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Brito F, Lagos C, Cubillos J, Orellana J, Gajardo M, Böhme D, Encina G, Repetto GM. Genomic analysis in Chilean patients with suspected Rett syndrome: keep a broad differential diagnosis. Front Genet 2024; 15:1278198. [PMID: 38566815 PMCID: PMC10986174 DOI: 10.3389/fgene.2024.1278198] [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: 08/15/2023] [Accepted: 02/12/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Rett syndrome (RTT, MIM #312750) is a rare genetic disorder that leads to developmental regression and severe disability and is caused by pathogenic variants in the MECP2 gene. The diagnosis of RTT is based on clinical features and, depending on resources and access, on molecular confirmation. There is scarce information on molecular diagnosis from patients in Latin America, mostly due to limited availability and coverage of genomic testing. This pilot study aimed to implement genomic testing and characterize clinical and molecular findings in a group of Chilean patients with a clinical diagnosis of RTT. Methods: Twenty-eight patients with suspected RTT underwent characterization of phenotypic manifestations and molecular testing using Clinical Exome SolutionTM CES_V2 by SOPHiA Genetics. Data was analyzed using the commercial bioinformatics platform, SOPHiA DDMTM. A virtual panel of 34 genes, including MECP2 and other genes that are in the differential diagnosis of RTT, was used to prioritize initial analyses, followed by evaluation of the complete exome sequence data. Results: Twelve patients (42.8% of participants) had variants in MECP2, of which 11 (39.2%) were interpreted as pathogenic/likely pathogenic (P/LP), thus confirming the diagnosis of RTT in them. Eight additional patients (28.5%) harbored ten variants in nine other genes. Four of these variants were interpreted as P/LP (14.2%) (GRIN2B, MADD, TRPM3 and ZEB2) resulting in alternative neurodevelopmental diagnoses, and six were considered of uncertain significance. No evident candidate variant was found for eight patients. Discussion: This study allowed to reach a diagnosis in half of the participants. The diagnosis of RTT was confirmed in over a third of them, while others were found to have alternative neurodevelopmental disorders. Further evaluation is needed to identify the cause in those with negative or uncertain results. This information is useful for the patients, families, and clinicians to guide clinical management, even more so since the development of novel therapies for RTT. We also show the feasibility of implementing a step-wide approach to genomic testing in a setting with limited resources.
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Affiliation(s)
- Florencia Brito
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Sciences and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Catalina Lagos
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Sciences and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | | | - Joan Orellana
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Sciences and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Mallen Gajardo
- Escuela de Ingeniería, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Daniela Böhme
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Sciences and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Biosoluciones-UDD, Santiago, Chile
| | | | - Gabriela M. Repetto
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Sciences and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
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Pramanik S, Bala A, Pradhan A. Zebrafish in understanding molecular pathophysiology, disease modeling, and developing effective treatments for Rett syndrome. J Gene Med 2024; 26:e3677. [PMID: 38380785 DOI: 10.1002/jgm.3677] [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: 11/14/2023] [Revised: 01/04/2024] [Accepted: 01/28/2024] [Indexed: 02/22/2024] Open
Abstract
Rett syndrome (RTT) is a rare but dreadful X-linked genetic disease that mainly affects young girls. It is a neurological disease that affects nerve cell development and function, resulting in severe motor and intellectual disabilities. To date, no cure is available for treating this disease. In 90% of the cases, RTT is caused by a mutation in methyl-CpG-binding protein 2 (MECP2), a transcription factor involved in the repression and activation of transcription. MECP2 is known to regulate several target genes and is involved in different physiological functions. Mouse models exhibit a broad range of phenotypes in recapitulating human RTT symptoms; however, understanding the disease mechanisms remains incomplete, and many potential RTT treatments developed in mouse models have not shown translational effectiveness in human trials. Recent data hint that the zebrafish model emulates similar disrupted neurological functions following mutation of the mecp2 gene. This suggests that zebrafish can be used to understand the onset and progression of RTT pathophysiology and develop a possible cure. In this review, we elaborate on the molecular basis of RTT pathophysiology in humans and model organisms, including rodents and zebrafish, focusing on the zebrafish model to understand the molecular pathophysiology and the development of therapeutic strategies for RTT. Finally, we propose a rational treatment strategy, including antisense oligonucleotides, small interfering RNA technology and induced pluripotent stem cell-derived cell therapy.
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Affiliation(s)
- Subrata Pramanik
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Asis Bala
- Pharmacology and Drug Discovery Research Laboratory, Division of Life Sciences; Institute of Advanced Study in Science and Technology (IASST), An Autonomous Institute Under - Department of Science & Technology (Govt. of India) Vigyan Path, Guwahati, Assam, India
| | - Ajay Pradhan
- Biology, The Life Science Center, School of Science and Technology, Örebro University, Örebro, Sweden
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Rong M, Benke T, Zulfiqar Ali Q, Aledo-Serrano Á, Bayat A, Rossi A, Devinsky O, Qaiser F, Ali AS, Fasano A, Bassett AS, Andrade DM. Adult Phenotype of SYNGAP1-DEE. Neurol Genet 2023; 9:e200105. [PMID: 38045990 PMCID: PMC10692795 DOI: 10.1212/nxg.0000000000200105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/20/2023] [Indexed: 12/05/2023]
Abstract
Background and Objectives SYNGAP1 variants are associated with rare developmental and epileptic encephalopathies (DEEs). Although SYNGAP1-related childhood phenotypes are well characterized, the adult phenotype remains ill-defined. We sought to investigate phenotypes and outcomes in adults with SYNGAP1 variants and epilepsy. Methods Patients 18 years or older with DEE carrying likely pathogenic and pathogenic (LP/P) SYNGAP1 variants were recruited through physicians' practices and patient organization groups. We used standardized questionnaires to evaluate current seizures, medication use, sleep, gastrointestinal symptoms, pain response, gait, social communication disorder and adaptive skills of patients. We also assessed caregiver burden. Results Fourteen unrelated adult patients (median: 21 years, range: 18-65 years) with SYNGAP1-DEE were identified, 11 with novel and 3 with known LP/P SYNGAP1 de novo variants. One patient with a partial exon 3 deletion had greater daily living skills and social skills than others with single-nucleotide variants. Ten of 14 (71%) patients had drug-resistant seizures, treated with a median of 2 antiseizure medications. All patients (100%) had abnormal pain processing. Sleep disturbances, social communication disorders, and aggressive/self-injurious behaviors were each reported in 86% of patients. Only half of adults could walk with minimal or no assistance. Toileting was normal in 29%, and 71% had constipation. No adult patients could read or understand verbal material at a sixth-grade level or higher. Aggressive/self-injurious behaviors were leading cause of caregiver burden. The oldest patient was aged 65 years; although nonambulant, she had walked independently when younger. Discussion Seventy-one percent of patients with SYNGAP1-DEEs continue to have seizures when adults. Nonseizure comorbidities, especially aggression and self-injurious behaviors, are major management challenges in adults with SYNGAP1-DEE. Only 50% of adults can ambulate with minimal or no assistance. Almost all adult patients depend on caregivers for many activities of daily living. Prompt diagnostic genetic testing of adults with DEE can inform clinical care and guide outcomes of precision therapies.
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Affiliation(s)
- Marlene Rong
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Tim Benke
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Quratulain Zulfiqar Ali
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Ángel Aledo-Serrano
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Allan Bayat
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Alessandra Rossi
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Orrin Devinsky
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Farah Qaiser
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Anum S Ali
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Alfonso Fasano
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Anne S Bassett
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
| | - Danielle M Andrade
- From the Institute of Medical Science (M.R.), University of Toronto; Adult Genetic Epilepsy (AGE) Program (M.R., Q.Z.A., F.Q., A.S.A., D.M.A.), Krembil Neurosciences Institute, Toronto Western Hospital, University Health Network, Ontario, Canada; Department of Pediatrics, Neurology, Pharmacology and Otolaryngology (T.B.), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora; Epilepsy and Neurogenetics Program (A.A.-S.), Neurology Department, Ruber Internacional Hospital, and Initiative for Neuroscience (INCE) Foundation, Madrid, Spain; Department of Drug Design and Pharmacology (A. Bayat), University of Copenhagen; Department for Genetics and Personalized Medicine (A. Bayat), Danish Epilepsy Centre, Dianalund; Institute for Regional Health Services (A. Bayat), University of Southern Denmark, Odense; Department of Epilepsy Genetics and Personalized Medicine (A.R.), Danish Epilepsy Centre, Dianalund, Denmark; Pediatric Clinic (A.R.), IRCCS San Matteo Hospital Foundation, University of Pavia, Italy; NYU Langone Epilepsy Center (O.D.), NY; Edmond J. Safra Program in Parkinson's Disease (A.F.), Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital; Division of Neurology (A.F.), University of Toronto; Krembil Brain Institute (A.F.); Clinical Genetics Research Program (A.S.B.), Centre for Addiction and Mental Health; The Dalglish Family 22q Clinic (A.S.B.), Toronto General Hospital, University Health Network; Department of Psychiatry (A.S.B.), University of Toronto; Toronto Congenital Cardiac Centre for Adults (A.S.B.), Division of Cardiology, Department of Medicine, and Department of Psychiatry, University Health Network; Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute (A.S.B.); Division of Neurology (D.M.A.), Department of Medicine, University of Toronto, Ontario, Canada
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Frankel E, Podder A, Sharifi M, Pillai R, Belnap N, Ramsey K, Dodson J, Venugopal P, Brzezinski M, Llaci L, Gerald B, Mills G, Sanchez-Castillo M, Balak CD, Szelinger S, Jepsen WM, Siniard AL, Richholt R, Naymik M, Schrauwen I, Craig DW, Piras IS, Huentelman MJ, Schork NJ, Narayanan V, Rangasamy S. Genetic and Protein Network Underlying the Convergence of Rett-Syndrome-like (RTT-L) Phenotype in Neurodevelopmental Disorders. Cells 2023; 12:1437. [PMID: 37408271 DOI: 10.3390/cells12101437] [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: 02/07/2023] [Revised: 04/20/2023] [Accepted: 04/29/2023] [Indexed: 07/07/2023] Open
Abstract
Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. A subset of patients who are recognized to have an overlapping neurological phenotype with RTT but are lacking a mutation in a gene that causes classical or atypical RTT can be described as having a 'Rett-syndrome-like phenotype (RTT-L). Here, we report eight patients from our cohort diagnosed as having RTT-L who carry mutations in genes unrelated to RTT. We annotated the list of genes associated with RTT-L from our patient cohort, considered them in the light of peer-reviewed articles on the genetics of RTT-L, and constructed an integrated protein-protein interaction network (PPIN) consisting of 2871 interactions connecting 2192 neighboring proteins among RTT- and RTT-L-associated genes. Functional enrichment analysis of RTT and RTT-L genes identified a number of intuitive biological processes. We also identified transcription factors (TFs) whose binding sites are common across the set of RTT and RTT-L genes and appear as important regulatory motifs for them. Investigation of the most significant over-represented pathway analysis suggests that HDAC1 and CHD4 likely play a central role in the interactome between RTT and RTT-L genes.
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Affiliation(s)
- Eric Frankel
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Avijit Podder
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Megan Sharifi
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Roshan Pillai
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Newell Belnap
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Julius Dodson
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Pooja Venugopal
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Molly Brzezinski
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Lorida Llaci
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Brittany Gerald
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Gabrielle Mills
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Meredith Sanchez-Castillo
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Chris D Balak
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Szabolcs Szelinger
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ryan Richholt
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Neurology, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90033, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Nicholas J Schork
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Vinodh Narayanan
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
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5
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Politano D, Gana S, Pezzotti E, Berardinelli A, Pasca L, Carmen Barbero V, Pichiecchio A, Maria Valente E, Errichiello E. A novel variant in NEUROD2 in a patient with Rett-like phenotype points to Glu130 codon as a mutational hotspot. Brain Dev 2023; 45:179-184. [PMID: 36446697 DOI: 10.1016/j.braindev.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/25/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND NEUROD2, encoding the neurogenic differentiation factor 2, is essential for neurodevelopment. To date, heterozygous missense variants in this gene have been identified in eight patients (from six unrelated families) with epileptic encephalopathy and developmental delay. CASE REPORT We describe a child with initial clinical suspicion of Rett/Rett-like syndrome, in whom exome sequencing detected a novel de novo variant (c.388G > A, p.Glu130Lys) in NEUROD2. Interestingly, a missense change affecting the same codon, c.388G > C (p.Glu130Gln), was previously identified in other two patients. CONCLUSIONS Our results suggest that Glu130 might represent a potential mutational hotspot of NEUROD2. Furthermore, the clinical findings (especially the absence of clinically overt seizures) strengthen the NEUROD2-phenotypic spectrum, implying that developmental delay may also manifest isolatedly. We suggest inclusion of NEUROD2-associated developmental and epileptic encephalopathies (DEEs) in the differential diagnosis of atypical Rett syndrome as well as gene panels related to autism spectrum disorder.
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Affiliation(s)
- Davide Politano
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Simone Gana
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Elena Pezzotti
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Angela Berardinelli
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia, Italy
| | - Ludovica Pasca
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy; Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Anna Pichiecchio
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy; Department of Neuroradiology, Advanced Imaging and Radiomics Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Enza Maria Valente
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Edoardo Errichiello
- Medical Genetics Unit, IRCCS Mondino Foundation, Pavia, Italy; Department of Molecular Medicine, University of Pavia, Pavia, Italy.
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6
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The Role of MEF2 Transcription Factor Family in Neuronal Survival and Degeneration. Int J Mol Sci 2023; 24:ijms24043120. [PMID: 36834528 PMCID: PMC9963821 DOI: 10.3390/ijms24043120] [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: 12/30/2022] [Revised: 01/15/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
The family of myocyte enhancer factor 2 (MEF2) transcription factors comprises four highly conserved members that play an important role in the nervous system. They appear in precisely defined time frames in the developing brain to turn on and turn off genes affecting growth, pruning and survival of neurons. MEF2s are known to dictate neuronal development, synaptic plasticity and restrict the number of synapses in the hippocampus, thus affecting learning and memory formation. In primary neurons, negative regulation of MEF2 activity by external stimuli or stress conditions is known to induce apoptosis, albeit the pro or antiapoptotic action of MEF2 depends on the neuronal maturation stage. By contrast, enhancement of MEF2 transcriptional activity protects neurons from apoptotic death both in vitro and in preclinical models of neurodegenerative diseases. A growing body of evidence places this transcription factor in the center of many neuropathologies associated with age-dependent neuronal dysfunctions or gradual but irreversible neuron loss. In this work, we discuss how the altered function of MEF2s during development and in adulthood affecting neuronal survival may be linked to neuropsychiatric disorders.
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7
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Comprehensive In Silico Functional Prediction Analysis of CDKL5 by Single Amino Acid Substitution in the Catalytic Domain. Int J Mol Sci 2022; 23:ijms232012281. [PMID: 36293137 PMCID: PMC9603577 DOI: 10.3390/ijms232012281] [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: 09/09/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Cyclin-dependent kinase-like 5 (CDKL5) is a serine/threonine protein kinase whose pathological mutations cause CDKL5 deficiency disorder. Most missense mutations are concentrated in the catalytic domain. Therefore, anticipating whether mutations in this region affect CDKL5 function is informative for clinical diagnosis. This study comprehensively predicted the pathogenicity of all 5700 missense substitutions in the catalytic domain of CDKL5 using in silico analysis and evaluating their accuracy. Each missense substitution was evaluated as “pathogenic” or “benign”. In silico tools PolyPhen-2 HumDiv mode/HumVar mode, PROVEAN, and SIFT were selected individually or in combination with one another to determine their performance using 36 previously reported mutations as a reference. Substitutions predicted as pathogenic were over 88.0% accurate using each of the three tools. The best performance score (accuracy, 97.2%; sensitivity, 100%; specificity, 66.7%; and Matthew’s correlation coefficient (MCC), 0.804) was achieved by combining PolyPhen-2 HumDiv, PolyPhen-2 HumVar, and PROVEAN. This provided comprehensive information that could accurately predict the pathogenicity of the disease, which might be used as an aid for clinical diagnosis.
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8
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Balamanikandan P, Bharathi SJ. A mathematical modelling to detect sickle cell anemia using Quantum graph theory and Aquila optimization classifier. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:10060-10077. [PMID: 36031983 DOI: 10.3934/mbe.2022470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recently genetic disorders are the most common reason for human fatality. Sickle Cell anemia is a monogenic disorder caused by A-to-T point mutations in the β-globin gene which produces abnormal hemoglobin S (Hgb S) that polymerizes at the state of deoxygenation thus resulting in the physical deformation or erythrocytes sickling. This shortens the expectancy of human life. Thus, the early diagnosis and identification of sickle cell will aid the people in recognizing signs and to take treatments. The manual identification is a time consuming one and might outcome in the misclassification of count as there is millions of red blood cells in one spell. So as to overcome this, data mining approaches like Quantum graph theory model and classifier is effective in detecting sickle cell anemia with high precision rate. The proposed work aims at presenting a mathematical modeling using Quantum graph theory to extract elasticity properties and to distinguish them as normal cells and sickle cell anemia (SCA) in red blood cells. Initially, input DNA sequence is taken and the elasticity property features are extracted by using Quantum graph theory model at which the formation of spanning tree is made followed by graph construction and Hemoglobin quantization. After which, the extracted properties are optimized using Aquila optimization and classified using cascaded Long Short-Term memory (LSTM) to attain the classified outcome of sickle cell and normal cells. Finally, the performance assessment is made and the outcomes attained in terms of accuracy, precision, sensitivity, specificity, and AUC are compared with existing classifier to validate the proposed system effectiveness.
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Affiliation(s)
- P Balamanikandan
- Department of Mathematics, Thiagarajar College of Engineering, Madurai, Tamilnadu, India
| | - S Jeya Bharathi
- Department of Mathematics, Thiagarajar College of Engineering, Madurai, Tamilnadu, India
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9
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Fernandez G, Yubero D, Palau F, Armstrong J. Molecular Modelling Hurdle in the Next-Generation Sequencing Era. Int J Mol Sci 2022; 23:ijms23137176. [PMID: 35806177 PMCID: PMC9266691 DOI: 10.3390/ijms23137176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
There are challenges in the genetic diagnosis of rare diseases, and pursuing an optimal strategy to identify the cause of the disease is one of the main objectives of any clinical genomics unit. A range of techniques are currently used to characterize the genomic variability within the human genome to detect causative variants of specific disorders. With the introduction of next-generation sequencing (NGS) in the clinical setting, geneticists can study single-nucleotide variants (SNVs) throughout the entire exome/genome. In turn, the number of variants to be evaluated per patient has increased significantly, and more information has to be processed and analyzed to determine a proper diagnosis. Roughly 50% of patients with a Mendelian genetic disorder are diagnosed using NGS, but a fair number of patients still suffer a diagnostic odyssey. Due to the inherent diversity of the human population, as more exomes or genomes are sequenced, variants of uncertain significance (VUSs) will increase exponentially. Thus, assigning relevance to a VUS (non-synonymous as well as synonymous) in an undiagnosed patient becomes crucial to assess the proper diagnosis. Multiple algorithms have been used to predict how a specific mutation might affect the protein’s function, but they are far from accurate enough to be conclusive. In this work, we highlight the difficulties of genomic variability determined by NGS that have arisen in diagnosing rare genetic diseases, and how molecular modelling has to be a key component to elucidate the relevance of a specific mutation in the protein’s loss of function or malfunction. We suggest that the creation of a multi-omics data model should improve the classification of pathogenicity for a significant amount of the detected genomic variability. Moreover, we argue how it should be incorporated systematically in the process of variant evaluation to be useful in the clinical setting and the diagnostic pipeline.
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Affiliation(s)
- Guerau Fernandez
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (G.F.); (F.P.); (J.A.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain
| | - Dèlia Yubero
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (G.F.); (F.P.); (J.A.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain
- Correspondence: ; Tel.: +34-93-600-9451; Fax: +34-93-600-9760
| | - Francesc Palau
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (G.F.); (F.P.); (J.A.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain
- Division of Pediatrics, University of Barcelona School of Medicine and Health Sciences, 08007 Barcelona, Spain
| | - Judith Armstrong
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (G.F.); (F.P.); (J.A.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain
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10
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Cali E, Rocca C, Salpietro V, Houlden H. Epileptic Phenotypes Associated With SNAREs and Related Synaptic Vesicle Exocytosis Machinery. Front Neurol 2022; 12:806506. [PMID: 35095745 PMCID: PMC8792400 DOI: 10.3389/fneur.2021.806506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 11/16/2021] [Indexed: 01/29/2023] Open
Abstract
SNAREs (soluble N-ethylmaleimide sensitive factor attachment protein receptor) are an heterogeneous family of proteins that, together with their key regulators, are implicated in synaptic vesicle exocytosis and synaptic transmission. SNAREs represent the core component of this protein complex. Although the specific mechanisms of the SNARE machinery is still not completely uncovered, studies in recent years have provided a clearer understanding of the interactions regulating the essential fusion machinery for neurotransmitter release. Mutations in genes encoding SNARE proteins or SNARE complex associated proteins have been associated with a variable spectrum of neurological conditions that have been recently defined as “SNAREopathies.” These include neurodevelopmental disorder, autism spectrum disorder (ASD), movement disorders, seizures and epileptiform abnormalities. The SNARE phenotypic spectrum associated with seizures ranges from simple febrile seizures and infantile spasms, to severe early-onset epileptic encephalopathies. Our study aims to review and delineate the epileptic phenotypes associated with dysregulation of synaptic vesicle exocytosis and transmission, focusing on the main proteins of the SNARE core complex (STX1B, VAMP2, SNAP25), tethering complex (STXBP1), and related downstream regulators.
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Affiliation(s)
- Elisa Cali
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Clarissa Rocca
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Vincenzo Salpietro
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Henry Houlden
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
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11
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Zhang Z, Zhao Y. Progress on the roles of MEF2C in neuropsychiatric diseases. Mol Brain 2022; 15:8. [PMID: 34991657 PMCID: PMC8740500 DOI: 10.1186/s13041-021-00892-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/23/2021] [Indexed: 12/15/2022] Open
Abstract
Myocyte Enhancer Factor 2 C (MEF2C), one of the transcription factors of the MADS-BOX family, is involved in embryonic brain development, neuronal formation and differentiation, as well as in the growth and pruning of axons and dendrites. MEF2C is also involved in the development of various neuropsychiatric disorders, such as autism spectrum disorders (ASD), epilepsy, schizophrenia and Alzheimer’s disease (AD). Here, we review the relationship between MEF2C and neuropsychiatric disorders, and provide further insights into the mechanism of these diseases.
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Affiliation(s)
- Zhikun Zhang
- National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.,Department of Mental Health, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, Guangxi, China
| | - Yongxiang Zhao
- National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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12
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Technological Improvements in the Genetic Diagnosis of Rett Syndrome Spectrum Disorders. Int J Mol Sci 2021; 22:ijms221910375. [PMID: 34638716 PMCID: PMC8508637 DOI: 10.3390/ijms221910375] [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: 07/30/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Rett syndrome (RTT) is a severe neurodevelopmental disorder that constitutes the second most common cause of intellectual disability in females worldwide. In the past few years, the advancements in genetic diagnosis brought by next generation sequencing (NGS), have made it possible to identify more than 90 causative genes for RTT and significantly overlapping phenotypes (RTT spectrum disorders). Therefore, the clinical entity known as RTT is evolving towards a spectrum of overlapping phenotypes with great genetic heterogeneity. Hence, simultaneous multiple gene testing and thorough phenotypic characterization are mandatory to achieve a fast and accurate genetic diagnosis. In this review, we revise the evolution of the diagnostic process of RTT spectrum disorders in the past decades, and we discuss the effectiveness of state-of-the-art genetic testing options, such as clinical exome sequencing and whole exome sequencing. Moreover, we introduce recent technological advancements that will very soon contribute to the increase in diagnostic yield in patients with RTT spectrum disorders. Techniques such as whole genome sequencing, integration of data from several “omics”, and mosaicism assessment will provide the tools for the detection and interpretation of genomic variants that will not only increase the diagnostic yield but also widen knowledge about the pathophysiology of these disorders.
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13
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Pascual-Alonso A, Martínez-Monseny AF, Xiol C, Armstrong J. MECP2-Related Disorders in Males. Int J Mol Sci 2021; 22:9610. [PMID: 34502518 PMCID: PMC8431762 DOI: 10.3390/ijms22179610] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 12/23/2022] Open
Abstract
Methyl CpG binding protein 2 (MECP2) is located at Xq28 and is a multifunctional gene with ubiquitous expression. Loss-of-function mutations in MECP2 are associated with Rett syndrome (RTT), which is a well-characterized disorder that affects mainly females. In boys, however, mutations in MECP2 can generate a wide spectrum of clinical presentations that range from mild intellectual impairment to severe neonatal encephalopathy and premature death. Thus, males can be more difficult to classify and diagnose than classical RTT females. In addition, there are some variants of unknown significance in MECP2, which further complicate the diagnosis of these children. Conversely, the entire duplication of the MECP2 gene is related to MECP2 duplication syndrome (MDS). Unlike in RTT, in MDS, males are predominantly affected. Usually, the duplication is inherited from an apparently asymptomatic carrier mother. Both syndromes share some characteristics, but also differ in some aspects regarding the clinical picture and evolution. In the following review, we present a thorough description of the different types of MECP2 variants and alterations that can be found in males, and explore several genotype-phenotype correlations, although there is still a lot to understand.
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Affiliation(s)
- Ainhoa Pascual-Alonso
- Fundació Per la Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (A.P.-A.); (C.X.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Antonio F. Martínez-Monseny
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
- Clinical Genetics, Molecular and Genetic Medicine Section, Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Clara Xiol
- Fundació Per la Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (A.P.-A.); (C.X.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Judith Armstrong
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
- Clinical Genetics, Molecular and Genetic Medicine Section, Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
- CIBER-ER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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14
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Saikia SJ, Nirmala SR. Identification of disease genes and assessment of eye-related diseases caused by disease genes using JMFC and GDLNN. Comput Methods Biomech Biomed Engin 2021; 25:359-370. [PMID: 34384296 DOI: 10.1080/10255842.2021.1955358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Early detection of disease genes helps humans to recover from certain gene-related diseases, like genetic eye diseases. This work identifies the possibility of eye diseasesfor the disease genes utilizing a Gaussian-activation function (G)-centric deeplearning neural network (GDLNN) model. In this work, human genes are selected by computing structural similarity and genes are clustered as disease genesand normal genes by using the JMFC clustering algorithm. Levy flight and Crossover and Mutation (LCM) centric Chicken Swarm Optimization (LCM-CSO) is employed for feature selection and GDLNN classifies the eye-related diseases for the input genes using the selected features.
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Affiliation(s)
- Samar Jyoti Saikia
- Department of Electronics and Communication Engineering, Gauhati University, Guwahati, Assam, India.,Department of Electronics and Communication Engineering, Assam Don Bosco University, Guwahati, Assam, India
| | - S R Nirmala
- Department of Electronics and Communication Engineering, Gauhati University, Guwahati, Assam, India.,School of Electronics and Communication Engineering, KLE Technological University, Hubli, Karnataka, India
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15
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Cooley Coleman JA, Sarasua SM, Boccuto L, Moore HW, Skinner SA, DeLuca JM. Comprehensive investigation of the phenotype of MEF2C-related disorders in human patients: A systematic review. Am J Med Genet A 2021; 185:3884-3894. [PMID: 34184825 DOI: 10.1002/ajmg.a.62412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/31/2022]
Abstract
MEF2C-related disorders (aka MEF2C-haploinsufficiency) are caused by variations in or involving the MEF2C gene and are characterized by intellectual disability, developmental delay, lack of speech, limited walking, and seizures. Despite these findings, the disorder is not easily recognized clinically. We performed a systematic review following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to assemble the most comprehensive list of patients and their phenotypes. Through searching PubMed, Web of Science, and MEDLINE, 43 articles met the inclusion criteria and were fully reviewed. One hundred and seventeen patients were identified from these publications with most having a phenotype of intellectual disability, developmental delay, seizures, hypotonia, absent speech, inability to walk, stereotypic movements, and MRI abnormalities. Nonclassical findings included one patient with a question mark ear, two patients with a jugular pit, one patient with a unique neuroendocrine finding, and nine patients that did not have MEF2C deletions or disruptions but may be affected due to a positional effect on MEF2C. This systematic review characterizes the phenotype of MEF2C-related disorders, documents the severity of this condition, and will help providers to better diagnose and care for patients and their families. Additionally, this compiled information provides a comprehensive resource for investigators interested in pursuing specific genotype-phenotype correlations.
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Affiliation(s)
- Jessica A Cooley Coleman
- School of Nursing, Clemson University, Clemson, South Carolina, USA.,Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Sara M Sarasua
- School of Nursing, Clemson University, Clemson, South Carolina, USA
| | - Luigi Boccuto
- School of Nursing, Clemson University, Clemson, South Carolina, USA
| | | | | | - Jane M DeLuca
- School of Nursing, Clemson University, Clemson, South Carolina, USA.,Greenwood Genetic Center, Greenwood, South Carolina, USA
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16
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Fontana A, Consentino MC, Motta M, Costanza G, Lo Bianco M, Marino S, Falsaperla R, Praticò AD. Syntaxin Binding Protein 1 Related Epilepsies. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1727259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractSyntaxin binding protein 1 (STXBP1), commonly known as MUNC18–1, is a member of SEC1 family membrane trafficking proteins; their function consists in controlling the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex assembly, making them essentials regulators of vesicle fusion. The precise function and molecular mechanism through which Munc18–1 contributes to neurotransmitter releasing is not entirely understood, but several evidences suggest its probable role in exocytosis. In 2008, heterozygous de novo mutations in neuronal protein Munc18–1 were first referred as a cause of Ohtahara syndrome development. Currently, a wide examination of the published data proved that 3.1% of patients with severe epilepsy carry a pathogenic de novo mutation including STXBP1 and approximately 10.2% of early onset epileptic encephalopathy is due to an aberrant STXBP1 form codified by the mutated gene. STXBP1 mutations can be associated to a wide clinical heterogeneity. All affected individuals show developmental delay and approximately the 95% of cases have seizures and early onset epileptic encephalopathy, characterized by infantile spasms as the main consistent feature. Burst suppression pattern and hypsarrhythmia are the most frequent EEG anomalies. Other neuronal disorders include Rett syndrome and behavioral and movement disorders. Mild dysmorphic features have been detected in a small number of cases. No genotype–phenotype correlation has been reported. Management of STXBP1 encephalopathy requires a multidisciplinary approach, including epilepsy control and neurological rehabilitation. About 25% of patients are refractory to standard therapy. A single or combined antiepileptic drugs may be required. Several studies described vigabatrin, valproic acid, levetiracetam, topiramate, clobazam, and oxcarbazepine as effective in seizure control. Lamotrigine, zonisamide, and phenobarbital are also commonly used. To date, it remains unclear which therapy is the most effective. Severe morbidity and high mortality are inevitable consequences in some of these patients.
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Affiliation(s)
- Alessandra Fontana
- Pediatrics Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Maria Chiara Consentino
- Pediatrics Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Milena Motta
- Pediatrics Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Giuseppe Costanza
- Pediatrics Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Manuela Lo Bianco
- Pediatrics Postgraduate Residency Program, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Simona Marino
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Andrea D. Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
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17
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MECP2-Related Disorders and Epilepsy Phenotypes. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1728643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
MECP2 (methyl-CpG binding protein-2) gene, located on chromosome Xq28, encodes for a protein particularly abundant in the brain that is required for maturation of astrocytes and neurons and is developmentally regulated. A defective homeostasis of MECP2 expression, either by haploinsufficiency or overexpression, leads to a neurodevelopmental phenotype. As MECP2 is located on chromosome X, the clinical presentation varies in males and females ranging from mild learning disabilities to severe encephalopathies and early death. Typical Rett syndrome (RTT), the most frequent phenotype associated with MECP2 mutations, primarily affects girls and it was previously thought to be lethal in males; however, MECP2 duplication syndrome, resulting from a duplication of the Xq28 region including MECP2, leads to a severe neurodevelopmental disorder in males. RTT and MECP2 duplication syndrome share overlapping clinical phenotypes including intellectual disabilities, motor deficits, hypotonia, progressive spasticity, and epilepsy. In this manuscript we reviewed literature on epilepsy related to MECP2 disorders, focusing on clinical presentation, genotype–phenotype correlation, and treatment.
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18
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Praticò AD, Giallongo A, Arrabito M, D'Amico S, Gauci MC, Lombardo G, Polizzi A, Falsaperla R, Ruggieri M. SCN2A and Its Related Epileptic Phenotypes. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1727097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractEpilepsies due to SCN2A mutations can present with a broad range of phenotypes that are still not fully understood. Clinical characteristics of SNC2A-related epilepsy may vary from neonatal benign epilepsy to early-onset epileptic encephalopathy, including Ohtahara syndrome and West syndrome, and epileptic encephalopathies occurring at later ages (usually within the first 10 years of life). Some patient may present with intellectual disability and/or autism or movement disorders and without epilepsy. The heterogeneity of the phenotypes associated to such genetic mutations does not always allow the clinician to address his suspect on this gene. For this reason, diagnosis is usually made after a multiple gene panel examination through next generation sequencing (NGS) or after whole exome sequencing (WES) or whole genome sequencing (WGS). Subsequently, confirmation by Sanger sequencing can be obtained. Mutations in SCN2A are inherited as an autosomal dominant trait. Most individuals diagnosed with SCN2A–benign familial neonatal-infantile seizures (BFNIS) have an affected parent; however, hypothetically, a child may present SCN2A-BNFNIS as the result of a de novo pathogenic variant. Almost all individuals with SCN2A and severe epileptic encephalopathies have a de novo pathogenic variant. SNC2A-related epilepsies have not shown a clear genotype–phenotype correlation; in some cases, a same variant may lead to different presentations even within the same family and this could be due to other genetic factors or to environmental causes. There is no “standardized” treatment for SCN2A-related epilepsy, as it varies in relation to the clinical presentation and the phenotype of the patient, according to its own gene mutation. Treatment is based mainly on antiepileptic drugs, which include classic wide-spectrum drugs, such as valproic acid, levetiracetam, and lamotrigine. However, specific agents, which act directly modulating the sodium channels activity (phenytoin, carbamazepine, oxcarbamazepine, lamotrigine, and zonisamide), have shown positive result, as other sodium channel blockers (lidocaine and mexiletine) or even other drugs with different targets (phenobarbital).
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Affiliation(s)
- Andrea D. Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Alessandro Giallongo
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Marta Arrabito
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Silvia D'Amico
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Maria Cristina Gauci
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
| | - Giulia Lombardo
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Agata Polizzi
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
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19
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Currò A, Doddato G, Bruttini M, Zollino M, Marangi G, Zappella M, Renieri A, Pinto AM. CDKL5 mutations may mimic Pitt-Hopkins syndrome phenotype. Eur J Med Genet 2020; 64:104102. [PMID: 33220470 DOI: 10.1016/j.ejmg.2020.104102] [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: 06/19/2020] [Revised: 10/30/2020] [Accepted: 11/08/2020] [Indexed: 11/28/2022]
Abstract
Genetic conditions comprise a wide spectrum of different phenotypes, rapidly expanding due to new diagnostic methodologies. Patients' facial features and clinical history represent the key elements leading clinicians to the right diagnosis. CDKL5-early onset epilepsy and Pitt-Hopkins syndrome are two well-known genetic conditions, with a defined phenotype sharing some common characteristics like early-onset epilepsy and hyperventilation episodes. Whilst facial features represent a diagnostic handle in patients with Pitt-Hopkins syndrome, clinical history is crucial in patients carrying a mutation in CDKL5. Here we present the clinical case of a girl evaluated for the first time when she was 24-years old, with a clinical phenotype mimicking Pitt-Hopkins syndrome. Her facial features have become coarser while she was growing up, leading geneticists to raise different clinical hypotheses and to perform several molecular tests before getting the diagnosis of CDKL5-early-epileptic encephalopathy. This finding highlights that although typical facial gestalt has not so far extensively been described in CDKL5 mutated adult patients, peculiar facial features could be present later in life and may let CDKL5-related disorder mimic Pitt Hopkins. Thus, considering atypical Rett syndrome in the differential diagnosis of Pitt Hopkins syndrome could be important to solve complex clinical cases.
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Affiliation(s)
- Aurora Currò
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Gabriella Doddato
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Marcella Zollino
- Università Cattolica del Sacro Cuore, Facoltà di Medicina e Chirurgia, Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Roma, Italy; Fondazione Policlinico Universitario A. Gemelli IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologico, Unità di Genetica Medica, Roma, Italy
| | - Giuseppe Marangi
- Università Cattolica del Sacro Cuore, Facoltà di Medicina e Chirurgia, Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Roma, Italy; Fondazione Policlinico Universitario A. Gemelli IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologico, Unità di Genetica Medica, Roma, Italy
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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20
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Mastrangelo M, Manti F, Giannini MT, Guerrini R, Leuzzi V. KCNQ2 encephalopathy manifesting with Rett-like features: A follow-up into adulthood. NEUROLOGY-GENETICS 2020; 6:e510. [PMID: 33134511 PMCID: PMC7577543 DOI: 10.1212/nxg.0000000000000510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/20/2020] [Indexed: 01/28/2023]
Affiliation(s)
- Mario Mastrangelo
- Child Neurology and Psychiatry Unit (M.M., F.M., M.T.G., V.L.), Department of Human Neuroscience, Sapienza University of Rome, Italy; and Neuroscience and Neurogenetics Excellence Centre (R.G.), Anna Meyer Children's Hospital, Florence, Italy
| | - Filippo Manti
- Child Neurology and Psychiatry Unit (M.M., F.M., M.T.G., V.L.), Department of Human Neuroscience, Sapienza University of Rome, Italy; and Neuroscience and Neurogenetics Excellence Centre (R.G.), Anna Meyer Children's Hospital, Florence, Italy
| | - Maria Teresa Giannini
- Child Neurology and Psychiatry Unit (M.M., F.M., M.T.G., V.L.), Department of Human Neuroscience, Sapienza University of Rome, Italy; and Neuroscience and Neurogenetics Excellence Centre (R.G.), Anna Meyer Children's Hospital, Florence, Italy
| | - Renzo Guerrini
- Child Neurology and Psychiatry Unit (M.M., F.M., M.T.G., V.L.), Department of Human Neuroscience, Sapienza University of Rome, Italy; and Neuroscience and Neurogenetics Excellence Centre (R.G.), Anna Meyer Children's Hospital, Florence, Italy
| | - Vincenzo Leuzzi
- Child Neurology and Psychiatry Unit (M.M., F.M., M.T.G., V.L.), Department of Human Neuroscience, Sapienza University of Rome, Italy; and Neuroscience and Neurogenetics Excellence Centre (R.G.), Anna Meyer Children's Hospital, Florence, Italy
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21
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Sandweiss AJ, Brandt VL, Zoghbi HY. Advances in understanding of Rett syndrome and MECP2 duplication syndrome: prospects for future therapies. Lancet Neurol 2020; 19:689-698. [PMID: 32702338 DOI: 10.1016/s1474-4422(20)30217-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 01/07/2023]
Abstract
The X-linked gene encoding MECP2 is involved in two severe and complex neurodevelopmental disorders. Loss of function of the MeCP2 protein underlies Rett syndrome, whereas duplications of the MECP2 locus cause MECP2 duplication syndrome. Research on the mechanisms by which MeCP2 exerts effects on gene expression in neurons, studies of animal models bearing different disease-causing mutations, and more in-depth observations of clinical presentations have clarified some issues even as they have raised further questions. Yet there is enough evidence so far to suggest possible approaches to therapy for these two diseases that could go beyond attempting to address specific signs and symptoms (of which there are many) and instead target the pathophysiology underlying MECP2 disorders. Further work could bring antisense oligonucleotides, deep brain stimulation, and gene therapy into the clinic within the next decade or so.
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Affiliation(s)
- Alexander J Sandweiss
- Department of Pediatrics, Section of Neurology and Developmental Neurosciences, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Vicky L Brandt
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Huda Y Zoghbi
- Department of Pediatrics, Section of Neurology and Developmental Neurosciences, Baylor College of Medicine, Houston, TX, USA; Howard Hughes Medical Institute, and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.
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22
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Kaur S, Van Bergen NJ, Verhey KJ, Nowell CJ, Budaitis B, Yue Y, Ellaway C, Brunetti-Pierri N, Cappuccio G, Bruno I, Boyle L, Nigro V, Torella A, Roscioli T, Cowley MJ, Massey S, Sonawane R, Burton MD, Schonewolf-Greulich B, Tümer Z, Chung WK, Gold WA, Christodoulou J. Expansion of the phenotypic spectrum of de novo missense variants in kinesin family member 1A (KIF1A). Hum Mutat 2020; 41:1761-1774. [PMID: 32652677 DOI: 10.1002/humu.24079] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Defects in the motor domain of kinesin family member 1A (KIF1A), a neuron-specific ATP-dependent anterograde axonal transporter of synaptic cargo, are well-recognized to cause a spectrum of neurological conditions, commonly known as KIF1A-associated neurological disorders (KAND). Here, we report one mutation-negative female with classic Rett syndrome (RTT) harboring a de novo heterozygous novel variant [NP_001230937.1:p.(Asp248Glu)] in the highly conserved motor domain of KIF1A. In addition, three individuals with severe neurodevelopmental disorder along with clinical features overlapping with KAND are also reported carrying de novo heterozygous novel [NP_001230937.1:p.(Cys92Arg) and p.(Pro305Leu)] or previously reported [NP_001230937.1:p.(Thr99Met)] variants in KIF1A. In silico tools predicted these variants to be likely pathogenic, and 3D molecular modeling predicted defective ATP hydrolysis and/or microtubule binding. Using the neurite tip accumulation assay, we demonstrated that all novel KIF1A variants significantly reduced the ability of the motor domain of KIF1A to accumulate along the neurite lengths of differentiated SH-SY5Y cells. In vitro microtubule gliding assays showed significantly reduced velocities for the variant p.(Asp248Glu) and reduced microtubule binding for the p.(Cys92Arg) and p.(Pro305Leu) variants, suggesting a decreased ability of KIF1A to move along microtubules. Thus, this study further expanded the phenotypic characteristics of KAND individuals with pathogenic variants in the KIF1A motor domain to include clinical features commonly seen in RTT individuals.
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Affiliation(s)
- Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Cameron J Nowell
- Drug Discover Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Breane Budaitis
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Carolyn Ellaway
- Discipline of Genomic Medicine, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Western Sydney Genetics Program, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Irene Bruno
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Lia Boyle
- Division of Molecular Genetics, Columbia University Irving Medical Center, New York, New York
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Tony Roscioli
- New South Wales Health Pathology, Randwick, New South Wales, Australia.,Neuroscience Research Australia, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia.,Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, New South Wales, Australia
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Rhea Sonawane
- Faculty of Science, Engineering and Built Environment, Deakin University, Melbourne, Australia
| | - Matthew D Burton
- Flow Cytometry and Imaging Facility, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Bitten Schonewolf-Greulich
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Wendy K Chung
- Departments of Paediatrics and Medicine, Columbia University Medical Center, New York, New York
| | - Wendy A Gold
- Molecular Neurobiology Research Laboratory, Kids Research, Children's Hospital at Westmead, and The Children's Medical Research Institute, Westmead, New South Wales, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia.,School of Medical Sciences and Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Discipline of Genomic Medicine, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
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23
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Cyclin-Dependent Kinase-Like 5 (CDKL5): Possible Cellular Signalling Targets and Involvement in CDKL5 Deficiency Disorder. Neural Plast 2020; 2020:6970190. [PMID: 32587608 PMCID: PMC7293752 DOI: 10.1155/2020/6970190] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/29/2022] Open
Abstract
Cyclin-dependent kinase-like 5 (CDKL5, also known as STK9) is a serine/threonine protein kinase originally identified in 1998 during a transcriptional mapping project of the human X chromosome. Thereafter, a mutation in CDKL5 was reported in individuals with the atypical Rett syndrome, a neurodevelopmental disorder, suggesting that CDKL5 plays an important regulatory role in neuronal function. The disease associated with CDKL5 mutation has recently been recognised as CDKL5 deficiency disorder (CDD) and has been distinguished from the Rett syndrome owing to its symptomatic manifestation. Because CDKL5 mutations identified in patients with CDD cause enzymatic loss of function, CDKL5 catalytic activity is likely strongly associated with the disease. Consequently, the exploration of CDKL5 substrate characteristics and regulatory mechanisms of its catalytic activity are important for identifying therapeutic target molecules and developing new treatment. In this review, we summarise recent findings on the phosphorylation of CDKL5 substrates and the mechanisms of CDKL5 phosphorylation and dephosphorylation. We also discuss the relationship between changes in the phosphorylation signalling pathways and the Cdkl5 knockout mouse phenotype and consider future prospects for the treatment of mental and neurological disease associated with CDKL5 mutations.
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24
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Vidal S, Xiol C, Pascual-Alonso A, O'Callaghan M, Pineda M, Armstrong J. Genetic Landscape of Rett Syndrome Spectrum: Improvements and Challenges. Int J Mol Sci 2019; 20:ijms20163925. [PMID: 31409060 PMCID: PMC6719047 DOI: 10.3390/ijms20163925] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/08/2019] [Accepted: 08/10/2019] [Indexed: 02/06/2023] Open
Abstract
Rett syndrome (RTT) is an early-onset neurodevelopmental disorder that primarily affects females, resulting in severe cognitive and physical disabilities, and is one of the most prevalent causes of intellectual disability in females. More than fifty years after the first publication on Rett syndrome, and almost two decades since the first report linking RTT to the MECP2 gene, the research community's effort is focused on obtaining a better understanding of the genetics and the complex biology of RTT and Rett-like phenotypes without MECP2 mutations. Herein, we review the current molecular genetic studies, which investigate the genetic causes of RTT or Rett-like phenotypes which overlap with other genetic disorders and document the swift evolution of the techniques and methodologies employed. This review also underlines the clinical and genetic heterogeneity of the Rett syndrome spectrum and provides an overview of the RTT-related genes described to date, many of which are involved in epigenetic gene regulation, neurotransmitter action or RNA transcription/translation. Finally, it discusses the importance of including both phenotypic and genetic diagnosis to provide proper genetic counselling from a patient's perspective and the appropriate treatment.
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Affiliation(s)
- Silvia Vidal
- Sant Joan de Déu Research Foundation, 08950 Barcelona, Spain
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Clara Xiol
- Sant Joan de Déu Research Foundation, 08950 Barcelona, Spain
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Ainhoa Pascual-Alonso
- Sant Joan de Déu Research Foundation, 08950 Barcelona, Spain
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - M O'Callaghan
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain
- Neurology Service, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
- CIBER-ER (Biomedical Network Research Center for Rare Diseases), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Mercè Pineda
- Sant Joan de Déu Research Foundation, 08950 Barcelona, Spain
| | - Judith Armstrong
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, 08950 Barcelona, Spain.
- CIBER-ER (Biomedical Network Research Center for Rare Diseases), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain.
- Molecular and Genetics Medicine Section, Hospital Sant Joan de Déu, 08950 Barcelona, Spain.
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