1
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Ponomareva NV, Klyushnikov SA, Abramycheva N, Konovalov RN, Krotenkova M, Kolesnikova E, Malina D, Urazgildeeva G, Kanavets E, Mitrofanov A, Fokin V, Rogaev E, Illarioshkin SN. Neurophysiological hallmarks of Huntington's disease progression: an EEG and fMRI connectivity study. Front Aging Neurosci 2023; 15:1270226. [PMID: 38161585 PMCID: PMC10755012 DOI: 10.3389/fnagi.2023.1270226] [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: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) can provide corroborative data on neurophysiological alterations in Huntington's disease (HD). However, the alterations in EEG and fMRI resting-state functional connectivity (rsFC), as well as their interrelations, at different stages of HD remain insufficiently investigated. This study aimed to identify neurophysiological alterations in individuals with preclinical HD (preHD) and early manifest HD (EMHD) by analyzing EEG and fMRI rsFC and examining their interrelationships. We found significant differences in EEG power between preHD individuals and healthy controls (HC), with a decrease in power in a specific frequency range at the theta-alpha border and slow alpha activity. In EMHD patients, in addition to the decrease in power in the 7-9 Hz range, a reduction in power within the classic alpha band compared to HC was observed. The fMRI analysis revealed disrupted functional connectivity in various brain networks, particularly within frontal lobe, putamen-cortical, and cortico-cerebellar networks, in individuals with the HD mutation compared to HC. The analysis of the relationship between EEG and fMRI rsFC revealed an association between decreased alpha power, observed in individuals with EMHD, and increased connectivity in large-scale brain networks. These networks include putamen-cortical, DMN-related and cortico-hippocampal circuits. Overall, the findings suggest that EEG and fMRI provide valuable information for monitoring pathological processes during the development of HD. A decrease in inhibitory control within the putamen-cortical, DMN-related and cortico-hippocampal circuits, accompanied by a reduction in alpha and theta-alpha border oscillatory activity, could potentially contribute to cognitive decline in HD.
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Affiliation(s)
- Natalya V. Ponomareva
- Research Center of Neurology, Moscow, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
| | | | | | | | | | | | | | | | | | | | | | - Evgeny Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
- Department of Psychiatry, Umass Chan Medical School, Shrewsbury, MA, United States
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2
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Mullari M, Fossat N, Skotte NH, Asenjo-Martinez A, Humphreys DT, Bukh J, Kirkeby A, Scheel TKH, Nielsen ML. Characterising the RNA-binding protein atlas of the mammalian brain uncovers RBM5 misregulation in mouse models of Huntington's disease. Nat Commun 2023; 14:4348. [PMID: 37468457 DOI: 10.1038/s41467-023-39936-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/30/2023] [Indexed: 07/21/2023] Open
Abstract
RNA-binding proteins (RBPs) are key players regulating RNA processing and are associated with disorders ranging from cancer to neurodegeneration. Here, we present a proteomics workflow for large-scale identification of RBPs and their RNA-binding regions in the mammalian brain identifying 526 RBPs. Analysing brain tissue from males of the Huntington's disease (HD) R6/2 mouse model uncovered differential RNA-binding of the alternative splicing regulator RBM5. Combining several omics workflows, we show that RBM5 binds differentially to transcripts enriched in pathways of neurodegeneration in R6/2 brain tissue. We further find these transcripts to undergo changes in splicing and demonstrate that RBM5 directly regulates these changes in human neurons derived from embryonic stem cells. Finally, we reveal that RBM5 interacts differently with several known huntingtin interactors and components of huntingtin aggregates. Collectively, we demonstrate the applicability of our method for capturing RNA interactor dynamics in the contexts of tissue and disease.
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Affiliation(s)
- Meeli Mullari
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- CO-HEP, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Niels H Skotte
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Asenjo-Martinez
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - David T Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- CO-HEP, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Agnete Kirkeby
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
- Wallenberg Center for Molecular Medicine (WCMM) and Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- CO-HEP, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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3
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Fang L, Monteys AM, Dürr A, Keiser M, Cheng C, Harapanahalli A, Gonzalez-Alegre P, Davidson BL, Wang K. Haplotyping SNPs for allele-specific gene editing of the expanded huntingtin allele using long-read sequencing. HGG ADVANCES 2023; 4:100146. [PMID: 36262216 PMCID: PMC9574884 DOI: 10.1016/j.xhgg.2022.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by CAG trinucleotide repeat expansions in exon-1 of huntingtin (HTT). Currently, there is no cure for HD, and the clinical care of individuals with HD is focused on symptom management. Previously, we showed allele-specific deletion of the expanded HTT allele (mHTT) using CRISPR-Cas9 by targeting nearby (<10 kb) SNPs that created or eliminated a protospacer adjacent motif (PAM) near exon-1. Here, we comprehensively analyzed all potential PAM sites within a 10.4-kb genomic region flanking exon-1 of HTT in 983 individuals with HD using a multiplex targeted long-read sequencing approach on the Oxford Nanopore platform. We developed computational tools (NanoBinner and NanoRepeat) to de-multiplex the data, detect repeats, and phase the reads on the expanded or the wild-type HTT allele. One SNP common to 30% of individuals with HD of European ancestry emerged through this analysis, which was confirmed as a strong candidate for allele-specific deletion of the mHTT in human HD cell lines. In addition, up to 57% HD individuals may be candidates for allele-specific editing through combinatorial SNP targeting. Cumulatively, we provide a haplotype map of the region surrounding exon-1 of HTT in individuals affected with HD. Our workflow can be applied to other repeat expansion diseases to facilitate the design of guide RNAs for allele-specific gene editing.
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Affiliation(s)
- Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alex Mas Monteys
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra Dürr
- Sorbonne Université, Paris Brain Institute, AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, Paris, France
| | - Megan Keiser
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Congsheng Cheng
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Akhil Harapanahalli
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pedro Gonzalez-Alegre
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Huntington’s Disease Center and Division of Movement Disorders, Department of Neurology, The University of Pennsylvania, Philadelphia, PA 19104, USA
- Spark Therapeutics, Philadelphia, PA 19104, USA
| | - Beverly L. Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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da Silva IDS, Apolinário TA, de Andrade Agostinho L, Paiva CLA. Investigation of the Influence of TBP CAG/CAA Repeats in Conjunction with HTT CAG Repeats on Huntington's Disease Age at Onset in a Brazilian Sample. J Mol Neurosci 2022; 72:1116-1124. [PMID: 35275350 DOI: 10.1007/s12031-021-01938-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022]
Abstract
Huntington's disease (HD) is a genetic neurodegenerative progressive and fatal disease characterized by motor disorder, cognitive impairment, and behavioral problems, caused by expanded repeats of CAG trinucleotides in the HTT gene. The aim of this study was to investigate the influence of TBP gene CAG/CAA repeats in conjunction with HTT gene CAG repeats, on the age at HD onset in Brazilian individuals. Individuals diagnosed as molecularly negative for HD presented 29-39 TBP CAG/CAA. Their most frequent allele had 36 repeats. In individuals diagnosed as molecularly positive for HD, a range of 25-40 TBP CAG/ CAA was found. The most frequent TBP allele had 38 repeats. We also conducted TBP direct Sanger sequencing of some samples which demonstrated other four TBP structures different from the basic TBP structure and others reported in the literature. The HTT expanded CAG and TBP CAG/CAA repeat sizes jointly explained 66% of the age at onset (AO) in our HD patients. The strongest variable in the model associated with AO was the number of expanded HTT CAG repeats. The difference between the association of HD AO with HTT expanded CAG together with TBP CAG/CAA and the association of HD AO with HTT expanded CAG was 0.001 (∆R2). Therefore, we found a weak association (0.1%) of TBP CAG/CAA repeats on HD AO, if any.
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Affiliation(s)
- Iane Dos Santos da Silva
- Programa de Pós-Graduação em Biologia Molecular e Celular (PPGBMC), Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brazil
| | | | - Luciana de Andrade Agostinho
- Programa de Pós-Graduação em Neurologia, (UNIRIO), Rio de Janeiro, RJ, Brazil.
- Centro Universitário UNIFAMINAS, Muriae, Minas Gerais, Brazil.
| | - Carmen Lucia Antão Paiva
- Programa de Pós-Graduação em Biologia Molecular e Celular (PPGBMC), Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brazil
- Programa de Pós-Graduação em Neurologia, (UNIRIO), Rio de Janeiro, RJ, Brazil
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5
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Stevanovski I, Chintalaphani SR, Gamaarachchi H, Ferguson JM, Pineda SS, Scriba CK, Tchan M, Fung V, Ng K, Cortese A, Houlden H, Dobson-Stone C, Fitzpatrick L, Halliday G, Ravenscroft G, Davis MR, Laing NG, Fellner A, Kennerson M, Kumar KR, Deveson IW. Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing. SCIENCE ADVANCES 2022; 8:eabm5386. [PMID: 35245110 PMCID: PMC8896783 DOI: 10.1126/sciadv.abm5386] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
More than 50 neurological and neuromuscular diseases are caused by short tandem repeat (STR) expansions, with 37 different genes implicated to date. We describe the use of programmable targeted long-read sequencing with Oxford Nanopore's ReadUntil function for parallel genotyping of all known neuropathogenic STRs in a single assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of STR sites, from a list of predetermined candidates. This correctly diagnoses all individuals in a small cohort (n = 37) including patients with various neurogenetic diseases (n = 25). Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing and identifies noncanonical STR motif conformations and internal sequence interruptions. We observe a diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of repeat disorders. Last, we show how the inclusion of pharmacogenomic genes as secondary ReadUntil targets can further inform patient care.
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Affiliation(s)
- Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sanjog R. Chintalaphani
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Medicine, University of New South Wales, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Hasindu Gamaarachchi
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - James M. Ferguson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Carolin K. Scriba
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
- Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Michel Tchan
- Westmead Hospital, Westmead, NSW, Australia and Sydney Medical School, The University of Sydney, NSW, Australia
| | - Victor Fung
- Westmead Hospital, Westmead, NSW, Australia and Sydney Medical School, The University of Sydney, NSW, Australia
| | - Karl Ng
- Department of Neurology, Royal North Shore Hospital and The University of Sydney, Sydney, NSW, Australia
| | - Andrea Cortese
- Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- The National Hospital for Neurology and Neurosurgery, London, UK
| | - Henry Houlden
- Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- The National Hospital for Neurology and Neurosurgery, London, UK
| | - Carol Dobson-Stone
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Lauren Fitzpatrick
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Glenda Halliday
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Mark R. Davis
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Nigel G. Laing
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
- Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Avi Fellner
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- The Neurology Department, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Faculty of Health and Medicine, University of Sydney, Camperdown, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
- Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW, Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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6
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De Luca A, Morella A, Consoli F, Fanelli S, Thibert JR, Statt S, Latham GJ, Squitieri F. A Novel Triplet-Primed PCR Assay to Detect the Full Range of Trinucleotide CAG Repeats in the Huntingtin Gene ( HTT). Int J Mol Sci 2021; 22:ijms22041689. [PMID: 33567536 PMCID: PMC7916029 DOI: 10.3390/ijms22041689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
The expanded CAG repeat number in HTT gene causes Huntington disease (HD), which is a severe, dominant neurodegenerative illness. The accurate determination of the expanded allele size is crucial to confirm the genetic status in symptomatic and presymptomatic at-risk subjects and avoid genetic polymorphism-related false-negative diagnoses. Precise CAG repeat number determination is critical to discriminate the cutoff between unexpanded and intermediate mutable alleles (IAs, 27–35 CAG) as well as between IAs and pathological, low-penetrance alleles (i.e., 36–39 CAG repeats), and it is also critical to detect large repeat expansions causing pediatric HD variants. We analyzed the HTT-CAG repeat number of 14 DNA reference materials and of a DNA collection of 43 additional samples carrying unexpanded, IAs, low and complete penetrance alleles, including large (>60 repeats) and very large (>100 repeats) expansions using a novel triplet-primed PCR-based assay, the AmplideX PCR/CE HTT Kit. The results demonstrate that the method accurately genotypes both normal and expanded HTT-CAG repeat numbers and reveals previously undisclosed and very large CAG expansions >200 repeats. We also show that this technique can improve genetic test reliability and accuracy by detecting CAG expansions in samples with sequence variations within or adjacent to the repeat tract that cause allele drop-outs or inaccuracies using other PCR methods.
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Affiliation(s)
- Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (A.D.L.); (A.M.); (F.C.)
| | - Annunziata Morella
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (A.D.L.); (A.M.); (F.C.)
| | - Federica Consoli
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy; (A.D.L.); (A.M.); (F.C.)
| | - Sergio Fanelli
- Huntington and Rare Diseases Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Julie R. Thibert
- Asuragen, Inc., Austin, TX 78744, USA; (J.R.T.); (S.S.); (G.J.L.)
| | - Sarah Statt
- Asuragen, Inc., Austin, TX 78744, USA; (J.R.T.); (S.S.); (G.J.L.)
| | - Gary J. Latham
- Asuragen, Inc., Austin, TX 78744, USA; (J.R.T.); (S.S.); (G.J.L.)
| | - Ferdinando Squitieri
- Huntington and Rare Diseases Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy;
- Correspondence: ; Tel.: +39-06-44160536
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7
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Magri S, Nanetti L, Mongelli A, Rizzo E, Taroni F, Mariotti C, Gellera C. Missing the pathological expansion in Huntington disease: de novo c.51C>G variant on the expanded allele causing intrafamilial allele dropout. Am J Med Genet A 2020; 185:397-400. [PMID: 33247537 DOI: 10.1002/ajmg.a.61973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/08/2020] [Accepted: 10/25/2020] [Indexed: 11/08/2022]
Abstract
Huntington disease (HD) is an autosomal dominant disease characterized by motor, behavioral, and cognitive symptoms, caused by the pathological expansion of more than 35 CAG/CAA repeats in the HTT gene. We describe the phenotype of a patient compatible with HD. Several family members were reported as affected, and a paternal cousin and his daughter carried 39 and 42 CAG/CAA. HD genetic testing in proband showed homozygosity for a 14 CAG/CAA allele. Considering the phenotype and family history, HTT gene sequence was performed, revealing heterozygosity for the c.51C>G variant that changes the last nucleotide before the CAG tract, causing misannealing of forward primer (HD344) and dropout of the expanded allele. Polymerase chain reaction (PCR) analysis performed with an alternative forward primer demonstrated a 41 CAG/CAA allele. The c.51C>G variant was not detected in the affected cousin, thus suggesting a de novo occurrence. The lack of biological samples from the proband father and grandmother prevented further investigations to establish in which family member the variant occurred. These data indicate that patients presenting HD phenotype, and homozygous for a normal HTT CAG/CAA allele should be thoroughly evaluated for the presence of a genetic variant, even de novo, within the repeat region that may hamper genetic diagnosis.
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Affiliation(s)
- Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Lorenzo Nanetti
- Unit of Medical Genetics and Neurogenetics, Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alessia Mongelli
- Unit of Medical Genetics and Neurogenetics, Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Elena Rizzo
- Unit of Medical Genetics and Neurogenetics, Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Caterina Mariotti
- Unit of Medical Genetics and Neurogenetics, Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Department of Diagnostics and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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8
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Compromised IGF signaling causes caspase-6 activation in Huntington disease. Exp Neurol 2020; 332:113396. [DOI: 10.1016/j.expneurol.2020.113396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 06/16/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022]
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9
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Skotte NH, Andersen JV, Santos A, Aldana BI, Willert CW, Nørremølle A, Waagepetersen HS, Nielsen ML. Integrative Characterization of the R6/2 Mouse Model of Huntington's Disease Reveals Dysfunctional Astrocyte Metabolism. Cell Rep 2019; 23:2211-2224. [PMID: 29768217 DOI: 10.1016/j.celrep.2018.04.052] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/23/2018] [Accepted: 04/12/2018] [Indexed: 01/05/2023] Open
Abstract
Huntington's disease is a fatal neurodegenerative disease, where dysfunction and loss of striatal and cortical neurons are central to the pathogenesis of the disease. Here, we integrated quantitative studies to investigate the underlying mechanisms behind HD pathology in a systems-wide manner. To this end, we used state-of-the-art mass spectrometry to establish a spatial brain proteome from late-stage R6/2 mice and compared this with wild-type littermates. We observed altered expression of proteins in pathways related to energy metabolism, synapse function, and neurotransmitter homeostasis. To support these findings, metabolic 13C labeling studies confirmed a compromised astrocytic metabolism and regulation of glutamate-GABA-glutamine cycling, resulting in impaired release of glutamine and GABA synthesis. In recent years, increasing attention has been focused on the role of astrocytes in HD, and our data support that therapeutic strategies to improve astrocytic glutamine homeostasis may help ameliorate symptoms in HD.
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Affiliation(s)
- Niels H Skotte
- Proteomics Program, The Novo Nordisk Foundation Centre for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens V Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Santos
- Proteomics Program, The Novo Nordisk Foundation Centre for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Blanca I Aldana
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie W Willert
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Nørremølle
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helle S Waagepetersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Program, The Novo Nordisk Foundation Centre for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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10
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Zhao M, Cheah FSH, Tan ASC, Lian M, Phang GP, Agarwal A, Chong SS. Robust Preimplantation Genetic Testing of Huntington Disease by Combined Triplet-Primed PCR Analysis of the HTT CAG Repeat and Multi-Microsatellite Haplotyping. Sci Rep 2019; 9:16481. [PMID: 31712634 PMCID: PMC6848083 DOI: 10.1038/s41598-019-52769-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Huntington disease (HD) is a lethal neurodegenerative disorder caused by expansion of a CAG repeat within the huntingtin (HTT) gene. Disease prevention can be facilitated by preimplantation genetic testing for this monogenic disorder (PGT-M). We developed a strategy for HD PGT-M, involving whole genome amplification (WGA) followed by combined triplet-primed PCR (TP-PCR) for HTT CAG repeat expansion detection and multi-microsatellite marker genotyping for disease haplotype phasing. The strategy was validated and tested pre-clinically in a simulated PGT-M case before clinical application in five cycles of a PGT-M case. The assay reliably and correctly diagnosed all embryos, even where allele dropout (ADO) occurred at the HTT CAG repeat locus or at one or more linked markers. Ten of the 27 embryos analyzed were diagnosed as unaffected. Four embryo transfers were performed, two of which involved fresh cycle double embryo transfers and two were frozen-thawed single embryo transfers. Pregnancies were achieved from each of the frozen-thawed single embryo transfers and confirmed to be unaffected by amniocentesis, culminating in live births at term. This strategy enhances diagnostic confidence for PGT-M of HD and can also be employed in situations where disease haplotype phase cannot be established prior to the start of PGT-M.
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Affiliation(s)
- Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Felicia Siew Hong Cheah
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Arnold Sia Chye Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Mulias Lian
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Gui Ping Phang
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Anupriya Agarwal
- Clinic for Human Reproduction, Department of Obstetrics and Gynecology, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore. .,Molecular Diagnosis Center and Clinical Cytogenetics Service, Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.
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11
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Tellone E, Galtieri A, Ficarra S. Reviewing Biochemical Implications of Normal and Mutated Huntingtin in Huntington's Disease. Curr Med Chem 2019; 27:5137-5158. [PMID: 31223078 DOI: 10.2174/0929867326666190621101909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/08/2019] [Accepted: 05/22/2019] [Indexed: 12/17/2022]
Abstract
Huntingtin (Htt) is a multi-function protein of the brain. Normal Htt shows a common alpha-helical structure but conformational changes in the form with beta strands are the principal cause of Huntington's disease. Huntington's disease is a genetic neurological disorder caused by a repeated expansion of the CAG trinucleotide, causing instability in the N-terminal of the gene coding for the Huntingtin protein. The mutation leads to the abnormal expansion of the production of the polyglutamine tract (polyQ) resulting in the form of an unstable Huntingtin protein commonly referred to as mutant Huntingtin. Mutant Huntingtin is the cause of the complex neurological metabolic alteration of Huntington's disease, resulting in both the loss of all the functions of normal Huntingtin and the genesis of abnormal interactions due to the presence of this mutation. One of the problems arising from the misfolded Huntingtin is the increase in oxidative stress, which is common in many neurological diseases such as Alzheimer's, Parkinson's, Amyotrophic Lateral Sclerosis and Creutzfeldt-Jakob disease. In the last few years, the use of antioxidants had a strong incentive to find valid therapies for defence against neurodegenerations. Although further studies are needed, the use of antioxidant mixtures to counteract neuronal damages seems promising.
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Affiliation(s)
- Ester Tellone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Antonio Galtieri
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Silvana Ficarra
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
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12
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Andersen JV, Skotte NH, Aldana BI, Nørremølle A, Waagepetersen HS. Enhanced cerebral branched-chain amino acid metabolism in R6/2 mouse model of Huntington's disease. Cell Mol Life Sci 2019; 76:2449-2461. [PMID: 30830240 PMCID: PMC11105563 DOI: 10.1007/s00018-019-03051-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/23/2019] [Accepted: 02/19/2019] [Indexed: 01/01/2023]
Abstract
Huntington's disease (HD) is a hereditary and fatal disease causing profound neurodegeneration. Deficits in cerebral energy and neurotransmitter metabolism have been suggested to play a central role in the neuronal dysfunction and death associated with HD. The branched-chain amino acids (BCAAs), leucine, isoleucine and valine, are important for cerebral nitrogen homeostasis, neurotransmitter recycling and can be utilized as energy substrates in the tricarboxylic acid (TCA) cycle. Reduced levels of BCAAs in HD have been validated by several reports. However, it is still unknown how cerebral BCAA metabolism is regulated in HD. Here we investigate the metabolism of leucine and isoleucine in the R6/2 mouse model of HD. Acutely isolated cerebral cortical and striatal slices of control and R6/2 mice were incubated in media containing 15N- or 13C-labeled leucine or isoleucine and slice extracts were analyzed by gas chromatography-mass spectrometry (GC-MS) to determine isotopic enrichment of derived metabolites. Elevated BCAA transamination was found from incubations with [15N]leucine and [15N]isoleucine, in both cerebral cortical and striatal slices of R6/2 mice compared to controls. Metabolism of [U-13C]leucine and [U-13C]isoleucine, entering oxidative metabolism as acetyl CoA, was maintained in R6/2 mice. However, metabolism of [U-13C]isoleucine, entering the TCA cycle as succinyl CoA, was elevated in both cerebral cortical and striatal slices of R6/2 mice, suggesting enhanced metabolic flux via this anaplerotic pathway. To support the metabolic studies, expression of enzymes in the BCAA metabolic pathway was assessed from a proteomic resource. Several enzymes related to BCAA metabolism were found to exhibit augmented expression in the R6/2 brain, particularly related to isoleucine metabolism, suggesting an increase in the BCAA metabolic machinery. Our results show that the capacity for cerebral BCAA metabolism, predominantly of isoleucine, is amplified in the R6/2 brain and indicates that perturbations in cerebral BCAA homeostasis could have functional consequences for HD pathology.
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Affiliation(s)
- Jens V Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Niels H Skotte
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Blanca I Aldana
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Anne Nørremølle
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helle S Waagepetersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark.
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13
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Höijer I, Tsai Y, Clark TA, Kotturi P, Dahl N, Stattin E, Bondeson M, Feuk L, Gyllensten U, Ameur A. Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing. Hum Mutat 2018; 39:1262-1272. [PMID: 29932473 PMCID: PMC6175010 DOI: 10.1002/humu.23580] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 12/24/2022]
Abstract
Amplification of DNA is required as a mandatory step during library preparation in most targeted sequencing protocols. This can be a critical limitation when targeting regions that are highly repetitive or with extreme guanine-cytosine (GC) content, including repeat expansions associated with human disease. Here, we used an amplification-free protocol for targeted enrichment utilizing the CRISPR/Cas9 system (No-Amp Targeted sequencing) in combination with single molecule, real-time (SMRT) sequencing for studying repeat elements in the huntingtin (HTT) gene, where an expanded CAG repeat is causative for Huntington disease. We also developed a robust data analysis pipeline for repeat element analysis that is independent of alignment of reads to a reference genome. The method was applied to 11 diagnostic blood samples, and for all 22 alleles the resulting CAG repeat count agreed with previous results based on fragment analysis. The amplification-free protocol also allowed for studying somatic variability of repeat elements in our samples, without the interference of PCR stutter. In summary, with No-Amp Targeted sequencing in combination with our analysis pipeline, we could accurately study repeat elements that are difficult to investigate using PCR-based methods.
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Affiliation(s)
- Ida Höijer
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | | | | | | | - Niklas Dahl
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Eva‐Lena Stattin
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Marie‐Louise Bondeson
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Lars Feuk
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Ulf Gyllensten
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
| | - Adam Ameur
- Science for Life LaboratoryDepartment of ImmunologyGenetics and PathologyUppsala UniversityUppsalaSweden
- School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
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14
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Zhao M, Cheah FSH, Chen M, Lee CG, Law HY, Chong SS. Improved high sensitivity screen for Huntington disease using a one-step triplet-primed PCR and melting curve assay. PLoS One 2017; 12:e0180984. [PMID: 28700716 PMCID: PMC5507316 DOI: 10.1371/journal.pone.0180984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 05/22/2017] [Indexed: 11/19/2022] Open
Abstract
Molecular diagnosis of Huntington disease (HD) is currently performed by fluorescent repeat-flanking or triplet-primed PCR (TP-PCR) with capillary electrophoresis (CE). However, CE requires multiple post-PCR steps and may result in high cost in high-throughput settings. We previously described a cost-effective single-step molecular screening strategy employing the use of melting curve analysis (MCA). However, because it relies on repeat-flanking PCR, its efficiency in detecting expansion mutations decreases with increasing size of the repeat, which could lead to false-negative results. To address this pitfall, we have developed an improved screening assay coupling TP-PCR, which has been shown in CE-based assays to detect all expanded alleles regardless of size, with MCA in a rapid one-step assay. A companion protocol for rapid size confirmation of expansion-positive samples is also described. The assay was optimized on 30 genotype-known DNAs, and two plasmids pHTT(CAG)26 and pHTT(CAG)33 were used to establish the threshold temperatures (TTs) distinguishing normal from expansion-positive samples. In contrast to repeat-flanking PCR MCA, TP-PCR MCA displayed much higher sensitivity for detecting large expansions. All 30 DNAs generated distinct melt peak Tms which correlated well with each sample's larger allele. Normal samples were clearly distinguished from affected samples. The companion sizing protocol accurately sized even the largest expanded allele of ~180 CAGs. Blinded analysis of 69 clinical samples enriched for HD demonstrated 100% assay sensitivity and specificity in sample segregation. The assay targets the HTT CAG repeat specifically, tolerates a wide range of input DNA, and works well using DNA from saliva and buccal swab in addition to blood. Therefore, rapid, accurate, reliable, and high-throughput detection/exclusion of HD can be achieved using this one-step screening assay, at less than half the cost of fluorescent PCR with CE.
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Affiliation(s)
- Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Felicia S. H. Cheah
- Khoo Teck Puat – National University Children’s Medical Institute, National University Health System, Singapore, Singapore
| | - Min Chen
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Caroline G. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Medical Sciences, National Cancer Center, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women’s and Children’s Hospital, Singapore, Singapore
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat – National University Children’s Medical Institute, National University Health System, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
- * E-mail:
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Kay C, Hayden MR, Leavitt BR. Epidemiology of Huntington disease. HANDBOOK OF CLINICAL NEUROLOGY 2017; 144:31-46. [DOI: 10.1016/b978-0-12-801893-4.00003-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Agostinho LA, Spitz M, Pereira JS, Paiva CLA. Clinical and genetic investigation of a Brazilian family with Huntington's disease. FUNCTIONAL NEUROLOGY 2016; 31:135-42. [PMID: 27678206 DOI: 10.11138/fneur/2016.31.3.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aim of this study was to investigate a Brazilian family carrying full penetrance alleles for Huntington's disease (HD) in order to correlate each member's genetic and clinical features. To this end, the following scales were administered in each patient: the Beck Depression Inventory, the Mini-Mental State Examination (MMSE) and the Unified Huntington's Disease Rating Scale (UHDRS). The patterns of CAG and CCG polymorphic regions in the HTT gene were determined, the disease burden score was calculated, and genotypes were correlated with phenotypes within this family. We suggest that HD duration, the number of years of formal education, and UHDRS status variables can explain 96.6% of the MMSE variability in HD patients. A strong significant correlation was found between the disease burden score and the UHDRS (r = 0.76; p-value = 0.049) and the MMSE (r = -0.90; p-value = 0.006). The correlations between CAG allele size and the three clinical evaluations performed in the HD patients were not statistically significant.
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Bastepe M, Xin W. Huntington Disease: Molecular Diagnostics Approach. ACTA ACUST UNITED AC 2015; 87:9.26.1-9.26.23. [DOI: 10.1002/0471142905.hg0926s87] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Murat Bastepe
- Neurogenetics DNA Diagnostic Laboratory, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Boston Massachusetts
- Genetics Training Program, Harvard Medical School Boston Massachusetts
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School Boston Massachusetts
| | - Winnie Xin
- Neurogenetics DNA Diagnostic Laboratory, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Boston Massachusetts
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School Boston Massachusetts
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18
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Bečanović K, Nørremølle A, Neal SJ, Kay C, Collins JA, Arenillas D, Lilja T, Gaudenzi G, Manoharan S, Doty CN, Beck J, Lahiri N, Portales-Casamar E, Warby SC, Connolly C, De Souza RAG, Tabrizi SJ, Hermanson O, Langbehn DR, Hayden MR, Wasserman WW, Leavitt BR. A SNP in the HTT promoter alters NF-κB binding and is a bidirectional genetic modifier of Huntington disease. Nat Neurosci 2015; 18:807-16. [PMID: 25938884 DOI: 10.1038/nn.4014] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/06/2015] [Indexed: 12/11/2022]
Abstract
Cis-regulatory variants that alter gene expression can modify disease expressivity, but none have previously been identified in Huntington disease (HD). Here we provide in vivo evidence in HD patients that cis-regulatory variants in the HTT promoter are bidirectional modifiers of HD age of onset. HTT promoter analysis identified a NF-κB binding site that regulates HTT promoter transcriptional activity. A non-coding SNP, rs13102260:G > A, in this binding site impaired NF-κB binding and reduced HTT transcriptional activity and HTT protein expression. The presence of the rs13102260 minor (A) variant on the HD disease allele was associated with delayed age of onset in familial cases, whereas the presence of the rs13102260 (A) variant on the wild-type HTT allele was associated with earlier age of onset in HD patients in an extreme case-based cohort. Our findings suggest a previously unknown mechanism linking allele-specific effects of rs13102260 on HTT expression to HD age of onset and have implications for HTT silencing treatments that are currently in development.
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Affiliation(s)
- Kristina Bečanović
- 1] Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada. [2] Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Anne Nørremølle
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Scott J Neal
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chris Kay
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer A Collins
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Arenillas
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tobias Lilja
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Giulia Gaudenzi
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Shiana Manoharan
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Crystal N Doty
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessalyn Beck
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nayana Lahiri
- UCL Institute of Neurology, University College London, London, UK
| | - Elodie Portales-Casamar
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon C Warby
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colúm Connolly
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rebecca A G De Souza
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah J Tabrizi
- UCL Institute of Neurology, University College London, London, UK
| | - Ola Hermanson
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Douglas R Langbehn
- Department of Psychiatry and Biostatistics, University of Iowa, Iowa City, Iowa, USA
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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McQuade LR, Balachandran A, Scott HA, Khaira S, Baker MS, Schmidt U. Proteomics of Huntington's disease-affected human embryonic stem cells reveals an evolving pathology involving mitochondrial dysfunction and metabolic disturbances. J Proteome Res 2014; 13:5648-59. [PMID: 25316320 DOI: 10.1021/pr500649m] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a mutation in the Huntingtin gene, where excessive (≥ 36) CAG repeats encode for glutamine expansion in the huntingtin protein. Research using mouse models and human pathological material has indicated dysfunctions in a myriad of systems, including mitochondrial and ubiquitin/proteasome complexes, cytoskeletal transport, signaling, and transcriptional regulation. Here, we examined the earliest biochemical and pathways involved in HD pathology. We conducted a proteomics study combined with immunocytochemical analysis of undifferentiated HD-affected and unaffected human embryonic stem cells (hESC). Analysis of 1883 identifications derived from membrane and cytosolic enriched fractions revealed mitochondria as the primary dysfunctional organ in HD-affected pluripotent cells in the absence of significant differences in huntingtin protein. Furthermore, on the basis of analysis of 645 proteins found in neurodifferentiated hESC, we show a shift to transcriptional dysregulation and cytoskeletal abnormalities as the primary pathologies in HD-affected cells differentiating along neural lineages in vitro. We also show this is concomitant with an up-regulation in expression of huntingtin protein in HD-affected cells. This study demonstrates the utility of a model that recapitulates HD pathology and offers insights into disease initiation, etiology, progression, and potential therapeutic intervention.
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Affiliation(s)
- Leon R McQuade
- Australian Proteome Analysis Facility, §Australian School of Advanced Medicine, Macquarie University , Sydney, New South Wales 2109, Australia
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Bean L, Bayrak-Toydemir P. American College of Medical Genetics and Genomics Standards and Guidelines for Clinical Genetics Laboratories, 2014 edition: technical standards and guidelines for Huntington disease. Genet Med 2014; 16:e2. [PMID: 25356969 DOI: 10.1038/gim.2014.146] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 09/15/2014] [Indexed: 11/09/2022] Open
Abstract
Huntington disease is an autosomal-dominant neurodegenerative disease of mid-life onset caused by expansion of a polymorphic trinucleotide (CAG) repeat. Variable penetrance for alleles carrying 36-39 repeats has been noted, but the disease appears fully penetrant when the repeat numbers are >40. An abnormal CAG repeat may expand, contract, or be stably transmitted when passed from parent to child. Assays used to diagnose Huntington disease must be optimized to ensure the accurate and unambiguous quantitation of CAG repeat length. This document provides an overview of Huntington disease and methodological considerations for Huntington disease testing. Examples of laboratory reports are also included.
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Affiliation(s)
- Lora Bean
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Pinar Bayrak-Toydemir
- Department of Pathology, University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah, USA
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Ponomareva N, Klyushnikov S, Abramycheva N, Malina D, Scheglova N, Fokin V, Ivanova-Smolenskaia I, Illarioshkin S. Alpha-theta border EEG abnormalities in preclinical Huntington's disease. J Neurol Sci 2014; 344:114-20. [PMID: 25015843 DOI: 10.1016/j.jns.2014.06.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 05/23/2014] [Accepted: 06/17/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND Brain dysfunction precedes clinical manifestation of Huntington's disease (HD) by decades. This study was aimed to determine whether resting EEG is altered in preclinical HD mutations carriers (pre-HD). METHODS We examined relative power of broad traditional EEG bands as well as 1-Hz sub-bands of theta and alpha from the resting-state EEG of 29 pre-HD individuals and of 29 age-matched normal controls. RESULTS The relative power of the narrow sub-band in the border of theta-alpha (7-8 Hz) was significantly reduced in pre-HD subjects as compared to normal controls, while the alterations in relative power of the broad frequency bands were not significant. In pre-HD subjects, the number of CAG repeats in the huntingtin (HTT) gene as well as the disease burden score (DBS) showed a positive correlation with relative power of the delta and theta frequency bands and their sub-bands and a negative correlation with alpha band relative power and the differences of relative power of the 7-8 Hz and 4-5 Hz frequency sub-bands. CONCLUSION The obtained results suggest that EEG alterations in pre-HD individuals may be related to the course of the pathological process and to HD endophenotype. Analysis of the narrow EEG bands was found to be more useful for assessing EEG alterations in pre-HD individuals than a more traditional approach using broad bandwidths.
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Affiliation(s)
- Natalya Ponomareva
- Department for Brain Research, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia.
| | - Sergey Klyushnikov
- Department of Neurogenetics, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Natalya Abramycheva
- Department of Neurogenetics, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Daria Malina
- Department for Brain Research, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Nadejda Scheglova
- Department for Brain Research, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Vitaly Fokin
- Department for Brain Research, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Irina Ivanova-Smolenskaia
- Department of Neurogenetics, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergey Illarioshkin
- Department for Brain Research, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia; Department of Neurogenetics, Research Center of Neurology, Russian Academy of Medical Sciences, Moscow, Russia
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Levin BC, Richie KL, Jakupciak JP. Advances in Huntington’s disease diagnostics: development of a standard reference material. Expert Rev Mol Diagn 2014; 6:587-96. [PMID: 16824032 DOI: 10.1586/14737159.6.4.587] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disease that affects four to seven individuals per 100,000. The onset of symptoms usually begins in middle age, although approximately 5% become symptomatic as juveniles. Death occurs approximately 15 years following the onset of symptoms, which include choreic movements, cognitive decline and psychiatric changes. HD is an autosomal dominant inherited disease that is associated with an expansion of a trinucleotide (CAG) repeat located on chromosome 4. Physicians rely on a positive family history, and diagnostic and genetic tests to detect the expansion in the number of CAG trinucleotide repeats in the HD gene to confirm the diagnosis. More than 99% of HD patients have 40 or more CAG triplet repeats and, therefore, targeted mutational analysis is greater than 99% sensitive. Individuals with 26 triplet repeats or less are normal, and while those with 27-35 repeats may not demonstrate symptoms themselves, their offspring may have the disease. Individuals with 36-39 repeats may or may not exhibit symptoms. The College of American Pathology/American College of Medical Genetics Biochemical and Molecular Genetics Resource Committee has emphasized the need to standardize the methodology for the determination of the accurate number of CAG repeats. This will prevent false-positive or -negative results when conducting predictive or prenatal testing of at-risk individuals. The National Institute of Standards and Technology is developing a standard reference material to provide these positive and negative controls needed by clinical testing laboratories. The use of a HD standard reference material will provide the quality control and assurance that data from different laboratories are both comparable and accurate.
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Affiliation(s)
- Barbara C Levin
- National Institute of Standards & Technology, 100 Bureau Drive, Mail Stop 8311, Biochemical Science Division, Chemical Science & Technology Laboratory, Gaithersburg, MD 20899-8311, USA.
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Vázquez-Mojena Y, Laguna-Salvia L, Laffita-Mesa JM, González-Zaldívar Y, Almaguer-Mederos LE, Rodríguez-Labrada R, Almaguer-Gotay D, Zayas-Feria P, Velázquez-Pérez L. Genetic features of Huntington disease in Cuban population: Implications for phenotype, epidemiology and predictive testing. J Neurol Sci 2013; 335:101-4. [DOI: 10.1016/j.jns.2013.08.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/22/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
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Semaka A, Kay C, Doty CN, Collins JA, Tam N, Hayden MR. High frequency of intermediate alleles on Huntington disease-associated haplotypes in British Columbia's general population. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:864-71. [PMID: 24038799 DOI: 10.1002/ajmg.b.32193] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 07/11/2013] [Indexed: 11/08/2022]
Abstract
Intermediate alleles (27-35 CAG, IAs) for Huntington disease (HD) usually do not confer the disease phenotype but are prone to CAG repeat instability. Consequently, offspring are at-risk of inheriting an expanded allele in the HD range (≥36 CAG). IAs that expand into a new mutation have been hypothesized to be more susceptible to instability compared to IAs identified on the non-HD side of a family from the general population. Frequency estimates for IAs are limited and have largely been determined using clinical samples of HD or related disorders, which may result in an ascertainment bias. This study aimed to establish the frequency of IAs in a sample of a British Columbia's (B.C.) general population with no known association to HD and examine the haplotype of new mutation and general population IAs. CAG sizing was performed on 1,600 DNA samples from B.C.'s general population. Haplotypes were determined using 22 tagging SNPs across the HTT gene. 5.8% of individuals were found to have an IA, of which 60% were on HD-associated haplotypes. There was no difference in the haplotype distribution of new mutation and general population IAs. These findings suggest that IAs are relatively frequent in the general population and are often found on haplotypes associated with expanded CAG lengths. There is likely no difference in the propensity of new mutation and general population IAs to expand into the disease range given that they are both found on disease-associated haplotypes. These findings have important implications for clinical practice.
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Affiliation(s)
- Alicia Semaka
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
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25
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Marchina E, Misasi S, Bozzato A, Ferraboli S, Agosti C, Rozzini L, Borsani G, Barlati S, Padovani A. Gene expression profile in fibroblasts of Huntington's disease patients and controls. J Neurol Sci 2013; 337:42-6. [PMID: 24296361 DOI: 10.1016/j.jns.2013.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/19/2013] [Accepted: 11/11/2013] [Indexed: 01/08/2023]
Abstract
Huntington's disease is an inherited disorder caused by expanded stretch of consecutive trinucleotides (cytosine-adenosine-guanine, CAG) within the first exon of the huntingtin (HTT) gene on chromosome 4 (p16.3). The mutated huntingtin (mHTT) gains toxic function, probably through mechanisms that involve aberrant interactions in several pathways, causing cytotoxicity. Pathophysiology of disease involves several tissues; indeed it has been shown that there is a broad toxic effect of mHTT in the peripheral tissue of patients with HD, not only in the central nervous system. In this study we compared gene expression profiles (GEP) of HD fibroblasts and matched controls using microarray technology. We used RT-PCR to test the consistency of the microarray data and we found four genes up-regulated in HD patients with respect to control individuals. The genes appear to be involved in different pathways that have been shown to be perturbed even in HD models and patients. Although our study is preliminary and has to be extended to a larger cohort of HD patients and controls, nevertheless it shows that gene expression profiles seem to be altered in the fibroblasts of HD patients. Validation of the differential expressions at the protein level is required to ascertain if this cell type can be considered a suitable model for the identification of HD biomarkers.
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Affiliation(s)
- Eleonora Marchina
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
| | - Silvia Misasi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Andrea Bozzato
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sergio Ferraboli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Chiara Agosti
- Division of Neurology, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Luca Rozzini
- Division of Neurology, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Giuseppe Borsani
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sergio Barlati
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandro Padovani
- Division of Neurology, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
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Semaka A, Kay C, Doty C, Collins JA, Bijlsma EK, Richards F, Goldberg YP, Hayden MR. CAG size-specific risk estimates for intermediate allele repeat instability in Huntington disease. J Med Genet 2013; 50:696-703. [PMID: 23896435 DOI: 10.1136/jmedgenet-2013-101796] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION New mutations for Huntington disease (HD) occur due to CAG repeat instability of intermediate alleles (IA). IAs have between 27 and 35 CAG repeats, a range just below the disease threshold of 36 repeats. While they usually do not confer the HD phenotype, IAs are prone to paternal germline CAG repeat instability. Consequently, they may expand into the HD range upon transmission to the next generation, producing a new mutation. Quantified risk estimates for IA repeat instability are extremely limited but needed to inform clinical practice. METHODS Using small-pool PCR of sperm DNA from Caucasian men, we examined the frequency and magnitude of CAG repeat instability across the entire range of intermediate CAG sizes. The CAG size-specific risk estimates generated are based on the largest sample size ever examined, including 30 IAs and 18 198 sperm. RESULTS Our findings demonstrate a significant risk of new mutations. While all intermediate CAG sizes demonstrated repeat expansion into the HD range, alleles with 34 and 35 CAG repeats were associated with the highest risk of a new mutation (2.4% and 21.0%, respectively). IAs with ≥33 CAG repeats showed a dramatic increase in the frequency of instability and a switch towards a preponderance of repeat expansions over contractions. CONCLUSIONS These data provide novel insights into the origins of new mutations for HD. The CAG size-specific risk estimates inform clinical practice and provide accurate risk information for persons who receive an IA predictive test result.
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Affiliation(s)
- Alicia Semaka
- Department of Medical Genetics, Centre for Molecular Medicine & Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
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Losekoot M, van Belzen MJ, Seneca S, Bauer P, Stenhouse SAR, Barton DE. EMQN/CMGS best practice guidelines for the molecular genetic testing of Huntington disease. Eur J Hum Genet 2013; 21:480-6. [PMID: 22990145 PMCID: PMC3641377 DOI: 10.1038/ejhg.2012.200] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Huntington disease (HD) is caused by the expansion of an unstable polymorphic trinucleotide (CAG)n repeat in exon 1 of the HTT gene, which translates into an extended polyglutamine tract in the protein. Laboratory diagnosis of HD involves estimation of the number of CAG repeats. Molecular genetic testing for HD is offered in a wide range of laboratories both within and outside the European community. In order to measure the quality and raise the standard of molecular genetic testing in these laboratories, the European Molecular Genetics Quality Network has organized a yearly external quality assessment (EQA) scheme for molecular genetic testing of HD for over 10 years. EQA compares a laboratory's output with a fixed standard both for genotyping and reporting of the results to the referring physicians. In general, the standard of genotyping is very high but the clarity of interpretation and reporting of the test result varies more widely. This emphasizes the need for best practice guidelines for this disorder. We have therefore developed these best practice guidelines for genetic testing for HD to assist in testing and reporting of results. The analytical methods and the potential pitfalls of molecular genetic testing are highlighted and the implications of the different test outcomes for the consultand and his or her family members are discussed.
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Affiliation(s)
- Monique Losekoot
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis, Leiden University Medical Centre, Leiden, The Netherlands.
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Baine FK, Kay C, Ketelaar ME, Collins JA, Semaka A, Doty CN, Krause A, Greenberg LJ, Hayden MR. Huntington disease in the South African population occurs on diverse and ethnically distinct genetic haplotypes. Eur J Hum Genet 2013; 21:1120-7. [PMID: 23463025 DOI: 10.1038/ejhg.2013.2] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 12/12/2012] [Accepted: 12/28/2012] [Indexed: 11/09/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder resulting from the expansion of a CAG trinucleotide repeat in the huntingtin (HTT) gene. Worldwide prevalence varies geographically with the highest figures reported in populations of European ancestry. HD in South Africa has been reported in Caucasian, black and mixed subpopulations, with similar estimated prevalence in the Caucasian and mixed groups and a lower estimate in the black subpopulation. Recent studies have associated specific HTT haplotypes with HD in distinct populations. Expanded HD alleles in Europe occur predominantly on haplogroup A (specifically high-risk variants A1/A2), whereas in East Asian populations, HD alleles are associated with haplogroup C. Whether specific HTT haplotypes associate with HD in black Africans and how these compare with haplotypes found in European and East Asian populations remains unknown. The current study genotyped the HTT region in unaffected individuals and HD patients from each of the South African subpopulations, and haplotypes were constructed. CAG repeat sizes were determined and phased to haplotype. Results indicate that HD alleles from Caucasian and mixed patients are predominantly associated with haplogroup A, signifying a similar European origin for HD. However, in black patients, HD occurs predominantly on haplogroup B, suggesting several distinct origins of the mutation in South Africa. The absence of high-risk variants (A1/A2) in the black subpopulation may also explain the reported low prevalence of HD. Identification of haplotypes associated with HD-expanded alleles is particularly relevant to the development of population-specific therapeutic targets for selective suppression of the expanded HTT transcript.
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Affiliation(s)
- Fiona K Baine
- 1] Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa [2] Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Jama M, Millson A, Miller CE, Lyon E. Triplet repeat primed PCR simplifies testing for Huntington disease. J Mol Diagn 2013; 15:255-62. [PMID: 23414820 DOI: 10.1016/j.jmoldx.2012.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 09/18/2012] [Accepted: 09/26/2012] [Indexed: 12/14/2022] Open
Abstract
Diagnostic and predictive testing for Huntington disease (HD) requires an accurate determination of the number of CAG repeats in the Huntingtin (HHT) gene. Currently, when a sample appears to be homozygous for a normal allele, additional testing is required to confirm amplification from both alleles. If the sample still appears homozygous, Southern blot analysis is performed to rule out an undetected expanded HTT allele. Southern blot analysis is expensive, time-consuming, and labor intensive and requires high concentrations of DNA. We have developed a chimeric PCR process to help streamline workflow; true homozygous alleles are easily distinguished by this simplified method, and only very large expanded alleles still require Southern blot analysis. Two hundred forty-six HD samples, previously run with a different fragment analysis method, were analyzed with our new method. All samples were correctly genotyped, resulting in 100% concordance between the methods. The chimeric PCR assay was able to identify expanded alleles up to >150 CAG repeats. This method offers a simple strategy to differentiate normal from expanded CAG alleles, thereby reducing the number of samples reflexed to Southern blot analysis. It also provides assurance that expanded alleles are not routinely missed because of allele dropout.
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Affiliation(s)
- Mohamed Jama
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, USA.
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30
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Kalathur RKR, Hernández-Prieto MA, Futschik ME. Huntington's disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database. BMC Neurol 2012; 12:47. [PMID: 22741533 PMCID: PMC3492045 DOI: 10.1186/1471-2377-12-47] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 06/05/2012] [Indexed: 01/09/2023] Open
Abstract
Background Huntington’s disease (HD) is a fatal progressive neurodegenerative disorder caused by the expansion of the polyglutamine repeat region in the huntingtin gene. Although the disease is triggered by the mutation of a single gene, intensive research has linked numerous other genes to its pathogenesis. To obtain a systematic overview of these genes, which may serve as therapeutic targets, CHDI Foundation has recently established the HD Research Crossroads database. With currently over 800 cataloged genes, this web-based resource constitutes the most extensive curation of genes relevant to HD. It provides us with an unprecedented opportunity to survey molecular mechanisms involved in HD in a holistic manner. Methods To gain a synoptic view of therapeutic targets for HD, we have carried out a variety of bioinformatical and statistical analyses to scrutinize the functional association of genes curated in the HD Research Crossroads database. In particular, enrichment analyses were performed with respect to Gene Ontology categories, KEGG signaling pathways, and Pfam protein families. For selected processes, we also analyzed differential expression, using published microarray data. Additionally, we generated a candidate set of novel genetic modifiers of HD by combining information from the HD Research Crossroads database with previous genome-wide linkage studies. Results Our analyses led to a comprehensive identification of molecular mechanisms associated with HD. Remarkably, we not only recovered processes and pathways, which have frequently been linked to HD (such as cytotoxicity, apoptosis, and calcium signaling), but also found strong indications for other potentially disease-relevant mechanisms that have been less intensively studied in the context of HD (such as the cell cycle and RNA splicing, as well as Wnt and ErbB signaling). For follow-up studies, we provide a regularly updated compendium of molecular mechanism, that are associated with HD, at http://hdtt.sysbiolab.eu Additionally, we derived a candidate set of 24 novel genetic modifiers, including histone deacetylase 3 (HDAC3), metabotropic glutamate receptor 1 (GRM1), CDK5 regulatory subunit 2 (CDK5R2), and coactivator 1ß of the peroxisome proliferator-activated receptor gamma (PPARGC1B). Conclusions The results of our study give us an intriguing picture of the molecular complexity of HD. Our analyses can be seen as a first step towards a comprehensive list of biological processes, molecular functions, and pathways involved in HD, and may provide a basis for the development of more holistic disease models and new therapeutics.
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Affiliation(s)
- Ravi Kiran Reddy Kalathur
- Centro de Biomedicina Molecular e Estrutural, Campus de Gambelas, Universidade do Algarve, Faro, Portugal
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31
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Abstract
BACKGROUND The primary aim of the present study was to determine the survival rates and identify predictors of disease duration in a cohort of Huntington's disease (HD) patients from Southern Italy. METHODS All medical records of HD patients followed between 1977 and 2008 at the Department of Neurological Sciences of Federico II University in Naples were retrospectively reviewed and 135 patients were enrolled in the analysis. At the time of data collection, 41 patients were deceased (19 males and 22 females) with a mean ± SD age at death of 56.6 ± 14.9 years (range 18-83). RESULTS The median survival time was 20 years (95% CI: 18.3-21.7). Cox regression analysis showed that the number of CAG in the expanded allele (HR 1.09 for 1 point triplet increase, p=0.002) and age of onset (HR 1.05 for 1 point year increase, p=0.002) were independent and significant predictors of lower survival rates. CONCLUSIONS We believe that these findings are important for a better understanding of the natural history of the disease and may be relevant in designing future therapeutic trials.
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32
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Variation within the Huntington's disease gene influences normal brain structure. PLoS One 2012; 7:e29809. [PMID: 22235343 PMCID: PMC3250493 DOI: 10.1371/journal.pone.0029809] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 12/05/2011] [Indexed: 01/18/2023] Open
Abstract
Genetics of the variability of normal and diseased brain structure largely remains to be elucidated. Expansions of certain trinucleotide repeats cause neurodegenerative disorders of which Huntington's disease constitutes the most common example. Here, we test the hypothesis that variation within the IT15 gene on chromosome 4, whose expansion causes Huntington's disease, influences normal human brain structure. In 278 normal subjects, we determined CAG repeat length within the IT15 gene on chromosome 4 and analyzed high-resolution T1-weighted magnetic resonance images by the use of voxel-based morphometry. We found an increase of GM with increasing long CAG repeat and its interaction with age within the pallidum, which is involved in Huntington's disease. Our study demonstrates that a certain trinucleotide repeat influences normal brain structure in humans. This result may have important implications for the understanding of both the healthy and diseased brain.
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Ramos Arroyo MA, Trujillo-Tiebas MJ, Milá M. [Recommendations of good practices for molecular diagnosis of Huntington disease]. Med Clin (Barc) 2011; 138:584-8. [PMID: 21524764 DOI: 10.1016/j.medcli.2011.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 02/10/2011] [Accepted: 03/10/2011] [Indexed: 11/16/2022]
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Repeat associated non-ATG translation initiation: one DNA, two transcripts, seven reading frames, potentially nine toxic entities! PLoS Genet 2011; 7:e1002018. [PMID: 21423665 PMCID: PMC3053344 DOI: 10.1371/journal.pgen.1002018] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Diseases associated with unstable repetitive elements in the DNA, RNA, and amino acids have consistently revealed scientific surprises. Most diseases are caused by expansions of trinucleotide repeats, which ultimately lead to diseases like Huntington's disease, myotonic dystrophy, fragile X syndrome, and a series of spinocerebellar ataxias. These repeat mutations are dynamic, changing through generations and within an individual, and the repeats can be bi-directionally transcribed. Unsuspected modes of pathogenesis involve aberrant loss of protein expression; aberrant over-expression of non-mutant proteins; toxic-gain-of-protein function through expanded polyglutamine tracts that are encoded by expanded CAG tracts; and RNA-toxic-gain-of-function caused by transcripts harboring expanded CUG, CAG, or CGG tracts. A recent advance reveals that RNA transcripts with expanded CAG repeats can be translated in the complete absence of a starting ATG, and this Repeat Associated Non-ATG translation (RAN-translation) occurs across expanded CAG repeats in all reading frames (CAG, AGC, and GCA) to produce homopolymeric proteins of long polyglutamine, polyserine, and polyalanine tracts. Expanded CTG tracts expressing CUG transcripts also show RAN-translation occurring in all three frames (CUG, UGC, and GCU), to produce polyleucine, polycysteine, and polyalanine. These RAN-translation products can be toxic. Thus, one unstable (CAG)•(CTG) DNA can produce two expanded repeat transcripts and homopolymeric proteins with reading frames (the AUG-directed polyGln and six RAN-translation proteins), yielding a total of potentially nine toxic entities. The occurrence of RAN-translation in patient tissues expands our horizons of modes of disease pathogenesis. Moreover, since RAN-translation counters the canonical requirements of translation initiation, many new questions are now posed that must be addressed. This review covers RAN-translation and some of the pertinent questions.
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Bradley CK, Scott HA, Chami O, Peura TT, Dumevska B, Schmidt U, Stojanov T. Derivation of Huntington's Disease-Affected Human Embryonic Stem Cell Lines. Stem Cells Dev 2011; 20:495-502. [DOI: 10.1089/scd.2010.0120] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Omar Chami
- Sydney IVF Stem Cells, Sydney, Australia
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36
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Cleavage at the 586 amino acid caspase-6 site in mutant huntingtin influences caspase-6 activation in vivo. J Neurosci 2010; 30:15019-29. [PMID: 21068307 DOI: 10.1523/jneurosci.2071-10.2010] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Caspase cleavage of huntingtin (htt) and nuclear htt accumulation represent early neuropathological changes in brains of patients with Huntington's disease (HD). However, the relationship between caspase cleavage of htt and caspase activation patterns in the pathogenesis of HD remains poorly understood. The lack of a phenotype in YAC mice expressing caspase-6-resistant (C6R) mutant htt (mhtt) highlights proteolysis of htt at the 586 aa caspase-6 (casp6) site as a key mechanism in the pathology of HD. The goal of this study was to investigate how proteolysis of htt at residue 586 plays a role in the pathogenesis of HD and determine whether inhibiting casp6 cleavage of mhtt alters cell-death pathways in vivo. Here we demonstrate that activation of casp6, and not caspase-3, is observed before onset of motor abnormalities in human and murine HD brain. Active casp6 levels correlate directly with CAG size and inversely with age of onset. In contrast, in vivo expression of C6R mhtt attenuates caspase activation. Increased casp6 activity and apoptotic cell death is evident in primary striatal neurons expressing caspase-cleavable, but not C6R, mhtt after NMDA application. Pretreatment with a casp6 inhibitor rescues the apoptotic cell death observed in this paradigm. These data demonstrate that activation of casp6 is an early marker of disease in HD. Furthermore, these data provide a clear link between excitotoxic pathways and proteolysis and suggest that C6R mhtt protects against neurodegeneration by influencing the activation of neuronal cell-death and excitotoxic pathways operative in HD.
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Sequeiros J, Ramos EM, Cerqueira J, Costa MC, Sousa A, Pinto-Basto J, Alonso I. Large normal and reduced penetrance alleles in Huntington disease: instability in families and frequency at the laboratory, at the clinic and in the population. Clin Genet 2010; 78:381-7. [DOI: 10.1111/j.1399-0004.2010.01388.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zuccato C, Valenza M, Cattaneo E. Molecular Mechanisms and Potential Therapeutical Targets in Huntington's Disease. Physiol Rev 2010; 90:905-81. [DOI: 10.1152/physrev.00041.2009] [Citation(s) in RCA: 626] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the gene encoding for huntingtin protein. A lot has been learned about this disease since its first description in 1872 and the identification of its causative gene and mutation in 1993. We now know that the disease is characterized by several molecular and cellular abnormalities whose precise timing and relative roles in pathogenesis have yet to be understood. HD is triggered by the mutant protein, and both gain-of-function (of the mutant protein) and loss-of-function (of the normal protein) mechanisms are involved. Here we review the data that describe the emergence of the ancient huntingtin gene and of the polyglutamine trait during the last 800 million years of evolution. We focus on the known functions of wild-type huntingtin that are fundamental for the survival and functioning of the brain neurons that predominantly degenerate in HD. We summarize data indicating how the loss of these beneficial activities reduces the ability of these neurons to survive. We also review the different mechanisms by which the mutation in huntingtin causes toxicity. This may arise both from cell-autonomous processes and dysfunction of neuronal circuitries. We then focus on novel therapeutical targets and pathways and on the attractive option to counteract HD at its primary source, i.e., by blocking the production of the mutant protein. Strategies and technologies used to screen for candidate HD biomarkers and their potential application are presented. Furthermore, we discuss the opportunities offered by intracerebral cell transplantation and the likely need for these multiple routes into therapies to converge at some point as, ideally, one would wish to stop the disease process and, at the same time, possibly replace the damaged neurons.
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Affiliation(s)
- Chiara Zuccato
- Department of Pharmacological Sciences and Centre for Stem Cell Research, Università degli Studi di Milano, Milan, Italy
| | - Marta Valenza
- Department of Pharmacological Sciences and Centre for Stem Cell Research, Università degli Studi di Milano, Milan, Italy
| | - Elena Cattaneo
- Department of Pharmacological Sciences and Centre for Stem Cell Research, Università degli Studi di Milano, Milan, Italy
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39
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Semaka A, Collins JA, Hayden MR. Unstable familial transmissions of Huntington disease alleles with 27-35 CAG repeats (intermediate alleles). Am J Med Genet B Neuropsychiatr Genet 2010; 153B:314-20. [PMID: 19455596 DOI: 10.1002/ajmg.b.30970] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
There are inconsistent reports regarding the likelihood of repeat instability for alleles with 27-35 CAG repeats in the Huntington disease (HD) gene. We have examined the intergenerational stability of such intermediate alleles in 51 families from the University of British Columbia's DNA and Tissue Bank for Huntington Disease Research (UBC-HD Databank). A total of 181 transmissions were identified, with 30% (n = 54/181) of the alleles being unstable upon transmission. The unstable transmissions included both expansions (n = 37) and contractions (n = 17) of CAG size. Of the expanded alleles, 68% (n = 25/37) expanded into the HD range (>36 CAG). Therefore, 14% (n = 25/181) of the 27-35 CAG allele transmissions examined expanded into the disease-associated range resulting in a new mutation for HD. Significantly, of these new mutations, 40% (n = 10/25) originated from an allele with 35 CAG repeats with CAG repeat expansions ranging from +1 CAG to +23 CAG. The proportion of new mutations in the UBC-HD Databank is consistent with the most recent new mutation rate for HD, estimated to be at least 10%. The observed difference in the stability of HD intermediate allele transmissions in this data set and in other studies may be a reflection of a small sample size. Alternately, these inconsistencies may indicate an underlying difference in genetic factors which influence repeat instability between the different populations examined. Additional studies determining the frequency and magnitude of repeat instability in this CAG repeat range and factors that influence instability are urgently needed. Until we understand the clinical implications of HD alleles with 27-35 CAG repeats and establish reliable risks of instability, we should exercise caution when translating these results to the clinic.
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Affiliation(s)
- A Semaka
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
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40
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Blanco S, Suarez A, Gandia-Pla S, Gómez-Llorente C, Antúnez A, Gómez-Capilla JA, Fárez-Vidal ME. Use of capillary electrophoresis for accurate determination of CAG repeats causing Huntington disease. An oligonucleotide design avoiding shadow bands. Scandinavian Journal of Clinical and Laboratory Investigation 2009; 68:577-84. [PMID: 19378429 DOI: 10.1080/00365510801915171] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Huntington disease (HD) is a neurodegenerative disorder associated with the expansion of a polymorphic trinucleotide CAG repeat in the HD gene. We have developed an assay to accurately determine CAG repeats that combines a novel oligonucleotide design and the resolution of capillary electrophoresis. A mismatch in the second nucleotide from the 3' end enhanced specificity by avoiding mispriming and diminishing shadow bands and artifactual PCR products. The coupling of capillary electrophoresis analysis with the assay added the advantages of accuracy, high resolution, semi-automation, rapid analysis and low sample consumption. Analysis of 200 chromosomes in the Spanish population sample studied (control group) gave a peak frequency for 16 CAG repeats and of 7 triplets for CCG repeats. Diagnosis of HD was confirmed in 22 of 34 individuals with a range of CAG repeats from 39 to 52. Predictive testing was also carried out for 19 relatives of the HD families diagnosed at our laboratory. The method proposed in this article provides an accurate sizing of DNA repeats that can be applied to the analysis of DNA size-related disorders.
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Affiliation(s)
- Sonia Blanco
- Departamento de Bioquímica y Biología Molecular, Universidad de Granada, Spain
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Nørremølle A, Budtz-Jørgensen E, Fenger K, Nielsen JE, Sørensen SA, Hasholt L. 4p16.3 haplotype modifying age at onset of Huntington disease. Clin Genet 2009; 75:244-50. [DOI: 10.1111/j.1399-0004.2008.01136.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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González-González MC, Garcia-Hoyos M, Trujillo-Tiebas MJ, Bustamante Aragonés A, Rodriguez de Alba M, Diego Alvarez D, Diaz-Recasens J, Ayuso C, Ramos C. Improvement in strategies for the non-invasive prenatal diagnosis of Huntington disease. J Assist Reprod Genet 2008; 25:477-81. [PMID: 18853247 DOI: 10.1007/s10815-008-9256-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 09/24/2008] [Indexed: 12/01/2022] Open
Abstract
PURPOSE We focused on the improvements of prenatal diagnosis by the analysis of DNA from maternal plasma, using Huntington disease as a model of disease. METHODS We studied plasma from a pregnancy at risk of having a fetus affected with Huntington disease by the use of two direct analysis of the mutation and polymorphic STRs. RESULTS Direct methods were not informative. Analysis with STRs revealed the presence of the allele that does not co-segregate with the disease, thus the fetus was healthy. CONCLUSIONS This strategy is very useful to face complex cases when the direct study is not informative not only for Huntington disease but also for many other disorders.
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Harvey JJ, Brant SR, Knutson JR, Han MK. SNP analysis using CataCleave probes. J Clin Lab Anal 2008; 22:192-203. [PMID: 18484652 DOI: 10.1002/jcla.20240] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
CataCleave probes are catalytically cleavable fluorescence probes having a chimeric deoxyribonucleic acid (DNA)-ribonucleic acid (RNA)-DNA structure that can be used for real-time detection of single nucleotide polymorphisms (SNPs), insertions, and deletions. Fluorescent donor emission is normally quenched by Förster resonance energy transfer (FRET). Upon binding to the target, if the RNA/DNA hybrid is correctly base-paired, ribonuclease (RNase) H will cleave the RNA moiety and the probe fragments will dissociate. FRET is lost and the donor fluorescence signal is recovered. A single-base mismatch within the hybrid region causes probe cleavage to be significantly reduced. We designed CataCleave probes to detect SNPs located in the insulin-like growth factor 2 (IGF-2) gene and at position 702 within the NOD2/CARD15 gene. Probes were also designed to detect a six-basepair deletion in the amelogenin gene and a partially methylated target DNA. Discrimination between wild-type and SNP is demonstrated for both genes in homogeneous reactions under isothermal and temperature cycling conditions. These probes were also able to identify a multibase deletion and methylated DNA. Cleavage rates were proportional to target concentration. Probe length and position of fluorescent labels may also be modified for use in multiplexing high-throughput SNP assays. This represents a novel method for the detection of SNPs.
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Affiliation(s)
- John J Harvey
- Excimus Biotech, Inc., 8510 Corridor Road, Savage, MD 20763, USA.
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Teo CRL, Wang W, Yang Law H, Lee CG, Chong SS. Single-step scalable-throughput molecular screening for Huntington disease. Clin Chem 2008; 54:964-72. [PMID: 18403567 DOI: 10.1373/clinchem.2007.096503] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Huntington disease (HD) is a fatal autosomal dominant neurodegenerative disorder caused by an unstable expansion of the CAG trinucleotide repeat in exon 1 of the HTT (huntingtin) gene and typically has an adult onset. Molecular diagnosis and screening for HD currently involve separate amplification and detection steps. METHODS We evaluated a novel, rapid microplate-based screening method for HD that combines the amplification and detection procedures in a single-step, closed-tube format. We carried out both the PCR for the HTT CAG-repeat region and the subsequent automated melting-curve analysis of the amplicon in the same wells on the plate. To establish cutoff melting temperatures (T(m)s) for each allelic class, we used a panel of reference DNA samples of known CAG-repeat sizes that represent a range of HTT alleles [normal (< or =26 repeats), intermediate (27-35 repeats), reduced penetrance expanded (36-39 repeats), and fully penetrant expanded (> or =40 repeats)]. We also measured well-to-well variation in T(m) across the thermal block and validated cutoff T(m)s with DNA samples from 5 different populations. We also conducted a blinded validation analysis of clinical samples from an additional 40 HD-affected and 30 unaffected individuals. RESULTS We observed a strong correlation between CAG-repeat size and amplicon T(m) among the reference DNA samples. Use of the T(m) cutoffs we established revealed that 5 samples from unaffected individuals had been misclassified as affected (1.1% false-positive rate). All samples from HD-affected and unaffected individuals were correctly identified in the blinded analysis. CONCLUSIONS This simple and scalable homogeneous assay may serve as a convenient, rapid, and accurate screen to detect the presence of pathologic expanded HD alleles in symptomatic patients.
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Affiliation(s)
- Clara R L Teo
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Paradisi I, Hernández A, Arias S. Huntington disease mutation in Venezuela: age of onset, haplotype analyses and geographic aggregation. J Hum Genet 2007; 53:127-135. [PMID: 18157708 DOI: 10.1007/s10038-007-0227-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 11/09/2007] [Indexed: 11/29/2022]
Abstract
The aggregation of patients with Huntington's disease (HD) around Lake Maracaibo, Zulia State, Venezuela, is widely recognized, but the epidemiology of HD in the whole country is relatively unstudied. We have examined 279 individuals from 60 unrelated affected families residing in various areas of Venezuela for the presence of CAG repeats and other features associated with HD. The number of expanded repeats in 139 carriers varied from 35 to 112. Based on our examination of 71 symptomatic individuals, we developed a log-transformed regression equation, y= -0.0238x + 2.6616, to enable the prediction of age of onset in asymptomatic carriers. Intragenic haplotypes were constructed with two VNTRs (variable number of tandem repeats) and two SNPs (single nucleotide polymorphisms) in the promoter region as well as CCG repeat and Delta2642 polymorphisms to assess kinship between families. In 43 of 45 tested families, the haplotype on the mutated chromosome was 1;G;C;7;(A). The other haplotypes observed, 1;G;C;7;(B) and 4;G;C;7;(A), were of Peruvian and French origins, respectively. The geographic source of the first affected ancestor was assessed in 54 families from 15 different states. Residents of the states of Miranda, Lara and Táchira, excluding those of Zulia, had a mutated allele prevalence five- to ninefold higher than that of other areas. A low (approx. 1/200,000) prevalence, a wide-spread distribution with aggregation in some states and a likely remote European Caucasoid origin are defining epidemiologic features of HD in Venezuela.
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Affiliation(s)
- Irene Paradisi
- Laboratorio de Genética Humana, Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas, 1020A, Venezuela
| | - Alba Hernández
- Laboratorio de Genética Humana, Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas, 1020A, Venezuela
| | - Sergio Arias
- Laboratorio de Genética Humana, Centro de Medicina Experimental, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas, 1020A, Venezuela.
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Allen RA, Gatalica Z, Knezetic J, Hatcher L, Vogel JS, Dunn ST. A common 1317TC polymorphism in MTHFR can lead to erroneous 1298AC genotyping by PCR-RE and TaqMan probe assays. ACTA ACUST UNITED AC 2007; 11:167-73. [PMID: 17627388 DOI: 10.1089/gte.2006.0513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Multiple polymorphisms of the methylenetetrahydrofolate reductase gene (MTHFR) have been documented, and some are associated with decreased enzyme activity. One polymorphism, 677CT, is commonly tested in the context of thrombosis. Recently, consideration has also been extended to 1298AC, which is also associated with reduced catalytic activity. This report describes problems arising during the development of a PCR restriction enzyme assay for 1298AC. In the process of validating a PCR-MboII assay, it was realized that a nearby 1317TC polymorphism rendered a restriction fragment length polymorphism (RFLP) pattern that was virtually indistinguishable from a 1298A allele. An alternate approach, involving primer mutagenesis and Fnu4HI digestion, resolved the problem. To validate the latter assay, samples were obtained from a CLIA-approved facility that had developed a multiplexed real-time PCR using TaqMan probes for simultaneous assessment of 677CT and 1298AC. Interlaboratory results concurred for 10 out of 11 samples; however, one sample was consistently heterozygous by PCR-Fnu4HI and homozygous 1298CC by real-time PCR. Bidirectional sequencing confirmed that the sample was a compound 1298AC/1317TC heterozygote. It is likely that the 1317C variant, residing with 1298A on one chromosome, disrupted primer annealing in the TaqMan assay, leading to preferential amplification of the 1298C/1317T chromosome and hence an aberrant homozygous 1298CC genotype. This validation exercise emphasizes the need for comprehensive appraisal and continual reassessment of the optimal performance of molecular diagnostic assays. It is hoped that laboratories offering MTHFR 1298AC testing are cognizant of some of the inherent problems in published methods.
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Affiliation(s)
- Richard A Allen
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
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Ichiba M, Nakamura M, Kusumoto A, Mizuno E, Kurano Y, Matsuda M, Kato M, Agemura A, Tomemori Y, Muroya S, Nakabeppu Y, Sano A. Clinical and molecular genetic assessment of a chorea-acanthocytosis pedigree. J Neurol Sci 2007; 263:124-32. [PMID: 17673232 DOI: 10.1016/j.jns.2007.07.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 06/26/2007] [Accepted: 07/03/2007] [Indexed: 10/23/2022]
Abstract
BACKGROUND Chorea-acanthocytosis (ChAc) is an autosomal recessive hereditary disease characterized by neurodegeneration in the striatum and acanthocytosis that is caused by mutations in the VPS13A gene. There are only few reports that studied clinical status of the obligate carriers of ChAc. Clinical courses with follow-up neuroradiological and neuropsychological evaluations in individuals with ChAc have been rarely reported. METHODS We followed an index patient with ChAc and evaluated the clinical features of the pedigree members. Genetic analyses of VPS13A and genes responsible for other neuroacanthocytotic and neurodegenerative diseases were performed. CONCLUSIONS The index patient was homozygous for a 3889C>T nonsense mutation in the VPS13A gene and presented with a typical ChAc phenotype. Neuropsychological evaluation with brain imaging in the patient over 3 years revealed atrophy and a decrease in blood flow at the basal ganglia and frontal lobe, and impairment in cognitive function reflecting frontal lobe dysfunction in progressive manners. Four out of five heterozygous mutation carriers in the pedigree showed signs or symptoms potentially attributable to a heterozygous VPS13A mutation.
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Affiliation(s)
- Mio Ichiba
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima University, Japan
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Woodman B, Butler R, Landles C, Lupton MK, Tse J, Hockly E, Moffitt H, Sathasivam K, Bates GP. The Hdh(Q150/Q150) knock-in mouse model of HD and the R6/2 exon 1 model develop comparable and widespread molecular phenotypes. Brain Res Bull 2007; 72:83-97. [PMID: 17352931 DOI: 10.1016/j.brainresbull.2006.11.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Indexed: 11/25/2022]
Abstract
The identification of the Huntington's disease (HD) mutation as a CAG/polyglutamine repeat expansion enabled the generation of transgenic rodent models and gene-targeted mouse models of HD. Of these, mice that are transgenic for an N-terminal huntingtin fragment have been used most extensively because they develop phenotypes with relatively early ages of onset and rapid disease progression. Although the fragment models have led to novel insights into the pathophysiology of HD, it is important that models expressing a mutant version of the full-length protein are analysed in parallel. We have generated congenic C57BL/6 and CBA strains for the HdhQ150 knock-in mouse model of HD so that homozygotes can be analysed on an F1 hybrid background. Although a significant impairment in grip strength could be detected from a very early age, the performance of these mice in the quantitative behavioural tests most frequently used in preclinical efficacy trials indicates that they are unlikely to be useful for preclinical screening using a battery of conventional tests. However, at 22 months of age, the Hdh(Q150/Q150) homozygotes showed unexpected widespread aggregate deposition throughout the brain, transcriptional dysregulation in the striatum and cerebellum and decreased levels of specific chaperones, all well-characterised molecular phenotypes present in R6/2 mice aged 12 weeks. Therefore, when strain background and CAG repeat length are controlled for, the knock-in and fragment models develop comparable phenotypes. This supports the continued use of the more high-throughput fragment models to identify mechanisms of pathogenesis and for preclinical screening.
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Affiliation(s)
- Ben Woodman
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, UK
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Orlacchio A, Calabresi P, Rum A, Tarzia A, Salvati AM, Kawarai T, Stefani A, Pisani A, Bernardi G, Cianciulli P, Caprari P. Neuroacanthocytosis associated with a defect of the 4.1R membrane protein. BMC Neurol 2007; 7:4. [PMID: 17298666 PMCID: PMC1805452 DOI: 10.1186/1471-2377-7-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2006] [Accepted: 02/13/2007] [Indexed: 11/10/2022] Open
Abstract
Background Neuroacanthocytosis (NA) denotes a heterogeneous group of diseases that are characterized by nervous system abnormalities in association with acanthocytosis in the patients' blood. The 4.1R protein of the erythrocyte membrane is critical for the membrane-associated cytoskeleton structure and in central neurons it regulates the stabilization of AMPA receptors on the neuronal surface at the postsynaptic density. We report clinical, biochemical, and genetic features in four patients from four unrelated families with NA in order to explain the cause of morphological abnormalities and the relationship with neurodegenerative processes. Case presentation All patients were characterised by atypical NA with a novel alteration of the erythrocyte membrane: a 4.1R protein deficiency. The 4.1R protein content was significantly lower in patients (3.40 ± 0.42) than in controls (4.41 ± 0.40, P < 0.0001), reflecting weakened interactions of the cytoskeleton with the membrane. In patients IV:1 (RM23), IV:3 (RM15), and IV:6 (RM16) the 4.1 deficiency seemed to affect the horizontal interactions of spectrin and an impairment of the dimer self-association into tetramers was detected. In patient IV:1 (RM16) the 4.1 deficiency seemed to affect the skeletal attachment to membrane and the protein band 3 was partially reduced. Conclusion A decreased expression pattern of the 4.1R protein was observed in the erythrocytes from patients with atypical NA, which might reflect the expression pattern in the central nervous system, especially basal ganglia, and might lead to dysfunction of AMPA-mediated glutamate transmission.
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Affiliation(s)
- Antonio Orlacchio
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) – Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy
- Dipartimento di Neuroscienze, Neurologia, Università di Roma "Tor Vergata", Rome, Italy
| | - Paolo Calabresi
- Dipartimento di Specialità Medico-Chirurgiche e Sanità Pubblica, Neurologia, Università di Perugia, Perugia, Italy
- Laboratorio di Neurofisiologia Sperimentale, Centro Europeo di Ricerca sul Cervello (CERC) – Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy
| | - Adriana Rum
- Dipartimento di Neuroscienze, Neurologia, Università di Roma "Tor Vergata", Rome, Italy
| | - Anna Tarzia
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Anna Maria Salvati
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Toshitaka Kawarai
- Department of Neurology, Hyogo Brain and Heart Center, Himeji city, Hyogo prefecture, Japan
| | - Alessandro Stefani
- Dipartimento di Neuroscienze, Neurologia, Università di Roma "Tor Vergata", Rome, Italy
| | - Antonio Pisani
- Dipartimento di Neuroscienze, Neurologia, Università di Roma "Tor Vergata", Rome, Italy
- Laboratorio di Neurofisiologia Sperimentale, Centro Europeo di Ricerca sul Cervello (CERC) – Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy
| | - Giorgio Bernardi
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) – Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy
- Dipartimento di Neuroscienze, Neurologia, Università di Roma "Tor Vergata", Rome, Italy
- Laboratorio di Neurofisiologia Sperimentale, Centro Europeo di Ricerca sul Cervello (CERC) – Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy
| | | | - Patrizia Caprari
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
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50
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Semaka A, Creighton S, Warby S, Hayden MR. Predictive testing for Huntington disease: interpretation and significance of intermediate alleles. Clin Genet 2006; 70:283-94. [PMID: 16965319 DOI: 10.1111/j.1399-0004.2006.00668.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Direct mutation analysis for Huntington disease (HD) became possible in 1993 with the identification of an expanded CAG trinucleotide repeat as the mutation underlying the disease. Expansion of CAG length beyond 35 repeats may be associated with the clinical presentation of HD. HD has never been seen in a person with a CAG size of <36 repeats. Intermediate alleles are defined as being below the affected CAG range but have the potential to expand to >35 CAG repeats within one generation. Thus, children of intermediate allele carriers have a low risk of developing HD. Currently, the intermediate allele range for HD is between 27 and 35 CAG repeats. In this study, we review the current knowledge on intermediate alleles for HD including the CAG repeat range, the intermediate allele frequency, and the clinical implications of an intermediate allele predictive test result. The factors influencing CAG repeat expansion, including the CAG size of the intermediate allele, the sex and age of the transmitting parent, the family history, and the HD gene sequence and haplotype, will also be reviewed.
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Affiliation(s)
- A Semaka
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
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