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Amiñoso C, Solera J. Genetic analysis of 76 Spanish Pompe disease patients: Identification of 12 novel pathogenic GAA variants and functional characterization of splicing variants. Gene 2022; 808:145967. [PMID: 34530085 DOI: 10.1016/j.gene.2021.145967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/14/2021] [Accepted: 09/09/2021] [Indexed: 11/04/2022]
Abstract
Glycogenosis type II (GSDII), or Pompe disease (MIM 232300), is an inherited autosomal recessive disorder caused by deficiency of the lysosomal acid-α-glucosidase. Mutations in the GAA gene alter normal enzyme production and lead to progressive buildup of intralysosomal glycogen, which plays an essential role in the severity and progression of the disease. We report here the study of 76 patients from Spain with either infantile or late onset form of Pompe disease. The analysis consisted in the molecular study of exons and intron flanking fragments of GAA gene. We have identified 55 different molecular pathogenic variants, 12 of them not previously described. In addition, we have determined a frequency of 84.37% for the c.-32-13T>G mutation in patients with the late-onset form of the disease. Functional characterization of some splice mutations showed deleterious mechanisms on the processing of mRNA.
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Affiliation(s)
- Cinthia Amiñoso
- Molecular Oncogenetics Section, INGEMM, Hospital La Paz, 28046 Madrid, Spain
| | - Jesús Solera
- Molecular Oncogenetics Section, INGEMM, Hospital La Paz, 28046 Madrid, Spain; Department of Biochemistry, Faculty of Medicine, Autonoma University of Madrid, 28046 Madrid, Spain.
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Pilot M, Moura AE, Okhlopkov IM, Mamaev NV, Manaseryan NH, Hayrapetyan V, Kopaliani N, Tsingarska E, Alagaili AN, Mohammed OB, Ostrander EA, Bogdanowicz W. Human-modified canids in human-modified landscapes: The evolutionary consequences of hybridization for grey wolves and free-ranging domestic dogs. Evol Appl 2021; 14:2433-2456. [PMID: 34745336 PMCID: PMC8549620 DOI: 10.1111/eva.13257] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 05/05/2021] [Accepted: 05/19/2021] [Indexed: 12/22/2022] Open
Abstract
Introgressive hybridization between domestic animals and their wild relatives is an indirect form of human-induced evolution, altering gene pools and phenotypic traits of wild and domestic populations. Although this process is well documented in many taxa, its evolutionary consequences are poorly understood. In this study, we assess introgression patterns in admixed populations of Eurasian wolves and free-ranging domestic dogs (FRDs), identifying chromosomal regions with significantly overrepresented hybrid ancestry and assessing whether genes located within these regions show signatures of selection. Although the dog admixture proportion in West Eurasian wolves (2.7%) was greater than the wolf admixture proportion in FRDs (0.75%), the number and average length of chromosomal blocks showing significant overrepresentation of hybrid ancestry were smaller in wolves than FRDs. In wolves, 6% of genes located within these blocks showed signatures of positive selection compared to 23% in FRDs. We found that introgression from wolves may provide a considerable adaptive advantage to FRDs, counterbalancing some of the negative effects of domestication, which can include reduced genetic diversity and excessive tameness. In wolves, introgression from FRDs is mostly driven by drift, with a small number of positively selected genes associated with brain function and behaviour. The predominance of drift may be the consequence of small effective size of wolf populations, which reduces efficiency of selection for weakly advantageous or against weakly disadvantageous introgressed variants. Small wolf population sizes result largely from human-induced habitat loss and hunting, thus linking introgression rates to anthropogenic processes. Our results imply that maintenance of large population sizes should be an important element of wolf management strategies aimed at reducing introgression rates of dog-derived variants.
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Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of ZoologyPolish Academy of SciencesWarsawPoland
| | - Andre E. Moura
- Museum and Institute of ZoologyPolish Academy of SciencesWarsawPoland
| | - Innokentiy M. Okhlopkov
- Institute of Biological Problems of CryolithozoneSiberian Branch of Russian Academy of SciencesYakutskRussia
| | - Nikolay V. Mamaev
- Institute of Biological Problems of CryolithozoneSiberian Branch of Russian Academy of SciencesYakutskRussia
| | - Ninna H. Manaseryan
- Scientific Center of Zoology and HydroecologyNational Academy of SciencesYerevanArmenia
| | | | | | | | - Abdulaziz N. Alagaili
- KSU Mammals Research ChairDepartment of ZoologyKing Saud UniversityRiyadhSaudi Arabia
| | - Osama B. Mohammed
- KSU Mammals Research ChairDepartment of ZoologyKing Saud UniversityRiyadhSaudi Arabia
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
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Gomes CP, Marins MM, Motta FL, Kyosen SO, Curiati MA, D'Almeida V, Martins AM, Pesquero JB. A New Mutation in IDS Gene Causing Hunter Syndrome: A Case Report. Front Genet 2020; 10:1383. [PMID: 32256517 PMCID: PMC7093562 DOI: 10.3389/fgene.2019.01383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/18/2019] [Indexed: 12/02/2022] Open
Abstract
Rationale Mucopolysaccharidosis type II (Hunter syndrome) is an X-linked multisystem disorder, caused by deficiency of the lysosomal enzyme iduronate-2-sulfatase (I2S). The clinical manifestations of this disease are severe skeletal deformities, airway obstruction, cardiomyopathy, and neurologic deterioration. Patient The patient was 5 years and 6 months boy, with developmental delay, hearing loss, hepatosplenomegaly, and skeletal dysplasia. He was diagnosed with mucopolysaccharidosis type II based on clinical manifestations, biochemical and genetic analysis. Outcomes The patient carries a new mutation (c.879-1210_1007-218del) in hemizygosis in the IDS gene, which was defined as pathogenic according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines and as responsible for the mucopolysaccharidosis type II phenotype in the patient.
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Affiliation(s)
- Caio Perez Gomes
- Center for Research and Molecular Diagnosis of Genetic Diseases, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maryana Mara Marins
- Center for Research and Molecular Diagnosis of Genetic Diseases, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fabiana Louise Motta
- Center for Research and Molecular Diagnosis of Genetic Diseases, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sandra Obikawa Kyosen
- Inborn Errors of Metabolism Reference Center, Department of Pediatrics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marco Antonio Curiati
- Inborn Errors of Metabolism Reference Center, Department of Pediatrics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vânia D'Almeida
- Inborn Errors of Metabolism Laboratory, Department of Psychobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Maria Martins
- Inborn Errors of Metabolism Reference Center, Department of Pediatrics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - João Bosco Pesquero
- Center for Research and Molecular Diagnosis of Genetic Diseases, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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Amiñoso C, Gordillo-Marañón M, Hernández J, Solera J. Reevaluating the pathogenicity of the mutation c.1194 +5 G>A in GAA gene by functional analysis of RNA in a 61-year-old woman diagnosed with Pompe disease by muscle biopsy. Neuromuscul Disord 2019; 29:187-191. [PMID: 30770309 DOI: 10.1016/j.nmd.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/05/2018] [Accepted: 12/09/2018] [Indexed: 11/18/2022]
Abstract
Glycogen storage disease type II, or Pompe disease, is an autosomal recessive disorder caused by deficiency of lysosomal acid alpha-glucosidase (GAA). We performed genetic analysis to confirm the diagnosis of Pompe disease in a 61-year-old patient with progressive weakness in extremities, severe Sleep Apnea-Hypopnea Syndrome, a significant reduction of alpha-glucosidase in liquid sample of peripheral blood and muscular biopsy diagnosis. GAA gene sequencing showed the patient is homozygous for the splice-site mutation c.1194+5G>A, considered as nonpathogenic in Pompe Center mutation database. Further molecular RNA characterization of GAA transcripts allowed us to identify abnormal processing of pre-mRNA, leading to aberrant transcripts and a significant reduction of GAA mRNA levels. Our results indicate that c.1194+5G>A is a pathogenic splice-site mutation and should be considered as such for diagnostic purposes. This study emphasizes the potential role of functional studies to determine the consequences of mutations with no evident pathogenicity.
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Affiliation(s)
- Cinthia Amiñoso
- Unidad de Oncogenética Molecular, Instituto de Genética Médica y Molecular (INGEMM), Edificio Quirúrgico Planta-2, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - María Gordillo-Marañón
- Unidad de Oncogenética Molecular, Instituto de Genética Médica y Molecular (INGEMM), Edificio Quirúrgico Planta-2, Hospital Universitario La Paz, 28046 Madrid, Spain; Institute of Cardiovascular Science, Faculty of Population Health, University College London, London WC1E 6BT, UK
| | - Jaime Hernández
- Neurology Department, University General Hospital of Guadalajara, Spain
| | - Jesús Solera
- Unidad de Oncogenética Molecular, Instituto de Genética Médica y Molecular (INGEMM), Edificio Quirúrgico Planta-2, Hospital Universitario La Paz, 28046 Madrid, Spain; Department of Biochemistry, Faculty of Medicine, Autonoma University of Madrid, 28046 Madrid, Spain.
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Kim S, Cho CS, Han K, Lee J. Structural Variation of Alu Element and Human Disease. Genomics Inform 2016; 14:70-77. [PMID: 27729835 PMCID: PMC5056899 DOI: 10.5808/gi.2016.14.3.70] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 01/04/2023] Open
Abstract
Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery. The 'master gene' model has been generally accepted to explain Alu element amplification in primate genomes. According to the model, different subfamilies of Alu elements are created by mutations on the master gene and most Alu elements are amplified from the hyperactive master genes. Alu element is frequently involved in genomic rearrangements in the human genome due to its abundance and sequence identity between them. The genomic rearrangements caused by Alu elements could lead to genetic disorders such as hereditary disease, blood disorder, and neurological disorder. In fact, Alu elements are associated with approximately 0.1% of human genetic disorders. The first part of this review discusses mechanisms of Alu amplification and diversity among different Alu subfamilies. The second part discusses the particular role of Alu elements in generating genomic rearrangements as well as human genetic disorders.
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Affiliation(s)
- Songmi Kim
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Korea.; BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
| | - Chun-Sung Cho
- Department of Neurosurgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Korea.; BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
| | - Jungnam Lee
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Florida, Gainesville, FL 32610, USA
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Gutiérrez-Rivas E, Bautista J, Vílchez J, Muelas N, Díaz-Manera J, Illa I, Martínez-Arroyo A, Olivé M, Sanz I, Arpa J, Fernández-Torrón R, López de Munáin A, Jiménez L, Solera J, Lukacs Z. Targeted screening for the detection of Pompe disease in patients with unclassified limb-girdle muscular dystrophy or asymptomatic hyperCKemia using dried blood: A Spanish cohort. Neuromuscul Disord 2015; 25:548-53. [DOI: 10.1016/j.nmd.2015.04.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 04/10/2015] [Accepted: 04/20/2015] [Indexed: 11/26/2022]
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