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Gottschalk I, Kölsch U, Wagner DL, Kath J, Martini S, Krüger R, Puel A, Casanova JL, Jezela-Stanek A, Rossi R, Chehadeh SE, Van Esch H, von Bernuth H. IRAK1 Duplication in MECP2 Duplication Syndrome Does Not Increase Canonical NF-κB-Induced Inflammation. J Clin Immunol 2023; 43:421-439. [PMID: 36319802 PMCID: PMC9628328 DOI: 10.1007/s10875-022-01390-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/20/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Besides their developmental and neurological phenotype, most patients with MECP2/IRAK1 duplication syndrome present with recurrent and severe infections, accompanied by strong inflammation. Respiratory infections are the most common cause of death. Standardized pneumological diagnostics, targeted anti-infectious treatment, and knowledge of the underlying pathomechanism that triggers strong inflammation are unmet clinical needs. We investigated the influence of IRAK1 overexpression on the canonical NF-κB signaling as a possible cause for excessive inflammation in these patients. METHODS NF-κB signaling was examined by measuring the production of proinflammatory cytokines and evaluating the IRAK1 phosphorylation and degradation as well as the IκBα degradation upon stimulation with IL-1β and TLR agonists in SV40-immortalized fibroblasts, PBMCs, and whole blood of 9 patients with MECP2/IRAK1 duplication syndrome, respectively. RESULTS Both, MECP2/IRAK1-duplicated patients and healthy controls, showed similar production of IL-6 and IL-8 upon activation with IL-1β and TLR2/6 agonists in immortalized fibroblasts. In PBMCs and whole blood, both patients and controls had a similar response of cytokine production after stimulation with IL-1β and TLR4/2/6 agonists. Patients and controls had equivalent patterns of IRAK1 phosphorylation and degradation as well as IκBα degradation upon stimulation with IL-1β. CONCLUSION Patients with MECP2/IRAK1 duplication syndrome do not show increased canonical NF-κB signaling in immortalized fibroblasts, PBMCs, and whole blood. Therefore, we assume that these patients do not benefit from a therapeutic suppression of this pathway.
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Affiliation(s)
- Ilona Gottschalk
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Uwe Kölsch
- Labor Berlin GmbH, Department of Immunology, Berlin, Germany
| | - Dimitrios L Wagner
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität, Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Institute of Transfusion Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Campus Virchow-Klinikum, Berlin, Germany
| | - Jonas Kath
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität, Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Stefania Martini
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Renate Krüger
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris, Paris, France
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Rainer Rossi
- Childrens' Hospital Neukölln, Vivantes GmbH, Berlin, Germany
| | | | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Louvain, Belgium
| | - Horst von Bernuth
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
- Labor Berlin GmbH, Department of Immunology, Berlin, Germany.
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Wang X, Junqing L, Huang T. CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data. Comput Biol Chem 2022; 99:107720. [DOI: 10.1016/j.compbiolchem.2022.107720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/03/2022]
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Salinas V, Martínez N, Maturo JP, Rodriguez-Quiroga SA, Zavala L, Medina N, Amartino H, Sfaello I, Agosta G, Serafín EM, Morón DG, Kauffman MA, Vega P. Clinical next generation sequencing in developmental and epileptic encephalopathies: Diagnostic relevance of data re-analysis and variants re-interpretation. Eur J Med Genet 2021; 64:104363. [PMID: 34673242 DOI: 10.1016/j.ejmg.2021.104363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 09/24/2021] [Accepted: 10/08/2021] [Indexed: 11/26/2022]
Abstract
Developmental and epileptic encephalopathies (DEE) are complex pediatric epilepsies, in which heterogeneous pathogenic factors play an important role. Next-generation-sequencing based tools have shown excellent effectiveness. The constant increase in the number of new genotype-phenotype associations suggests the periodic need for re-interpretation and re-analysis of genetic studies without positive results. In this study, we report the diagnostic utility of targeted gene panel sequencing and whole exome sequencing in 55 Argentine subjects with DEE, focusing on the utility of re-interpretation and re-analysis of undetermined and negative genetic diagnoses. The new information in biomedical literature and databases was used for the re-interpretation. For re-analysis, sequencing data processing was repeated using updated bioinformatics tools. Initially, pathogenic variants were detected in 21 subjects (38%). After an average time of 29 months, 25% of the subjects without a genetic diagnosis were re-categorized as diagnosed. Finally, the overall diagnostic yield increased to 53% (29 subjects). In consequence of the re-interpretation and re-analysis, we identified novel variants in the genes: CHD2, COL4A1, FOXG1, GABRA1, GRIN2B, HNRNPU, KCNQ2, MECP2, PCDH19, SCN1A, SCN2A, SCN8A, SLC6A1, STXBP1 and WWOX. Our results expand the diagnostic yield of this subgroup of infantile and childhood seizures and demonstrate the importance of re-evaluation of genetic tests in subjects without an identified causative etiology.
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Affiliation(s)
- Valeria Salinas
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | - Nerina Martínez
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Josefina Pérez Maturo
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | | | - Lucia Zavala
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Nancy Medina
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Hernán Amartino
- Paediatric Neurology Unit, Hospital Universitario Austral, Buenos Aires, Argentina.
| | - Ignacio Sfaello
- CETES, Instituto de Neurología Infanto-Juvenil, Córdoba, Argentina.
| | - Guillermo Agosta
- Paediatric Neurology Unit, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina.
| | | | | | - Marcelo A Kauffman
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | - Patricia Vega
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
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Albuz B, Ozdemir O, Silan F. The high frequency of chromosomal copy number variations and candidate genes in epilepsy patients. Clin Neurol Neurosurg 2021; 202:106487. [PMID: 33484953 DOI: 10.1016/j.clineuro.2021.106487] [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: 07/09/2020] [Revised: 11/29/2020] [Accepted: 01/07/2021] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Epilepsy is a chronic brain disease and is estimated to affect more than 50 million people worldwide.Epilepsy is a polygenic and multifactorial disease.Genetic causes play a major role in 40-60 % of all epilepsies.Copy number variations(CNVs) have been reported in approximately 5-12 % of patients with different types of epilepsy.Here we aimed to determine the diagnostic yield of the aCGH in epilepsy and to reveal new candidate genes and CNVs by analyzing aCGH data retrospectively. METHODS The clinical data of 80 patients with the diagnosis of epilepsy were examined retrospectively and the raw data of aCGH of these patients were reanalyzed in the light of current literature. RESULTS Pathogenic/likely pathogenic CNVs were detected in 14 of 80 patients and 12 of these CNVs (15 %) were associated with epilepsy phenotype. In addition, 18 CNVs in 16 different chromosomal loci that were evaluated as the variant of unknown clinical significance(VOUS). In four cases (5%), CNVs associated with epilepsy were less than 100 kb and these accounted for 13.3 % of all epilepsy associated CNVs. CONCLUSION The diagnostic yield of aCGH in epilepsy patients was found to be higher than most studies in the literature. MACROD2,ADGRB3(BAI3),SOX8,HIP1,PARK2 and TAFA2 genes were evaluated as potential epilepsy-related genes and NEDD9,RASAL2 and TNR genes thought to be the candidate genes for epilepsy. Our study showed that the diagnostic efficiency of aCGH in epilepsy is high and with more comprehensive studies, it will contribute to the elucidation of genes involved in genetic etiology in epilepsy patients.
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Affiliation(s)
- Burcu Albuz
- Department of Medical Genetics, Faculty of Medicine, Canakkale Onsekiz Mart University, 17020, Canakkale, Turkey.
| | - Ozturk Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Canakkale Onsekiz Mart University, 17020, Canakkale, Turkey.
| | - Fatma Silan
- Department of Medical Genetics, Faculty of Medicine, Canakkale Onsekiz Mart University, 17020, Canakkale, Turkey.
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Gursoy S, Ataman E, Baysal BT, Özyılmaz B, Gençpınar P, Hız AS, Yiş U, Ünalp A, Dündar NO, Ülgenalp A, Erçal D. Identification of PCDH19 Gene Mutations/Deletions in Patients with Early Onset Epilepsy. Ann Indian Acad Neurol 2020; 23:206-210. [PMID: 32189863 PMCID: PMC7061497 DOI: 10.4103/aian.aian_465_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 11/06/2022] Open
Abstract
Background and Aims: PCDH19 gene, which encodes protocadherin 19, is associated with epilepsy and intellectual disability, mainly in affected females. The clinical manifestations are heterogeneous and the main features include early onset seizure, generalized or focal seizures sensitive to fever, and brief seizures occurring in clusters. The disorders exhibit a unique and unusual X-linked pattern of expression. We aimed to investigate PCDH19 mutations/deletions in patients with epilepsy and describe the clinical/molecular features. Methods: PCDH19 gene was analyzed in 35 Turkish female patients from 34 families with early-onset epilepsy via direct sequencing and multiplex ligation-dependent probe amplification analysis. Additionally, array comparative genomic hybridization analysis was performed in patients with whole gene deletion. Results: We identified 2 different heterozygous mutations in 2 unrelated probands (5. 7%) which were located in exon 1. Additionally, whole gene deletions were detected in dizygotic twin girls (5. 7%), who had distinct clinical features and the deletion was inherited from the unaffected father. The second twin suffered more severe clinical manifestations including autistic features, behavioral problems, mild-moderate mental retardation and seizures, which were under control with multidrug regimen when compared with the first twin. Conclusion: PCDH19 is a major causative gene in patients with epilepsy and further data is required to gain a better understanding of phenotype-genotype correlation. In addition to gene sequencing, deletion/duplication analysis will improve the molecular diagnosis in patients with clinical findings.
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Affiliation(s)
- Semra Gursoy
- Department of Pediatric Genetics, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Esra Ataman
- Department of Medical Genetics, Dokuz Eylül University Medical School, Izmir, Turkey
| | - Bahar Toklu Baysal
- Department of Pediatric Neurology, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Berk Özyılmaz
- Department of Medical Genetics, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Pınar Gençpınar
- Department of Pediatric Neurology, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Ayşe Semra Hız
- Department of Pediatric Neurology, Dokuz Eylül University Medical School, Izmir, Turkey
| | - Uluç Yiş
- Department of Pediatric Neurology, Dokuz Eylül University Medical School, Izmir, Turkey
| | - Aycan Ünalp
- Department of Pediatric Neurology, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Nihal Olgaç Dündar
- Department of Pediatric Neurology, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Ayfer Ülgenalp
- Department of Medical Genetics, Dokuz Eylül University Medical School, Izmir, Turkey
| | - Derya Erçal
- Department of Pediatric Genetics, Dokuz Eylül University Medical School, Izmir, Turkey
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Casamassa A, Ferrari D, Gelati M, Carella M, Vescovi AL, Rosati J. A Link between Genetic Disorders and Cellular Impairment, Using Human Induced Pluripotent Stem Cells to Reveal the Functional Consequences of Copy Number Variations in the Central Nervous System-A Close Look at Chromosome 15. Int J Mol Sci 2020; 21:ijms21051860. [PMID: 32182809 PMCID: PMC7084702 DOI: 10.3390/ijms21051860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 12/28/2022] Open
Abstract
Recent cutting-edge human genetics technology has allowed us to identify copy number variations (CNVs) and has provided new insights for understanding causative mechanisms of human diseases. A growing number of studies show that CNVs could be associated with physiological mechanisms linked to evolutionary trigger, as well as to the pathogenesis of various diseases, including cancer, autoimmune disease and mental disorders such as autism spectrum disorders, schizophrenia, intellectual disabilities or attention-deficit/hyperactivity disorder. Their incomplete penetrance and variable expressivity make diagnosis difficult and hinder comprehension of the mechanistic bases of these disorders. Additional elements such as co-presence of other CNVs, genomic background and environmental factors are involved in determining the final phenotype associated with a CNV. Genetically engineered animal models are helpful tools for understanding the behavioral consequences of CNVs. However, the genetic background and the biology of these animal model systems have sometimes led to confusing results. New cellular models obtained through somatic cellular reprogramming technology that produce induced pluripotent stem cells (iPSCs) from human subjects are being used to explore the mechanisms involved in the pathogenic consequences of CNVs. Considering the vast quantity of CNVs found in the human genome, we intend to focus on reviewing the current literature on the use of iPSCs carrying CNVs on chromosome 15, highlighting advantages and limits of this system with respect to mouse model systems.
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Affiliation(s)
- Alessia Casamassa
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy;
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, Viale Abramo Lincoln 5, 81100 Caserta, Italy
| | - Daniela Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy;
| | - Maurizio Gelati
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
| | - Massimo Carella
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
| | - Angelo Luigi Vescovi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy;
- Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy; (M.G.); (M.C.)
- Correspondence: (A.L.V.); (J.R.)
| | - Jessica Rosati
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, Foggia, Italy;
- Correspondence: (A.L.V.); (J.R.)
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Esposito M, Lagorio I, Peroni D, Bonuccelli A, Orsini A, Striano P. Genomic sequencing in severe epilepsy: a step closer to precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1732203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Mariagrazia Esposito
- Pediatric Neurology Unit, “A.O.U. Pisana” University Hospital of Pisa, Pisa, Italy
| | - Ilaria Lagorio
- Department of Neurology, University of Siena, Siena, Italy
| | - Diego Peroni
- Pediatric Department, “A.O.U. Pisana”, University Hospital of Pisa, Pisa, Italy
| | - Alice Bonuccelli
- Pediatric Neurology Unit, “A.O.U. Pisana” University Hospital of Pisa, Pisa, Italy
| | - Alessandro Orsini
- Pediatric Neurology Unit, “A.O.U. Pisana” University Hospital of Pisa, Pisa, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS “G. Gaslini” Institute, Genova, Italy
- Department Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health University of Genoa, Genova, Italy
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