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Lee S, Kang M, So KH, Jang R, Shin YW, Jang SS, Yoon JG, Kim S, Kim M, Chu K, Lee SK, Kim KJ, Baek ST, Lim BC, Moon J. Broadening the scope of multigene panel analysis for adult epilepsy patients. Epilepsia Open 2024; 9:1538-1549. [PMID: 38946282 PMCID: PMC11296137 DOI: 10.1002/epi4.12993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024] Open
Abstract
OBJECTIVE Epilepsy is a suitable target for gene panel sequencing because a considerable portion of epilepsy is now explained by genetic components, especially in syndromic cases. However, previous gene panel studies on epilepsy have mostly focused on pediatric patients. METHODS We enrolled adult epilepsy patients meeting any of the following criteria: family history of epilepsy, seizure onset age ≤ 19 years, neuronal migration disorder, and seizure freedom not achieved by dual anti-seizure medications. We sequenced the exonic regions of 211 epilepsy genes in these patients. To confirm the pathogenicity of a novel MTOR truncating variant, we electroporated vectors with different MTOR variants into developing mouse brains. RESULTS A total of 92 probands and 4 affected relatives were tested, and the proportion of intellectual disability (ID) and/or developmental disability (DD) was 21.7%. As a result, twelve probands (13.0%) had pathogenic or likely pathogenic variants in the following genes or regions: DEPDC5, 15q12-q13 duplication (n = 2), SLC6A1, SYNGAP1, EEF1A2, LGI1, MTOR, KCNQ2, MEF2C, and TSC1 (n = 1). We confirmed the functional impact of a novel truncating mutation in the MTOR gene (c.7570C > T, p.Gln2524Ter) that disrupted neuronal migration in a mouse model. The diagnostic yield was higher in patients with ID/DD or childhood-onset seizures. We also identified additional candidate variants in 20 patients that could be reassessed by further studies. SIGNIFICANCE Our findings underscore the clinical utility of gene panel sequencing in adult epilepsy patients suspected of having genetic etiology, especially those with ID/DD or early-onset seizures. Gene panel sequencing could not only lead to genetic diagnosis in a substantial portion of adult epilepsy patients but also inform more precise therapeutic decisions based on their genetic background. PLAIN LANGUAGE SUMMARY This study demonstrated the effectiveness of gene panel sequencing in adults with epilepsy, revealing pathogenic or likely pathogenic variants in 13.0% of patients. Higher diagnostic yields were observed in those with neurodevelopmental disorders or childhood-onset seizures. Additionally, we have shown that expanding genetic studies into adult patients would uncover new types of pathogenic variants for epilepsy, contributing to the advancement of precision medicine for individuals with epilepsy. In conclusion, our results highlight the practical value of employing gene panel sequencing in adult epilepsy patients, particularly when genetic etiology is clinically suspected.
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Affiliation(s)
- Seungbok Lee
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
- Department of PediatricsSeoul National University College of Medicine, Seoul National University Children's HospitalSeoulKorea
| | - Mi‐Kyoung Kang
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Ki Hurn So
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangKorea
| | - Riyul Jang
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangKorea
| | - Yong Woo Shin
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Se Song Jang
- Department of PediatricsSeoul National University College of Medicine, Seoul National University Children's HospitalSeoulKorea
| | - Jihoon G. Yoon
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
| | - Sheehyun Kim
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
| | - Manjin Kim
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
- Department of Laboratory MedicineSeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Kon Chu
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Sang Kun Lee
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
| | - Ki Joong Kim
- Department of PediatricsSeoul National University College of Medicine, Seoul National University Children's HospitalSeoulKorea
| | - Seung Tae Baek
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangKorea
| | - Byung Chan Lim
- Department of PediatricsSeoul National University College of Medicine, Seoul National University Children's HospitalSeoulKorea
| | - Jangsup Moon
- Department of Genomic MedicineSeoul National University HospitalSeoulKorea
- Department of NeurologySeoul National University College of Medicine, Seoul National University HospitalSeoulKorea
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Chengyan L, Chupeng X, You W, Yinhui C, Binglong H, Dang A, Ling L, Chuan T. Identification of genetic causes in children with unexplained epilepsy based on trio-whole exome sequencing. Clin Genet 2024; 106:140-149. [PMID: 38468460 DOI: 10.1111/cge.14519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Genotype and clinical phenotype analyses of 128 children were performed based on whole exome sequencing (WES), providing a reference for the provision of genetic counseling and the precise diagnosis and treatment of epilepsy. A total of 128 children with unexplained epilepsy were included in this study, and all their clinical data were analyzed. The children's treatments, epilepsy control, and neurodevelopmental levels were regularly followed up every 3 months. The genetic diagnostic yield of the 128 children with epilepsy is 50.8%, with an SNV diagnostic yield of 39.8% and a CNV diagnostic yield of 12.5%. Among the 128 children with epilepsy, 57.0% had onset of epilepsy in infancy, 25.8% have more than two clinical seizure forms, 62.5% require two or more anti-epileptic drug treatments, and 72.7% of the children have varying degrees of psychomotor development retardation. There are significant differences between ages of onset, neurodevelopmental levels and the presence of drug resistance in the genetic diagnostic yield (all p < 0.05). The 52 pathogenic/likely pathogenic SNVs involve 31 genes, with genes encoding ion channels having the largest number of mutations (30.8%). There were 16 cases of pathogenic/possibly pathogenic CNVs, among which the main proportions of CNVs were located in chromosome 15 and chromosome 16. Trio-WES is an essential tool for the genetic diagnosis of unexplained epilepsy, with a genetic diagnostic yield of up to 50.8%. Early genetic testing can provide an initiate appropriate therapies and accurate molecular diagnosis.
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Affiliation(s)
- Li Chengyan
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Xue Chupeng
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
- Department of Pediatrics, Shantou Central Hospital, Shantou, People's Republic of China
| | - Wang You
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Chen Yinhui
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Huang Binglong
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Ao Dang
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Liu Ling
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Tian Chuan
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
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3
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Mayfield JM, Hitefield NL, Czajewski I, Vanhye L, Holden L, Morava E, van Aalten DMF, Wells L. O-GlcNAc transferase congenital disorder of glycosylation (OGT-CDG): Potential mechanistic targets revealed by evaluating the OGT interactome. J Biol Chem 2024; 300:107599. [PMID: 39059494 DOI: 10.1016/j.jbc.2024.107599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
O-GlcNAc transferase (OGT) is the sole enzyme responsible for the post-translational modification of O-GlcNAc on thousands of target nucleocytoplasmic proteins. To date, nine variants of OGT that segregate with OGT Congenital Disorder of Glycosylation (OGT-CDG) have been reported and characterized. Numerous additional variants have been associated with OGT-CDG, some of which are currently undergoing investigation. This disorder primarily presents with global developmental delay and intellectual disability (ID), alongside other variable neurological features and subtle facial dysmorphisms in patients. Several hypotheses aim to explain the etiology of OGT-CDG, with a prominent hypothesis attributing the pathophysiology of OGT-CDG to mutations segregating with this disorder disrupting the OGT interactome. The OGT interactome consists of thousands of proteins, including substrates as well as interactors that require noncatalytic functions of OGT. A key aim in the field is to identify which interactors and substrates contribute to the primarily neural-specific phenotype of OGT-CDG. In this review, we will discuss the heterogenous phenotypic features of OGT-CDG seen clinically, the variable biochemical effects of mutations associated with OGT-CDG, and the use of animal models to understand this disorder. Furthermore, we will discuss how previously identified OGT interactors causal for ID provide mechanistic targets for investigation that could explain the dysregulated gene expression seen in OGT-CDG models. Identifying shared or unique altered pathways impacted in OGT-CDG patients will provide a better understanding of the disorder as well as potential therapeutic targets.
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Affiliation(s)
- Johnathan M Mayfield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Naomi L Hitefield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | - Lotte Vanhye
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Laura Holden
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Eva Morava
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Daan M F van Aalten
- School of Life Sciences, University of Dundee, Dundee, UK; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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Majethia P, Kaur N, Mascarenhas S, Rao LP, Pande S, Narayanan DL, Bhat V, Nayak SS, Nair KV, Prasannakumar AP, Chaurasia A, Hunakunti B, Jadhav N, Farooqui S, Yeole M, Kothiwale V, Naik R, Bhat V, Aroor S, Lewis L, Purkayastha J, Bhat YR, Praveen BK, Yatheesha BL, Patil SJ, Nampoothiri S, Kamath N, Siddiqui S, Bielas S, Girisha KM, Sharma S, Shukla A. Genetic and phenotypic landscape of pediatric-onset epilepsy in 142 Indian families: Counseling and therapeutic implications. Clin Genet 2024; 105:639-654. [PMID: 38374498 PMCID: PMC7615923 DOI: 10.1111/cge.14495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 02/21/2024]
Abstract
The application of genomic technologies has led to unraveling of the complex genetic landscape of disorders of epilepsy, gaining insights into their underlying disease mechanisms, aiding precision medicine, and providing informed genetic counseling. We herein present the phenotypic and genotypic insights from 142 Indian families with epilepsy with or without comorbidities. Based on the electroclinical findings, epilepsy syndrome diagnosis could be made in 44% (63/142) of the families adopting the latest proposal for the classification by the ILAE task force (2022). Of these, 95% (60/63) of the families exhibited syndromes with developmental epileptic encephalopathy or progressive neurological deterioration. A definitive molecular diagnosis was achieved in 74 of 142 (52%) families. Infantile-onset epilepsy was noted in 81% of these families (61/74). Fifty-five monogenic, four chromosomal, and one imprinting disorder were identified in 74 families. The genetic variants included 65 (96%) single-nucleotide variants/small insertion-deletions, 1 (2%) copy-number variant, and 1 (2%) triplet-repeat expansion in 53 epilepsy-associated genes causing monogenic disorders. Of these, 35 (52%) variants were novel. Therapeutic implications were noted in 51% of families (38/74) with definitive diagnosis. Forty-one out of 66 families with monogenic disorders exhibited autosomal recessive and inherited autosomal dominant disorders with high risk of recurrence.
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Affiliation(s)
- Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Namanpreet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vivekananda Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shalini S. Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Vijay Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Adarsh Pooradan Prasannakumar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ankur Chaurasia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Bhagesh Hunakunti
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nalesh Jadhav
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sheeba Farooqui
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Mayuri Yeole
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vishaka Kothiwale
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rohit Naik
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Veena Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran Aroor
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Jayashree Purkayastha
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Y. Ramesh Bhat
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - B. K. Praveen
- Department of Pediatrics, Father Muller Medical College Hospital, Mangalore, India
| | - B. L. Yatheesha
- Paediatric neurology, Dheemahi Child Neurology and Development Center, Shimoga, India
| | - Siddaramappa J. Patil
- Division of Medical Genetics, Narayana Hrudayalaya Hospitals/Mazumdar-Shaw Medical Center, Bangalore, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shahyan Siddiqui
- Department of Neuro and Vascular Interventional Radiology, Yashoda Hospitals, Hyderabad, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Suma Genomics Private Limited, Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Suvasini Sharma
- Neurology Division, Department of Pediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children’s Hospital, New Delhi, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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5
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Li S, Ouyang X, Sun H, Jin J, Chen Y, Li L, Wang Q, He Y, Wang J, Chen T, Zhong Q, Liang Y, Pierre P, Zou Q, Ye Y, Su B. DEPDC5 protects CD8 + T cells from ferroptosis by limiting mTORC1-mediated purine catabolism. Cell Discov 2024; 10:53. [PMID: 38763950 PMCID: PMC11102918 DOI: 10.1038/s41421-024-00682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/10/2024] [Indexed: 05/21/2024] Open
Abstract
Peripheral CD8+ T cell number is tightly controlled but the precise molecular mechanism regulating this process is still not fully understood. In this study, we found that epilepsy patients with loss of function mutation of DEPDC5 had reduced peripheral CD8+ T cells, and DEPDC5 expression positively correlated with tumor-infiltrating CD8+ T cells as well as overall cancer patient survival, indicating that DEPDC5 may control peripheral CD8+ T cell homeostasis. Significantly, mice with T cell-specific Depdc5 deletion also had reduced peripheral CD8+ T cells and impaired anti-tumor immunity. Mechanistically, Depdc5-deficient CD8+ T cells produced high levels of xanthine oxidase and lipid ROS due to hyper-mTORC1-induced expression of ATF4, leading to spontaneous ferroptosis. Together, our study links DEPDC5-mediated mTORC1 signaling with CD8+ T cell protection from ferroptosis, thereby revealing a novel strategy for enhancing anti-tumor immunity via suppression of ferroptosis.
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Affiliation(s)
- Song Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Gastroenterology and Center for Immune-Related Diseases Research at Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinxing Ouyang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Chest Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongxiang Sun
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Gastroenterology and Center for Immune-Related Diseases Research at Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingsi Jin
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yao Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Gastroenterology and Center for Immune-Related Diseases Research at Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Gastroenterology and Center for Immune-Related Diseases Research at Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qijun Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingzhong He
- Department of Neurology of Shanghai Children's Medical Center affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiwen Wang
- Department of Neurology of Shanghai Children's Medical Center affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tongxin Chen
- Department of Allergy and Immunology, Division of Immunology and Multidisciplinary Specialty Clinic, Institute of Pediatric Translational Medicine at Shanghai Children's Medical Center affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Zhong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinming Liang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Philippe Pierre
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Aix Marseille Université, CNRS, INSERM, CIML, Marseille, cedex 9, France
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Qiang Zou
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Gastroenterology and Center for Immune-Related Diseases Research at Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Gastroenterology and Center for Immune-Related Diseases Research at Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.
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Triono A, Herini ES, Gunadi. Genetic exploration of Dravet syndrome: two case report. J Med Case Rep 2024; 18:215. [PMID: 38649973 PMCID: PMC11036636 DOI: 10.1186/s13256-024-04514-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Dravet syndrome is an infantile-onset developmental and epileptic encephalopathy (DEE) characterized by drug resistance, intractable seizures, and developmental comorbidities. This article focuses on manifestations in two Indonesian children with Javanese ethnicity who experienced Dravet syndrome with an SCN1A gene mutation, presenting genetic analysis findings using next-generation sequencing. CASE PRESENTATION We present a case series involving two Indonesian children with Javanese ethnicity whom had their first febrile seizure at the age of 3 months, triggered after immunization. Both patients had global developmental delay and intractable seizures. We observed distinct genetic findings in both our cases. The first patient revealed heterozygous deletion mutation in three genes (TTC21B, SCN1A, and SCN9A). In our second patient, previously unreported mutation was discovered at canonical splice site upstream of exon 24 of the SCN1A gene. Our patient's outcomes improved after therapeutic evaluation based on mutation findings When comparing clinical manifestations in our first and second patients, we found that the more severe the genetic mutation discovered, the more severe the patient's clinical manifestations. CONCLUSION These findings emphasize the importance of comprehensive genetic testing beyond SCN1A, providing valuable insights for personalized management and tailored therapeutic interventions in patients with Dravet syndrome. Our study underscores the potential of next-generation sequencing in advancing genotype-phenotype correlations and enhancing diagnostic precision for effective disease management.
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Affiliation(s)
- Agung Triono
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia
| | - Elisabeth Siti Herini
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia.
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Dr. Sardjito Hospital, Yogyakarta, 55281, Indonesia
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Zhang X, Xiang F, Li D, Yang F, Yu S, Wang X. Adult-onset combined oxidative phosphorylation deficiency type 14 manifests as epileptic status: a new phenotype and literature review. BMC Neurol 2024; 24:15. [PMID: 38166857 PMCID: PMC10759640 DOI: 10.1186/s12883-023-03480-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Combined oxidative phosphorylation deficiency (COXPD) is a severe disorder with early onset and autosomal recessive inheritance, and has been divided into 51 types (COXPD1-COXPD51). COXPD14 is caused by a mutation in the FARS2 gene, which encodes mitochondrial phenylalanyl-tRNA synthetase (mt-PheRS), an enzyme that transfers phenylalanine to its cognate tRNA in mitochondria. Since the first case was reported in 2012, an increasing number of FARS2 variations have been subsequently identified, which present three main phenotypic manifestations: early onset epileptic encephalopathy, hereditary spastic paraplegia, and juvenile-onset epilepsy. To our knowledge, no adult cases have been reported in the literature. METHODS We report in detail a case of genetically confirmed COXPD14 and review the relevant literature. RESULTS Approximately 58 subjects with disease-causing variants of FARS2 have been reported, including 31 cases of early onset epileptic encephalopathy, 16 cases of hereditary spastic paraplegia, 3 cases of juvenile-onset epilepsy, and 8 cases of unknown phenotype. We report a case of autosomal recessive COXPD14 in an adult with status epilepticus as the only manifestation with a good prognosis, which is different from that in neonatal or infant patients reported in the literature. c.467C > T (p.T156M) has been previously reported, while c.119_120del (p.E40Vfs*87) is novel, and, both mutations are pathogenic. CONCLUSIONS This case of autosomal recessive COXPD14 in an adult only presented as status epilepticus, which is different from the patients reported previously. Our study expands the mutation spectrum of FARS2, and we tended to define the phenotypes based on the clinical manifestation rather than the age of onset.
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Affiliation(s)
- Xu Zhang
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Feng Xiang
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Desheng Li
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Fei Yang
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Shengyuan Yu
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China
| | - Xiangqing Wang
- Department of Neurology, The First Medical Center of Chinese PLA General Hospital, 28# Fuxing Road, Beijing, People's Republic of China.
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8
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Khan R, Chaturvedi P, Sahu P, Ludhiadch A, Singh P, Singh G, Munshi A. Role of Potassium Ion Channels in Epilepsy: Focus on Current Therapeutic Strategies. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:67-87. [PMID: 36578258 DOI: 10.2174/1871527322666221227112621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Epilepsy is one of the prevalent neurological disorders characterized by disrupted synchronization between inhibitory and excitatory neurons. Disturbed membrane potential due to abnormal regulation of neurotransmitters and ion transport across the neural cell membrane significantly contributes to the pathophysiology of epilepsy. Potassium ion channels (KCN) regulate the resting membrane potential and are involved in neuronal excitability. Genetic alterations in the potassium ion channels (KCN) have been reported to result in the enhancement of the release of neurotransmitters, the excitability of neurons, and abnormal rapid firing rate, which lead to epileptic phenotypes, making these ion channels a potential therapeutic target for epilepsy. The aim of this study is to explore the variations reported in different classes of potassium ion channels (KCN) in epilepsy patients, their functional evaluation, and therapeutic strategies to treat epilepsy targeting KCN. METHODOLOGY A review of all the relevant literature was carried out to compile this article. RESULTS A large number of variations have been reported in different genes encoding various classes of KCN. These genetic alterations in KCN have been shown to be responsible for disrupted firing properties of neurons. Antiepileptic drugs (AEDs) are the main therapeutic strategy to treat epilepsy. Some patients do not respond favorably to the AEDs treatment, resulting in pharmacoresistant epilepsy. CONCLUSION Further to address the challenges faced in treating epilepsy, recent approaches like optogenetics, chemogenetics, and genome editing, such as clustered regularly interspaced short palindromic repeats (CRISPR), are emerging as target-specific therapeutic strategies.
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Affiliation(s)
- Rahul Khan
- Department of Human Genetics and Molecular Medicine Central University of Punjab, Bathinda 151401, India
| | - Pragya Chaturvedi
- Department of Human Genetics and Molecular Medicine Central University of Punjab, Bathinda 151401, India
| | - Prachi Sahu
- Department of Human Genetics and Molecular Medicine Central University of Punjab, Bathinda 151401, India
| | - Abhilash Ludhiadch
- Department of Human Genetics and Molecular Medicine Central University of Punjab, Bathinda 151401, India
| | - Paramdeep Singh
- Department of Radiology, All India Institute of Medical Sciences, Bathinda, Punjab, 151001 India
| | - Gagandeep Singh
- Department of Neurology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine Central University of Punjab, Bathinda 151401, India
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9
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Poggio E, Barazzuol L, Salmaso A, Milani C, Deligiannopoulou A, Cazorla ÁG, Jang SS, Juliá-Palacios N, Keren B, Kopajtich R, Lynch SA, Mignot C, Moorwood C, Neuhofer C, Nigro V, Oostra A, Prokisch H, Saillour V, Schuermans N, Torella A, Verloo P, Yazbeck E, Zollino M, Jech R, Winkelmann J, Necpal J, Calì T, Brini M, Zech M. ATP2B2 de novo variants as a cause of variable neurodevelopmental disorders that feature dystonia, ataxia, intellectual disability, behavioral symptoms, and seizures. Genet Med 2023; 25:100971. [PMID: 37675773 DOI: 10.1016/j.gim.2023.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023] Open
Abstract
PURPOSE ATP2B2 encodes the variant-constrained plasma-membrane calcium-transporting ATPase-2, expressed in sensory ear cells and specialized neurons. ATP2B2/Atp2b2 variants were previously linked to isolated hearing loss in patients and neurodevelopmental deficits with ataxia in mice. We aimed to establish the association between ATP2B2 and human neurological disorders. METHODS Multinational case recruitment, scrutiny of trio-based genomics data, in silico analyses, and functional variant characterization were performed. RESULTS We assembled 7 individuals harboring rare, predicted deleterious heterozygous ATP2B2 variants. The alleles comprised 5 missense substitutions that affected evolutionarily conserved sites and 2 frameshift variants in the penultimate exon. For 6 variants, a de novo status was confirmed. Unlike described patients with hearing loss, the individuals displayed a spectrum of neurological abnormalities, ranging from ataxia with dystonic features to complex neurodevelopmental manifestations with intellectual disability, autism, and seizures. Two cases with recurrent amino-acid variation showed distinctive overlap with cerebellar atrophy-associated ataxia and epilepsy. In cell-based studies, all variants caused significant alterations in cytosolic calcium handling with both loss- and gain-of-function effects. CONCLUSION Presentations in our series recapitulate key phenotypic aspects of Atp2b2-mouse models and underline the importance of precise calcium regulation for neurodevelopment and cerebellar function. Our study documents a role for ATP2B2 variants in causing heterogeneous neurodevelopmental and movement-disorder syndromes.
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Affiliation(s)
- Elena Poggio
- Department of Biology, University of Padua, Padua, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Andrea Salmaso
- Department of Biology, University of Padua, Padua, Italy
| | - Celeste Milani
- Department of Biology, University of Padua, Padua, Italy
| | | | - Ángeles García Cazorla
- European Reference Network for Hereditary Metabolic Diseases (MetabERN), Madrid, Spain; Neurometabolic Unit and Synaptic Metabolism Laboratory, Neurology Department Sant Joan de Déu Hospital, IPR, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Se Song Jang
- Seoul National University (SNU) College of Medicine, Seoul, South Korea
| | - Natalia Juliá-Palacios
- Neurology Department, Neurometabolic Unit, Institut de Recerca, CIBERER and MetabERN, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Boris Keren
- APHP.Sorbonne Université, Department of Medical Genetics, Pitié-Salpêtrière University Hospital, and Centre de Référence Maladies Rares Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Robert Kopajtich
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sally Ann Lynch
- Department of Clinical Genetics, Temple Street Children's University Hospital, Dublin, Ireland
| | - Cyril Mignot
- APHP.Sorbonne Université, Department of Medical Genetics, Pitié-Salpêtrière University Hospital, and Centre de Référence Maladies Rares Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Catherine Moorwood
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Christiane Neuhofer
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, Napoli, Italy
| | - Anna Oostra
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Virginie Saillour
- Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France
| | - Nika Schuermans
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, Napoli, Italy
| | - Patrick Verloo
- Department of Pediatric Neurology, Center for Inherited Metabolic Disorders and metabERN, University Hospital Ghent, Ghent, Belgium
| | - Elise Yazbeck
- Pediatric Neurology Department, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Paris Saclay, Bicêtre Hospital, Le Kremlin Bicêtre, France
| | - Marcella Zollino
- Unit of Medical Genetics, Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Robert Jech
- Department of Neurology, Charles University in Prague, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Jan Necpal
- 2nd Department of Neurology, Faculty of Medicine, Comenius University, Bratislava, Slovakia; Department of Neurology, Zvolen Hospital, Zvolen, Slovakia
| | - Tito Calì
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Centro Studi per la Neurodegenerazione (CESNE), University of Padua, Padua, Italy; Neuroscience Center (PNC), University of Padua, Padua, Italy
| | - Marisa Brini
- Department of Biology, University of Padua, Padua, Italy; Centro Studi per la Neurodegenerazione (CESNE), University of Padua, Padua, Italy
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute for Advanced Study, Technical University of Munich, Garching, Germany.
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Arslan A. Pathogenic variants of human GABRA1 gene associated with epilepsy: A computational approach. Heliyon 2023; 9:e20218. [PMID: 37809401 PMCID: PMC10559982 DOI: 10.1016/j.heliyon.2023.e20218] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/17/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Critical for brain development, neurodevelopmental and network disorders, the GABRA1 gene encodes for the α1 subunit, an abundantly and developmentally expressed subunit of heteropentameric gamma-aminobutyric acid A receptors (GABAARs) mediating primary inhibition in the brain. Mutations of the GABAAR subunit genes including GABRA1 gene are associated with epilepsy, a group of syndromes, characterized by unprovoked seizures and diagnosed by integrative approach, that involves genetic testing. Despite the diagnostic use of genetic testing, a large fraction of the GABAAR subunit gene variants including the variants of GABRA1 gene is not known in terms of their molecular consequence, a challenge for precision and personalized medicine. Addressing this, one hundred thirty-seven GABRA1 gene variants of unknown clinical significance have been extracted from the ClinVar database and computationally analyzed for pathogenicity. Eight variants (L49H, P59L, W97R, D99G, G152S, V270G, T294R, P305L) are predicted as pathogenic and mapped to the α1 subunit's extracellular domain (ECD), transmembrane domains (TMDs) and extracellular linker. This is followed by the integration with relevant data for cellular pathology and severity of the epilepsy syndromes retrieved from the literature. Our results suggest that the pathogenic variants in the ECD of GABRA1 (L49H, P59L, W97R, D99G, G152S) will probably manifest decreased surface expression and reduced current with mild epilepsy phenotypes while V270G, T294R in the TMDs and P305L in the linker between the second and the third TMDs will likely cause reduced cell current with severe epilepsy phenotypes. The results presented in this study provides insights for clinical genetics and wet lab experimentation.
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Affiliation(s)
- Ayla Arslan
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Üsküdar University, Istanbul, Turkey
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11
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Ko YJ, Kim SY, Lee S, Yoon JG, Kim MJ, Jun H, Kim H, Chae JH, Kim KJ, Kim K, Lim BC. Epilepsy phenotype and gene ontology analysis of the 129 genes in a large neurodevelopmental disorders cohort. Front Neurol 2023; 14:1218706. [PMID: 37645600 PMCID: PMC10461058 DOI: 10.3389/fneur.2023.1218706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/19/2023] [Indexed: 08/31/2023] Open
Abstract
Objective Although pediatric epilepsy is an independent disease entity, it is often observed in pediatric neurodevelopmental disorders (NDDs) as a major or minor clinical feature, which might provide diagnostic clues. This study aimed to identify the clinical and genetic characteristics of patients with epilepsy in an NDD cohort and demonstrate the importance of genetic testing. Methods We retrospectively analyzed the detailed clinical differences of pediatric NDD patients with epilepsy according to their genetic etiology. Among 1,213 patients with NDDs, 477 were genetically diagnosed by exome sequencing, and 168 had epilepsy and causative variants in 129 genes. Causative genes were classified into two groups: (i) the "epilepsy-genes" group resulting in epilepsy as the main phenotype listed in OMIM, Epi25, and ClinGen (67 patients) and (ii) the "NDD-genes" group not included in the "epilepsy-genes" group (101 patients). Results Patients in the "epilepsy-genes" group started having seizures, often characterized by epilepsy syndrome, at a younger age. However, overall clinical features, including treatment responses and all neurologic manifestations, showed no significant differences between the two groups. Gene ontology analysis revealed the close interactions of epilepsy genes associated with ion channels and neurotransmitters. Conclusion We demonstrated a similar clinical presentation of different gene groups regarding biological/molecular processes in a large NDDs cohort with epilepsy. Phenotype-driven genetic analysis should cover a broad scope, and further studies are required to elucidate integrated pathomechanisms.
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Affiliation(s)
- Young Jun Ko
- Department of Pediatrics, Chung-Ang University Gwangmyeong Hospital, Gwangmyeong, Republic of Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seungbok Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jihoon G. Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyeji Jun
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hunmin Kim
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ki Joong Kim
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Byung Chan Lim
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea
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12
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Ko YJ, Cho A, Kim WJ, Kim SY, Lim BC, Kim H, Hwang H, Choi JE, Kim KJ, Chae JH. Broad spectrum of phenotype and genotype in Korean alpha dystroglycan related muscular dystrophy presenting to a tertiary pediatric neuromuscular center. Neuromuscul Disord 2023; 33:425-431. [PMID: 37087885 DOI: 10.1016/j.nmd.2023.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
α-Dystroglycanopathies are a clinically and genetically heterogeneous group of muscular dystrophies associated with the defective glycosylation of α-dystroglycan (α-DG). Eighteen genes associated with α-dystroglycanopathies have been identified, and the relative prevalence of genetic subtypes varies with ethnicity. Here, we investigated the clinical and genetic characteristics of α-DG-related muscular dystrophy in the Korean pediatric population. We analyzed the clinical characteristics and variant profiles of 42 patients with α-DG-related muscular dystrophies diagnosed by either reduced glycosylation of α-DG and/or genetic confirmation. Genotype-phenotype correlations were explored by a retrospective medical record review. The muscle-eye-brain disease/Fukuyama congenital muscular dystrophy was the most common phenotype (28/42, 66.7%). Homozygous or compound heterozygous variants were detected in 37 patients belonging to 34 unrelated families (37/42; 88.1%). Pathogenic variants were identified in FKTN (n = 24), POMGNT1 (n = 4), GMPPB (n = 4), FKRP (n = 2), POMT1 (n = 2), and ISPD (n = 1). Compound heterozygous retrotransposal insertions and deep-intronic variants in FKTN were the most common genotypes and were associated with severe phenotypes. This study suggests that α-DG-related muscular dystrophy has a wide range of genotypes and phenotypes according to ethnicity. A stratified genetic test according to ethnicity should be considered to diagnose α-DG-related muscular dystrophy.
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Félix TM, Fischinger Moura de Souza C, Oliveira JB, Rico-Restrepo M, Zanoteli E, Zatz M, Giugliani R. Challenges and recommendations to increasing the use of exome sequencing and whole genome sequencing for diagnosing rare diseases in Brazil: an expert perspective. Int J Equity Health 2023; 22:11. [PMID: 36639662 PMCID: PMC9837951 DOI: 10.1186/s12939-022-01809-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023] Open
Abstract
Early diagnosis of genetic rare diseases is an unmet need in Brazil, where an estimated 10-13 million people live with these conditions. Increased use of chromosome microarray assays, exome sequencing, and whole genome sequencing as first-tier testing techniques in suitable indications can shorten the diagnostic odyssey, eliminate unnecessary tests, procedures, and treatments, and lower healthcare expenditures. A selected panel of Brazilian experts in fields related to rare diseases was provided with a series of relevant questions to address before a multi-day conference. Within this conference, each narrative was discussed and edited through numerous rounds of discussion until agreement was achieved. The widespread adoption of exome sequencing and whole genome sequencing in Brazil is limited by various factors: cost and lack of funding, reimbursement, awareness and education, specialist shortages, and policy issues. To reduce the burden of rare diseases and increase early diagnosis, the Brazilian healthcare authorities/government must address the barriers to equitable access to early diagnostic methods for these conditions. Recommendations are provided, including broadening approved testing indications, increasing awareness and education efforts, increasing specialist training opportunities, and ensuring sufficient funding for genetic testing.
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Affiliation(s)
- Têmis Maria Félix
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil
| | - Carolina Fischinger Moura de Souza
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil
| | - João Bosco Oliveira
- grid.413562.70000 0001 0385 1941Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Edmar Zanoteli
- grid.11899.380000 0004 1937 0722Faculdade de Medicina, Universidade de São Paulo (FMUSP), São Paulo, Brazil
| | - Mayana Zatz
- grid.11899.380000 0004 1937 0722Human Genome and Stem-cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Roberto Giugliani
- grid.414449.80000 0001 0125 3761Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos, 2350, Porto Alegre, 90,035–903 Brazil ,House of Rares, Porto Alegre, Rio Grande do Sul Brazil
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14
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Li N, Song YM, Zhang XD, Zhao XS, He XY, Yu LF, Zou DW. Pseudoileus caused by primary visceral myopathy in a Han Chinese patient with a rare MYH11 mutation: A case report. World J Clin Cases 2022; 10:12623-12630. [PMID: 36579105 PMCID: PMC9791514 DOI: 10.12998/wjcc.v10.i34.12623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/17/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Chronic intestinal pseudo-obstruction (CIPO) is a syndrome of intestinal motor dysfunction caused by intestinal nerve, muscle, and/or Cajal stromal cell lesions. CIPO is a serious category of gastrointestinal dynamic dysfunction, which can eventually lead to the death of patients with intestinal failure. Due to considerable phenotypic heterogeneity, the estimated incidence of CIPO is 1/476190 and 1/416666 in men and women, respectively. According to the etiology, CIPO can be divided into idiopathic and secondary, of which the latter is the most common, often secondary to tumor, virus infection, connective tissue disease, neurological diseases, and endocrine diseases. Idiopathic CIPO in the intestinal tract is divided into visceral myopathy, neuropathy, and stromal cell lesions according to the location. Surgery is usually not recommended for CIPO, because it often does not benefit patients with CIPO, and postoperative intestinal obstruction is likely to occur, which may even worsen the condition.
CASE SUMMARY Here, we describe the case of a 43-year-old male Han Chinese patient with a 15-year history of recurrent abdominal distention with no clear cause. The results of physical, biochemical, and other relevant examinations showed no clear abnormalities. Contrast-enhanced computed tomography (CT) indicated a large duodenum, clear expansion of the intestinal lumen, and CIPO. Whole exome sequencing (WES) of the patient and his mother confirmed the diagnosis of primary familial visceral myopathy type 2 chronic pseudoileus with a rare heterozygous gene mutation in MYH11. This is the second reported case of CIPO with a heterozygous MYH11 [NM_001040113.1: c.5819delC (p.Pro1940Hisfs*91)] mutation.
CONCLUSION This case report indicates that physicians can perform routine clinical examinations, CT, and WES to achieve a diagnosis and treatment of CIPO in early disease stages.
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Affiliation(s)
- Na Li
- Department of Geriatrics, Qinghai Provincial People’s Hospital, Xining 810007, Qinghai Province, China
| | - Yi-Ming Song
- Department of Gastroenterology, Fenghua District People’s Hospital, Ningbo 315000, Zhejiang Province, China
| | - Xian-Da Zhang
- Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xue-Song Zhao
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiang-Yi He
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Li-Fen Yu
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Duo-Wu Zou
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Sochacka M, Karelus R, Opalinski L, Krowarsch D, Biadun M, Otlewski J, Zakrzewska M. FGF12 is a novel component of the nucleolar NOLC1/TCOF1 ribosome biogenesis complex. Cell Commun Signal 2022; 20:182. [PMID: 36411431 PMCID: PMC9677703 DOI: 10.1186/s12964-022-01000-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
Among the FGF proteins, the least characterized superfamily is the group of fibroblast growth factor homologous factors (FHFs). To date, the main role of FHFs has been primarily seen in the modulation of voltage-gated ion channels, but a full picture of the function of FHFs inside the cell is far from complete. In the present study, we focused on identifying novel FGF12 binding partners to indicate its intracellular functions. Among the identified proteins, a significant number were nuclear proteins, especially RNA-binding proteins involved in translational processes, such as ribosomal processing and modification. We have demonstrated that FGF12 is localized to the nucleolus, where it interacts with NOLC1 and TCOF1, proteins involved in the assembly of functional ribosomes. Interactions with both NOLC1 and TCOF1 are unique to FGF12, as other FHF proteins only bind to TCOF1. The formation of nucleolar FGF12 complexes with NOLC1 and TCOF1 is phosphorylation-dependent and requires the C-terminal region of FGF12. Surprisingly, NOLC1 and TCOF1 are unable to interact with each other in the absence of FGF12. Taken together, our data link FHF proteins to nucleoli for the first time and suggest a novel and unexpected role for FGF12 in ribosome biogenesis. Video Abstract.
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Affiliation(s)
- Martyna Sochacka
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Radoslaw Karelus
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Lukasz Opalinski
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Daniel Krowarsch
- grid.8505.80000 0001 1010 5103Department of Protein Biotechnology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Martyna Biadun
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Jacek Otlewski
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Malgorzata Zakrzewska
- grid.8505.80000 0001 1010 5103Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wrocław, Poland
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16
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D'Onofrio G, Riva A, Di Rosa G, Cali' E, Efthymiou S, Gitto E, Madia F, Accogli A, Zara F, Houlden H, Salpietro V, Striano P, Soler D. Paroxysmal limb dystonias associated with GABBR2 pathogenic variant: A case-based literature review. Brain Dev 2022; 44:469-473. [PMID: 35414446 DOI: 10.1016/j.braindev.2022.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND De novo mutations in the GABBR2 (Gamma-Aminobutyric acid Type B Receptor Subunit 2) gene have recently been reported to be associated with a form of early-infantile epileptic encephalopathy (EIEE59; OMIM# 617904), as well as a Rett syndrome (RTT)-like disorder defined as a neurodevelopmental disorder with poor language and loss of hand skills (NDPLHS; OMIM# 617903). METHODS We describe a pediatric case carrying a de novo GABBR2 pathogenic variant and showing a phenotype encompassing RTT, epilepsy, generalized hypotonia with a paroxysmal limb dystonia. RESULTS A 11-year-old girl, born to non-consanguineous parents after an uneventful pregnancy, had developmental delay and generalized hypotonia. At age 3.5 months she presented with infantile spasms with an electroencephalographic pattern of hypsarrhythmia. After treatment with clonazepam and prednisolone, she became seizure-free with a slow background electrical activity. Brain magnetic resonance imaging was normal. Paroxysmal dystonic posturing of the extremities, especially the upper limbs, have been observed since the age of 3 years. Motor stereotypies, non-epileptic episodes of hyperventilation and breath-holding were also reported. The girl suffered from feeding difficulties requiring gastrostomy at the age of 8. Exome sequencing (ES) revealed a de novo GABBR2 pathogenic variant (NM_005458:c.G2077T:p.G693W). CONCLUSION Paroxysmal limb dystonias, especially in the context of neurodevelopmental disorder featuring epilepsy, generalized hypotonia and RTT-like features should lead to the suspect of GABBR2 mutations.
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Affiliation(s)
- Gianluca D'Onofrio
- Department of Neurosciences Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "Giannina Gaslini", Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Antonella Riva
- Department of Neurosciences Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "Giannina Gaslini", Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Gabriella Di Rosa
- Child Neuropsychiatry Unit, Department of Pediatrics, University of Messina, Messina 98100, Italy
| | - Elisa Cali'
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, Gower Street, London WC1E 6BT, United Kingdom
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, Gower Street, London WC1E 6BT, United Kingdom
| | - Eloisa Gitto
- Intensive Neonatal and Pediatric Care Unit, Department of Pediatrics, University of Messina, Messina 98100, Italy
| | - Francesca Madia
- Unit of Medical Genetics, IRCCS Istituto "Giannina Gaslini", Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Federico Zara
- Department of Neurosciences Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; Unit of Medical Genetics, IRCCS Istituto "Giannina Gaslini", Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, Gower Street, London WC1E 6BT, United Kingdom
| | - Vincenzo Salpietro
- Department of Neurosciences Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "Giannina Gaslini", Via Gerolamo Gaslini 5, 16147 Genoa, Italy; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, Gower Street, London WC1E 6BT, United Kingdom
| | - Pasquale Striano
- Department of Neurosciences Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "Giannina Gaslini", Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Doriette Soler
- Department of Paediatrics, Mater dei Hospital, Msida, Malta.
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Chen X, Liu F, Li B, Wang Y, Yuan L, Yin A, Chen Q, Hu W, Yao Y, Zhang M, Wu Y, Chen K. Neuropathy-associated Fars2 deficiency affects neuronal development and potentiates neuronal apoptosis by impairing mitochondrial function. Cell Biosci 2022; 12:103. [PMID: 35794642 PMCID: PMC9258231 DOI: 10.1186/s13578-022-00838-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/23/2022] [Indexed: 11/22/2022] Open
Abstract
Background Neurodegenerative diseases encompass an extensive and heterogeneous group of nervous system disorders which are characterized by progressive degeneration and death of neurons. Many lines of evidence suggest the participation of mitochondria dysfunction in these diseases. Mitochondrial phenylalanyl-tRNA synthetase, encoded by FARS2, catalyzes the transfer of phenylalanine to its cognate tRNA for protein synthesis. As a member of mt-aaRSs genes, FARS2 missense homozygous mutation c.424G > T (p.D142Y) found in a Chinese consanguineous family first built the relationship between pure hereditary spastic paraplegia (HSP) and FARS2 gene. More FARS2 variations were subsequently found to cause heterogeneous group of neurologic disorders presenting three main phenotypic manifestations: infantile-onset epileptic mitochondrial encephalopathy, later-onset spastic paraplegia and juvenile onset refractory epilepsy. Studies showed that aminoacylation activity is frequently disrupt in cases with FARS2 mutations, indicating a loss-of-function mechanism. However, the underlying pathogenesis of neuropathy-associated Fars2 deficiency is still largely unknown. Results Early gestation lethality of global Fars2 knockout mice was observed prior to neurogenesis. The conditional Fars2 knockout-mouse model delayed lethality to late-gestation, resulting in a thinner cortex and an enlarged ventricle which is consist with the MRI results revealing cortical atrophy and reduced cerebral white matter volume in FARS2-deficient patients. Delayed development of neurite outgrowth followed by neuronal apoptosis was confirmed in Fars2-knockdown mouse primary cultured neurons. Zebrafish, in which fars2 was knocked down, exhibited aberrant motor neuron function including reduced locomotor capacity which well restored the spastic paraplegia phenotype of FARS2-deficient patients. Altered mitochondrial protein synthesis and reduced levels of oxidative phosphorylation complexes were detected in Fars2-deficient samples. And thus, reduced ATP, total NAD levels and mitochondrial membrane potential, together with increased ROS production, revealed mitochondrial dysfunction both in vitro and in vivo. Dctn3 is a potential downstream molecule in responds to Fars2 deficient in neurons, which may provide some evidence for the development of pathogenesis study and therapeutic schedule. Conclusions The Fars2 deficiency genetic models developed in this study cover the typical clinical manifestations in FARS2 patients, and help clarify how neuropathy-associated Fars2 deficiency, by damaging the mitochondrial respiratory chain and impairing mitochondrial function, affects neuronal development and potentiates neuronal cell apoptosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00838-y.
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Affiliation(s)
- Xihui Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Fangfang Liu
- Department of Neurobiology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Bowen Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Yufeng Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Medical Genetics, Yan'an University, Yan'an, Shaanxi, People's Republic of China
| | - Lijuan Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Department of General Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Anan Yin
- Department of Neurosurgery, Xijing Institute of Clinical Neuroscience, Department of Plastic surgery, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Qi Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China
| | - Weihong Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Medical Genetics, Yan'an University, Yan'an, Shaanxi, People's Republic of China
| | - Yan Yao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Medical Genetics, Yan'an University, Yan'an, Shaanxi, People's Republic of China
| | - Mengjie Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.,Medical Genetics, Yan'an University, Yan'an, Shaanxi, People's Republic of China
| | - YuanMing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China. .,Shaanxi Provincial Key Laboratory of Clinic Genetics, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.
| | - Kun Chen
- Department of Anatomy, Histology and Embryology and K.K. Leung Brain Research Centre, School of Basic Medicine, Air Force Medical University, Xi'an, Shaanxi, People's Republic of China.
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18
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Wu J, Zhu S, Zhao C, Xu X. Comprehensive investigation of molecular signatures and pathways linking Alzheimer's disease and Epilepsy via bioinformatic approaches. Curr Alzheimer Res 2022; 19:146-160. [PMID: 35114922 DOI: 10.2174/1567205019666220202120638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/22/2021] [Accepted: 12/03/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Epileptic activity is frequent in patients with Alzheimer's disease (AD), and this may accelerate AD progression; however, the relationship between AD and epilepsy remains unclear. OBJECTIVE We aimed to investigate the molecular pathways and genes linking AD and epilepsy using bioinformatics approaches. METHODS Gene expression profiles of AD (GSE1297) and epilepsy (GSE28674) were derived from the Gene Expression Omnibus (GEO) database. The top 50% expression variants were subjected to weighted gene co-expression network analysis (WGCNA) to identify key modules associated with these diseases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for the key modules were performed, and the intersected terms of functional enrichment and common genes within the key modules were selected. The overlapping genes were subjected to analyses of protein-protein interaction (PPI) network, transcription factor (TF)-mRNA network, microRNA (miRNA)-mRNA network, and drug prediction. RESULTS We identified 229 and 1187 genes in the AD-associated purple and epilepsy-associated blue modules, respectively. Six shared functional terms between the two modules included "calcium ion binding" and "calcium signaling pathway." According to 17 common genes discovered, 130 TF-mRNA pairs and 56 miRNA-mRNA pairs were established. The topological analyses of the constructed regulatory networks suggested that TF - FOXC1 and miRNA - hsa-mir-335-5p might be vital co-regulators of gene expression in AD and epilepsy. In addition, CXCR4 was identified as a hub gene, becoming the putative target for 20 drugs. CONCLUSION Our study provided novel insights into the molecular connection between AD and epilepsy, which might be beneficial for exploring shared mechanisms and designing disease-modifying therapies.
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Affiliation(s)
- Jiao Wu
- Department of Neurology, the First Hospital of China Medical University, Shenyang, China
- Department of Neurology, The People's Hospital of China Medical University, Shenyang, China
- Department of Neurology, The People's Hospital of Liaoning Province, Shenyang, China
| | - Shu Zhu
- Department of Pediatric Dentistry, School of Stomatology, China Medical University, Shenyang, China
| | - Chenyang Zhao
- Department of Neurology, the First Hospital of China Medical University, Shenyang, China
| | - Xiaoxue Xu
- Department of Neurology, the First Hospital of China Medical University, Shenyang, China
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19
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Umlai UKI, Bangarusamy DK, Estivill X, Jithesh PV. Genome sequencing data analysis for rare disease gene discovery. Brief Bioinform 2021; 23:6366880. [PMID: 34498682 DOI: 10.1093/bib/bbab363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/24/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022] Open
Abstract
Rare diseases occur in a smaller proportion of the general population, which is variedly defined as less than 200 000 individuals (US) or in less than 1 in 2000 individuals (Europe). Although rare, they collectively make up to approximately 7000 different disorders, with majority having a genetic origin, and affect roughly 300 million people globally. Most of the patients and their families undergo a long and frustrating diagnostic odyssey. However, advances in the field of genomics have started to facilitate the process of diagnosis, though it is hindered by the difficulty in genome data analysis and interpretation. A major impediment in diagnosis is in the understanding of the diverse approaches, tools and datasets available for variant prioritization, the most important step in the analysis of millions of variants to select a few potential variants. Here we present a review of the latest methodological developments and spectrum of tools available for rare disease genetic variant discovery and recommend appropriate data interpretation methods for variant prioritization. We have categorized the resources based on various steps of the variant interpretation workflow, starting from data processing, variant calling, annotation, filtration and finally prioritization, with a special emphasis on the last two steps. The methods discussed here pertain to elucidating the genetic basis of disease in individual patient cases via trio- or family-based analysis of the genome data. We advocate the use of a combination of tools and datasets and to follow multiple iterative approaches to elucidate the potential causative variant.
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Affiliation(s)
- Umm-Kulthum Ismail Umlai
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
| | - Dhinoth Kumar Bangarusamy
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
| | - Xavier Estivill
- Quantitative Genomics Laboratories (qGenomics), Barcelona, Catalonia, Spain
| | - Puthen Veettil Jithesh
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
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