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Fasaludeen A, McTague A, Jose M, Banerjee M, Sundaram S, Madhusoodanan UK, Radhakrishnan A, Menon RN. Genetic variant interpretation for the neurologist - A pragmatic approach in the next-generation sequencing era in childhood epilepsy. Epilepsy Res 2024; 201:107341. [PMID: 38447235 DOI: 10.1016/j.eplepsyres.2024.107341] [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: 11/27/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Genetic advances over the past decade have enhanced our understanding of the genetic landscape of childhood epilepsy. However a major challenge for clinicians ha been understanding the rationale and systematic approach towards interpretation of the clinical significance of variant(s) detected in their patients. As the clinical paradigm evolves from gene panels to whole exome or whole genome testing including rapid genome sequencing, the number of patients tested and variants identified per patient will only increase. Each step in the process of variant interpretation has limitations and there is no single criterion which enables the clinician to draw reliable conclusions on a causal relationship between the variant and disease without robust clinical phenotyping. Although many automated online analysis software tools are available, these carry a risk of misinterpretation. This guideline provides a pragmatic, real-world approach to variant interpretation for the child neurologist. The focus will be on ascertaining aspects such as variant frequency, subtype, inheritance pattern, structural and functional consequence with regard to genotype-phenotype correlations, while refraining from mere interpretation of the classification provided in a genetic test report. It will not replace the expert advice of colleagues in clinical genetics, however as genomic investigations become a first-line test for epilepsy, it is vital that neurologists and epileptologists are equipped to navigate this landscape.
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Affiliation(s)
- Alfiya Fasaludeen
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Amy McTague
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Manna Jose
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Soumya Sundaram
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - U K Madhusoodanan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ashalatha Radhakrishnan
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ramshekhar N Menon
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India.
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2
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Burgis NE, VanWormer K, Robbins D, Smith J. An ITPA Enzyme with Improved Substrate Selectivity. Protein J 2024; 43:62-71. [PMID: 38066288 PMCID: PMC10901923 DOI: 10.1007/s10930-023-10162-0] [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] [Accepted: 10/03/2023] [Indexed: 02/29/2024]
Abstract
Recent clinical data have identified infant patients with lethal ITPA deficiencies. ITPA is known to modulate ITP concentrations in cells and has a critical function in neural development which is not understood. Polymorphism of the ITPA gene affects outcomes for both ribavirin and thiopurine based therapies and nearly one third of the human population is thought to harbor ITPA polymorphism. In a previous site-directed mutagenesis alanine screen of the ITPA substrate selectivity pocket, we identified the ITPA mutant, E22A, as a gain-of function mutant with enhanced ITP hydrolysis activity. Here we report a rational enzyme engineering experiment to investigate the biochemical properties of position 22 ITPA mutants and find that the E22D ITPA has two- and four-fold improved substrate selectivity for ITP over the canonical purine triphosphates ATP and GTP, respectively, while maintaining biological activity. The novel E22D ITPA should be considered as a platform for further development of ITPA therapies.
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Affiliation(s)
- Nicholas E Burgis
- Department of Chemistry, Biochemistry & Physics, Eastern Washington University, Cheney, WA, 99004, USA.
| | - Kandise VanWormer
- Department of Chemistry, Biochemistry & Physics, Eastern Washington University, Cheney, WA, 99004, USA
| | - Devin Robbins
- Department of Chemistry, Biochemistry & Physics, Eastern Washington University, Cheney, WA, 99004, USA
| | - Jonathan Smith
- Department of Chemistry, Biochemistry & Physics, Eastern Washington University, Cheney, WA, 99004, USA
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3
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Schroader JH, Handley MT, Reddy K. Inosine triphosphate pyrophosphatase: A guardian of the cellular nucleotide pool and potential mediator of RNA function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1790. [PMID: 37092460 DOI: 10.1002/wrna.1790] [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: 11/30/2022] [Revised: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
Inosine triphosphate pyrophosphatase (ITPase), encoded by the ITPA gene in humans, is an important enzyme that preserves the integrity of cellular nucleotide pools by hydrolyzing the noncanonical purine nucleotides (deoxy)inosine and (deoxy)xanthosine triphosphate into monophosphates and pyrophosphate. Variants in the ITPA gene can cause partial or complete ITPase deficiency. Partial ITPase deficiency is benign but clinically relevant as it is linked to altered drug responses. Complete ITPase deficiency causes a severe multisystem disorder characterized by seizures and encephalopathy that is frequently associated with fatal infantile dilated cardiomyopathy. In the absence of ITPase activity, its substrate noncanonical nucleotides have the potential to accumulate and become aberrantly incorporated into DNA and RNA. Hence, the pathophysiology of ITPase deficiency could arise from metabolic imbalance, altered DNA or RNA regulation, or from a combination of these factors. Here, we review the known functions of ITPase and highlight recent work aimed at determining the molecular basis for ITPA-associated pathogenesis which provides evidence for RNA dysfunction. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jacob H Schroader
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Mark T Handley
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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4
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Garg M, Goraya J, Kochar G, Jain V. ITPA-associated developmental and epileptic encephalopathy: characteristic neuroradiological features with novel clinical and biochemical findings. Epileptic Disord 2022; 24:583-588. [PMID: 35770779 DOI: 10.1684/epd.2022.1424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/08/2022] [Indexed: 11/17/2022]
Abstract
Developmental and epileptic encephalopathies (DEE) in children have an everexpanding range of rare causes. Mutations in ITPA have been recently described as causative of DEE, but only a small number of patients have been reported so far. We describe two Indian children with novel variants in the ITPA gene. Both patients had characteristic, previously described, neuroradiological findings that helped us suspect this condition even before genetic evaluation. In addition, we present new and rarely reported clinical findings associated with this condition: migrating partial epilepsy, fever-triggered seizures, movement disorder including oculogyria and dystonic tremor. One of the patients also had high cerebrospinal fluid glycine levels. Both patients had drug-responsive epilepsy, in contrast to drug-resistant seizures in previously reported patients. These patients reiterate the utility of awareness of specific neuroradiological findings and subsequent genetic evaluation to help make a precise diagnosis. Our report also extends the clinical spectrum and provides insight into possible biochemical causes for the neuroimaging findings seen in this condition.
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5
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Scala M, Wortmann SB, Kaya N, Stellingwerff MD, Pistorio A, Glamuzina E, van Karnebeek CD, Skrypnyk C, Iwanicka‐Pronicka K, Piekutowska‐Abramczuk D, Ciara E, Tort F, Sheidley B, Poduri A, Jayakar P, Jayakar A, Upadia J, Walano N, Haack TB, Prokisch H, Aldhalaan H, Karimiani EG, Yildiz Y, Ceylan AC, Santiago‐Sim T, Dameron A, Yang H, Toosi MB, Ashrafzadeh F, Akhondian J, Imannezhad S, Mirzadeh HS, Maqbool S, Farid A, Al‐Muhaizea MA, Alshwameen MO, Aldowsari L, Alsagob M, Alyousef A, AlMass R, AlHargan A, Alwadei AH, AlRasheed MM, Colak D, Alqudairy H, Khan S, Lines MA, García Cazorla MÁ, Ribes A, Morava E, Bibi F, Haider S, Ferla MP, Taylor JC, Alsaif HS, Firdous A, Hashem M, Shashkin C, Koneev K, Kaiyrzhanov R, Efthymiou S, Genomics QS, Schmitt‐Mechelke T, Ziegler A, Issa MY, Elbendary HM, Striano P, Alkuraya FS, Zaki MS, Gleeson JG, Barakat TS, Bierau J, van der Knaap MS, Maroofian R, Houlden H. Clinico-radiological features, molecular spectrum, and identification of prognostic factors in developmental and epileptic encephalopathy due to inosine triphosphate pyrophosphatase (ITPase) deficiency. Hum Mutat 2022; 43:403-419. [PMID: 34989426 PMCID: PMC9152572 DOI: 10.1002/humu.24326] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022]
Abstract
Developmental and epileptic encephalopathy 35 (DEE 35) is a severe neurological condition caused by biallelic variants in ITPA, encoding inosine triphosphate pyrophosphatase, an essential enzyme in purine metabolism. We delineate the genotypic and phenotypic spectrum of DEE 35, analyzing possible predictors for adverse clinical outcomes. We investigated a cohort of 28 new patients and reviewed previously described cases, providing a comprehensive characterization of 40 subjects. Exome sequencing was performed to identify underlying ITPA pathogenic variants. Brain MRI (magnetic resonance imaging) scans were systematically analyzed to delineate the neuroradiological spectrum. Survival curves according to the Kaplan-Meier method and log-rank test were used to investigate outcome predictors in different subgroups of patients. We identified 18 distinct ITPA pathogenic variants, including 14 novel variants, and two deletions. All subjects showed profound developmental delay, microcephaly, and refractory epilepsy followed by neurodevelopmental regression. Brain MRI revision revealed a recurrent pattern of delayed myelination and restricted diffusion of early myelinating structures. Congenital microcephaly and cardiac involvement were statistically significant novel clinical predictors of adverse outcomes. We refined the molecular, clinical, and neuroradiological characterization of ITPase deficiency, and identified new clinical predictors which may have a potentially important impact on diagnosis, counseling, and follow-up of affected individuals.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthUniversità Degli Studi di GenovaGenoaItaly
- Pediatric Neurology and Muscular Diseases UnitIRCCS Istituto Giannina GasliniGenoaItaly
- UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Saskia B. Wortmann
- Amalia Children's HospitalRadboud University NijmegenNijmegenThe Netherlands
- University Children's HospitalParacelsus Medical UniversitySalzburgAustria
| | - Namik Kaya
- Department of GeneticsKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
- Department of Translational Genomics, Center for Genomics MedicineKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Menno D. Stellingwerff
- Department of Child Neurology, Emma Children's Hospital, Amsterdam Leukodystrophy Center, Amsterdam University Medical CentersVrije Universiteit and Amsterdam NeuroscienceAmsterdamThe Netherlands
| | - Angela Pistorio
- Clinical Epidemiology and Biostatistics UnitIRCCS Istituto Giannina GasliniGenoaItaly
| | - Emma Glamuzina
- Adult and Paediatric National Metabolic ServiceStarship Children's HospitalAucklandNew Zealand
| | - Clara D. van Karnebeek
- Departments of Pediatrics and Clinical GeneticsAcademic Medical CentreAmsterdamThe Netherlands
| | - Cristina Skrypnyk
- Department of Molecular Medicine, Al‐Jawhara Centre for Molecular MedicineArabian Gulf UniversityManamaKingdom of Bahrain
| | - Katarzyna Iwanicka‐Pronicka
- Department of Medical GeneticsThe Children's Memorial Health InstituteWarsawPoland
- Department of Audiology and PhoniatricsThe Children's Memorial Health InstituteWarsawPoland
| | | | - Elżbieta Ciara
- Department of Medical GeneticsThe Children's Memorial Health InstituteWarsawPoland
| | - Frederic Tort
- Secció d'Errors Congènits del Metabolisme‐IBC, Servei de Bioquímica iGenètica MolecularHospital Clínic, IDIBAPS, CIBERERBarcelonaSpain
| | - Beth Sheidley
- Department of NeurologyF.M. Kirby Neurobiology Center, Boston Children's HospitalBostonMassachusettesUSA
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics ProgramBoston Children's HospitalBostonMassachusettesUSA
| | - Annapurna Poduri
- Department of NeurologyF.M. Kirby Neurobiology Center, Boston Children's HospitalBostonMassachusettesUSA
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics ProgramBoston Children's HospitalBostonMassachusettesUSA
- Department of NeurologyHarvard Medical SchoolBostonMassachusettesUSA
| | | | | | - Jariya Upadia
- Tulane University School of MedicineNew OrleansLouisianaUSA
| | | | - Tobias B. Haack
- Institute of Medical Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
| | - Holger Prokisch
- Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Hesham Aldhalaan
- Department of NeurosciencesKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Ehsan G. Karimiani
- Department of Medical GeneticsNext Generation Genetic PolyclinicMashhadIran
- Molecular and Clinical Sciences InstituteSt. George's University of London, Cranmer TerraceLondonUK
- Innovative Medical Research CenterIslamic Azad University, Mashhad BranchMashhadIran
| | - Yilmaz Yildiz
- Pediatric Metabolic Diseases ClinicDr. Sami Ulus Training and Research Hospital for Maternity and ChildrenAnkaraTurkey
| | - Ahmet C. Ceylan
- Department of Medical GeneticsAnkara City HospitalAnkaraTurkey
| | | | | | | | - Mehran B. Toosi
- Pediatric Neurology Department, Ghaem HospitalMashhad University of Medical SciencesMashhadIran
| | - Farah Ashrafzadeh
- Department of PediatricsMashhad University of Medical SciencesMashhadIran
| | - Javad Akhondian
- Pediatric Neurology Department, Ghaem HospitalMashhad University of Medical SciencesMashhadIran
| | - Shima Imannezhad
- Department of Pediatric DiseasesMashhad University of Medical SciencesMashhadIran
| | - Hanieh S. Mirzadeh
- Department of Pediatric DiseasesMashhad University of Medical SciencesMashhadIran
| | - Shazia Maqbool
- Development and Behavioral Pediatrics DepartmentInstitute of Child Health and The Children HospitalLahorePakistan
| | - Aisha Farid
- Development and Behavioral Pediatrics DepartmentInstitute of Child Health and The Children HospitalLahorePakistan
| | - Mohamed A. Al‐Muhaizea
- Department of NeurosciencesKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Meznah O. Alshwameen
- Department of NeurosciencesKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Lama Aldowsari
- Department of GeneticsKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Maysoon Alsagob
- Department of GeneticsKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Ashwaq Alyousef
- Department of GeneticsKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Rawan AlMass
- Department of GeneticsKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Aljouhra AlHargan
- Department of GeneticsKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Ali H. Alwadei
- Neurosciences DepartmentKing Fahad Medical CityRiyadhSaudi Arabia
| | - Maha M. AlRasheed
- Department of Clinical PharmacyKing Saud UniversityRiyadhSaudi Arabia
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific ComputingKFSHRCRiyadhKingdom of Saudi Arabia
| | - Hanan Alqudairy
- Department of GeneticsKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Sameena Khan
- Department of NeurosciencesKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Matthew A. Lines
- Medical Genetics, Department of PediatricsAlberta Children's HospitalCalgaryCanada
| | | | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme‐IBC, Servei de Bioquímica iGenètica MolecularHospital Clínic, IDIBAPS, CIBERERBarcelonaSpain
| | - Eva Morava
- Department of Clinical Genomics, Laboratory of Medicine and PathologyCenter for Individualized Medicine, Mayo ClinicRochesterMinnesotaUSA
| | - Farah Bibi
- Institute of Biochemistry and BiotechnologyPir Mehar Ali Shah Arid Agriculture UniversityRawalpindiPakistan
| | - Shahzad Haider
- Izzat Ali Shah HospitalLalarukh Wah CanttRawalpindiPakistan
| | - Matteo P. Ferla
- NIHR Oxford BRC Genomic Medicine, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Jenny C. Taylor
- NIHR Oxford BRC Genomic Medicine, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Hessa S. Alsaif
- Department of Translational Genomics, Center for Genomics MedicineKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Abdulwahab Firdous
- Department of Translational Genomics, Center for Genomics MedicineKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomics MedicineKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Chingiz Shashkin
- International University of Postgraduate EducationAlmatyKazakhstan
| | - Kairgali Koneev
- Department of Neurology and NeurosurgeryAsfendiyarov Kazakh National Medical UniversityAlmatyKazakhstan
| | - Rauan Kaiyrzhanov
- UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | | | | | | | - Andreas Ziegler
- Zentrum für Kinder und Jugendmedizin Heidelberg, Sektion Neuropädiatrie und StoffwechselmedizinUniversitätsklinikum HeidelbergHeidelbergGermany
| | - Mahmoud Y. Issa
- Clinical Genetics Department, Human Genetics and Genome Research DivisionNational Research CentreCairoEgypt
| | - Hasnaa M. Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research DivisionNational Research CentreCairoEgypt
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child HealthUniversità Degli Studi di GenovaGenoaItaly
- Pediatric Neurology and Muscular Diseases UnitIRCCS Istituto Giannina GasliniGenoaItaly
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomics MedicineKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
- Department of Anatomy and Cell BiologyAlfaisal UniversityRiyadhSaudi Arabia
| | - Maha S. Zaki
- Clinical Genetics Department, Human Genetics and Genome Research DivisionNational Research CentreCairoEgypt
| | - Joseph G. Gleeson
- Department of Neuroscience, Rady Children's Institute for Genomic Medicine, Howard Hughes Medical InstituteUniversity of CaliforniaSan DiegoCaliforniaUSA
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MCUniversity Medical CenterRotterdamThe Netherlands
| | - Jorgen Bierau
- Laboratory of Biochemical Genetics, Department of Clinical GeneticsMaastricht University HospitalMaastrichtThe Netherlands
| | - Marjo S. van der Knaap
- Department of Child Neurology, Emma Children's Hospital, Amsterdam Leukodystrophy Center, Amsterdam University Medical CentersVrije Universiteit and Amsterdam NeuroscienceAmsterdamThe Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive ResearchVU UniversityAmsterdamThe Netherlands
| | - Reza Maroofian
- UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Henry Houlden
- UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
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6
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Zamzami MA. Inosine Triphosphate Pyrophosphatase (ITPase): Functions, Mutations, Polymorphisms and Its Impact on Cancer Therapies. Cells 2022; 11:384. [PMID: 35159194 PMCID: PMC8833965 DOI: 10.3390/cells11030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Inosine triphosphate pyrophosphatase (ITPase) is an enzyme encoded by the ITPA gene and functions to prevent the incorporation of noncanonical purine nucleotides into DNA and RNA. Specifically, the ITPase catalyzed the hydrolysis of (deoxy) nucleoside triphosphates ((d) NTPs) into the corresponding nucleoside monophosphate with the concomitant release of pyrophosphate. Recently, thiopurine drug metabolites such as azathioprine have been included in the lists of ITPase substrates. Interestingly, inosine or xanthosine triphosphate (ITP/XTP) and their deoxy analogs, deoxy inosine or xanthosine triphosphate (dITP/dXTP), are products of important biological reactions such as deamination that take place within the cellular compartments. However, the incorporation of ITP/XTP, dITP/dXTP, or the genetic deficiency or polymorphism of the ITPA gene have been implicated in many human diseases, including infantile epileptic encephalopathy, early onset of tuberculosis, and the responsiveness of patients to cancer therapy. This review provides an up-to-date report on the ITPase enzyme, including information regarding its discovery, analysis, and cellular localization, its implication in human diseases including cancer, and its therapeutic potential, amongst others.
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Affiliation(s)
- Mazin A. Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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7
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Kaur P, do Rosario MC, Hebbar M, Sharma S, Kausthubham N, Nair K, A S, Bhat Y R, Lewis LES, Nampoothiri S, Patil SJ, Suresh N, Bijarnia Mahay S, Dua Puri R, Pai S, Kaur A, Kc R, Kamath N, Bajaj S, Kumble A, Shetty R, Shenoy R, Kamate M, Shah H, Muranjan MN, Bl Y, Avabratha KS, Subramaniam G, Kadavigere R, Bielas S, Girisha KM, Shukla A. Clinical and genetic spectrum of 104 Indian families with central nervous system white matter abnormalities. Clin Genet 2021; 100:542-550. [PMID: 34302356 PMCID: PMC8918360 DOI: 10.1111/cge.14037] [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: 04/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022]
Abstract
Genetic disorders with predominant central nervous system white matter abnormalities (CNS WMAs), also called leukodystrophies, are heterogeneous entities. We ascertained 117 individuals with CNS WMAs from 104 unrelated families. Targeted genetic testing was carried out in 16 families and 13 of them received a diagnosis. Chromosomal microarray (CMA) was performed for three families and one received a diagnosis. Mendeliome sequencing was used for testing 11 families and all received a diagnosis. Whole exome sequencing (WES) was performed in 80 families and was diagnostic in 52 (65%). Singleton WES was diagnostic for 50/75 (66.67%) families. Overall, genetic diagnoses were obtained in 77 families (74.03%). Twenty-two of 47 distinct disorders observed in this cohort have not been reported in Indian individuals previously. Notably, disorders of nuclear mitochondrial pathology were most frequent (9 disorders in 20 families). Thirty-seven of 75 (49.33%) disease-causing variants are novel. To sum up, the present cohort describes the phenotypic and genotypic spectrum of genetic disorders with CNS WMAs in our population. It demonstrates WES, especially singleton WES, as an efficient tool in the diagnosis of these heterogeneous entities. It also highlights possible founder events and recurrent disease-causing variants in our population and their implications on the testing strategy.
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Affiliation(s)
- Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran A
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ramesh Bhat Y
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie Edward S Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sheela Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Kochi, India
| | | | - Narayanaswami Suresh
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Shivanand Pai
- Department of Neurology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Anupriya Kaur
- Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakshith Kc
- Department of Neurology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Bajaj
- Jaslok Hospital and Research Centre, Mumbai, India
| | - Ali Kumble
- Department of Paediatrics, Indiana Hospital and Heart Institute, Mangalore, India
| | | | - Rathika Shenoy
- Department of Paediatrics, K.S. Hegde Medical Academy, NITTE University, Mangalore, India
| | - Mahesh Kamate
- Department of Paediatrics, Jawaharlal Nehru Medical College, Belgaum, India
| | - Hitesh Shah
- Department of Orthopaedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Mamta N Muranjan
- Department of Pediatrics, Genetics Division, Seth Gordhandas Sunderdas Medical College and King Edward VII Memorial Hospital, Mumbai, Maharashtra, India
| | - Yatheesha Bl
- Dheemahi Child Neurology and Development Center, Shimoga, India
| | | | | | - Rajagopal Kadavigere
- Department of Radiodiagnosis, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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James AM, Seal SE, Bailey AM, Foster GD. Viral inosine triphosphatase: A mysterious enzyme with typical activity, but an atypical function. MOLECULAR PLANT PATHOLOGY 2021; 22:382-389. [PMID: 33471956 PMCID: PMC7865087 DOI: 10.1111/mpp.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 05/03/2023]
Abstract
Plant viruses typically have highly condensed genomes, yet the plant-pathogenic viruses Cassava brown streak virus, Ugandan cassava brown streak virus, and Euphorbia ringspot virus are unusual in encoding an enzyme not yet found in any other virus, the "house-cleaning" enzyme inosine triphosphatase. Inosine triphosphatases (ITPases) are highly conserved enzymes that occur in all kingdoms of life and perform a house-cleaning function by hydrolysing the noncanonical nucleotide inosine triphosphate to inosine monophosphate. The ITPases encoded by cassava brown streak virus and Ugandan cassava brown streak virus have been characterized biochemically and are shown to have typical ITPase activity. However, their biological role in virus infection has yet to be elucidated. Here we review what is known of viral-encoded ITPases and speculate on potential roles in infection with the aim of generating a greater understanding of cassava brown streak viruses, a group of the world's most devastating viruses.
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Affiliation(s)
- Amy M. James
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Susan E. Seal
- Natural Resources Institute, Chatham MaritimeGillinghamUK
| | - Andy M. Bailey
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
| | - Gary D. Foster
- School of Biological SciencesLife Sciences BuildingUniversity of BristolBristolUK
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Koga Y, Tsuchimoto D, Hayashi Y, Abolhassani N, Yoneshima Y, Sakumi K, Nakanishi H, Toyokuni S, Nakabeppu Y. Neural stem cell-specific ITPA deficiency causes neural depolarization and epilepsy. JCI Insight 2020; 5:140229. [PMID: 33208550 PMCID: PMC7710303 DOI: 10.1172/jci.insight.140229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/15/2020] [Indexed: 11/17/2022] Open
Abstract
Inosine triphosphate pyrophosphatase (ITPA) hydrolyzes inosine triphosphate (ITP) and other deaminated purine nucleotides to the corresponding nucleoside monophosphates. In humans, ITPA deficiency causes severe encephalopathy with epileptic seizure, microcephaly, and developmental retardation. In this study, we established neural stem cell-specific Itpa-conditional KO mice (Itpa-cKO mice) to clarify the effects of ITPA deficiency on the neural system. The Itpa-cKO mice showed growth retardation and died within 3 weeks of birth. We did not observe any microcephaly in the Itpa-cKO mice, although the female Itpa-cKO mice did show adrenal hypoplasia. The Itpa-cKO mice showed limb-clasping upon tail suspension and spontaneous and/or audiogenic seizure. Whole-cell patch-clamp recordings from entorhinal cortex neurons in brain slices revealed a depolarized resting membrane potential, increased firing, and frequent spontaneous miniature excitatory postsynaptic current and miniature inhibitory postsynaptic current in the Itpa-cKO mice compared with ITPA-proficient controls. Accumulated ITP or its metabolites, such as cyclic inosine monophosphates, or RNA containing inosines may cause membrane depolarization and hyperexcitability in neurons and induce the phenotype of ITPA-deficient mice, including seizure.
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Affiliation(s)
- Yuichiro Koga
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, and
| | - Daisuke Tsuchimoto
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, and
| | - Yoshinori Hayashi
- Department of Aging Science and Pharmacology, Faculty of Dental Sciences, Kyushu University, Fukuoka, Japan
- Department of Physiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Nona Abolhassani
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, and
| | - Yasuto Yoneshima
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, and
| | - Kunihiko Sakumi
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, and
| | - Hiroshi Nakanishi
- Department of Pharmacology, Faculty of Pharmacy, Yasuda Women’s University, Hiroshima, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, and
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Sakamoto M, Kouhei D, Haniffa M, Silva S, Troncoso M, Santander P, Schonstedt V, Stecher X, Okamoto N, Hamanaka K, Mizuguchi T, Mitsuhashi S, Miyake N, Matsumoto N. A novel ITPA variant causes epileptic encephalopathy with multiple-organ dysfunction. J Hum Genet 2020; 65:751-757. [PMID: 32405030 DOI: 10.1038/s10038-020-0765-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 11/09/2022]
Abstract
Inborn errors of metabolism can cause epileptic encephalopathies. Biallelic loss-of-function variants in the ITPA gene, encoding inosine triphosphate pyrophosphatase (ITPase), have been reported in epileptic encephalopathies with lack of myelination of the posterior limb of the internal capsule, brainstem tracts, and tracts to the primary visual and motor cortices (MIM:616647). ITPase plays an important role in purine metabolism. In this study, we identified two novel homozygous ITPA variants, c.264-1 G > A and c.489-1 G > A, in two unrelated consanguineous families. The probands had epilepsy, microcephaly with characteristic magnetic resonance imaging findings (T2 hyperintensity signals in the pyramidal tracts of the internal capsule, delayed myelination, and thin corpus callosum), hypotonia, and developmental delay; both died in early infancy. Our report expands the knowledge of clinical consequences of biallelic ITPA variants.
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Affiliation(s)
- Masamune Sakamoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Pediatrics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Den Kouhei
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Muzhirah Haniffa
- Department of Genetics, Hospital Kuala Lumpur, Jalan Pahang, Malaysia
| | - Sebastián Silva
- Child Neurology Service, Hospital de Puerto Montt, Puerto Montt, Chile
| | - Mónica Troncoso
- Child Neurology Service, Hospital San Borja Arriarán, Universidad de Chile, Santiago, Chile
| | - Paola Santander
- Child Neurology Service, Hospital San Borja Arriarán, Universidad de Chile, Santiago, Chile
| | | | - Ximena Stecher
- Department of Radiology, Clínica Alemana de Santiago, Santiago, Chile.,Department of Radiology, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | | | - Kohei Hamanaka
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.
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11
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Houndonougbo Y, Pugh B, VanWormer K, April C, Burgis N. Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:1236-1247. [PMID: 32129147 DOI: 10.1080/07391102.2020.1727363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The inosine triphosphate pyrophosphatase (ITPA) protein is responsible for removing noncanonical purine nucleoside triphosphates from intracellular nucleotide pools. Absence of ITPA results in genomic instability and increased levels of inosine in DNA and RNA. The proline to threonine substitution at position 32 (P32T) affects roughly 15% of the global population and can modulate treatment outcomes for cancer, lupus, and hepatitis C patients. The substitution of arginine with cysteine at position 178 (R178C) is extremely uncommon and has only been reported in a small cohort of early infantile encephalopathy patients suggesting that a functional ITPA protein is required for life in humans. Here we present molecular dynamic simulations that describe the structure and dynamics of the wild-type ITPA homodimer and two of its clinically relevant mutants, P32T and R178C. The simulation results indicate that both the P32T and R178C mutations alter the structure and dynamic properties of the protein and provide a possible explanation of the experimentally observed effect of the mutations on ITPA activity. Specifically, the mutations increased the overall flexibility of the protein and changed the dominant collective motions of the top lobe as well as the helix 2 of the lower lobe. Moreover, we have identified key active-site residues that are classified as essential or intermediate for inosine triphosphate (ITP) hydrolyzing activity based on their hydrogen bond occupancy. Here we also present biochemical data indicating that the R178C mutant has very low ITP hydrolyzing activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yao Houndonougbo
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Bethany Pugh
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Kandise VanWormer
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Caitlin April
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
| | - Nicholas Burgis
- Department of Chemistry and Biochemistry, Eastern Washington University, Cheney, WA, USA
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