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Uribe-Carretero E, Rey V, Fuentes JM, Tamargo-Gómez I. Lysosomal Dysfunction: Connecting the Dots in the Landscape of Human Diseases. BIOLOGY 2024; 13:34. [PMID: 38248465 PMCID: PMC10813815 DOI: 10.3390/biology13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Lysosomes are the main organelles responsible for the degradation of macromolecules in eukaryotic cells. Beyond their fundamental role in degradation, lysosomes are involved in different physiological processes such as autophagy, nutrient sensing, and intracellular signaling. In some circumstances, lysosomal abnormalities underlie several human pathologies with different etiologies known as known as lysosomal storage disorders (LSDs). These disorders can result from deficiencies in primary lysosomal enzymes, dysfunction of lysosomal enzyme activators, alterations in modifiers that impact lysosomal function, or changes in membrane-associated proteins, among other factors. The clinical phenotype observed in affected patients hinges on the type and location of the accumulating substrate, influenced by genetic mutations and residual enzyme activity. In this context, the scientific community is dedicated to exploring potential therapeutic approaches, striving not only to extend lifespan but also to enhance the overall quality of life for individuals afflicted with LSDs. This review provides insights into lysosomal dysfunction from a molecular perspective, particularly in the context of human diseases, and highlights recent advancements and breakthroughs in this field.
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Affiliation(s)
- Elisabet Uribe-Carretero
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Verónica Rey
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Jose Manuel Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Audet S, Triassi V, Gelinas M, Legault-Cadieux N, Ferraro V, Duquette A, Tetreault M. Integration of multi-omics technologies for molecular diagnosis in ataxia patients. Front Genet 2024; 14:1304711. [PMID: 38239855 PMCID: PMC10794629 DOI: 10.3389/fgene.2023.1304711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Background: Episodic ataxias are rare neurological disorders characterized by recurring episodes of imbalance and coordination difficulties. Obtaining definitive molecular diagnoses poses challenges, as clinical presentation is highly heterogeneous, and literature on the underlying genetics is limited. While the advent of high-throughput sequencing technologies has significantly contributed to Mendelian disorders genetics, interpretation of variants of uncertain significance and other limitations inherent to individual methods still leaves many patients undiagnosed. This study aimed to investigate the utility of multi-omics for the identification and validation of molecular candidates in a cohort of complex cases of ataxia with episodic presentation. Methods: Eight patients lacking molecular diagnosis despite extensive clinical examination were recruited following standard genetic testing. Whole genome and RNA sequencing were performed on samples isolated from peripheral blood mononuclear cells. Integration of expression and splicing data facilitated genomic variants prioritization. Subsequently, long-read sequencing played a crucial role in the validation of those candidate variants. Results: Whole genome sequencing uncovered pathogenic variants in four genes (SPG7, ATXN2, ELOVL4, PMPCB). A missense and a nonsense variant, both previously reported as likely pathogenic, configured in trans in individual #1 (SPG7: c.2228T>C/p.I743T, c.1861C>T/p.Q621*). An ATXN2 microsatellite expansion (CAG32) in another late-onset case. In two separate individuals, intronic variants near splice sites (ELOVL4: c.541 + 5G>A; PMPCB: c.1154 + 5G>C) were predicted to induce loss-of-function splicing, but had never been reported as disease-causing. Long-read sequencing confirmed the compound heterozygous variants configuration, repeat expansion length, as well as splicing landscape for those pathogenic variants. A potential genetic modifier of the ATXN2 expansion was discovered in ZFYVE26 (c.3022C>T/p.R1008*). Conclusion: Despite failure to identify pathogenic variants through clinical genetic testing, the multi-omics approach enabled the molecular diagnosis in 50% of patients, also giving valuable insights for variant prioritization in remaining cases. The findings demonstrate the value of long-read sequencing for the validation of candidate variants in various scenarios. Our study demonstrates the effectiveness of leveraging complementary omics technologies to unravel the underlying genetics in patients with unresolved rare diseases such as ataxia. Molecular diagnoses not only hold significant promise in improving patient care management, but also alleviates the burden of diagnostic odysseys, more broadly enhancing quality of life.
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Affiliation(s)
- Sebastien Audet
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
| | - Valerie Triassi
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
| | - Myriam Gelinas
- Department of Medicine, University of Montreal Hospital Centre (CHUM), Montreal, QC, Canada
| | - Nab Legault-Cadieux
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
| | - Vincent Ferraro
- Department of Medicine, University of Montreal Hospital Centre (CHUM), Montreal, QC, Canada
| | - Antoine Duquette
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
- Neurology Service, Department of Medicine, André-Barbeau Movement Disorders Unit, University of Montreal Hospital (CHUM), Montreal, QC, Canada
- Genetic Service, Department of Medicine, University of Montreal Hospital (CHUM), Montreal, QC, Canada
| | - Martine Tetreault
- University of Montreal Hospital Research Center (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
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Lopergolo D, Salvatore S, Sorrentino V, Malandrini A, Santorelli FM, Battisti C. Early-onset motor polyneuropathy associated with a novel dominant NAGLU mutation. Neurol Sci 2023; 44:1415-1418. [PMID: 36648562 DOI: 10.1007/s10072-023-06607-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/08/2023] [Indexed: 01/18/2023]
Abstract
INTRODUCTION NAGLU encodes N-acetyl-alpha-glucosaminidase, an enzyme that degrades heparan sulfate. Biallelic NAGLU mutations cause mucopolysaccharidosis IIIB, a severe childhood-onset neurodegenerative disease, while monoallelic mutations are associated to late-onset, dominantly inherited painful sensory neuropathy. However, to date, only one family with a dominant NAGLU-related neuropathy has been described. CASE REPORT Here we describe a patient with early-onset motor polyneuropathy harboring a novel monoallelic NAGLU mutation. We found reduced NAGLU enzymatic activity thus corroborating the pathogenic role of the new variant. DISCUSSION Our report represents the second ever described case with dominant NAGLU-related neuropathy and the first case with early-onset motor symptoms. We underlie the importance of a thorough clinical description of this probably underestimated new clinical entity.
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Affiliation(s)
- Diego Lopergolo
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy.
- UOC Neurologia E Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100, Siena, Italy.
| | - Simona Salvatore
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- UOC Neurologia E Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100, Siena, Italy
| | - Vincenzo Sorrentino
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
- Interdepartmental Program of Molecular Diagnosis and Pathogenetic Mechanisms of Rare Genetic Diseases, Azienda Ospedaliero Universitaria Senese, Siena, Italy
| | - Alessandro Malandrini
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- UOC Neurologia E Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100, Siena, Italy
| | | | - Carla Battisti
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- UOC Neurologia E Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 16, 53100, Siena, Italy
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García-Pérez R, Ramirez JM, Ripoll-Cladellas A, Chazarra-Gil R, Oliveros W, Soldatkina O, Bosio M, Rognon PJ, Capella-Gutierrez S, Calvo M, Reverter F, Guigó R, Aguet F, Ferreira PG, Ardlie KG, Melé M. The landscape of expression and alternative splicing variation across human traits. CELL GENOMICS 2022; 3:100244. [PMID: 36777183 PMCID: PMC9903719 DOI: 10.1016/j.xgen.2022.100244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022]
Abstract
Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.
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Affiliation(s)
- Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Jose Miguel Ramirez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Aida Ripoll-Cladellas
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Ruben Chazarra-Gil
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Winona Oliveros
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Oleksandra Soldatkina
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Mattia Bosio
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Paul Joris Rognon
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Department of Economics and Business, Universitat Pompeu Fabra, Barcelona, Catalonia 08005, Spain,Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia 08034, Spain
| | - Salvador Capella-Gutierrez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Miquel Calvo
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Ferran Reverter
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalonia 08003, Spain
| | | | - Pedro G. Ferreira
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal,Laboratory of Artificial Intelligence and Decision Support, INESC TEC, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal,Institute of Molecular Pathology and Immunology of the University of Porto, Institute for Research and Innovation in Health (i3s), R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | | | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Corresponding author
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Estimated prevalence of Niemann-Pick type C disease in Quebec. Sci Rep 2021; 11:22621. [PMID: 34799641 PMCID: PMC8604933 DOI: 10.1038/s41598-021-01966-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022] Open
Abstract
Niemann–Pick type C (NP-C) disease is an autosomal recessive disease caused by variants in the NPC1 or NPC2 genes. It has a large range of symptoms depending on age of onset, thus making it difficult to diagnose. In adults, symptoms appear mainly in the form of psychiatric problems. The prevalence varies from 0.35 to 2.2 per 100,000 births depending on the country. The aim of this study is to calculate the estimated prevalence of NP-C in Quebec to determine if it is underdiagnosed in this population. The CARTaGENE database is a unique database that regroups individuals between 40 and 69 years old from metropolitan regions of Quebec. RNA-sequencing data was available for 911 individuals and exome sequencing for 198 individuals. We used a bioinformatic pipeline on those individuals to extract the variants in the NPC1/2 genes. The prevalence in Quebec was estimated assuming Hardy–Weinberg Equilibrium. Two pathogenic variants were used. The variant p.Pro543Leu was found in three heterozygous individuals that share a common haplotype, which suggests a founder French-Canadian pathogenic variant. The variant p.Ile1061Thr was found in two heterozygous individuals. Both variants have previously been reported and are usually associated with infantile onset. The estimated prevalence calculated using those two variants is 0.61:100,000 births. This study represents the first estimate of NP-C in Quebec. The estimated prevalence for NP-C is likely underestimated due to misdiagnosis or missed cases. It is therefore important to diagnose all NP-C patients to initiate early treatment.
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Schiavon CR, Shadel GS, Manor U. Impaired Mitochondrial Mobility in Charcot-Marie-Tooth Disease. Front Cell Dev Biol 2021; 9:624823. [PMID: 33598463 PMCID: PMC7882694 DOI: 10.3389/fcell.2021.624823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Charcot-Marie-Tooth (CMT) disease is a progressive, peripheral neuropathy and the most commonly inherited neurological disorder. Clinical manifestations of CMT mutations are typically limited to peripheral neurons, the longest cells in the body. Currently, mutations in at least 80 different genes are associated with CMT and new mutations are regularly being discovered. A large portion of the proteins mutated in axonal CMT have documented roles in mitochondrial mobility, suggesting that organelle trafficking defects may be a common underlying disease mechanism. This review will focus on the potential role of altered mitochondrial mobility in the pathogenesis of axonal CMT, highlighting the conceptional challenges and potential experimental and therapeutic opportunities presented by this "impaired mobility" model of the disease.
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Affiliation(s)
- Cara R. Schiavon
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, United States
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Gerald S. Shadel
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Uri Manor
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, United States
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Harm TA, Hostetter SJ, Nenninger AS, Valentine BN, Ellinwood NM, Smith JD. Temporospatial Development of Neuropathologic Findings in a Canine Model of Mucopolysaccharidosis IIIB. Vet Pathol 2020; 58:205-222. [PMID: 33205707 DOI: 10.1177/0300985820960128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mucopolysaccharidosis (MPS) IIIB is a neuropathic lysosomal storage disease characterized by the deficient activity of a lysosomal enzyme obligate for the degradation of the glycosaminoglycan (GAG) heparan sulfate (HS). The pathogenesis of neurodegeneration in MPS IIIB is incompletely understood. Large animal models are attractive for pathogenesis and therapeutic studies due to their larger size, outbred genetics, longer lifespan, and naturally occurring MPS IIIB disease. However, the temporospatial development of neuropathologic changes has not been reported for canine MPS IIIB. Here we describe lesions in 8 brain regions, cervical spinal cord, and dorsal root ganglion (DRG) in a canine model of MPS IIIB that includes dogs aged from 2 to 26 months of age. Pathological changes in the brain included early microscopic vacuolation of glial cells initially observed at 2 months, and vacuolation of neurons initially observed at 10 months. Inclusions within affected cells variably stained positively with PAS and LFB stains. Quantitative immunohistochemistry demonstrated increased glial expression of GFAP and Iba1 in dogs with MPS IIIB compared to age-matched controls at all time points, suggesting neuroinflammation occurs early in disease. Loss of Purkinje cells was initially observed at 10 months and was pronounced in 18- and 26-month-old dogs with MPS IIIB. Our results support the dog as a replicative model of MPS IIIB neurologic lesions and detail the pathologic and neuroinflammatory changes in the spinal cord and DRG of MPS IIIB-affected dogs.
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Affiliation(s)
| | - Shannon J Hostetter
- 70724Iowa State University, Ames, IA, USA.,Current address: Department of Veterinary Pathology, University of Georgia, Athens, GA, USA
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Neuropathophysiology of Lysosomal Storage Diseases: Synaptic Dysfunction as a Starting Point for Disease Progression. J Clin Med 2020; 9:jcm9030616. [PMID: 32106459 PMCID: PMC7141115 DOI: 10.3390/jcm9030616] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022] Open
Abstract
About two thirds of the patients affected with lysosomal storage diseases (LSD) experience neurological manifestations, such as developmental delay, seizures, or psychiatric problems. In order to develop efficient therapies, it is crucial to understand the neuropathophysiology underlying these symptoms. How exactly lysosomal storage affects biogenesis and function of neurons is still under investigation however recent research highlights a substantial role played by synaptic defects, such as alterations in synaptic spines, synaptic proteins, postsynaptic densities, and synaptic vesicles that might lead to functional impairments in synaptic transmission and neurodegeneration, finally culminating in massive neuronal death and manifestation of cognitive symptoms. Unveiling how the synaptic components are affected in neurological LSD will thus enable a better understanding of the complexity of disease progression as well as identify crucial targets of therapeutic relevance and optimal time windows for targeted intervention.
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Nam SH, Choi BO. Clinical and genetic aspects of Charcot-Marie-Tooth disease subtypes. PRECISION AND FUTURE MEDICINE 2019. [DOI: 10.23838/pfm.2018.00163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Jain S, Chaitanya V, Faruq M. A novel frameshift deletion in NAGLU causing sanfilipo type III-B in an Indian family. Clin Case Rep 2018; 6:2399-2402. [PMID: 30564336 PMCID: PMC6293137 DOI: 10.1002/ccr3.1844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/10/2018] [Accepted: 09/13/2018] [Indexed: 11/09/2022] Open
Abstract
Mucopolysaccharidoses are group of inherited lysosomal storage disorder. Two siblings of a family manifested behavioral abnormalities; hepatosplenomegaly and hypotonia of infantile onset were found to have a novel homozygous frameshift variation, p.Leu280TrpfsTer19 in NAGLU. This variant was predicted to cause the loss of TIM-barrel and alpha-helical region of NAGLU protein.
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Affiliation(s)
- Sweta Jain
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
| | | | - Mohammed Faruq
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
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Zorina-Lichtenwalter K, Parisien M, Diatchenko L. Genetic studies of human neuropathic pain conditions: a review. Pain 2018; 159:583-594. [PMID: 29240606 PMCID: PMC5828382 DOI: 10.1097/j.pain.0000000000001099] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 10/20/2017] [Accepted: 10/26/2017] [Indexed: 12/12/2022]
Abstract
Numerous studies have shown associations between genetic variants and neuropathic pain disorders. Rare monogenic disorders are caused by mutations of substantial effect size in a single gene, whereas common disorders are likely to have a contribution from multiple genetic variants of mild effect size, representing different biological pathways. In this review, we survey the reported genetic contributors to neuropathic pain and submit them for validation in a 150,000-participant sample of the U.K. Biobank cohort. Successfully replicated association with a neuropathic pain construct for 2 variants in IL10 underscores the importance of neuroimmune interactions, whereas genome-wide significant association with low back pain (P = 1.3e-8) and false discovery rate 5% significant associations with hip, knee, and neck pain for variant rs7734804 upstream of the MAT2B gene provide evidence of shared contributing mechanisms to overlapping pain conditions at the molecular genetic level.
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Affiliation(s)
| | - Marc Parisien
- Alan Edwards Pain Centre, McGill University, Montreal, QC, Canada
| | - Luda Diatchenko
- Alan Edwards Pain Centre, McGill University, Montreal, QC, Canada
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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Abstract
PURPOSE OF REVIEW Charcot-Marie-Tooth disease (CMT) is one of the commonest inherited neuromuscular diseases with a population prevalence of 1 in 2500. This review will cover recent advances in the genetics and pathomechanisms of CMT and how these are leading to the development of rational therapies. RECENT FINDINGS Pathomechanistic and therapeutic target advances in CMT include the identification of the ErbB receptor signalling pathway as a therapeutic target in CMT1A and pharmacological modification of the unfolded protein response in CMT1B. In CMT2D, due to mutations in glycyl-tRNA synthetase, vascular endothelial growth factor-mediated stimulation of the Nrp1 receptor has been identified as a therapeutic target. Preclinical advances have been accompanied by the publication of large natural history cohorts and the identification of a sensitive biomarker of disease (muscle MRI) that is able to detect disease progression in CMT1A over 1 year. SUMMARY Advances in next-generation sequencing technology, cell biology and animal models of CMT are paving the way for rational treatments. The combination of robust natural history data and the identification of sensitive biomarkers mean that we are now entering an exciting therapeutic era in the field of the genetic neuropathies.
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Yassaee VR, Hashemi-Gorji F, Miryounesi M, Rezayi A, Ravesh Z, Yassaee F, Salehpour S. Clinical, biochemical and molecular features of Iranian families with mucopolysaccharidosis: A case series. Clin Chim Acta 2017; 474:88-95. [PMID: 28844463 DOI: 10.1016/j.cca.2017.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 12/15/2022]
Abstract
This study aims to ascertain the genetic variants which contribute to the most common types of MPS in eleven Iranian families. Clinical and biochemical features were obtained during initial examination and patients were further investigated for genetic defects in the MPS genes. Peripheral blood samples were obtained from all family members after obtaining written informed consent. Based on the patient's clinical diagnosis, three different genetic tests including Sanger sequencing of four genes (IDUA, IDS, SGSH, and GALNS), targeted panel (10 genes) and Whole Exome Sequencing (WES) techniques were applied to identify the causative variants. A total of 12 different mutations were identified in five genes, including nine novel mutations and three previously reported missense mutations. Sanger sequencing confirmation of the identified mutations determined one case of compound heterozygous in the NAGLU gene. In this study, novel mutations in MPS related genes were identified attempting to characterize the type and subtype of the disease using molecular approaches. Results of the study positively contribute to mutation spectrum of IDUA, IDS, SGSH, NAGLU, and GALNS genes in the Iranian cohort. It may also enrich genetic counseling for rapid risk assessment and disease management.
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Affiliation(s)
- Vahid Reza Yassaee
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Miryounesi
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Rezayi
- Department of Pediatrics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Ravesh
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fakhrolmolouk Yassaee
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Obstetrics and Gynecology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shadab Salehpour
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Pediatrics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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15
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Beck M. The Link Between Lysosomal Storage Disorders and More Common Diseases. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2016. [DOI: 10.1177/2326409816682767] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Michael Beck
- Institute of Human Genetics, University Medical Center, Mainz, Germany
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16
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Stojkovic T. Hereditary neuropathies: An update. Rev Neurol (Paris) 2016; 172:775-778. [PMID: 27866730 DOI: 10.1016/j.neurol.2016.06.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/10/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
Hereditary neuropathies are the most common inherited neuromuscular diseases. Charcot-Marie-Tooth (CMT) disease represents the most common form with an average prevalence ranging from 1/2500 to 1/1200, depending on the studies. To date and with the advances of the latest generation sequencing, more than 80 genes have been identified. Although the common clinical phenotype comprises a progressive distal muscle weakness and sensory loss, foot deformities and decreased or absent tendon reflexes, clinical and electrophysiological phenotypes exhibit great variability. Moreover, atypical phenotypes are arising, overlapping with spastic paraplegia, hereditary sensory neuropathies or amyotrophic lateral sclerosis. The causative genes are involved in various biological processes such as myelin development and maintenance, biosynthesis and degradation of proteins, neuronal structural maintenance, axonal transport, endocytosis, membrane dynamics, ion-channel function and the mitochondrial network. An accurate genetic diagnosis is important for appropriate genetic counselling and treatment options. Therapeutic advances, particularly small interfering RNA therapy, are encouraging in hereditary transthyretin amyloid neuropathy.
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Affiliation(s)
- T Stojkovic
- Centre de référence des maladies neuromusculaires Paris Est, AP-HP, groupe hospitalier Pitié-Salpêtrière, 47-83, boulevard de l'Hôpital, 75013 Paris, France.
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17
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Delineation of New Disorders and Phenotypic Expansion of Known Disorders Through Whole Exome Sequencing. CURRENT GENETIC MEDICINE REPORTS 2015. [DOI: 10.1007/s40142-015-0079-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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