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Tolonen JP, Parolin Schnekenberg R, McGowan S, Sims D, McEntagart M, Elmslie F, Shears D, Stewart H, Tofaris GK, Dabir T, Morrison PJ, Johnson D, Hadjivassiliou M, Ellard S, Shaw‐Smith C, Znaczko A, Dixit A, Suri M, Sarkar A, Harrison RE, Jones G, Houlden H, Ceravolo G, Jarvis J, Williams J, Shanks ME, Clouston P, Rankin J, Blumkin L, Lerman‐Sagie T, Ponger P, Raskin S, Granath K, Uusimaa J, Conti H, McCann E, Joss S, Blakes AJ, Metcalfe K, Kingston H, Bertoli M, Kneen R, Lynch SA, Martínez Albaladejo I, Moore AP, Jones WD, Becker EB, Németh AH. Detailed Analysis of ITPR1 Missense Variants Guides Diagnostics and Therapeutic Design. Mov Disord 2024; 39:141-151. [PMID: 37964426 PMCID: PMC10952845 DOI: 10.1002/mds.29651] [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: 07/30/2023] [Revised: 09/16/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND The ITPR1 gene encodes the inositol 1,4,5-trisphosphate (IP3 ) receptor type 1 (IP3 R1), a critical player in cerebellar intracellular calcium signaling. Pathogenic missense variants in ITPR1 cause congenital spinocerebellar ataxia type 29 (SCA29), Gillespie syndrome (GLSP), and severe pontine/cerebellar hypoplasia. The pathophysiological basis of the different phenotypes is poorly understood. OBJECTIVES We aimed to identify novel SCA29 and GLSP cases to define core phenotypes, describe the spectrum of missense variation across ITPR1, standardize the ITPR1 variant nomenclature, and investigate disease progression in relation to cerebellar atrophy. METHODS Cases were identified using next-generation sequencing through the Deciphering Developmental Disorders study, the 100,000 Genomes project, and clinical collaborations. ITPR1 alternative splicing in the human cerebellum was investigated by quantitative polymerase chain reaction. RESULTS We report the largest, multinational case series of 46 patients with 28 unique ITPR1 missense variants. Variants clustered in functional domains of the protein, especially in the N-terminal IP3 -binding domain, the carbonic anhydrase 8 (CA8)-binding region, and the C-terminal transmembrane channel domain. Variants outside these domains were of questionable clinical significance. Standardized transcript annotation, based on our ITPR1 transcript expression data, greatly facilitated analysis. Genotype-phenotype associations were highly variable. Importantly, while cerebellar atrophy was common, cerebellar volume loss did not correlate with symptom progression. CONCLUSIONS This dataset represents the largest cohort of patients with ITPR1 missense variants, expanding the clinical spectrum of SCA29 and GLSP. Standardized transcript annotation is essential for future reporting. Our findings will aid in diagnostic interpretation in the clinic and guide selection of variants for preclinical studies. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Jussi Pekka Tolonen
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Kavli Institute of Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | - Ricardo Parolin Schnekenberg
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Oxford Center for Genomic MedicineOxford University Hospitals National Health Service Foundation Trust, University of OxfordOxfordUK
| | - Simon McGowan
- Centre for Computational Biology, MRC Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - David Sims
- Centre for Computational Biology, MRC Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Meriel McEntagart
- South West Regional Genetics ServiceSt. George's University HospitalsLondonUK
| | - Frances Elmslie
- South West Regional Genetics ServiceSt. George's University HospitalsLondonUK
| | - Debbie Shears
- Oxford Center for Genomic MedicineOxford University Hospitals National Health Service Foundation Trust, University of OxfordOxfordUK
| | - Helen Stewart
- Oxford Center for Genomic MedicineOxford University Hospitals National Health Service Foundation Trust, University of OxfordOxfordUK
| | - George K. Tofaris
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Kavli Institute of Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | - Tabib Dabir
- Northern Ireland Regional Genetics ServiceBelfast City HospitalBelfastUK
| | - Patrick J. Morrison
- Patrick G. Johnston Centre for Cancer Research and Cell BiologyQueen's University BelfastBelfastUK
| | - Diana Johnson
- Sheffield Clinical Genetics ServiceSheffield Children's NHS Foundation TrustSheffieldUK
| | - Marios Hadjivassiliou
- Department of NeurologyRoyal Hallamshire Hospital, Sheffield Teaching Hospital NHS Foundation TrustSheffieldUK
| | - Sian Ellard
- Exeter Genomics LaboratoryRoyal Devon University Healthcare NHS Foundation TrustUK
| | - Charles Shaw‐Smith
- Peninsula Clinical Genetics Service, Royal Devon University HospitalRoyal Devon University Healthcare NHS Foundation TrustExeterUK
| | - Anna Znaczko
- Peninsula Clinical Genetics Service, Royal Devon University HospitalRoyal Devon University Healthcare NHS Foundation TrustExeterUK
| | - Abhijit Dixit
- Department of Clinical GeneticsNottingham University Hospitals NHS TrustNottinghamUK
| | - Mohnish Suri
- Department of Clinical GeneticsNottingham University Hospitals NHS TrustNottinghamUK
| | - Ajoy Sarkar
- Department of Clinical GeneticsNottingham University Hospitals NHS TrustNottinghamUK
| | - Rachel E. Harrison
- Department of Clinical GeneticsNottingham University Hospitals NHS TrustNottinghamUK
| | - Gabriela Jones
- Department of Clinical GeneticsNottingham University Hospitals NHS TrustNottinghamUK
| | - Henry Houlden
- Department of Neuromuscular DisordersUCL Queen Square Institute of Neurology, University College LondonLondonUK
| | - Giorgia Ceravolo
- Department of Neuromuscular DisordersUCL Queen Square Institute of Neurology, University College LondonLondonUK
- Unit of Pediatric Emergency, Department of Adult and Childhood Human PathologyUniversity Hospital of MessinaMessinaItaly
| | - Joanna Jarvis
- Birmingham Women's and Children's NHS Foundation TrustBirminghamUK
| | - Jonathan Williams
- Oxford Regional Genetics Laboratory, Churchill HospitalOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Morag E. Shanks
- Oxford Regional Genetics Laboratory, Churchill HospitalOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Penny Clouston
- Oxford Regional Genetics Laboratory, Churchill HospitalOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Julia Rankin
- Department of Clinical GeneticsRoyal Devon and Exeter NHS Foundation TrustExeterUK
| | - Lubov Blumkin
- Sackler School of MedicineTel Aviv UniversityTel AvivIsrael
- Pediatric Movement Disorders Service, Pediatric Neurology UnitEdith Wolfson Medical CenterHolonIsrael
| | - Tally Lerman‐Sagie
- Sackler School of MedicineTel Aviv UniversityTel AvivIsrael
- Magen Center for Rare Diseases‐Metabolic, NeurogeneticWolfson Medical CenterHolonIsrael
| | - Penina Ponger
- Sackler School of MedicineTel Aviv UniversityTel AvivIsrael
- Movement Disorders Unit, Department of NeurologyTel Aviv Sourasky Medical CenterTel AvivIsrael
| | - Salmo Raskin
- Genetika Centro de Aconselhamento e LaboratórioCuritibaBrazil
| | - Katariina Granath
- Research Unit of Clinical MedicineMedical Research Center, Oulu University Hospital and University of OuluOuluFinland
| | - Johanna Uusimaa
- Research Unit of Clinical MedicineMedical Research Center, Oulu University Hospital and University of OuluOuluFinland
| | - Hector Conti
- All Wales Medical Genomics ServiceWrexham Maelor HospitalWrexhamUK
| | - Emma McCann
- Liverpool Women's Hospital Foundation TrustLiverpoolUK
| | - Shelagh Joss
- West of Scotland Centre for Genomic MedicineQueen Elizabeth University HospitalGlasgowUK
| | - Alexander J.M. Blakes
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of BiologyMedicine and Health, University of ManchesterManchesterUK
- Manchester Centre for Genomic MedicineUniversity of Manchester, St. Mary's Hospital, Manchester Academic Health Science CentreManchesterUK
| | - Kay Metcalfe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of BiologyMedicine and Health, University of ManchesterManchesterUK
- Manchester Centre for Genomic MedicineUniversity of Manchester, St. Mary's Hospital, Manchester Academic Health Science CentreManchesterUK
| | - Helen Kingston
- Manchester Centre for Genomic MedicineUniversity of Manchester, St. Mary's Hospital, Manchester Academic Health Science CentreManchesterUK
| | - Marta Bertoli
- Northern Genetics ServiceInternational Centre for LifeNewcastle upon TyneUK
| | - Rachel Kneen
- Department of NeurologyAlder Hey Children's NHS Foundation TrustLiverpoolUK
| | - Sally Ann Lynch
- Department of Clinical GeneticsChildren's Health Ireland (CHI) at CrumlinDublinIreland
| | | | | | - Wendy D. Jones
- North East Thames Regional Genetics ServiceGreat Ormond Street Hospital for Children, Great Ormond Street NHS Foundation TrustLondonUK
| | | | - Esther B.E. Becker
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Kavli Institute of Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | - Andrea H. Németh
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Oxford Center for Genomic MedicineOxford University Hospitals National Health Service Foundation Trust, University of OxfordOxfordUK
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Moritsugu K, Ito T, Kidera A. Allosteric response to ligand binding: Molecular dynamics study of the N-terminal domains in IP 3 receptor. Biophys Physicobiol 2019; 16:232-239. [PMID: 31984176 PMCID: PMC6975907 DOI: 10.2142/biophysico.16.0_232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/13/2019] [Indexed: 02/07/2023] Open
Abstract
Inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) is a huge tetrameric intracellular Ca2+ channel that mediates cytoplasmic Ca2+ signaling. The structural basis of the gating in IP3R has been studied by X-ray crystallography and cryo-electron microscopy, focusing on the domain rearrangements triggered by IP3 binding. Here, we conducted molecular dynamics (MD) simulations of the three N-terminal domains of IP3R responsible for IP3 binding (IBC/SD; two domains of the IP3 binding core, IBCβ and IBCα, and suppressor domain, SD) as a model system to study the initial gating stage. The response upon removal of IP3 from the IP3-bound form of IBC/SD was traced in MD trajectories. The two IBC domains showed an immediate response of opening after removal of IP3, and SD showed a simultaneous opening motion indicating a tight dynamic coupling with IBC. However, when IBC remained in a more closed form, the dynamic coupling broke and SD exhibited a more amplified closing motion independently of IBC. This amplified SD motion was caused by the break of connection between SD and IBCβ at the hinge region, but was suppressed in the native tetrameric state. The analyses using Motion Tree and the linear response theory clarified that in the open form, SD and IBCα moved collectively relative to IBCβ with a response upon IP3 binding within the linear regime, whereas in the closed form, such collectiveness disappeared. These results suggest that the regulation of dynamics via the domain arrangement and multimerization is requisite for large-scale allosteric communication in IP3R gating machinery.
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Affiliation(s)
- Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Tsubasa Ito
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Akinori Kidera
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
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Abstract
In the body, extracellular stimuli produce inositol 1,4,5-trisphosphate (IP3), an intracellular chemical signal that binds to the IP3 receptor (IP3R) to release calcium ions (Ca2+) from the endoplasmic reticulum. In the past 40 years, the wide-ranging functions mediated by IP3R and its genetic defects causing a variety of disorders have been unveiled. Recent cryo-electron microscopy and X-ray crystallography have resolved IP3R structures and begun to integrate with concurrent functional studies, which can explicate IP3-dependent opening of Ca2+-conducting gates placed ∼90 Å away from IP3-binding sites and its regulation by Ca2+. This review highlights recent research progress on the IP3R structure and function. We also propose how protein plasticity within IP3R, which involves allosteric gating and assembly transformations accompanied by rapid and chronic structural changes, would enable it to regulate diverse functions at cellular microdomains in pathophysiological states.
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Affiliation(s)
- Kozo Hamada
- Laboratory of Cell Calcium Signaling, Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, 201210, China; ,
| | - Katsuhiko Mikoshiba
- Laboratory of Cell Calcium Signaling, Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, 201210, China; ,
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Chandran A, Chee X, Prole DL, Rahman T. Exploration of inositol 1,4,5-trisphosphate (IP 3) regulated dynamics of N-terminal domain of IP 3 receptor reveals early phase molecular events during receptor activation. Sci Rep 2019; 9:2454. [PMID: 30792485 PMCID: PMC6385359 DOI: 10.1038/s41598-019-39301-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/22/2019] [Indexed: 01/12/2023] Open
Abstract
Inositol 1, 4, 5-trisphosphate (IP3) binding at the N-terminus (NT) of IP3 receptor (IP3R) allosterically triggers the opening of a Ca2+-conducting pore located ~100 Å away from the IP3-binding core (IBC). However, the precise mechanism of IP3 binding and correlated domain dynamics in the NT that are central to the IP3R activation, remains unknown. Our all-atom molecular dynamics (MD) simulations recapitulate the characteristic twist motion of the suppressor domain (SD) and reveal correlated ‘clam closure’ dynamics of IBC with IP3-binding, complementing existing suggestions on IP3R activation mechanism. Our study further reveals the existence of inter-domain dynamic correlation in the NT and establishes the SD to be critical for the conformational dynamics of IBC. Also, a tripartite interaction involving Glu283-Arg54-Asp444 at the SD – IBC interface seemed critical for IP3R activation. Intriguingly, during the sub-microsecond long simulation, we observed Arg269 undergoing an SD-dependent flipping of hydrogen bonding between the first and fifth phosphate groups of IP3. This seems to play a major role in determining the IP3 binding affinity of IBC in the presence/absence of the SD. Our study thus provides atomistic details of early molecular events occurring within the NT during and following IP3 binding that lead to channel gating.
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Affiliation(s)
- Aneesh Chandran
- Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD, Cambridge, UK. .,Molecular Biophysics Unit, Indian Institute of Science, 560 012, Bangalore, India.
| | - Xavier Chee
- Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD, Cambridge, UK
| | - David L Prole
- Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD, Cambridge, UK
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD, Cambridge, UK.
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