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Zhou X, Yang Y, Tai Z, Zhang H, Yang J, Luo Z, Xu Z. The mechanism of mitochondrial autophagy regulating Clathrin-mediated endocytosis in epilepsy. Epilepsia Open 2024; 9:1252-1264. [PMID: 38700951 PMCID: PMC11296089 DOI: 10.1002/epi4.12945] [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: 07/08/2023] [Revised: 03/10/2024] [Accepted: 03/31/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVE The objective of this study is to determine whether inhibition of mitophagy affects seizures through Clathrin-mediated endocytosis (CME). METHODS Pentylenetetrazol (PTZ) was intraperitoneally injected daily to establish a chronic PTZ-kindled seizure. The Western blot (WB) was used to compare the differences in Parkin protein expression between the epilepsy group and the control group. Immunofluorescence was used to detect the expression of MitoTracker and LysoTracker. Transferrin-Alexa488 (Tf-A488) was injected into the hippocampus of mice. We evaluated the effect of 3-methyladenine (3-MA) on epilepsy behavior through observation in PTZ-kindled models. RESULTS The methylated derivative of adenine, known as 3-MA, has been extensively utilized in the field of autophagy research. The transferrin protein is internalized from the extracellular environment into the intracellular space via the CME pathway. Tf-A488 uses a fluorescent marker to track CME. Western blot showed that the expression of Parkin was significantly increased in the PTZ-kindled model (p < 0.05), while 3-MA could reduce the expression (p < 0.05). The fluorescence uptake of MitoTracker and LysoTracker was increased in the primary cultured neurons induced by magnesium-free extracellular fluid (p < 0.05); the fluorescence uptake of Tf-A488 was significantly decreased in the 3-MA group compared with the control group (p < 0.05). Following hippocampal injection of Tf-A488, both the epilepsy group and the 3-MA group exhibited decreased fluorescence uptake, with a more pronounced effect observed in the 3-MA group. Inhibition of mitophagy by 3-MA from day 3 to day 9 progressively exacerbated seizure severity and shortened latency. SIGNIFICANCE It is speculated that the aggravation of seizures by 3-MA may be related to the failure to remove damaged mitochondria in time and effectively after inhibiting mitochondrial autophagy, affecting the vesicle endocytosis function of CME and increasing the susceptibility to epilepsy. SUMMARY Abnormal mitophagy was observed in a chronic pentylenetetrazol-induced seizure model and a Mg2+-free-induced spontaneous recurrent epileptiform discharge model. A fluorescent transferrin marker was utilized to track clathrin-mediated endocytosis. Using an autophagy inhibitor (3-methyladenine) on primary cultured neurons, we discovered that inhibition of autophagy led to a reduction in fluorescent transferrin uptake, while impairing clathrin-mediated endocytosis function mediated by mitophagy. Finally, we examined the effects of 3-methyladenine in an animal model of seizures showing that it exacerbated seizure severity. Ultimately, this study provides insights into potential mechanisms through which mitophagy regulates clathrin-mediated endocytosis in epilepsy.
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Affiliation(s)
- Xuejiao Zhou
- Department of NeurologyThe Affiliated Hospital of Zunyi Medical UniversityZunyiChina
- The Collaborative Innovation Center of Tissue Damage Repair and RegenerationZunyi Medical UniversityZunyiChina
| | - Yu Yang
- Department of NeurologyThe Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Zhenzhen Tai
- Department of NeurologyThe Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Haiqing Zhang
- Department of NeurologyThe Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Juan Yang
- Department of NeurologyThe Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Zhong Luo
- Department of NeurologyThe Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Zucai Xu
- Department of NeurologyThe Affiliated Hospital of Zunyi Medical UniversityZunyiChina
- The Collaborative Innovation Center of Tissue Damage Repair and RegenerationZunyi Medical UniversityZunyiChina
- Key Laboratory of Brain ScienceZunyi Medical UniversityZunyiChina
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Diarra S, Ghosh S, Cissé L, Coulibaly T, Yalcouyé A, Harmison G, Diallo S, Diallo SH, Coulibaly O, Schindler A, Cissé CAK, Maiga AB, Bamba S, Samassekou O, Khokha MK, Mis EK, Lakhani SA, Donovan FX, Jacobson S, Blackstone C, Guinto CO, Landouré G, Bonifacino JS, Fischbeck KH, Grunseich C. AP2A2 mutation and defective endocytosis in a Malian family with hereditary spastic paraplegia. Neurobiol Dis 2024; 198:106537. [PMID: 38772452 PMCID: PMC11209852 DOI: 10.1016/j.nbd.2024.106537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/17/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
Hereditary spastic paraplegia (HSP) comprises a large group of neurogenetic disorders characterized by progressive lower extremity spasticity. Neurological evaluation and genetic testing were completed in a Malian family with early-onset HSP. Three children with unaffected consanguineous parents presented with symptoms consistent with childhood-onset complicated HSP. Neurological evaluation found lower limb weakness, spasticity, dysarthria, seizures, and intellectual disability. Brain MRI showed corpus callosum thinning with cortical and spinal cord atrophy, and an EEG detected slow background in the index patient. Whole exome sequencing identified a homozygous missense variant in the adaptor protein (AP) complex 2 alpha-2 subunit (AP2A2) gene. Western blot analysis showed reduced levels of AP2A2 in patient-iPSC derived neuronal cells. Endocytosis of transferrin receptor (TfR) was decreased in patient-derived neurons. In addition, we observed increased axon initial segment length in patient-derived neurons. Xenopus tropicalis tadpoles with ap2a2 knockout showed cerebral edema and progressive seizures. Immunoprecipitation of the mutant human AP-2-appendage alpha-C construct showed defective binding to accessory proteins. We report AP2A2 as a novel genetic entity associated with HSP and provide functional data in patient-derived neuron cells and a frog model. These findings expand our understanding of the mechanism of HSP and improve the genetic diagnosis of this condition.
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Affiliation(s)
- Salimata Diarra
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States; Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Saikat Ghosh
- Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
| | - Lassana Cissé
- Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Thomas Coulibaly
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
| | - Abdoulaye Yalcouyé
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - George Harmison
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | | | | | - Oumar Coulibaly
- Service de Chirurgie Pédiatrique, CHU du Gabriel Touré, Bamako, Mali
| | - Alice Schindler
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - Cheick A K Cissé
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Alassane B Maiga
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Salia Bamba
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Oumar Samassekou
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Mustafa K Khokha
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Emily K Mis
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Saquib A Lakhani
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, NHGRI, NIH, Bethesda, MD, United States
| | - Steve Jacobson
- Neuroimmunology Division, NINDS, NIH, Bethesda, MD, United States
| | - Craig Blackstone
- Movement Disorders Division, Department of Neurology, Harvard Medicine School, Massachusetts General Hospital, Boston, MA, United States
| | - Cheick O Guinto
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Guida Landouré
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
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Magielski J, McSalley I, Parthasarathy S, McKee J, Ganesan S, Helbig I. Advances in big data and omics: Paving the way for discovery in childhood epilepsies. Curr Probl Pediatr Adolesc Health Care 2024; 54:101634. [PMID: 38825428 DOI: 10.1016/j.cppeds.2024.101634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The insights gained from big data and omics approaches have transformed the field of childhood genetic epilepsy. With an increasing number of individuals receiving genetic testing for seizures, we are provided with an opportunity to identify clinically relevant subgroups and extract meaningful observations from this large-scale clinical data. However, the volume of data from electronic medical records and omics (e.g., genomics, transcriptomics) is so vast that standardized methods, such as the Human Phenotype Ontology, are necessary for reliable and comprehensive characterization. Here, we explore the integration of clinical and omics data, highlighting how these approaches pave the way for discovery in childhood epilepsies.
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Affiliation(s)
- Jan Magielski
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Ian McSalley
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Shridhar Parthasarathy
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jillian McKee
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA; Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shiva Ganesan
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19014, USA
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, 19146, USA; Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Fatima N, Dillen L, Hommersom MP, Çepni E, Fatima F, van Beusekom E, Albert S, Ali Khan A, de Brouwer APM, van Bokhoven H. Generation of induced pluripotent stem cell line (UCSFi001-A-77) carrying a biallelic frameshift variant in exon 4 of SGIP1 through CRISPR/Cas9. Stem Cell Res 2024; 80:103511. [PMID: 39098170 DOI: 10.1016/j.scr.2024.103511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024] Open
Abstract
SGIP1 encodes a protein Src homology 3-domain growth factor receptor-bound 2-like endophilin interacting protein 1. It is involved in the regulation of clathrin-mediated endocytosis along with having a role in energy homeostasis in neuronal systems. We generated an isogenic human induced pluripotent stem cell (iPSC) line with a biallelic frameshift variant in SGIP1. This exon has been shown to be subject to alternative splicing, leading to an isoform lacking 24 amino acids that are present in the longest SGIP isoform. The newly generated iPSC line will be helpful to dissect the differential properties of the two SGIP isoforms.
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Affiliation(s)
- Neelam Fatima
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Lieke Dillen
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Marina P Hommersom
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Ece Çepni
- Institute of Health Sciences, Koç University,Istanbul 34010, Turkey
| | - Fareeha Fatima
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Ellen van Beusekom
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Silvia Albert
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Asma Ali Khan
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Department of Cognitive (c)Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center,Nijmegen 6500 HB, Netherlands.
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Lee C, Chang Y, Lin H, Lee H, Yeh T, Fang L, Lee N, Tsai J, Lin S. Multisystem disorder associated with a pathogenic variant in CLCN7 in the absence of osteopetrosis. Mol Genet Genomic Med 2024; 12:e2494. [PMID: 39056574 PMCID: PMC11273547 DOI: 10.1002/mgg3.2494] [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: 02/06/2024] [Revised: 05/08/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND We clinically and genetically evaluated a Taiwanese boy presenting with developmental delay, organomegaly, hypogammaglobulinemia and hypopigmentation without osteopetrosis. Whole-exome sequencing revealed a de novo gain-of-function variant, p.Tyr715Cys, in the C-terminal domain of ClC-7 encoded by CLCN7. METHODS Nicoli et al. (2019) assessed the functional impact of p.Tyr715Cys by heterologous expression in Xenopus oocytes and evaluating resulting currents. RESULTS The variant led to increased outward currents, indicating it underlies the patient's phenotype of lysosomal hyperacidity, storage defects and vacuolization. This demonstrates the crucial physiological role of ClC-7 antiporter activity in maintaining appropriate lysosomal pH. CONCLUSION Elucidating mechanisms by which CLCN7 variants lead to lysosomal dysfunction will advance understanding of genotype-phenotype correlations. Identifying modifier genes and compensatory pathways may reveal therapeutic targets. Ongoing functional characterization of variants along with longitudinal clinical evaluations will continue advancing knowledge of ClC-7's critical roles and disease mechanisms resulting from its dysfunction. Expanded cohort studies are warranted to delineate the full spectrum of associated phenotypes.
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Affiliation(s)
- Chung‐Lin Lee
- Department of PediatricsMacKay Memorial HospitalTaipeiTaiwan
- Department and Institute of Clinical MedicineNational Yang‐Ming Chiao‐Tung UniversityTaipeiTaiwan
- Department of Rare Disease CenterMacKay Memorial HospitalTaipeiTaiwan
- Department of MedicineMackay Medical CollegeNew Taipei CityTaiwan
- Mackay Junior College of Medicine, Nursing, and ManagementTaipeiTaiwan
| | - Yeun‐Wen Chang
- Department of PediatricsMacKay Memorial HospitalTaipeiTaiwan
- Department of PediatricsTaipei Tzu Chi Hospital, Buddhist Tzu Chi Medical FoundationNew Taipei CityTaiwan
| | - Hsiang‐Yu Lin
- Department of PediatricsMacKay Memorial HospitalTaipeiTaiwan
- Department of Rare Disease CenterMacKay Memorial HospitalTaipeiTaiwan
- Department of MedicineMackay Medical CollegeNew Taipei CityTaiwan
- Mackay Junior College of Medicine, Nursing, and ManagementTaipeiTaiwan
- Division of Genetics and Metabolism, Department of Medical ResearchMacKay Memorial HospitalTaipeiTaiwan
- Department of Medical ResearchChina Medical University Hospital, China Medical UniversityTaichungTaiwan
| | - Hung‐Chang Lee
- Department of PediatricsMacKay Memorial HospitalTaipeiTaiwan
| | - Ting‐Chi Yeh
- Department of PediatricsMacKay Memorial HospitalTaipeiTaiwan
| | - Li‐Ching Fang
- Department of PediatricsMacKay Memorial HospitalTaipeiTaiwan
| | - Ni‐Chung Lee
- Department of PediatricsNational Taiwan University HospitalTaipeiTaiwan
| | - Jeng‐Daw Tsai
- Department of PediatricsMacKay Memorial HospitalTaipeiTaiwan
- Department of MedicineMackay Medical CollegeNew Taipei CityTaiwan
| | - Shuan‐Pei Lin
- Department of PediatricsMacKay Memorial HospitalTaipeiTaiwan
- Department of Rare Disease CenterMacKay Memorial HospitalTaipeiTaiwan
- Department of MedicineMackay Medical CollegeNew Taipei CityTaiwan
- Division of Genetics and Metabolism, Department of Medical ResearchMacKay Memorial HospitalTaipeiTaiwan
- Department of Infant and Child CareNational Taipei University of Nursing and Health SciencesTaipeiTaiwan
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Yang Z, Yang C, Xu P, Han L, Li Y, Peng L, Wei X, Schmid SL, Svitkina T, Chen Z. CCDC32 stabilizes clathrin-coated pits and drives their invagination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600785. [PMID: 38979322 PMCID: PMC11230434 DOI: 10.1101/2024.06.26.600785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Clathrin-mediated endocytosis (CME) is essential for maintaining cellular homeostasis. Previous studies have reported more than 50 CME accessory proteins; however, the mechanism driving the invagination of clathrin-coated pits (CCPs) remains elusive. Quantitative live cell imaging reveals that CCDC32, a poorly characterized endocytic accessory protein, regulates CCP stabilization and is required for efficient CCP invagination. CCDC32 interacts with the α-appendage domain (AD) of AP2 via its coiled-coil domain to exert this function. Furthermore, we showed that the clinically observed nonsense mutations in CCDC32, which result in the development of cardio-facio-neuro-developmental syndrome (CFNDS), inhibit CME by abolishing CCDC32-AP2 interactions. Overall, our data demonstrates the function and molecular mechanism of a novel endocytic accessory protein, CCDC32, in CME regulation. Significance Statement Clathrin-mediated endocytosis (CME) happens via the initiation, stabilization, and invagination of clathrin-coated pits (CCPs). In this study, we used a combination of quantitative live cell imaging, ultrastructure electron microscopy and biochemical experiments to show that CCDC32, a poorly studied and functional ambiguous protein, acts as an important endocytic accessory protein that regulates CCP stabilization and invagination. Specifically, CCDC32 exerts this function via its interactions with AP2, and the coiled-coil domain of CCDC32 and the α-appendage domain (AD) of AP2 are essential in mediating CCDC32-AP2 interactions. Importantly, we demonstrate that clinically observed loss-of-function mutations in CCDC32 lose AP2 interaction capacity and inhibit CME, resulting in the development of cardio-facio-neuro-developmental syndrome (CFNDS).
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Schaare D, Lusk L, Karlin A, Kaufman MC, Magielski J, Sarasua SM, Allison K, Boccuto L, Helbig I. A Longitudinal Exploration of CACNA1A -related Hemiplegic Migraine in Children. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.14.24308953. [PMID: 38946946 PMCID: PMC11213092 DOI: 10.1101/2024.06.14.24308953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Introduction Since the initial description of CACNA1A- related hemiplegic migraine (HM), the phenotypic spectrum has expanded from mild episodes in neurotypical individuals to potentially life-threatening events frequently seen in individuals with developmental and epileptic encephalopathies. However, the overall longitudinal course throughout childhood remains unknown. Methods We analyzed HM and seizure history in individuals with CACNA1A -related HM, delineating frequency and severity of events in monthly increments through a standardized approach. Combining these data with medication prescription information, we assessed the response of HM to different agents. Results Our cohort involved 15 individuals between 3 and 29 years (163 patient years) and included 11 unique and two recurrent variants (p.R1349Q and p.V1393M; both n= 2). The age of first confirmed HM ranged from 14 months to 13 years (average 3 years). 25% of all HM events were severe (lasting >3 days) and 73% of individuals had at least 1 severe occurrence. Spacing of HM events ranged from 1 month to 14 years and changes in HM severity over time of showed increases or decreases of >2 severity levels in 12/122 events. Eight individuals had epilepsy, but severity of epilepsy did not correlate with frequency and severity of HM events. While levetiracetam ( n= 6) and acetazolamide ( n= 5) were the most frequently used medications, they did not show efficacy in HM prevention or HM severity reduction. However, verapamil ( n= 3) showed efficacy in preventing HM episodes (OR 2.68, CI 1.39-5.67). Significance The longitudinal course of CACNA1A -related HM lacks recognizable patterns for timing and severity of HM events or correlation with seizure patterns. Our data underscores the unpredictability of CACNA1A -related HM, highlighting the need for close surveillance for reoccurring HM events even in individuals with symptom-free periods. Key points 24% of hemiplegic migraines (HM) in CACNA1A- related disorders are severe, involving cerebral edema and greater than 4 days to recover Timing and severity of HM are unpredictable, with large changes in severity between events, and age of onset ranging from 1-13 yearsEpilepsy occurred in 53% of individuals, with neither the timing nor severity of seizures correlated with HM.
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Abela L, Gianfrancesco L, Tagliatti E, Rossignoli G, Barwick K, Zourray C, Reid KM, Budinger D, Ng J, Counsell J, Simpson A, Pearson TS, Edvardson S, Elpeleg O, Brodsky FM, Lignani G, Barral S, Kurian MA. Neurodevelopmental and synaptic defects in DNAJC6 parkinsonism, amenable to gene therapy. Brain 2024; 147:2023-2037. [PMID: 38242634 PMCID: PMC11146427 DOI: 10.1093/brain/awae020] [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: 07/06/2023] [Revised: 11/10/2023] [Accepted: 12/16/2023] [Indexed: 01/21/2024] Open
Abstract
DNAJC6 encodes auxilin, a co-chaperone protein involved in clathrin-mediated endocytosis (CME) at the presynaptic terminal. Biallelic mutations in DNAJC6 cause a complex, early-onset neurodegenerative disorder characterized by rapidly progressive parkinsonism-dystonia in childhood. The disease is commonly associated with additional neurodevelopmental, neurological and neuropsychiatric features. Currently, there are no disease-modifying treatments for this condition, resulting in significant morbidity and risk of premature mortality. To investigate the underlying disease mechanisms in childhood-onset DNAJC6 parkinsonism, we generated induced pluripotent stem cells (iPSC) from three patients harbouring pathogenic loss-of-function DNAJC6 mutations and subsequently developed a midbrain dopaminergic neuronal model of disease. When compared to age-matched and CRISPR-corrected isogenic controls, the neuronal cell model revealed disease-specific auxilin deficiency as well as disturbance of synaptic vesicle recycling and homeostasis. We also observed neurodevelopmental dysregulation affecting ventral midbrain patterning and neuronal maturation. To explore the feasibility of a viral vector-mediated gene therapy approach, iPSC-derived neuronal cultures were treated with lentiviral DNAJC6 gene transfer, which restored auxilin expression and rescued CME. Our patient-derived neuronal model provides deeper insights into the molecular mechanisms of auxilin deficiency as well as a robust platform for the development of targeted precision therapy approaches.
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Affiliation(s)
- Lucia Abela
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Lorita Gianfrancesco
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Erica Tagliatti
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- Laboratory of Pharmacology and Brain Pathology, Humanitas Clinical and Research Center, 20089 Milano, Italy
| | - Giada Rossignoli
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Katy Barwick
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Clara Zourray
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Kimberley M Reid
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Dimitri Budinger
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Joanne Ng
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
- Genetic Therapy Accelerator Centre, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - John Counsell
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Arlo Simpson
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Toni S Pearson
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032-3784, USA
- Department of Pediatrics, Nationwide Children’s Hospital, Ohio State University, Columbus, OH 43210, USA
- Department of Neurology, Nationwide Children’s Hospital, Ohio State University, Columbus, OH 43210, USA
| | - Simon Edvardson
- Department of Genetics, Hadassah, Hebrew University Medical Center, 9574869 Jerusalem, Israel
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, 9574869 Jerusalem, Israel
| | - Frances M Brodsky
- Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Gabriele Lignani
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Serena Barral
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, London, WC1N 1DZ, UK
- Department of Neurology, Great Ormond Street Hospital, London, WC1N 3JH, UK
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9
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Dillen L, Fatima N, Hommersom MP, Çepni E, Fatima F, van Beusekom E, Albert S, van Hagen JM, de Vries BBA, Khan AA, de Brouwer APM, van Bokhoven H. Generation of induced pluripotent stem cell lines from two unrelated patients affected by intellectual disability carrying homozygous variants in SGIP1. Stem Cell Res 2024; 77:103442. [PMID: 38739972 DOI: 10.1016/j.scr.2024.103442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
Intellectual disability (ID) is a diverse neurodevelopmental condition and almost half of the cases have a genetic etiology. SGIP1 acts as an endocytic protein that influences the signaling of receptors in neuronal systems related to energy homeostasis through its interaction with endophilins. This study focuses on the generation and characterization of induced pluripotent stem cells (iPSC) from two unrelated patients due to a frameshift variant (c.764dupA, NM_032291.4) and a splice donor site variant (c.74 + 1G > A, NM_032291.4) in the SGIP1 gene.
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Affiliation(s)
- Lieke Dillen
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Neelam Fatima
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Marina P Hommersom
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
| | - Ece Çepni
- Institute of Health Sciences, Koç University, 34010 Istanbul, Turkey
| | - Fareeha Fatima
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Ellen van Beusekom
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Silvia Albert
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Asma Ali Khan
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, Netherlands.
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10
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Magielski J, Ruggiero SM, Xian J, Parthasarathy S, Galer P, Ganesan S, Back A, McKee J, McSalley I, Gonzalez AK, Morgan A, Donaher J, Helbig I. The clinical and genetic spectrum of paediatric speech and language disorders in 52,143 individuals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.23.24306192. [PMID: 38712155 PMCID: PMC11071575 DOI: 10.1101/2024.04.23.24306192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Speech and language disorders are known to have a substantial genetic contribution. Although frequently examined as components of other conditions, research on the genetic basis of linguistic differences as separate phenotypic subgroups has been limited so far. Here, we performed an in-depth characterization of speech and language disorders in 52,143 individuals, reconstructing clinical histories using a large-scale data mining approach of the Electronic Medical Records (EMR) from an entire large paediatric healthcare network. The reported frequency of these disorders was the highest between 2 and 5 years old and spanned a spectrum of twenty-six broad speech and language diagnoses. We used Natural Language Processing to assess to which degree clinical diagnosis in full-text notes were reflected in ICD-10 diagnosis codes. We found that aphasia and speech apraxia could be easily retrieved through ICD-10 diagnosis codes, while stuttering as a speech phenotype was only coded in 12% of individuals through appropriate ICD-10 codes. We found significant comorbidity of speech and language disorders in neurodevelopmental conditions (30.31%) and to a lesser degree with epilepsies (6.07%) and movement disorders (2.05%). The most common genetic disorders retrievable in our EMR analysis were STXBP1 (n=21), PTEN (n=20), and CACNA1A (n=18). When assessing associations of genetic diagnoses with specific linguistic phenotypes, we observed associations of STXBP1 and aphasia (P=8.57 × 10-7, CI=18.62-130.39) and MYO7A with speech and language development delay due to hearing loss (P=1.24 × 10-5, CI=17.46-Inf). Finally, in a sub-cohort of 726 individuals with whole exome sequencing data, we identified an enrichment of rare variants in synaptic protein and neuronal receptor pathways and associations of UQCRC1 with expressive aphasia and WASHC4 with abnormality of speech or vocalization. In summary, our study outlines the landscape of paediatric speech and language disorders, confirming the phenotypic complexity of linguistic traits and novel genotype-phenotype associations. Subgroups of paediatric speech and language disorders differ significantly with respect to the composition of monogenic aetiologies.
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Affiliation(s)
- Jan Magielski
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Sarah M. Ruggiero
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Julie Xian
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Shridhar Parthasarathy
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Peter Galer
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shiva Ganesan
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Amanda Back
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jillian McKee
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Ian McSalley
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Alexander K. Gonzalez
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Angela Morgan
- Murdoch Children’s Research Institute, Parkville 3052, Australia
- Department of Audiology and Speech Pathology, University of Melbourne, Parkville 3052, Australia
| | - Joseph Donaher
- Center for Childhood Communication, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Otorhinolaryngology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
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11
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Gu X, Lin L. Spatiotemporal expression of AP-2/myosin Ⅵ in mouse cochlear IHCs and correlation with auditory function. Acta Otolaryngol 2024; 144:198-206. [PMID: 38662892 DOI: 10.1080/00016489.2024.2341126] [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: 02/19/2024] [Accepted: 04/04/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Recycling of synaptic vesicles plays an important role in vesicle pool replenishment, neurotransmitter release and synaptic plasticity. Clathrin-mediated endocytosis (CME) is considered to be the main mechanism for synaptic vesicle replenishment. AP-2 (adaptor-related protein complex 2) and myosin Ⅵ are known as key proteins that regulate the structure and dynamics of CME. OBJECTIVE This study aims to reveal the spatiotemporal expression of AP-2/myosin Ⅵ in inner hair cells (IHCs) of the mouse cochlea and its correlation with auditory function. MATERIAL AND METHODS Immunofluorescence was used to detect the localization and expression of AP-2 and myosin Ⅵ in cochlear hair cells (HCs) of CBA/CaJ mice of various ages. qRT-PCR was used to verify the differential expression of AP-2 and myosin Ⅵ mRNA in the mouse cochlea, and ABR tests were administered to mice of various ages. A preliminary analysis of the correlation between AP-2/myosin Ⅵ levels and auditory function was conducted. RESULTS AP-2 was located in the cytoplasmic region of IHCs and was mainly expressed in the basal region of IHCs and the area near ribbon synapses, while myosin Ⅵ was expressed in the cytoplasmic region of IHCs and OHCs. Furthermore, AP-2 and myosin Ⅵ were not significant detected in the cochleae of P7 mice; the expression level reached a peak at P35 and then decreased significantly with age. The expression patterns and expression levels of AP-2 and myosin Ⅵ in the cochleae of the mice were consistent with the development of the auditory system. CONCLUSIONS AND SIGNIFICANCE AP-2 and myosin Ⅵ protein expression may differ in mice of different ages, and this variation probably leads to a difference in the efficiency in CME; it may also cause a defect in IHC function.
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Affiliation(s)
- Xiang Gu
- Department of Otolaryngology Head and Neck Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Lin
- Department of Otolaryngology Head and Neck Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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12
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Chan CWF, Wang B, Nan L, Huang X, Mao T, Chu HY, Luo C, Chu H, Choi GCG, Shum HC, Wong ASL. High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2. Nat Biomed Eng 2024; 8:291-309. [PMID: 37996617 DOI: 10.1038/s41551-023-01140-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
Mapping mutations and discovering cellular determinants that cause the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to induce infected cells to form syncytia would facilitate the development of strategies for blocking the formation of such cell-cell fusion. Here we describe high-throughput screening methods based on droplet microfluidics and the size-exclusion selection of syncytia, coupled with large-scale mutagenesis and genome-wide knockout screening via clustered regularly interspaced short palindromic repeats (CRISPR), for the large-scale identification of determinants of cell-cell fusion. We used the methods to perform deep mutational scans in spike-presenting cells to pinpoint mutable syncytium-enhancing substitutions in two regions of the spike protein (the fusion peptide proximal region and the furin-cleavage site). We also used a genome-wide CRISPR screen in cells expressing the receptor angiotensin-converting enzyme 2 to identify inhibitors of clathrin-mediated endocytosis that impede syncytium formation, which we validated in hamsters infected with SARS-CoV-2. Finding genetic and cellular determinants of the formation of syncytia may reveal insights into the physiological and pathological consequences of cell-cell fusion.
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Affiliation(s)
- Charles W F Chan
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Bei Wang
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tianjiao Mao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Hoi Yee Chu
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People's Republic of China.
| | - Gigi C G Choi
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
| | - Alan S L Wong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Shatin, Hong Kong SAR, China.
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13
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Sengül GF, Mishra R, Candiello E, Schu P. Hsc70 phosphorylation patterns and calmodulin regulate AP2 Clathrin-Coated-Vesicle life span for cell adhesion protein transport. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119611. [PMID: 37926156 DOI: 10.1016/j.bbamcr.2023.119611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
AP2 forms AP2 CCV with clathrin and over 60 additional coat proteins. Due to this complexity, we have a limited understanding of CCV life cycle regulation. Synapses contain canonical AP2 CCV, canCCV, and more stable, thereby longer lived, AP2 CCV. The more stable AP2 CCV can be distinguished from canCCV due to the stable binding of Hsc70 to clathrin. The AP1/σ1B complex knockout leads to impaired synaptic vesicle recycling and altered endosomal protein sorting. This causes as a secondary phenotype the twofold upregulation of endocytosis by canCCV and by more stable AP2 CCV. These stable CCV are more stabilized than their wt counterpart, hence stCCV. They have less of the uncoating proteins synaptojanin1 and Hsc70, and more of the coat stabilizing AAK1. Hsc70 clathrin dissociation activity is regulated by complex phosphorylation patterns. Two major groups of hyper- and of hypo-phosphorylated Hsc70 proteins are formed. The latter are enriched in wt stable CCV and stabilized stCCV. Hsc70 T265 phosphorylation regulates binding of CaM/Ca2+. CaM/Ca2+ binding to the T265 domain blocks Hsc70 homodimerization and its concentration in stCCV required for clathrin disassembly. Kinases DYRK1A and CaMK-IIδ can phosphorylate T265 preventing CaM/Ca2+ binding. Their and the levels of STK38L and STK39/Cab39, which are able to phosphorylate additional Hsc70 residues are reduced in stCCV. The stCCV pathway sorts specifically the cell adhesion proteins CHL1 and Neurocan, supporting our model of that the stCCV pathway fulfills specific functions in synaptic plasticity.
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Affiliation(s)
- G F Sengül
- Georg-August-University Göttingen, University Medical Center, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Ankara Medipol University, Faculty of Medicine, Department of Medical Biochemistry, Turkey
| | - R Mishra
- Georg-August-University Göttingen, University Medical Center, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; Dept. of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, England, United Kingdom
| | - E Candiello
- Georg-August-University Göttingen, University Medical Center, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany; University of Turin, Tumor Immunology Laboratory, Torino, Italy
| | - P Schu
- Georg-August-University Göttingen, University Medical Center, Department of Cellular Biochemistry, Humboldtallee 23, 37073 Göttingen, Germany.
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14
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Wu C, Ruan T, Yuan Y, Xu C, Du L, Wang F, Xu S. Alterations in Synaptic Connectivity and Synaptic Transmission in Alzheimer's Disease with High Physical Activity. J Alzheimers Dis 2024; 99:1005-1022. [PMID: 38759013 DOI: 10.3233/jad-240123] [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] [Indexed: 05/19/2024]
Abstract
Background Alzheimer's disease (AD) is a progressive neurodegeneration disease. Physical activity is one of the most promising modifiable lifestyles that can be effective in slowing down the progression of AD at an early stage. Objective Explore the molecular processes impaired in AD that were conversely preserved and enhanced by physical activity. Methods Integrated transcriptomic analyses were performed in datasets that contain AD patients and elders with different degrees of physical activity. The changes of the hub genes were validated through analyzing another two datasets. The expression of the hub genes was further detected in the hippocampus and cortexes of APP/PS1 transgenic mice with or without physical activity by Quantitative polymerase chain reaction (qPCR). Results Cross-comparison highlighted 195 DEGs displaying opposed regulation patterns between AD and high physical activity (HPA). The common DEGs were predominantly involved in synaptic vesicle recycling and synaptic transmission, largely downregulated in AD patients but upregulated in the elders with HPA. Two key modules and four hub genes that were related to synaptic vesicle turnover were obtained from the PPI network. The expression of these hub genes (SYT1, SYT4, SH3GL2, and AP2M1) was significantly decreased in AD transgenic mice and was reversed by HPA training. Conclusions HPA may reverse AD pathology by upregulating a range of synaptic vesicle transport related proteins which might improve the efficiency of synaptic vesicle turnover and facilitate inter-neuronal information transfer. The study provides novel insights into the mechanisms underlining the protective effects of HPA on AD.
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Affiliation(s)
- Can Wu
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Tingting Ruan
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Yalan Yuan
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Chunshuang Xu
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Lijuan Du
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
- Faculty of Physical Education, Ningbo University, Ningbo, Zhejiang, China
| | - Fang Wang
- Department of Pharmacy, Zhejiang Pharmaceutical University, Ningbo, Zhejiang, China
| | - Shujun Xu
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
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15
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Sigrist SJ, Haucke V. Orchestrating vesicular and nonvesicular membrane dynamics by intrinsically disordered proteins. EMBO Rep 2023; 24:e57758. [PMID: 37680133 PMCID: PMC10626433 DOI: 10.15252/embr.202357758] [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: 07/05/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
Compartmentalization by membranes is a common feature of eukaryotic cells and serves to spatiotemporally confine biochemical reactions to control physiology. Membrane-bound organelles such as the endoplasmic reticulum (ER), the Golgi complex, endosomes and lysosomes, and the plasma membrane, continuously exchange material via vesicular carriers. In addition to vesicular trafficking entailing budding, fission, and fusion processes, organelles can form membrane contact sites (MCSs) that enable the nonvesicular exchange of lipids, ions, and metabolites, or the secretion of neurotransmitters via subsequent membrane fusion. Recent data suggest that biomolecule and information transfer via vesicular carriers and via MCSs share common organizational principles and are often mediated by proteins with intrinsically disordered regions (IDRs). Intrinsically disordered proteins (IDPs) can assemble via low-affinity, multivalent interactions to facilitate membrane tethering, deformation, fission, or fusion. Here, we review our current understanding of how IDPs drive the formation of multivalent protein assemblies and protein condensates to orchestrate vesicular and nonvesicular transport with a special focus on presynaptic neurotransmission. We further discuss how dysfunction of IDPs causes disease and outline perspectives for future research.
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Affiliation(s)
- Stephan J Sigrist
- Department of Biology, Chemistry, PharmacyFreie Universität BerlinBerlinGermany
| | - Volker Haucke
- Department of Biology, Chemistry, PharmacyFreie Universität BerlinBerlinGermany
- Department of Molecular Pharmacology and Cell BiologyLeibniz Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
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16
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Song DY, Yuan L, Cui N, Feng C, Meng L, Wang XH, Xiang M, Liu D, Wang C, Zhang Z, Li JY, Li W. α-Synuclein induces deficiency in clathrin-mediated endocytosis through inhibiting synaptojanin1 expression. J Neurochem 2023; 167:461-484. [PMID: 37788328 DOI: 10.1111/jnc.15974] [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: 06/15/2023] [Revised: 08/13/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023]
Abstract
Parkinson's disease (PD) is an age-related chronic neurological disorder, mainly characterized by the pathological feature of α-synuclein (α-syn) aggregation, with the exact disease pathogenesis unclear. During the onset and progression of PD, synaptic dysfunction, including dysregulation of axonal transport, impaired exocytosis, and endocytosis are identified as crucial events of PD pathogenesis. It has been reported that over-expression of α-syn impairs clathrin-mediated endocytosis (CME) in the synapses. However, the underlying mechanisms still needs to be explored. In this study, we investigated the molecular events underlying the synaptic dysfunction caused by over-expression of wild-type human α-syn and its mutant form, involving series of proteins participating in CME. We found that excessive human α-syn causes impaired fission and uncoating of clathrin-coated vesicles during synaptic vesicle recycling, leading to reduced clustering of synaptic vesicles near the active zone and increased size of plasma membrane and number of endocytic intermediates. Furthermore, over-expressed human α-syn induced changes of CME-associated proteins, among which synaptojanin1 (SYNJ1) showed significant reduction in various brain regions. Over-expression of SYNJ1 in primary hippocampal neurons from α-syn transgenic mice recovered the synaptic vesicle density, clustering and endocytosis. Using fluorescence-conjugated transferrin, we demonstrated that SYNJ1 re-boosted the CME activity by restoring the phosphatidylinositol-4,5-bisphosphate homeostasis. Our data suggested that over-expression of α-syn disrupts synaptic function through interfering with vesicle recycling, which could be alleviated by re-availing of SYNJ1. Our study unrevealed a molecular mechanism of the synaptic dysfunction in PD pathogenesis and provided a potential therapeutic target for treating PD.
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Affiliation(s)
- Dong-Yan Song
- Institute of Neuroscience, College of Life and Health Sciences, Northeastern University, Shenyang, China
- Laboratory of Research in Parkinson's Disease and Related Disorders, Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders, Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
| | - Na Cui
- Laboratory of Research in Parkinson's Disease and Related Disorders, Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
| | - Cong Feng
- Laboratory of Research in Parkinson's Disease and Related Disorders, Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
| | - Lanxia Meng
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xin-He Wang
- Institute of Neuroscience, College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Man Xiang
- Laboratory of Research in Parkinson's Disease and Related Disorders, Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
| | - Di Liu
- Institute of Neuroscience, College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Chun Wang
- Laboratory of Research in Parkinson's Disease and Related Disorders, Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
| | - Zhentao Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jia-Yi Li
- Laboratory of Research in Parkinson's Disease and Related Disorders, Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
- Neural Plasticity and Repair Unit, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Wen Li
- Laboratory of Research in Parkinson's Disease and Related Disorders, Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
- Neural Plasticity and Repair Unit, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
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17
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Afsar T, Huang X, Shah AA, Abbas S, Bano S, Mahmood A, Hu J, Razak S, Umair M. Truncated DNM1 variant underlines developmental delay and epileptic encephalopathy. Front Pediatr 2023; 11:1266376. [PMID: 37900685 PMCID: PMC10601988 DOI: 10.3389/fped.2023.1266376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/06/2023] [Indexed: 10/31/2023] Open
Abstract
Background Developmental and epileptic encephalopathies (DEEs) signify a group of heterogeneous neurodevelopmental disorder associated with early-onset seizures accompanied by developmental delay, hypotonia, mild to severe intellectual disability, and developmental regression. Variants in the DNM1 gene have been associated with autosomal dominant DEE type 31A and autosomal recessive DEE type 31B. Methods In the current study, a consanguineous Pakistani family consisting of a proband (IV-2) was clinically evaluated and genetically analyzed manifesting in severe neurodevelopmental phenotypes. WES followed by Sanger sequencing was performed to identify the disease-causing variant. Furthermore, 3D protein modeling and dynamic simulation of wild-type and mutant proteins along with reverse transcriptase (RT)-based mRNA expression were checked using standard methods. Results Data analysis of WES revealed a novel homozygous non-sense variant (c.1402G>T; p. Glu468*) in exon 11 of the DNM1 gene that was predicted as pathogenic class I. Variants in the DNM1 gene have been associated with DEE types 31A and B. Different bioinformatics prediction tools and American College of Medical Genetics guidelines were used to verify the identified variant. Sanger sequencing was used to validate the disease-causing variant. Our approach validated the pathogenesis of the variant as a cause of heterogeneous neurodevelopmental disorders. In addition, 3D protein modeling showed that the mutant protein would lose most of the amino acids and might not perform the proper function if the surveillance non-sense-mediated decay mechanism was skipped. Molecular dynamics analysis showed varied trajectories of wild-type and mutant DNM1 proteins in terms of root mean square deviation, root mean square fluctuation and radius of gyration. Similarly, RT-qPCR revealed a substantial reduction of the DNM1 gene in the index patient. Conclusion Our finding further confirms the association of homozygous, loss-of-function variants in DNM1 associated with DEE type 31B. The study expands the genotypic and phenotypic spectrum of pathogenic DNM1 variants related to DNM1-associated pathogenesis.
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Affiliation(s)
- Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Xiaoyun Huang
- Department of Neurology, SSL Central Hospital of Dongguan City, Affiliated Dongguan Shilong People’s Hospital of Southern Medical University, Dongguan, China
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Safdar Abbas
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Shazia Bano
- Department of Optometry and Vision Sciences, University of Lahore, Lahore, Pakistan
| | - Arif Mahmood
- Department of Neurology, SSL Central Hospital of Dongguan City, Affiliated Dongguan Shilong People’s Hospital of Southern Medical University, Dongguan, China
| | - Junjian Hu
- Department of Central Laboratory, SSL Central Hospital of Dongguan City, Affiliated Dongguan Shilong People’s Hospital of Southern Medical University, Dongguan, China
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Muhammad Umair
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
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18
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Bonnycastle K, Dobson KL, Blumrich EM, Gajbhiye A, Davenport EC, Pronot M, Steinruecke M, Trost M, Gonzalez-Sulser A, Cousin MA. Reversal of cell, circuit and seizure phenotypes in a mouse model of DNM1 epileptic encephalopathy. Nat Commun 2023; 14:5285. [PMID: 37648685 PMCID: PMC10468497 DOI: 10.1038/s41467-023-41035-w] [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: 02/20/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
Dynamin-1 is a large GTPase with an obligatory role in synaptic vesicle endocytosis at mammalian nerve terminals. Heterozygous missense mutations in the dynamin-1 gene (DNM1) cause a novel form of epileptic encephalopathy, with pathogenic mutations clustering within regions required for its essential GTPase activity. We reveal the most prevalent pathogenic DNM1 mutation, R237W, disrupts dynamin-1 enzyme activity and endocytosis when overexpressed in central neurons. To determine how this mutation impacted cell, circuit and behavioural function, we generated a mouse carrying the R237W mutation. Neurons from heterozygous mice display dysfunctional endocytosis, in addition to altered excitatory neurotransmission and seizure-like phenotypes. Importantly, these phenotypes are corrected at the cell, circuit and in vivo level by the drug, BMS-204352, which accelerates endocytosis. Here, we demonstrate a credible link between dysfunctional endocytosis and epileptic encephalopathy, and importantly reveal that synaptic vesicle recycling may be a viable therapeutic target for monogenic intractable epilepsies.
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Affiliation(s)
- Katherine Bonnycastle
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK.
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK.
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK.
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) Sainte-Justine, Université de Montréal, Montreal, QC, Canada.
| | - Katharine L Dobson
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
| | - Eva-Maria Blumrich
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
| | - Akshada Gajbhiye
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, NE2 4HH, Newcastle upon Tyne, UK
| | - Elizabeth C Davenport
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
| | - Marie Pronot
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
| | - Moritz Steinruecke
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
| | - Matthias Trost
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, NE2 4HH, Newcastle upon Tyne, UK
| | - Alfredo Gonzalez-Sulser
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK.
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK.
- Muir Maxwell Epilepsy Centre, Hugh Robson Building, George Square, University of Edinburgh, EH8 9XD, Edinburgh, Scotland, UK.
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Leonardsen EH, Vidal-Piñeiro D, Roe JM, Frei O, Shadrin AA, Iakunchykova O, de Lange AMG, Kaufmann T, Taschler B, Smith SM, Andreassen OA, Wolfers T, Westlye LT, Wang Y. Genetic architecture of brain age and its causal relations with brain and mental disorders. Mol Psychiatry 2023; 28:3111-3120. [PMID: 37165155 PMCID: PMC10615751 DOI: 10.1038/s41380-023-02087-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/12/2023]
Abstract
The difference between chronological age and the apparent age of the brain estimated from brain imaging data-the brain age gap (BAG)-is widely considered a general indicator of brain health. Converging evidence supports that BAG is sensitive to an array of genetic and nongenetic traits and diseases, yet few studies have examined the genetic architecture and its corresponding causal relationships with common brain disorders. Here, we estimate BAG using state-of-the-art neural networks trained on brain scans from 53,542 individuals (age range 3-95 years). A genome-wide association analysis across 28,104 individuals (40-84 years) from the UK Biobank revealed eight independent genomic regions significantly associated with BAG (p < 5 × 10-8) implicating neurological, metabolic, and immunological pathways - among which seven are novel. No significant genetic correlations or causal relationships with BAG were found for Parkinson's disease, major depressive disorder, or schizophrenia, but two-sample Mendelian randomization indicated a causal influence of AD (p = 7.9 × 10-4) and bipolar disorder (p = 1.35 × 10-2) on BAG. These results emphasize the polygenic architecture of brain age and provide insights into the causal relationship between selected neurological and neuropsychiatric disorders and BAG.
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Affiliation(s)
- Esten H Leonardsen
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
| | - Didac Vidal-Piñeiro
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - James M Roe
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Oleksandr Frei
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
| | - Alexey A Shadrin
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Olena Iakunchykova
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Ann-Marie G de Lange
- Department of Psychology, University of Oslo, 0317, Oslo, Norway
- LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, 1015, Lausanne, Switzerland
- Department of Psychiatry, University of Oxford, OX1 2JD, Oxford, UK
| | - Tobias Kaufmann
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, 72074, Tübingen, Germany
| | - Bernd Taschler
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, OX3 9DU, Oxford, United Kingdom
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging (WIN FMRIB), University of Oxford, OX3 9DU, Oxford, United Kingdom
| | - Ole A Andreassen
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Thomas Wolfers
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- Department of Psychology, University of Oslo, 0317, Oslo, Norway
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, 72074, Tübingen, Germany
| | - Lars T Westlye
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Yunpeng Wang
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway.
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20
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Henry OJ, Stödberg T, Båtelson S, Rasi C, Stranneheim H, Wedell A. Individualised human phenotype ontology gene panels improve clinical whole exome and genome sequencing analytical efficacy in a cohort of developmental and epileptic encephalopathies. Mol Genet Genomic Med 2023; 11:e2167. [PMID: 36967109 PMCID: PMC10337286 DOI: 10.1002/mgg3.2167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/21/2023] [Accepted: 03/01/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND The majority of genetic epilepsies remain unsolved in terms of specific genotype. Phenotype-based genomic analyses have shown potential to strengthen genomic analysis in various ways, including improving analytical efficacy. METHODS We have tested a standardised phenotyping method termed 'Phenomodels' for integrating deep-phenotyping information with our in-house developed clinical whole exome/genome sequencing analytical pipeline. Phenomodels includes a user-friendly epilepsy phenotyping template and an objective measure for selecting which template terms to include in individualised Human Phenotype Ontology (HPO) gene panels. In a pilot study of 38 previously solved cases of developmental and epileptic encephalopathies, we compared the sensitivity and specificity of the individualised HPO gene panels with the clinical epilepsy gene panel. RESULTS The Phenomodels template showed high sensitivity for capturing relevant phenotypic information, where 37/38 individuals' HPO gene panels included the causative gene. The HPO gene panels also had far fewer variants to assess than the epilepsy gene panel. CONCLUSION We have demonstrated a viable approach for incorporating standardised phenotype information into clinical genomic analyses, which may enable more efficient analysis.
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Affiliation(s)
- Olivia J. Henry
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | - Tommy Stödberg
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Department of Pediatric NeurologyKarolinska University HospitalStockholmSweden
| | - Sofia Båtelson
- Department of Pediatric NeurologyKarolinska University HospitalStockholmSweden
| | - Chiara Rasi
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell BiologyKarolinska InstitutetStockholmSweden
- Centre for Inherited Metabolic DiseasesKarolinska University HospitalStockholmSweden
| | - Anna Wedell
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
- Centre for Inherited Metabolic DiseasesKarolinska University HospitalStockholmSweden
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21
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Jiang ZJ, Gong LW. The SphK1/S1P Axis Regulates Synaptic Vesicle Endocytosis via TRPC5 Channels. J Neurosci 2023; 43:3807-3824. [PMID: 37185099 PMCID: PMC10217994 DOI: 10.1523/jneurosci.1494-22.2023] [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: 08/03/2022] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Sphingosine-1-phosphate (S1P), a bioactive sphingolipid concentrated in the brain, is essential for normal brain functions, such as learning and memory and feeding behaviors. Sphingosine kinase 1 (SphK1), the primary kinase responsible for S1P production in the brain, is abundant within presynaptic terminals, indicating a potential role of the SphK1/S1P axis in presynaptic physiology. Altered S1P levels have been highlighted in many neurologic diseases with endocytic malfunctions. However, it remains unknown whether the SphK1/S1P axis may regulate synaptic vesicle endocytosis in neurons. The present study evaluates potential functions of the SphK1/S1P axis in synaptic vesicle endocytosis by determining effects of a dominant negative catalytically inactive SphK1. Our data for the first time identify a critical role of the SphK1/S1P axis in endocytosis in both neuroendocrine chromaffin cells and neurons from mice of both sexes. Furthermore, our Ca2+ imaging data indicate that the SphK1/S1P axis may be important for presynaptic Ca2+ increases during prolonged stimulations by regulating the Ca2+ permeable TRPC5 channels, which per se regulate synaptic vesicle endocytosis. Collectively, our data point out a critical role of the regulation of TRPC5 by the SphK1/S1P axis in synaptic vesicle endocytosis.SIGNIFICANCE STATEMENT Sphingosine kinase 1 (SphK1), the primary kinase responsible for brain sphingosine-1-phosphate (S1P) production, is abundant within presynaptic terminals. Altered SphK1/S1P metabolisms has been highlighted in many neurologic disorders with defective synaptic vesicle endocytosis. However, whether the SphK1/S1P axis may regulate synaptic vesicle endocytosis is unknown. Here, we identify that the SphK1/S1P axis regulates the kinetics of synaptic vesicle endocytosis in neurons, in addition to controlling fission-pore duration during single vesicle endocytosis in neuroendocrine chromaffin cells. The regulation of the SphK1/S1P axis in synaptic vesicle endocytosis is specific since it has a distinguished signaling pathway, which involves regulation of Ca2+ influx via TRPC5 channels. This discovery may provide novel mechanistic implications for the SphK1/S1P axis in brain functions under physiological and pathologic conditions.
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Affiliation(s)
- Zhong-Jiao Jiang
- Department of Biological Sciences, University of Illinois Chicago, Chicago, Illinois 60607
| | - Liang-Wei Gong
- Department of Biological Sciences, University of Illinois Chicago, Chicago, Illinois 60607
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22
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Daniali M, Galer PD, Lewis-Smith D, Parthasarathy S, Kim E, Salvucci DD, Miller JM, Haag S, Helbig I. Enriching representation learning using 53 million patient notes through human phenotype ontology embedding. Artif Intell Med 2023; 139:102523. [PMID: 37100502 PMCID: PMC10782859 DOI: 10.1016/j.artmed.2023.102523] [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: 07/01/2022] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
The Human Phenotype Ontology (HPO) is a dictionary of >15,000 clinical phenotypic terms with defined semantic relationships, developed to standardize phenotypic analysis. Over the last decade, the HPO has been used to accelerate the implementation of precision medicine into clinical practice. In addition, recent research in representation learning, specifically in graph embedding, has led to notable progress in automated prediction via learned features. Here, we present a novel approach to phenotype representation by incorporating phenotypic frequencies based on 53 million full-text health care notes from >1.5 million individuals. We demonstrate the efficacy of our proposed phenotype embedding technique by comparing our work to existing phenotypic similarity-measuring methods. Using phenotype frequencies in our embedding technique, we are able to identify phenotypic similarities that surpass current computational models. Furthermore, our embedding technique exhibits a high degree of agreement with domain experts' judgment. By transforming complex and multidimensional phenotypes from the HPO format into vectors, our proposed method enables efficient representation of these phenotypes for downstream tasks that require deep phenotyping. This is demonstrated in a patient similarity analysis and can further be applied to disease trajectory and risk prediction.
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Affiliation(s)
- Maryam Daniali
- Department of Computer Science, Drexel University, Philadelphia, PA, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter D Galer
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; The Epilepsy Neuro Genetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - David Lewis-Smith
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; The Epilepsy Neuro Genetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK; Department of Clinical Neurosciences, Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
| | - Shridhar Parthasarathy
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; The Epilepsy Neuro Genetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edward Kim
- Department of Computer Science, Drexel University, Philadelphia, PA, USA
| | - Dario D Salvucci
- Department of Computer Science, Drexel University, Philadelphia, PA, USA
| | - Jeffrey M Miller
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Scott Haag
- Department of Computer Science, Drexel University, Philadelphia, PA, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ingo Helbig
- Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; The Epilepsy Neuro Genetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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23
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Xiao T, Dong X, Lu Y, Zhou W. High-Resolution and Multidimensional Phenotypes Can Complement Genomics Data to Diagnose Diseases in the Neonatal Population. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:204-215. [PMID: 37197647 PMCID: PMC10110825 DOI: 10.1007/s43657-022-00071-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 05/19/2023]
Abstract
Advances in genomic medicine have greatly improved our understanding of human diseases. However, phenome is not well understood. High-resolution and multidimensional phenotypes have shed light on the mechanisms underlying neonatal diseases in greater details and have the potential to optimize clinical strategies. In this review, we first highlight the value of analyzing traditional phenotypes using a data science approach in the neonatal population. We then discuss recent research on high-resolution, multidimensional, and structured phenotypes in neonatal critical diseases. Finally, we briefly introduce current technologies available for the analysis of multidimensional data and the value that can be provided by integrating these data into clinical practice. In summary, a time series of multidimensional phenome can improve our understanding of disease mechanisms and diagnostic decision-making, stratify patients, and provide clinicians with optimized strategies for therapeutic intervention; however, the available technologies for collecting multidimensional data and the best platform for connecting multiple modalities should be considered.
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Affiliation(s)
- Tiantian Xiao
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai, 201102 China
- Department of Neonatology, Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610000 China
| | - Xinran Dong
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
| | - Yulan Lu
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
| | - Wenhao Zhou
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai, 201102 China
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
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24
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Ruggiero SM, Xian J, Helbig I. The current landscape of epilepsy genetics: where are we, and where are we going? Curr Opin Neurol 2023; 36:86-94. [PMID: 36762645 PMCID: PMC10088099 DOI: 10.1097/wco.0000000000001141] [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] [Indexed: 02/11/2023]
Abstract
PURPOSE OF REVIEW In this review, we aim to analyse the progress in understanding the genetic basis of the epilepsies, as well as ongoing efforts to define the increasingly diverse and novel presentations, phenotypes and divergences from the expected that have continually characterized the field. RECENT FINDINGS A genetic workup is now considered to be standard of care for individuals with an unexplained epilepsy, due to mounting evidence that genetic diagnoses significantly influence treatment choices, prognostication, community support, and increasingly, access to clinical trials. As more individuals with epilepsy are tested, novel presentations of known epilepsy genes are being discovered, and more individuals with self-limited epilepsy are able to attain genetic diagnoses. In addition, new genes causative of epilepsy are being uncovered through both traditional and novel methods, including large international data-sharing collaborations and massive sequencing efforts as well as computational methods and analyses driven by the Human Phenotype Ontology (HPO). SUMMARY New approaches to gene discovery and characterization are advancing rapidly our understanding of the genetic and phenotypic architecture of the epilepsies. This review highlights relevant and groundbreaking studies published recently that have pushed forward the field of epilepsy genetics.
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Affiliation(s)
- Sarah M Ruggiero
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Julie Xian
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, 19146, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
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Liu X, Zhao X, Yang J, Wang H, Piao Y, Wang L. High expression of AP2M1 correlates with worse prognosis by regulating immune microenvironment and drug resistance to R-CHOP in diffuse large B cell lymphoma. Eur J Haematol 2023; 110:198-208. [PMID: 36335584 DOI: 10.1111/ejh.13895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND First-line treatment with R-CHOP has cured 50%-60% patients of diffuse large B cell lymphoma (DLBCL), and more than one-third patients will eventually progressed to relapsed/refractory disease with dismal outcomes. Adaptor Related Protein Complex 2 Subunit Mu 1 (AP2M1) is required for the activity of a vacuolar ATPase and may also play an important role in regulating the intracellular trafficking and function of CTLA-4 protein. Herein, using both public databases and our own tumor samples, we aimed to demonstrate the prognostic role of AP2M1 and the potential tumor-promoting mechanisms in DLBCL. METHOD Using public datasets of DLBCL from both GEO and TCGA databases, we analyzed the role of AP2M1 in mediating chemoresistance to R-CHOP and its correlation with various clinical parameters and prognosis. By using various R packages, we evaluated the role of AP2M1 on regulating tumor immune microenvironment. Moreover, tumor samples of DLBCL from Beijing TongRen Hospital were used to validate our findings by immunohistochemistry staining. RESULT Expression of AP2M1 was significantly increased in DLBCL, which was correlated with poor prognosis and a variety of clinical indicators. On the basis of enrichment analysis, it was found that AP2M1 may be related to intracellular receptor signaling pathway. Through immune analysis and drug prediction, we found that the expression of AP2M1 affected the immune environment and drug response of DLBCL, which further revealed the important role of AP2M1 in DLBCL. By analyzing 61 patients treated uniformly with R-CHOP regimen in our center, we validated the above findings that high expression of AP2M1 correlated with inferior survival outcomes and affected sensitivity to R-CHOP treatment. CONCLUSION Expression of AP2M1 may affect the prognosis of DLBCL patients probably by affecting the immune environment and the responses to many drugs in treating DLBCL, indicating AP2M1 as a potential therapy target in DLBCL.
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Affiliation(s)
- Xindi Liu
- Department of Hematology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Xiaoli Zhao
- Department of Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Jing Yang
- Department of Hematology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Henan Wang
- Department of Hematology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Yingshi Piao
- Department of Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Liang Wang
- Department of Hematology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
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Routine Diagnostics Confirm Novel Neurodevelopmental Disorders. Genes (Basel) 2022; 13:genes13122305. [PMID: 36553572 PMCID: PMC9778535 DOI: 10.3390/genes13122305] [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: 10/21/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Routine diagnostics is biased towards genes and variants with satisfactory evidence, but rare disorders with only little confirmation of their pathogenicity might be missed. Many of these genes can, however, be considered relevant, although they may have less evidence because they lack OMIM entries or comprise only a small number of publicly available variants from one or a few studies. Here, we present 89 individuals harbouring variants in 77 genes for which only a small amount of public evidence on their clinical significance is available but which we still found to be relevant enough to be reported in routine diagnostics. For 21 genes, we present case reports that confirm the lack or provisionality of OMIM associations (ATP6V0A1, CNTN2, GABRD, NCKAP1, RHEB, TCF7L2), broaden the phenotypic spectrum (CC2D1A, KCTD17, YAP1) or substantially strengthen the confirmation of genes with limited evidence in the medical literature (ADARB1, AP2M1, BCKDK, BCORL1, CARS2, FBXO38, GABRB1, KAT8, PRKD1, RAB11B, RUSC2, ZNF142). Routine diagnostics can provide valuable information on disease associations and support for genes without requiring tremendous research efforts. Thus, our results validate and delineate gene-disorder associations with the aim of motivating clinicians and scientists in diagnostic departments to provide additional evidence via publicly available databases or by publishing short case reports.
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Parthasarathy S, Ruggiero SM, Gelot A, Soardi FC, Ribeiro BFR, Pires DEV, Ascher DB, Schmitt A, Rambaud C, Represa A, Xie HM, Lusk L, Wilmarth O, McDonnell PP, Juarez OA, Grace AN, Buratti J, Mignot C, Gras D, Nava C, Pierce SR, Keren B, Kennedy BC, Pena SDJ, Helbig I, Cuddapah VA. A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism. Am J Hum Genet 2022; 109:2253-2269. [PMID: 36413998 PMCID: PMC9748255 DOI: 10.1016/j.ajhg.2022.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
Heterozygous pathogenic variants in DNM1 cause developmental and epileptic encephalopathy (DEE) as a result of a dominant-negative mechanism impeding vesicular fission. Thus far, pathogenic variants in DNM1 have been studied with a canonical transcript that includes the alternatively spliced exon 10b. However, after performing RNA sequencing in 39 pediatric brain samples, we find the primary transcript expressed in the brain includes the downstream exon 10a instead. Using this information, we evaluated genotype-phenotype correlations of variants affecting exon 10a and identified a cohort of eleven previously unreported individuals. Eight individuals harbor a recurrent de novo splice site variant, c.1197-8G>A (GenBank: NM_001288739.1), which affects exon 10a and leads to DEE consistent with the classical DNM1 phenotype. We find this splice site variant leads to disease through an unexpected dominant-negative mechanism. Functional testing reveals an in-frame upstream splice acceptor causing insertion of two amino acids predicted to impair oligomerization-dependent activity. This is supported by neuropathological samples showing accumulation of enlarged synaptic vesicles adherent to the plasma membrane consistent with impaired vesicular fission. Two additional individuals with missense variants affecting exon 10a, p.Arg399Trp and p.Gly401Asp, had a similar DEE phenotype. In contrast, one individual with a missense variant affecting exon 10b, p.Pro405Leu, which is less expressed in the brain, had a correspondingly less severe presentation. Thus, we implicate variants affecting exon 10a as causing the severe DEE typically associated with DNM1-related disorders. We highlight the importance of considering relevant isoforms for disease-causing variants as well as the possibility of splice site variants acting through a dominant-negative mechanism.
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Affiliation(s)
- Shridhar Parthasarathy
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Sarah McKeown Ruggiero
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Antoinette Gelot
- AP-HP, Hôpital Armand-Trousseau, Service d'Anatomie Pathologique, 75012 Paris, France; INMED INSERM U 901 Parc Scientifique de Luminy, 13273 Marseille, France; Centre de Recherche Clinique ConCer-LD, Paris, France
| | - Fernanda C Soardi
- GENE - Núcleo de Genética Médica, Belo Horizonte, MG, Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC 3052, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3053, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC 3052, Australia; School of Chemistry and Molecular Biology, University of Queensland, St Lucia, QLD 4072, Australia
| | - Alain Schmitt
- INSERM U 1016, Institut Cochin, Paris, France; CNRS UMR 8104, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Caroline Rambaud
- AP-HP, Hôpital Raymond-Poincaré, Laboratoire Anatomie Pathologique, Garches, France
| | - Alfonso Represa
- INMED, INSERM, Aix-Marseille Université, Campus de Luminy, 13009 Marseille, France
| | - Hongbo M Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Laina Lusk
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Olivia Wilmarth
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pamela Pojomovsky McDonnell
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Olivia A Juarez
- Baylor College of Medicine Genetics Clinic, Children's Hospital of San Antonio, San Antonio, TX, USA
| | - Alexandra N Grace
- Baylor College of Medicine Genetics Clinic, Children's Hospital of San Antonio, San Antonio, TX, USA
| | - Julien Buratti
- AP-HP, Hôpital de la Pitié Salpêtrière, Département de Génétique, 75013 Paris, France
| | - Cyril Mignot
- AP-HP, Hôpital de la Pitié Salpêtrière, Département de Génétique, 75013 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, INSERM U 1127, CNRS UMR 7225, ICM, 75013 Paris, France; AP-HP, Hôpital Robert Debré, Service de Neurologie Pediatrique et de Maladies Métaboliques, 75019 Paris, France
| | - Domitille Gras
- AP-HP, Hôpital Robert Debré, Service de Neurologie Pediatrique et de Maladies Métaboliques, 75019 Paris, France
| | - Caroline Nava
- AP-HP, Hôpital de la Pitié Salpêtrière, Département de Génétique, 75013 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, INSERM U 1127, CNRS UMR 7225, ICM, 75013 Paris, France; AP-HP, Hôpital Robert Debré, Service de Neurologie Pediatrique et de Maladies Métaboliques, 75019 Paris, France
| | - Samuel R Pierce
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Physical Therapy, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Boris Keren
- AP-HP, Hôpital de la Pitié Salpêtrière, Département de Génétique, 75013 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, INSERM U 1127, CNRS UMR 7225, ICM, 75013 Paris, France; AP-HP, Hôpital Robert Debré, Service de Neurologie Pediatrique et de Maladies Métaboliques, 75019 Paris, France
| | - Benjamin C Kennedy
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA; Department of Neurosurgery, The University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sergio D J Pena
- GENE - Núcleo de Genética Médica, Belo Horizonte, MG, Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19146, USA; Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Vishnu Anand Cuddapah
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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Lewis-Smith D, Parthasarathy S, Xian J, Kaufman MC, Ganesan S, Galer PD, Thomas RH, Helbig I. Computational analysis of neurodevelopmental phenotypes: Harmonization empowers clinical discovery. Hum Mutat 2022; 43:1642-1658. [PMID: 35460582 PMCID: PMC9560951 DOI: 10.1002/humu.24389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/23/2022] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
Abstract
Making a specific diagnosis in neurodevelopmental disorders is traditionally based on recognizing clinical features of a distinct syndrome, which guides testing of its possible genetic etiologies. Scalable frameworks for genomic diagnostics, however, have struggled to integrate meaningful measurements of clinical phenotypic features. While standardization has enabled generation and interpretation of genomic data for clinical diagnostics at unprecedented scale, making the equivalent breakthrough for clinical data has proven challenging. However, increasingly clinical features are being recorded using controlled dictionaries with machine readable formats such as the Human Phenotype Ontology (HPO), which greatly facilitates their use in the diagnostic space. Improving the tractability of large-scale clinical information will present new opportunities to inform genomic research and diagnostics from a clinical perspective. Here, we describe novel approaches for computational phenotyping to harmonize clinical features, improve data translation through revising domain-specific dictionaries, quantify phenotypic features, and determine clinical relatedness. We demonstrate how these concepts can be applied to longitudinal phenotypic information, which represents a critical element of developmental disorders and pediatric conditions. Finally, we expand our discussion to clinical data derived from electronic medical records, a largely untapped resource of deep clinical information with distinct strengths and weaknesses.
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Affiliation(s)
- David Lewis-Smith
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK
- Department of Clinical Neurosciences, Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shridhar Parthasarathy
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julie Xian
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael C. Kaufman
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiva Ganesan
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter D. Galer
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Rhys H. Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK
- Department of Clinical Neurosciences, Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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29
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Straka B, Hermanovska B, Krskova L, Zamecnik J, Vlckova M, Balascakova M, Tesner P, Jezdik P, Tichy M, Kyncl M, Musilova A, Lassuthova P, Marusic P, Krsek P. Genetic Testing for Malformations of Cortical Development. Neurol Genet 2022; 8:e200032. [PMID: 36324633 PMCID: PMC9621608 DOI: 10.1212/nxg.0000000000200032] [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: 06/14/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022]
Abstract
Background and Objectives Malformations of cortical development (MCD), though individually rare, constitute a significant burden of disease. The diagnostic yield of next-generation sequencing (NGS) in these patients varies across studies and methods, and novel genes and variants continue to emerge. Methods Patients (n = 123) with a definite radiologic or histopathologic diagnosis of MCD, with or without epilepsy were included in this study. They underwent NGS-based targeted gene panel (TGP) testing, whole-exome sequencing (WES), or WES-based virtual panel testing. Selected patients who underwent epilepsy surgery (n = 69) also had somatic gene testing of brain tissue–derived DNA. We analyzed predictors of positive germline genetic finding and diagnostic yield of respective methods. Results Pathogenic or likely pathogenic germline genetic variants were detected in 21% of patients (26/123). In the surgical subgroup (69/123), we performed somatic sequencing in 40% of cases (28/69) and detected causal variants in 18% (5/28). Diagnostic yield did not differ between TGP, WES-based virtual gene panel, and open WES (p = 0.69). Diagnosis of focal cortical dysplasia type 2A, epilepsy, and intellectual disability were associated with positive results of germline testing. We report previously unpublished variants in 16/26 patients and 4 cases of MCD with likely pathogenic variants in non-MCD genes. Discussion In this study, we are reporting genetic findings of a large cohort of MCD patients with epilepsy or potentially epileptogenic MCD. We determine predictors of successful ascertainment of a genetic diagnosis in real-life setting and report novel, likely pathogenic variants in MCD and non-MCD genes alike.
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30
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Havrilla JM, Singaravelu A, Driscoll DM, Minkovsky L, Helbig I, Medne L, Wang K, Krantz I, Desai BR. PheNominal: an EHR-integrated web application for structured deep phenotyping at the point of care. BMC Med Inform Decis Mak 2022; 22:198. [PMID: 35902925 PMCID: PMC9335954 DOI: 10.1186/s12911-022-01927-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/06/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Clinical phenotype information greatly facilitates genetic diagnostic interpretations pipelines in disease. While post-hoc extraction using natural language processing on unstructured clinical notes continues to improve, there is a need to improve point-of-care collection of patient phenotypes. Therefore, we developed "PheNominal", a point-of-care web application, embedded within Epic electronic health record (EHR) workflows, to permit capture of standardized phenotype data. METHODS Using bi-directional web services available within commercial EHRs, we developed a lightweight web application that allows users to rapidly browse and identify relevant terms from the Human Phenotype Ontology (HPO). Selected terms are saved discretely within the patient's EHR, permitting reuse both in clinical notes as well as in downstream diagnostic and research pipelines. RESULTS In the 16 months since implementation, PheNominal was used to capture discrete phenotype data for over 1500 individuals and 11,000 HPO terms during clinic and inpatient encounters for a genetic diagnostic consultation service within a quaternary-care pediatric academic medical center. An average of 7 HPO terms were captured per patient. Compared to a manual workflow, the average time to enter terms for a patient was reduced from 15 to 5 min per patient, and there were fewer annotation errors. CONCLUSIONS Modern EHRs support integration of external applications using application programming interfaces. We describe a practical application of these interfaces to facilitate deep phenotype capture in a discrete, structured format within a busy clinical workflow. Future versions will include a vendor-agnostic implementation using FHIR. We describe pilot efforts to integrate structured phenotyping through controlled dictionaries into diagnostic and research pipelines, reducing manual effort for phenotype documentation and reducing errors in data entry.
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Affiliation(s)
- James M. Havrilla
- grid.239552.a0000 0001 0680 8770Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Anbumalar Singaravelu
- grid.239552.a0000 0001 0680 8770Emerging Technology and Transformation Team, Information Services, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Dennis M. Driscoll
- grid.239552.a0000 0001 0680 8770Emerging Technology and Transformation Team, Information Services, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Leonard Minkovsky
- grid.239552.a0000 0001 0680 8770Emerging Technology and Transformation Team, Information Services, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Ingo Helbig
- grid.239552.a0000 0001 0680 8770Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, USA ,grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104 USA
| | - Livija Medne
- grid.239552.a0000 0001 0680 8770Roberts Individualized Medical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Kai Wang
- grid.239552.a0000 0001 0680 8770Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
| | - Ian Krantz
- grid.239552.a0000 0001 0680 8770Roberts Individualized Medical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Bimal R. Desai
- grid.25879.310000 0004 1936 8972Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
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Khan MQ, Mubeen H, Khan ZQ, Masood A, Zafar A, Wattoo JI, Nisa AU. Computational insights into missense mutations in HTT gene causing Huntington's disease and its interactome networks. Ir J Med Sci 2022:10.1007/s11845-022-03043-5. [PMID: 35829908 DOI: 10.1007/s11845-022-03043-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Huntington's disease is a rare neurodegenerative illness of the central nervous system that is inherited in an autosomal dominant pattern. Mutant huntingtin protein is produced as a result of enlargement of CAG repeat in the N-terminal of the polyglutamine tract. AIM OF THE STUDY Herein, we aim to investigate the mutations and their effects on the HTT gene and its genetic variants. Additionally, the protein-protein interaction of HTT with other proteins and receptor-ligand interaction with the three-dimensional structure of huntingtin protein were identified. METHODS A comprehensive analysis of the HTT interactome and protein-ligand interaction has been carried out to provide a global picture of structure-function analysis of huntingtin protein. Mutations were analyzed and mutation verification tools were used to check the effect of mutation on protein function. RESULTS The results showed, mutations in a single gene are not only responsible for causing a particular disease but may also cause other hereditary disorders as well. Moreover, the modification at the nucleotide level also cause the change in the specific amino acid which may disrupt the function of HTT and its interacting proteins contributing in disease pathogenesis. Furthermore, the interaction between MECP2 and BDNF lowers the rate of transcriptional activity. Molecular docking further confirmed the strong interaction between MECP2 and BDNF with highest affinity. Amino acid residues of the HTT protein, involved in the interaction with tetrabenazine were N912, Y890, G2385, and V2320. These findings proved, tetrabenazine as one of the potential therapeutic agent for treatment of Huntington's disease. CONCLUSION These results give further insights into the genetics of Huntington's disease for a better understanding of disease models which will be beneficial for the future therapeutic studies.
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Affiliation(s)
| | - Hira Mubeen
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan.
| | | | - Ammara Masood
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Asma Zafar
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Javed Iqbal Wattoo
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Alim Un Nisa
- Pakistan Council of Scientific and Industrial Research, Lahore, Pakistan
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Yates T, Lain A, Campbell J, FitzPatrick DR, Simpson TI. Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders. Database (Oxford) 2022; 2022:baac038. [PMID: 35670729 PMCID: PMC9216525 DOI: 10.1093/database/baac038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/26/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022]
Abstract
There are >2500 different genetically determined developmental disorders (DD), which, as a group, show very high levels of both locus and allelic heterogeneity. This has led to the wide-spread use of evidence-based filtering of genome-wide sequence data as a diagnostic tool in DD. Determining whether the association of a filtered variant at a specific locus is a plausible explanation of the phenotype in the proband is crucial and commonly requires extensive manual literature review by both clinical scientists and clinicians. Access to a database of weighted clinical features extracted from rigorously curated literature would increase the efficiency of this process and facilitate the development of robust phenotypic similarity metrics. However, given the large and rapidly increasing volume of published information, conventional biocuration approaches are becoming impractical. Here, we present a scalable, automated method for the extraction of categorical phenotypic descriptors from the full-text literature. Papers identified through literature review were downloaded and parsed using the Cadmus custom retrieval package. Human Phenotype Ontology terms were extracted using MetaMap, with 76-84% precision and 65-73% recall. Mean terms per paper increased from 9 in title + abstract, to 68 using full text. We demonstrate that these literature-derived disease models plausibly reflect true disease expressivity more accurately than widely used manually curated models, through comparison with prospectively gathered data from the Deciphering Developmental Disorders study. The area under the curve for receiver operating characteristic (ROC) curves increased by 5-10% through the use of literature-derived models. This work shows that scalable automated literature curation increases performance and adds weight to the need for this strategy to be integrated into informatic variant analysis pipelines. Database URL: https://doi.org/10.1093/database/baac038.
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Affiliation(s)
- T.M Yates
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
- Transforming Genetic Medicine Initiative, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - A Lain
- Institute for Adaptive and Neural Computation, Informatics Forum, The University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
| | - J Campbell
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XF, UK
| | - D R FitzPatrick
- MRC Human Genetics Unit, Western General Hospital, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
- Transforming Genetic Medicine Initiative, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XF, UK
| | - T I Simpson
- Institute for Adaptive and Neural Computation, Informatics Forum, The University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XF, UK
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33
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Xian J, Parthasarathy S, Ruggiero SM, Balagura G, Fitch E, Helbig K, Gan J, Ganesan S, Kaufman MC, Ellis CA, Lewis-Smith D, Galer P, Cunningham K, O’Brien M, Cosico M, Baker K, Darling A, Veiga de Goes F, El Achkar CM, Doering JH, Furia F, García-Cazorla Á, Gardella E, Geertjens L, Klein C, Kolesnik-Taylor A, Lammertse H, Lee J, Mackie A, Misra-Isrie M, Olson H, Sexton E, Sheidley B, Smith L, Sotero L, Stamberger H, Syrbe S, Thalwitzer KM, van Berkel A, van Haelst M, Yuskaitis C, Weckhuysen S, Prosser B, Son Rigby C, Demarest S, Pierce S, Zhang Y, Møller RS, Bruining H, Poduri A, Zara F, Verhage M, Striano P, Helbig I. Assessing the landscape of STXBP1-related disorders in 534 individuals. Brain 2022; 145:1668-1683. [PMID: 35190816 PMCID: PMC9166568 DOI: 10.1093/brain/awab327] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/30/2021] [Accepted: 08/10/2021] [Indexed: 01/18/2023] Open
Abstract
Disease-causing variants in STXBP1 are among the most common genetic causes of neurodevelopmental disorders. However, the phenotypic spectrum in STXBP1-related disorders is wide and clear correlations between variant type and clinical features have not been observed so far. Here, we harmonized clinical data across 534 individuals with STXBP1-related disorders and analysed 19 973 derived phenotypic terms, including phenotypes of 253 individuals previously unreported in the scientific literature. The overall phenotypic landscape in STXBP1-related disorders is characterized by neurodevelopmental abnormalities in 95% and seizures in 89% of individuals, including focal-onset seizures as the most common seizure type (47%). More than 88% of individuals with STXBP1-related disorders have seizure onset in the first year of life, including neonatal seizure onset in 47%. Individuals with protein-truncating variants and deletions in STXBP1 (n = 261) were almost twice as likely to present with West syndrome and were more phenotypically similar than expected by chance. Five genetic hotspots with recurrent variants were identified in more than 10 individuals, including p.Arg406Cys/His (n = 40), p.Arg292Cys/His/Leu/Pro (n = 30), p.Arg551Cys/Gly/His/Leu (n = 24), p.Pro139Leu (n = 12), and p.Arg190Trp (n = 11). None of the recurrent variants were significantly associated with distinct electroclinical syndromes, single phenotypic features, or showed overall clinical similarity, indicating that the baseline variability in STXBP1-related disorders is too high for discrete phenotypic subgroups to emerge. We then reconstructed the seizure history in 62 individuals with STXBP1-related disorders in detail, retrospectively assigning seizure type and seizure frequency monthly across 4433 time intervals, and retrieved 251 anti-seizure medication prescriptions from the electronic medical records. We demonstrate a dynamic pattern of seizure control and complex interplay with response to specific medications particularly in the first year of life when seizures in STXBP1-related disorders are the most prominent. Adrenocorticotropic hormone and phenobarbital were more likely to initially reduce seizure frequency in infantile spasms and focal seizures compared to other treatment options, while the ketogenic diet was most effective in maintaining seizure freedom. In summary, we demonstrate how the multidimensional spectrum of phenotypic features in STXBP1-related disorders can be assessed using a computational phenotype framework to facilitate the development of future precision-medicine approaches.
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Affiliation(s)
- Julie Xian
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
- Neuroscience Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shridhar Parthasarathy
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Sarah M Ruggiero
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ganna Balagura
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS ‘G. Gaslini’ Institute, Genoa, Italy
| | - Eryn Fitch
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Katherine Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Jing Gan
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shiva Ganesan
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Michael C Kaufman
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
| | - Colin A Ellis
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David Lewis-Smith
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
- Royal Victoria Infirmary, Newcastle-upon-Tyne NE1 4LP, UK
| | - Peter Galer
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristin Cunningham
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Margaret O’Brien
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Mahgenn Cosico
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kate Baker
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Alejandra Darling
- Pediatric Neurology Department, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Fernanda Veiga de Goes
- Department of Pediatrics and Pediatric Neurology Laboratory, Instituto Fernandes Figueira, Rio de Janeiro 22250-020, Brazil
| | - Christelle M El Achkar
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Jan Henje Doering
- Division of Pediatric Epileptology, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Francesca Furia
- Department of Clinical Neurophysiology, Danish Epilepsy Center Filadelfia, Dianalund 4293, Denmark
| | - Ángeles García-Cazorla
- Pediatric Neurology Department, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Elena Gardella
- Department of Clinical Neurophysiology, Danish Epilepsy Center Filadelfia, Dianalund 4293, Denmark
| | - Lisa Geertjens
- Department of Child and Adolescent Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Courtney Klein
- Departments of Pediatrics and Neurology, Children's Hospital Colorado, Aurora, CO 80045, USA
| | | | - Hanna Lammertse
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam University Medical Center, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
| | - Alexandra Mackie
- Departments of Pediatrics and Neurology, Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Mala Misra-Isrie
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam University Medical Center, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Heather Olson
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Emma Sexton
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Beth Sheidley
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Lacey Smith
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Luiza Sotero
- Department of Pediatrics and Pediatric Neurology Laboratory, Instituto Fernandes Figueira, Rio de Janeiro 22250-020, Brazil
| | - Hannah Stamberger
- Division of Neurology, University Hospital Antwerp, Antwerp, Belgium
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Steffen Syrbe
- Division of Pediatric Epileptology, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Kim Marie Thalwitzer
- Division of Pediatric Epileptology, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Annemiek van Berkel
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Mieke van Haelst
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam University Medical Center, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Christopher Yuskaitis
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Sarah Weckhuysen
- Division of Neurology, University Hospital Antwerp, Antwerp, Belgium
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
| | - Ben Prosser
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Scott Demarest
- Departments of Pediatrics and Neurology, Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Samuel Pierce
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yuehua Zhang
- Department of Pediatrics, Beijing University First Hospital, Beijing, China
| | - Rikke S Møller
- Department of Clinical Neurophysiology, Danish Epilepsy Center Filadelfia, Dianalund 4293, Denmark
| | - Hilgo Bruining
- Department of Child and Adolescent Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Annapurna Poduri
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, Genoa, Italy
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Matthijs Verhage
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam University Medical Center, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS ‘G. Gaslini’ Institute, Genoa, Italy
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA 19146, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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Zechner C, Henne WM, Sathe AA, Xing C, Hernandez G, Sun S, Cheong MC. Cellular abundance of sodium phosphate cotransporter SLC20A1/PiT1 and phosphate uptake are controlled post-transcriptionally by ESCRT. J Biol Chem 2022; 298:101945. [PMID: 35447110 PMCID: PMC9123275 DOI: 10.1016/j.jbc.2022.101945] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Inorganic phosphate is essential for human life. The widely expressed mammalian sodium/phosphate cotransporter SLC20A1/PiT1 mediates phosphate uptake into most cell types; however, while SLC20A1 is required for development, and elevated SLC20A1 expression is associated with vascular calcification and aggressive tumor growth, the mechanisms regulating SLC20A1 protein abundance are unknown. Here, we found that SLC20A1 protein expression is low in phosphate-replete cultured cells but is strikingly induced following phosphate starvation, whereas mRNA expression is high in phosphate-replete cells and only mildly increased by phosphate starvation. To identify regulators of SLC20A1 protein levels, we performed a genome-wide CRISPR-based loss-of-function genetic screen in phosphate-replete cells using SLC20A1 protein induction as readout. Our screen revealed that endosomal sorting complexes required for transport (ESCRT) machinery was essential for proper SLC20A1 protein downregulation in phosphate-replete cells. We show that SLC20A1 colocalizes with ESCRT and that ESCRT deficiency increases SLC20A1 protein and phosphate uptake into cells. We also found numerous additional candidate regulators of mammalian phosphate homeostasis, including genes modifying protein ubiquitination and the Krebs cycle and oxidative phosphorylation pathways. Many of these targets have not been previously implicated in this process. We present here a model in which SLC20A1 protein abundance and phosphate uptake are tonically negatively regulated post-transcriptionally in phosphate-replete cells through direct ESCRT-mediated SLC20A1 degradation. Moreover, our screening results provide a comprehensive resource for future studies to elucidate the mechanisms governing cellular phosphate homeostasis. We conclude that genome-wide CRISPR-based genetic screening is a powerful tool to discover proteins and pathways relevant to physiological processes.
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Affiliation(s)
- Christoph Zechner
- Division of Endocrinology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Charles and Jane Pak Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
| | - W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Adwait A Sathe
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Genaro Hernandez
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shengyi Sun
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Mi Cheong Cheong
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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35
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Abdalla E, Alawi M, Meinecke P, Kutsche K, Harms FL. Cardiofacioneurodevelopmental syndrome: Report of a novel patient and expansion of the phenotype. Am J Med Genet A 2022; 188:2448-2453. [PMID: 35451546 DOI: 10.1002/ajmg.a.62762] [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: 01/28/2022] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 11/11/2022]
Abstract
The cardiofacioneurodevelopmental syndrome (CFNDS) is characterized by craniofacial anomalies including bilateral cleft lip and palate, cardiac, skeletal, and neurodevelopmental features and additional variable manifestations. Whole-exome sequencing revealed homozygous loss-of-function variants in CCDC32 (alternative name: C15orf57) in both previously described patients. ccdc32 deletion in zebrafish suggests a ciliary contribution to the pathomechanism. We report a 9-year-old female patient with CFNDS caused by a homozygous 32,583-bp deletion affecting CCDC32. Independent of the affected CCDC32 transcript variant this deletion likely leads to loss of the encoded protein. The patient had intellectual disability, marked hypertelorism, bilateral cleft lip and palate, and short stature. She had bilateral conductive hearing loss, small hands and feet, and finger abnormalities. Brain imaging disclosed hypoplastic corpus callosum. We describe a core phenotype comprising developmental delay and bilateral cleft lip and palate in the three individuals with CFNDS. Variable abnormalities of the face, brain, heart, fingers, and toes and postnatal growth retardation or microcephaly can be present. Possible involvement of the uncharacterized CCDC32 protein in the adapter protein 2 (AP2) complex regulating clathrin-mediated endocytosis has been reported. Cleft palate and cardiac defects observed in mice deficient of different AP2 subunits support a CCDC32 function in the AP2 complex.
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Affiliation(s)
- Ebtesam Abdalla
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt.,Genetics Department, Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Meinecke
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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36
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Wang H, Xu H, Chen W, Cheng M, Zou L, Yang Q, Chan CB, Zhu H, Chen C, Nie JY, Jiao B. Rab13 sustains breast cancer stem cells by supporting tumor-stroma crosstalk. Cancer Res 2022; 82:2124-2140. [PMID: 35395074 DOI: 10.1158/0008-5472.can-21-4097] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/02/2022] [Accepted: 04/05/2022] [Indexed: 11/16/2022]
Abstract
Cancer stem cells (CSC) are supported by the tumor microenvironment, and non-CSCs can regain CSC phenotypes in certain niches, leading to limited clinical benefits of CSC-targeted therapy. A better understanding of the mechanisms governing the orchestration of the CSC niche could help improve the therapeutic targeting of CSCs. Here, we report that Rab13, a small GTPase, is highly expressed in breast CSCs (BCSCs). Rab13 depletion suppressed breast cancer cell stemness, tumorigenesis, and chemoresistance by reducing tumor-stroma crosstalk. Accordingly, Rab13 controlled the membrane translocation of CXCR1/2, allowing tumor cells to interact with tumor-associated macrophages and cancer-associated fibroblasts to establish a supportive BCSC niche. Targeting the Rab13-mediated BCSC niche with bardoxolone-methyl (CDDO-Me) prevented BCSC stemness in vitro and in vivo. These findings highlight the novel regulatory mechanism of Rab13 in BCSC, with important implications for the development of therapeutic strategies for disrupting the BCSC niche.
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Affiliation(s)
- Hui Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Haibo Xu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, 518035, China., Shenzhen, Guangdong, China
| | - Wei Chen
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
| | - Mei Cheng
- Kunming Institute of Zoology, Chinese Academy of Sciences, China
| | - Li Zou
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qin Yang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | - Hao Zhu
- Southern Medical University, Guangzhou, China
| | - Ceshi Chen
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jian-Yun Nie
- The Third Affiliated Hospital of Kunming Medical University, KUNMING, Yunnan, China
| | - Baowei Jiao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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37
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Tagliatti E, Cortese K. Imaging Endocytosis Dynamics in Health and Disease. MEMBRANES 2022; 12:membranes12040393. [PMID: 35448364 PMCID: PMC9028293 DOI: 10.3390/membranes12040393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023]
Abstract
Endocytosis is a critical process for cell growth and viability. It mediates nutrient uptake, guarantees plasma membrane homeostasis, and generates intracellular signaling cascades. Moreover, it plays an important role in dead cell clearance and defense against external microbes. Finally, endocytosis is an important cellular route for the delivery of nanomedicines for therapeutic treatments. Thus, it is not surprising that both environmental and genetic perturbation of endocytosis have been associated with several human conditions such as cancer, neurological disorders, and virus infections, among others. Over the last decades, a lot of research has been focused on developing advanced imaging methods to monitor endocytosis events with high resolution in living cells and tissues. These include fluorescence imaging, electron microscopy, and correlative and super-resolution microscopy. In this review, we outline the major endocytic pathways and briefly discuss how defects in the molecular machinery of these pathways lead to disease. We then discuss the current imaging methodologies used to study endocytosis in different contexts, highlighting strengths and weaknesses.
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Affiliation(s)
- Erica Tagliatti
- Laboratory of Pharmacology and Brain Pathology, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Milano, Italy
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London WC1E 6BT, UK
- Correspondence: (E.T.); (K.C.)
| | - Katia Cortese
- Cellular Electron Microscopy Laboratory, Department of Experimental Medicine (DIMES), Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132 Genova, Italy
- Correspondence: (E.T.); (K.C.)
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38
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Shor O, Rabinowitz R, Offen D, Benninger F. Computational normal mode analysis accurately replicates the activity and specificity profiles of CRISPR-Cas9 and high-fidelity variants. Comput Struct Biotechnol J 2022; 20:2013-2019. [PMID: 35521548 PMCID: PMC9062324 DOI: 10.1016/j.csbj.2022.04.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/16/2022] [Accepted: 04/17/2022] [Indexed: 12/01/2022] Open
Abstract
The CRISPR-Cas system has transformed the field of gene-editing and created opportunities for novel genome engineering therapeutics. The field has significantly progressed, and recently, CRISPR-Cas9 was utilized in clinical trials to target disease-causing mutations. Existing tools aim to predict the on-target efficacy and potential genome-wide off-targets by scoring a particular gRNA according to an array of gRNA design principles or machine learning algorithms based on empirical results of large numbers of gRNAs. However, such tools are unable to predict the editing outcome by variant Cas enzymes and can only assess potential off-targets related to reference genomes. Here, we employ normal mode analysis (NMA) to investigate the structure of the Cas9 protein complexed with its gRNA and target DNA and explore the function of the protein. Our results demonstrate the feasibility and validity of NMA to predict the activity and specificity of SpyCas9 in the presence of mismatches by comparison to empirical data. Furthermore, despite the absence of their exact structures, this method accurately predicts the enzymatic activity of known high-fidelity engineered Cas9 variants.
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Affiliation(s)
- Oded Shor
- Department of Neurology, Rabin Medical Center, Petach Tikva 4941492, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Felsenstein Medical Research Center, Tel Aviv University, Petach Tikva 4941492, Israel
| | - Roy Rabinowitz
- Felsenstein Medical Research Center, Tel Aviv University, Petach Tikva 4941492, Israel
- Sackler School of Medicine, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Daniel Offen
- Felsenstein Medical Research Center, Tel Aviv University, Petach Tikva 4941492, Israel
- Sackler School of Medicine, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Felix Benninger
- Department of Neurology, Rabin Medical Center, Petach Tikva 4941492, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Felsenstein Medical Research Center, Tel Aviv University, Petach Tikva 4941492, Israel
- Corresponding author at: Department of Neurology, Rabin Medical Center, Petach Tikva 4941492, Israel.
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Distinct Epileptogenic Mechanisms Associated with Seizures in Wolf-Hirschhorn Syndrome. Mol Neurobiol 2022; 59:3159-3169. [DOI: 10.1007/s12035-022-02792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 03/04/2022] [Indexed: 11/25/2022]
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40
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Barua S, Pereira EM, Jobanputra V, Anyane-Yeboa K, Levy B, Liao J. 3q27.1 microdeletion causes prenatal and postnatal growth restriction and neurodevelopmental abnormalities. Mol Cytogenet 2022; 15:7. [PMID: 35241116 PMCID: PMC8895857 DOI: 10.1186/s13039-022-00587-0] [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: 08/27/2021] [Accepted: 02/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Overlapping microdeletions of chromosome 3q26-3q28 have been reported in eight individuals. The common phenotype observed in these individuals include intrauterine growth restriction, short stature, microcephaly, feeding difficulties, facial dysmorphisms, limb abnormalities and developmental delay. The most striking clinical features shared among all reported cases is prenatal and postnatal growth restriction and neurodevelopmental abnormalities. CASE PRESENTATION We identified two additional individuals with overlapping deletions and shared clinical features by high-resolution SNP oligonucleotide microarray, and refined the smallest region of overlap (SRO) to a 1.2 Mb genomic location in chromosome 3q27.1 by reviewing and comparing all published cases. We evaluated the SRO using ACMG/ClinGen current recommendations for classifying copy number variants (CNVs), and discussed the contribution of the genes deleted in the SRO to the abnormal phenotype observed in these individuals. CONCLUSIONS This study provides further evidence supporting the existence of a novel 3q27.1 microdeletion syndrome and suggests that haploinsufficiency of potential candidate genes, DVL3, AP2M1, and PARL in the SRO in 3q27.1 is responsible for the phenotype.
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Affiliation(s)
- Subit Barua
- Department of Pathology, Anatomy, and Laboratory Medicine, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Elaine M Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jun Liao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
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41
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He Q, Shen H, Shao X, Chen W, Wu Y, Liu R, Li S, Zhou Z. Cardiovascular Phenotypes Profiling for L-Transposition of the Great Arteries and Prognosis Analysis. Front Cardiovasc Med 2022; 8:781041. [PMID: 35127856 PMCID: PMC8814104 DOI: 10.3389/fcvm.2021.781041] [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: 09/22/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
Objectives Congenitally corrected transposition of the great arteries (ccTGA) is a rare and complex congenital heart disease with the characteristics of double discordance. Enormous co-existed anomalies are the culprit of prognosis evaluation and clinical decision. We aim at delineating a novel ccTGA clustering modality under human phenotype ontology (HPO) instruction and elucidating the relationship between phenotypes and prognosis in patients with ccTGA. Methods A retrospective review of 270 patients diagnosed with ccTGA in Fuwai hospital from 2009 to 2020 and cross-sectional follow-up were performed. HPO-instructed clustering method was administered in ccTGA risk stratification. Kaplan-Meier survival, Landmark analysis, and cox regression analysis were used to investigate the difference of outcomes among clusters. Results The median follow-up time was 4.29 (2.07–7.37) years. A total of three distinct phenotypic clusters were obtained after HPO-instructed clustering with 21 in cluster 1, 136 in cluster 2, and 113 in cluster 3. Landmark analysis revealed significantly worse mid-term outcomes in all-cause mortality (p = 0.021) and composite endpoints (p = 0.004) of cluster 3 in comparison with cluster 1 and cluster 2. Multivariate analysis indicated that pulmonary arterial hypertension (PAH), atrioventricular septal defect (AVSD), and arrhythmia were risk factors for composite endpoints. Moreover, the surgical treatment was significantly different among the three groups (p < 0.001) and surgical strategies had different effects on the prognosis of the different phenotypic clusters. Conclusions Human phenotype ontology-instructed clustering can be a potentially powerful tool for phenotypic risk stratification in patients with complex congenital heart diseases, which may improve prognosis prediction and clinical decision.
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Affiliation(s)
- Qiyu He
- Pediatric Cardiac Center, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huayan Shen
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyang Shao
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen Chen
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafeng Wu
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Rui Liu
- Pediatric Cardiac Center, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shoujun Li
- Pediatric Cardiac Center, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Shoujun Li
| | - Zhou Zhou
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Zhou Zhou
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42
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López-Hernández T, Takenaka KI, Mori Y, Kongpracha P, Nagamori S, Haucke V, Takamori S. Clathrin-independent endocytic retrieval of SV proteins mediated by the clathrin adaptor AP-2 at mammalian central synapses. eLife 2022; 11:e71198. [PMID: 35014951 PMCID: PMC8752090 DOI: 10.7554/elife.71198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/28/2021] [Indexed: 12/25/2022] Open
Abstract
Neurotransmission is based on the exocytic fusion of synaptic vesicles (SVs) followed by endocytic membrane retrieval and the reformation of SVs. Conflicting models have been proposed regarding the mechanisms of SV endocytosis, most notably clathrin/adaptor protein complex 2 (AP-2)-mediated endocytosis and clathrin-independent ultrafast endocytosis. Partitioning between these pathways has been suggested to be controlled by temperature and stimulus paradigm. We report on the comprehensive survey of six major SV proteins to show that SV endocytosis in mouse hippocampal neurons at physiological temperature occurs independent of clathrin while the endocytic retrieval of a subset of SV proteins including the vesicular transporters for glutamate and GABA depend on sorting by the clathrin adaptor AP-2. Our findings highlight a clathrin-independent role of the clathrin adaptor AP-2 in the endocytic retrieval of select SV cargos from the presynaptic cell surface and suggest a revised model for the endocytosis of SV membranes at mammalian central synapses.
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Affiliation(s)
| | - Koh-ichiro Takenaka
- Laboratory of Neural Membrane Biology, Graduate School of Brain Science, Doshisha UniversityKyotoJapan
| | - Yasunori Mori
- Laboratory of Neural Membrane Biology, Graduate School of Brain Science, Doshisha UniversityKyotoJapan
| | - Pornparn Kongpracha
- Department of Laboratory Medicine, The Jikei University School of MedicineTokyoJapan
| | - Shushi Nagamori
- Department of Laboratory Medicine, The Jikei University School of MedicineTokyoJapan
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Shigeo Takamori
- Laboratory of Neural Membrane Biology, Graduate School of Brain Science, Doshisha UniversityKyotoJapan
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43
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Fellner A, Goldberg Y, Lev D, Basel-Salmon L, Shor O, Benninger F. In-silico phenotype prediction by normal mode variant analysis in TUBB4A-related disease. Sci Rep 2022; 12:58. [PMID: 34997144 PMCID: PMC8741991 DOI: 10.1038/s41598-021-04337-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/21/2021] [Indexed: 11/09/2022] Open
Abstract
TUBB4A-associated disorder is a rare condition affecting the central nervous system. It displays a wide phenotypic spectrum, ranging from isolated late-onset torsion dystonia to a severe early-onset disease with developmental delay, neurological deficits, and atrophy of the basal ganglia and cerebellum, therefore complicating variant interpretation and phenotype prediction in patients carrying TUBB4A variants. We applied entropy-based normal mode analysis (NMA) to investigate genotype–phenotype correlations in TUBB4A-releated disease and to develop an in-silico approach to assist in variant interpretation and phenotype prediction in this disorder. Variants included in our analysis were those reported prior to the conclusion of data collection for this study in October 2019. All TUBB4A pathogenic missense variants reported in ClinVar and Pubmed, for which associated clinical information was available, and all benign/likely benign TUBB4A missense variants reported in ClinVar, were included in the analysis. Pathogenic variants were divided into five phenotypic subgroups. In-silico point mutagenesis in the wild-type modeled protein structure was performed for each variant. Wild-type and mutated structures were analyzed by coarse-grained NMA to quantify protein stability as entropy difference value (ΔG) for each variant. Pairwise ΔG differences between all variant pairs in each structural cluster were calculated and clustered into dendrograms. Our search yielded 41 TUBB4A pathogenic variants in 126 patients, divided into 11 partially overlapping structural clusters across the TUBB4A protein. ΔG-based cluster analysis of the NMA results revealed a continuum of genotype–phenotype correlation across each structural cluster, as well as in transition areas of partially overlapping structural clusters. Benign/likely benign variants were integrated into the genotype–phenotype continuum as expected and were clearly separated from pathogenic variants. We conclude that our results support the incorporation of the NMA-based approach used in this study in the interpretation of variant pathogenicity and phenotype prediction in TUBB4A-related disease. Moreover, our results suggest that NMA may be of value in variant interpretation in additional monogenic conditions.
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Affiliation(s)
- Avi Fellner
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, 49100, Petah Tikva, Israel. .,Department of Neurology, Rabin Medical Center, Beilinson Hospital, 49100, Petah Tikva, Israel.
| | - Yael Goldberg
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, 49100, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Dorit Lev
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.,Metabolic-Neurogenetic Clinic, Wolfson Medical Center, 58220, Holon, Israel.,Rina Mor Institute of Medical Genetics, Wolfson Medical Center, 58220, Holon, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, 49100, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.,Felsenstein Medical Research Center, 49100, Petah Tikva, Israel
| | - Oded Shor
- Department of Neurology, Rabin Medical Center, Beilinson Hospital, 49100, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.,Felsenstein Medical Research Center, 49100, Petah Tikva, Israel
| | - Felix Benninger
- Department of Neurology, Rabin Medical Center, Beilinson Hospital, 49100, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.,Felsenstein Medical Research Center, 49100, Petah Tikva, Israel
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44
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Yap ZY, Efthymiou S, Seiffert S, Vargas Parra K, Lee S, Nasca A, Maroofian R, Schrauwen I, Pendziwiat M, Jung S, Bhoj E, Striano P, Mankad K, Vona B, Cuddapah S, Wagner A, Alvi JR, Davoudi-Dehaghani E, Fallah MS, Gannavarapu S, Lamperti C, Legati A, Murtaza BN, Nadeem MS, Rehman MU, Saeidi K, Salpietro V, von Spiczak S, Sandoval A, Zeinali S, Zeviani M, Reich A, Jang C, Helbig I, Barakat TS, Ghezzi D, Leal SM, Weber Y, Houlden H, Yoon WH, Houlden H, Yoon WH. Bi-allelic variants in OGDHL cause a neurodevelopmental spectrum disease featuring epilepsy, hearing loss, visual impairment, and ataxia. Am J Hum Genet 2021; 108:2368-2384. [PMID: 34800363 DOI: 10.1016/j.ajhg.2021.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022] Open
Abstract
The 2-oxoglutarate dehydrogenase-like (OGDHL) protein is a rate-limiting enzyme in the Krebs cycle that plays a pivotal role in mitochondrial metabolism. OGDHL expression is restricted mainly to the brain in humans. Here, we report nine individuals from eight unrelated families carrying bi-allelic variants in OGDHL with a range of neurological and neurodevelopmental phenotypes including epilepsy, hearing loss, visual impairment, gait ataxia, microcephaly, and hypoplastic corpus callosum. The variants include three homozygous missense variants (p.Pro852Ala, p.Arg244Trp, and p.Arg299Gly), three compound heterozygous single-nucleotide variants (p.Arg673Gln/p.Val488Val, p.Phe734Ser/p.Ala327Val, and p.Trp220Cys/p.Asp491Val), one homozygous frameshift variant (p.Cys553Leufs∗16), and one homozygous stop-gain variant (p.Arg440Ter). To support the pathogenicity of the variants, we developed a novel CRISPR-Cas9-mediated tissue-specific knockout with cDNA rescue system for dOgdh, the Drosophila ortholog of human OGDHL. Pan-neuronal knockout of dOgdh led to developmental lethality as well as defects in Krebs cycle metabolism, which was fully rescued by expression of wild-type dOgdh. Studies using the Drosophila system indicate that p.Arg673Gln, p.Phe734Ser, and p.Arg299Gly are severe loss-of-function alleles, leading to developmental lethality, whereas p.Pro852Ala, p.Ala327Val, p.Trp220Cys, p.Asp491Val, and p.Arg244Trp are hypomorphic alleles, causing behavioral defects. Transcript analysis from fibroblasts obtained from the individual carrying the synonymous variant (c.1464T>C [p.Val488Val]) in family 2 showed that the synonymous variant affects splicing of exon 11 in OGDHL. Human neuronal cells with OGDHL knockout exhibited defects in mitochondrial respiration, indicating the essential role of OGDHL in mitochondrial metabolism in humans. Together, our data establish that the bi-allelic variants in OGDHL are pathogenic, leading to a Mendelian neurodevelopmental disease in humans.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Wan Hee Yoon
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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45
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Ayagama T, Bose SJ, Capel RA, Priestman DA, Berridge G, Fischer R, Galione A, Platt FM, Kramer H, Burton RA. A modified density gradient proteomic-based method to analyze endolysosomal proteins in cardiac tissue. iScience 2021; 24:102949. [PMID: 34466782 PMCID: PMC8384914 DOI: 10.1016/j.isci.2021.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/04/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022] Open
Abstract
The importance of lysosomes in cardiac physiology and pathology is well established, and evidence for roles in calcium signaling is emerging. We describe a label-free proteomics method suitable for small cardiac tissue biopsies based on density-separated fractionation, which allows study of endolysosomal (EL) proteins. Density gradient fractions corresponding to tissue lysate; sarcoplasmic reticulum (SR), mitochondria (Mito) (1.3 g/mL); and EL with negligible contamination from SR or Mito (1.04 g/mL) were analyzed using Western blot, enzyme activity assay, and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis (adapted discontinuous Percoll and sucrose differential density gradient). Kyoto Encyclopedia of Genes and Genomes, Reactome, Panther, and Gene Ontology pathway analysis showed good coverage of RAB proteins and lysosomal cathepsins (including cardiac-specific cathepsin D) in the purified EL fraction. Significant EL proteins recovered included catalytic activity proteins. We thus present a comprehensive protocol and data set of guinea pig atrial EL organelle proteomics using techniques also applicable for non-cardiac tissue.
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Affiliation(s)
- Thamali Ayagama
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Samuel J. Bose
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Rebecca A. Capel
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | | | - Georgina Berridge
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Antony Galione
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Frances M. Platt
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, W12 0NN UK
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46
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Yechieli M, Gulsuner S, Ben-Pazi H, Fattal A, Aran A, Kuzminsky A, Sagi L, Guttman D, Schneebaum Sender N, Gross-Tsur V, Klopstock T, Walsh T, Renbaum P, Zeligson S, Shemer Meiri L, Lev D, Shmueli D, Blumkin L, Lahad A, King MC, Levy EL, Segel R. Diagnostic yield of chromosomal microarray and trio whole exome sequencing in cryptogenic cerebral palsy. J Med Genet 2021; 59:759-767. [PMID: 34321325 DOI: 10.1136/jmedgenet-2021-107884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/14/2021] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To determine the yield of genetic diagnoses using chromosomal microarray (CMA) and trio whole exome sequencing (WES), separately and combined, among patients with cryptogenic cerebral palsy (CP). METHODS Trio WES of patients with prior CMA analysis for cryptogenic CP, defined as disabling, non-progressive motor symptoms beginning before the age of 3 years without known cause. RESULTS Given both CMA analysis and trio WES, clinically significant genetic findings were identified for 58% of patients (26 of 45). Diagnoses were eight large CNVs detected by CMA and 18 point mutations detected by trio WES. None had more than one severe mutation. Approximately half of events (14 of 26) were de novo. Yield was significantly higher in patients with CP with comorbidities (69%, 22 of 32) than in those with pure motor CP (31%, 4 of 13; p=0.02). Among patients with genetic diagnoses, CNVs were more frequent than point mutations among patients with congenital anomalies (OR 7.8, 95% CI 1.2 to 52.4) or major dysmorphic features (OR 10.5, 95% CI 1.4 to 73.7). Clinically significant mutations were identified in 18 different genes: 14 with known involvement in CP-related disorders and 4 responsible for other neurodevelopmental conditions. Three possible new candidate genes for CP were ARGEF10, RTF1 and TAOK3. CONCLUSIONS Cryptogenic CP is genetically highly heterogeneous. Genomic analysis has a high yield and is warranted in all these patients. Trio WES has higher yield than CMA, except in patients with congenital anomalies or major dysmorphic features, but these methods are complementary. Patients with negative results with one approach should also be tested by the other.
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Affiliation(s)
- Michal Yechieli
- Obstetrics and Gynecology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Hilla Ben-Pazi
- Pediatric Neurology, Shaare Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aviva Fattal
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Aran
- Pediatric Neurology, Shaare Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alla Kuzminsky
- Pediatric Neurology Institute, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Liora Sagi
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dafna Guttman
- Pediatric Rehabilitation Department, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Nira Schneebaum Sender
- Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Varda Gross-Tsur
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Pediatric Neurology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tehila Klopstock
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tom Walsh
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Paul Renbaum
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Dorit Lev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Institute of Medical Genetics, Edith Wolfson Medical Center, Holon, Israel
| | - Dorit Shmueli
- Child Development Services, Clalit Health Services, Tel Aviv, Israel
| | - Luba Blumkin
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Neurology, Edith Wolfson Hospital, Holon, Israel
| | - Amnon Lahad
- Braun School of Public Health, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Family Medicine, Clalit Health Services, Jerusalem, Israel
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ephrat Lahad Levy
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Reeval Segel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel .,Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
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47
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Phenotypic homogeneity in childhood epilepsies evolves in gene-specific patterns across 3251 patient-years of clinical data. Eur J Hum Genet 2021; 29:1690-1700. [PMID: 34031551 PMCID: PMC8560769 DOI: 10.1038/s41431-021-00908-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/25/2022] Open
Abstract
While genetic studies of epilepsies can be performed in thousands of individuals, phenotyping remains a manual, non-scalable task. A particular challenge is capturing the evolution of complex phenotypes with age. Here, we present a novel approach, applying phenotypic similarity analysis to a total of 3251 patient-years of longitudinal electronic medical record data from a previously reported cohort of 658 individuals with genetic epilepsies. After mapping clinical data to the Human Phenotype Ontology, we determined the phenotypic similarity of individuals sharing each genetic etiology within each 3-month age interval from birth up to a maximum age of 25 years. 140 of 600 (23%) of all 27 genes and 3-month age intervals with sufficient data for calculation of phenotypic similarity were significantly higher than expect by chance. 11 of 27 genetic etiologies had significant overall phenotypic similarity trajectories. These do not simply reflect strong statistical associations with single phenotypic features but appear to emerge from complex clinical constellations of features that may not be strongly associated individually. As an attempt to reconstruct the cognitive framework of syndrome recognition in clinical practice, longitudinal phenotypic similarity analysis extends the traditional phenotyping approach by utilizing data from electronic medical records at a scale that is far beyond the capabilities of manual phenotyping. Delineation of how the phenotypic homogeneity of genetic epilepsies varies with age could improve the phenotypic classification of these disorders, the accuracy of prognostic counseling, and by providing historical control data, the design and interpretation of precision clinical trials in rare diseases.
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48
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Lewis-Smith D, Galer PD, Balagura G, Kearney H, Ganesan S, Cosico M, O'Brien M, Vaidiswaran P, Krause R, Ellis CA, Thomas RH, Robinson PN, Helbig I. Modeling seizures in the Human Phenotype Ontology according to contemporary ILAE concepts makes big phenotypic data tractable. Epilepsia 2021; 62:1293-1305. [PMID: 33949685 PMCID: PMC8272408 DOI: 10.1111/epi.16908] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/19/2021] [Accepted: 04/01/2021] [Indexed: 01/08/2023]
Abstract
Objective: The clinical features of epilepsy determine how it is defined, which in turn guides management. Therefore, consideration of the fundamental clinical entities that comprise an epilepsy is essential in the study of causes, trajectories, and treatment responses. The Human Phenotype Ontology (HPO) is used widely in clinical and research genetics for concise communication and modeling of clinical features, allowing extracted data to be harmonized using logical inference. We sought to redesign the HPO seizure subontology to improve its consistency with current epileptological concepts, supporting the use of large clinical data sets in high-throughput clinical and research genomics. Methods: We created a new HPO seizure subontology based on the 2017 International League Against Epilepsy (ILAE) Operational Classification of Seizure Types, and integrated concepts of status epilepticus, febrile, reflex, and neonatal seizures at different levels of detail. We compared the HPO seizure subontology prior to, and following, our revision, according to the information that could be inferred about the seizures of 791 individuals from three independent cohorts: 2 previously published and 150 newly recruited individuals. Each cohort’s data were provided in a different format and harmonized using the two versions of the HPO. Results: The new seizure subontology increased the number of descriptive concepts for seizures 5-fold. The number of seizure descriptors that could be annotated to the cohort increased by 40% and the total amount of information about individuals’ seizures increased by 38%. The most important qualitative difference was the relationship of focal to bilateral tonic-clonic seizure to generalized-onset and focal-onset seizures.
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Affiliation(s)
- David Lewis-Smith
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK.,Department of Clinical Neurosciences, Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
| | - Peter D Galer
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ganna Balagura
- Medical Genetics Unit, IRCSS Giannina Gaslini Institute, Genoa, Italy
| | - Hugh Kearney
- FutureNeuro the SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Shiva Ganesan
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mahgenn Cosico
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Margaret O'Brien
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Priya Vaidiswaran
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Colin A Ellis
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Rhys H Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK.,Department of Clinical Neurosciences, Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
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Wilf-Yarkoni A, Shor O, Fellner A, Hellmann MA, Pras E, Yonath H, Shkedi-Rafid S, Basel-Salmon L, Bazak L, Eliahou R, Greenbaum L, Stiebel-Kalish H, Benninger F, Goldberg Y. Mild Phenotype of Wolfram Syndrome Associated With a Common Pathogenic Variant Is Predicted by a Structural Model of Wolframin. NEUROLOGY-GENETICS 2021; 7:e578. [PMID: 33763535 PMCID: PMC7983365 DOI: 10.1212/nxg.0000000000000578] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/27/2021] [Indexed: 11/15/2022]
Abstract
Objective To describe the WFS1 c.1672C>T; p.R558C missense variant, found in 1.34% of Ashkenazi Jews, that has a relatively mild phenotype and to use computational normal mode analysis (NMA) to explain the genotype-phenotype relationship. Methods The clinical, laboratory, and genetic features of 8 homozygotes were collected. A model of the wolframin protein was constructed, and NMA was used to simulate the effect of the variant on protein thermodynamics. Results Mean age at Wolfram syndrome (WS) diagnosis among homozygotes was 30 years; diabetes (7/8) was diagnosed at mean age 19 years (15–21 years), and bilateral optic atrophy (with MRI evidence of optic/chiasm atrophy) (6/8) at mean age 29 years (15–48 years). The oldest patient (62 years) also had gait difficulties, memory problems, parietal and cerebellar atrophy, and white matter hyperintense lesions. All retained functional vision with independent ambulation and self-care; none had diabetes insipidus or hearing loss. The p.R558C variant caused less impairment of protein entropy than WFS1 variants associated with a more severe phenotype. Conclusions The p.R558C variant causes a milder, late-onset phenotype of WS. We report a structural model of wolframin protein based on empirical functional studies and use NMA modeling to show a genotype-phenotype correlation across all homozygotes. Clinicians should be alert to this condition in patients with juvenile diabetes and patients of any age with a combination of diabetes and optic atrophy. Computational NMA has potential benefit for prediction of the genotype-phenotype relationship.
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Affiliation(s)
- Adi Wilf-Yarkoni
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Oded Shor
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Avi Fellner
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Mark Andrew Hellmann
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Elon Pras
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Hagit Yonath
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Shiri Shkedi-Rafid
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Lina Basel-Salmon
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Lili Bazak
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Ruth Eliahou
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Lior Greenbaum
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Hadas Stiebel-Kalish
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Felix Benninger
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
| | - Yael Goldberg
- Neuro-Immunology Unit (A.W-.Y., M.A.H.), Department of Neurology (O.S., A.F., F.B.), Department of Radiology (R.E.), and Neuro-Ophthalmology Unit, Department of Ophthalmology (H.S.K.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine (O.S., E.P., H.Y., L.B.-S., L.G., H.S.-K., F.B., Y.G.), Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute (A.F., Y.G., L.B.-S., L.B.), Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel; The Danek Gertner Institute of Human Genetics (E.P., H.Y., L.G.), Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center (E.P., L.G.), Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A (H.Y.), Sheba Medical Center, Tel Hashomer, Israel; Department of Genetics and Faculty of Medicine (S.S.-R.), Hadassah-Hebrew University Hospital, Jerusalem, Israel; Felsenstein Medical Research Center (O.S., L.B.-S., F.B.), Petach Tikva, Israel
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50
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Hannan FM, Stevenson M, Bayliss AL, Stokes VJ, Stewart M, Kooblall KG, Gorvin CM, Codner G, Teboul L, Wells S, Thakker RV. Ap2s1 mutation causes hypercalcaemia in mice and impairs interaction between calcium-sensing receptor and adaptor protein-2. Hum Mol Genet 2021; 30:880-892. [PMID: 33729479 PMCID: PMC8165646 DOI: 10.1093/hmg/ddab076] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/09/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Adaptor protein 2 (AP2), a heterotetrameric complex comprising AP2α, AP2β2, AP2μ2 and AP2σ2 subunits, is ubiquitously expressed and involved in endocytosis and trafficking of membrane proteins, such as the calcium-sensing receptor (CaSR), a G-protein coupled receptor that signals via Gα11. Mutations of CaSR, Gα11 and AP2σ2, encoded by AP2S1, cause familial hypocalciuric hypercalcaemia types 1–3 (FHH1–3), respectively. FHH3 patients have heterozygous AP2S1 missense Arg15 mutations (p.Arg15Cys, p.Arg15His or p.Arg15Leu) with hypercalcaemia, which may be marked and symptomatic, and occasional hypophosphataemia and osteomalacia. To further characterize the phenotypic spectrum and calcitropic pathophysiology of FHH3, we used CRISPR/Cas9 genome editing to generate mice harboring the AP2S1 p.Arg15Leu mutation, which causes the most severe FHH3 phenotype. Heterozygous (Ap2s1+/L15) mice were viable, and had marked hypercalcaemia, hypermagnesaemia, hypophosphataemia, and increases in alkaline phosphatase activity and fibroblast growth factor-23. Plasma 1,25-dihydroxyvitamin D was normal, and no alterations in bone mineral density or bone turnover were noted. Homozygous (Ap2s1L15/L15) mice invariably died perinatally. Co-immunoprecipitation studies showed that the AP2S1 p.Arg15Leu mutation impaired protein–protein interactions between AP2σ2 and the other AP2 subunits, and also with the CaSR. Cinacalcet, a CaSR positive allosteric modulator, decreased plasma calcium and parathyroid hormone concentrations in Ap2s1+/L15 mice, but had no effect on the diminished AP2σ2-CaSR interaction in vitro. Thus, our studies have established a mouse model that is representative for FHH3 in humans, and demonstrated that the AP2S1 p.Arg15Leu mutation causes a predominantly calcitropic phenotype, which can be ameliorated by treatment with cinacalcet.
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Affiliation(s)
- Fadil M Hannan
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK.,Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Asha L Bayliss
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Victoria J Stokes
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Michelle Stewart
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Kreepa G Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Caroline M Gorvin
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
| | - Gemma Codner
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Lydia Teboul
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Sara Wells
- Mammalian Genetics Unit and Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7LJ, UK
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