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K P, Madhana PN, Eswaramoorthy R, Ramasamy M. A computational approach to analyzing the functional and structural impacts of Tripeptidyl-Peptidase 1 missense mutations in neuronal ceroid lipofuscinosis. Metab Brain Dis 2024; 39:545-558. [PMID: 38185715 DOI: 10.1007/s11011-024-01341-8] [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: 10/25/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Neuronal ceroid-lipofuscinosis (NCLs) are a group of severe neurodegenerative conditions, most likely present in infantile, late infantile, juvenile, and adult-onset forms. Their phenotypic characteristics comprise eyesight damage, reduced motor activity and cognitive function, and sometimes tend to die in the initial stage. In recent studies, NCLs have been categorized into at least 14 genetic collections (CLN1-14). CLN2 gene encodes Tripeptidyl peptidase 1 (TPP1), which affects late infantile-onset form. In this study, we retrieved a mutational dataset screening for TPP1 protein from various databases (ClinVar, UniProt, HGMD). Fifty-six missense mutants were enumerated with computational methods to perceive the significant mutants (G475R and G501C) and correlated with clinical and literature data. A structure-based screening method was initiated to understand protein-ligand interaction and dynamic simulation. The docking procedure was performed for the native (3EDY) and mutant (G473R and G501C) structures with Gemfibrozil (gem), which lowers the lipid level, decreases the triglycerides amount in the blood circulation, and controls hyperlipidemia. The Native had an interaction score of -5.57 kcal/mol, and the mutants had respective average binding scores of -6.24 (G473R) and - 5.17 (G501C) kcal/mol. Finally, molecular dynamics simulation showed that G473R and G501C mutants had better flexible and stable orientation in all trajectory analyses. Therefore, this work gives an extended understanding of both functional and structural levels of influence for the mutant form that leads to NCL disorder.
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Affiliation(s)
- Priyanka K
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India
| | - Priya N Madhana
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India
| | - Rajalakshmanan Eswaramoorthy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, TamilNadu, India
| | - Magesh Ramasamy
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India.
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Hay Mele B, Rossetti F, Cubellis MV, Monticelli M, Andreotti G. Drug Repurposing and Lysosomal Storage Disorders: A Trick to Treat. Genes (Basel) 2024; 15:290. [PMID: 38540351 PMCID: PMC10970111 DOI: 10.3390/genes15030290] [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: 01/22/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 06/14/2024] Open
Abstract
Rare diseases, or orphan diseases, are defined as diseases affecting a small number of people compared to the general population. Among these, we find lysosomal storage disorders (LSDs), a cluster of rare metabolic diseases characterized by enzyme mutations causing abnormal glycolipid storage. Drug repositioning involves repurposing existing approved drugs for new therapeutic applications, offering advantages in cost, time savings, and a lower risk of failure. We present a comprehensive analysis of existing drugs, their repurposing potential, and their clinical implications in the context of LSDs, highlighting the necessity of mutation-specific approaches. Our review systematically explores the landscape of drug repositioning as a means to enhance LSDs therapies. The findings advocate for the strategic repositioning of drugs, accentuating its role in expediting the discovery of effective treatments. We conclude that drug repurposing represents a viable pathway for accelerating therapeutic discovery for LSDs, emphasizing the need for the careful evaluation of drug efficacy and toxicity in disease-specific contexts.
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Affiliation(s)
- Bruno Hay Mele
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (B.H.M.); (F.R.); (M.V.C.)
| | - Federica Rossetti
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (B.H.M.); (F.R.); (M.V.C.)
| | - Maria Vittoria Cubellis
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (B.H.M.); (F.R.); (M.V.C.)
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
- Stazione Zoologica “Anton Dohrn”, Villa Comunale, 80121 Naples, Italy
| | - Maria Monticelli
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (B.H.M.); (F.R.); (M.V.C.)
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
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Sakti DH, Cornish EE, Fraser CL, Nash BM, Sandercoe TM, Jones MM, Rowe NA, Jamieson RV, Johnson AM, Grigg JR. Early recognition of CLN3 disease facilitated by visual electrophysiology and multimodal imaging. Doc Ophthalmol 2023:10.1007/s10633-023-09930-1. [PMID: 36964447 DOI: 10.1007/s10633-023-09930-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/07/2023] [Indexed: 03/26/2023]
Abstract
BACKGROUND Neuronal ceroid lipofuscinosis is a group of neurodegenerative disorders with varying visual dysfunction. CLN3 is a subtype which commonly presents with visual decline. Visual symptomatology can be indistinct making early diagnosis difficult. This study reports ocular biomarkers of CLN3 patients to assist clinicians in early diagnosis, disease monitoring, and future therapy. METHODS Retrospective review of 5 confirmed CLN3 patients in our eye clinic. Best corrected visual acuity (BCVA), electroretinogram (ERG), ultra-widefield (UWF) fundus photography and fundus autofluorescence (FAF), and optical coherence tomography (OCT) studies were undertaken. RESULTS Five unrelated children, 4 females and 1 male, with median age of 6.2 years (4.6-11.7) at first assessment were investigated at the clinic from 2016 to 2021. Four homozygous and one heterozygous pathogenic CLN3 variants were found. Best corrected visual acuities (BCVAs) ranged from 0.18 to 0.88 logMAR at first presentation. Electronegative ERGs were identified in all patients. Bull's eye maculopathies found in all patients. Hyper-autofluorescence ring surrounding hypo-autofluorescence fovea on FAF was found. Foveal ellipsoid zone (EZ) disruptions were found in all patients with additional inner and outer retinal microcystic changes in one patient. Neurological problems noted included autism, anxiety, motor dyspraxia, behavioural issue, and psychomotor regression. CONCLUSIONS CLN3 patients presented at median age 6.2 years with visual decline. Early onset maculopathy with an electronegative ERG and variable cognitive and motor decline should prompt further investigations including neuropaediatric evaluation and genetic assessment for CLN3 disease. The structural parameters such as EZ and FAF will facilitate ocular monitoring.
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Affiliation(s)
- Dhimas H Sakti
- Save Sight Institute, Speciality of Clinical Ophthalmology and Eye Health, Faculty of Medicine and Health, The University of Sydney, Sydney Eye Hospital Campus, 8 Macquarie St, Sydney, NSW, 2001, Australia
- Department of Ophthalmology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elisa E Cornish
- Save Sight Institute, Speciality of Clinical Ophthalmology and Eye Health, Faculty of Medicine and Health, The University of Sydney, Sydney Eye Hospital Campus, 8 Macquarie St, Sydney, NSW, 2001, Australia
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Clare L Fraser
- Save Sight Institute, Speciality of Clinical Ophthalmology and Eye Health, Faculty of Medicine and Health, The University of Sydney, Sydney Eye Hospital Campus, 8 Macquarie St, Sydney, NSW, 2001, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
- Sydney Genome Diagnostics, Sydney Children's Hospital Network (Westmead), Sydney, Australia
| | - Trent M Sandercoe
- Department of Ophthalmology, Sydney Children's Hospital Network (Westmead), Sydney, Australia
| | - Michael M Jones
- Department of Ophthalmology, Sydney Children's Hospital Network (Westmead), Sydney, Australia
| | - Neil A Rowe
- Department of Ophthalmology, Sydney Children's Hospital Network (Westmead), Sydney, Australia
| | - Robyn V Jamieson
- Save Sight Institute, Speciality of Clinical Ophthalmology and Eye Health, Faculty of Medicine and Health, The University of Sydney, Sydney Eye Hospital Campus, 8 Macquarie St, Sydney, NSW, 2001, Australia
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Alexandra M Johnson
- Department of Neurology, Sydney Children's Hospital, University of New South Wales, Sydney, Australia
| | - John R Grigg
- Save Sight Institute, Speciality of Clinical Ophthalmology and Eye Health, Faculty of Medicine and Health, The University of Sydney, Sydney Eye Hospital Campus, 8 Macquarie St, Sydney, NSW, 2001, Australia.
- Eye Genetics Research Unit, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia.
- Department of Ophthalmology, Sydney Children's Hospital Network (Westmead), Sydney, Australia.
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Wibbeler E, Nickel M, Schwering C, Schulz A, Mink JW. The Unified Batten Disease Rating Scale (UBDRS): Validation and reliability in an independent CLN3 disease sample. Eur J Paediatr Neurol 2022; 38:62-65. [PMID: 35427884 PMCID: PMC9879304 DOI: 10.1016/j.ejpn.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND The neuronal ceroid lipofuscinoses (NCLs) are a group of disorders characterized by neurodegeneration and intracellular accumulation of an auto-fluorescent lipopigment. Together, NCLs represent the most common cause of cerebral neurodegenerative disease in children. CLN3 disease, the classic juvenile-onset form (JNCL) due to mutations in CLN3, is characterized by progressive vision loss, epilepsy, dementia, behavioral difficulties, and motor impairment. The Unified Batten Disease Rating Scale (UBDRS) is a disease-specific rating scale that was developed to assess disease severity in 4 domains: physical, behavior, seizures, and functional capability. Validity and reliability of the UBDRS has been established in a large North American cohort of over 130 individuals. The purpose of this study was to determine whether the UBDRS is valid and reliable when tested in an independent sample. METHODS Over the course of one week, 13 individuals with genetically confirmed CLN3 disease were evaluated with the UBDRS by 5 examiners at the University Medical Center Hamburg Eppendorf (UKE). One rater (JWM), one of the developers of the UBDRS, served as the reference standard. The other 4 raters were physicians with expertise in various forms of Batten Disease. After a formal training session, 13 individuals (age 16.5 ± 5.6 yrs) were evaluated simultaneous in parallel by the 5 raters. Inter-rater reliability of the Physical subscale was assessed with Intra-class Correlation (ICC) analysis. The relationship between age and severity was assessed and compared to previously published data from the North American cohort. FINDINGS The ICC among the 5 independent raters was 0.92, demonstrating excellent inter-rater reliability. The individual correlations of each UKE rater compared to the reference standard rater were all >0.95. The average UBDRS Physical Subscale score in this sample was 28 ± 21 (mean ± SD) with a range from 1 to 61. When evaluated as a function of participant age, the slope was 3.06 points/year (R2 = 0.66). INTERPRETATION We have shown excellent interrater reliability for the UBDRS as a clinical rating scale for CLN3 disease in a sample independent from previous work. The results of this study are comparable to those published by Kwon et al., 2011 in a North American cohort showing a slope of 2.86 points per year with a 95% CI of 2.27-3.45 (N = 82). Our results demonstrate excellence inter-rater reliability after training a new group of raters and provide additional evidence for construct validity of the UBDRS. The UBDRS is a valid and reliable rating scale that can used by trained raters to assess the severity and rate of progression of CLN3 disease.
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Affiliation(s)
- Eva Wibbeler
- University Medical Center Hamburg Eppendorf (UKE), Hamburg, Germany.
| | - Miriam Nickel
- University Medical Center Hamburg Eppendorf (UKE), Hamburg, Germany
| | | | - Angela Schulz
- University Medical Center Hamburg Eppendorf (UKE), Hamburg, Germany
| | - Jonathan W Mink
- Department of Neurology, University of Rochester, 601 Elmwood Avenue, Rochester, NY, 14642, USA
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Augustine EF, Adams HR, de Los Reyes E, Drago K, Frazier M, Guelbert N, Laine M, Levin T, Mink JW, Nickel M, Peifer D, Schulz A, Simonati A, Topcu M, Turunen JA, Williams R, Wirrell EC, King S. Management of CLN1 Disease: International Clinical Consensus. Pediatr Neurol 2021; 120:38-51. [PMID: 34000449 DOI: 10.1016/j.pediatrneurol.2021.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND CLN1 disease (neuronal ceroid lipofuscinosis type 1) is a rare, genetic, neurodegenerative lysosomal storage disorder caused by palmitoyl-protein thioesterase 1 (PPT1) enzyme deficiency. Clinical features include developmental delay, psychomotor regression, seizures, ataxia, movement disorders, visual impairment, and early death. In general, the later the age at symptom onset, the more protracted the disease course. We sought to evaluate current evidence and to develop expert practice consensus to support clinicians who have not previously encountered patients with this rare disease. METHODS We searched the literature for guidelines and evidence to support clinical practice recommendations. We surveyed CLN1 disease experts and caregivers regarding their experiences and recommendations, and a meeting of experts was conducted to ascertain points of consensus and clinical practice differences. RESULTS We found a limited evidence base for treatment and no clinical management guidelines specific to CLN1 disease. Fifteen CLN1 disease experts and 39 caregivers responded to the surveys, and 14 experts met to develop consensus-based recommendations. The resulting management recommendations are uniquely informed by family perspectives, due to the inclusion of caregiver and advocate perspectives. A family-centered approach is supported, and individualized, multidisciplinary care is emphasized in the recommendations. Ascertainment of the specific CLN1 disease phenotype (infantile-, late infantile-, juvenile-, or adult-onset) is of key importance in informing the anticipated clinical course, prognosis, and care needs. Goals and strategies should be periodically reevaluated and adapted to patients' current needs, with a primary aim of optimizing patient and family quality of life.
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Affiliation(s)
- Erika F Augustine
- Department of Neurology and Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland; Departments of Neurology and Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York.
| | - Heather R Adams
- Departments of Neurology and Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Emily de Los Reyes
- Department of Pediatrics and Neurology, Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio
| | | | | | - Norberto Guelbert
- Metabolic Diseases Section, Children's Hospital of Cordoba, Cordoba, Argentina
| | - Minna Laine
- Department of Pediatric Neurology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tanya Levin
- Medical Writing Consultant, Atlanta, Georgia
| | - Jonathan W Mink
- Departments of Neurology, Neuroscience, and Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Miriam Nickel
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Angela Schulz
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandro Simonati
- Department of Surgery, Dentistry, Paediatrics and Gynaecology, University of Verona School of Medicine, Verona, Italy
| | - Meral Topcu
- Professor Emeritus, Department of Pediatric Neurology, Hacettepe University, Ankara, Turkey
| | - Joni A Turunen
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ruth Williams
- Children's Neurosciences Centre, Evelina London Children's Hospital, London, United Kingdom
| | - Elaine C Wirrell
- Divisions of Epilepsy and Child and Adolescent Neurology, Department of Neurology, Mayo Clinic, Rochester, Minnesota
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Li D, McIntosh CS, Mastaglia FL, Wilton SD, Aung-Htut MT. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl Neurodegener 2021; 10:16. [PMID: 34016162 PMCID: PMC8136212 DOI: 10.1186/s40035-021-00240-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is a fundamental step in eukaryotic gene expression that systematically removes non-coding regions (introns) and ligates coding regions (exons) into a continuous message (mature mRNA). This process is highly regulated and can be highly flexible through a process known as alternative splicing, which allows for several transcripts to arise from a single gene, thereby greatly increasing genetic plasticity and the diversity of proteome. Alternative splicing is particularly prevalent in neuronal cells, where the splicing patterns are continuously changing to maintain cellular homeostasis and promote neurogenesis, migration and synaptic function. The continuous changes in splicing patterns and a high demand on many cis- and trans-splicing factors contribute to the susceptibility of neuronal tissues to splicing defects. The resultant neurodegenerative diseases are a large group of disorders defined by a gradual loss of neurons and a progressive impairment in neuronal function. Several of the most common neurodegenerative diseases involve some form of splicing defect(s), such as Alzheimer's disease, Parkinson's disease and spinal muscular atrophy. Our growing understanding of RNA splicing has led to the explosion of research in the field of splice-switching antisense oligonucleotide therapeutics. Here we review our current understanding of the effects alternative splicing has on neuronal differentiation, neuronal migration, synaptic maturation and regulation, as well as the impact on neurodegenerative diseases. We will also review the current landscape of splice-switching antisense oligonucleotides as a therapeutic strategy for a number of common neurodegenerative disorders.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Craig Stewart McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Frank Louis Mastaglia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Steve Donald Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia. .,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia.
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