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Mayfield JM, Hitefield NL, Czajewski I, Vanhye L, Holden L, Morava E, van Aalten DMF, Wells L. O-GlcNAc Transferase Congenital Disorder of Glycosylation (OGT-CDG): Potential mechanistic targets revealed by evaluating the OGT interactome. J Biol Chem 2024:107599. [PMID: 39059494 DOI: 10.1016/j.jbc.2024.107599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
O-GlcNAc transferase (OGT) is the sole enzyme responsible for the post-translational modification O-GlcNAc on thousands of target nucleocytoplasmic proteins. To date, nine variants of OGT that segregate with OGT Congenital Disorder of Glycosylation (OGT-CDG) have been reported and characterized. Numerous additional variants have been associated with OGT-CDG, some of which are currently undergoing investigation. This disorder primarily presents with global developmental delay and intellectual disability (ID), alongside other variable neurological features and subtle facial dysmorphisms in patients. Several hypotheses aim to explain the etiology of OGT-CDG, with a prominent hypothesis attributing the pathophysiology of OGT-CDG to mutations segregating with this disorder disrupting the OGT interactome. The OGT interactome consists of thousands of proteins, including substrates as well as interactors that require noncatalytic functions of OGT. A key aim in the field is to identify which interactors and substrates contribute to the primarily neural-specific phenotype of OGT-CDG. In this review, we will discuss the heterogenous phenotypic features of OGT-CDG seen clinically, the variable biochemical effects of mutations associated with OGT-CDG, and the use of animal models to understand this disorder. Furthermore, we will discuss how previously identified OGT interactors causal for ID provide mechanistic targets for investigation that could explain the dysregulated gene expression seen in OGT-CDG models. Identifying shared or unique altered pathways impacted in OGT-CDG patients will provide a better understanding of the disorder as well as potential therapeutic targets.
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Affiliation(s)
- Johnathan M Mayfield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Naomi L Hitefield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Ignacy Czajewski
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Lotte Vanhye
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Laura Holden
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Eva Morava
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Daan M F van Aalten
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, DK.
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America.
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Baskar D, Preethish-Kumar V, Polavarapu K, Vengalil S, Nashi S, Menon D, Ganaraja VH, Girija MS, Nandeesh BN, Arunachal G, Nalini A. Clinical and Genetic Heterogeneity of Nuclear Envelopathy Related Muscular Dystrophies in an Indian Cohort. J Neuromuscul Dis 2024:JND230172. [PMID: 39058449 DOI: 10.3233/jnd-230172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Introduction Nuclear envelopathies occur due to structural and/or functional defects in various nuclear envelope proteins such as lamin A/C and lamin related proteins. This study is the first report on the phenotype-genotype patterns of nuclear envelopathy-related muscular dystrophies from India. Methods In this retrospective study, we have described patients with genetically confirmed muscular dystrophy associated with nuclear envelopathy. Data on clinical, laboratory findings and muscle MRI were collected. Results Sixteen patients were included with median age at onset of 3 years (range: 1 month - 17 years). Three genes were involved: LMNA (11, 68.75%), EMD (4, 25%) and SYNE1 (1, 6.25%). The 11 patients with LMNA variants were Congenital muscular dystrophy (MDCL)=4, Limb Girdle Muscular Dystrophy (LGMD1B)=4 and Emery-Dreifuss Muscular Dystrophy (EDMD2)=3. On muscle biopsy, one patient from each laminopathy phenotype (n = 3) revealed focal perivascular inflammatory infiltrate. Other notable features were ophthalmoparesis in one and facial weakness in one. None had cardiac involvement. Patients with EDMD1 had both upper (UL) and lower limb (LL) proximo-distal weakness. Cardiac rhythm disturbances such as sick sinus syndrome and atrial arrhythmias were noted in two patients with EDMD1. Only one patient with variant c.654_658dup (EMD) lost ambulation in the 3rd decade, 18 years after disease onset. Two had finger contractures with EMD and SYNE1 variants respectively. All patients with LMNA and SYNE1 variants were ambulant at the time of evaluation. Mean duration of illness (years) was 11.6±13 (MDCL), 3.2±1.0 (EDMD2), 10.4±12.8 (LGMD1B), 11.8±8.4 (EDMD1) and 3 (EDMD4). One patient had a novel SYNE1 mutation (c.22472dupA, exon 123) and presented with UL phenotype and prominent finger and wrist contractures. Conclusion The salient features included ophthalmoparesis and facial weakness in LMNA, prominent finger contractures in EMD and SYNE1 and upper limb phenotype with the novel pathogenic variant in SYNE1.
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Affiliation(s)
- Dipti Baskar
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | | | - Kiran Polavarapu
- Department of Medicine, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa and Division of Neurology, The Ottawa Hospital, Ottawa, Canada
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Deepak Menon
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | | | - Manu Santhappan Girija
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | | | - Gautham Arunachal
- Department of Human Genetics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
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3
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Chen P, Long J, Hua T, Zheng Z, Xiao Y, Chen L, Yu K, Wu W, Zhang S. Transcriptome and open chromatin analysis reveals the process of myocardial cell development and key pathogenic target proteins in Long QT syndrome type 7. J Transl Med 2024; 22:307. [PMID: 38528561 PMCID: PMC10964537 DOI: 10.1186/s12967-024-05125-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 03/20/2024] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Long QT syndrome type 7 (Andersen-Tawil syndrome, ATS), which is caused by KCNJ2 gene mutation, often leads to ventricular arrhythmia, periodic paralysis and skeletal malformations. The development, differentiation and electrophysiological maturation of cardiomyocytes (CMs) changes promote the pathophysiology of Long QT syndrome type 7(LQT7). We aimed to specifically reproduce the ATS disease phenotype and study the pathogenic mechanism. METHODS AND RESULTS We established a cardiac cell model derived from human induced pluripotent stem cells (hiPSCs) to the phenotypes and electrophysiological function, and the establishment of a human myocardial cell model that specifically reproduces the symptoms of ATS provides a reliable platform for exploring the mechanism of this disease or potential drugs. The spontaneous pulsation rate of myocardial cells in the mutation group was significantly lower than that in the repair CRISPR group, the action potential duration was prolonged, and the Kir2.1 current of the inward rectifier potassium ion channel was decreased, which is consistent with the clinical symptoms of ATS patients. Only ZNF528, a chromatin-accessible TF related to pathogenicity, was continuously regulated beginning from the cardiac mesodermal precursor cell stage (day 4), and continued to be expressed at low levels, which was identified by WGCNA method and verified with ATAC-seq data in the mutation group. Subsequently, it indicated that seven pathways were downregulated (all p < 0.05) by used single sample Gene Set Enrichment Analysis to evaluate the overall regulation of potassium-related pathways enriched in the transcriptome and proteome of late mature CMs. Among them, the three pathways (GO: 0008076, GO: 1990573 and GO: 0030007) containing the mutated gene KCNJ2 is involved that are related to the whole process by which a potassium ion enters the cell via the inward rectifier potassium channel to exert its effect were inhibited. The other four pathways are related to regulation of the potassium transmembrane pathway and sodium:potassium exchange ATPase (p < 0.05). ZNF528 small interfering (si)-RNA was applied to hiPSC-derived cardiomyocytes for CRISPR group to explore changes in potassium ion currents and growth and development related target protein levels that affect disease phenotype. Three consistently downregulated proteins (KCNJ2, CTTN and ATP1B1) associated with pathogenicity were verificated through correlation and intersection analysis. CONCLUSION This study uncovers TFs and target proteins related to electrophysiology and developmental pathogenicity in ATS myocardial cells, obtaining novel targets for potential therapeutic candidate development that does not rely on gene editing.
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Affiliation(s)
- Peipei Chen
- Department of Clinical Nutrition & Health Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Junyu Long
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianrui Hua
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhifa Zheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Xiao
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lianfeng Chen
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Kang Yu
- Department of Clinical Nutrition & Health Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Wei Wu
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Hussain SI, Muhammad N, Shah SUD, Fardous F, Khan SA, Khan N, Rehman AU, Siddique M, Wasan SA, Niaz R, Ullah H, Khan N, Muhammad N, Mirza MU, Wasif N, Khan S. Structural and functional implications of SLC13A3 and SLC9A6 mutations: an in silico approach to understanding intellectual disability. BMC Neurol 2023; 23:353. [PMID: 37794328 PMCID: PMC10548666 DOI: 10.1186/s12883-023-03397-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Intellectual disability (ID) is a condition that varies widely in both its clinical presentation and its genetic underpinnings. It significantly impacts patients' learning capacities and lowers their IQ below 70. The solute carrier (SLC) family is the most abundant class of transmembrane transporters and is responsible for the translocation of various substances across cell membranes, including nutrients, ions, metabolites, and medicines. The SLC13A3 gene encodes a plasma membrane-localized Na+/dicarboxylate cotransporter 3 (NaDC3) primarily expressed in the kidney, astrocytes, and the choroid plexus. In addition to three Na + ions, it brings four to six carbon dicarboxylates into the cytosol. Recently, it was discovered that patients with acute reversible leukoencephalopathy and a-ketoglutarate accumulation (ARLIAK) carry pathogenic mutations in the SLC13A3 gene, and the X-linked neurodevelopmental condition Christianson Syndrome is caused by mutations in the SLC9A6 gene, which encodes the recycling endosomal alkali cation/proton exchanger NHE6, also called sodium-hydrogen exchanger-6. As a result, there are severe impairments in the patient's mental capacity, physical skills, and adaptive behavior. METHODS AND RESULTS Two Pakistani families (A and B) with autosomal recessive and X-linked intellectual disorders were clinically evaluated, and two novel disease-causing variants in the SLC13A3 gene (NM 022829.5) and the SLC9A6 gene (NM 001042537.2) were identified using whole exome sequencing. Family-A segregated a novel homozygous missense variant (c.1478 C > T; p. Pro493Leu) in the exon-11 of the SLC13A3 gene. At the same time, family-B segregated a novel missense variant (c.1342G > A; p.Gly448Arg) in the exon-10 of the SLC9A6 gene. By integrating computational approaches, our findings provided insights into the molecular mechanisms underlying the development of ID in individuals with SLC13A3 and SLC9A6 mutations. CONCLUSION We have utilized in-silico tools in the current study to examine the deleterious effects of the identified variants, which carry the potential to understand the genotype-phenotype relationships in neurodevelopmental disorders.
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Affiliation(s)
- Syeda Iqra Hussain
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Nazif Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Salah Ud Din Shah
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Fardous Fardous
- Department of Medical Lab Technology, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Sher Alam Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Niamatullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Adil U Rehman
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Mehwish Siddique
- Department of Zoology, Government Post Graduate College for Women, Satellite Town, Gujranwala, Pakistan
| | - Shoukat Ali Wasan
- Department of Botany, Faculty of Natural Sciences, Shah Abdul Latif University, Khairpur, Sindh, Pakistan
| | - Rooh Niaz
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Hafiz Ullah
- Gomal Center of Biochemistry and Biotechnology (GCBB), Gomal University D. I. Khan, D. I. Khan, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Noor Muhammad
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, N9B 1C4, Canada
| | - Naveed Wasif
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, 89081, Ulm, Germany.
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology (KUST), Kohat, Khyber Pakhtunkhwa, Pakistan.
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5
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Oishi T, Pagano J, Sellers C, Jerath NU. Two Cases of Periodic Paralysis Associated With MCM3AP Variants. J Clin Neuromuscul Dis 2023; 25:36-41. [PMID: 37611268 DOI: 10.1097/cnd.0000000000000454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
OBJECTIVES Periodic paralysis is a rare genetic condition characterized by episodes of neuromuscular weakness, often provoked by electrolyte abnormalities, physiologic stress, physical exertion, and diet. In addition to mutations in genes coding for skeletal muscle ion channels, in 2019, Gustavasson et al discovered that the MCM3AP gene could be responsible for periodic paralysis. In this study, we present 2 individuals with clinical episodes of periodic paralysis who have variants in the MCM3AP gene. METHODS Two unrelated probands were independently evaluated with clinical, genetic, and electrodiagnostic testing. RESULTS Proband 1 is a 46-year-old man who presented with decades of ongoing episodic weakness and fatigue, clinically diagnosed with periodic paralysis and supported by electrodiagnostic studies. Proband 2 is a 34-year-old woman with a history of episodic paralysis since childhood. Genetic testing in both individuals revealed potentially pathogenic variants in the MCM3AP gene. CONCLUSIONS Periodic paralysis is a condition that significantly affects the lives of those diagnosed. The results illustrate that MCM3AP gene variants can been associated with a clinical and electrodiagnostic presentation of periodic paralysis. Additional future research should focus on clarifying any relationship between these genetic variants and the disease, as well as other possible genetic causes.
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Affiliation(s)
| | | | - Cody Sellers
- Nova Southeastern University, Fort Lauderdale, FL
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Ballesta-Martínez MJ, Pérez-Fernández V, López-González V, Sánchez-Soler MJ, Serrano-Antón AT, Rodríguez-Peña LI, Barreda-Sánchez M, Armengol-Dulcet L, Guillén-Navarro E. Validation of clinical exome sequencing in the diagnostic procedure of patients with intellectual disability in clinical practice. Orphanet J Rare Dis 2023; 18:201. [PMID: 37480025 PMCID: PMC10362575 DOI: 10.1186/s13023-023-02809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of 1-3% and aproximately 30-50% of ID cases have a genetic cause. Development of next-generation sequencing has shown a high diagnostic potential. The aim of this work was to evaluate the diagnostic yield of clinical exome sequencing in 188 ID patients and the economic impact of its introduction in clinical practice. An analysis of diagnostic yield according to the different clinical variables was performed in order to establish an efficient diagnostic protocol for ID patients. Diagnostic yield of clinical exome sequencing was significant (34%) supporting its utility in diagnosis of ID patients. Wide genetic heterogeneity and predominance of autosomal dominant de novo variants in ID patients were observed. Time to diagnosis was shortened and diagnostic study costs decreased by 62% after implementation of clinical exome sequencing. No association was found between any of the variables analyzed and a higher diagnostic yield; added to the fact that many of the diagnoses weren't clinically detectable, the reduction of time to diagnosis and the economic savings with respect to classical diagnostic studies, strengthen the clinical and economical convenience of early implementation of clinical exome sequencing in the diagnostic workup of ID patients in clinical practice.
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Affiliation(s)
- María Juliana Ballesta-Martínez
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain.
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain.
| | - Virginia Pérez-Fernández
- Departamento de Ciencias Sociosanitarias-Área de Bioestadística, Facultad de Medicina, Universidad de Murcia, Murcia, Spain
| | - Vanesa López-González
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain
| | - María José Sánchez-Soler
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
| | - Ana Teresa Serrano-Antón
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
| | - Lidia Isolina Rodríguez-Peña
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | - Lluís Armengol-Dulcet
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Catalonia, Spain
| | - Encarna Guillén-Navarro
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain.
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain.
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Lyulcheva-Bennett E, Genomics England Research Consortium, Bennett D. A retrospective analysis of phosphatase catalytic subunit gene variants in patients with rare disorders identifies novel candidate neurodevelopmental disease genes. Front Cell Dev Biol 2023; 11:1107930. [PMID: 37056996 PMCID: PMC10086149 DOI: 10.3389/fcell.2023.1107930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
Rare genetic disorders represent some of the most severe and life-limiting conditions that constitute a considerable burden on global healthcare systems and societies. Most individuals affected by rare disorders remain undiagnosed, highlighting the unmet need for improved disease gene discovery and novel variant interpretation. Aberrant (de) phosphorylation can have profound pathological consequences underpinning many disease processes. Numerous phosphatases and associated proteins have been identified as disease genes, with many more likely to have gone undiscovered thus far. To begin to address these issues, we have performed a systematic survey of de novo variants amongst 189 genes encoding phosphatase catalytic subunits found in rare disease patients recruited to the 100,000 Genomes Project (100 kGP), the largest national sequencing project of its kind in the United Kingdom. We found that 49% of phosphatases were found to carry de novo mutation(s) in this cohort. Only 25% of these phosphatases have been previously linked to genetic disorders. A gene-to-patient approach matching variants to phenotypic data identified 9 novel candidate rare-disease genes: PTPRD, PTPRG, PTPRT, PTPRU, PTPRZ1, MTMR3, GAK, TPTE2, PTPN18. As the number of patients undergoing whole genome sequencing increases and information sharing improves, we anticipate that reiterative analysis of genomic and phenotypic data will continue to identify candidate phosphatase disease genes for functional validation. This is the first step towards delineating the aetiology of rare genetic disorders associated with altered phosphatase function, leading to new biological insights and improved clinical outcomes for the affected individuals and their families.
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Affiliation(s)
| | | | - Daimark Bennett
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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8
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Liu S, Zhang Z, Li L, Yao L, Ma Z, Li J. ADAM10- and γ-secretase-dependent cleavage of the transmembrane protein PTPRT attenuates neurodegeneration in the mouse model of Alzheimer's disease. FASEB J 2023; 37:e22734. [PMID: 36583697 DOI: 10.1096/fj.202201396r] [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: 08/25/2022] [Revised: 11/20/2022] [Accepted: 12/14/2022] [Indexed: 12/31/2022]
Abstract
PTPRT (receptor-type tyrosine-protein phosphatase T), a brain-specific type 1 transmembrane protein, plays an important role in neurodevelopment and synapse formation. However, whether abnormal PTPRT signaling is associated with Alzheimer's disease (AD) remains elusive. Here, we report that Ptprt mRNA expression is found to be downregulated in the brains of both human and mouse models of AD. We further identified that the PTPRT intracellular domain (PICD), which is released by ADAM10- and γ-secretase-dependent cleavage of PTPRT, efficiently translocates to the nucleus via a conserved nuclear localization signal (NLS). We show that inhibition of nuclear translocation of PICD leads to an accumulation of phosphorylated signal transducer and activator of transcription 3 (pSTAT3), a substrate of PTPRT-eventually resulting in neuronal cell death. Consistently, RNA sequencing reveals that overexpression of PICD leads to changes in the expression of genes that are functionally associated with synapse formation, cell adhesion, and protein dephosphorylation. Moreover, overexpression of PICD not only decreases the level of phospho-STAT3Y705 and amyloid β production in the hippocampus of APP/PS1 mice but also partially improves synaptic function and behavioral deficits in this mouse model of AD. These findings suggest that a novel role of the ADAM 10- and γ-secretase-dependent cleavage of PTPRT may alleviate the AD-like neurodegenerative processes.
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Affiliation(s)
- Siling Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhongyu Zhang
- National Institute on Drug Dependence, Peking University, Beijing, China
| | - Lianwei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Li Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jiali Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,National Institute on Drug Dependence, Peking University, Beijing, China.,IDG/McGovern Institute for Brain Research, Peking University, Beijing, China.,Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming, China.,National Research Facility for Phenotypic and Genetic Analysis of Model Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
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9
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The Genetics of Intellectual Disability. Brain Sci 2023; 13:brainsci13020231. [PMID: 36831774 PMCID: PMC9953898 DOI: 10.3390/brainsci13020231] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/23/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of ~2-3% in the general population, having a large societal impact. The underlying cause of ID is largely of genetic origin; however, identifying this genetic cause has in the past often led to long diagnostic Odysseys. Over the past decades, improvements in genetic diagnostic technologies and strategies have led to these causes being more and more detectable: from cytogenetic analysis in 1959, we moved in the first decade of the 21st century from genomic microarrays with a diagnostic yield of ~20% to next-generation sequencing platforms with a yield of up to 60%. In this review, we discuss these various developments, as well as their associated challenges and implications for the field of ID, which highlight the revolutionizing shift in clinical practice from a phenotype-first into genotype-first approach.
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10
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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11
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Schwartz CE, Louie RJ, Toutain A, Skinner C, Friez MJ, Stevenson RE. X-Linked intellectual disability update 2022. Am J Med Genet A 2023; 191:144-159. [PMID: 36300573 DOI: 10.1002/ajmg.a.63008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/28/2022] [Accepted: 09/29/2022] [Indexed: 12/14/2022]
Abstract
Genes that are involved in the transcription process, mitochondrial function, glycoprotein metabolism, and ubiquitination dominate the list of 21 new genes associated with X-linked intellectual disability since the last update in 2017. The new genes were identified by sequencing of candidate genes (2), the entire X-chromosome (2), the whole exome (15), or the whole genome (2). With these additions, 42 (21%) of the 199 named XLID syndromes and 27 (25%) of the 108 numbered nonsyndromic XLID families remain to be resolved at the molecular level. Although the pace of discovery of new XLID genes has slowed during the past 5 years, the density of genes on the X chromosome that cause intellectual disability still appears to be twice the density of intellectual disability genes on the autosomes.
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Affiliation(s)
| | | | - Annick Toutain
- Department of Medical Genetics, Centre Hospitalier Universitaire, Tours, France
| | - Cindy Skinner
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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12
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RINGs, DUBs and Abnormal Brain Growth-Histone H2A Ubiquitination in Brain Development and Disease. EPIGENOMES 2022; 6:epigenomes6040042. [PMID: 36547251 PMCID: PMC9778336 DOI: 10.3390/epigenomes6040042] [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: 11/03/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
During mammalian neurodevelopment, signaling pathways converge upon transcription factors (TFs) to establish appropriate gene expression programmes leading to the production of distinct neural and glial cell types. This process is partially regulated by the dynamic modulation of chromatin states by epigenetic systems, including the polycomb group (PcG) family of co-repressors. PcG proteins form multi-subunit assemblies that sub-divide into distinct, yet functionally related families. Polycomb repressive complexes 1 and 2 (PRC1 and 2) modify the chemical properties of chromatin by covalently modifying histone tails via H2A ubiquitination (H2AK119ub1) and H3 methylation, respectively. In contrast to the PRCs, the Polycomb repressive deubiquitinase (PR-DUB) complex removes H2AK119ub1 from chromatin through the action of the C-terminal hydrolase BAP1. Genetic screening has identified several PcG mutations that are causally associated with a range of congenital neuropathologies associated with both localised and/or systemic growth abnormalities. As PRC1 and PR-DUB hold opposing functions to control H2AK119ub1 levels across the genome, it is plausible that such neurodevelopmental disorders arise through a common mechanism. In this review, we will focus on advancements regarding the composition and opposing molecular functions of mammalian PRC1 and PR-DUB, and explore how their dysfunction contributes to the emergence of neurodevelopmental disorders.
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13
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Nishi K, Fu W, Kiyama R. Novel estrogen-responsive genes (ERGs) for the evaluation of estrogenic activity. PLoS One 2022; 17:e0273164. [PMID: 35976950 PMCID: PMC9385026 DOI: 10.1371/journal.pone.0273164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/03/2022] [Indexed: 11/19/2022] Open
Abstract
Estrogen action is mediated by various genes, including estrogen-responsive genes (ERGs). ERGs have been used as reporter-genes and markers for gene expression. Gene expression profiling using a set of ERGs has been used to examine statistically reliable transcriptomic assays such as DNA microarray assays and RNA sequencing (RNA-seq). However, the quality of ERGs has not been extensively examined. Here, we obtained a set of 300 ERGs that were newly identified by six sets of RNA-seq data from estrogen-treated and control human breast cancer MCF-7 cells. The ERGs exhibited statistical stability, which was based on the coefficient of variation (CV) analysis, correlation analysis, and examination of the functional association with estrogen action using database searches. A set of the top 30 genes based on CV ranking were further evaluated quantitatively by RT-PCR and qualitatively by a functional analysis using the GO and KEGG databases and by a mechanistic analysis to classify ERα/β-dependent or ER-independent types of transcriptional regulation. The 30 ERGs were characterized according to (1) the enzymes, such as metabolic enzymes, proteases, and protein kinases, (2) the genes with specific cell functions, such as cell-signaling mediators, tumor-suppressors, and the roles in breast cancer, (3) the association with transcriptional regulation, and (4) estrogen-responsiveness. Therefore, the ERGs identified here represent various cell functions and cell signaling pathways, including estrogen signaling, and thus, may be useful to evaluate estrogenic activity.
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Affiliation(s)
- Kentaro Nishi
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
| | - Wenqiang Fu
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
| | - Ryoiti Kiyama
- Department of Life Science, Faculty of Life Science, Kyushu Sangyo University Matsukadai, Higashi-ku, Fukuoka, Japan
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14
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Yang XZ, Wan MY, Zhang DD, Dai Y, Pan ZA, Zhai FF, Han F, Liu JY, Zhou LX, Ni J, Yao M, Jin ZY, Cui LY, Zhang SY, Zhu YC. Investigating the Genetic Characteristics of Hippocampal Volume and Plasma β-Amyloid in a Chinese Community-Dwelling Population. Neurology 2022; 99:e234-e244. [PMID: 35623891 DOI: 10.1212/wnl.0000000000200554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/02/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES The genetic characteristics and correlations of hippocampal volume (HV) and plasma β-amyloid (Aβ), probable endophenotypes for dementia, remain to be explored in a Chinese community cohort. Using whole-exome sequencing (WES) and single nucleotide polymorphism (SNP) array genotyping, we sought to identify rare and common variants and genes influencing these 2 endophenotypes and calculate their heritability and genetic correlation. METHODS Association analyses with both WES and SNP array genotyping data were performed for HV and plasma Aβ with mixed-effect linear regression model adjusted for sex, age, and total intracranial volume or APOE ε4 while considering familial relatedness. We also performed gene-level analysis for common and gene burden analysis for rare variants. Heritability and genetic correlation were examined further. RESULTS A total of 1,261 participants from a Chinese community cohort were included and we identified 1 gene, PTPRT, for HV, with the top significant SNPs by whole genome-wide association study (GWAS). rs6030076 (p = 5.48 × 10-8, β = -0.092, SE 0.017) from WES and rs6030088 (p = 8.24 × 10-9, β = -105.22, SE 18.09) from SNP array data were both located in this gene. Gene burden analysis based on rare mutations detected 6 genes to be significantly associated with Aβ. The SNP-based heritability was 0.43 ± 0.13 for HV and 0.2-0.3 for plasma Aβ. The SNP-based genetic correlation between HV and plasma Aβ was negative. DISCUSSION In this study, we identified several SNPs and 1 gene, PTPRT, which were not reported in previous GWAS, associated with HV. The heritability and the genetic correlation gave an overview of HV and plasma Aβ. Our findings provide insights into the mechanisms behind the individual variances in these endophenotypes.
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Affiliation(s)
- Xin-Zhuang Yang
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng-Yao Wan
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ding-Ding Zhang
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Dai
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zi-Ang Pan
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei-Fei Zhai
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Han
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing-Yi Liu
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Xin Zhou
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Ni
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ming Yao
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng-Yu Jin
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Ying Cui
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shu-Yang Zhang
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Cheng Zhu
- From the Department of Neurology (X.-Z.Y., M.-Y.W., D.-D.Z., Y.D., Z.-A.P., F.-F.Z., F.H., J.-Y.L., L.-X.Z., J.N., M.Y., L.-Y.C., Y.-C.Z.), Medical Research Center (X.-Z.Y., D.-D.Z.), and Departments of Radiology (Z.-Y.J.) and Cardiology (S.-Y.Z.), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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15
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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16
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Major brain malformations: corpus callosum dysgenesis, agenesis of septum pellucidum and polymicrogyria in patients with BCORL1-related disorders. J Hum Genet 2022; 67:95-101. [PMID: 34400773 DOI: 10.1038/s10038-021-00971-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/14/2021] [Accepted: 08/02/2021] [Indexed: 11/08/2022]
Abstract
OBJECTIVE BCORL1, a transcriptional co-repressor, has a role in cortical migration, neuronal differentiation, maturation, and cerebellar development. We describe BCORL1 as a new genetic cause for major brain malformations. METHODS AND RESULTS We report three patients from two unrelated families with neonatal onset intractable epilepsy and profound global developmental delay. Brain MRI of two siblings from the first family depicted hypoplastic corpus callosum and septal agenesis (ASP) in the older brother and unilateral perisylvian polymicrogyria (PMG) in the younger one. MRI of the patient from the second family demonstrated complete agenesis of corpus callosum (CC). Whole Exome Sequencing revealed a novel hemizygous variant in NM_021946.5 (BCORL1):c.796C>T (p.Pro266Ser) in the two siblings from the first family and the NM_021946.5 (BCORL1): c.3376G>A; p.Asp1126Asn variant in the patient from the second family, both variants inherited from healthy mothers. We reviewed the patients' charts and MRIs and compared the phenotype to the other published BCORL1-related cases. Brain malformations have not been previously described in association with the BCORL1 phenotype. We discuss the potential influence of BCORL1 on brain development. CONCLUSIONS We suggest that BCORL1 variants present with a spectrum of neurodevelopmental disorders and can lead to major brain malformations originating at different stages of fetal development. We suggest adding BCORL1 to the genetic causes of PMG, ASP, and CC dysgenesis.
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17
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Chen CW, Huang RL, Do AQ, Wang HC, Lee YX, Wang CW, Hsieh CC, Tzeng CR, Hu YM, Chen CH, Weng YC, Su PH, Chen LY, Lai HC. Genome-wide analysis of cervical secretions obtained during embryo transfer reveals the association between deoxyribonucleic acid methylation and pregnancy outcomes. F&S SCIENCE 2022; 3:74-83. [PMID: 35559997 DOI: 10.1016/j.xfss.2021.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To study whether the methylation status of cervical secretions can reflect the ability of the endometrium to allow embryo implantation. DESIGN Case-control study. SETTING In vitro fertilization centers. PATIENT(S) Women undergoing embryo transfer cycles, in which at least 1 good-quality embryo was transferred. INTERVENTION(S) Collection of cervical secretions during the procedure of embryo transfer. MAIN OUTCOME MEASURE(S) Methylation profiles of cervical secretions in relation to pregnancy outcomes. RESULT(S) Genome-wide methylation profiles differ between cervical secretions from pregnancy and nonpregnancy cycles. Clustering analysis on the basis of the top 2,000 differentially methylated probes of cervical secretions from 28 pregnancy and 29 nonpregnancy cycles correctly categorized 86.0% of the samples in terms of conceptional status, which was verified in selected genes by quantitative methylation-specific polymerase chain reaction and validated in another independent sample set. The combination of selected genes was estimated to predict pregnancy outcomes with a maximal area under the receiver operating characteristic curve of 0.83. CONCLUSION(S) The methylation profiles of cervical secretions were associated with pregnancy outcomes in embryo transfer cycles. Although not clinically useful at present, deoxyribonucleic acid methylation in cervical secretions may shed new light on the less invasive assessment of endometrial receptivity.
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Affiliation(s)
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Anh Q Do
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Obstetrics and Gynecology, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam; International Ph.D. Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hui-Chen Wang
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Xuan Lee
- Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Graduate Institute of Clinical Medicine, Taipei Medical University, Taipei, Taiwan; Taipei Fertility Center, Taipei, Taiwan
| | | | | | | | | | - Chi-Huang Chen
- Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yu-Chun Weng
- Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Po-Hsuan Su
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Lin-Yu Chen
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Translational Epigenetic Center, Shuang Ho Hospital, Taipei Medical University, New Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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18
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Xu X, Lu F, Du S, Zhao X, Li H, Zhang L, Tang J. Case report: Novel compound heterozygous missense mutations in the DDHD2 gene in a Chinese patient associated with spastic paraplegia type 54. Front Pediatr 2022; 10:997274. [PMID: 36090575 PMCID: PMC9458848 DOI: 10.3389/fped.2022.997274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/10/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Spastic paraplegia type 54 (SPG54) is a rare inherited autosomal recessive disorder, and a complex hereditary spastic paraplegia (HSP) caused by mutations in the phospholipase DDHD2 gene. SPG54 is characterized by early onset of spastic paraplegia, intellectual disability and dysplasia of corpus callosum. CASE PRESENTATION We report a 9 years and 5 months old Chinese girl with progressive spasm of the lower limbs, muscle weakness and intellectual disability. Brain magnetic resonance imaging (MRI) showed periventricular leukomalacia and thinning of the corpus callosum. According to the Wechsler Intelligence Scale, her IQ is 42. By whole exome sequencing, novel compound heterozygous missense mutations in the DDHD2 gene [c.168G>C, p.(Trp56Cys) and c.1505T>C, p.(Phe502Ser)] were identified in the proband. Comparative amino acid sequence alignment across different species revealed that Trp56 and Phe502 in the DDHD2 protein were highly conserved during evolution. And multiple in silico prediction tools suggested that both mutations were deleterious. CONCLUSIONS Our study reports a very rare case of complicated HSP caused by two novel compound heterozygous mutations in the DDHD2 gene. Our findings expand the genetic spectrum of SPG54.
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Affiliation(s)
- Xin Xu
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Fen Lu
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Senjie Du
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoke Zhao
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hongying Li
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Li Zhang
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jian Tang
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
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Maia N, Nabais Sá MJ, Melo-Pires M, de Brouwer APM, Jorge P. Intellectual disability genomics: current state, pitfalls and future challenges. BMC Genomics 2021; 22:909. [PMID: 34930158 PMCID: PMC8686650 DOI: 10.1186/s12864-021-08227-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Intellectual disability (ID) can be caused by non-genetic and genetic factors, the latter being responsible for more than 1700 ID-related disorders. The broad ID phenotypic and genetic heterogeneity, as well as the difficulty in the establishment of the inheritance pattern, often result in a delay in the diagnosis. It has become apparent that massive parallel sequencing can overcome these difficulties. In this review we address: (i) ID genetic aetiology, (ii) clinical/medical settings testing, (iii) massive parallel sequencing, (iv) variant filtering and prioritization, (v) variant classification guidelines and functional studies, and (vi) ID diagnostic yield. Furthermore, the need for a constant update of the methodologies and functional tests, is essential. Thus, international collaborations, to gather expertise, data and resources through multidisciplinary contributions, are fundamental to keep track of the fast progress in ID gene discovery.
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Affiliation(s)
- Nuno Maia
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal. .,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal.
| | - Maria João Nabais Sá
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Manuel Melo-Pires
- Serviço de Neuropatologia, Centro Hospitalar e Universitário do Porto (CHUPorto), Porto, Portugal
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
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20
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Lim SH, Sung YJ, Jo N, Lee NY, Kim KS, Lee DY, Kim NS, Lee J, Byun JY, Shin YB, Lee JR. Nanoplasmonic immunosensor for the detection of SCG2, a candidate serum biomarker for the early diagnosis of neurodevelopmental disorder. Sci Rep 2021; 11:22764. [PMID: 34815513 PMCID: PMC8610996 DOI: 10.1038/s41598-021-02262-7] [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: 08/05/2021] [Accepted: 11/12/2021] [Indexed: 11/09/2022] Open
Abstract
The neural circuits of the infant brain are rapidly established near 6 months of age, but neurodevelopmental disorders can be diagnosed only at the age of 2-3 years using existing diagnostic methods. Early diagnosis is very important to alleviate life-long disability in patients through appropriate early intervention, and it is imperative to develop new diagnostic methods for early detection of neurodevelopmental disorders. We examined the serum level of secretogranin II (SCG2) in pediatric patients to evaluate its potential role as a biomarker for neurodevelopmental disorders. A plasmonic immunosensor performing an enzyme-linked immunosorbent assay (ELISA) on a gold nanodot array was developed to detect SCG2 in small volumes of serum. This nanoplasmonic immunosensor combined with tyramide signal amplification was highly sensitive to detect SCG2 in only 5 μL serum samples. The analysis using the nanoplasmonic immunosensor revealed higher serum SCG2 levels in pediatric patients with developmental delay than in the control group. Overexpression or knockdown of SCG2 in hippocampal neurons significantly attenuated dendritic arborization and synaptic formation. These results suggest that dysregulated SCG2 expression impairs neural development. In conclusion, we developed a highly sensitive nanoplasmonic immunosensor to detect serum SCG2, a candidate biomarker for the early diagnosis of neurodevelopmental disorders.
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Affiliation(s)
- So-Hee Lim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Yun-Ju Sung
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Narae Jo
- BioNano Health Guard Research Center (H-GUARD), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Na-Yoon Lee
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea.,Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Korea
| | - Kyoung-Shim Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Da Yong Lee
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Nam-Soon Kim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Korea
| | - Ju-Young Byun
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
| | - Yong-Beom Shin
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea. .,BioNano Health Guard Research Center (H-GUARD), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
| | - Jae-Ran Lee
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
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21
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Zhang X, Wu X, Liu H, Song T, Jiang Y, He H, Yang S, Xie Y. Christianson syndrome: A novel splicing variant of SLC9A6 causes exon skipping in a Chinese boy and a literature review. J Clin Lab Anal 2021; 36:e24123. [PMID: 34791706 PMCID: PMC8761434 DOI: 10.1002/jcla.24123] [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: 09/17/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Variants in the endosomal solute carrier family 9 member A6 (SLC9A6)/(Na+ ,K+ )/H+ exchanger 6 (NHE6) gene have been linked to epilepsy, speech loss, truncal ataxia, hyperkinesia, and postnatal microcephaly. METHODS In the present study, we evaluated genetic alterations in a 3-year-old Chinese boy displayed features of epilepsy, psychomotor retardation, microcephaly, low body weight, difficulty in feeding, excessive movement, attention loss, ataxia, and cerebellar atrophy and his healthy family using WES method. The identified variant was further confirmed by Sanger sequencing method. Finally, minigene assays were used to verify whether the novel SLC9A6 intronic variant influenced the normal splicing of mRNA. RESULTS We identified a novel hemizygous splicing variant [NM_001042537.1: c.1463-1G>A] in SLC9A6 by trio-based exome sequencing. The minigene expression in vitro confirmed the splicing variant altered a consensus splice acceptor site of SLC9A6 intron 11, resulting in skipping over exon 12. CONCLUSIONS Our finding extends the catalog of pathogenic intronic variants affecting SLC9A6 pre-mRNA splicing and provides a basis for the genetic diagnosis of CS.
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Affiliation(s)
- Xiaoge Zhang
- Department of pediatrics, Northwest Women's and Children's Hospital, Xi'an, China
| | - Xiaofang Wu
- Department of pediatrics, Northwest Women's and Children's Hospital, Xi'an, China
| | - Hongli Liu
- Department of pediatrics, Northwest Women's and Children's Hospital, Xi'an, China
| | - Tingting Song
- Department of pediatrics, Northwest Women's and Children's Hospital, Xi'an, China
| | - Yongsheng Jiang
- Department of pediatrics, Northwest Women's and Children's Hospital, Xi'an, China
| | - Hanhan He
- Department of pediatrics, Northwest Women's and Children's Hospital, Xi'an, China
| | - Shaoqing Yang
- State Key Laboratory of Military Stomatology, Department of Oral Biology, School of Stomatology, Clinic of Oral Rare and Genetic Diseases, National Clinical Research Center for Oral Diseases, The Fourth Military Medical University, Xi'an, China
| | - Yun Xie
- Department of clinical laboratory, Northwest Women's and Children's Hospital, Xi'an, China
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22
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Mitani T, Isikay S, Gezdirici A, Gulec EY, Punetha J, Fatih JM, Herman I, Akay G, Du H, Calame DG, Ayaz A, Tos T, Yesil G, Aydin H, Geckinli B, Elcioglu N, Candan S, Sezer O, Erdem HB, Gul D, Demiral E, Elmas M, Yesilbas O, Kilic B, Gungor S, Ceylan AC, Bozdogan S, Ozalp O, Cicek S, Aslan H, Yalcintepe S, Topcu V, Bayram Y, Grochowski CM, Jolly A, Dawood M, Duan R, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Marafi D, Akdemir ZC, Karaca E, Carvalho CMB, Gibbs RA, Posey JE, Lupski JR, Pehlivan D. High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population. Am J Hum Genet 2021; 108:1981-2005. [PMID: 34582790 PMCID: PMC8546040 DOI: 10.1016/j.ajhg.2021.08.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
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Affiliation(s)
- Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, University of Gaziantep, Gaziantep 27310, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303 Istanbul, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Isabella Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Akif Ayaz
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey; Departments of Medical Genetics, School of Medicine, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Tulay Tos
- University of Health Sciences Zubeyde Hanim Research and Training Hospital of Women's Health and Diseases, Department of Medical Genetics, Ankara 06080, Turkey
| | - Gozde Yesil
- Istanbul Faculty of Medicine, Department of Medical Genetics, Istanbul University, Istanbul 34093, Turkey
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Private Reyap Istanbul Hospital, Istanbul 34515, Turkey
| | - Bilgen Geckinli
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Department of Medical Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey; Eastern Mediterranean University Medical School, Magosa, Mersin 10, Turkey
| | - Sukru Candan
- Medical Genetics Section, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Ozlem Sezer
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun 55100, Turkey
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Emine Demiral
- Department of Medical Genetics, School of Medicine, University of Inonu, Malatya 44280, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Bezmialem Foundation University, Istanbul 34093, Turkey; Department of Pediatrics, Division of Pediatric Critical Care Medicine, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Betul Kilic
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Serdal Gungor
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Ahmet C Ceylan
- Department of Medical Genetics, University of Health Sciences, Ankara Training and Research Hospital, Ankara 06110, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Cukurova University Faculty of Medicine, Adana 01330, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Salih Cicek
- Department of Medical Genetics, Konya Training and Research Hospital, Konya 42250, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, School of Medicine, Trakya University, Edirne 22130, Turkey
| | - Vehap Topcu
- Department of Medical Genetics, Ankara City Hospital, Ankara 06800, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
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23
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Van Bergen NJ, Bell KM, Carey K, Gear R, Massey S, Murrell EK, Gallacher L, Pope K, Lockhart PJ, Kornberg A, Pais L, Walkiewicz M, Simons C, Wickramasinghe VO, White SM, Christodoulou J. Pathogenic variants in nucleoporin TPR (translocated promoter region, nuclear basket protein) cause severe intellectual disability in humans. Hum Mol Genet 2021; 31:362-375. [PMID: 34494102 DOI: 10.1093/hmg/ddab248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/10/2021] [Accepted: 08/23/2021] [Indexed: 01/16/2023] Open
Abstract
The nuclear pore complex (NPC) is a multi-protein complex that regulates the trafficking of macromolecules between the nucleus and cytoplasm. Genetic variants in components of the NPC have been shown to cause a range of neurological disorders, including intellectual disability and microcephaly. Translocated promoter region, nuclear basket protein (TPR) is a critical scaffolding element of the nuclear facing interior of the NPC. Here we present two siblings with biallelic variants in TPR who present with a phenotype of microcephaly, ataxia and severe intellectual disability. The variants result in a premature truncation variant, and a splice variant leading to a 12-amino acid deletion respectively. Functional analyses in patient fibroblasts demonstrate significantly reduced TPR levels, and decreased TPR-containing NPC density. A compensatory increase in total NPC levels was observed, and decreased global RNA intensity in the nucleus. The discovery of variants that partly disable TPR function provide valuable insight into this essential protein in human disease, and our findings suggest that TPR variants are the cause of the siblings' neurological disorder.
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Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Katrina M Bell
- Bioinformatics, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia
| | - Kirsty Carey
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Russell Gear
- Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Edward K Murrell
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Lyndon Gallacher
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Andrew Kornberg
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Neurology Department, Royal Children's Hospital, Melbourne, Australia.,Neurosciences Research, Murdoch Children's Research Institute, Victoria, Australia
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Marzena Walkiewicz
- Translational Genomics Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Cas Simons
- Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia.,Translational Genomics Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | | | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Susan M White
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, VIC, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
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24
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Biallelic SYNE2 Missense Mutations Leading to Nesprin-2 Giant Hypo-Expression Are Associated with Intellectual Disability and Autism. Genes (Basel) 2021; 12:genes12091294. [PMID: 34573277 PMCID: PMC8470961 DOI: 10.3390/genes12091294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/06/2021] [Accepted: 08/20/2021] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurological and developmental disabilities characterised by clinical and genetic heterogeneity. The current study aimed to expand ASD genotyping by investigating potential associations with SYNE2 mutations. Specifically, the disease-causing variants of SYNE2 in 410 trios manifesting neurodevelopmental disorders using whole-exome sequencing were explored. The consequences of the identified variants were studied at the transcript level using quantitative polymerase chain reaction (qPCR). For validation, immunofluorescence and immunoblotting were performed to analyse mutational effects at the protein level. The compound heterozygous variants of SYNE2 (NM_182914.3:c.2483T>G; p.(Val828Gly) and NM_182914.3:c.2362G>A; p.(Glu788Lys)) were identified in a 4.5-year-old male, clinically diagnosed with autism spectrum disorder, developmental delay and intellectual disability. Both variants reside within the nesprin-2 giant spectrin repeat (SR5) domain and are predicted to be highly damaging using in silico tools. Specifically, a significant reduction of nesprin-2 giant protein levels is revealed in patient cells. SYNE2 transcription and the nuclear envelope localisation of the mutant proteins was however unaffected as compared to parental control cells. Collectively, these data provide novel insights into the cardinal role of the nesprin-2 giant in neurodevelopment and suggest that the biallelic hypomorphic SYNE2 mutations may be a new cause of intellectual disability and ASD.
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25
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SCAMP5 plays a critical role in axonal trafficking and synaptic localization of NHE6 to adjust quantal size at glutamatergic synapses. Proc Natl Acad Sci U S A 2021; 118:2011371118. [PMID: 33372133 DOI: 10.1073/pnas.2011371118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Glutamate uptake into synaptic vesicles (SVs) depends on cation/H+ exchange activity, which converts the chemical gradient (ΔpH) into membrane potential (Δψ) across the SV membrane at the presynaptic terminals. Thus, the proper recruitment of cation/H+ exchanger to SVs is important in determining glutamate quantal size, yet little is known about its localization mechanism. Here, we found that secretory carrier membrane protein 5 (SCAMP5) interacted with the cation/H+ exchanger NHE6, and this interaction regulated NHE6 recruitment to glutamatergic presynaptic terminals. Protein-protein interaction analysis with truncated constructs revealed that the 2/3 loop domain of SCAMP5 is directly associated with the C-terminal region of NHE6. The use of optical imaging and electrophysiological recording showed that small hairpin RNA-mediated knockdown (KD) of SCAMP5 or perturbation of SCAMP5/NHE6 interaction markedly inhibited axonal trafficking and the presynaptic localization of NHE6, leading to hyperacidification of SVs and a reduction in the quantal size of glutamate release. Knockout of NHE6 occluded the effect of SCAMP5 KD without causing additional defects. Together, our results reveal that as a key regulator of axonal trafficking and synaptic localization of NHE6, SCAMP5 could adjust presynaptic strength by regulating quantal size at glutamatergic synapses. Since both proteins are autism candidate genes, the reduced quantal size by interrupting their interaction may underscore synaptic dysfunction observed in autism.
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26
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BCOR gene alterations in hematological diseases. Blood 2021; 138:2455-2468. [PMID: 33945606 DOI: 10.1182/blood.2021010958] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
The BCL6 co-repressor (BCOR) is a transcription factor involved in the control of embryogenesis, mesenchymal stem cells function, hematopoiesis and lymphoid development. Recurrent somatic clonal mutations of the BCOR gene and its homologue BCORL1 have been detected in several hematological malignancies and aplastic anemia. They are scattered across the whole gene length and mostly represent frameshifts (deletions, insertions), nonsense and missence mutations. These disruptive events lead to the loss of full-length BCOR protein and to the lack or low expression of a truncated form of the protein, both consistent with the tumor suppressor role of BCOR. BCOR and BCORL1 mutations are similar to those causing two rare X-linked diseases: the oculo-facio-cardio-dental (OFCD) and the Shukla-Vernon syndromes, respectively. Here, we focus on the structure and function of normal BCOR and BCORL1 in normal hematopoietic and lymphoid tissues and review the frequency and clinical significance of the mutations of these genes in malignant and non-malignant hematological diseases. Moreover, we discuss the importance of mouse models to better understand the role of Bcor loss, alone and combined with alterations of other genes (e.g. Dnmt3a and Tet2), in promoting hematological malignancies and in providing a useful platform for the development of new targeted therapies.
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Muthusamy B, Bellad A, Girimaji SC, Pandey A. Shukla-Vernon Syndrome: A Second Family with a Novel Variant in the BCORL1 Gene. Genes (Basel) 2021; 12:genes12030452. [PMID: 33810051 PMCID: PMC8005212 DOI: 10.3390/genes12030452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/31/2022] Open
Abstract
Shukla-Vernon syndrome (SHUVER) is an extremely rare neurodevelopmental disorder characterized by global developmental delay, intellectual disability, behavioral anomalies, and dysmorphic features. Pathogenic variants in the BCORL1 gene have been identified as the molecular cause for this disorder. The BCORL1 gene encodes for BCL-6 corepressor-like protein 1, a transcriptional corepressor that is an integral component of protein complexes involved in transcription repression. In this study, we report an Indian family with two male siblings with features of Shukla-Vernon syndrome. The patients exhibited global developmental delay, intellectual disability, kyphosis, seizures, and dysmorphic features including bushy prominent eyebrows with synophrys, sharp beaked prominent nose, protuberant lower jaw, squint, and hypoplastic ears with fused ear lobes. No behavioral abnormalities were observed. Whole exome sequencing revealed a novel potentially pathogenic arginine to cysteine substitution (p.Arg1265Cys) in the BCORL1 protein. This is the second report of Shukla-Vernon syndrome with a novel missense variant in the BCORL1 gene. Our study confirms and expands the phenotypes and genotypes described previously for this syndrome and should aid in diagnosis and genetic counselling of patients and their families.
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Affiliation(s)
- Babylakshmi Muthusamy
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Manipal Academy of Higher Education, Manipal 576104, India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India
- Correspondence: (B.M.); (S.C.G.); (A.P.)
| | - Anikha Bellad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Manipal Academy of Higher Education, Manipal 576104, India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India
| | - Satish Chandra Girimaji
- Department of Child and Adolescent Psychiatry, NIMHANS, Hosur Road, Bangalore 560029, India
- Correspondence: (B.M.); (S.C.G.); (A.P.)
| | - Akhilesh Pandey
- Manipal Academy of Higher Education, Manipal 576104, India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: (B.M.); (S.C.G.); (A.P.)
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Szpisjak L, Szaraz G, Salamon A, Nemeth VL, Szepfalusi N, Veres G, Kincses B, Maroti Z, Kalmar T, Rydzanicz M, Ploski R, Klivenyi P, Zadori D. Eye-tracking-aided characterization of saccades and antisaccades in SYNE1 ataxia patients: a pilot study. BMC Neurosci 2021; 22:7. [PMID: 33526008 PMCID: PMC7852103 DOI: 10.1186/s12868-021-00612-9] [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: 09/17/2020] [Accepted: 01/13/2021] [Indexed: 11/11/2022] Open
Abstract
Background SYNE1 ataxia is an autosomal recessive hereditary condition, the main characteristic features of which are gait and limb ataxia and cerebellar dysarthria. Reports have revealed that the clinical phenotype of SYNE1 ataxia is more complex than the first published cases with pure cerebellar signs indicated. The aim of this study was to characterize eye movement alterations in the first diagnosed Hungarian SYNE1 ataxia patients. Results Saccades and antisaccades were examined with an eye tracker device in 3 SYNE1 (one patient has two frameshift mutations [c.8515_8516insA, p.Met2839Asnfs*53 and c.11594_11595insG, p.Glu3866*] in a compound heterozygous state, whereas two subjects have a splicing variant [c.23146-2A > G] in a homozygous state), 6 Friedreich ataxia (FA) patients and 12 healthy controls. Besides that, detailed clinical phenotyping and comprehensive neuropsychological assessment were carried out in all patients with ataxia. In addition to the characteristic cerebellar alterations, pyramidal signs and polyneuropathy were observed at least in 2 SYNE1 ataxia patients, for which no other underlying reason was found. The eye tracking assessment revealed hypometric saccades in the longer amplitude (18.4°) saccadic paradigm in all SYNE1 patients, whereas 2 out of 3 SYNE1 subjects performed slow saccades as well. In the antisaccade task, higher incorrect ratios of antisaccades were demonstrated in SYNE1 patients compared to healthy controls, showing inverse correlation with working memory test results. The corresponding data of FA patients was dispersed over a wide range, partially overlapping with control data. Conclusions The current study draws attention to the presence of eye movement disorders in patients with SYNE1 ataxia and demonstrates that alterations in the antisaccade paradigm may be related to working memory deficits.
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Affiliation(s)
- Laszlo Szpisjak
- Department of Neurology, University of Szeged, Semmelweis u. 6, 6725, Szeged, Hungary
| | - Gabor Szaraz
- Department of Neurology, University of Szeged, Semmelweis u. 6, 6725, Szeged, Hungary
| | - Andras Salamon
- Department of Neurology, University of Szeged, Semmelweis u. 6, 6725, Szeged, Hungary
| | - Viola L Nemeth
- Department of Neurology, University of Szeged, Semmelweis u. 6, 6725, Szeged, Hungary
| | - Noemi Szepfalusi
- Department of Neurology, University of Szeged, Semmelweis u. 6, 6725, Szeged, Hungary
| | - Gabor Veres
- Department of Neurology, University of Szeged, Semmelweis u. 6, 6725, Szeged, Hungary.,MTA-SZTE Neuroscience Research Group, Szeged, Hungary
| | - Balint Kincses
- Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Zoltan Maroti
- Genetic Diagnostic Laboratory, Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Hungary
| | - Tibor Kalmar
- Genetic Diagnostic Laboratory, Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Hungary
| | | | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Peter Klivenyi
- Department of Neurology, University of Szeged, Semmelweis u. 6, 6725, Szeged, Hungary
| | - Denes Zadori
- Department of Neurology, University of Szeged, Semmelweis u. 6, 6725, Szeged, Hungary.
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Lim SH, Shin S, Kim MH, Kim EC, Lee DY, Moon J, Park HY, Ryu YK, Kang YM, Kang YJ, Kim TH, Lee NY, Kim NS, Yu DY, Shim I, Gondo Y, Satake M, Kim E, Kim KS, Min SS, Lee JR. Depression-like behaviors induced by defective PTPRT activity through dysregulated synaptic functions and neurogenesis. J Cell Sci 2020; 133:jcs243972. [PMID: 32938684 DOI: 10.1242/jcs.243972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 09/07/2020] [Indexed: 12/27/2022] Open
Abstract
PTPRT has been known to regulate synaptic formation and dendritic arborization of hippocampal neurons. PTPRT-/- null and PTPRT-D401A mutant mice displayed enhanced depression-like behaviors compared with wild-type mice. Transient knockdown of PTPRT in the dentate gyrus enhanced the depression-like behaviors of wild-type mice, whereas rescued expression of PTPRT ameliorated the behaviors of PTPRT-null mice. Chronic stress exposure reduced expression of PTPRT in the hippocampus of mice. In PTPRT-deficient mice the expression of GluR2 (also known as GRIA2) was attenuated as a consequence of dysregulated tyrosine phosphorylation, and the long-term potentiation at perforant-dentate gyrus synapses was augmented. The inhibitory synaptic transmission of the dentate gyrus and hippocampal GABA concentration were reduced in PTPRT-deficient mice. In addition, the hippocampal expression of GABA transporter GAT3 (also known as SLC6A11) was decreased, and its tyrosine phosphorylation was increased in PTPRT-deficient mice. PTPRT-deficient mice displayed reduced numbers and neurite length of newborn granule cells in the dentate gyrus and had attenuated neurogenic ability of embryonic hippocampal neural stem cells. In conclusion, our findings show that the physiological roles of PTPRT in hippocampal neurogenesis, as well as synaptic functions, are involved in the pathogenesis of depressive disorder.
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Affiliation(s)
- So-Hee Lim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Sangyep Shin
- Department of Physiology and Biophysics, School of Medicine, Eulji University, Daejeon 34824, Korea
| | - Myoung-Hwan Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Eung Chang Kim
- Department of Physiology and Biophysics, School of Medicine, Eulji University, Daejeon 34824, Korea
| | - Da Yong Lee
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jeonghee Moon
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Hye-Yeon Park
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Young-Kyoung Ryu
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Young-Mi Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Yu Jeong Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Tae Hwan Kim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Na-Yoon Lee
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Nam-Soon Kim
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Dae-Yeul Yu
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Insop Shim
- Department of Physiology, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Yoichi Gondo
- Department of Molecular Life Sciences, Tokai University School of Medicine, Shimo-Kasuya, Isehara 259-1193, Japan
| | - Masanobu Satake
- Department of Molecular Immunology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Eunhee Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Kyoung-Shim Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Sun Seek Min
- Department of Physiology and Biophysics, School of Medicine, Eulji University, Daejeon 34824, Korea
| | - Jae-Ran Lee
- Rare Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
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Woldegebriel R, Kvist J, Andersson N, Õunap K, Reinson K, Wojcik MH, Bijlsma EK, Hoffer MJV, Ryan MM, Stark Z, Walsh M, Cuppen I, van den Boogaard MJH, Bharucha-Goebel D, Donkervoort S, Winchester S, Zori R, Bönnemann CG, Maroofian R, O’Connor E, Houlden H, Zhao F, Carpén O, White M, Sreedharan J, Stewart M, Ylikallio E, Tyynismaa H. Distinct effects on mRNA export factor GANP underlie neurological disease phenotypes and alter gene expression depending on intron content. Hum Mol Genet 2020; 29:1426-1439. [PMID: 32202298 PMCID: PMC7297229 DOI: 10.1093/hmg/ddaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/15/2022] Open
Abstract
Defects in the mRNA export scaffold protein GANP, encoded by the MCM3AP gene, cause autosomal recessive early-onset peripheral neuropathy with or without intellectual disability. We extend here the phenotypic range associated with MCM3AP variants, by describing a severely hypotonic child and a sibling pair with a progressive encephalopathic syndrome. In addition, our analysis of skin fibroblasts from affected individuals from seven unrelated families indicates that disease variants result in depletion of GANP except when they alter critical residues in the Sac3 mRNA binding domain. GANP depletion was associated with more severe phenotypes compared with the Sac3 variants. Patient fibroblasts showed transcriptome alterations that suggested intron content-dependent regulation of gene expression. For example, all differentially expressed intronless genes were downregulated, including ATXN7L3B, which couples mRNA export to transcription activation by association with the TREX-2 and SAGA complexes. Our results provide insight into the molecular basis behind genotype-phenotype correlations in MCM3AP-associated disease and suggest mechanisms by which GANP defects might alter RNA metabolism.
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Affiliation(s)
- Rosa Woldegebriel
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jouni Kvist
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
| | - Noora Andersson
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H Wojcik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Genomics and Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique M Ryan
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Royal Children’s Hospital, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne 3052, Australia
| | - Zornitza Stark
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne 3052, Australia
| | - Maie Walsh
- Murdoch Children’s Research Institute, Melbourne 3052, Australia
| | - Inge Cuppen
- Department of Pediatric Neurology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Division of Neurology, Children's National Health System, Washington, DC, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sara Winchester
- Child Neurology Center of Northwest Florida, Pensacola, FL, USA
| | - Roberto Zori
- Division of Genetics and Metabolism, University of Florida, Gainesville, FL, USA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Emer O’Connor
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Fang Zhao
- Department of Pathology and Genetics, HUSLAB Laboratories, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland
| | - Matthew White
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jemeen Sreedharan
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, 00290 Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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31
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Mesman S, Bakker R, Smidt MP. Tcf4 is required for correct brain development during embryogenesis. Mol Cell Neurosci 2020; 106:103502. [PMID: 32474139 DOI: 10.1016/j.mcn.2020.103502] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/28/2020] [Accepted: 05/19/2020] [Indexed: 01/02/2023] Open
Abstract
Tcf4 has been linked to autism, schizophrenia, and Pitt-Hopkins Syndrome (PTHS) in humans, suggesting a role for Tcf4 in brain development and importantly cortical development. However, the mechanisms behind its role in disease and brain development are still elusive. We provide evidence that Tcf4 has a critical function in the differentiation of cortical regions, corpus callosum and anterior commissure formation, and development of the hippocampus during murine embryonic development. In the present study, we show that Tcf4 is expressed throughout the developing brain at the peak of neurogenesis. Deletion of Tcf4 results in mis-specification of the cortical neurons, malformation of the corpus callosum and anterior commissure, and hypoplasia of the hippocampus. Furthermore, the Tcf4 mutant shows an absence of midline remodeling, underlined by the loss of GFAP-expressing midline glia in the indusium griseum and callosal wedge and midline zipper glia in the telencephalic midline. RNA-sequencing on E14.5 cortex material shows that Tcf4 functions as a transcriptional activator and loss of Tcf4 results in downregulation of genes linked to neurogenesis and neuronal maturation. Furthermore, many genes that are differentially expressed after Tcf4 ablation are linked to other neurodevelopmental disorders. Taken together, we show that correct brain development and neuronal differentiation are severely affected in Tcf4 mutants, phenocopying morphological brain defects detected in PTHS patients. The presented data identifies new leads to understand the mechanisms behind brain and specifically cortical development and can provide novel insights in developmental mechanisms underlying human brain defects.
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Affiliation(s)
- Simone Mesman
- Swammerdam Institute for Life Sciences, FNWI University of Amsterdam, Science Park 904, 1098XH Amsterdam, the Netherlands
| | - Reinier Bakker
- Swammerdam Institute for Life Sciences, FNWI University of Amsterdam, Science Park 904, 1098XH Amsterdam, the Netherlands
| | - Marten P Smidt
- Swammerdam Institute for Life Sciences, FNWI University of Amsterdam, Science Park 904, 1098XH Amsterdam, the Netherlands.
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32
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Ilie A, Boucher A, Park J, Berghuis AM, McKinney RA, Orlowski J. Assorted dysfunctions of endosomal alkali cation/proton exchanger SLC9A6 variants linked to Christianson syndrome. J Biol Chem 2020; 295:7075-7095. [PMID: 32277048 PMCID: PMC7242699 DOI: 10.1074/jbc.ra120.012614] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic screening has identified numerous variants of the endosomal solute carrier family 9 member A6 (SLC9A6)/(Na+,K+)/H+ exchanger 6 (NHE6) gene that cause Christianson syndrome, a debilitating X-linked developmental disorder associated with a range of neurological, somatic, and behavioral symptoms. Many of these variants cause complete loss of NHE6 expression, but how subtler missense substitutions or nonsense mutations that partially truncate its C-terminal cytoplasmic regulatory domain impair NHE6 activity and endosomal function are poorly understood. Here, we describe the molecular and cellular consequences of six unique mutations located in the N-terminal cytoplasmic segment (A9S), the membrane ion translocation domain (L188P and G383D), and the C-terminal regulatory domain (E547*, R568Q, and W570*) of human NHE6 that purportedly cause disease. Using a heterologous NHE6-deficient cell expression system, we show that the biochemical, catalytic, and cellular properties of the A9S and R568Q variants were largely indistinguishable from those of the WT transporter, which obscured their disease significance. By contrast, the L188P, G383D, E547*, and W570* mutants exhibited variable deficiencies in biosynthetic post-translational maturation, membrane sorting, pH homeostasis in recycling endosomes, and cargo trafficking, and they also triggered apoptosis. These findings broaden our understanding of the molecular dysfunctions of distinct NHE6 variants associated with Christianson syndrome.
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Affiliation(s)
- Alina Ilie
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Annie Boucher
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | | | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - John Orlowski
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
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33
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Lu C, Zhang Y, Qin Y, Xu Q, Zhou R, Cui Y, Zhu Y, Zhang X, Zhang J, Wei X, Wang M, Hang B, Mao JH, Snijders AM, Liu M, Hu Z, Shen H, Zhou Z, Guo X, Wu X, Wang X, Xia Y. Human X chromosome exome sequencing identifies BCORL1 as contributor to spermatogenesis. J Med Genet 2020; 58:56-65. [PMID: 32376790 DOI: 10.1136/jmedgenet-2019-106598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 03/16/2020] [Accepted: 03/21/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Infertility affects approximately 15% of couples worldwide with male infertility being responsible for approximately 50% of cases. Although accumulating evidence demonstrates the critical role of the X chromosome in spermatogenesis during the last few decades, the expression patterns and potential impact of the X chromosome, together with X linked genes, on male infertility are less well understood. METHODS We performed X chromosome exome sequencing followed by a two-stage independent population validation in 1333 non-obstructive azoospermia cases and 1141 healthy controls to identify variant classes with high likelihood of pathogenicity. To explore the functions of these candidate genes in spermatogenesis, we first knocked down these candidate genes individually in mouse spermatogonial stem cells (SSCs) using short interfering RNA oligonucleotides and then generated candidate genes knockout mice by CRISPR-Cas9 system. RESULTS Four low-frequency variants were identified in four genes (BCORL1, MAP7D3, ARMCX4 and H2BFWT) associated with male infertility. Functional studies of the mouse SSCs revealed that knocking down Bcorl1 or Mtap7d3 could inhibit SSCs self-renewal and knocking down Armcx4 could repress SSCs differentiation in vitro. Using CRISPR-Cas9 system, Bcorl1 and Mtap7d3 knockout mice were generated. Excitingly, Bcorl1 knockout mice were infertile with impaired spermatogenesis. Moreover, Bcorl1 knockout mice exhibited impaired sperm motility and sperm cells displayed abnormal mitochondrial structure. CONCLUSION Our data indicate that the X-linked genes are associated with male infertility and involved in regulating SSCs, which provides a new insight into the role of X-linked genes in spermatogenesis.
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Affiliation(s)
- Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yan Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Qiaoqiao Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ran Zhou
- Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jintao Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiang Wei
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Min Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bo Hang
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jian-Hua Mao
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Antoine M Snijders
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zuomin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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Chen CP, Chen CY, Chern SR, Wu PS, Chen SW, Chuang TY, Wang W. Detection of a familial 21q22.3 microduplication in a fetus associated with congenital heart defects. Taiwan J Obstet Gynecol 2020; 58:869-871. [PMID: 31759545 DOI: 10.1016/j.tjog.2019.09.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2019] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE We present a familial 21q22.3 microduplication in a fetus associated with prenatally detected congenital heart defects (CHD). CASE REPORT A 38-year-old woman underwent amniocentesis at 22 weeks of gestation because of sonographic findings of double outlet of right ventricle, ventricular septal defect and transposition of great artery in the fetus. Her husband was 42 years old, and there was no CHD and congenital malformation in the family. Cytogenetic analysis revealed a karyotype of 46,XY in the fetus. Simultaneous array comparative genomic hybridization (aCGH) analysis using uncultured amniocytes revealed a 0.56-Mb microduplication of 21q22.3 or arr 21q22.3 (47,482,210-48,043,704)×3.0 [GRCh37 (hg19)] encompassing nine Online Mendelian Inheritance in Man (OMIM) genes of FTCD, SPATC1L, LSS, MCM3AP, YBEY, PCNT, DIP2A, S100B and PRMT2. aCGH analysis of the parental bloods revealed that the phenotypically normal father carried the same microduplication. The parents decided to continue the pregnancy, and a 3168-g male baby was delivered at term without Down syndrome phenotype except CHD. Mutational analysis of the CRELD1 gene on the DNA extracted from the cord blood showed no mutation in CRELD1. Postnatal molecular cytogenetic analysis of the cord blood confirmed the prenatal diagnosis. The infant underwent a successful heart surgery to correct the CHD and was doing well without psychomotor or developmental delay at six months of age. CONCLUSION Prenatal diagnosis of 21q22.3 microduplication associated with CHD should include a differential diagnosis of Down syndrome.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Chen-Yu Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Yun Chuang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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35
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Al-Naama N, Mackeh R, Kino T. C 2H 2-Type Zinc Finger Proteins in Brain Development, Neurodevelopmental, and Other Neuropsychiatric Disorders: Systematic Literature-Based Analysis. Front Neurol 2020; 11:32. [PMID: 32117005 PMCID: PMC7034409 DOI: 10.3389/fneur.2020.00032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are multifaceted pathologic conditions manifested with intellectual disability, autistic features, psychiatric problems, motor dysfunction, and/or genetic/chromosomal abnormalities. They are associated with skewed neurogenesis and brain development, in part through dysfunction of the neural stem cells (NSCs) where abnormal transcriptional regulation on key genes play significant roles. Recent accumulated evidence highlights C2H2-type zinc finger proteins (C2H2-ZNFs), the largest transcription factor family in humans, as important targets for the pathologic processes associated with NDDs. In this review, we identified their significant accumulation (74 C2H2-ZNFs: ~10% of all human member proteins) in brain physiology and pathology. Specifically, we discuss their physiologic contribution to brain development, particularly focusing on their actions in NSCs. We then explain their pathologic implications in various forms of NDDs, such as morphological brain abnormalities, intellectual disabilities, and psychiatric disorders. We found an important tendency that poly-ZNFs and KRAB-ZNFs tend to be involved in the diseases that compromise gross brain structure and human-specific higher-order functions, respectively. This may be consistent with their characteristic appearance in the course of species evolution and corresponding contribution to these brain activities.
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Affiliation(s)
- Njoud Al-Naama
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Rafah Mackeh
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Tomoshige Kino
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
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36
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Functional Assessment In Vivo of the Mouse Homolog of the Human Ala-9-Ser NHE6 Variant. eNeuro 2019; 6:ENEURO.0046-19.2019. [PMID: 31676550 PMCID: PMC6893231 DOI: 10.1523/eneuro.0046-19.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 11/21/2022] Open
Abstract
Christianson syndrome (CS) is an X-linked neurogenetic disorder resulting from loss-of-function (LoF) mutations in SLC9A6, which encodes the endosomal Na+/H+ exchanger 6 (NHE6). NHE6 regulates proton efflux from endosomes and, thus, participates in regulating cargo processing and trafficking. LoF mutations in NHE6 cause aberrant acidification of endosomes. While CS arises in males generally due to clear LoF mutations, other potentially hypomorphic variants have emerged, yet most of these variants have not been evaluated for functional effects, particularly in vivo Here we characterize an SLC9A6 variant that has been previously reported in patients, yet now also appears in exome datasets of largely control individuals-c.25G>T, p.A9S. By heterologous expression in cell lines, we show that human NHE6A9S is expressed and localizes in a manner comparable to control NHE6. By genome editing, we generated the equivalent NHE6 mutation in mouse-p.A11S-and determined that male NHE6A11S mice have normal brain size at 6 months of age and do not show cerebellar degeneration or defective neuronal arborization. Neurons from male NHE6A11S mice also did not demonstrate an abnormality in intraendosomal pH compared with controls. These findings are in contrast to findings in NHE6-null mice previously reported and indicate that the NHE6A11S variant functions at a level equivalent to control NHE6 for many of the assays performed. These data stand in support of the population genetic data, which are also evaluated here, indicating that the A9S variant is unlikely to confer disease susceptibility with high penetrance.
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37
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Zhang DL, Blair MP, Zeid JL, Basith SST, Shapiro MJ. FEVR phenotype associated with septo-optic dysplasia. Ophthalmic Genet 2019; 40:449-452. [PMID: 31755341 DOI: 10.1080/13816810.2019.1660380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: Septo-optic dysplasia, also known as de Morsier syndrome, is a disorder of brain development characterized by optic nerve hypoplasia, hypopituitarism, and midline brain defects.Materials and Methods: Single retrospective case report.Results: An infant born at 38 5/7 weeks gestation age weighing 3125 g developed respiratory distress shortly after birth. Systemic findings included myocardial dysfunction, hypopituitarism, feeding intolerance, microphallus, and dysmorphic features. Eye examination revealed tractional retinal detachments and optic nerve hypoplasia. In addition, peripheral non-perfusion and peripheral neovascularization were consistent with Familial Exudative Vitreoretinopathy (FEVR) phenotype. MRI showed hypoplastic optic nerves, ectopic posterior pituitary with hypoplastic pituitary infundibulum, and slightly thin corpus callosum, diagnostic of septo-optic dysplasia. Genetic testing revealed no pathogenic variants and two variants of uncertain significance.Conclusion: FEVR findings can be associated with septo-optic dysplasia and may point to an etiologic connection between neural development and subsequent vascular development.
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Affiliation(s)
| | - Michael P Blair
- Retina Consultants Ltd., Des Plaines, Illinois, USA.,Department of Ophthalmology and Visual Science, University of Chicago, Chicago, Illinois, USA
| | - Janice L Zeid
- Department of Pediatric Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Syeda S T Basith
- Department of Pediatric Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
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38
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Kerner-Rossi M, Gulinello M, Walkley S, Dobrenis K. Pathobiology of Christianson syndrome: Linking disrupted endosomal-lysosomal function with intellectual disability and sensory impairments. Neurobiol Learn Mem 2019; 165:106867. [PMID: 29772390 PMCID: PMC6235725 DOI: 10.1016/j.nlm.2018.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/04/2018] [Accepted: 05/12/2018] [Indexed: 11/18/2022]
Abstract
Christianson syndrome (CS) is a recently described rare neurogenetic disorder presenting early in life with a broad range of neurological symptoms, including severe intellectual disability with nonverbal status, hyperactivity, epilepsy, and progressive ataxia due to cerebellar atrophy. CS is due to loss-of-function mutations in SLC9A6, encoding NHE6, a sodium-hydrogen exchanger involved in the regulation of early endosomal pH. Here we review what is currently known about the neuropathogenesis of CS, based on insights from experimental models, which to date have focused on mechanisms that affect the CNS, specifically the brain. In addition, parental reports of sensory disturbances in their children with CS, including an apparent insensitivity to pain, led us to explore sensory function and related neuropathology in Slc9a6 KO mice. We present new data showing sensory deficits in Slc9a6 KO mice, which had reduced behavioral responses to noxious thermal and mechanical stimuli (Hargreaves and Von Frey assays, respectively) compared to wild type (WT) littermates. Immunohistochemical and ultrastructural analysis of the spinal cord and peripheral nervous system revealed intracellular accumulation of the glycosphingolipid GM2 ganglioside in KO but not WT mice. This cellular storage phenotype was most abundant in neurons of lamina I-II of the dorsal horn, a major relay site in the processing of painful stimuli. Spinal cords of KO mice also exhibited changes in astroglial and microglial populations throughout the gray matter suggestive of a neuroinflammatory process. Our findings establish the Slc9a6 KO mouse as a relevant tool for studying the sensory deficits in CS, and highlight selective vulnerabilities in relevant cell populations that may contribute to this phenotype. How NHE6 loss of function leads to such a multifaceted neurological syndrome is still undefined, and it is likely that NHE6 is involved with many cellular processes critical to normal nervous system development and function. In addition, the sensory issues exhibited by Slc9a6 KO mice, in combination with our neuropathological findings, are consistent with NHE6 loss of function impacting the entire nervous system. Sensory dysfunction in intellectually disabled individuals is challenging to assess and may impair patient safety and quality of life. Further mechanistic studies of the neurological impairments underlying CS and other genetic intellectual disability disorders must also take into account mechanisms affecting broader nervous system function in order to understand the full range of associated disabilities.
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Affiliation(s)
- Mallory Kerner-Rossi
- Dominick P. Purpura Dept. of Neuroscience, Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Maria Gulinello
- Dominick P. Purpura Dept. of Neuroscience, Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA; IDDRC Behavioral Core Facility, Neuroscience Department, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven Walkley
- Dominick P. Purpura Dept. of Neuroscience, Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Kostantin Dobrenis
- Dominick P. Purpura Dept. of Neuroscience, Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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39
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Sedghi M, Moslemi AR, Cabrera-Serrano M, Ansari B, Ghasemi M, Baktashian M, Fattahpour A, Tajsharghi H. Recessive Charcot-Marie-Tooth and multiple sclerosis associated with a variant in MCM3AP. Brain Commun 2019; 1:fcz011. [PMID: 32954258 PMCID: PMC7425404 DOI: 10.1093/braincomms/fcz011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/09/2023] Open
Abstract
Variants in MCM3AP, encoding the germinal-centre associated nuclear protein, have been associated with progressive polyneuropathy with or without intellectual disability and ptosis in some cases, and with a complex phenotype with immunodeficiency, skin changes and myelodysplasia. MCM3AP encoded protein functions as an acetyltransferase that acetylates the replication protein, MCM3, and plays a key role in the regulation of DNA replication. In this study, we report a novel variant in MCM3AP (p.Ile954Thr), in a family including three affected individuals with characteristic features of Charcot-Marie-Tooth neuropathy and multiple sclerosis, an inflammatory condition of the central nervous system without known genetic cause. The affected individuals were homozygous for a missense MCM3AP variant, located at the Sac3 domain, which was predicted to affect conserved amino acid likely important for the function of the germinal-centre associated nuclear protein. Our data support further expansion of the clinical spectrum linked to MCM3AP variant and highlight that MCM3AP should be considered in patients with accompaniment of recessive motor axonal Charcot-Marie-Tooth neuropathy and multiple sclerosis.
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Affiliation(s)
- Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali-Reza Moslemi
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg University, Gothenburg, Sweden
| | - Macarena Cabrera-Serrano
- Department of Neurology, Hospital Universitario Virgen del Rocio, Sevilla, Spain.,Instituto de Biomedicina de Sevilla, Universidad de Sevilla, Sevilla, Spain
| | - Behnaz Ansari
- Department of neurology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majid Ghasemi
- Department of neurology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mojtaba Baktashian
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Fattahpour
- Radiology Resident, Department of Radiology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Homa Tajsharghi
- Division of Biomedicine, School of Health Science, University of Skovde, SE-541 28 Skovde, Sweden
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40
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Nicita F, Stregapede F, Tessa A, Bassi MT, Jezela-Stanek A, Primiano G, Pizzuti A, Barghigiani M, Nardella M, Zanni G, Servidei S, Astrea G, Panzeri E, Maghini C, Losito L, Ploski R, Gasperowicz P, Santorelli FM, Bertini E, Travaglini L. Defining the clinical-genetic and neuroradiological features in SPG54: description of eight additional cases and nine novel DDHD2 variants. J Neurol 2019; 266:2657-2664. [DOI: 10.1007/s00415-019-09466-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 11/29/2022]
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41
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Ylikallio E, Woldegebriel R, Tyynismaa H. Reply: A novel MCM3AP mutation in a Lebanese family with recessive Charcot-Marie-Tooth neuropathy. Brain 2019; 141:e67. [PMID: 29982292 DOI: 10.1093/brain/awy185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emil Ylikallio
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Rosa Woldegebriel
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Henna Tyynismaa
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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42
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Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M, Lipkowitz B, Akhtarkhavari T, Mehvari S, Otto S, Mohseni M, Arzhangi S, Jamali P, Mojahedi F, Taghdiri M, Papari E, Soltani Banavandi MJ, Akbari S, Tonekaboni SH, Dehghani H, Ebrahimpour MR, Bader I, Davarnia B, Cohen M, Khodaei H, Albrecht B, Azimi S, Zirn B, Bastami M, Wieczorek D, Bahrami G, Keleman K, Vahid LN, Tzschach A, Gärtner J, Gillessen-Kaesbach G, Varaghchi JR, Timmermann B, Pourfatemi F, Jankhah A, Chen W, Nikuei P, Kalscheuer VM, Oladnabi M, Wienker TF, Ropers HH, Najmabadi H. Genetics of intellectual disability in consanguineous families. Mol Psychiatry 2019; 24:1027-1039. [PMID: 29302074 DOI: 10.1038/s41380-017-0012-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 01/17/2023]
Abstract
Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.
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Affiliation(s)
- Hao Hu
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Guangzhou Women and Children's Medical Center, 510623, Guangzhou, China
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Luciana Musante
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ralf Herwig
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Cornelia Oppitz
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Vanessa Suckow
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Farzaneh Larti
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sabine Otto
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Payman Jamali
- Shahrood Genetic Counseling Center, Welfare Office, Semnan, 36156, Iran
| | - Faezeh Mojahedi
- Mashhad Medical Genetic Counseling Center, Mashhad, 91767, Iran
| | - Maryam Taghdiri
- Shiraz Genetic Counseling Center, Welfare Office, Shiraz, Iran
| | - Elaheh Papari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Saeide Akbari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Seyed Hassan Tonekaboni
- Pediatric Neurology Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, 15468, Iran
| | - Hossein Dehghani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Mohammad Reza Ebrahimpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ingrid Bader
- Kinderzentrum München, Technische Universität München, 81377, München, Germany
| | - Behzad Davarnia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Monika Cohen
- Children's Center Munich, 81377, Munich, Germany
| | - Hossein Khodaei
- Meybod Genetics Research Center, Welfare Organization, Yazd, 89651, Iran
| | - Beate Albrecht
- Institute of Human Genetics, University Hospital Essen, 45122, Essen, Germany
| | - Sarah Azimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Birgit Zirn
- Genetikum Counseling Center, 70173, Stuttgart, Germany
| | - Milad Bastami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Dagmar Wieczorek
- Institute of Human Genetics and Anthropology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Gholamreza Bahrami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Krystyna Keleman
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Leila Nouri Vahid
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Andreas Tzschach
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Institute of Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | - Jutta Gärtner
- University Medical Center, Georg August University Göttingen, 37075, Göttingen, Germany
| | | | | | - Bernd Timmermann
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | | | - Aria Jankhah
- Shiraz Genetic Counseling Center, Shiraz, 71346, Iran
| | - Wei Chen
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, 13125, Berlin, Germany
| | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Thomas F Wienker
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Hans-Hilger Ropers
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany. .,Institute of Human Genetics, University Medicine, Mainz, Germany.
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran. .,Kariminejad - Najmabadi Pathology & Genetics Centre, Tehran, 14667-13713, Iran.
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43
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Karakaya M, Mazaheri N, Polat I, Bharucha-Goebel D, Donkervoort S, Maroofian R, Shariati G, Hoelker I, Monaghan K, Winchester S, Zori R, Galehdari H, Bönnemann CG, Yis U, Wirth B. Biallelic MCM3AP mutations cause Charcot-Marie-Tooth neuropathy with variable clinical presentation. Brain 2019; 140:e65. [PMID: 28969388 DOI: 10.1093/brain/awx222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Neda Mazaheri
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, East Mihan Ave., Kianpars, Ahvaz, Iran
| | - Ipek Polat
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Diana Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, USA.,Division of Neurology, Children's National Health System, Washington, DC, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, USA
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, Cranmer, 16 Terrace, London, UK.,Medical Research, RILD Welcome Wolfson Centre, Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, East Mihan Ave., Kianpars, Ahvaz, Iran.,Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Irmgard Hoelker
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | | | - Sara Winchester
- Child Neurology Center of Northwest Florida, Pensacola, FL, USA
| | - Robert Zori
- Division of Genetics and Metabolism, University of Florida, Gainesville, FL, USA
| | - Hamid Galehdari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, USA
| | - Uluc Yis
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
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Shukla A, Girisha KM, Somashekar PH, Nampoothiri S, McClellan R, Vernon HJ. Variants in the transcriptional corepressor BCORL1 are associated with an X-linked disorder of intellectual disability, dysmorphic features, and behavioral abnormalities. Am J Med Genet A 2019; 179:870-874. [PMID: 30941876 DOI: 10.1002/ajmg.a.61118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/08/2019] [Accepted: 02/25/2019] [Indexed: 11/05/2022]
Abstract
BCORL1, a transcriptional corepressor, is involved in negative gene regulation through associations with several protein complexes including Class II histone deacetylases (HDACs). Acquired somatic mutations in BCORL1 have been implicated in the pathogenesis of several malignancies, but germline mutations of BCORL1 have not been associated with a specific genetic syndrome. We report five individuals from three pedigrees with phenotypes including intellectual disability, behavioral difficulties, and dysmorphic features who were found via whole exome sequencing to have variants in BCORL1. In silico analysis of these variants strongly suggests pathogenicity. We propose that hemizygous pathogenic variants in BCORL1 underlie a newly identified X-linked epigenetic syndrome.
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Affiliation(s)
- Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Puneeth H Somashekar
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sheela Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Rebecca McClellan
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | - Hilary J Vernon
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland.,Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland
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45
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Levchenko OA, Lavrov AV. [Massive parallel sequencing for molecular-genetic diagnosis of mental retardation]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 118:65-71. [PMID: 30698565 DOI: 10.17116/jnevro201811812165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene mutations occur with high frequency in children with mental retardation. Standard diagnostic methods, such as TMS, Sanger's sequencing of individual genes, MLPA analysis of deletions, and investigation of methylation status in Martin-Bell syndrome are not informative in the majority of cases that hampered further diagnostic efforts. Massive parallel sequencing (MPS) allowed physicians to continue diagnostic search in previously undiagnosed cases and to find molecular causes of disease. MPS permits to discover a large number of new genes and understand the pathogenesis of mental retardation and brain development more deeply. It became possible to perform prenatal and pre-implantation diagnostics. However, big data generate big problems with their interpretation the genetic counselor faces with. This review reflects the advantages and disadvantages of MPS. Different variants of MPS, including gene panels, whole exome and whole genome sequencing as well as sequencing of trios, are described. In addition, the authors discuss the difficulties of interpretation of the results and recommendations for obtaining the most accurate results.
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Affiliation(s)
- O A Levchenko
- Research Centre for Medical Genetics, Moscow, Russia
| | - A V Lavrov
- Research Centre for Medical Genetics, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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46
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Blum S, Ji Y, Pennisi D, Li Z, Leo P, McCombe P, Brown MA. Genome-wide association study in Guillain-Barré syndrome. J Neuroimmunol 2018; 323:109-114. [DOI: 10.1016/j.jneuroim.2018.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 10/28/2022]
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Fu XN, Xiong H. Genetic and Clinical Advances of Congenital Muscular Dystrophy. Chin Med J (Engl) 2018; 130:2624-2631. [PMID: 29067961 PMCID: PMC5678264 DOI: 10.4103/0366-6999.217091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Objective: The aim was to update the genetic and clinical advances of congenital muscular dystrophy (CMD), based on a systematic review of the literature from 1991 to 2017. Data Sources: Articles in English published in PubMed from 1991 to 2017 English were searched. The terms used in the literature searches were CMD. Study Selection: The task force initially identified citations for 98 published articles. Of the 98 articles, 52 studies were selected after further detailed review. Three articles, which were not written in English, were excluded from the study. This study referred to all the important and English literature in full. Results: CMD is a group of early-onset disorders encompassing great clinical and genetic heterogeneity. Patients present with muscle weakness typically from birth to early infancy, delay or arrest of gross motor development, and joint and/or spinal rigidity. The diagnosis of CMD relies on clinical findings, brain and muscle imaging, muscle biopsy histology, muscle and/or skin immunohistochemical staining, and molecular genetic testing. Conclusions: Advances in next-generation sequencing and histopathological techniques have enabled the recognition of distinct CMD subtypes supported by specific gene identification. Genetic counseling and multidisciplinary management of CMD play an important role in help patients and their family. Further elucidation of the significant clinical and genetic heterogeneity, therapeutic targets, and the clinical care for patients remains our challenge for the future.
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Affiliation(s)
- Xiao-Na Fu
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
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48
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Ylikallio E, Woldegebriel R, Tumiati M, Isohanni P, Ryan MM, Stark Z, Walsh M, Sawyer SL, Bell KM, Oshlack A, Lockhart PJ, Shcherbii M, Estrada-Cuzcano A, Atkinson D, Hartley T, Tetreault M, Cuppen I, van der Pol WL, Candayan A, Battaloglu E, Parman Y, van Gassen KLI, van den Boogaard MJH, Boycott KM, Kauppi L, Jordanova A, Lönnqvist T, Tyynismaa H. MCM3AP in recessive Charcot-Marie-Tooth neuropathy and mild intellectual disability. Brain 2017. [PMID: 28633435 DOI: 10.1093/brain/awx138] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Defects in mRNA export from the nucleus have been linked to various neurodegenerative disorders. We report mutations in the gene MCM3AP, encoding the germinal center associated nuclear protein (GANP), in nine affected individuals from five unrelated families. The variants were associated with severe childhood onset primarily axonal (four families) or demyelinating (one family) Charcot-Marie-Tooth neuropathy. Mild to moderate intellectual disability was present in seven of nine affected individuals. The affected individuals were either compound heterozygous or homozygous for different MCM3AP variants, which were predicted to cause depletion of GANP or affect conserved amino acids with likely importance for its function. Accordingly, fibroblasts of affected individuals from one family demonstrated severe depletion of GANP. GANP has been described to function as an mRNA export factor, and to suppress TDP-43-mediated motor neuron degeneration in flies. Thus our results suggest defective mRNA export from nucleus as a potential pathogenic mechanism of axonal degeneration in these patients. The identification of MCM3AP variants in affected individuals from multiple centres establishes it as a disease gene for childhood-onset recessively inherited Charcot-Marie-Tooth neuropathy with intellectual disability.
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Affiliation(s)
- Emil Ylikallio
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Rosa Woldegebriel
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland
| | - Manuela Tumiati
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, 00290 Helsinki, Finland
| | - Pirjo Isohanni
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Department of Child Neurology, Children's Hospital and Pediatric Research Center, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Monique M Ryan
- Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Maie Walsh
- Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Sarah L Sawyer
- Department of Genetics and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, Canada
| | - Katrina M Bell
- Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Alicia Oshlack
- Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia
| | - Paul J Lockhart
- Murdoch Children's Research Institute, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, 3052, Australia.,Bruce Lefroy Centre, Murdoch Childrens Research Institute, Melbourne, Victoria, 3052, Australia
| | - Mariia Shcherbii
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland
| | - Alejandro Estrada-Cuzcano
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, 2610 Antwerpen, Belgium
| | - Derek Atkinson
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, 2610 Antwerpen, Belgium
| | - Taila Hartley
- Department of Genetics and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, Canada
| | - Martine Tetreault
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada.,McGill University and Genome Quebec Innovation Center, Montreal, QC H3A 1A4, Canada
| | - Inge Cuppen
- Department of Paediatric Neurology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - W Ludo van der Pol
- Brain Centre Rudolf Magnus, Department of Neurology and Neurosurgery, University Medical Centre Utrecht, 3508 Utrecht, The Netherlands
| | - Ayse Candayan
- Bogazici University, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Esra Battaloglu
- Bogazici University, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Yesim Parman
- Istanbul University, Istanbul Medical School, Department of Neurology, Istanbul, Turkey
| | - Koen L I van Gassen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Kym M Boycott
- Department of Genetics and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, Canada
| | - Liisa Kauppi
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, 00290 Helsinki, Finland
| | - Albena Jordanova
- Molecular Neurogenomics Group, VIB Department of Molecular Genetics, University of Antwerp, 2610 Antwerpen, Belgium
| | - Tuula Lönnqvist
- Department of Child Neurology, Children's Hospital and Pediatric Research Center, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Henna Tyynismaa
- Research Programs Unit, Molecular Neurology, University of Helsinki, 00290 Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, 00290 Helsinki, Finland
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49
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Chen Z, Ren Z, Mei W, Ma Q, Shi Y, Zhang Y, Li S, Xiang L, Zhang J. A novel SYNE1 gene mutation in a Chinese family of Emery-Dreifuss muscular dystrophy-like. BMC MEDICAL GENETICS 2017; 18:63. [PMID: 28583108 PMCID: PMC5460548 DOI: 10.1186/s12881-017-0424-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 05/21/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND In the present study, a novel mutation in exon 46 at codon 2304 (G2304R) of the SYNE1 gene is described in a Chinese family (proband, mother, and sister) with Emery-Dreifuss muscular dystrophy-like, which clinically manifests as muscle weakness, muscle atrophy, joint contracture, and without significant cardiac abnormalities. METHODS Clinical examination and neuroimaging of the captured target region and high-throughput sequencing were performed in a family of four generations. Muscle changes were evaluated using magnetic resonance imaging and muscle biopsies. RESULTS Target region capture sequencing yielded a novel missense mutation in codon 2304 (G2304R), which is a heterozygous A to G point mutation at position 6910 (c.6910A > G) in exon 46 of SYNE1 leading to a glycine-to-arginine substitution (p.Gly2304Arg). The results were also identified by Sanger sequencing in three family members but not in the other three unaffected family members and 100 control subjects. CONCLUSIONS This mutation is probably pathogenic and is the first of its kind reported in a familial Emery-Dreifuss muscular dystrophy-like.
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Affiliation(s)
- Zuzhi Chen
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Zhixia Ren
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Wenli Mei
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Qiankun Ma
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Yingying Shi
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Yuanxing Zhang
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Shujian Li
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Li Xiang
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Jiewen Zhang
- Department of Neurology, People's Hospital of Zhengzhou University, No. 7 Weiwu Road, Zhengzhou, Henan, 450003, China.
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50
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Povysil G, Tzika A, Vogt J, Haunschmid V, Messiaen L, Zschocke J, Klambauer G, Hochreiter S, Wimmer K. panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics. Hum Mutat 2017; 38:889-897. [PMID: 28449315 PMCID: PMC5518446 DOI: 10.1002/humu.23237] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/21/2017] [Accepted: 04/22/2017] [Indexed: 11/10/2022]
Abstract
Targeted next‐generation‐sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy‐number variations (CNVs) in addition to single‐nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user‐friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state‐of‐the‐art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user‐selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user‐friendliness rendering it highly suitable for routine clinical diagnostics.
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Affiliation(s)
- Gundula Povysil
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Antigoni Tzika
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Julia Vogt
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Verena Haunschmid
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Johannes Zschocke
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Günter Klambauer
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Sepp Hochreiter
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
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