1
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Lin X. Genomic Variation Prediction: A Summary From Different Views. Front Cell Dev Biol 2021; 9:795883. [PMID: 34901036 PMCID: PMC8656232 DOI: 10.3389/fcell.2021.795883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/11/2021] [Indexed: 12/02/2022] Open
Abstract
Structural variations in the genome are closely related to human health and the occurrence and development of various diseases. To understand the mechanisms of diseases, find pathogenic targets, and carry out personalized precision medicine, it is critical to detect such variations. The rapid development of high-throughput sequencing technologies has accelerated the accumulation of large amounts of genomic mutation data, including synonymous mutations. Identifying pathogenic synonymous mutations that play important roles in the occurrence and development of diseases from all the available mutation data is of great importance. In this paper, machine learning theories and methods are reviewed, efficient and accurate pathogenic synonymous mutation prediction methods are developed, and a standardized three-level variant analysis framework is constructed. In addition, multiple variation tolerance prediction models are studied and integrated, and new ideas for structural variation detection based on deep information mining are explored.
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Affiliation(s)
- Xiuchun Lin
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
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2
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Ithal D, Sukumaran SK, Bhattacharjee D, Vemula A, Nadella R, Mahadevan J, Sud R, Viswanath B, Purushottam M, Jain S. Exome hits demystified: The next frontier. Asian J Psychiatr 2021; 59:102640. [PMID: 33892377 DOI: 10.1016/j.ajp.2021.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Severe mental illnesses such as schizophrenia and bipolar disorder have complex inheritance patterns, involving both common and rare variants. Whole exome sequencing is a promising approach to find out the rare genetic variants. We had previously reported several rare variants in multiplex families with severe mental illnesses. The current article tries to summarise the biological processes and pattern of expression of genes harbouring the aforementioned variants, linking them to known clinical manifestations through a methodical narrative review. Of the 28 genes considered for this review from 7 families with multiple affected individuals, 6 genes are implicated in various neuropsychiatric manifestations including some variations in the brain morphology assessed by magnetic resonance imaging. Another 15 genes, though associated with neuropsychiatric manifestations, did not have established brain morphological changes whereas the remaining 7 genes did not have any previously recorded neuropsychiatric manifestations at all. Wnt/b-catenin signaling pathway was associated with 6 of these genes and PI3K/AKT, calcium signaling, ERK, RhoA and notch signaling pathways had at least 2 gene associations. We present a comprehensive review of biological and clinical knowledge about the genes previously reported in multiplex families with severe mental illness. A 'disease in dish approach' can be helpful to further explore the fundamental mechanisms.
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Affiliation(s)
- Dhruva Ithal
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Salil K Sukumaran
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Debanjan Bhattacharjee
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Alekhya Vemula
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Ravi Nadella
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Reeteka Sud
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India.
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
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3
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Praticò AD, Giallongo A, Arrabito M, D'Amico S, Gauci MC, Lombardo G, Polizzi A, Falsaperla R, Ruggieri M. SCN2A and Its Related Epileptic Phenotypes. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1727097] [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
AbstractEpilepsies due to SCN2A mutations can present with a broad range of phenotypes that are still not fully understood. Clinical characteristics of SNC2A-related epilepsy may vary from neonatal benign epilepsy to early-onset epileptic encephalopathy, including Ohtahara syndrome and West syndrome, and epileptic encephalopathies occurring at later ages (usually within the first 10 years of life). Some patient may present with intellectual disability and/or autism or movement disorders and without epilepsy. The heterogeneity of the phenotypes associated to such genetic mutations does not always allow the clinician to address his suspect on this gene. For this reason, diagnosis is usually made after a multiple gene panel examination through next generation sequencing (NGS) or after whole exome sequencing (WES) or whole genome sequencing (WGS). Subsequently, confirmation by Sanger sequencing can be obtained. Mutations in SCN2A are inherited as an autosomal dominant trait. Most individuals diagnosed with SCN2A–benign familial neonatal-infantile seizures (BFNIS) have an affected parent; however, hypothetically, a child may present SCN2A-BNFNIS as the result of a de novo pathogenic variant. Almost all individuals with SCN2A and severe epileptic encephalopathies have a de novo pathogenic variant. SNC2A-related epilepsies have not shown a clear genotype–phenotype correlation; in some cases, a same variant may lead to different presentations even within the same family and this could be due to other genetic factors or to environmental causes. There is no “standardized” treatment for SCN2A-related epilepsy, as it varies in relation to the clinical presentation and the phenotype of the patient, according to its own gene mutation. Treatment is based mainly on antiepileptic drugs, which include classic wide-spectrum drugs, such as valproic acid, levetiracetam, and lamotrigine. However, specific agents, which act directly modulating the sodium channels activity (phenytoin, carbamazepine, oxcarbamazepine, lamotrigine, and zonisamide), have shown positive result, as other sodium channel blockers (lidocaine and mexiletine) or even other drugs with different targets (phenobarbital).
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Affiliation(s)
- Andrea D. 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
| | - Alessandro Giallongo
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Marta Arrabito
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Silvia D'Amico
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Maria Cristina Gauci
- 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
| | - Giulia Lombardo
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Agata Polizzi
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco,” 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
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4
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Mantegazza M, Cestèle S, Catterall WA. Sodium channelopathies of skeletal muscle and brain. Physiol Rev 2021; 101:1633-1689. [PMID: 33769100 DOI: 10.1152/physrev.00025.2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Voltage-gated sodium channels initiate action potentials in nerve, skeletal muscle, and other electrically excitable cells. Mutations in them cause a wide range of diseases. These channelopathy mutations affect every aspect of sodium channel function, including voltage sensing, voltage-dependent activation, ion conductance, fast and slow inactivation, and both biosynthesis and assembly. Mutations that cause different forms of periodic paralysis in skeletal muscle were discovered first and have provided a template for understanding structure, function, and pathophysiology at the molecular level. More recent work has revealed multiple sodium channelopathies in the brain. Here we review the well-characterized genetics and pathophysiology of the periodic paralyses of skeletal muscle and then use this information as a foundation for advancing our understanding of mutations in the structurally homologous α-subunits of brain sodium channels that cause epilepsy, migraine, autism, and related comorbidities. We include studies based on molecular and structural biology, cell biology and physiology, pharmacology, and mouse genetics. Our review reveals unexpected connections among these different types of sodium channelopathies.
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Affiliation(s)
- Massimo Mantegazza
- Université Cote d'Azur, Valbonne-Sophia Antipolis, France.,CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne-Sophia Antipolis, France.,INSERM, Valbonne-Sophia Antipolis, France
| | - Sandrine Cestèle
- Université Cote d'Azur, Valbonne-Sophia Antipolis, France.,CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne-Sophia Antipolis, France
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5
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Ademuwagun IA, Rotimi SO, Syrbe S, Ajamma YU, Adebiyi E. Voltage Gated Sodium Channel Genes in Epilepsy: Mutations, Functional Studies, and Treatment Dimensions. Front Neurol 2021; 12:600050. [PMID: 33841294 PMCID: PMC8024648 DOI: 10.3389/fneur.2021.600050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/01/2021] [Indexed: 12/19/2022] Open
Abstract
Genetic epilepsy occurs as a result of mutations in either a single gene or an interplay of different genes. These mutations have been detected in ion channel and non-ion channel genes. A noteworthy class of ion channel genes are the voltage gated sodium channels (VGSCs) that play key roles in the depolarization phase of action potentials in neurons. Of huge significance are SCN1A, SCN1B, SCN2A, SCN3A, and SCN8A genes that are highly expressed in the brain. Genomic studies have revealed inherited and de novo mutations in sodium channels that are linked to different forms of epilepsies. Due to the high frequency of sodium channel mutations in epilepsy, this review discusses the pathogenic mutations in the sodium channel genes that lead to epilepsy. In addition, it explores the functional studies on some known mutations and the clinical significance of VGSC mutations in the medical management of epilepsy. The understanding of these channel mutations may serve as a strong guide in making effective treatment decisions in patient management.
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Affiliation(s)
- Ibitayo Abigail Ademuwagun
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Solomon Oladapo Rotimi
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Steffen Syrbe
- Clinic for Pediatric and Adolescent Medicine, Heidelberg University, Heidelberg, Germany
| | | | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research, Covenant University, Ota, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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6
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Trollmann R. Neuromonitoring in Neonatal-Onset Epileptic Encephalopathies. Front Neurol 2021; 12:623625. [PMID: 33603712 PMCID: PMC7884638 DOI: 10.3389/fneur.2021.623625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/12/2021] [Indexed: 12/31/2022] Open
Abstract
Considering the wide spectrum of etiologies of neonatal-onset epileptic encephalopathies (EE) and their unfavorable consequences for neurodevelopmental prognoses, neuromonitoring at-risk neonates is increasingly important. EEG is highly sensitive for early identification of electrographic seizures and abnormal background activity. Amplitude-integrated EEG (aEEG) is recommended as a useful bedside monitoring method but as a complementary tool because of methodical limitations. It is of special significance in monitoring neonates with acute symptomatic as well as structural, metabolic and genetic neonatal-onset EE, being at high risk of electrographic-only and prolonged seizures. EEG/aEEG monitoring is established as an adjunctive tool to confirm perinatal hypoxic-ischemic encephalopathy (HIE). In neonates with HIE undergoing therapeutic hypothermia, burst suppression pattern is associated with good outcomes in about 40% of the patients. The prognostic specificity of EEG/aEEG is lower compared to cMRI. As infants with HIE may develop seizures after cessation of hypothermia, recording for at least 24 h after the last seizure is recommended. Progress in the identification of genetic etiology of neonatal EE constantly increases. However, presently, no specific EEG changes indicative of a genetic variant have been characterized, except for individual variants associated with typical EEG patterns (e.g., KCNQ2, KCNT1). Long-term monitoring studies are necessary to define and classify electro-clinical patterns of neonatal-onset EE.
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Affiliation(s)
- Regina Trollmann
- Department of Pediatrics and Pediatric Neurology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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7
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Uchiyama Y, Yamaguchi D, Iwama K, Miyatake S, Hamanaka K, Tsuchida N, Aoi H, Azuma Y, Itai T, Saida K, Fukuda H, Sekiguchi F, Sakaguchi T, Lei M, Ohori S, Sakamoto M, Kato M, Koike T, Takahashi Y, Tanda K, Hyodo Y, Honjo RS, Bertola DR, Kim CA, Goto M, Okazaki T, Yamada H, Maegaki Y, Osaka H, Ngu LH, Siew CG, Teik KW, Akasaka M, Doi H, Tanaka F, Goto T, Guo L, Ikegawa S, Haginoya K, Haniffa M, Hiraishi N, Hiraki Y, Ikemoto S, Daida A, Hamano SI, Miura M, Ishiyama A, Kawano O, Kondo A, Matsumoto H, Okamoto N, Okanishi T, Oyoshi Y, Takeshita E, Suzuki T, Ogawa Y, Handa H, Miyazono Y, Koshimizu E, Fujita A, Takata A, Miyake N, Mizuguchi T, Matsumoto N. Efficient detection of copy-number variations using exome data: Batch- and sex-based analyses. Hum Mutat 2020; 42:50-65. [PMID: 33131168 DOI: 10.1002/humu.24129] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/29/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Many algorithms to detect copy number variations (CNVs) using exome sequencing (ES) data have been reported and evaluated on their sensitivity and specificity, reproducibility, and precision. However, operational optimization of such algorithms for a better performance has not been fully addressed. ES of 1199 samples including 763 patients with different disease profiles was performed. ES data were analyzed to detect CNVs by both the eXome Hidden Markov Model (XHMM) and modified Nord's method. To efficiently detect rare CNVs, we aimed to decrease sequencing biases by analyzing, at the same time, the data of all unrelated samples sequenced in the same flow cell as a batch, and to eliminate sex effects of X-linked CNVs by analyzing female and male sequences separately. We also applied several filtering steps for more efficient CNV selection. The average number of CNVs detected in one sample was <5. This optimization together with targeted CNV analysis by Nord's method identified pathogenic/likely pathogenic CNVs in 34 patients (4.5%, 34/763). In particular, among 142 patients with epilepsy, the current protocol detected clinically relevant CNVs in 19 (13.4%) patients, whereas the previous protocol identified them in only 14 (9.9%) patients. Thus, this batch-based XHMM analysis efficiently selected rare pathogenic CNVs in genetic diseases.
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Affiliation(s)
- Yuri Uchiyama
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan.,Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | | | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan.,Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine Juntendo University, Tokyo, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomohiro Sakaguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ming Lei
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Takayoshi Koike
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Yukitoshi Takahashi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Koichi Tanda
- Department of Pediatrics, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Yuki Hyodo
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan
| | - Rachel S Honjo
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Debora Romeo Bertola
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Masahide Goto
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | - Tetsuya Okazaki
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Hiroyuki Yamada
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Yoshihiro Maegaki
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | - Lock-Hock Ngu
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Ch'ng G Siew
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Keng W Teik
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Manami Akasaka
- Department of Pediatrics, Iwate Medical University School of Medicine, Morioka, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomohide Goto
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Long Guo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - Muzhirah Haniffa
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Nozomi Hiraishi
- Department of Pediatrics, Yokohama City University Medical Center, Yokohama, Japan
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | - Satoru Ikemoto
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Atsuro Daida
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Shin-Ichiro Hamano
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Masaki Miura
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Pediatrics, Nagaoka Red Cross Hospital, Nagaoka, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Osamu Kawano
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Akane Kondo
- Clinical Genetics Center, Shikoku Medical Center for Children and Adults, National Hospital Organization, Kagawa, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Tohru Okanishi
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan.,Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Hamamatsu, Japan
| | - Yukimi Oyoshi
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Faculty of Medicine Juntendo University, Tokyo, Japan
| | - Yoshiyuki Ogawa
- Department of Hematology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Hiroshi Handa
- Department of Hematology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yayoi Miyazono
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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8
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Brunklaus A, Du J, Steckler F, Ghanty II, Johannesen KM, Fenger CD, Schorge S, Baez-Nieto D, Wang HR, Allen A, Pan JQ, Lerche H, Heyne H, Symonds JD, Zuberi SM, Sanders S, Sheidley BR, Craiu D, Olson HE, Weckhuysen S, DeJonge P, Helbig I, Van Esch H, Busa T, Milh M, Isidor B, Depienne C, Poduri A, Campbell AJ, Dimidschstein J, Møller RS, Lal D. Biological concepts in human sodium channel epilepsies and their relevance in clinical practice. Epilepsia 2020; 61:387-399. [PMID: 32090326 DOI: 10.1111/epi.16438] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Voltage-gated sodium channels (SCNs) share similar amino acid sequence, structure, and function. Genetic variants in the four human brain-expressed SCN genes SCN1A/2A/3A/8A have been associated with heterogeneous epilepsy phenotypes and neurodevelopmental disorders. To better understand the biology of seizure susceptibility in SCN-related epilepsies, our aim was to determine similarities and differences between sodium channel disorders, allowing us to develop a broader perspective on precision treatment than on an individual gene level alone. METHODS We analyzed genotype-phenotype correlations in large SCN-patient cohorts and applied variant constraint analysis to identify severe sodium channel disease. We examined temporal patterns of human SCN expression and correlated functional data from in vitro studies with clinical phenotypes across different sodium channel disorders. RESULTS Comparing 865 epilepsy patients (504 SCN1A, 140 SCN2A, 171 SCN8A, four SCN3A, 46 copy number variation [CNV] cases) and analysis of 114 functional studies allowed us to identify common patterns of presentation. All four epilepsy-associated SCN genes demonstrated significant constraint in both protein truncating and missense variation when compared to other SCN genes. We observed that age at seizure onset is related to SCN gene expression over time. Individuals with gain-of-function SCN2A/3A/8A missense variants or CNV duplications share similar characteristics, most frequently present with early onset epilepsy (<3 months), and demonstrate good response to sodium channel blockers (SCBs). Direct comparison of corresponding SCN variants across different SCN subtypes illustrates that the functional effects of variants in corresponding channel locations are similar; however, their clinical manifestation differs, depending on their role in different types of neurons in which they are expressed. SIGNIFICANCE Variant function and location within one channel can serve as a surrogate for variant effects across related sodium channels. Taking a broader view on precision treatment suggests that in those patients with a suspected underlying genetic epilepsy presenting with neonatal or early onset seizures (<3 months), SCBs should be considered.
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Affiliation(s)
- Andreas Brunklaus
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | - Juanjiangmeng Du
- Cologne Center for Genomics, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Felix Steckler
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | - Ismael I Ghanty
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | - Katrine M Johannesen
- Deparment of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Christina Dühring Fenger
- Deparment of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center Filadelfia, Dianalund, Denmark.,Amplexa Genetics, Odense, Denmark
| | - Stephanie Schorge
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK.,School of Pharmacy, University College London, London, UK
| | - David Baez-Nieto
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Hao-Ran Wang
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Andrew Allen
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Germany
| | - Henrike Heyne
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Joseph D Symonds
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | - Stephan Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California
| | - Beth R Sheidley
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Dana Craiu
- Carol Davila University of Medicine, Department of Clinical Neurosciences, Pediatric Neurology Discipline, Bucharest, Romania.,Alexandru Obregia Hospital, Pediatric Neurology Clinic, Bucharest, Romania
| | - Heather E Olson
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Sarah Weckhuysen
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Peter DeJonge
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Neuropediatrics, University of Kiel, Kiel, Germany
| | - Hilde Van Esch
- Department of Human Genetics and Center for Human Genetics, Laboratory for Genetics of Cognition, University Hospitals Leuven, Leuven, Belgium
| | - Tiffany Busa
- Genetics Department, Timone Enfants University Hospital Center, Public Assistance-Marseille Hospitals, Marseille, France
| | - Matthieu Milh
- Medical Genetics and Functional Genomics, National Institute of Health and Medical Research, Mixed Unit of Research S910, Aix-Marseille University, Marseille, France.,Hematology Laboratory, Le Mans Hospital Center, Le Mans, France
| | - Bertrand Isidor
- Medical Genetics Department, Nantes University Hospital Center, Nantes, France
| | - Christel Depienne
- Institute of Human Genetics, Essen University Hospital, Essen, Germany.,Brain and Spinal Cord Institute, National Institute of Health and Medical Research, Unit 1127, National Center for Scientific Research, Mixed Unit of Research 7225, Sorbonne Universities, Pierre and Marie Curie University, Mixed Unit of Research S 1127, Brain & Spine Institute, Paris, France
| | - Annapurna Poduri
- Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Jordane Dimidschstein
- Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Rikke S Møller
- Deparment of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, University Hospital Cologne, Cologne, Germany.,Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, Ohio.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
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9
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AlSaif S, Umair M, Alfadhel M. Biallelic SCN2A Gene Mutation Causing Early Infantile Epileptic Encephalopathy: Case Report and Review. J Cent Nerv Syst Dis 2019; 11:1179573519849938. [PMID: 31205438 PMCID: PMC6537489 DOI: 10.1177/1179573519849938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 04/20/2019] [Indexed: 01/13/2023] Open
Abstract
The voltage-gated sodium channel neuronal type 2 alpha subunit (Navα1.2) encoded by the SCN2A gene causes early infantile epileptic encephalopathy (EIEE) inherited in an autosomal dominant manner. Clinically, it has variable presentations, ranging from benign familial infantile seizures (BFIS) to severe EIEE. Diagnosis is achieved through molecular DNA testing of the SCN2A gene. Herein, we report on a 30-month-old Saudi girl who presented on the fourth day of life with EIEE, normal brain magnetic resonance imaging (MRI), normal electroencephalography (EEG), and well-controlled seizures. Genetic investigation revealed a novel homozygous missense mutation (c.5242A > G; p.Asn1748Asp) in the SCN2A gene (NM_001040142.1). This is the first reported autosomal recessive inheritance of a disease allele in the SCN2A and therefore expands the molecular and inheritance spectrum of the SCN2A gene defects.
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Affiliation(s)
- Shahad AlSaif
- College of Medicine, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
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10
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Sanders SJ, Campbell AJ, Cottrell JR, Moller RS, Wagner FF, Auldridge AL, Bernier RA, Catterall WA, Chung WK, Empfield JR, George AL, Hipp JF, Khwaja O, Kiskinis E, Lal D, Malhotra D, Millichap JJ, Otis TS, Petrou S, Pitt G, Schust LF, Taylor CM, Tjernagel J, Spiro JE, Bender KJ. Progress in Understanding and Treating SCN2A-Mediated Disorders. Trends Neurosci 2018; 41:442-456. [PMID: 29691040 DOI: 10.1016/j.tins.2018.03.011] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/09/2018] [Accepted: 03/14/2018] [Indexed: 01/20/2023]
Abstract
Advances in gene discovery for neurodevelopmental disorders have identified SCN2A dysfunction as a leading cause of infantile seizures, autism spectrum disorder, and intellectual disability. SCN2A encodes the neuronal sodium channel NaV1.2. Functional assays demonstrate strong correlation between genotype and phenotype. This insight can help guide therapeutic decisions and raises the possibility that ligands that selectively enhance or diminish channel function may improve symptoms. The well-defined function of sodium channels makes SCN2A an important test case for investigating the neurobiology of neurodevelopmental disorders more generally. Here, we discuss the progress made, through the concerted efforts of a diverse group of academic and industry scientists as well as policy advocates, in understanding and treating SCN2A-related disorders.
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Affiliation(s)
- Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Arthur J Campbell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA
| | - Jeffrey R Cottrell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA
| | - Rikke S Moller
- The Danish Epilepsy Centre, Dianalund, Denmark; Institute for Regional Health Services, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Florence F Wagner
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA
| | - Angie L Auldridge
- FamilieSCN2a Foundation, P.O. Box 82, East Longmeadow, MA 01028, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA 98195-7280, USA
| | - Wendy K Chung
- Simons Foundation, New York, NY 10010, USA; Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - James R Empfield
- Xenon Pharmaceuticals Inc., 3650 Gilmore Way, Burnaby, BC V5G 4W8, Canada
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joerg F Hipp
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Omar Khwaja
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Evangelos Kiskinis
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Dennis Lal
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA 02142, USA
| | - Dheeraj Malhotra
- Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - John J Millichap
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Epilepsy Center and Division of Neurology, Ann & Robert H. Lurie Children's Hospital of Chicago, IL 60611, USA; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Thomas S Otis
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, 25 Howland Street, London W1T 4JG, UK
| | - Steven Petrou
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Geoffrey Pitt
- Cardiovascular Research Institute, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Leah F Schust
- FamilieSCN2a Foundation, P.O. Box 82, East Longmeadow, MA 01028, USA
| | - Cora M Taylor
- Geisinger Health System, 100 North Academy Avenue, Danville, PA 17822, USA
| | | | | | - Kevin J Bender
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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