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Ruiz de Sabando A, Urrutia Lafuente E, Galbete A, Ciosi M, García Amigot F, García Solaesa V, Monckton DG, Ramos-Arroyo MA. Spanish HTT gene study reveals haplotype and allelic diversity with possible implications for germline expansion dynamics in Huntington disease. Hum Mol Genet 2023; 32:897-906. [PMID: 36130218 PMCID: PMC9990985 DOI: 10.1093/hmg/ddac224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
We aimed to determine the genetic diversity and molecular characteristics of the Huntington disease (HD) gene (HTT) in Spain. We performed an extended haplotype and exon one deep sequencing analysis of the HTT gene in a nationwide cohort of population-based controls (n = 520) and families with symptomatic individuals referred for HD genetic testing. This group included 331 HD cases and 140 carriers of intermediate alleles. Clinical and family history data were obtained when available. Spanish normal alleles are enriched in C haplotypes (40.1%), whereas A1 (39.8%) and A2 (31.6%) prevail among intermediate and expanded alleles, respectively. Alleles ≥ 50 CAG repeats are primarily associated with haplotypes A2 (38.9%) and C (32%), which are also present in 50% and 21.4%, respectively, of HD families with large intergenerational expansions. Non-canonical variants of exon one sequence are less frequent, but much more diverse, in alleles of ≥27 CAG repeats. The deletion of CAACAG, one of the six rare variants not observed among smaller normal alleles, is associated with haplotype C and appears to correlate with larger intergenerational expansions and early onset of symptoms. Spanish HD haplotypes are characterized by a high genetic diversity, potentially admixed with other non-Caucasian populations, with a higher representation of A2 and C haplotypes than most European populations. Differences in haplotype distributions across the CAG length range support differential germline expansion dynamics, with A2 and C showing the largest intergenerational expansions. This haplotype-dependent germline instability may be driven by specific cis-elements, such as the CAACAG deletion.
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Affiliation(s)
- Ainara Ruiz de Sabando
- Department of Medical Genetics, Hospital Universitario de Navarra, IdiSNA, Pamplona 31008, Spain.,Department of Health Sciences, Universidad Pública de Navarra, IdiSNA, Pamplona 31008, Spain.,Fundación Miguel Servet-Navarrabiomed, IdiSNA, Pamplona 31008, Spain
| | | | - Arkaitz Galbete
- Department of Statistics, Informatics and Mathematics, Universidad Pública de Navarra, IdiSNA, Pamplona 31006, Spain
| | - Marc Ciosi
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Fermín García Amigot
- Department of Medical Genetics, Hospital Universitario de Navarra, IdiSNA, Pamplona 31008, Spain
| | - Virginia García Solaesa
- Department of Medical Genetics, Hospital Universitario de Navarra, IdiSNA, Pamplona 31008, Spain
| | | | - Darren G Monckton
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Maria A Ramos-Arroyo
- Department of Medical Genetics, Hospital Universitario de Navarra, IdiSNA, Pamplona 31008, Spain.,Fundación Miguel Servet-Navarrabiomed, IdiSNA, Pamplona 31008, Spain
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Kay C, Collins JA, Caron NS, Agostinho LDA, Findlay-Black H, Casal L, Sumathipala D, Dissanayake VHW, Cornejo-Olivas M, Baine F, Krause A, Greenberg JL, Paiva CLA, Squitieri F, Hayden MR. A Comprehensive Haplotype-Targeting Strategy for Allele-Specific HTT Suppression in Huntington Disease. Am J Hum Genet 2019; 105:1112-1125. [PMID: 31708117 PMCID: PMC6904807 DOI: 10.1016/j.ajhg.2019.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/11/2019] [Indexed: 11/20/2022] Open
Abstract
Huntington disease (HD) is a fatal neurodegenerative disorder caused by a gain-of-function mutation in HTT. Suppression of mutant HTT has emerged as a leading therapeutic strategy for HD, with allele-selective approaches targeting HTT SNPs now in clinical trials. Haplotypes associated with the HD mutation (A1, A2, A3a) represent panels of allele-specific gene silencing targets for efficient treatment of individuals with HD of Northern European and indigenous South American ancestry. Here we extend comprehensive haplotype analysis of the HD mutation to key populations of Southern European, South Asian, Middle Eastern, and admixed African ancestry. In each of these populations, the HD mutation occurs predominantly on the A2 HTT haplotype. Analysis of HD haplotypes across all affected population groups enables rational selection of candidate target SNPs for development of allele-selective gene silencing therapeutics worldwide. Targeting SNPs on the A1 and A2 haplotypes in parallel is essential to achieve treatment of the most HD-affected subjects in populations where HD is most prevalent. Current allele-specific approaches will leave a majority of individuals with HD untreated in populations where the HD mutation occurs most frequently on the A2 haplotype. We further demonstrate preclinical development of potent and selective ASOs targeting SNPs on the A2 HTT haplotype, representing an allele-specific treatment strategy for these individuals. On the basis of comprehensive haplotype analysis, we show the maximum proportion of HD-affected subjects that may be treated with three or four allele targets in different populations worldwide, informing current allele-specific HTT silencing strategies.
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Affiliation(s)
- Chris Kay
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | - Jennifer A Collins
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | - Nicholas S Caron
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | - Luciana de Andrade Agostinho
- PPGNEURO, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ 20270-004, Brazil; Centro Universitário UNIFAMINAS, Muriaé, MG 36880-000, Brazil; Hospital do Câncer de Muriaé, Muriaé, MG 36880-000, Brazil
| | - Hailey Findlay-Black
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | - Lorenzo Casal
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z4H4, Canada
| | | | | | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima 15003, Peru; Center for Global Health, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Fiona Baine
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa; Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
| | - Jacquie L Greenberg
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Carmen Lúcia Antão Paiva
- PPGNEURO, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ 20270-004, Brazil
| | - Ferdinando Squitieri
- Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | - Michael R Hayden
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z4H4, Canada.
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Population-specific genetic modification of Huntington's disease in Venezuela. PLoS Genet 2018; 14:e1007274. [PMID: 29750799 PMCID: PMC5965898 DOI: 10.1371/journal.pgen.1007274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 05/23/2018] [Accepted: 02/23/2018] [Indexed: 12/21/2022] Open
Abstract
Modifiers of Mendelian disorders can provide insights into disease mechanisms and guide therapeutic strategies. A recent genome-wide association (GWA) study discovered genetic modifiers of Huntington's disease (HD) onset in Europeans. Here, we performed whole genome sequencing and GWA analysis of a Venezuelan HD cluster whose families were crucial for the original mapping of the HD gene defect. The Venezuelan HD subjects develop motor symptoms earlier than their European counterparts, implying the potential for population-specific modifiers. The main Venezuelan HD family inherits HTT haplotype hap.03, which differs subtly at the sequence level from European HD hap.03, suggesting a different ancestral origin but not explaining the earlier age at onset in these Venezuelans. GWA analysis of the Venezuelan HD cluster suggests both population-specific and population-shared genetic modifiers. Genome-wide significant signals at 7p21.2-21.1 and suggestive association signals at 4p14 and 17q21.2 are evident only in Venezuelan HD, but genome-wide significant association signals at the established European chromosome 15 modifier locus are improved when Venezuelan HD data are included in the meta-analysis. Venezuelan-specific association signals on chromosome 7 center on SOSTDC1, which encodes a bone morphogenetic protein antagonist. The corresponding SNPs are associated with reduced expression of SOSTDC1 in non-Venezuelan tissue samples, suggesting that interaction of reduced SOSTDC1 expression with a population-specific genetic or environmental factor may be responsible for modification of HD onset in Venezuela. Detection of population-specific modification in Venezuelan HD supports the value of distinct disease populations in revealing novel aspects of a disease and population-relevant therapeutic strategies.
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Genetic Contributors to Intergenerational CAG Repeat Instability in Huntington's Disease Knock-In Mice. Genetics 2016; 205:503-516. [PMID: 27913616 PMCID: PMC5289832 DOI: 10.1534/genetics.116.195578] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/12/2016] [Indexed: 12/11/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by the expansion of a CAG trinucleotide repeat in exon 1 of the HTT gene. Longer repeat sizes are associated with increased disease penetrance and earlier ages of onset. Intergenerationally unstable transmissions are common in HD families, partly underlying the genetic anticipation seen in this disorder. HD CAG knock-in mouse models also exhibit a propensity for intergenerational repeat size changes. In this work, we examine intergenerational instability of the CAG repeat in over 20,000 transmissions in the largest HD knock-in mouse model breeding datasets reported to date. We confirmed previous observations that parental sex drives the relative ratio of expansions and contractions. The large datasets further allowed us to distinguish effects of paternal CAG repeat length on the magnitude and frequency of expansions and contractions, as well as the identification of large repeat size jumps in the knock-in models. Distinct degrees of intergenerational instability were observed between knock-in mice of six background strains, indicating the occurrence of trans-acting genetic modifiers. We also found that lines harboring a neomycin resistance cassette upstream of Htt showed reduced expansion frequency, indicative of a contributing role for sequences in cis, with the expanded repeat as modifiers of intergenerational instability. These results provide a basis for further understanding of the mechanisms underlying intergenerational repeat instability.
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Ramos EM, Gillis T, Mysore JS, Lee J, Gögele M, D'Elia Y, Pichler I, Sequeiros J, Pramstaller PP, Gusella JF, MacDonald ME, Alonso I. Haplotype analysis of the 4p16.3 region in Portuguese families with Huntington's disease. Am J Med Genet B Neuropsychiatr Genet 2015; 168B:135-43. [PMID: 25656686 PMCID: PMC5006842 DOI: 10.1002/ajmg.b.32289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 11/25/2014] [Indexed: 12/12/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder characterized by involuntary choreic movements, cognitive impairment, and behavioral changes, caused by the expansion of an unstable CAG repeat in HTT. We characterized the genetic diversity of the HD mutation by performing an extensive haplotype analysis of ∼1Mb region flanking HTT in over 300 HD families of Portuguese origin. We observed that haplotype A, marked by HTT delta2642, was enriched in HD chromosomes and carried the two largest expansions reported in the Portuguese population. However, the most frequent HD haplotype B carried one of the largest (+12 CAGs) expansions, which resulted in an allele class change to full penetrance. Despite having a normal CAG distribution skewed to the higher end of the range, these two core haplotypes had similar expanded CAG repeat sizes compared to the other major core haplotypes (C and D) and there was no statistical difference in transmitted repeat instability across haplotypes. We observed a diversity of HTT region haplotypes in both normal and expanded chromosomes, representative of more than one ancestral chromosome underlying HD in Portugal, where multiple independent events on distinct chromosome 4 haplotypes have given rise to expansion into the pathogenic range.
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Affiliation(s)
- Eliana Marisa Ramos
- Center for Human Genetic ResearchMassachusetts General HospitalBostonMassachusettsUSA,UnIGENeIBMC–Institute for Molecular and Cell BiologyUniversity of PortoPortoPortugal
| | - Tammy Gillis
- Center for Human Genetic ResearchMassachusetts General HospitalBostonMassachusettsUSA
| | - Jayalakshmi S. Mysore
- Center for Human Genetic ResearchMassachusetts General HospitalBostonMassachusettsUSA
| | - Jong‐Min Lee
- Center for Human Genetic ResearchMassachusetts General HospitalBostonMassachusettsUSA
| | - Martin Gögele
- Center for BiomedicineEuropean Academy of Bozen/Bolzano (EURAC)BolzanoItaly
| | - Yuri D'Elia
- Center for BiomedicineEuropean Academy of Bozen/Bolzano (EURAC)BolzanoItaly
| | - Irene Pichler
- Center for BiomedicineEuropean Academy of Bozen/Bolzano (EURAC)BolzanoItaly
| | - Jorge Sequeiros
- UnIGENeIBMC–Institute for Molecular and Cell BiologyUniversity of PortoPortoPortugal,CGPPIBMC–Institute for Molecular and Cell BiologyUniversity of PortoPortoPortugal,ICBAS–Instituto de Ciências Biomédicas Abel SalazarUniversity of PortoPortoPortugal
| | - Peter P. Pramstaller
- Center for BiomedicineEuropean Academy of Bozen/Bolzano (EURAC)BolzanoItaly,Department of NeurologyCentral HospitalBolzanoItaly,Department of NeurologyUniversity of LübeckLübeckGermany
| | - James F. Gusella
- Center for Human Genetic ResearchMassachusetts General HospitalBostonMassachusettsUSA
| | - Marcy E. MacDonald
- Center for Human Genetic ResearchMassachusetts General HospitalBostonMassachusettsUSA
| | - Isabel Alonso
- UnIGENeIBMC–Institute for Molecular and Cell BiologyUniversity of PortoPortoPortugal,CGPPIBMC–Institute for Molecular and Cell BiologyUniversity of PortoPortoPortugal,ICBAS–Instituto de Ciências Biomédicas Abel SalazarUniversity of PortoPortoPortugal
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