1
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Kouzu K, Tsujimoto H, Ishinuki T, Shinji S, Shinkawa H, Tamura K, Uchino M, Ohge H, Shimizu J, Haji S, Mohri Y, Yamashita C, Kitagawa Y, Suzuki K, Kobayashi M, Kobayashi M, Hanai Y, Nobuhara H, Imaoka H, Yoshida M, Mizuguchi T, Mayumi T, Kitagawa Y. The effectiveness of fascial closure with antimicrobial-coated sutures in preventing incisional surgical site infections in gastrointestinal surgery: a systematic review and meta-analysis. J Hosp Infect 2024; 146:174-182. [PMID: 37734678 DOI: 10.1016/j.jhin.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
The aim of this study was to conduct a systematic review and meta-analysis of the efficacy of fascial closure using antimicrobial-sutures specifically for the prevention of surgical site infections (SSIs) in gastrointestinal surgery, as part of the revision of the SSI prevention guidelines of the Japanese Society of Surgical Infectious Diseases (JSSI). We searched CENTRAL, PubMed and ICHUSHI-Web in May 2023, and included randomized controlled trials (RCTs) comparing antimicrobial-coated and non-coated sutures for fascial closure in gastrointestinal surgery (PROSPERO No. CRD42023430377). Three authors independently screened the RCTs. We assessed the risk of bias and the GRADE criteria for the extracted data. The primary outcome was incisional SSI and the secondary outcomes were abdominal wall dehiscence and the length of postoperative hospital stay. This study was supported partially by the JSSI. A total of 10 RCTs and 5396 patients were included. The use of antimicrobial-coated sutures significantly lowered the risk of incisional SSIs compared with non-coated suture (risk ratio: 0.79, 95% confidence intervals: 0.64-0.98). In subgroup analyses, antimicrobial-coated sutures reduced the risk of SSIs for open surgeries, and when monofilament sutures were used. Antimicrobial-coated sutures did not reduce the incidence of abdominal wall dehiscence and the length of hospital stay compared with non-coated sutures. The certainty of the evidence was rated as moderate according to the GRADE criteria, because of risk of bias. In conclusion, the use of antimicrobial-coated sutures for fascial closure in gastrointestinal surgery is associated with a significantly lower risk of SSI than non-coated sutures.
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Affiliation(s)
- K Kouzu
- Department of Surgery, National Defense Medical College, Japan
| | - H Tsujimoto
- Department of Surgery, National Defense Medical College, Japan.
| | - T Ishinuki
- Department of Nursing, Division of Surgical Science, Sapporo Medical University, Japan
| | - S Shinji
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - H Shinkawa
- Department of Hepatobiliary-Pancreatic Surgery, Osaka Metropolitan University Graduate School of Medicine, Japan
| | - K Tamura
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Japan
| | - M Uchino
- Department of Gastroenterological Surgery, Division of Inflammatory Bowel Disease, Hyogo Medical University, Japan
| | - H Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
| | - J Shimizu
- Department of Surgery, Toyonaka Municipal Hospital, Japan
| | - S Haji
- Department of Surgery, Soseikai General Hospital, Japan
| | - Y Mohri
- Department of Surgery, Mie Prefectural General Medical Center, Japan
| | - C Yamashita
- Department of Anesthesiology and Critical Care Medicine, Fujita Health University School of Medicine, Japan
| | - Y Kitagawa
- Department of Infection Control, National Center for Geriatrics and Gerontology, Japan
| | - K Suzuki
- Department of Infectious Disease Medicine, School of Medicine, University of Occupational and Environmental Health, Japan
| | - M Kobayashi
- Department of Anesthesiology, Hokushinkai Megumino Hospital, Japan
| | - M Kobayashi
- Laboratory of Clinical Pharmacokinetics, School of Pharmacy, Kitasato University, Japan
| | - Y Hanai
- Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Toho University, Japan
| | - H Nobuhara
- Department of Dentistry, Hiroshima Prefectural Hospital, Japan
| | - H Imaoka
- Department of Gastrointestinal and Pediatric Surgery, Mie University Graduate School of Medicine, Japan
| | - M Yoshida
- Department of Hepato-Biliary-Pancreatic and Gastrointestinal Surgery, International University of Health and Welfare, School of Medicine, Japan
| | - T Mizuguchi
- Department of Nursing, Division of Surgical Science, Sapporo Medical University, Japan
| | - T Mayumi
- Department of Intensive Care Unit, Japan Community Healthcare Organization Chukyo Hospital, Japan
| | - Y Kitagawa
- Keio University, School of Medicine, Japan
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2
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Inoue Y, Tsuchida N, Kim CA, de Oliveira Stephan B, Castro MAA, Honjo RS, Bertola DR, Uchiyama Y, Hamanaka K, Fujita A, Koshimizu E, Misawa K, Miyatake S, Mizuguchi T, Matsumoto N. Novel compound heterozygous ABCA2 variants cause IDPOGSA, a variable phenotypic syndrome with intellectual disability. J Hum Genet 2024; 69:163-167. [PMID: 38228874 DOI: 10.1038/s10038-024-01219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/07/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024]
Abstract
The gene for ATP binding cassette subfamily A member 2 (ABCA2) is located at chromosome 9q34.3. Biallelic ABCA2 variants lead to intellectual developmental disorder with poor growth and with or without seizures or ataxia (IDPOGSA). In this study, we identified novel compound heterozygous ABCA2 variants (NM_001606.5:c.[5300-17C>A];[6379C>T]) by whole exome sequencing in a 28-year-old Korean female patient with intellectual disability. These variants included intronic and nonsense variants of paternal and maternal origin, respectively, and are absent from gnomAD. SpliceAI predicted that the intron variant creates a cryptic acceptor site. Reverse transcription-PCR using RNA extracted from a lymphoblastoid cell line of the patient confirmed two aberrant transcripts. Her clinical features are compatible with those of IDPOGSA.
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Affiliation(s)
- Yuta Inoue
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Chong Ae Kim
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HC-FMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Bruno de Oliveira Stephan
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HC-FMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Matheus Augusto Araujo Castro
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HC-FMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Rachel Sayuri Honjo
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HC-FMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Debora Romeo Bertola
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HC-FMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- 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
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, 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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3
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Koshimizu E, Kato M, Misawa K, Uchiyama Y, Tsuchida N, Hamanaka K, Fujita A, Mizuguchi T, Miyatake S, Matsumoto N. Detection of hidden intronic DDC variant in aromatic L-amino acid decarboxylase deficiency by adaptive sampling. J Hum Genet 2024; 69:153-157. [PMID: 38216729 DOI: 10.1038/s10038-023-01217-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Aromatic l-amino acid decarboxylase (AADC) deficiency is an autosomal recessive neurotransmitter disorder caused by pathogenic DOPA decarboxylase (DDC) variants. We previously reported Japanese siblings with AADC deficiency, which was confirmed by the lack of enzyme activity; however, only a heterozygous missense variant was detected. We therefore performed targeted long-read sequencing by adaptive sampling to identify any missing variants. Haplotype phasing and variant calling identified a novel deep intronic variant (c.714+255 C > A), which was predicted to potentially activate the noncanonical splicing acceptor site. Minigene assay revealed that wild-type and c.714+255 C > A alleles had different impacts on splicing. Three transcripts, including the canonical transcript, were detected from the wild-type allele, but only the noncanonical cryptic exon was produced from the variant allele, indicating that c.714+255 C > A was pathogenic. Target long-read sequencing may be used to detect hidden pathogenic variants in unresolved autosomal recessive cases with only one disclosed hit variant.
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Affiliation(s)
- Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Fujita
- 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
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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4
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Lee GH, Jung E, Jung NY, Mizuguchi T, Matsumoto N, Kim EJ. Case report: Neuronal intranuclear inclusion disease initially mimicking reversible cerebral vasoconstriction syndrome: serial neuroimaging findings during an 11-year follow-up. Front Neurol 2024; 15:1347646. [PMID: 38405405 PMCID: PMC10884197 DOI: 10.3389/fneur.2024.1347646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 02/27/2024] Open
Abstract
Neuronal intranuclear inclusion disease (NIID) is a rare, progressive neurodegenerative disorder known for its diverse clinical manifestations. Although episodic neurogenic events can be associated with NIID, no reported cases have demonstrated concurrent clinical features or MRI findings resembling reversible cerebral vasoconstriction syndrome (RCVS). Here, we present the inaugural case of an adult-onset NIID patient who initially displayed symptoms reminiscent of RCVS. The 59-year-old male patient's initial presentation included a thunderclap headache, right visual field deficit, and confusion. Although his brain MRI appeared normal, MR angiography unveiled left posterior cerebral artery occlusion, subsequently followed by recanalization, culminating in an RCVS diagnosis. Over an 11-year period, the patient encountered 10 additional episodes, each escalating in duration and intensity, accompanied by seizures. Simultaneously, cognitive impairment progressed. Genetic testing for NIID revealed an abnormal expansion of GGC repeats in NOTCH2NLC, with a count of 115 (normal range, <60), and this patient was diagnosed with NIID. Our report highlights that NIID can clinically and radiologically mimic RCVS. Therefore, in the differential diagnosis of RCVS, particularly in cases with atypical features or recurrent episodes, consideration of NIID is warranted. Additionally, the longitudinal neuroimaging findings provided the course of NIID over an 11-year follow-up period.
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Affiliation(s)
- Gha-Hyun Lee
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Medical Research Institute, Pusan, Republic of Korea
| | - Eugene Jung
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Medical Research Institute, Pusan, Republic of Korea
| | - Na-Yeon Jung
- Department of Neurology, Pusan National University Yangsan Hospital, Pusan National University School of Medicine and Medical Research Institute, Yangsan, Republic of Korea
| | - 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
| | - Eun-Joo Kim
- Department of Neurology, Pusan National University Hospital, Pusan National University School of Medicine and Medical Research Institute, Pusan, Republic of Korea
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5
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Utsuno Y, Hamada K, Hamanaka K, Miyoshi K, Tsuchimoto K, Sunada S, Itai T, Sakamoto M, Tsuchida N, Uchiyama Y, Koshimizu E, Fujita A, Miyatake S, Misawa K, Mizuguchi T, Kato Y, Saito K, Ogata K, Matsumoto N. Novel missense variants cause intermediate phenotypes in the phenotypic spectrum of SLC5A6-related disorders. J Hum Genet 2024; 69:69-77. [PMID: 38012394 DOI: 10.1038/s10038-023-01206-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 11/05/2023] [Accepted: 11/05/2023] [Indexed: 11/29/2023]
Abstract
SLC5A6 encodes the sodium-dependent multivitamin transporter, a transmembrane protein that uptakes biotin, pantothenic acid, and lipoic acid. Biallelic SLC5A6 variants cause sodium-dependent multivitamin transporter deficiency (SMVTD) and childhood-onset biotin-responsive peripheral motor neuropathy (COMNB), which both respond well to replacement therapy with the above three nutrients. SMVTD usually presents with various symptoms in multiple organs, such as gastrointestinal hemorrhage, brain atrophy, and global developmental delay, at birth or in infancy. Without nutrient replacement therapy, SMVTD can be lethal in early childhood. COMNB is clinically milder and has a later onset than SMVTD, at approximately 10 years of age. COMNB symptoms are mostly limited to peripheral motor neuropathy. Here we report three patients from one Japanese family harboring novel compound heterozygous missense variants in SLC5A6, namely NM_021095.4:c.[221C>T];[642G>C] p.[(Ser74Phe)];[(Gln214His)]. Both variants were predicted to be deleterious through multiple lines of evidence, including amino acid conservation, in silico predictions of pathogenicity, and protein structure considerations. Drosophila analysis also showed c.221C>T to be pathogenic. All three patients had congenital brain cysts on neonatal cranial imaging, but no other morphological abnormalities. They also had a mild motor developmental delay that almost completely resolved despite no treatment. In terms of severity, their phenotypes were intermediate between SMVTD and COMNB. From these findings we propose a new SLC5A6-related disorder, spontaneously remitting developmental delay with brain cysts (SRDDBC) whose phenotypic severity is between that of SMVTD and COMNB. Further clinical and genetic evidence is needed to support our suggestion.
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Affiliation(s)
- Yasuhiro Utsuno
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Asahikawa Medical University, Hokkaido, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Keita Miyoshi
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Shizuoka, Japan
| | - Keiji Tsuchimoto
- Department of Pediatrics, Kochi Health Sciences Center, Kochi, Japan
| | - Satoshi Sunada
- Department of Pediatrics, Kurashiki Central Hospital, Okayama, Japan
| | - Toshiyuki Itai
- 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 Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 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
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yasuhito Kato
- Department of Obstetrics and Gynecology, Asahikawa Medical University, Hokkaido, Japan
| | - Kuniaki Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Shizuoka, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, 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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6
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Matsubara K, Kuki I, Ishioka R, Yamada N, Fukuoka M, Inoue T, Nukui M, Okamoto N, Mizuguchi T, Matsumoto N, Okazaki S. Abnormal axonal development and severe epileptic phenotype in Dynamin-1 (DNM1) encephalopathy. Epileptic Disord 2024; 26:139-143. [PMID: 38009673 DOI: 10.1002/epd2.20181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/09/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Dynamin-1 (DNM1) is involved in synaptic vesicle recycling, and DNM1 mutations can lead to developmental and epileptic encephalopathy. The neuroimaging of DNM1 encephalopathy has not been reported in detail. We describe a severe phenotype of DNM1 encephalopathy showing characteristic neuroradiological features. In addition, we reviewed previously reported cases who have DNM1 pathogenic variants with white matter abnormalities. Our case presented drug-resistant seizures from 1 month of age and epileptic spasms at 2 years of age. Brain MRI showed no progression of myelination, progression of diffuse cerebral atrophy, and a thin corpus callosum. Proton magnetic resonance spectroscopy showed a decreased N-acetylaspartate peak and diffusion tensor imaging presented with less pyramidal decussation. Whole-exome sequencing revealed a recurrent de novo heterozygous variant of DNM1. So far, more than 50 cases of DNM1 encephalopathy have been reported. Among these patients, delayed myelination occurred in two cases of GTPase-domain DNM1 encephalopathy and in six cases of middle-domain DNM1 encephalopathy. The neuroimaging findings in this case suggest inadequate axonal development. DNM1 is involved in the release of synaptic vesicles with the inhibitory transmitter GABA, suggesting that GABAergic neuron dysfunction is the mechanism of refractory epilepsy in DNM1 encephalopathy. GABA-mediated signaling mechanisms play important roles in axonal development and GABAergic neuron dysfunction may be cause of white matter abnormalities in DNM1 encephalopathy.
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Affiliation(s)
- Kohei Matsubara
- Division of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Ichiro Kuki
- Division of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Risako Ishioka
- Division of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Naoki Yamada
- Division of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Masataka Fukuoka
- Division of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Takeshi Inoue
- Division of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Megumi Nukui
- Division of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Nobuhiko Okamoto
- Division of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Takeshi Mizuguchi
- Division of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Division of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shin Okazaki
- Division of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
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7
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Sakamoto M, Kurosawa K, Tanoue K, Iwama K, Ishida F, Watanabe Y, Okamoto N, Tsuchida N, Uchiyama Y, Koshimizu E, Fujita A, Misawa K, Miyatake S, Mizuguchi T, Matsumoto N. A heterozygous germline deletion within USP8 causes severe neurodevelopmental delay with multiorgan abnormalities. J Hum Genet 2024; 69:85-90. [PMID: 38030753 DOI: 10.1038/s10038-023-01209-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023]
Abstract
Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme involved in deubiquitinating the enhanced epidermal growth factor receptor for escape from degradation. Somatic variants at a hotspot in USP8 are a cause of Cushing's disease, and a de novo germline USP8 variant at this hotspot has been described only once previously, in a girl with Cushing's disease and developmental delay. In this study, we investigated an exome-negative patient with severe developmental delay, dysmorphic features, and multiorgan dysfunction by long-read sequencing, and identified a 22-kb de novo germline deletion within USP8 (chr15:50469966-50491995 [GRCh38]). The deletion involved the variant hotspot, one rhodanese domain, and two SH3 binding motifs, and was presumed to be generated through nonallelic homologous recombination through Alu elements. Thus, the patient may have perturbation of the endosomal sorting system and mitochondrial autophagy through the USP8 defect. This is the second reported case of a germline variant in USP8.
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Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Koji Tanoue
- Department of General Medicine, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Perinatal Center for Maternity and Neonate, Yokohama City University Medical Center, Yokohama, Japan
| | - Fumihiko Ishida
- Perinatal Center for Maternity and Neonate, Yokohama City University Medical Center, Yokohama, Japan
| | - Yoshihiro Watanabe
- Children's Medical Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Riken Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.
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8
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Higashimoto K, Sun F, Imagawa E, Saida K, Miyake N, Hara S, Yatsuki H, Kubiura-Ichimaru M, Fujita A, Mizuguchi T, Matsumoto N, Soejima H. Whole-exome sequencing reveals causative genetic variants for several overgrowth syndromes in molecularly negative Beckwith-Wiedemann spectrum. J Med Genet 2024:jmg-2023-109621. [PMID: 38228391 DOI: 10.1136/jmg-2023-109621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024]
Abstract
Background Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder caused by (epi)genetic alterations at 11p15. Because approximately 20% of patients test negative via molecular testing of peripheral blood leukocytes, the concept of Beckwith-Wiedemann spectrum (BWSp) was established to encompass a broader cohort with diverse and overlapping phenotypes. The prevalence of other overgrowth syndromes concealed within molecularly negative BWSp remains unexplored.Methods We conducted whole-exome sequencing (WES) on 69 singleton patients exhibiting molecularly negative BWSp. Variants were confirmed by Sanger sequencing or quantitative genomic PCR. We compared BWSp scores and clinical features between groups with classical BWS (cBWS), atypical BWS or isolated lateralised overgrowth (aBWS+ILO) and overgrowth syndromes identified via WES.Results Ten patients, one classified as aBWS and nine as cBWS, showed causative gene variants for Simpson-Golabi-Behmel syndrome (five patients), Sotos syndrome (two), Imagawa-Matsumoto syndrome (one), glycosylphosphatidylinositol biosynthesis defect 11 (one) or 8q duplication/9p deletion (one). BWSp scores did not distinguish between cBWS and other overgrowth syndromes. Birth weight and height in other overgrowth syndromes were significantly larger than in aBWS+ILO and cBWS, with varying intergroup frequencies of clinical features.Conclusion Molecularly negative BWSp encapsulates other syndromes, and considering both WES and clinical features may facilitate accurate diagnosis.
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Affiliation(s)
- Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Feifei Sun
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, China
| | - Eri Imagawa
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo, Japan
| | - Ken Saida
- 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
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Satoshi Hara
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Musashi Kubiura-Ichimaru
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Atsushi Fujita
- 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
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
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9
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Mizuguchi T, Toyota T, Koshimizu E, Kameyama S, Fukuda H, Tsuchida N, Uchiyama Y, Hamanaka K, Fujita A, Misawa K, Miyatake S, Adachi H, Matsumoto N. Complete SAMD12 repeat expansion sequencing in a four-generation BAFME1 family with anticipation. J Hum Genet 2023; 68:875-878. [PMID: 37592133 DOI: 10.1038/s10038-023-01187-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/29/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023]
Abstract
Benign adult familial myoclonic epilepsy type 1 (BAFME1) is an autosomal dominant, adult-onset neurological disease caused by SAMD12 repeat expansion. In BAFME1, anticipation, such as the earlier onset of tremor and/or seizures in the next generation, was reported. This could be explained by intergenerational repeat instability, leading to larger expansions in successive generations. We report a four-generation BAFME1-affected family with anticipation. Using Nanopore long-read sequencing, detailed information regarding the sizes, configurations, and compositions of the expanded SAMD12 repeats across generations was obtained. Unexpectedly, a grandmother-mother-daughter triad showed similar repeat structures but with slight repeat expansions, despite quite variable age of onset of seizures (range: 52-14 years old), implying a complex relationship between the SAMD12 repeat expansion sequence and anticipation. This study suggests that different factor(s) from repeat expansion could modify the anticipation in BAFME1.
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Affiliation(s)
- Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
| | - Tomoko Toyota
- Department of Neurology, University of Occupational and Environmental Health School of Medicine, Kitakyushu, 807-8555, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Shinichi Kameyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Hiroaki Adachi
- Department of Neurology, University of Occupational and Environmental Health School of Medicine, Kitakyushu, 807-8555, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
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10
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Fukuda H, Mizuguchi T, Doi H, Kameyama S, Kunii M, Joki H, Takahashi T, Komiya H, Sasaki M, Miyaji Y, Ohori S, Koshimizu E, Uchiyama Y, Tsuchida N, Fujita A, Hamanaka K, Misawa K, Miyatake S, Tanaka F, Matsumoto N. Long-read sequencing revealing intragenic deletions in exome-negative spastic paraplegias. J Hum Genet 2023; 68:689-697. [PMID: 37308565 DOI: 10.1038/s10038-023-01170-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/01/2023] [Accepted: 06/04/2023] [Indexed: 06/14/2023]
Abstract
Hereditary spastic paraplegias (HSPs) are a heterogeneous group of neurodegenerative disorders characterized by progressive spasticity and weakness in the lower extremities. To date, a total of 88 types of SPG are known. To diagnose HSP, multiple technologies, including microarray, direct sequencing, multiplex ligation-dependent probe amplification, and short-read next-generation sequencing, are often chosen based on the frequency of HSP subtypes. Exome sequencing (ES) is commonly used. We used ES to analyze ten cases of HSP from eight families. We identified pathogenic variants in three cases (from three different families); however, we were unable to determine the cause of the other seven cases using ES. We therefore applied long-read sequencing to the seven undetermined HSP cases (from five families). We detected intragenic deletions within the SPAST gene in four families, and a deletion within PSEN1 in the remaining family. The size of the deletion ranged from 4.7 to 12.5 kb and involved 1-7 exons. All deletions were entirely included in one long read. We retrospectively performed an ES-based copy number variation analysis focusing on pathogenic deletions, but were not able to accurately detect these deletions. This study demonstrated the efficiency of long-read sequencing in detecting intragenic pathogenic deletions in ES-negative HSP patients.
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Affiliation(s)
- Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Shinichi Kameyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Pathology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Misako Kunii
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Hideto Joki
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Neurology, National Hospital Organization Yokohama Medical Center, Yokohama, Kanagawa, 245-8575, Japan
| | - Tatsuya Takahashi
- Department of Neurology, National Hospital Organization Yokohama Medical Center, Yokohama, Kanagawa, 245-8575, Japan
| | - Hiroyasu Komiya
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Mei Sasaki
- Department of Neurology, Yokohama Minami Kyosai Hospital, Yokohama, 236-0037, Japan
| | - Yosuke Miyaji
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
- Department of Genetics, Kitasato University Hospital, Sagamihara, 252-0375, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
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11
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Ohori S, Miyauchi A, Osaka H, Lourenco CM, Arakaki N, Sengoku T, Ogata K, Honjo RS, Kim CA, Mitsuhashi S, Frith MC, Seyama R, Tsuchida N, Uchiyama Y, Koshimizu E, Hamanaka K, Misawa K, Miyatake S, Mizuguchi T, Saito K, Fujita A, Matsumoto N. Biallelic structural variations within FGF12 detected by long-read sequencing in epilepsy. Life Sci Alliance 2023; 6:e202302025. [PMID: 37286232 PMCID: PMC10248215 DOI: 10.26508/lsa.202302025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
We discovered biallelic intragenic structural variations (SVs) in FGF12 by applying long-read whole genome sequencing to an exome-negative patient with developmental and epileptic encephalopathy (DEE). We also found another DEE patient carrying a biallelic (homozygous) single-nucleotide variant (SNV) in FGF12 that was detected by exome sequencing. FGF12 heterozygous recurrent missense variants with gain-of-function or heterozygous entire duplication of FGF12 are known causes of epilepsy, but biallelic SNVs/SVs have never been described. FGF12 encodes intracellular proteins interacting with the C-terminal domain of the alpha subunit of voltage-gated sodium channels 1.2, 1.5, and 1.6, promoting excitability by delaying fast inactivation of the channels. To validate the molecular pathomechanisms of these biallelic FGF12 SVs/SNV, highly sensitive gene expression analyses using lymphoblastoid cells from the patient with biallelic SVs, structural considerations, and Drosophila in vivo functional analysis of the SNV were performed, confirming loss-of-function. Our study highlights the importance of small SVs in Mendelian disorders, which may be overlooked by exome sequencing but can be detected efficiently by long-read whole genome sequencing, providing new insights into the pathomechanisms of human diseases.
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Affiliation(s)
- Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Genetics, Kitasato University Hospital, Sagamihara, Japan
| | - Akihiko Miyauchi
- Department of Pediatrics, Jichi Medical School, Shimotsuke, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical School, Shimotsuke, Japan
| | - Charles Marques Lourenco
- Neurogenetics Department, Faculdade de Medicina de São José do Rio Preto, São Jose do Rio Preto, Brazil
- Personalized Medicine Department, Special Education Sector at DLE/Grupo Pardini, Belo Horizonte, Brazil
| | - Naohiro Arakaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Shizuoka, Japan
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Rachel Sayuri Honjo
- Unidade de Genética Médica do Instituto da Criança, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Unidade de Genética Médica do Instituto da Criança, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Satomi Mitsuhashi
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Martin C Frith
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST, Tokyo, Japan
| | - Rie Seyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kuniaki Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Shizuoka, Japan
| | - Atsushi Fujita
- 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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12
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Seyama R, Nishikawa M, Uchiyama Y, Hamada K, Yamamoto Y, Takeda M, Ochi T, Kishi M, Suzuki T, Hamanaka K, Fujita A, Tsuchida N, Koshimizu E, Misawa K, Miyatake S, Mizuguchi T, Makino S, Yao T, Ito H, Itakura A, Ogata K, Nagata KI, Matsumoto N. A missense variant at the RAC1-PAK1 binding site of RAC1 inactivates downstream signaling in VACTERL association. Sci Rep 2023; 13:9789. [PMID: 37328543 PMCID: PMC10275923 DOI: 10.1038/s41598-023-36381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Abstract
RAC1 at 7p22.1 encodes a RAC family small GTPase that regulates actin cytoskeleton organization and intracellular signaling pathways. Pathogenic RAC1 variants result in developmental delay and multiple anomalies. Here, exome sequencing identified a rare de novo RAC1 variant [NM_018890.4:c.118T > C p.(Tyr40His)] in a male patient. Fetal ultrasonography indicated the patient to have multiple anomalies, including persistent left superior vena cava, total anomalous pulmonary venous return, esophageal atresia, scoliosis, and right-hand polydactyly. After birth, craniofacial dysmorphism and esophagobronchial fistula were confirmed and VACTERL association was suspected. One day after birth, the patient died of respiratory failure caused by tracheal aplasia type III. The molecular mechanisms of pathogenic RAC1 variants remain largely unclear; therefore, we biochemically examined the pathophysiological significance of RAC1-p.Tyr40His by focusing on the best characterized downstream effector of RAC1, PAK1, which activates Hedgehog signaling. RAC1-p.Tyr40His interacted minimally with PAK1, and did not enable PAK1 activation. Variants in the RAC1 Switch II region consistently activate downstream signals, whereas the p.Tyr40His variant at the RAC1-PAK1 binding site and adjacent to the Switch I region may deactivate the signals. It is important to accumulate data from individuals with different RAC1 variants to gain a full understanding of their varied clinical presentations.
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Affiliation(s)
- Rie Seyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Masashi Nishikawa
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, Aichi, 480-0392, Japan
- Department of Biological Sciences, Nagoya University, Nagoya, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuka Yamamoto
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Masahiro Takeda
- Department of Pediatric Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Takanori Ochi
- Department of Pediatric Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Monami Kishi
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
- Department of Obstetrics and Gynecology, Keiai Hospital, Saitama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Shintaro Makino
- Department of Obstetrics and Gynecology, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Takashi Yao
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hidenori Ito
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, Aichi, 480-0392, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai, Aichi, 480-0392, Japan.
- Department of Neurochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Nagoya, Japan, 466-8550.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan.
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13
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Miyake N, Tsurusaki Y, Fukai R, Kushima I, Okamoto N, Ohashi K, Nakamura K, Hashimoto R, Hiraki Y, Son S, Kato M, Sakai Y, Osaka H, Deguchi K, Matsuishi T, Takeshita S, Fattal-Valevski A, Ekhilevitch N, Tohyama J, Yap P, Keng WT, Kobayashi H, Takubo K, Okada T, Saitoh S, Yasuda Y, Murai T, Nakamura K, Ohga S, Matsumoto A, Inoue K, Saikusa T, Hershkovitz T, Kobayashi Y, Morikawa M, Ito A, Hara T, Uno Y, Seiwa C, Ishizuka K, Shirahata E, Fujita A, Koshimizu E, Miyatake S, Takata A, Mizuguchi T, Ozaki N, Matsumoto N. Molecular diagnosis of 405 individuals with autism spectrum disorder. Eur J Hum Genet 2023:10.1038/s41431-023-01335-7. [PMID: 36973392 DOI: 10.1038/s41431-023-01335-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/08/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Autism spectrum disorder (ASD) is caused by combined genetic and environmental factors. Genetic heritability in ASD is estimated as 60-90%, and genetic investigations have revealed many monogenic factors. We analyzed 405 patients with ASD using family-based exome sequencing to detect disease-causing single-nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variations (CNVs) for molecular diagnoses. All candidate variants were validated by Sanger sequencing or quantitative polymerase chain reaction and were evaluated using the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines for molecular diagnosis. We identified 55 disease-causing SNVs/indels in 53 affected individuals and 13 disease-causing CNVs in 13 affected individuals, achieving a molecular diagnosis in 66 of 405 affected individuals (16.3%). Among the 55 disease-causing SNVs/indels, 51 occurred de novo, 2 were compound heterozygous (in one patient), and 2 were X-linked hemizygous variants inherited from unaffected mothers. The molecular diagnosis rate in females was significantly higher than that in males. We analyzed affected sibling cases of 24 quads and 2 quintets, but only one pair of siblings shared an identical pathogenic variant. Notably, there was a higher molecular diagnostic rate in simplex cases than in multiplex families. Our simulation indicated that the diagnostic yield is increasing by 0.63% (range 0-2.5%) per year. Based on our simple simulation, diagnostic yield is improving over time. Thus, periodical reevaluation of ES data should be strongly encouraged in undiagnosed ASD patients.
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Affiliation(s)
- Noriko Miyake
- Department of Human Genetics, National Center for Global Health and Medicine, Tokyo, Japan.
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Ryoko Fukai
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kei Ohashi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kazuhiko Nakamura
- Department of Neuropsychiatry, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | - Shuraku Son
- Department of Psychiatry, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | | | - Toyojiro Matsuishi
- Departments of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
- Department of Pediatrics, St. Mary's Hospital, Kurume, Japan
| | - Saoko Takeshita
- Department of Pediatrics, Yokohama City University Medical Center, Yokohama, Japan
| | - Aviva Fattal-Valevski
- Pediatric Neurology Institute, Dana-Dwek Children's Hospital, Tel Aviv Medical Center & Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nina Ekhilevitch
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Patrick Yap
- Genetic Health Service New Zealand, Auckland, New Zealand
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Wee Teik Keng
- Genetic Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Hiroshi Kobayashi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Takashi Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yuka Yasuda
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Toshiya Murai
- Department of Psychiatry, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ayumi Matsumoto
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | - Ken Inoue
- Deguchi Pediatric Clinic, Omura, Japan
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Tomoko Saikusa
- Departments of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
- Department of Pediatrics, St. Mary's Hospital, Kurume, Japan
| | - Tova Hershkovitz
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Yu Kobayashi
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Mako Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Aiko Ito
- Department of Pediatrics, Yamagata Prefectural Rehabilitation Center for Children with Disabilities, Yamagata, Japan
| | | | - Yota Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chizuru Seiwa
- Department of Pediatrics, Yamagata Prefectural Rehabilitation Center for Children with Disabilities, Yamagata, Japan
| | - Kanako Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Emi Shirahata
- Department of Pediatrics, Yamagata Prefectural Rehabilitation Center for Children with Disabilities, Yamagata, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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14
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Mori T, Sakamoto M, Tayama T, Goji A, Toda Y, Fujita A, Mizuguchi T, Urushihara M, Matsumoto N. A case of epilepsy with myoclonic atonic seizures caused by SLC6A1 gene mutation due to balanced chromosomal translocation. Brain Dev 2023:S0387-7604(23)00044-X. [PMID: 36966012 DOI: 10.1016/j.braindev.2023.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/27/2023]
Abstract
INTRODUCTION Epilepsy with myoclonic atonic seizures (EMAtS) was previously thought to occur in normally developing children. We report a female case of EMAtS and mild developmental delay before onset. Importantly, a de novo balanced chromosomal translocation was recognized in the patient. CASE PRESENTATION The patient was a 4-year-old girl. Mild developmental delay was observed during infancy. At the age of one and a half years, she developed atonic seizures once a month. At 4 years of age, her seizures increased to more than 10 times per hour. An ictal electroencephalogram (EEG) showed a 3-4-Hz spike-and-wave complex, which was consistent with atonic and myoclonic seizures of the trunk, eyelids, and lips. Therefore, EMAtS was diagnosed based on the symptoms and EEG findings. After administration of valproic acid (VPA), the epileptic seizures disappeared immediately. At the age of 5 years and 2 months, the seizures recurred but disappeared again when the dose of VPA was increased. Subsequently, no recurrence was observed until 6 years and 3 months of age on VPA and lamotrigine. Chromosome analysis of the patient disclosed 46,XX,t(3;11)(p25;q13.1)dn. Long-read sequencing of the the patient's genomic DNA revealed that the 3p25.3 translocation breakpoint disrupted the intron 7 of the SLC6A1 gene. CONCLUSION The SLC6A1 disruption by chromosome translocation well explains the clinical features of this patient. Long-read sequencing is a powerful technique to determine genomic abnormality at the nucleotide level for disease-associated chromosomal abnormality.
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Affiliation(s)
- Tatsuo Mori
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Japan; Division of Epilepsy Center, Tokushima University Hospital, Japan.
| | - Masamune Sakamoto
- Department of Human Genetics, Yokohama City University, Graduate School of Medicine, Japan; Department of Pediatrics, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Takahiro Tayama
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Japan; Division of Epilepsy Center, Tokushima University Hospital, Japan
| | - Aya Goji
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Japan; Division of Epilepsy Center, Tokushima University Hospital, Japan
| | - Yoshihiro Toda
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Japan; Division of Epilepsy Center, Tokushima University Hospital, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University, Graduate School of Medicine, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University, Graduate School of Medicine, Japan
| | - Maki Urushihara
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Japan
| | - Naomichi Matsumoto
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Japan
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15
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Liao YC, Wei CY, Chang FP, Chou YT, Hsu SL, Chung CP, Mizuguchi T, Matsumoto N, Yet SF, Lee YC. NOTCH2NLC GGC Repeat Expansion in Patients With Vascular Leukoencephalopathy. Stroke 2023; 54:1236-1245. [PMID: 36942588 DOI: 10.1161/strokeaha.122.041848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
BACKGROUND Neuronal intranuclear inclusion disease (NIID), caused by GGC (guanine-guanine-cytosine) repeat expansion in NOTCH2NLC, has several clinical and radiological features akin to cerebral small vessel disease (cSVD). The present study tested the hypothesis that NOTCH2NLC GGC expansion may contribute to cSVD. METHODS One hundred and ninety-seven unrelated patients with genetically unsolved vascular leukoencephalopathy without NOTCH3, HTRA1, and mitochondrial m.3243A>G mutations and 730 healthy individuals were screened for NOTCH2NLC GGC repeat expansion using repeat-primed polymerase chain reaction, fragment analysis, Southern blot analysis, or nanopore sequencing with Cas9 (CRISPR associated protein 9)-mediated enrichment. The clinical and neuroimaging features of the patients were compared between individuals with and without NOTCH2NLC GGC repeat expansion. RESULTS Six of the 197 (3.0%) patients with unsolved vascular leukoencephalopathy and none of the controls carried the GGC repeat expansion (P=0.00009). Skin biopsy of 1 patient revealed eosinophilic, ubiquitin-positive, and p62-positive intranuclear inclusions in the cells of sweat gland and capillary, providing pathologic evidence for the involvement of small vessels in NIID. For the 6 patients, gait disturbance and cognitive decline were common manifestations with a median onset age of 65 (59-69) years. They all had multiple neuroimaging features suggestive of cSVD, including diffuse white matter hyperintensities, lacunes, and enlarged perivascular space in all 6 patients, cerebral microbleeds in 5, and old intracerebral hemorrhage in 4. Four patients had linear hyperintensity in the corticomedullary junction on diffusion-weighted imaging-the characteristic neuroimaging feature of NIID. There was no difference in the severity of cSVD imaging features between the patients with and without the GGC expansion but more pronounced brain atrophy in the patients with the GGC expansion. CONCLUSIONS NOTCH2NLC GGC repeat expansion accounted for 3% of genetically unsolved Taiwanese vascular leukoencephalopathy cases after excluding participants with cerebral autosomal dominant arteriopathy with subcortical infarct and leukoencephalopathy (CADASIL), cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL), and mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS). NIID should be considered in patients manifesting cSVD, especially in those with characteristic neuroimaging feature of NIID.
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Affiliation(s)
- Yi-Chu Liao
- Departments of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
- Taipei Veterans General Hospital, Taiwan. Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
- Brain Research Center, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-C. Lee)
| | - Cheng-Yu Wei
- Department of Exercise and Health Promotion, College of Kinesiology and Health, Chinese Culture University, Taipei, Taiwan (C.-Y.W.)
- Department of Neurology, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan (C.-Y.W.)
| | - Fu-Pang Chang
- Department of Pathology and Laboratory Medicine, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (F.-P.C.)
- Institute of Clinical Medicine, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (F.-P.C.)
| | - Ying-Tsen Chou
- Departments of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
- Taipei Veterans General Hospital, Taiwan. Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
| | - Shao-Lun Hsu
- Departments of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
- Taipei Veterans General Hospital, Taiwan. Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
| | - Chih-Ping Chung
- Departments of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
- Taipei Veterans General Hospital, Taiwan. Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan (T.M., N.M.)
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan (T.M., N.M.)
| | - Shaw-Fang Yet
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan, Taiwan (S.-F.Y.)
| | - Yi-Chung Lee
- Departments of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
- Taipei Veterans General Hospital, Taiwan. Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-T.C., S.-L.H., C.-P.C., Y.-C. Lee)
- Brain Research Center, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan. (Y.-C. Liao, Y.-C. Lee)
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16
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Fujita A, Kato M, Sugano H, Iimura Y, Suzuki H, Tohyama J, Fukuda M, Ito Y, Baba S, Okanishi T, Enoki H, Fujimoto A, Yamamoto A, Kawamura K, Kato S, Honda R, Ono T, Shiraishi H, Egawa K, Shirai K, Yamamoto S, Hayakawa I, Kawawaki H, Saida K, Tsuchida N, Uchiyama Y, Hamanaka K, Miyatake S, Mizuguchi T, Nakashima M, Saitsu H, Miyake N, Kakita A, Matsumoto N. An integrated genetic analysis of epileptogenic brain malformed lesions. Acta Neuropathol Commun 2023; 11:33. [PMID: 36864519 PMCID: PMC9983246 DOI: 10.1186/s40478-023-01532-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/17/2023] [Indexed: 03/04/2023] Open
Abstract
Focal cortical dysplasia is the most common malformation during cortical development, sometimes excised by epilepsy surgery and often caused by somatic variants of the mTOR pathway genes. In this study, we performed a genetic analysis of epileptogenic brain malformed lesions from 64 patients with focal cortical dysplasia, hemimegalencephy, brain tumors, or hippocampal sclerosis. Targeted sequencing, whole-exome sequencing, and single nucleotide polymorphism microarray detected four germline and 35 somatic variants, comprising three copy number variants and 36 single nucleotide variants and indels in 37 patients. One of the somatic variants in focal cortical dysplasia type IIB was an in-frame deletion in MTOR, in which only gain-of-function missense variants have been reported. In focal cortical dysplasia type I, somatic variants of MAP2K1 and PTPN11 involved in the RAS/MAPK pathway were detected. The in-frame deletions of MTOR and MAP2K1 in this study resulted in the activation of the mTOR pathway in transiently transfected cells. In addition, the PTPN11 missense variant tended to elongate activation of the mTOR or RAS/MAPK pathway, depending on culture conditions. We demonstrate that epileptogenic brain malformed lesions except for focal cortical dysplasia type II arose from somatic variants of diverse genes but were eventually linked to the mTOR pathway.
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Affiliation(s)
- Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, 142-8666, Japan
| | - Hidenori Sugano
- Department of Neurosurgery, Epilepsy Center, Juntendo University, Tokyo, 113-8421, Japan
| | - Yasushi Iimura
- Department of Neurosurgery, Epilepsy Center, Juntendo University, Tokyo, 113-8421, Japan
| | - Hiroharu Suzuki
- Department of Neurosurgery, Epilepsy Center, Juntendo University, Tokyo, 113-8421, Japan
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, 950-2085, Japan
| | - Masafumi Fukuda
- Department of Functional Neurosurgery, Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, 950-2085, Japan
| | - Yosuke Ito
- Department of Functional Neurosurgery, Epilepsy Center, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, 950-2085, Japan
| | - Shimpei Baba
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Hamamatsu, 430-8558, Japan
| | - Tohru Okanishi
- Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Yonago, 683-8503, Japan
| | - Hideo Enoki
- Department of Pediatrics, Kawasaki Medical School, Kurashiki, 701-0192, Japan
| | - Ayataka Fujimoto
- Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Hamamatsu, 430-8558, Japan
| | - Akiyo Yamamoto
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Kentaro Kawamura
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Shinsuke Kato
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, 060-8543, Japan
| | - Ryoko Honda
- Department of Pediatrics, National Hospital Organization Nagasaki Medical Center, Omura, 856-8562, Japan
| | - Tomonori Ono
- Epilepsy Center, National Hospital Organization Nagasaki Medical Center, Omura, 856-8562, Japan
| | - Hideaki Shiraishi
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Kiyoshi Egawa
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Kentaro Shirai
- Department of Pediatrics, Tsuchiura Kyodo General Hospital, Tsuchiura, 300-0028, Japan
| | - Shinji Yamamoto
- Department of Neurosurgery, Tsuchiura Kyodo General Hospital, Tsuchiura, 300-0028, Japan
| | - Itaru Hayakawa
- Division of Neurology, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Hisashi Kawawaki
- Department of Pediatric Neurology, Children's Medical Center, Osaka City General Hospital, Osaka, 534-0021, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.,Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan.
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17
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Hamanaka K, Yamauchi D, Koshimizu E, Watase K, Mogushi K, Ishikawa K, Mizusawa H, Tsuchida N, Uchiyama Y, Fujita A, Misawa K, Mizuguchi T, Miyatake S, Matsumoto N. Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans. Genome Res 2023; 33:435-447. [PMID: 37307504 PMCID: PMC10078293 DOI: 10.1101/gr.277335.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
Tandem repeats (TRs) are one of the largest sources of polymorphism, and their length is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a genome-wide catalog of 9537 spl-TRs with a total of 58,290 significant TR-splicing associations across 49 tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci for repeat expansion diseases, spinocerebellar ataxia 6 (SCA6) and 12 (SCA12). Splicing alterations by these spl-TRs were compatible with those observed in SCA6 and SCA12. Thus, our comprehensive spl-TR catalog may help elucidate the pathomechanism of genetic diseases.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | | | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kei Watase
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kaoru Mogushi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kinya Ishikawa
- The Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hidehiro Mizusawa
- Department of Neurology, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
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18
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Yamamoto K, Baba S, Saito T, Nakagawa E, Sugai K, Iwasaki M, Fujita A, Fukuda H, Mizuguchi T, Kato M, Matsumoto N, Sasaki M. Synchronous heart rate reduction with suppression-burst pattern in KCNT1-related developmental and epileptic encephalopathies. Epilepsia Open 2023. [PMID: 36740266 DOI: 10.1002/epi4.12705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/28/2023] [Indexed: 02/07/2023] Open
Abstract
Suppression-burst (SB) is an electroencephalographic pattern observed in neonatal- and infantile-onset developmental and epileptic encephalopathies (DEEs), which are associated with high mortality in early life. However, the relation of SB electroencephalogram (SB-EEG) with autonomic function requires clarification. We investigated the relationship between heart rate (HR) and phasic transition during SB-EEG in DEEs to explore the mechanism of early death. Seven patients (two with KCNT1-DEE) with neonatal- and infantile-onset DEE who presented with SB-EEG were retrospectively identified. Five-minute SB-EEGs were analyzed with simultaneous recording of electrocardiograms. Mean HR, suppression duration, and burst period were calculated by measuring RR intervals. Two patients with KCNT1-DEE exhibited synchronous HR fluctuations, with an HR decrease during suppression and an increase during burst. The HR decrease was larger (-6.1% and -7.7%) and the median duration of suppression was longer (4.0 and 8.2 s) in patients with KCNT1-DEE than the other five (range: -2.9% to 0.9% and 0.7-1.7s, respectively). A strong negative correlation was confirmed between suppression duration and HR reduction rates in one patient with KCNT1-DEE. SB phases may influence HR regulation in patients with KCTN1-DEE.
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Affiliation(s)
- Kaoru Yamamoto
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Shimpei Baba
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Takashi Saito
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Eiji Nakagawa
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.,Department of Epileptology, National Center Hospital, NCNP, Tokyo, Japan
| | - Kenji Sugai
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan.,Division of Pediatrics, Soleil Kawasaki Medical Center for the Handicapped, Kawasaki, Japan
| | - Masaki Iwasaki
- Department of Neurosurgery, National Center Hospital, NCNP, Tokyo, Japan
| | - Atsushi Fujita
- 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
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine and Epilepsy Medical Center, Showa University Hospital, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
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19
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Sakamoto M, Shiiki T, Matsui S, Okamoto N, Koshimizu E, Tsuchida N, Uchiyama Y, Hamanaka K, Fujita A, Miyatake S, Misawa K, Mizuguchi T, Matsumoto N. Correction: A novel homozygous CHMP1A variant arising from segmental uniparental disomy causes pontocerebellar hypoplasia type 8. J Hum Genet 2023; 68:299. [PMID: 36694001 DOI: 10.1038/s10038-023-01125-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Toshihide Shiiki
- Department of Pediatrics, Tokyo Children Rehabilitation Hospital, Tokyo, Japan
| | - Shuji Matsui
- Department of Pediatrics, Tokyo Children Rehabilitation Hospital, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Riken Center for Advanced Intelligence Project, Tokyo, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.
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20
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Kodama K, Aoyama H, Murakami Y, Takanashi JI, Koshimizu E, Miyatake S, Iwama K, Mizuguchi T, Matsumoto N, Omata T. A case of early-infantile onset, rapidly progressive leukoencephalopathy with calcifications and cysts caused by biallelic SNORD118 variants. Radiol Case Rep 2023; 18:1217-1220. [PMID: 36660574 PMCID: PMC9842793 DOI: 10.1016/j.radcr.2022.11.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 01/13/2023] Open
Abstract
Leukoencephalopathy with calcifications and cysts is a rare autosomal recessive genetic disorder neuroradiologically characterized by intracranial calcification, cerebral white matter disease, and multiple cysts. Although SNORD118 genes have recently been identified as a cause of this disorder, its clinical course varies for each patient. We report an early infantile case of this disease that progressed rapidly with confirmed SNORD118 variants. A 3-month-old female infant presented with epileptic seizures. Computed tomography revealed intracranial calcifications in the basal ganglia and thalamus. Magnetic resonance imaging demonstrated hyperintense lesions in the diffuse white matter on T2-weighted images starting at 7 months of age. Calcifications developed in the cerebral white matter, pons, and cerebellum. Small cysts appeared in the cerebral white matter at 1 year and 6 months. These cysts then began to increase bilaterally and expand rapidly. Although her epilepsy was controlled, she exhibited severe developmental delays and was unable to speak or walk at the age of 4 years. Whole-exome sequencing did not reveal any causal variants in the coding sequences. Further, Sanger sequencing revealed biallelic SNORD118 variants. Clinical features of this disease have not been established. To date, no cases with rapid changes in imaging results have been reported in detail prior to the appearance of cysts. Thus, we report a novel case that had an early infantile-onset and progressed rapidly with sequential appearance of calcification, white matter lesions and cysts. As SNORD118 variants might be missed by regular whole-exome sequencing, careful neuroimaging follow-up may be necessary to diagnose this disease.
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Affiliation(s)
- Kazuo Kodama
- Division of Child Neurology, Chiba Children's Hospital, 579-1, Heta-cho, Midori-ku, Chiba 266-0007, Japan
- Corresponding author.
| | - Hiromi Aoyama
- Division of Child Neurology, Chiba Children's Hospital, 579-1, Heta-cho, Midori-ku, Chiba 266-0007, Japan
| | - Yoshimi Murakami
- Division of Child Neurology, Chiba Children's Hospital, 579-1, Heta-cho, Midori-ku, Chiba 266-0007, Japan
| | - Jun-ichi Takanashi
- Department of Pediatrics, Tokyo Women's Medical University, Yachiyo Medical Center, Yachiyo, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | | | - Taku Omata
- Division of Child Neurology, Chiba Children's Hospital, 579-1, Heta-cho, Midori-ku, Chiba 266-0007, Japan
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21
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Saida K, Maroofian R, Sengoku T, Mitani T, Pagnamenta AT, Marafi D, Zaki MS, O'Brien TJ, Karimiani EG, Kaiyrzhanov R, Takizawa M, Ohori S, Leong HY, Akay G, Galehdari H, Zamani M, Romy R, Carroll CJ, Toosi MB, Ashrafzadeh F, Imannezhad S, Malek H, Ahangari N, Tomoum H, Gowda VK, Srinivasan VM, Murphy D, Dominik N, Elbendary HM, Rafat K, Yilmaz S, Kanmaz S, Serin M, Krishnakumar D, Gardham A, Maw A, Rao TS, Alsubhi S, Srour M, Buhas D, Jewett T, Goldberg RE, Shamseldin H, Frengen E, Misceo D, Strømme P, Magliocco Ceroni JR, Kim CA, Yesil G, Sengenc E, Guler S, Hull M, Parnes M, Aktas D, Anlar B, Bayram Y, Pehlivan D, Posey JE, Alavi S, Madani Manshadi SA, Alzaidan H, Al-Owain M, Alabdi L, Abdulwahab F, Sekiguchi F, Hamanaka K, Fujita A, Uchiyama Y, Mizuguchi T, Miyatake S, Miyake N, Elshafie RM, Salayev K, Guliyeva U, Alkuraya FS, Gleeson JG, Monaghan KG, Langley KG, Yang H, Motavaf M, Safari S, Alipour M, Ogata K, Brown AEX, Lupski JR, Houlden H, Matsumoto N. Brain monoamine vesicular transport disease caused by homozygous SLC18A2 variants: A study in 42 affected individuals. Genet Med 2023; 25:90-102. [PMID: 36318270 DOI: 10.1016/j.gim.2022.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Brain monoamine vesicular transport disease is an infantile-onset movement disorder that mimics cerebral palsy. In 2013, the homozygous SLC18A2 variant, p.Pro387Leu, was first reported as a cause of this rare disorder, and dopamine agonists were efficient for treating affected individuals from a single large family. To date, only 6 variants have been reported. In this study, we evaluated genotype-phenotype correlations in individuals with biallelic SLC18A2 variants. METHODS A total of 42 affected individuals with homozygous SLC18A2 variant alleles were identified. We evaluated genotype-phenotype correlations and the missense variants in the affected individuals based on the structural modeling of rat VMAT2 encoded by Slc18a2, with cytoplasm- and lumen-facing conformations. A Caenorhabditis elegans model was created for functional studies. RESULTS A total of 19 homozygous SLC18A2 variants, including 3 recurrent variants, were identified using exome sequencing. The affected individuals typically showed global developmental delay, hypotonia, dystonia, oculogyric crisis, and autonomic nervous system involvement (temperature dysregulation/sweating, hypersalivation, and gastrointestinal dysmotility). Among the 58 affected individuals described to date, 16 (28%) died before the age of 13 years. Of the 17 patients with p.Pro237His, 9 died, whereas all 14 patients with p.Pro387Leu survived. Although a dopamine agonist mildly improved the disease symptoms in 18 of 21 patients (86%), some affected individuals with p.Ile43Phe and p.Pro387Leu showed milder phenotypes and presented prolonged survival even without treatment. The C. elegans model showed behavioral abnormalities. CONCLUSION These data expand the phenotypic and genotypic spectra of SLC18A2-related disorders.
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Affiliation(s)
- Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Alistair T Pagnamenta
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Thomas J O'Brien
- MRC London Institute of Medical Sciences, London, United Kingdom; Faculty of Medicine, Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, United Kingdom; Innovative Medical Research Center, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Marina Takizawa
- 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
| | - Huey Yin Leong
- Genetics Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Ratna Romy
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, United Kingdom
| | - Christopher J Carroll
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, United Kingdom
| | - Mehran Beiraghi Toosi
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farah Ashrafzadeh
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shima Imannezhad
- Department of Pediatric Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadis Malek
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Najmeh Ahangari
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Hoda Tomoum
- Department of Pediatrics, Ain Shams University, Cairo, Egypt
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | | | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Karima Rafat
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Sanem Yilmaz
- Division of Pediatric Neurology, Department of Pediatrics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Seda Kanmaz
- Division of Pediatric Neurology, Department of Pediatrics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Mine Serin
- Division of Pediatric Neurology, Department of Pediatrics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Deepa Krishnakumar
- North West Thames Regional Genetics Service, Northwick Park Hospital, London, United Kingdom
| | - Alice Gardham
- North West Thames Regional Genetics Service, Northwick Park Hospital, London, United Kingdom
| | - Anna Maw
- Department of Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Tekki Sreenivasa Rao
- Department of Paediatrics, Luton and Dunstable University Hospital, Luton, United Kingdom
| | - Sarah Alsubhi
- Division of Pediatric Neurology, Departments of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Myriam Srour
- Division of Pediatric Neurology, Departments of Pediatrics, McGill University, Montreal, Quebec, Canada; Research Institute of the McGill University Health Center (MUHC), Montreal, Quebec, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Center (MUHC), Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tamison Jewett
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Rachel E Goldberg
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Hanan Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Petter Strømme
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital and University of Oslo, Oslo, Norway
| | | | - Chong Ae Kim
- Genetic Unit, Instituto da Crianca, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Gozde Yesil
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Esma Sengenc
- Department of Pediatric Neurology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Serhat Guler
- Department of Child Neurology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | | | | | - Dilek Aktas
- Damagen Genetic Diagnostic Center, Ankara, Turkey
| | - Banu Anlar
- Department of Pediatric Neurology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yavuz Bayram
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Division of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Shahryar Alavi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Hamad Alzaidan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammad Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lama Alabdi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ferdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- 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
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, 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
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Kamran Salayev
- Department of Neurology, Azerbaijan Medical University, Baku, Azerbaijan
| | | | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, San Diego, CA; Rady Children's Institute for Genomic Medicine, San Diego, CA
| | | | | | | | - Mahsa Motavaf
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Safari
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mozhgan Alipour
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - André E X Brown
- MRC London Institute of Medical Sciences, London, United Kingdom; Faculty of Medicine, Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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22
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Inoue Y, Tsuchida N, Okamoto N, Shuichi S, Ohashi K, Saitoh S, Ogawa A, Hamada K, Sakamoto M, Miyake N, Hamanaka K, Fujita A, Koshimizu E, Miyatake S, Mizuguchi T, Ogata K, Uchiyama Y, Matsumoto N. Three KINSSHIP syndrome patients with mosaic and germline AFF3 variants. Clin Genet 2022; 103:590-595. [PMID: 36576140 DOI: 10.1111/cge.14292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022]
Abstract
AFF3 at 2q11.2 encodes the nuclear transcriptional activator AF4/FMR2 Family Member 3. AFF3 constitutes super elongation complex like 3, which plays a role in promoting the expression of genes involved in neurogenesis and development. The degron motif in AFF3 with nine highly conserved amino acids is recognized by E3 ubiquitin ligase to induce protein degradation. Recently, AFF3 missense variants in this region and variants featuring deletion including this region were identified and shown to cause KINSSHIP syndrome. In this study, we identified two novel and one previously reported missense variants in the degron of AFF3 in three unrelated Japanese patients. Notably, two of these three variants exhibited mosaicism in the examined tissues. This study suggests that mosaic variants also cause KINSSHIP syndrome, showing various phenotypes.
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Affiliation(s)
- Yuta Inoue
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Shimakawa Shuichi
- Department of Pediatrics, Osaka Medical and Pharmaceutical University Hospital, Osaka, Japan
| | - Kei Ohashi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Atsushi Ogawa
- Department of Pediatrics, Chikushi Hospital, Fukuoka University, Fukuoka, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masamune Sakamoto
- 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.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kohei Hamanaka
- 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
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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23
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Sakamoto M, Shiiki T, Matsui S, Okamoto N, Koshimizu E, Tsuchida N, Uchiyama Y, Hamanaka K, Fujita A, Miyatake S, Misawa K, Mizuguchi T, Matsumoto N. A novel homozygous CHMP1A variant arising from segmental uniparental disomy causes pontocerebellar hypoplasia type 8. J Hum Genet 2022; 68:247-253. [PMID: 36509868 DOI: 10.1038/s10038-022-01098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/23/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
Pontocerebellar hypoplasia (PCH) is currently classified into 16 subgroups. Using mostly next-generation sequencing, pathogenic variants have been identified in as many as 24 PCH-associated genes. PCH type 8 (PCH8) is a rare heterogeneous disorder. Its clinical presentation includes severe development delay, increased muscle tone, microcephaly, and magnetic resonance imaging (MRI) abnormalities such as reduced cerebral white matter, a thin corpus callosum, and brainstem and cerebellar hypoplasia. To date, only two variants in the CHMP1A gene (MIM: 164010), NM_002768.5: c.88 C > T (p.Glu30*) and c.28-13 G > A, have been identified homozygously in seven patients with PCH8 from four families (MIM: 614961). CHMP1A is a subunit of the endosomal sorting complex required for transport III (ESCRT-III), which regulates the formation and release of extracellular vesicles. Biallelic CHMP1A loss of function impairs the ESCRT-III-mediated release of extracellular vesicles, which causes impaired progenitor proliferation in the developing brain. Herein, we report a patient with PCH8 who had a homozygous CHMP1A variant, c.122delA (p.Asn41Metfs*2), which arose from segmental uniparental disomy. Although our patient had similar MRI findings to those of previously reported patients, with no progression, we report some novel neurological and developmental findings that expand our knowledge of the clinical consequences associated with CHMP1A variants.
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Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Toshihide Shiiki
- Department of Pediatrics, Tokyo Children Rehabilitation Hospital, Tokyo, Japan
| | - Shuji Matsui
- Department of Pediatrics, Tokyo Children Rehabilitation Hospital, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Riken Center for Advanced Intelligence Project, Tokyo, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.
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24
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Sakamoto M, Iwama K, Sasaki M, Ishiyama A, Komaki H, Saito T, Takeshita E, Shimizu-Motohashi Y, Haginoya K, Kobayashi T, Goto T, Tsuyusaki Y, Iai M, Kurosawa K, Osaka H, Tohyama J, Kobayashi Y, Okamoto N, Suzuki Y, Kumada S, Inoue K, Mashimo H, Arisaka A, Kuki I, Saijo H, Yokochi K, Kato M, Inaba Y, Gomi Y, Saitoh S, Shirai K, Morimoto M, Izumi Y, Watanabe Y, Nagamitsu SI, Sakai Y, Fukumura S, Muramatsu K, Ogata T, Yamada K, Ishigaki K, Hirasawa K, Shimoda K, Akasaka M, Kohashi K, Sakakibara T, Ikuno M, Sugino N, Yonekawa T, Gürsoy S, Cinleti T, Kim CA, Teik KW, Yan CM, Haniffa M, Ohba C, Ito S, Saitsu H, Saida K, Tsuchida N, Uchiyama Y, Koshimizu E, Fujita A, Hamanaka K, Misawa K, Miyatake S, Mizuguchi T, Miyake N, Matsumoto N. Genetic and clinical landscape of childhood cerebellar hypoplasia and atrophy. Genet Med 2022; 24:2453-2463. [PMID: 36305856 DOI: 10.1016/j.gim.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 11/06/2022] Open
Abstract
PURPOSE Cerebellar hypoplasia and atrophy (CBHA) in children is an extremely heterogeneous group of disorders, but few comprehensive genetic studies have been reported. Comprehensive genetic analysis of CBHA patients may help differentiating atrophy and hypoplasia and potentially improve their prognostic aspects. METHODS Patients with CBHA in 176 families were genetically examined using exome sequencing. Patients with disease-causing variants were clinically evaluated. RESULTS Disease-causing variants were identified in 96 of the 176 families (54.5%). After excluding 6 families, 48 patients from 42 families were categorized as having syndromic associations with CBHA, whereas the remaining 51 patients from 48 families had isolated CBHA. In 51 patients, 26 aberrant genes were identified, of which, 20 (76.9%) caused disease in 1 family each. The most prevalent genes were CACNA1A, ITPR1, and KIF1A. Of the 26 aberrant genes, 21 and 1 were functionally annotated to atrophy and hypoplasia, respectively. CBHA+S was more clinically severe than CBHA-S. Notably, ARG1 and FOLR1 variants were identified in 2 families, leading to medical treatments. CONCLUSION A wide genetic and clinical diversity of CBHA was revealed through exome sequencing in this cohort, which highlights the importance of comprehensive genetic analyses. Furthermore, molecular-based treatment was available for 2 families.
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Affiliation(s)
- 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
| | - 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
| | - Masayuki Sasaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Hirofumi Komaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takashi Saito
- 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
| | - Yuko Shimizu-Motohashi
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - Tomoko Kobayashi
- Department of Pediatrics, Tohoku University Hospital, Tohoku University, Sendai, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohide Goto
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yu Tsuyusaki
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mizue Iai
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hitoshi Osaka
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan; Department of Pediatrics, Jichi Medical University, Tochigi, Japan
| | - Jun Tohyama
- Department of Child Neurology, NHO Nishiniigata Chuo Hospital, Niigata, Japan
| | - Yu Kobayashi
- Department of Child Neurology, NHO Nishiniigata Chuo Hospital, Niigata, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Yume Suzuki
- Department of Pediatrics, Jichi Medical University, Tochigi, Japan
| | - Satoko Kumada
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Kenji Inoue
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Hideaki Mashimo
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Atsuko Arisaka
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Ichiro Kuki
- Department of Pediatric Neurology, Children's Medical Center, Osaka City General Hospital, Osaka, Japan
| | - Harumi Saijo
- Department of Pediatrics, Tokyo Metropolitan Higashiyamato Medical Center for Developmental/Multiple Disabilities, Tokyo, Japan
| | - Kenji Yokochi
- Department of Pediatric Neurology, Seirei-Mikatahara General Hospital, Hamamatsu, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Yuji Inaba
- Division of Neurology, Nagano Children's Hospital, Azumino, Nagano, Japan
| | - Yuko Gomi
- Division of Rehabilitation, Nagano Children's Hospital, Azumino, Nagano, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kentaro Shirai
- Department of Pediatrics, Tsuchiura Kyodo General Hospital, Ibaraki, Japan
| | - Masafumi Morimoto
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuishin Izumi
- Department of Clinical Neuroscience, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Yoriko Watanabe
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
| | | | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shinobu Fukumura
- Department of Pediatrics, School of Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kazuhiro Muramatsu
- Department of Pediatrics, Jichi Medical University, Tochigi, Japan; Department of Pediatrics, Graduate School of Medicine, Gunma University, Gunma, Japan
| | - Tomomi Ogata
- Department of Pediatrics, Graduate School of Medicine, Gunma University, Gunma, Japan
| | - Keitaro Yamada
- Department of Pediatric Neurology, Aichi Developmental Disability Center Central Hospital, Aichi, Japan
| | - Keiko Ishigaki
- Department of Pediatrics, School of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Kyoko Hirasawa
- Department of Pediatrics, School of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Konomi Shimoda
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Manami Akasaka
- Department of Pediatrics, School of Medicine, Iwate Medical University, Iwate, Japan
| | - Kosuke Kohashi
- Department of Pediatrics, Matsudo City General Hospital, Matsudo, Japan
| | | | - Masashi Ikuno
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Noriko Sugino
- Department of Neonatology, Mie Chuo Medical Center, National Hospital Organization, Tsu, Japan
| | - Takahiro Yonekawa
- Department of Pediatrics, Mie University School of Medicine, Mie, Japan
| | - Semra Gürsoy
- Department of Pediatric Genetics, S.B.Ü. Dr. Behçet Uz Children's Education and Research Hospital, Izmir, Turkey
| | - Tayfun Cinleti
- Department of Pediatric Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Chong Ae Kim
- Unidade de Genética Clínica, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Keng Wee Teik
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Chan Mei Yan
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Muzhirah Haniffa
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Chihiro Ohba
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shuuichi Ito
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 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
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Takeshi Mizuguchi
- 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; Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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25
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Suzuki T, Osaka H, Miyake N, Fujita A, Uchiyama Y, Seyama R, Koshimizu E, Miyatake S, Mizuguchi T, Takeda S, Matsumoto N. Distal 2q duplication in a patient with intellectual disability. Hum Genome Var 2022; 9:39. [PMID: 36357380 PMCID: PMC9649592 DOI: 10.1038/s41439-022-00215-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/11/2022] Open
Abstract
We report on a patient with a distal 16.4-Mb duplication at 2q36.3-qter, who presented with severe intellectual disability, microcephaly, brachycephaly, prominent forehead, hypertelorism, prominent eyes, thin upper lip, and progenia. Copy number analysis using whole exome data detected a distal 2q duplication. This is the first report describing a distal 2q duplication at the molecular level.
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Affiliation(s)
- Toshifumi Suzuki
- grid.258269.20000 0004 1762 2738Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, 113-8421 Japan ,Department of Obstetrics and Gynecology, Keiai Hospital, Saitama, 354-0017 Japan
| | - Hitoshi Osaka
- grid.410804.90000000123090000Department of Pediatrics, Jichi Medical University, Shimotsuke, 329-0498 Japan
| | - Noriko Miyake
- grid.45203.300000 0004 0489 0290Department of Human Genetics, Research Institute National Center for Global Health and Medicine, Tokyo, Japan
| | - Atsushi Fujita
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Yuri Uchiyama
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan ,grid.470126.60000 0004 1767 0473Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004 Japan
| | - Rie Seyama
- grid.258269.20000 0004 1762 2738Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, 113-8421 Japan ,grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Eriko Koshimizu
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Satoko Miyatake
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan ,grid.470126.60000 0004 1767 0473Clinical Genetics Department, Yokohama City University Hospital, Yokohama, 236-0004 Japan
| | - Takeshi Mizuguchi
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
| | - Satoru Takeda
- grid.258269.20000 0004 1762 2738Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, 113-8421 Japan ,Aiiku Research Institute for Maternal, Child Health and Welfare, Tokyo, Japan
| | - Naomichi Matsumoto
- grid.268441.d0000 0001 1033 6139Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004 Japan
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26
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Kameyama S, Mizuguchi T, Doi H, Koyano S, Okubo M, Tada M, Shimizu H, Fukuda H, Tsuchida N, Uchiyama Y, Koshimizu E, Hamanaka K, Fujita A, Misawa K, Miyatake S, Kanai K, Tanaka F, Matsumoto N. Patients with biallelic GGC repeat expansions in NOTCH2NLC exhibiting a typical neuronal intranuclear inclusion disease phenotype. Genomics 2022; 114:110469. [PMID: 36041634 DOI: 10.1016/j.ygeno.2022.110469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/16/2022] [Accepted: 08/26/2022] [Indexed: 11/27/2022]
Abstract
We report two patients with autosomal dominant neuronal intranuclear inclusion disease (NIID) harboring the biallelic GGC repeat expansion in NOTCH2NLC to uncover the impact of repeat expansion zygosity on the clinical phenotype. The zygosity of the entire NOTCH2NLC GGC repeat expansion and DNA methylation were comprehensively evaluated using fluorescent amplicon length PCR (AL-PCR), Southern blotting and targeted long-read sequencing, and detailed genetic/epigenetic and clinical features were described. In AL-PCR, we could not recognize the wild-type allele in both patients. Targeted long-read sequencing revealed that one patient harbored a homozygous repeat expansion. The other patient harbored compound heterozygous repeat expansions. The GGC repeats and the nearest CpG island were hypomethylated in all expanded alleles in both patients. Both patients harboring the biallelic GGC repeat expansion showed a typical dementia-dominant NIID phenotype. In conclusion, the biallelic GGC repeat expansion in two typical NIID patients indicated that NOTCH2NLC-related diseases could be completely dominant.
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Affiliation(s)
- Shinichi Kameyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shigeru Koyano
- Department of Neurology, Yokohama Minami Kyosai Hospital, Yokohama 236-0037, Japan
| | - Masaki Okubo
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Mikiko Tada
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hiroshi Shimizu
- Department of Pathology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Clinical Genetics Department, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Kazuaki Kanai
- Department of Neurology, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.
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27
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Jung NY, Lee HJ, Mizuguchi T, Matsumoto N. Genetic and Imaging Characteristics of a Family With Neuronal Intranuclear Inclusion Disease. J Clin Neurol 2022; 18:358-360. [PMID: 35589323 PMCID: PMC9163938 DOI: 10.3988/jcn.2022.18.3.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Na-Yeon Jung
- Department of Neurology, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan, Korea.,Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea.
| | - Hyun Jung Lee
- Department of Pathology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - 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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28
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Saida K, Chong PF, Yamaguchi A, Saito N, Ikehara H, Koshimizu E, Miyata R, Ishiko A, Nakamura K, Ohnishi H, Fujioka K, Sakakibara T, Asada H, Ogawa K, Kudo K, Ohashi E, Kawai M, Abe Y, Tsuchida N, Uchiyama Y, Hamanaka K, Fujita A, Mizuguchi T, Miyatake S, Miyake N, Kato M, Kira R, Matsumoto N. Monogenic causes of pigmentary mosaicism. Hum Genet 2022; 141:1771-1784. [PMID: 35503477 DOI: 10.1007/s00439-022-02437-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/28/2022] [Indexed: 12/30/2022]
Abstract
Pigmentary mosaicism of the Ito type, also known as hypomelanosis of Ito, is a neurocutaneous syndrome considered to be predominantly caused by somatic chromosomal mosaicism. However, a few monogenic causes of pigmentary mosaicism have been recently reported. Eleven unrelated individuals with pigmentary mosaicism (mostly hypopigmented skin) were recruited for this study. Skin punch biopsies of the probands and trio-based blood samples (from probands and both biological parents) were collected, and genomic DNA was extracted and analyzed by exome sequencing. In all patients, plausible monogenic causes were detected with somatic and germline variants identified in five and six patients, respectively. Among the somatic variants, four patients had MTOR variant (36%) and another had an RHOA variant. De novo germline variants in USP9X, TFE3, and KCNQ5 were detected in two, one, and one patients, respectively. A maternally inherited PHF6 variant was detected in one patient with hyperpigmented skin. Compound heterozygous GTF3C5 variants were highlighted as strong candidates in the remaining patient. Exome sequencing, using patients' blood and skin samples is highly recommended as the first choice for detecting causative genetic variants of pigmentary mosaicism.
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Affiliation(s)
- Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Pin Fee Chong
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Asuka Yamaguchi
- Department of Pediatrics, Tokyo-Kita Medical Center, Tokyo, Japan
| | - Naka Saito
- Department of Pediatrics, Tsuruoka Municipal Shonai Hospital, Yamagata, Japan
| | - Hajime Ikehara
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Rie Miyata
- Department of Pediatrics, Tokyo-Kita Medical Center, Tokyo, Japan
| | - Akira Ishiko
- Department of Dermatology, Toho University School of Medicine, Tokyo, Japan
| | - Kazuyuki Nakamura
- Department of Pediatrics, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kei Fujioka
- Center of General Internal Medicine and Rheumatology, Gifu Municipal Hospital, Gifu, Japan
| | - Takafumi Sakakibara
- Department of Pediatrics, Nara Medical University School of Medicine, Nara, Japan
| | - Hideo Asada
- Department of Dermatology, Nara Medical University School of Medicine, Nara, Japan
| | - Kohei Ogawa
- Department of Dermatology, Nara Medical University School of Medicine, Nara, Japan
| | - Kyoko Kudo
- Department of Dermatology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Eri Ohashi
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Michiko Kawai
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Yuichi Abe
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Shinagawa-ku, Tokyo, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.
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29
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Hamanaka K, Miyake N, Mizuguchi T, Miyatake S, Uchiyama Y, Tsuchida N, Sekiguchi F, Mitsuhashi S, Tsurusaki Y, Nakashima M, Saitsu H, Yamada K, Sakamoto M, Fukuda H, Ohori S, Saida K, Itai T, Azuma Y, Koshimizu E, Fujita A, Erturk B, Hiraki Y, Ch'ng GS, Kato M, Okamoto N, Takata A, Matsumoto N. Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants. Genome Med 2022; 14:40. [PMID: 35468861 PMCID: PMC9040275 DOI: 10.1186/s13073-022-01042-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Background Previous large-scale studies of de novo variants identified a number of genes associated with neurodevelopmental disorders (NDDs); however, it was also predicted that many NDD-associated genes await discovery. Such genes can be discovered by integrating copy number variants (CNVs), which have not been fully considered in previous studies, and increasing the sample size. Methods We first constructed a model estimating the rates of de novo CNVs per gene from several factors such as gene length and number of exons. Second, we compiled a comprehensive list of de novo single-nucleotide variants (SNVs) in 41,165 individuals and de novo CNVs in 3675 individuals with NDDs by aggregating our own and publicly available datasets, including denovo-db and the Deciphering Developmental Disorders study data. Third, summing up the de novo CNV rates that we estimated and SNV rates previously established, gene-based enrichment of de novo deleterious SNVs and CNVs were assessed in the 41,165 cases. Significantly enriched genes were further prioritized according to their similarity to known NDD genes using a deep learning model that considers functional characteristics (e.g., gene ontology and expression patterns). Results We identified a total of 380 genes achieving statistical significance (5% false discovery rate), including 31 genes affected by de novo CNVs. Of the 380 genes, 52 have not previously been reported as NDD genes, and the data of de novo CNVs contributed to the significance of three genes (GLTSCR1, MARK2, and UBR3). Among the 52 genes, we reasonably excluded 18 genes [a number almost identical to the theoretically expected false positives (i.e., 380 × 0.05 = 19)] given their constraints against deleterious variants and extracted 34 “plausible” candidate genes. Their validity as NDD genes was consistently supported by their similarity in function and gene expression patterns to known NDD genes. Quantifying the overall similarity using deep learning, we identified 11 high-confidence (> 90% true-positive probabilities) candidate genes: HDAC2, SUPT16H, HECTD4, CHD5, XPO1, GSK3B, NLGN2, ADGRB1, CTR9, BRD3, and MARK2. Conclusions We identified dozens of new candidates for NDD genes. Both the methods and the resources developed here will contribute to the further identification of novel NDD-associated genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01042-w.
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Affiliation(s)
- Kohei Hamanaka
- 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
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kohei Yamada
- 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
| | - Hiromi Fukuda
- 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
| | - Ken Saida
- 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
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Aichi Medical University, Nagakute, 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
| | - Biray Erturk
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey.,Current affiliation: Department of Medical Genetics, Prof. Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | | | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan. .,Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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30
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Liu YH, Chou YT, Chang FP, Lee WJ, Guo YC, Chou CT, Huang HC, Mizuguchi T, Chou CC, Yu HY, Yu KW, Wu HM, Tsai PC, Matsumoto N, Lee YC, Liao YC. Neuronal intranuclear inclusion disease in patients with adult-onset non-vascular leukoencephalopathy. Brain 2022; 145:3010-3021. [PMID: 35411397 DOI: 10.1093/brain/awac135] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 11/12/2022] Open
Abstract
Neuronal intranuclear inclusion disease (NIID), caused by an expansion of GGC repeats in the 5'-untranslated region of NOTCH2NLC, is an important but underdiagnosed cause of adult-onset leukoencephalopathies. The present study aimed to investigate the prevalence, clinical spectrum, and brain MRI characteristics of NIID in adult-onset nonvascular leukoencephalopathies and assess the diagnostic performance of neuroimaging features. One hundred and sixty-one unrelated Taiwanese patients with genetically undetermined nonvascular leukoencephalopathies were screened for the NOTCH2NLC GGC repeat expansions using fragment analysis, repeat-primed PCR, southern blot analysis and/or nanopore sequencing with Cas9-mediated enrichment. Among them, 32 (19.9%) patients had an expanded NOTCH2NLC allele and diagnosed with NIID. We enrolled another two affected family members from one patient for further analysis. The size of the expanded NOTCH2NLC GGC repeats in the 34 patients ranged from 73 to 323 repeats. Skin biopsy from five patients all showed eosinophilic, p62-positive intranuclear inclusions in the sweat gland cells and dermal adipocytes. Among the 34 NIID patents presenting with nonvascular leukoencephalopathies, the median age at symptom onset was 61 years (range, 41-78 years) and the initial presentations included cognitive decline (44.1%; 15/34), acute encephalitis-like episodes (32.4%; 11/34), limb weakness (11.8%, 4/34), and parkinsonism (11.8%; 4/34). Cognitive decline (64.7%; 22/34) and acute encephalitis-like episodes (55.9%; 19/34) were also the most common overall manifestations. Two-thirds of the patients had either bladder dysfunction or visual disturbance. Comparing the brain MRI features between the NIID patients and individuals with other undetermined leukoencephalopathies, corticomedullary junction curvilinear lesion on diffusion weighted imaging (DWI) was the best biomarker to diagnose NIID with high specificity (98.4%) and sensitivity (88.2%). However, such DWI abnormality was absent in 11.8% of the NIID patients. When only fluid-attenuated inversion recovery images were available, presence of white matter hyperintensity lesions (WMH) either in paravermis or middle cerebellar peduncles also favored the diagnosis of NIID with a specificity of 85.3% and a sensitivity of 76.5%. Among the ten patients' MRI performed within 5 days of the onset of acute encephalitis-like episodes, five showed cortical DWI hyperintense lesions and two revealed focal brain edema. In conclusion, NIID accounts for 19.9% (32/161) of patients with adult-onset genetically undiagnosed nonvascular leukoencephalopathies in Taiwan. Half of the NIID patients ever developed encephalitis-like episodes with restricted diffusion in the cortical regions at the acute stage DWI. Corticomedullary junction hyperintense lesions, WMH in paravermis or middle cerebellar peduncles, bladder dysfunction and visual disturbance are useful hints to diagnose NIID.
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Affiliation(s)
- Yi-Hong Liu
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Ying-Tsen Chou
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Fu-Pang Chang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Wei-Ju Lee
- Neurological Institute, Taichung Veterans General Hospital, Taichung 40705, Taiwan.,Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,College of Medicine, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yuh-Cherng Guo
- Department of Neurology, China Medical University Hospital, Taichung 404332, Taiwan.,School of Medicine, College of Medicine, China Medical University, Taichung 404333, Taiwan
| | - Cheng-Ta Chou
- Neurological Institute, Taichung Veterans General Hospital, Taichung 40705, Taiwan.,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan
| | - Hui-Chun Huang
- Department of Neurology, China Medical University Hospital, Taichung 404332, Taiwan.,School of Medicine, College of Medicine, China Medical University, Taichung 404333, Taiwan
| | - Takeshi Mizuguchi
- Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Chien-Chen Chou
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Hsiang-Yu Yu
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Kai-Wei Yu
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,Department of Radiology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Hsiu-Mei Wu
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,Department of Radiology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Pei-Chien Tsai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Naomichi Matsumoto
- Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Yi-Chu Liao
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
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31
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Miyatake S, Yoshida K, Koshimizu E, Doi H, Yamada M, Miyaji Y, Ueda N, Tsuyuzaki J, Kodaira M, Onoue H, Taguri M, Imamura S, Fukuda H, Hamanaka K, Fujita A, Satoh M, Miyama T, Watanabe N, Kurita Y, Okubo M, Tanaka K, Kishida H, Koyano S, Takahashi T, Ono Y, Higashida K, Yoshikura N, Ogata K, Kato R, Tsuchida N, Uchiyama Y, Miyake N, Shimohata T, Tanaka F, Mizuguchi T, Matsumoto N. Repeat conformation heterogeneity in cerebellar ataxia, neuropathy, vestibular areflexia syndrome. Brain 2022; 145:1139-1150. [PMID: 35355059 DOI: 10.1093/brain/awab363] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022] Open
Abstract
Cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) is a late-onset, slow-progressing multisystem neurodegenerative disorder. Biallelic AAGGG repeat expansion in RFC1 has been identified as causative of this disease, and repeat conformation heterogeneity (ACAGG repeat) was also recently implied. To molecularly characterize this disease in Japanese patients with adult-onset ataxia, we accumulated and screened 212 candidate families by an integrated approach consisting of flanking PCR, repeat-primed PCR, Southern blotting and long-read sequencing using Sequel II, GridION or PromethION. We identified 16 patients from 11 families, of whom seven had ACAGG expansions [(ACAGG)exp/(ACAGG)exp] (ACAGG homozygotes), two had ACAGG and AAGGG expansions [(ACAGG)exp/(AAGGG)exp] (ACAGG/AAGGG compound heterozygotes) and seven had AAGGG expansions [(AAGGG)exp/(AAGGG)exp] (AAGGG homozygotes). The overall detection rate was 5.2% (11/212 families including one family having two expansion genotypes). Long-read sequencers revealed the entire sequence of both AAGGG and ACAGG repeat expansions at the nucleotide level of resolution. Clinical assessment and neuropathology results suggested that patients with ACAGG expansions have similar clinical features to previously reported patients with homozygous AAGGG expansions, although motor neuron involvement was more notable in patients with ACAGG expansions (even if one allele was involved). Furthermore, a later age of onset and slower clinical progression were implied in patients with ACAGG/AAGGG compound heterozygous expansions compared with either ACAGG or AAGGG homozygotes in our very limited cohort. Our study clearly shows the occurrence of repeat conformation heterogeneity, with possible different impacts on the affected nervous systems. The difference in disease onset and progression between compound heterozygotes and homozygotes might also be suspected but with very limited certainty due to the small sample number of cases in our study. Studies of additional patients are needed to confirm this.
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Affiliation(s)
- Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Kunihiro Yoshida
- Division of Neurogenetics, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Mitsunori Yamada
- Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Yosuke Miyaji
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Naohisa Ueda
- Department of Neurology, Yokohama City University Medical Center, Yokohama, Kanagawa 232-0024, Japan
| | - Jun Tsuyuzaki
- Department of Neurology, Asama Nanroku Komoro Medical Center, Komoro, Nagano 384-8588, Japan
| | - Minori Kodaira
- Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Hiroyuki Onoue
- Department of Neurology, Dokkyo Medical University Saitama Medical Center, Koshigaya, Saitama 343-8555, Japan
| | - Masataka Taguri
- Department of Data Science, Yokohama City University School of Data Science, Yokohama, Kanagawa 236-0027, Japan
| | - Shintaro Imamura
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan.,Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Mai Satoh
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takabumi Miyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Nobuko Watanabe
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Yusuke Kurita
- Department of Neurology, National Hospital Organization Yokohama Medical Center, Yokohama, Kanagawa 245-8575, Japan
| | - Masaki Okubo
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kenichi Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Hitaru Kishida
- Department of Neurology, Yokohama City University Medical Center, Yokohama, Kanagawa 232-0024, Japan
| | - Shigeru Koyano
- Department of Neurology, Yokohama Minami Kyosai Hospital, Yokohama, Kanagawa 236-0037, Japan
| | - Tatsuya Takahashi
- Department of Neurology, National Hospital Organization Yokohama Medical Center, Yokohama, Kanagawa 245-8575, Japan
| | - Yoya Ono
- Department of Neurology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Kazuhiro Higashida
- Department of Neurology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Nobuaki Yoshikura
- Department of Neurology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Katsuhisa Ogata
- Department of Neurology, National Hospital Organization Higashisaitama National Hospital, Hasuda, Saitama 349-0196, Japan
| | - Rumiko Kato
- Department of Pediatrics, National Hospital Organization Higashisaitama National Hospital, Hasuda, Saitama 349-0196, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takayoshi Shimohata
- Department of Neurology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
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32
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Kawazoe T, Tobisawa S, Sugaya K, Uruha A, Miyamoto K, Komori T, Goto YI, Nishino I, Yoshihashi H, Mizuguchi T, Matsumoto N, Egawa N, Kawata A, Isozaki E. Myoclonic Epilepsy with Ragged-red Fibers with Intranuclear Inclusions. Intern Med 2022; 61:547-552. [PMID: 34433719 PMCID: PMC8907771 DOI: 10.2169/internalmedicine.7767-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We herein report a case of myoclonic epilepsy with ragged-red fibers (MERRF) harboring a novel variant in mitochondrial cysteine transfer RNA (MT-TC). A 68-year-old woman presented with progressive myoclonic epilepsy with optic atrophy and peripheral neuropathy. A skin biopsy revealed p62-positive intranuclear inclusions. No mutations were found in the causative genes for diseases known to be related to intranuclear inclusions; however, a novel variant in MT-TC was found. The association between intranuclear inclusions and this newly identified MERRF-associated variant is unclear; however, the rare complication of intranuclear inclusions in a patient with typical MERRF symptoms should be noted for future studies.
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Affiliation(s)
- Tomoya Kawazoe
- Department of Neurology, Tokyo Metropolitan Neurological Hospital (TMNH), Japan
| | - Shinsuke Tobisawa
- Department of Neurology, Tokyo Metropolitan Neurological Hospital (TMNH), Japan
| | - Keizo Sugaya
- Department of Neurology, Tokyo Metropolitan Neurological Hospital (TMNH), Japan
| | - Akinori Uruha
- Department of Neurology, Tokyo Metropolitan Neurological Hospital (TMNH), Japan
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Germany
| | - Kazuhito Miyamoto
- Department of Neurology, Tokyo Metropolitan Neurological Hospital (TMNH), Japan
| | - Takashi Komori
- Department of Laboratory Medicine and Pathology (Neuropathology), TMNH, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Japan
- Medical Genome Center, NCNP, Japan
| | - Ichizo Nishino
- Medical Genome Center, NCNP, Japan
- Department of Neuromuscular Research, National Institute of Neuroscience, NCNP, Japan
| | - Hiroshi Yoshihashi
- Department of Clinical Genetics, Tokyo Metropolitan Children's Medical Center, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Naohiro Egawa
- Department of Neurology, Kyoto University Graduate School of Medicine, Japan
| | - Akihiro Kawata
- Department of Neurology, Tokyo Metropolitan Neurological Hospital (TMNH), Japan
| | - Eiji Isozaki
- Department of Neurology, Tokyo Metropolitan Neurological Hospital (TMNH), Japan
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33
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Hamanaka K, Miyoshi K, Sun JH, Hamada K, Komatsubara T, Saida K, Tsuchida N, Uchiyama Y, Fujita A, Mizuguchi T, Gerard B, Bayat A, Rinaldi B, Kato M, Tohyama J, Ogata K, Shi YS, Saito K, Miyatake S, Matsumoto N. Amelioration of a neurodevelopmental disorder by carbamazepine in a case having a gain-of-function GRIA3 variant. Hum Genet 2022; 141:283-293. [PMID: 35031858 DOI: 10.1007/s00439-021-02416-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022]
Abstract
GRIA3 at Xq25 encodes glutamate ionotropic receptor AMPA type 3 (GluA3), a subunit of postsynaptic glutamate-gated ion channels mediating neurotransmission. Hemizygous loss-of-function (LOF) variants in GRIA3 cause a neurodevelopmental disorder (NDD) in male individuals. Here, we report a gain-of-function (GOF) variant at GRIA3 in a male patient. We identified a hemizygous de novo missense variant in GRIA3 in a boy with an NDD: c.1844C > T (p.Ala615Val) using whole-exome sequencing. His neurological signs, such as hypertonia and hyperreflexia, were opposite to those in previous cases having LOF GRIA3 variants. His seizures and hypertonia were ameliorated by carbamazepine, inhibiting glutamate release from presynapses. Patch-clamp recordings showed that the human GluA3 mutant (p.Ala615Val) had slower desensitization and deactivation kinetics. A fly line expressing a human GluA3 mutant possessing our variant and the Lurcher variant, which makes ion channels leaky, showed developmental defects, while one expressing a mutant possessing either of them did not. Collectively, these results suggest that p.Ala615Val has GOF effects. GRIA3 GOF variants may cause an NDD phenotype distinctive from that of LOF variants, and drugs suppressing glutamatergic neurotransmission may ameliorate this phenotype. This study should help in refining the clinical management of GRIA3-related NDDs.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Keita Miyoshi
- Invertebrate Genetics Laboratory, Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, Japan.,Division of Invertebrate Genetics, Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Jia-Hui Sun
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Takao Komatsubara
- Department of Child Neurology, NHO Nishiniigata Chuo Hospital, Niigata, Niigata, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Benedicte Gerard
- Laboratoires de Diagnostic Génétique, Institut Medical d'Alsace, Hôpitaux Universitaire de Strasbourg, Strasbourg, France
| | - Allan Bayat
- Department for Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark.,Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Berardo Rinaldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Jun Tohyama
- Department of Child Neurology, NHO Nishiniigata Chuo Hospital, Niigata, Niigata, Japan.,Niigata University Medical and Dental Hospital, Niigata, Niigata, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yun Stone Shi
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China
| | - Kuniaki Saito
- Invertebrate Genetics Laboratory, Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, Japan.,Division of Invertebrate Genetics, Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.
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Yamada H, Okanishi T, Okazaki T, Oguri M, Fukuda H, Uchiyama Y, Mizuguchi T, Matsumoto N, Maegaki Y. Gait disturbance in a patient with de novo 1.0-kb SOX2 microdeletion. Brain Dev 2022; 44:68-72. [PMID: 34332824 DOI: 10.1016/j.braindev.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/07/2021] [Accepted: 07/15/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Sex-determining region Y-box 2 (SOX2) plays an important role in the early embryogenesis of the eye, forebrain, and hypothalamic-pituitary axis. Anophthalmia, microphthalmia, and hormonal abnormalities are commonly observed in patients with SOX2-related disorders. Although gait disturbance, particularly ataxic gait, has recently been observed in several cases, detailed data regarding the clinical course of gait disturbance in SOX2-related disorders are limited. CASE REPORT A 9-year-old Japanese boy presented with focal dyskinesia only during walking and running after he started walking at the age of 3 years. He also exhibited intellectual disability and mild dysmorphic features, including microcephaly, micropenis, and short stature associated with hormonal abnormalities. Gait disturbance with involuntary extremity movements only during walking and running was indicative of choreoathetosis and dystonia. Genetic analysis detected a de novo heterozygous 1.0-kb deletion including SOX2 at 3q26.32, as described in a previous technical paper. CONCLUSIONS SOX2-related disorders should be considered in patients with some anomalies having a differential diagnosis of dyskinesia. Focal dyskinesia only during walking and running may be a characteristic feature of SOX2-related disorders.
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Affiliation(s)
- Hiroyuki Yamada
- Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Yonago, Japan.
| | - Tohru Okanishi
- Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Tetsuya Okazaki
- Division of Clinical Genetics, Tottori University Hospital, Yonago, Japan
| | - Masayoshi Oguri
- Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Yonago, Japan; Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Takamatsu, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, 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
| | - Yoshihiro Maegaki
- Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Yonago, Japan
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Fukuda H, Yamaguchi D, Nyquist K, Yabuki Y, Miyatake S, Uchiyama Y, Hamanaka K, Saida K, Koshimizu E, Tsuchida N, Fujita A, Mitsuhashi S, Ohbo K, Satake Y, Sone J, Doi H, Morihara K, Okamoto T, Takahashi Y, Wenger AM, Shioda N, Tanaka F, Matsumoto N, Mizuguchi T. Father-to-offspring transmission of extremely long NOTCH2NLC repeat expansions with contractions: genetic and epigenetic profiling with long-read sequencing. Clin Epigenetics 2021; 13:204. [PMID: 34774111 PMCID: PMC8590777 DOI: 10.1186/s13148-021-01192-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/27/2021] [Indexed: 12/11/2022] Open
Abstract
Background GGC repeat expansions in NOTCH2NLC are associated with neuronal intranuclear inclusion disease. Very recently, asymptomatic carriers with NOTCH2NLC repeat expansions were reported. In these asymptomatic individuals, the CpG island in NOTCH2NLC is hypermethylated, suggesting that two factors repeat length and DNA methylation status should be considered to evaluate pathogenicity. Long-read sequencing can be used to simultaneously profile genomic and epigenomic alterations. We analyzed four sporadic cases with NOTCH2NLC repeat expansion and their phenotypically normal parents. The native genomic DNA that retains base modification was sequenced on a per-trio basis using both PacBio and Oxford Nanopore long-read sequencing technologies. A custom workflow was developed to evaluate DNA modifications. With these two technologies combined, long-range DNA methylation information was integrated with complete repeat DNA sequences to investigate the genetic origins of expanded GGC repeats in these sporadic cases. Results In all four families, asymptomatic fathers had longer expansions (median: 522, 390, 528 and 650 repeats) compared with their affected offspring (median: 93, 117, 162 and 140 repeats, respectively). These expansions are much longer than the disease-causing range previously reported (in general, 41–300 repeats). Repeat lengths were extremely variable in the father, suggesting somatic mosaicism. Instability is more frequent in alleles with uninterrupted pure GGCs. Single molecule epigenetic analysis revealed complex DNA methylation patterns and epigenetic heterogeneity. We identified an aberrant gain-of-methylation region (2.2 kb in size beyond the CpG island and GGC repeats) in asymptomatic fathers. This methylated region was unmethylated in the normal allele with bilateral transitional zones with both methylated and unmethylated CpG dinucleotides, which may be protected from methylation to ensure NOTCH2NLC expression. Conclusions We clearly demonstrate that the four sporadic NOTCH2NLC-related cases are derived from the paternal GGC repeat contraction associated with demethylation. The entire genetic and epigenetic landscape of the NOTCH2NLC region was uncovered using the custom workflow of long-read sequence data, demonstrating the utility of this method for revealing epigenetic/mutational changes in repetitive elements, which are difficult to characterize by conventional short-read/bisulfite sequencing methods. Our approach should be useful for biomedical research, aiding the discovery of DNA methylation abnormalities through the entire genome. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01192-5.
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Affiliation(s)
- Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | | | | | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Satomi Mitsuhashi
- Department of Genomic Function and Diversity, Medical Research Institute Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuyuki Ohbo
- Department of Histology and Cell Biology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuki Satake
- Department of Neurology, Yokkaichi Municipal Hospital, Yokkaichi, Japan
| | - Jun Sone
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan.,Department of Neurology, National Hospital Organization Suzuka National Hospital, Suzuka, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Keisuke Morihara
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomoko Okamoto
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yuji Takahashi
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | | | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.
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36
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Seyama R, Tsuchida N, Okada Y, Sakata S, Hamada K, Azuma Y, Hamanaka K, Fujita A, Koshimizu E, Miyatake S, Mizuguchi T, Makino S, Itakura A, Okada S, Okamoto N, Ogata K, Uchiyama Y, Matsumoto N. Two families with TET3-related disorder showing neurodevelopmental delay with craniofacial dysmorphisms. J Hum Genet 2021; 67:157-164. [PMID: 34719681 DOI: 10.1038/s10038-021-00986-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/25/2021] [Accepted: 10/09/2021] [Indexed: 01/21/2023]
Abstract
TET3 at 2p13.1 encodes tet methylcytosine dioxygenase 3, a demethylation enzyme that converts 5-methylcytosine to 5-hydroxymethylcytosine. Beck et al. reported that patients with TET3 abnormalities in either an autosomal dominant or recessive inheritance fashion clinically showed global developmental delay, intellectual disability, and dysmorphisms. In this study, exome sequencing identified both mono- and biallelic TET3 variants in two families: a de novo variant NM_001287491.1:c.3028 A > G:p.(Asn1010Asp), and compound heterozygous variants NM_001287491.1:c.[2077 C > T];[2896 T > G],p.[Gln693*];[Cys966Gly]. Despite the different inheritance modes, the affected individuals showed similar phenotypic features. Including these three patients, only 14 affected individuals have been reported to date. The accumulation of data regarding individuals with TET3-related disorder is necessary to describe their clinical spectrum.
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Affiliation(s)
- Rie Seyama
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.,Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yasuyuki Okada
- Department of Pediatrics, National Hospital Organization Higashihiroshima Medical Center, Higashihiroshima, Japan
| | - Sonoko Sakata
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University, Yokohama, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.,Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Shintaro Makino
- Department of Obstetrics and Gynecology, Juntendo University Urayasu Hospital, Chiba, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.
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Liao YC, Chang FP, Huang HW, Chen TB, Chou YT, Hsu SL, Jih K, Liu YH, Hsiao CT, Fukukda H, Mizuguchi T, Lin KPK, Lin CCK, Matsumoto N, Kennerson M, Lee YC. GGC Repeat Expansion of NOTCH2NLC in Taiwanese Patients With Inherited Neuropathies. Neurology 2021; 98:e199-e206. [PMID: 34675106 DOI: 10.1212/wnl.0000000000013008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/15/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVE The GGC repeat expansion in the 5' untranslated region of NOTCH2NLC was recently identified as the cause of neuronal intranuclear inclusion disease (NIID), which may manifest with peripheral neuropathy. The aim of this study is to investigate its contribution to inherited neuropathy. METHODS This cohort study screened patients with molecularly undiagnosed Charcot-Marie-Tooth disease (CMT) and healthy control individuals for the GGC repeat expansion in NOTCH2NLC using repeat-primed PCR and fragment analysis. The clinical and electrophysiological features of the patients harboring the GGC repeat expansion were scrutinized. Skin biopsy with immunohistochemistry staining and electric microscopic imaging were performed. RESULTS One hundred and twenty-seven unrelated patients with CMT, including 66 cases with axonal CMT (CMT2), and 200 healthy control individuals were included.Among them, seven CMT patients carried a mutant NOTCH2NLC allele with GGC repeat expansion, but it was absent in controls. The sizes of the expanded GGC repeats ranged from 80 to 104 repeats. All seven patients developed sensory predominant neuropathy with an average age at disease onset of 37.1 years (range 21-55). The electrophysiological studies revealed mild axonal sensorimotor polyneuropathy. Leukoencephalopathy was absent in the five patients who received a brain MRI. Skin biopsy from two patients showed eosinophilic, ubiquitin- and p62-positive intranuclear inclusions in the sweat gland cells and dermal fibroblasts. Two of the seven patients had a family history of NIID. DISCUSSION The NOTCH2NLC GGC repeat expansions are an underdiagnosed and important cause of inherited neuropathy. The expansion accounts for 10.6% (7/66) of molecularly unassigned CMT2 cases in the Taiwanese CMT cohort. CLASSIFICATION OF EVIDENCE This study provides Class III evidence that in Taiwanese patients with genetically undiagnosed CMT, 10.6% of the CMT2 cases have the GGC repeat expansion in NOTCH2NLC.
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Affiliation(s)
- Yi-Chu Liao
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan.,Brain Research Center,National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan
| | - Fu-Pang Chang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan
| | - Han-Wei Huang
- Department of Neurology, School of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Ting-Bing Chen
- Department of Neurology, Neurological Institute, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ying-Tsen Chou
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shao-Lun Hsu
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kangyang Jih
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan
| | - Yi-Hong Liu
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Cheng-Tsung Hsiao
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan
| | - Hiromi Fukukda
- 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
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kon-Ping Kp Lin
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan
| | - Chou-Ching K Lin
- Department of Neurology, School of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan .,Department of Neurology, National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan.,Brain Research Center,National Yang Ming Chao Tung University School of Medicine, Taipei, Taiwan
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Nagai K, Niihori T, Okamoto N, Kondo A, Suga K, Ohhira T, Hayabuchi Y, Homma Y, Nakagawa R, Ifuku T, Abe T, Mizuguchi T, Matsumoto N, Aoki Y. Duplications in the G3 domain or switch II region in HRAS identified in patients with Costello syndrome. Hum Mutat 2021; 43:3-15. [PMID: 34618388 DOI: 10.1002/humu.24287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022]
Abstract
Costello syndrome (CS) is an autosomal-dominant disorder characterized by distinctive facial features, hypertrophic cardiomyopathy, skeletal abnormalities, intellectual disability, and predisposition to cancers. Germline variants in HRAS have been identified in patients with CS. Intragenic HRAS duplications have been reported in three patients with a milder phenotype of CS. In this study, we identified two known HRAS variants, p.(Glu63_Asp69dup), p.(Glu62_Arg68dup), and one novel HRAS variant, p.(Ile55_Asp57dup), in patients with CS, including a patient with craniosynostosis. These intragenic duplications are located in the G3 domain and the switch II region. Cells expressing cDNA with these three intragenic duplications showed an increase in ELK-1 transactivation. Injection of wild-type or mutant HRAS mRNAs with intragenic duplications in zebrafish embryos showed significant elongation of the yolk at 11 h postfertilization, which was improved by MEK inhibitor treatment, and a variety of developmental abnormalities at 3 days post fertilization was observed. These results indicate that small in-frame duplications affecting the G3 domain and switch II region of HRAS increase the activation of the ERK pathway, resulting in developmental abnormalities in zebrafish or patients with CS.
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Affiliation(s)
- Koki Nagai
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Akane Kondo
- Perinatal Medical Center, Shikoku Medical Center for Children and Adults, National Hospital Organization, Kagawa, Japan
| | - Kenichi Suga
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Tomoko Ohhira
- Department of Pediatrics, Miyazaki Prefectural Miyazaki Hospital, Miyazaki, Japan
| | - Yasunobu Hayabuchi
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yukako Homma
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Ryuji Nakagawa
- Department of Pediatrics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Toshinobu Ifuku
- Department of Pediatrics, Miyazaki Prefectural Miyazaki Hospital, Miyazaki, Japan
| | - Taiki Abe
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, 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
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
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39
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Saida K, Tamaoki J, Sasaki M, Haniffa M, Koshimizu E, Sengoku T, Maeda H, Kikuchi M, Yokoyama H, Sakamoto M, Iwama K, Sekiguchi F, Hamanaka K, Fujita A, Mizuguchi T, Ogata K, Miyake N, Miyatake S, Kobayashi M, Matsumoto N. Pathogenic variants in the survival of motor neurons complex gene GEMIN5 cause cerebellar atrophy. Clin Genet 2021; 100:722-730. [PMID: 34569062 DOI: 10.1111/cge.14066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/05/2021] [Accepted: 09/24/2021] [Indexed: 12/31/2022]
Abstract
Cerebellar ataxia is a genetically heterogeneous disorder. GEMIN5 encoding an RNA-binding protein of the survival of motor neuron complex, is essential for small nuclear ribonucleoprotein biogenesis, and it was recently reported that biallelic loss-of-function variants cause neurodevelopmental delay, hypotonia, and cerebellar ataxia. Here, whole-exome analysis revealed compound heterozygous GEMIN5 variants in two individuals from our cohort of 162 patients with cerebellar atrophy/hypoplasia. Three novel truncating variants and one previously reported missense variant were identified: c.2196dupA, p.(Arg733Thrfs*6) and c.1831G > A, p.(Val611Met) in individual 1, and c.3913delG, p.(Ala1305Leufs*14) and c.4496dupA, p.(Tyr1499*) in individual 2. Western blotting analysis using lymphoblastoid cell lines derived from both affected individuals showed significantly reduced levels of GEMIN5 protein. Zebrafish model for null variants p.(Arg733Thrfs*6) and p.(Ala1305Leufs*14) exhibited complete lethality at 2 weeks and recapitulated a distinct dysplastic phenotype. The phenotypes of affected individuals and the zebrafish mutant models strongly suggest that biallelic loss-of-function variants in GEMIN5 cause cerebellar atrophy/hypoplasia.
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Affiliation(s)
- Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Junya Tamaoki
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Muzhirah Haniffa
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiroki Maeda
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masahiro Kikuchi
- Department of Pediatrics, Hitachi General Hospital, Hitachi, Japan
| | - Haruna Yokoyama
- Department of Child Neurology, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Masamune Sakamoto
- 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
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- 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
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Toyama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Makoto Kobayashi
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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40
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Kameyama S, Mizuguchi T, Fukuda H, Moey LH, Keng WT, Okamoto N, Tsuchida N, Uchiyama Y, Koshimizu E, Hamanaka K, Fujita A, Miyatake S, Matsumoto N. Biallelic null variants in ZNF142 cause global developmental delay with familial epilepsy and dysmorphic features. J Hum Genet 2021; 67:169-173. [PMID: 34531528 DOI: 10.1038/s10038-021-00978-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/09/2022]
Abstract
Biallelic variants in ZNF142 at 2q35, which encodes zinc-finger protein 142, cause neurodevelopmental disorder with seizures or dystonia. We identified compound heterozygous null variants in ZNF142, NM_001105537.4:c.[1252C>T];[1274-2A>G],p.[Arg418*];[Glu426*], in Malaysian siblings suffering from global developmental delay with epilepsy and dysmorphism. cDNA analysis showed the marked reduction of ZNF142 transcript level through nonsense-mediated mRNA decay by these novel biallelic variants. The affected siblings present with global developmental delay and epilepsy in common, which were previously described, as well as dysmorphism, which was not recognized. It is important to collect patients with ZNF142 abnormality to define its phenotypic spectrum.
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Affiliation(s)
- Shinichi Kameyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Mizuguchi
- 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
| | - Lip Hen Moey
- Department of Genetics, Penang General Hospital, George Town, Penang, Malaysia
| | - Wee Teik Keng
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- 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
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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41
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Sakurai Y, Watanabe T, Abe Y, Nawa T, Uchida T, Aoi H, Mizuguchi T, Matsumoto N, Haginoya K. Head titubation and irritability as early symptoms of Joubert syndrome with a homozygous NPHP1 variant. Brain Dev 2021; 43:863-866. [PMID: 34090716 DOI: 10.1016/j.braindev.2021.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Joubert syndrome is an autosomal recessive or X-linked genetic disease with a cerebellar vermis defect or hypoplasia, hypotonia, ocular dyskinesia, and mental retardation. In neonates, respiratory problems such as apnea and tachypnea are notable. CASE REPORT We report a patient Joubert syndrome with a homozygous NPHP1 variant, who had head titubation with irritability, including exaggerated jitteriness and a marked Morrow reflex appeared soon after birth without neonatal respiratory problems. These symptoms decreased gradually and disappeared until 1 year. CONCLUSION Irritability with head titubation may be an early clinical clue for the clinician to suspect Joubert syndrome.
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Affiliation(s)
- Yoshie Sakurai
- Department of Neonatology, Miyagi Children's Hospital, Japan.
| | | | - Yuki Abe
- Department of Neonatology, Miyagi Children's Hospital, Japan
| | - Tatsuro Nawa
- Department of Neonatology, Miyagi Children's Hospital, Japan
| | | | - Hiromi Aoi
- 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
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Japan
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42
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Sakamoto M, Sasaki K, Sugie A, Nitta Y, Kimura T, Gürsoy S, Cinleti T, Iai M, Sengoku T, Ogata K, Suzuki A, Okamoto N, Iwama K, Tsuchida N, Uchiyama Y, Koshimizu E, Fujita A, Hamanaka K, Miyatake S, Mizuguchi T, Taguri M, Ito S, Takahashi H, Miyake N, Matsumoto N. De novo ARF3 variants cause neurodevelopmental disorder with brain abnormality. Hum Mol Genet 2021; 31:69-81. [PMID: 34346499 DOI: 10.1093/hmg/ddab224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
An optimal Golgi transport system is important for mammalian cells. The adenosine diphosphate (ADP) ribosylation factors (ARF) are key proteins for regulating cargo sorting at the Golgi network. In this family, ARF3 mainly works at the trans-Golgi network (TGN), and no ARF3-related phenotypes have yet been described in humans. We here report the clinical and genetic evaluations of two unrelated children with de novo pathogenic variants in the ARF3 gene: c.200A > T (p.Asp67Val) and c.296G > T (p.Arg99Leu). Although the affected individuals presented commonly with developmental delay, epilepsy, and brain abnormalities, there were differences in severity, clinical course, and brain lesions. In vitro subcellular localization assays revealed that the p.Arg99Leu mutant localized to Golgi apparatus, similar to the wild-type, whereas the p.Asp67Val mutant tended to show a disperse cytosolic pattern together with abnormally dispersed Golgi localization, similar to that observed in a known dominant negative variant (p.Thr31Asn). Pull-down assays revealed that the p.Asp67Val had a loss-of-function effect and the p.Arg99Leu variant had increased binding of the adaptor protein, Golgi-localized, γ-adaptin ear-containing, ARF-binding protein 1 (GGA1), supporting the gain of function. Furthermore, in vivo studies revealed that p.Asp67Val transfection led to lethality in flies. In contrast, flies expressing p.Arg99Leu had abnormal rough eye, as observed in the gain-of-function variant p.Gln71Leu. These data indicate that two ARF3 variants, the possibly loss-of-function p.Asp67Val and the gain-of-function p.Arg99Leu, both impair the Golgi transport system. Therefore, it may not be unreasonable that they showed different clinical features like diffuse brain atrophy (p.Asp67Val) and cerebellar hypoplasia (p.Arg99Leu).
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Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazunori Sasaki
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Sugie
- Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Yohei Nitta
- Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Tetsuaki Kimura
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Semra Gürsoy
- Department of Pediatric Genetics, S.B.Ü. Dr. Behçet Uz Children's Education and Research Hospital, Izmir, 35210, Turkey
| | - Tayfun Cinleti
- Department of Pediatric Genetics, Dokuz Eylul University, Faculty of Medicine, Izumir, 35340, Turkey
| | - Mizue Iai
- Department of Neurology, Kanagawa Children's Medical Center, Yokohama, 232-8555, Japan
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Suzuki
- Molecular Cellular Biology Laboratory, Yokohama City University Graduate School of Medical Life Science, Yokohama, 230-0045, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, 594-1101, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Masataka Taguri
- Department of Data Science, Yokohama City University School of Data Science, Yokohama, 236-0027, Japan
| | - Shuuichi Ito
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.,Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
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43
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Itai T, Miyatake S, Tsuchida N, Saida K, Narahara S, Tsuyusaki Y, Castro MAA, Kim CA, Okamoto N, Uchiyama Y, Koshimizu E, Hamanaka K, Fujita A, Mizuguchi T, Matsumoto N. Novel CLTC variants cause new brain and kidney phenotypes. J Hum Genet 2021; 67:1-7. [PMID: 34230591 DOI: 10.1038/s10038-021-00957-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/12/2021] [Accepted: 06/21/2021] [Indexed: 11/09/2022]
Abstract
Heterozygous variants in CLTC, which encode the clathrin heavy chain protein, cause neurodevelopmental delay of varying severity, and often accompanied by dysmorphic features, seizures, hypotonia, and ataxia. To date, 28 affected individuals with CLTC variants have been reported, although their phenotypes have not been fully elucidated. Here, we report three novel de novo CLTC (NM_001288653.1) variants in three individuals with previously unreported clinical symptoms: c.3662_3664del:p.(Leu1221del) in individual 1, c.2878T>C:p.(Trp960Arg) in individual 2, and c.2430+1G>T:p.(Glu769_Lys810del) in individual 3. Consistent with previous reports, individuals with missense or small in-frame variants were more severely affected. Unreported symptoms included a brain defect (cystic lesions along the lateral ventricles of the brain in individuals 1 and 3), kidney findings (high-echogenic kidneys in individual 1 and agenesis of the left kidney and right vesicoureteral reflux in individual 3), respiratory abnormality (recurrent pneumonia in individual 1), and abnormal hematological findings (anemia in individual 1 and pancytopenia in individual 3). Of note, individual 1 even exhibited prenatal abnormality (fetal growth restriction, cystic brain lesions, high-echogenic kidneys, and a heart defect), suggesting that CLTC variants should be considered when abnormal prenatal findings in multiple organs are detected.
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Affiliation(s)
- Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Sho Narahara
- Department of Pediatrics, Anjo Kosei Hospital, Anjo, Aichi, Japan
| | - Yu Tsuyusaki
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Kanagawa, Japan
| | - Matheus Augusto Araujo Castro
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.
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44
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Parenti I, Lehalle D, Nava C, Torti E, Leitão E, Person R, Mizuguchi T, Matsumoto N, Kato M, Nakamura K, de Man SA, Cope H, Shashi V, Friedman J, Joset P, Steindl K, Rauch A, Muffels I, van Hasselt PM, Petit F, Smol T, Le Guyader G, Bilan F, Sorlin A, Vitobello A, Philippe C, van de Laar IMBH, van Slegtenhorst MA, Campeau PM, Au PYB, Nakashima M, Saitsu H, Yamamoto T, Nomura Y, Louie RJ, Lyons MJ, Dobson A, Plomp AS, Motazacker MM, Kaiser FJ, Timberlake AT, Fuchs SA, Depienne C, Mignot C. Missense and truncating variants in CHD5 in a dominant neurodevelopmental disorder with intellectual disability, behavioral disturbances, and epilepsy. Hum Genet 2021; 140:1109-1120. [PMID: 33944996 PMCID: PMC8197709 DOI: 10.1007/s00439-021-02283-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/15/2021] [Indexed: 12/27/2022]
Abstract
Located in the critical 1p36 microdeletion region, the chromodomain helicase DNA-binding protein 5 (CHD5) gene encodes a subunit of the nucleosome remodeling and deacetylation (NuRD) complex required for neuronal development. Pathogenic variants in six of nine chromodomain (CHD) genes cause autosomal dominant neurodevelopmental disorders, while CHD5-related disorders are still unknown. Thanks to GeneMatcher and international collaborations, we assembled a cohort of 16 unrelated individuals harboring heterozygous CHD5 variants, all identified by exome sequencing. Twelve patients had de novo CHD5 variants, including ten missense and two splice site variants. Three familial cases had nonsense or missense variants segregating with speech delay, learning disabilities, and/or craniosynostosis. One patient carried a frameshift variant of unknown inheritance due to unavailability of the father. The most common clinical features included language deficits (81%), behavioral symptoms (69%), intellectual disability (64%), epilepsy (62%), and motor delay (56%). Epilepsy types were variable, with West syndrome observed in three patients, generalized tonic-clonic seizures in two, and other subtypes observed in one individual each. Our findings suggest that, in line with other CHD-related disorders, heterozygous CHD5 variants are associated with a variable neurodevelopmental syndrome that includes intellectual disability with speech delay, epilepsy, and behavioral problems as main features.
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Affiliation(s)
- Ilaria Parenti
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daphné Lehalle
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Caroline Nava
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France
| | | | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, 142-8666, Japan
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University Faculty of Medicine, Yamagata, 990-9585, Japan
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer Friedman
- Departments of Neuroscience and Pediatrics, Division of Neurology, Rady Children's Hospital, UCSD, San Diego and Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Irena Muffels
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Peter M van Hasselt
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Thomas Smol
- Institut de Génétique Médicale, CHRU Lille, Université de Lille, Lille, France
| | - Gwenaël Le Guyader
- Service de Génétique Médicale, CHU de Poitiers, Poitiers, France
- EA3808 NEUVACOD, University of Poitiers, Poitiers, France
| | - Frédéric Bilan
- Service de Génétique Médicale, CHU de Poitiers, Poitiers, France
- EA3808 NEUVACOD, University of Poitiers, Poitiers, France
| | - Arthur Sorlin
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
- Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
- Sainte-Justine Hospital, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Ping Yee Billie Au
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Tatsuya Yamamoto
- Department of Pediatrics, Hirosaki University Graduate School of Medicine and School of Medicine, Hirosaki, 036-8562, Japan
| | - Yumiko Nomura
- Department of Pediatrics, Hirosaki National Hospital, Hirosaki, 036-8545, Japan
- Aomori City Health Center, Aomori, 030-0962, Japan
| | | | | | - Amy Dobson
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M Mahdi Motazacker
- Laboratory of Genome Diagnostics, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Health, New York, NY, USA
| | - Sabine A Fuchs
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France.
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, APHP, Sorbonne Université, Paris, France.
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France.
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Mizuguchi T, Toyota T, Miyatake S, Mitsuhashi S, Doi H, Kudo Y, Kishida H, Hayashi N, Tsuburaya RS, Kinoshita M, Fukuyama T, Fukuda H, Koshimizu E, Tsuchida N, Uchiyama Y, Fujita A, Takata A, Miyake N, Kato M, Tanaka F, Adachi H, Matsumoto N. Erratum to: Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment. Brain 2021; 144:e67. [PMID: 34037746 DOI: 10.1093/brain/awab183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Indexed: 11/13/2022] Open
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46
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Otoshi R, Baba T, Shintani R, Kitamura H, Yamaguchi Y, Hamanoue H, Mizuguchi T, Matsumoto N, Okudela K, Takemura T, Ogura T. Diverse Pathological Findings of Interstitial Lung Disease in a Patient with Dyskeratosis Congenita. Intern Med 2021; 60:1257-1263. [PMID: 33191321 PMCID: PMC8112977 DOI: 10.2169/internalmedicine.5143-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A 42-year-old man with a history of surgery for tongue cancer was referred to our hospital due to an abnormal chest shadow. High-resolution computed tomography showed lower lobe reticulation. A physical examination revealed nail dystrophy, oral leukoplakia, and reticulated hypopigmentation. Lung biopsy revealed subpleural and perilobular fibrosis, suggestive of usual interstitial pneumonia. However, multiple pathological findings, including homogenous fibrosis and cell infiltration in the centrilobular region, which were compatible with nonspecific interstitial pneumonia, and bronchiolitis were also seen. Genetic testing showed a hemizygous missense mutation in the DKC1 gene, and the patient was diagnosed with dyskeratosis congenita. Although anti-fibrotic therapy was initiated, the patient's respiratory function has continued to decrease.
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Affiliation(s)
- Ryota Otoshi
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Japan
| | - Tomohisa Baba
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Japan
| | - Ryota Shintani
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Japan
| | - Hideya Kitamura
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Japan
| | - Yukie Yamaguchi
- Department of Environmental Immuno-Dermatology, Yokohama City University Hospital, Japan
| | - Haruka Hamanoue
- Department of Clinical Genetics, Yokohama City University Hospital, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Japan
| | - Koji Okudela
- Department of Pathology, Yokohama City University Graduate School of Medicine, Japan
| | - Tamiko Takemura
- Department of Pathology, Kanagawa Cardiovascular and Respiratory Center, Japan
| | - Takashi Ogura
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Japan
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47
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Aoto K, Kato M, Akita T, Nakashima M, Mutoh H, Akasaka N, Tohyama J, Nomura Y, Hoshino K, Ago Y, Tanaka R, Epstein O, Ben-Haim R, Heyman E, Miyazaki T, Belal H, Takabayashi S, Ohba C, Takata A, Mizuguchi T, Miyatake S, Miyake N, Fukuda A, Matsumoto N, Saitsu H. ATP6V0A1 encoding the a1-subunit of the V0 domain of vacuolar H +-ATPases is essential for brain development in humans and mice. Nat Commun 2021; 12:2107. [PMID: 33833240 PMCID: PMC8032687 DOI: 10.1038/s41467-021-22389-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 03/05/2021] [Indexed: 02/01/2023] Open
Abstract
Vacuolar H+-ATPases (V-ATPases) transport protons across cellular membranes to acidify various organelles. ATP6V0A1 encodes the a1-subunit of the V0 domain of V-ATPases, which is strongly expressed in neurons. However, its role in brain development is unknown. Here we report four individuals with developmental and epileptic encephalopathy with ATP6V0A1 variants: two individuals with a de novo missense variant (R741Q) and the other two individuals with biallelic variants comprising one almost complete loss-of-function variant and one missense variant (A512P and N534D). Lysosomal acidification is significantly impaired in cell lines expressing three missense ATP6V0A1 mutants. Homozygous mutant mice harboring human R741Q (Atp6v0a1R741Q) and A512P (Atp6v0a1A512P) variants show embryonic lethality and early postnatal mortality, respectively, suggesting that R741Q affects V-ATPase function more severely. Lysosomal dysfunction resulting in cell death, accumulated autophagosomes and lysosomes, reduced mTORC1 signaling and synaptic connectivity, and lowered neurotransmitter contents of synaptic vesicles are observed in the brains of Atp6v0a1A512P/A512P mice. These findings demonstrate the essential roles of ATP6V0A1/Atp6v0a1 in neuronal development in terms of integrity and connectivity of neurons in both humans and mice. A member of the vacuolar H+-ATPase family, ATP6V0A1 is involved in lysosomal activity. Here, the authors report that ATP6V0A1 variants identified in individuals with developmental and epileptic encephalopathy are associated with impairment of lysosomal acidification, autophagy and mTORC1 signaling, suggesting an essential role of ATP6V0A1 in brain development.
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Affiliation(s)
- Kazushi Aoto
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Tenpei Akita
- Department of Neurophysiology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroki Mutoh
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Noriyuki Akasaka
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan.,Department of Pediatrics, Niigata Prefecture Hamagumi Medical Rehabilitation Center for Disabled Children, Niigata, Japan
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Yoshiko Nomura
- Segawa Neurological Clinic for Children, Tokyo, Japan.,Yoshiko Nomura Neurological Clinic for Children, Tokyo, Japan
| | - Kyoko Hoshino
- Segawa Neurological Clinic for Children, Tokyo, Japan.,Segawa Memorial Neurological Clinic for Children, Tokyo, Japan
| | - Yasuhiko Ago
- Department of Neonatology, Ibaraki Children's Hospital, Mito, Japan.,Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Ryuta Tanaka
- Ibaraki Pediatric Education and Training Station, University of Tsukuba, Mito, Japan
| | - Orna Epstein
- Pediatric Neurology and Development Center, Shamir Medical Center, Tzrifin, Beer Yaakov, Israel
| | - Revital Ben-Haim
- Pediatric Neurology and Development Center, Shamir Medical Center, Tzrifin, Beer Yaakov, Israel
| | - Eli Heyman
- Pediatric Neurology and Development Center, Shamir Medical Center, Tzrifin, Beer Yaakov, Israel
| | - Takehiro Miyazaki
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hazrat Belal
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shuji Takabayashi
- Laboratory Animal Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Chihiro Ohba
- 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
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- 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
| | - Atsuo Fukuda
- Department of Neurophysiology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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48
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Mizuguchi T, Toyota T, Miyatake S, Mitsuhashi S, Doi H, Kudo Y, Kishida H, Hayashi N, Tsuburaya RS, Kinoshita M, Fukuyama T, Fukuda H, Koshimizu E, Tsuchida N, Uchiyama Y, Fujita A, Takata A, Miyake N, Kato M, Tanaka F, Adachi H, Matsumoto N. Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment. Brain 2021; 144:1103-1117. [PMID: 33791773 DOI: 10.1093/brain/awab021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 11/14/2022] Open
Abstract
A pentanucleotide TTTCA repeat insertion into a polymorphic TTTTA repeat element in SAMD12 causes benign adult familial myoclonic epilepsy. Although the precise determination of the entire SAMD12 repeat sequence is important for molecular diagnosis and research, obtaining this sequence remains challenging when using conventional genomic/genetic methods, and even short-read and long-read next-generation sequencing technologies have been insufficient. Incomplete information regarding expanded repeat sequences may hamper our understanding of the pathogenic roles played by varying numbers of repeat units, genotype-phenotype correlations, and mutational mechanisms. Here, we report a new approach for the precise determination of the entire expanded repeat sequence and present a workflow designed to improve the diagnostic rates in various repeat expansion diseases. We examined 34 clinically diagnosed benign adult familial myoclonic epilepsy patients, from 29 families using repeat-primed PCR, Southern blot, and long-read sequencing with Cas9-mediated enrichment. Two cases with questionable results from repeat-primed PCR and/or Southern blot were confirmed as pathogenic using long-read sequencing with Cas9-mediated enrichment, resulting in the identification of pathogenic SAMD12 repeat expansions in 76% of examined families (22/29). Importantly, long-read sequencing with Cas9-mediated enrichment was able to provide detailed information regarding the sizes, configurations, and compositions of the expanded repeats. The inserted TTTCA repeat size and the proportion of TTTCA sequences among the overall repeat sequences were highly variable, and a novel repeat configuration was identified. A genotype-phenotype correlation study suggested that the insertion of even short (TTTCA)14 repeats contributed to the development of benign adult familial myoclonic epilepsy. However, the sizes of the overall TTTTA and TTTCA repeat units are also likely to be involved in the pathology of benign adult familial myoclonic epilepsy. Seven unsolved SAMD12-negative cases were investigated using whole-genome long-read sequencing, and infrequent, disease-associated, repeat expansions were identified in two cases. The strategic workflow resolved two questionable SAMD12-positive cases and two previously SAMD12-negative cases, increasing the diagnostic yield from 69% (20/29 families) to 83% (24/29 families). This study indicates the significant utility of long-read sequencing technologies to explore the pathogenic contributions made by various repeat units in complex repeat expansions and to improve the overall diagnostic rate.
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Affiliation(s)
- Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Tomoko Toyota
- Department of Neurology, University of Occupational and Environmental Health School of Medicine, Kitakyushu 807-8555, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama 236-0004, Japan
| | - Satomi Mitsuhashi
- Department of Genomic Function and Diversity, Medical Research Institute Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yosuke Kudo
- Department of Neurology, Yokohama Brain and Spine Center, Yokohama 235-0012, Japan
| | - Hitaru Kishida
- Department of Neurology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Noriko Hayashi
- Department of Neurology, Yamato Municipal Hospital, Yamato 242-8602, Japan
| | - Rie S Tsuburaya
- Department of Pediatric Neurology, National Hospital Organization Utano National Hospital, Kyoto 616-8255, Japan
| | - Masako Kinoshita
- Department of Neurology, National Hospital Organization Utano National Hospital, Kyoto 616-8255, Japan
| | - Tetsuhiro Fukuyama
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto 390-8621, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.,Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo 142-8666, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hiroaki Adachi
- Department of Neurology, University of Occupational and Environmental Health School of Medicine, Kitakyushu 807-8555, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
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49
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Saida K, Fukuda T, Scott DA, Sengoku T, Ogata K, Nicosia A, Hernandez-Garcia A, Lalani SR, Azamian MS, Streff H, Liu P, Dai H, Mizuguchi T, Miyatake S, Asahina M, Ogata T, Miyake N, Matsumoto N. OTUD5 Variants Associated With X-Linked Intellectual Disability and Congenital Malformation. Front Cell Dev Biol 2021; 9:631428. [PMID: 33748114 PMCID: PMC7965969 DOI: 10.3389/fcell.2021.631428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND X-linked intellectual disability (XLID), which occurs predominantly in males, is a relatively common and genetically heterogeneous disorder in which over 100 mutated genes have been reported. The OTUD5 gene at Xp11.23 encodes ovarian tumor deubiquitinase 5 protein, which is a deubiquitinating enzyme member of the ovarian tumor family. LINKage-specific-deubiquitylation-deficiency-induced embryonic defects (LINKED) syndrome, arising from pathogenic OTUD5 variants, was recently reported as a new XLID with additional congenital anomalies. METHODS We investigated three affected males (49- and 47-year-old brothers [Individuals 1 and 2] and a 2-year-old boy [Individual 3]) from two families who showed developmental delay. Their common clinical features included developmental delay, hypotonia, short stature, and distinctive facial features, such as telecanthus and a depressed nasal bridge. Individuals 1 and 2 showed epilepsy and brain magnetic resonance imaging showed a thin corpus callosum and mild ventriculomegaly. Individual 3 showed congenital malformations, including tetralogy of Fallot, hypospadias, and bilateral cryptorchidism. To identify the genetic cause of these features, we performed whole-exome sequencing. RESULTS A hemizygous OTUD5 missense variant, c.878A>T, p.Asn293Ile [NM_017602.4], was identified in one family with Individuals 1 and 2, and another missense variant, c.1210 C>T, p.Arg404Trp, in the other family with Individual 3, respectively. The former variant has not been registered in public databases and was predicted to be pathogenic by multiple in silico prediction tools. The latter variant p.Arg404Trp was previously reported as a pathogenic OTUD5 variant, and Individual 3 showed a typical LINKED syndrome phenotype. However, Individuals 1 and 2, with the novel variant (p.Asn293Ile), showed no cardiac or genitourinary malformations. CONCLUSIONS Unlike previous reports of LINKED syndrome, which described early lethality with congenital cardiac anomalies, our three cases are still alive. Notably, the adult brothers with the novel missense OTUD5 variant have lived into their forties. This may be indicative of a milder phenotype as a possible genotype-phenotype correlation. These findings imply a possible long-term prognosis for individuals with this new XLID syndrome, and a wider phenotypic variation than initially thought.
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Affiliation(s)
- Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tokiko Fukuda
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Texas Children’s Hospital, Houston, TX, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, United States
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Annarita Nicosia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, United States
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Texas Children’s Hospital, Houston, TX, United States
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Texas Children’s Hospital, Houston, TX, United States
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Baylor Genetics, Houston, TX, United States
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Baylor Genetics, Houston, TX, United States
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Miki Asahina
- Department of Pediatrics, Hamamatsu City Welfare and Medical Center for Development, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Noriko Miyake
- 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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50
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Morita A, Enokizono T, Ohto T, Tanaka M, Watanabe S, Takada Y, Iwama K, Mizuguchi T, Matsumoto N, Morita M, Takashima S, Shimozawa N, Takada H. Novel ACOX1 mutations in two siblings with peroxisomal acyl-CoA oxidase deficiency. Brain Dev 2021; 43:475-481. [PMID: 33234382 DOI: 10.1016/j.braindev.2020.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/21/2020] [Accepted: 10/25/2020] [Indexed: 11/16/2022]
Abstract
Peroxisomal acyl-CoA oxidase (ACOX1) deficiency is a rare autosomal recessive single enzyme deficiency characterized by hypotonia, seizures, failure to thrive, developmental delay, and neurological regression starting from approximately 3 years of age. Here, we report two siblings with ACOX1 deficiency born to non-consanguineous Japanese parents. They showed mild global developmental delay from infancy and began to regress at 5 years 10 months and 5 years 6 months of age respectively. They gradually manifested with cerebellar ataxia, dysarthria, pyramidal signs, and dysphasia. Brain MRI revealed T2 high-intensity areas in the cerebellar white matter, bilateral middle cerebellar peduncle, and transverse tracts of the pons, followed by progressive atrophy of these areas. Intriguingly, the ratios of C24:0, C25:0, and C26:0 to C22:0 in plasma, which usually increase in ACOX1 deficiency were within normal ranges in both patients. On the other hand, whole exome sequencing revealed novel compound heterozygous variants in ACOX1: a frameshift variant (c.160delC:p.Leu54Serfs*18) and a missense variant (c.1259 T > C:p.Phe420Ser). The plasma concentration of individual very long chain fatty acids (C24:0, C25:0, and C26:0) was elevated, and we found that peroxisomes in fibroblasts of the patients were larger in size and fewer in number as previously reported in patients with ACOX1 deficiency. Furthermore, the C24:0 β-oxidation activity was dramatically reduced. Our findings suggest that the elevation of individual plasma very long chain fatty acids concentration, genetic analysis including whole exome analysis, and biochemical studies on the patient's fibroblasts should be considered for the correct diagnosis of ACOX1 deficiency.
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Affiliation(s)
- Atsushi Morita
- Department of Pediatrics, University of Tsukuba Hospital, Japan
| | | | - Tatsuyuki Ohto
- Department of Pediatrics, University of Tsukuba Hospital, Japan; Department of Child Health, Faculty of Medicine, University of Tsukuba, Japan
| | - Mai Tanaka
- Department of Pediatrics, University of Tsukuba Hospital, Japan
| | - Shiena Watanabe
- Department of Pediatrics, University of Tsukuba Hospital, Japan
| | - Yui Takada
- Department of Pediatrics, Ibaraki Western Medical Center, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Japan
| | - Masashi Morita
- Graduate School of Medicine and Pharmaceutical Science, University of Toyama, Japan
| | - Shigeo Takashima
- Division of Genomic Research, Life Science Research Center, Gifu University, Japan
| | - Nobuyuki Shimozawa
- Division of Genomic Research, Life Science Research Center, Gifu University, Japan
| | - Hidetoshi Takada
- Department of Pediatrics, University of Tsukuba Hospital, Japan; Department of Child Health, Faculty of Medicine, University of Tsukuba, Japan
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