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Geroldi A, Mammi A, Gaudio A, Patrone S, La Barbera A, Origone P, Ponti C, Sanguineri F, Massucco S, Marinelli L, Grandis M, Schenone A, Mandich P, Bellone E, Gotta F. Next-generation sequencing in Charcot-Marie-Tooth: a proposal for improvement of ACMG guidelines for variant evaluation. J Med Genet 2024:jmg-2024-110019. [PMID: 38871447 DOI: 10.1136/jmg-2024-110019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND The application of massive parallel sequencing technologies in the molecular analysis of Charcot-Marie-Tooth (CMT) has enabled the rapid and cost-effective identification of numerous potentially significant variants for diagnostic purposes. The objective is to reduce the number of variants, focusing only on those with pathogenic significance. The 2015 American College of Medical Genetics and Genomics (ACMG) guidelines aid in achieving this goal, but it is now evident that a pathology or gene-specific review of these rules is essential to avoid misinterpretations that may result from blindly applying the criteria. This study demonstrates how revised ACMG criteria, combined with CMT-specific literature data and expertise, can alter the final classification of a variant. METHODS We reviewed ACMG criteria based on current knowledge of CMT and provided suggestions for adapting them to the specificities of CMT. RESULTS Of the 226 index patients analysed, a diagnostic yield of 20% was obtained. It is worth noting that the 9% of cases had their final diagnosis changed with the application of the revised criteria, often resulting in the loss of the pathogenic classification of a variant. CONCLUSIONS The widespread availability of high-throughput sequencing technologies has enabled genetic testing even for laboratories without specific disease expertise. Disease-specific ACMG criteria can be a valuable tool to prevent the proliferation of variants of uncertain significance and the misinterpretation of variants.
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Affiliation(s)
- Alessandro Geroldi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
| | - Alessia Mammi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Andrea Gaudio
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Serena Patrone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
| | - Andrea La Barbera
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Paola Origone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Clarissa Ponti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Francesca Sanguineri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Sara Massucco
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Neurology Clinic, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Lucio Marinelli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Neurology Clinic, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Marina Grandis
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Neurology Clinic, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Angelo Schenone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Neurology Clinic, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Emilia Bellone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Fabio Gotta
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
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Grosz BR, Parmar JM, Ellis M, Bryen S, Simons C, Reis ALM, Stevanovski I, Deveson IW, Nicholson G, Laing N, Wallis M, Ravenscroft G, Kumar KR, Vucic S, Kennerson ML. A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing. J Peripher Nerv Syst 2024; 29:262-274. [PMID: 38860315 DOI: 10.1111/jns.12637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Loss-of-function variants in MME (membrane metalloendopeptidase) are a known cause of recessive Charcot-Marie-Tooth Neuropathy (CMT). A deep intronic variant, MME c.1188+428A>G (NM_000902.5), was identified through whole genome sequencing (WGS) of two Australian families with recessive inheritance of axonal CMT using the seqr platform. MME c.1188+428A>G was detected in a homozygous state in Family 1, and in a compound heterozygous state with a known pathogenic MME variant (c.467del; p.Pro156Leufs*14) in Family 2. AIMS We aimed to determine the pathogenicity of the MME c.1188+428A>G variant through segregation and splicing analysis. METHODS The splicing impact of the deep intronic MME variant c.1188+428A>G was assessed using an in vitro exon-trapping assay. RESULTS The exon-trapping assay demonstrated that the MME c.1188+428A>G variant created a novel splice donor site resulting in the inclusion of an 83 bp pseudoexon between MME exons 12 and 13. The incorporation of the pseudoexon into MME transcript is predicted to lead to a coding frameshift and premature termination codon (PTC) in MME exon 14 (p.Ala397ProfsTer47). This PTC is likely to result in nonsense mediated decay (NMD) of MME transcript leading to a pathogenic loss-of-function. INTERPRETATION To our knowledge, this is the first report of a pathogenic deep intronic MME variant causing CMT. This is of significance as deep intronic variants are missed using whole exome sequencing screening methods. Individuals with CMT should be reassessed for deep intronic variants, with splicing impacts being considered in relation to the potential pathogenicity of variants.
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Affiliation(s)
- Bianca R Grosz
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
| | - Jevin M Parmar
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Melina Ellis
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
| | - Samantha Bryen
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andre L M Reis
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Garth Nicholson
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Nigel Laing
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Gianina Ravenscroft
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Kishore R Kumar
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
- Translational Neurogenomics Group, Genomic and Inherited Disease Program, The Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Healthcare Campus, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales, Australia
| | - Steve Vucic
- The University of Sydney, Camperdown, New South Wales, Australia
- Brain and Nerve Research Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
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Sadr Z, Rohani M, Jamali P, Alavi A. A case report of concurrent occurrence of two inherited axonopathies within a family: the benefit of whole-exome sequencing. Int J Neurosci 2023:1-6. [PMID: 37712628 DOI: 10.1080/00207454.2023.2260091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
Mutations in ERLIN2 and MFN2 lead to the development of spastic paraplegia-18 (SPG18) and Charcot-Marie-Tooth type-2A (CMT2A), respectively. These disorders are unified by the fact that both can be termed inherited axonopathies. With whole-exome sequencing (WES), more patients of neurological disorders with clinical overlaps receive a genetic result than ever before. This study describes an Iranian family who harbor mutations in ERLIN2 and MFN2, simultaneously. The proband was a 73-year old man who has experienced weakness and spasticity of lower limbs since late childhood. He was diagnosed with hereditary spastic paraplegia (HSP). His WES identified a novel homozygous variant in ERLIN2 as well as a known heterozygous variant in MFN2. These variants were cosegregated with the phenotypes among the family members. His sister with a similar phenotype just carried the homozygous ERLIN2 variant, whereas, his asymptomatic brother and daughter carried the heterozygous variant of MFN2. Re-evaluation of the MFN2 variant carriers by nerve conduction study revealed that only the proband's daughter has peripheral neuropathy. Herein, using WES two distinct disease-causing variants with different modes of inheritance in ERLIN2 and MFN2 were detected in the proband. As expected, individuals with a defined MFN2 variant, p.Arg468His, were asymptomatic or had a mild phenotype. The co-occurrence of such diseases, SPG18 and CMT2A, may result in the milder phenotype to be overlooked or its features considered as a part of the symptoms of other disease. Certainly, providing genetic counseling in such cases can be challenging. These cases reveal the importance of WES.
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Affiliation(s)
- Zahra Sadr
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Rohani
- Department of Neurology, Hazrat Rasool Hospital, School of Medicines, Iran University of Medical Sciences, Tehran, Iran
| | | | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran
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4
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Goleyjani Moghadam M, Elahi Z, Soveyzi M, Arzhangi S, Nafissi S, Najmabadi H, Kahrizi K, Fattahi Z. Expanding the Molecular Spectrum of HK1-Related Charcot-Marie-Tooth Disease, Type 4G; the First Report in Iran. ARCHIVES OF IRANIAN MEDICINE 2023; 26:279-284. [PMID: 38301092 PMCID: PMC10685863 DOI: 10.34172/aim.2023.43] [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: 01/08/2023] [Accepted: 03/05/2023] [Indexed: 02/03/2024]
Abstract
Charcot-Marie-Tooth disease type 4G (CMT4G) was first reported in Balkan Gypsies as a myelinopathy starting with progressive distal lower limb weakness, followed by upper limb involvement and prominent distal sensory impairment later in the patient's life. So far, CMT4G has been only reported in European Roma communities with two founder homozygous variants; g.9712G>C and g.11027G>A, located in the 5'-UTR of the HK1 gene. Here, we present the first Iranian CMT4G patient manifesting progressive distal lower limb weakness from 11 years of age and diagnosed with chronic demyelinating sensorimotor polyneuropathy. Whole-exome sequencing for this patient revealed a homozygous c.19C>T (p. Arg7*) variant in the HK1 gene. This report expands the mutational spectrum of the HK1-related CMT disorder and provides supporting evidence for the observation of CMT4G outside the Roma population. Interestingly, the same Arg7* variant is recently observed in another unrelated Pakistani CMT patient, proposing a possible prevalence of this variant in the Middle Eastern populations.
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Affiliation(s)
| | - Zohreh Elahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Mohamad Soveyzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Iranian Neuromuscular Research Center (INMRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Neurology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
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5
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Gao J, He J, Zhang F, Xiao Q, Cai X, Yi X, Zheng S, Zhang Y, Wang D, Zhu G, Wang J, Shen B, Ralser M, Guo T, Zhu Y. Integration of protein context improves protein-based COVID-19 patient stratification. Clin Proteomics 2022; 19:31. [PMID: 35953823 PMCID: PMC9366758 DOI: 10.1186/s12014-022-09370-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/30/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Classification of disease severity is crucial for the management of COVID-19. Several studies have shown that individual proteins can be used to classify the severity of COVID-19. Here, we aimed to investigate whether integrating four types of protein context data, namely, protein complexes, stoichiometric ratios, pathways and network degrees will improve the severity classification of COVID-19. METHODS We performed machine learning based on three previously published datasets. The first was a SWATH (sequential window acquisition of all theoretical fragment ion spectra) MS (mass spectrometry) based proteomic dataset. The second was a TMTpro 16plex labeled shotgun proteomics dataset. The third was a SWATH dataset of an independent patient cohort. RESULTS Besides twelve proteins, machine learning also prioritized two complexes, one stoichiometric ratio, five pathways, and five network degrees, resulting a 25-feature panel. As a result, a model based on the 25 features led to effective classification of severe cases with an AUC of 0.965, outperforming the models with proteins only. Complement component C9, transthyretin (TTR) and TTR-RBP (transthyretin-retinol binding protein) complex, the stoichiometric ratio of SAA2 (serum amyloid A proteins 2)/YLPM1 (YLP Motif Containing 1), and the network degree of SIRT7 (Sirtuin 7) and A2M (alpha-2-macroglobulin) were highlighted as potential markers by this classifier. This classifier was further validated with a TMT-based proteomic data set from the same cohort (test dataset 1) and an independent SWATH-based proteomic data set from Germany (test dataset 2), reaching an AUC of 0.900 and 0.908, respectively. Machine learning models integrating protein context information achieved higher AUCs than models with only one feature type. CONCLUSION Our results show that the integration of protein context including protein complexes, stoichiometric ratios, pathways, network degrees, and proteins improves phenotype prediction.
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Affiliation(s)
- Jinlong Gao
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Jiale He
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Fangfei Zhang
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Qi Xiao
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Xue Cai
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Xiao Yi
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Siqi Zheng
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Ying Zhang
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Donglian Wang
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Guangjun Zhu
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Jing Wang
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Bo Shen
- grid.268099.c0000 0001 0348 3990Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang China
| | - Markus Ralser
- grid.451388.30000 0004 1795 1830Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK ,grid.6363.00000 0001 2218 4662Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Tiannan Guo
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
| | - Yi Zhu
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang China
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Jamiri Z, Khosravi R, Heidari MM, Kiani E, Gharechahi J. A nonsense mutation in MME gene associates with autosomal recessive late-onset Charcot-Marie-Tooth disease. Mol Genet Genomic Med 2022; 10:e1913. [PMID: 35212467 PMCID: PMC9034668 DOI: 10.1002/mgg3.1913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 01/02/2023] Open
Abstract
Background The genetic cause for the majority of patients with late‐onset axonal form of neuropathies have remained unknown. In this study we aimed to identify the causal mutation in a family with multiple affected individuals manifesting a range of phenotypic features consistent with late‐onset sensorimotor axonal polyneuropathy. Methods Whole exome sequencing (WES) followed by targeted variant screening and prioritization was performed to identify the candidate mutation. The co‐segregation of the mutation with the phenotype was confirmed by Sanger sequencing. Results We identified a nonsense mutation (c.1564C>T; p.Q522*) in membrane metalloendopeptidase (MME) gene as the cause of the disease condition. The mutation has a combined annotation‐ dependent depletion (CADD) score 45 and predicted to be deleterious based on various algorithms. The mutation was inherited in an autosomal recessive mode and further confirmed to co‐segregate with the disease phenotype in the family and showed to has the required criteria including rarity and deleteriousness to be considered as pathogenic. Conclusion The MME gene encodes for the membrane bound endopeptidase neprilysin (NEP) which is involved in processing of various peptide substrates. The identified mutation causes a complete loss of carboxy‐terminal region of the NEP protein which contains the zinc binding site and the catalytic domain and thus considered to be a loss‐of‐function mutation. The loss of NEP activity is likely associated with impaired myelination and axonal injury which is hallmark of CMT diseases.
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Affiliation(s)
- Zeinab Jamiri
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - Rana Khosravi
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran
| | | | - Ebrahim Kiani
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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A National French Consensus on Gene List for the Diagnosis of Charcot–Marie–Tooth Disease and Related Disorders Using Next-Generation Sequencing. Genes (Basel) 2022; 13:genes13020318. [PMID: 35205364 PMCID: PMC8871532 DOI: 10.3390/genes13020318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/10/2022] Open
Abstract
Next generation sequencing (NGS) is strategically used for genetic diagnosis in patients with Charcot–Marie–Tooth disease (CMT) and related disorders called non-syndromic inherited peripheral neuropathies (NSIPN) in this paper. With over 100 different CMT-associated genes involved and ongoing discoveries, an important interlaboratory diversity of gene panels exists at national and international levels. Here, we present the work of the French National Network for Rare Neuromuscular Diseases (FILNEMUS) genetic diagnosis section which coordinates the seven French diagnosis laboratories using NGS for peripheral neuropathies. This work aimed to establish a unique, simple and accurate gene classification based on literature evidence. In NSIPN, three subgroups were usually distinguished: (1) HMSN, Hereditary Motor Sensory Neuropathy, (2) dHMN, distal Hereditary Motor Neuropathy, and (3) HSAN, Hereditary Sensory Autonomic Neuropathy. First, we reported ClinGen evaluation, and second, for the genes not evaluated yet by ClinGen, we classified them as “definitive” if reported in at least two clinical publications and associated with one report of functional evidence, or “limited” otherwise. In total, we report a unique consensus gene list for NSIPN including the three subgroups with 93 genes definitive and 34 limited, which is a good rate for our gene’s panel for molecular diagnostic use.
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Karayel-Basar M, Uras I, Kiris I, Sahin B, Akgun E, Baykal AT. Spatial proteomic alterations detected via MALDI-MS imaging implicate neuronal loss in a Huntington's disease mouse (YAC128) brain. Mol Omics 2022; 18:336-347. [PMID: 35129568 DOI: 10.1039/d1mo00440a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that occurs with the increase of CAG trinucleotide repeats in the huntingtin gene. To understand the mechanisms of HD, powerful proteomics techniques, such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) were employed. However, one major drawback of these methods is loss of the region-specific quantitative information of the proteins due to analysis of total tissue lysates. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a MS-based label-free technique that works directly on tissue sections and gathers m/z values with their respective regional information. In this study, we established a data processing protocol that includes several software programs and methods to determine spatial protein alterations between the brain samples of a 12 month-old YAC128 HD mouse model and their non-transgenic littermates. 22 differentially expressed proteins were revealed with their respective regional information, and possible relationships of several proteins were discussed. As a validation of the MALDI-MSI analysis, a differentially expressed protein (GFAP) was verified using immunohistochemical staining. Furthermore, since several proteins detected in this study have previously been associated with neuronal loss, neuronal loss in the cortical region was demonstrated using an anti-NeuN immunohistochemical staining method. In conclusion, the findings of this research have provided insights into the spatial proteomic changes between HD transgenic and non-transgenic littermates and therefore, we suggest that MALDI-MSI is a powerful technique to determine spatial proteomic alterations between biological samples, and the data processing that we present here can be employed as a complementary tool for the data analysis.
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Affiliation(s)
- Merve Karayel-Basar
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irep Uras
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irem Kiris
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Betul Sahin
- Acibadem Labmed Clinical Laboratories, R&D Center, Istanbul, Turkey
| | - Emel Akgun
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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Nagappa M, Sharma S, Govindaraj P, Chickabasaviah Y, Siram R, Shroti A, Seshagiri D, Debnath M, Bindu P, Taly A. Genetic spectrum of inherited neuropathies in India. Ann Indian Acad Neurol 2022; 25:407-416. [PMID: 35936615 PMCID: PMC9350795 DOI: 10.4103/aian.aian_269_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
Background and Objectives: Charcot-Marie-Tooth (CMT) disease is the commonest inherited neuromuscular disorder and has heterogeneous manifestations. Data regarding genetic basis of CMT from India is limited. This study aims to report the variations by using high throughput sequencing in Indian CMT cohort. Methods: Fifty-five probands (M:F 29:26) with suspected inherited neuropathy underwent genetic testing (whole exome: 31, clinical exome: 17 and targeted panel: 7). Their clinical and genetic data were analysed. Results: Age at onset ranged from infancy to 54 years. Clinical features included early-onset neuropathy (n=23), skeletal deformities (n=45), impaired vision (n=8), impaired hearing (n=6), facial palsy (n=8), thickened nerves (n=4), impaired cognition (n=5), seizures (n=5), pyramidal signs (n=7), ataxia (n=8) and vocal cord palsy, slow tongue movements and psychosis in one patient each. Twenty-eight patients had demyelinating electrophysiology. Abnormal visual and auditory evoked potentials were noted in 60.60% and 37.5% respectively. Sixty two variants were identified in 37 genes including variants of uncertain significance (n=34) and novel variants (n=45). Eleven patients had additional variations in genes implicated in CMTs/ other neurological disorders. Ten patients did not have variations in neuropathy associated genes, but had variations in genes implicated in other neurological disorders. In seven patients, no variations were detected. Conclusion: In this single centre cohort study from India, genetic diagnosis could be established in 87% of patients with inherited neuropathy. The identified spectrum of genetic variations adds to the pool of existing data and provides a platform for validation studies in cell culture or animal model systems.
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