points of 100 days in vitro. Neurons from FTD patients with the 10 + 16 mutation in MAPT express both 0N3R and 0N4R tau isoforms, demonstrating that this mutation overrides the developmental regulation of exon 10 inclusion in our in vitro model. Further, at extended time points of 365 days in vitro, we observe a switch in tau splicing to include six tau isoforms as seen in the adult human CNS. Our results demonstrate the importance of neuronal maturity for use in in vitro modeling and provide a system that will be important for understanding the functional consequences of altered tau splicing.
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Affiliation(s)
- Teresa Sposito
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK
| | - Elisavet Preza
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK
| | - Colin J Mahoney
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Núria Setó-Salvia
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK
| | - Natalie S Ryan
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Huw R Morris
- Department of Clinical Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Charles Arber
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK
| | - Michael J Devine
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK, Division of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK
| | - Thomas T Warner
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK
| | - Trevor J Bushell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Michele Zagnoni
- Centre for Microsystems and Photonics, Electronic and Electrical Engineering, University of Strathclyde, Glasgow G1 1XW, UK
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK and
| | - Frederick J Livesey
- Gurdon Institute, Cambridge Stem Cell Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Nick C Fox
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Martin N Rossor
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK
| | - Selina Wray
- Department of Molecular Neuroscience, UCL Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK,
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29
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Duan W, Zhang YP, Hou Z, Huang C, Zhu H, Zhang CQ, Yin Q. Novel Insights into NeuN: from Neuronal Marker to Splicing Regulator. Mol Neurobiol 2015; 53:1637-1647. [PMID: 25680637 DOI: 10.1007/s12035-015-9122-5] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/01/2015] [Indexed: 01/07/2023]
Abstract
Neuronal nuclei (NeuN) is a well-recognized "marker" that is detected exclusively in post-mitotic neurons and was initially identified through an immunological screen to produce neuron-specific antibodies. Immunostaining evidence indicates that NeuN is distributed in the nuclei of mature neurons in nearly all parts of the vertebrate nervous system. NeuN is highly conserved among species and is stably expressed during specific stages of development. Therefore, NeuN has been considered to be a reliable marker of mature neurons for the past two decades. However, this role has been challenged by recent studies indicating that NeuN staining is variable and even absent during certain diseases and specific physiological states. More importantly, despite the widespread use of the anti-NeuN antibody, the natural identity of the NeuN protein remained elusive for 17 years. NeuN was recently eventually identified as an epitope of Rbfox3, which is a novel member of the Rbfox1 family of splicing factors. This identification might provide a novel perspective on NeuN expression during both physiological and pathological conditions. This review summarizes the current progress on the biochemical identity and biological significance of NeuN and recommends caution when applying NeuN immunoreactivity as a definitive marker of mature neurons in certain diseases and specific physiological states.
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Affiliation(s)
- Wei Duan
- Department of Neurology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China
| | - Yu-Ping Zhang
- Department of Pediatrics, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China
| | - Zhi Hou
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China
| | - Chen Huang
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - He Zhu
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA.,Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.,The Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN, 37232, USA
| | - Chun-Qing Zhang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China.
| | - Qing Yin
- Department of Rehabilitation and Physical Therapy, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, People's Republic of China.
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Ohba C, Kato M, Takahashi S, Lerman-Sagie T, Lev D, Terashima H, Kubota M, Kawawaki H, Matsufuji M, Kojima Y, Tateno A, Goldberg-Stern H, Straussberg R, Marom D, Leshinsky-Silver E, Nakashima M, Nishiyama K, Tsurusaki Y, Miyake N, Tanaka F, Matsumoto N, Saitsu H. Early onset epileptic encephalopathy caused by de novoSCN8Amutations. Epilepsia 2014; 55:994-1000. [DOI: 10.1111/epi.12668] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Chihiro Ohba
- Department of Human Genetics; Graduate School of Medicine; Yokohama City University; Yokohama Japan
- Department of Clinical Neurology and Stroke Medicine; Yokohama City University; Yokohama Japan
| | - Mitsuhiro Kato
- Department of Pediatrics; Yamagata University Faculty of Medicine; Yamagata Japan
| | - Satoru Takahashi
- Department of Pediatrics; Asahikawa Medical University; Asahikawa Japan
| | | | - Dorit Lev
- Metabolic Neurogenetic Clinic; Wolfson Medical Center; Holon Israel
| | - Hiroshi Terashima
- Division of Neurology; National Center for Child Health and Development; Tokyo Japan
| | - Masaya Kubota
- Division of Neurology; National Center for Child Health and Development; Tokyo Japan
| | - Hisashi Kawawaki
- Department of Pediatric Neurology; Osaka City General Hospital; Osaka Japan
| | - Mayumi Matsufuji
- Department of Pediatrics; Japan Community Health Care Organization Kyusyu Hospital; Kitakyushu Japan
| | - Yasuko Kojima
- Department of Pediatrics; Toho University Sakura Medical Center; Chiba Japan
| | - Akihiko Tateno
- Department of Pediatrics; Toho University Sakura Medical Center; Chiba Japan
| | | | - Rachel Straussberg
- Department of Neurogenetics; Schneider's Children Medical Center; Petah Tiqwa Israel
| | - Dafna Marom
- Department of Neurogenetics; Schneider's Children Medical Center; Petah Tiqwa Israel
| | | | - Mitsuko Nakashima
- Department of Human Genetics; Graduate School of Medicine; Yokohama City University; Yokohama Japan
| | - Kiyomi Nishiyama
- Department of Human Genetics; Graduate School of Medicine; Yokohama City University; Yokohama Japan
| | - Yoshinori Tsurusaki
- Department of Human Genetics; Graduate School of Medicine; Yokohama City University; Yokohama Japan
| | - Noriko Miyake
- Department of Human Genetics; Graduate School of Medicine; Yokohama City University; Yokohama Japan
| | - Fumiaki Tanaka
- Department of Clinical Neurology and Stroke Medicine; Yokohama City University; Yokohama Japan
| | - Naomichi Matsumoto
- Department of Human Genetics; Graduate School of Medicine; Yokohama City University; Yokohama Japan
| | - Hirotomo Saitsu
- Department of Human Genetics; Graduate School of Medicine; Yokohama City University; Yokohama Japan
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Ulzi G, Sansone VA, Magri F, Corti S, Bresolin N, Comi GP, Lucchiari S. In vitro analysis of splice site mutations in the CLCN1 gene using the minigene assay. Mol Biol Rep 2014; 41:2865-74. [PMID: 24452722 DOI: 10.1007/s11033-014-3142-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/11/2014] [Indexed: 12/21/2022]
Abstract
Mutations in the chloride channel gene CLCN1 cause the allelic disorders Thomsen (dominant) and Becker (recessive) myotonia congenita (MC). The encoded protein, ClC-1, is the primary channel that mediates chloride (Cl-) conductance in skeletal muscle. Mutations in CLCN1 lower the channel's threshold voltage, leading to spontaneous action potentials that are not coupled to neuromuscular transmission and resulting in myotonia. Over 120 mutations in CLCN1 have been described, 10% of which are splicing defects. Biological specimens suitable for RNA extraction are not always available, but obtaining genomic DNA for analysis is easy and non-invasive. This is the first study to evaluate the pathogenic potential of novel splicing mutations using the minigene approach, which is based on genomic DNA analysis. Splicing mutations accounted for 23% of all pathogenic variants in our cohort of MC patients. Four were heterozygous mutations in four unrelated individuals, belonging to this cohort: c.563G>T in exon 5; c.1169-5T>G in intron 10; c.1251+1G>A in intron 11, and c.1931-2A>G in intron 16. These variants were expressed in HEK 293 cells, and aberrant splicing was verified by in vitro transcription and sequencing of the cDNA. Our findings confirm the need to further investigate the nature of rearrangements associated with this class of mutations and their effects on mature transcripts. In particular, splicing mutations predicted to generate in-frame transcripts may generate out-of-frame mRNA transcripts that do not produce functional ClC-1. Clinically, incomplete molecular evaluation could lead to delayed or faulty diagnosis.
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Affiliation(s)
- Gianna Ulzi
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Via Sforza 35, 20122, Milan, Italy
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32
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O'Brien JE, Meisler MH. Sodium channel SCN8A (Nav1.6): properties and de novo mutations in epileptic encephalopathy and intellectual disability. Front Genet 2013; 4:213. [PMID: 24194747 PMCID: PMC3809569 DOI: 10.3389/fgene.2013.00213] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/04/2013] [Indexed: 11/13/2022] Open
Abstract
The sodium channel Nav1.6, encoded by the gene SCN8A, is one of the major voltage-gated channels in human brain. The sequences of sodium channels have been highly conserved during evolution, and minor changes in biophysical properties can have a major impact in vivo. Insight into the role of Nav1.6 has come from analysis of spontaneous and induced mutations of mouse Scn8a during the past 18 years. Only within the past year has the role of SCN8A in human disease become apparent from whole exome and genome sequences of patients with sporadic disease. Unique features of Nav1.6 include its contribution to persistent current, resurgent current, repetitive neuronal firing, and subcellular localization at the axon initial segment (AIS) and nodes of Ranvier. Loss of Nav1.6 activity results in reduced neuronal excitability, while gain-of-function mutations can increase neuronal excitability. Mouse Scn8a (med) mutants exhibit movement disorders including ataxia, tremor and dystonia. Thus far, more than ten human de novo mutations have been identified in patients with two types of disorders, epileptic encephalopathy and intellectual disability. We review these human mutations as well as the unique features of Nav1.6 that contribute to its role in determining neuronal excitability in vivo. A supplemental figure illustrating the positions of amino acid residues within the four domains and 24 transmembrane segments of Nav1.6 is provided to facilitate the location of novel mutations within the channel protein.
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Affiliation(s)
- Janelle E O'Brien
- Department of Human Genetics, University of Michigan Ann Arbor, MI, USA
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33
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Lal D, Reinthaler EM, Altmüller J, Toliat MR, Thiele H, Nürnberg P, Lerche H, Hahn A, Møller RS, Muhle H, Sander T, Zimprich F, Neubauer BA. RBFOX1 and RBFOX3 mutations in rolandic epilepsy. PLoS One 2013; 8:e73323. [PMID: 24039908 PMCID: PMC3765197 DOI: 10.1371/journal.pone.0073323] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/19/2013] [Indexed: 12/20/2022] Open
Abstract
Partial deletions of the gene encoding the neuronal splicing regulator RBFOX1 have been reported in a range of neurodevelopmental diseases, including idiopathic generalized epilepsy. The RBFOX1 protein and its homologues (RBFOX2 and RBFOX3) regulate alternative splicing of many neuronal transcripts involved in the homeostatic control of neuronal excitability. In this study, we explored if structural microdeletions and exonic sequence variations in RBFOX1, RBFOX2, RBFOX3 confer susceptibility to rolandic epilepsy (RE), a common idiopathic focal childhood epilepsy. By high-density SNP array screening of 289 unrelated RE patients, we identified two hemizygous deletions, a 365 kb deletion affecting two untranslated 5′-terminal exons of RBFOX1 and a 43 kb deletion spanning exon 3 of RBFOX3. Exome sequencing of 242 RE patients revealed two novel probably deleterious variants in RBFOX1, a frameshift mutation (p.A233Vfs*74) and a hexanucleotide deletion (p.A299_A300del), and a novel nonsense mutation in RBFOX3 (p.Y287*). Although the three variants were inherited from unaffected parents, they were present in all family members exhibiting the RE trait clinically or electroencephalographically with only one exception. In contrast, no deleterious mutations of RBFOX1 and RBFOX3 were found in the exomes of 6503 non-RE subjects deposited in the Exome Variant Server database. The observed RBFOX3 exon 3 deletion and nonsense mutation suggest that RBFOX3 represents a novel risk factor for RE, indicating that exon deletions and truncating mutations of RBFOX1 and RBFOX3 contribute to the genetic variance of partial and generalized idiopathic epilepsy syndromes.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neuropediatrics, University Medical Clinic Giessen, Giessen, Germany
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | | | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, Eberhard-Karls University, Tuebingen, Germany
| | - Andreas Hahn
- Department of Neuropediatrics, University Medical Clinic Giessen, Giessen, Germany
| | | | - Hiltrud Muhle
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts University, Kiel, Germany
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Clinic Giessen, Giessen, Germany
- * E-mail:
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Zheng S, Black DL. Alternative pre-mRNA splicing in neurons: growing up and extending its reach. Trends Genet 2013; 29:442-8. [PMID: 23648015 PMCID: PMC3959871 DOI: 10.1016/j.tig.2013.04.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 03/20/2013] [Accepted: 04/04/2013] [Indexed: 11/18/2022]
Abstract
Alternative pre-mRNA splicing determines the protein output of most neuronally expressed genes. Many examples have been described of protein function being modulated by coding changes in different mRNA isoforms. Several recent studies demonstrate that, through the coupling of splicing to other processes of mRNA metabolism, alternative splicing can also act as an on/off switch for gene expression. Other regulated splicing events may determine how an mRNA is utilized in its later cytoplasmic life by changing its localization or translation. These studies make clear that the multiple steps of post-transcriptional gene regulation are strongly linked. Together, these regulatory process play key roles in all aspects of the cell biology of neurons, from their initial differentiation, to their choice of connections, and finally to their function with mature circuits.
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Affiliation(s)
- Sika Zheng
- Department of Microbiology, Immunology, and Molecular Genetics, Howard Hughes Medical Institute, UCLA, David Geffen School of Medicine, UCLA, 6780 MRL Bldg, 675 Charles Young Dr. S. Los Angeles, CA 90095-1662, (310) 794-7644
| | - Douglas L. Black
- Department of Microbiology, Immunology, and Molecular Genetics, Howard Hughes Medical Institute, UCLA, David Geffen School of Medicine, UCLA, 6780 MRL Bldg, 675 Charles Young Dr. S. Los Angeles, CA 90095-1662, (310) 794-7644
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Yap K, Makeyev EV. Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms. Mol Cell Neurosci 2013; 56:420-8. [PMID: 23357783 DOI: 10.1016/j.mcn.2013.01.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/15/2013] [Accepted: 01/17/2013] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic gene expression is orchestrated on a genome-wide scale through several post-transcriptional mechanisms. Of these, alternative pre-mRNA splicing expands the proteome diversity and modulates mRNA stability through downstream RNA quality control (QC) pathways including nonsense-mediated decay (NMD) of mRNAs containing premature termination codons and nuclear retention and elimination (NRE) of intron-containing transcripts. Although originally identified as mechanisms for eliminating aberrant transcripts, a growing body of evidence suggests that NMD and NRE coupled with deliberate changes in pre-mRNA splicing patterns are also used in a number of biological contexts for deterministic control of gene expression. Here we review recent studies elucidating molecular mechanisms and biological significance of these gene regulation strategies with a specific focus on their roles in nervous system development and physiology. This article is part of a Special Issue entitled 'RNA and splicing regulation in neurodegeneration'.
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Affiliation(s)
- Karen Yap
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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O'Brien JE, Sharkey LM, Vallianatos CN, Han C, Blossom JC, Yu T, Waxman SG, Dib-Hajj SD, Meisler MH. Interaction of voltage-gated sodium channel Nav1.6 (SCN8A) with microtubule-associated protein Map1b. J Biol Chem 2012; 287:18459-66. [PMID: 22474336 DOI: 10.1074/jbc.m111.336024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The mechanism by which voltage-gated sodium channels are trafficked to the surface of neurons is not well understood. Our previous work implicated the cytoplasmic N terminus of the sodium channel Na(v)1.6 in this process. We report that the N terminus plus the first transmembrane segment (residues 1-153) is sufficient to direct a reporter to the cell surface. To identify proteins that interact with the 117-residue N-terminal domain, we carried out a yeast two-hybrid screen of a mouse brain cDNA library. Three clones containing overlapping portions of the light chain of microtubule-associated protein Map1b (Mtap1b) were recovered from the screen. Interaction between endogenous Na(v)1.6 channels and Map1b in mouse brain was confirmed by co-immunoprecipitation. Map1b did not interact with the N terminus of the related channel Na(v)1.1. Alanine-scanning mutagenesis of the Na(v)1.6 N terminus demonstrated that residues 77-80 (VAVP) contribute to interaction with Map1b. Co-expression of Na(v)1.6 with Map1b in neuronal cell line ND7/23 resulted in a 50% increase in current density, demonstrating a functional role for this interaction. Mutation of the Map1b binding site of Na(v)1.6 prevented generation of sodium current in transfected cells. The data indicate that Map1b facilitates trafficking of Na(v)1.6 to the neuronal cell surface.
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Affiliation(s)
- Janelle E O'Brien
- Department of Human Genetics, the University of Michigan, Ann Arbor, Michigan 48109-5618, USA
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37
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Veeramah KR, O'Brien JE, Meisler MH, Cheng X, Dib-Hajj SD, Waxman SG, Talwar D, Girirajan S, Eichler EE, Restifo LL, Erickson RP, Hammer MF. De novo pathogenic SCN8A mutation identified by whole-genome sequencing of a family quartet affected by infantile epileptic encephalopathy and SUDEP. Am J Hum Genet 2012; 90:502-10. [PMID: 22365152 DOI: 10.1016/j.ajhg.2012.01.006] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 12/20/2011] [Accepted: 01/09/2012] [Indexed: 12/25/2022] Open
Abstract
Individuals with severe, sporadic disorders of infantile onset represent an important class of disease for which discovery of the underlying genetic architecture is not amenable to traditional genetic analysis. Full-genome sequencing of affected individuals and their parents provides a powerful alternative strategy for gene discovery. We performed whole-genome sequencing (WGS) on a family quartet containing an affected proband and her unaffected parents and sibling. The 15-year-old female proband had a severe epileptic encephalopathy consisting of early-onset seizures, features of autism, intellectual disability, ataxia, and sudden unexplained death in epilepsy. We discovered a de novo heterozygous missense mutation (c.5302A>G [p.Asn1768Asp]) in the voltage-gated sodium-channel gene SCN8A in the proband. This mutation alters an evolutionarily conserved residue in Nav1.6, one of the most abundant sodium channels in the brain. Analysis of the biophysical properties of the mutant channel demonstrated a dramatic increase in persistent sodium current, incomplete channel inactivation, and a depolarizing shift in the voltage dependence of steady-state fast inactivation. Current-clamp analysis in hippocampal neurons transfected with p.Asn1768Asp channels revealed increased spontaneous firing, paroxysmal-depolarizing-shift-like complexes, and an increased firing frequency, consistent with a dominant gain-of-function phenotype in the heterozygous proband. This work identifies SCN8A as the fifth sodium-channel gene to be mutated in epilepsy and demonstrates the value of WGS for the identification of pathogenic mutations causing severe, sporadic neurological disorders.
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Affiliation(s)
- Krishna R Veeramah
- Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, 85721, USA
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Gehman LT, Meera P, Stoilov P, Shiue L, O'Brien JE, Meisler MH, Ares M, Otis TS, Black DL. The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes Dev 2012; 26:445-60. [PMID: 22357600 DOI: 10.1101/gad.182477.111] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Rbfox proteins (Rbfox1, Rbfox2, and Rbfox3) regulate the alternative splicing of many important neuronal transcripts and have been implicated in a variety of neurological disorders. However, their roles in brain development and function are not well understood, in part due to redundancy in their activities. Here we show that, unlike Rbfox1 deletion, the CNS-specific deletion of Rbfox2 disrupts cerebellar development. Genome-wide analysis of Rbfox2(-/-) brain RNA identifies numerous splicing changes altering proteins important both for brain development and mature neuronal function. To separate developmental defects from alterations in the physiology of mature cells, Rbfox1 and Rbfox2 were deleted from mature Purkinje cells, resulting in highly irregular firing. Notably, the Scn8a mRNA encoding the Na(v)1.6 sodium channel, a key mediator of Purkinje cell pacemaking, is improperly spliced in RbFox2 and Rbfox1 mutant brains, leading to highly reduced protein expression. Thus, Rbfox2 protein controls a post-transcriptional program required for proper brain development. Rbfox2 is subsequently required with Rbfox1 to maintain mature neuronal physiology, specifically Purkinje cell pacemaking, through their shared control of sodium channel transcript splicing.
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Affiliation(s)
- Lauren T Gehman
- Molecular Biology Institute, University of California at Los Angeles, CA 90095, USA
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