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Lockwood C, Vo AS, Bellafard H, Carter AJR. More evidence for widespread antagonistic pleiotropy in polymorphic disease alleles. Front Genet 2024; 15:1404516. [PMID: 38952711 PMCID: PMC11215129 DOI: 10.3389/fgene.2024.1404516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/29/2024] [Indexed: 07/03/2024] Open
Abstract
Introduction Many loci segregate alleles classified as "genetic diseases" due to their deleterious effects on health. However, some disease alleles have been reported to show beneficial effects under certain conditions or in certain populations. The beneficial effects of these antagonistically pleiotropic alleles may explain their continued prevalence, but the degree to which antagonistic pleiotropy is common or rare is unresolved. We surveyed the medical literature to identify examples of antagonistic pleiotropy to help determine whether antagonistic pleiotropy appears to be rare or common. Results We identified ten examples of loci with polymorphisms for which the presence of antagonistic pleiotropy is well supported by detailed genetic or epidemiological information in humans. One additional locus was identified for which the supporting evidence comes from animal studies. These examples complement over 20 others reported in other reviews. Discussion The existence of more than 30 identified antagonistically pleiotropic human disease alleles suggests that this phenomenon may be widespread. This poses important implications for both our understanding of human evolutionary genetics and our approaches to clinical treatment and disease prevention, especially therapies based on genetic modification.
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Affiliation(s)
| | | | | | - Ashley J. R. Carter
- California State University Long Beach, Department of Biological Sciences, Long Beach, CA, United States
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Sena LS, Lemes RB, Furtado GV, Saraiva-Pereira ML, Jardim LB. A model for the dynamics of expanded CAG repeat alleles: ATXN2 and ATXN3 as prototypes. Front Genet 2023; 14:1296614. [PMID: 38034492 PMCID: PMC10682950 DOI: 10.3389/fgene.2023.1296614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Background: Spinocerebellar ataxia types 2 (SCA2) and 3 (SCA3/MJD) are diseases due to dominant unstable expansions of CAG repeats (CAGexp). Age of onset of symptoms (AO) correlates with the CAGexp length. Repeat instability leads to increases in the expanded repeats, to important AO anticipations and to the eventual extinction of lineages. Because of that, compensatory forces are expected to act on the maintenance of expanded alleles, but they are poorly understood. Objectives: we described the CAGexp dynamics, adapting a classical equation and aiming to estimate for how many generations will the descendants of a de novo expansion last. Methods: A mathematical model was adapted to encompass anticipation, fitness, and allelic segregation; and empirical data fed the model. The arbitrated ancestral mutations included in the model had the lowest CAGexp and the highest AO described in the literature. One thousand generations were simulated until the alleles were eliminated, fixed, or 650 generations had passed. Results: All SCA2 lineages were eliminated in a median of 10 generations. In SCA3/MJD lineages, 593 were eliminated in a median of 29 generations. The other ones were eliminated due to anticipation after the 650th generation or remained indefinitely with CAG repeats transitioning between expanded and unexpanded ranges. Discussion: the model predicted outcomes compatible with empirical data - the very old ancestral SCA3/MJD haplotype, and the de novo SCA2 expansions -, which previously seemed to be contradictory. This model accommodates these data into understandable dynamics and might be useful for other CAGexp disorders.
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Affiliation(s)
- Lucas Schenatto Sena
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | | | - Gabriel Vasata Furtado
- Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Maria Luiza Saraiva-Pereira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Laura Bannach Jardim
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Departamento de Medicina Interna, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Rossi M, Hamed M, Rodríguez-Antigüedad J, Cornejo-Olivas M, Breza M, Lohmann K, Klein C, Rajalingam R, Marras C, van de Warrenburg BP. Genotype-Phenotype Correlations for ATX-TBP (SCA17): MDSGene Systematic Review. Mov Disord 2023; 38:368-377. [PMID: 36374860 DOI: 10.1002/mds.29278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
Spinocerebellar ataxia type 17 or ATX-TBP is a CAG/CAA repeat expansion disorder characterized by marked clinical heterogeneity. Reports of affected carriers with subthreshold repeat expansions and of patients with Parkinson's disease (PD) with expanded repeats have cast doubt on the established cutoff values of the expansions and the phenotypic spectrum of this disorder. The objective of this systematic review was to explore the genotype-phenotype relationships for repeat expansions in TBP to delineate the ATX-TBP phenotype and reevaluate the pathological range of repeat expansions. The International Parkinson and Movement Disorder Society Genetic Mutation Database (MDSGene) standardized data extraction protocol was followed. Clinically affected carriers of reported ATX-TBP expansions were included. Publications that contained repeat sizes in screened cohorts of patients with PD and/or healthy individuals were included for a separate evaluation of cutoff values. Phenotypic and genotypic data for 346 ATX-TBP patients were curated. Overall, 97.7% of the patients had ≥41 repeats, while 99.6% of patients with PD and 99.9% of healthy individuals had ≤42 repeats, with a gray zone of reduced penetrance between 41 and 45 repeats. Pure parkinsonism was more common in ATX-TBP patients with 41 to 45 repeats than in the group with ≥46 repeats, which conversely more often presented with a complex phenotype with mixed movement disorders. An updated genotype-phenotype assessment for ATX-TBP is provided, and new repeat expansion cutoff values of reduced penetrance (41-45 expanded repeats) and full penetrance (46-66 expanded repeats) are proposed. These adjusted cutoff values will have diagnostic and counseling implications and may guide future clinical trial protocol. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Malco Rossi
- Sección de Movimientos Anormales, Departamento de Neurología, Fleni, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Moath Hamed
- New York-Presbyterian Brooklyn Methodist Hospital, Brooklyn, New York, USA
| | - Jon Rodríguez-Antigüedad
- Movement Disorders Unit, Neurology Department, Sant Pau Hospital, Barcelona, Spain
- Institut d'Investigacions Biomediques-Sant Pau, Barcelona, Spain
| | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Carrera de Medicina, Universidad Científica del Sur, Lima, Peru
| | - Marianthi Breza
- 1st Department of Neurology, School of Medicine, Eginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Rajasumi Rajalingam
- Edmond J. Safra Program in Parkinson's Disease, Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, UHN, Toronto, Ontario, Canada
| | - Connie Marras
- Edmond J. Safra Program in Parkinson's Disease, Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, UHN, Toronto, Ontario, Canada
| | - Bart P van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition & Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
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Bypassing Mendel's First Law: Transmission Ratio Distortion in Mammals. Int J Mol Sci 2023; 24:ijms24021600. [PMID: 36675116 PMCID: PMC9863905 DOI: 10.3390/ijms24021600] [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: 11/29/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Mendel's law of segregation states that the two alleles at a diploid locus should be transmitted equally to the progeny. A genetic segregation distortion, also referred to as transmission ratio distortion (TRD), is a statistically significant deviation from this rule. TRD has been observed in several mammal species and may be due to different biological mechanisms occurring at diverse time points ranging from gamete formation to lethality at post-natal stages. In this review, we describe examples of TRD and their possible mechanisms in mammals based on current knowledge. We first focus on the differences between TRD in male and female gametogenesis in the house mouse, in which some of the most well studied TRD systems have been characterized. We then describe known TRD in other mammals, with a special focus on the farmed species and in the peculiar common shrew species. Finally, we discuss TRD in human diseases. Thus far, to our knowledge, this is the first time that such description is proposed. This review will help better comprehend the processes involved in TRD. A better understanding of these molecular mechanisms will imply a better comprehension of their impact on fertility and on genome evolution. In turn, this should allow for better genetic counseling and lead to better care for human families.
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LaGrappe D, Massey L, Kruavit A, Howarth T, Lalara G, Daniels B, Wunungmurra JG, Flavell K, Barker R, Flavell H, Heraganahally SS. Sleep disorders among Aboriginal Australians with Machado-Joseph Disease: Quantitative results from a multiple methods study to assess the experience of people living with the disease and their caregivers. Neurobiol Sleep Circadian Rhythms 2022; 12:100075. [PMID: 35516836 PMCID: PMC9062757 DOI: 10.1016/j.nbscr.2022.100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 12/31/2022] Open
Abstract
Background Machado-Joseph Disease (MJD), or Spinocerebellar Ataxia Type 3 (SCA3), is a genetic disorder that causes progressive muscle weakness, loss of motor control, ataxia and permanent physical disability. Sleep disturbances are associated with MJD but remain poorly understood. Objective To investigate frequency and characteristics of sleep disorders and their association with health-related quality of life and psychosocial wellbeing for Aboriginal Australians living with MJD. Methods A convenience sample of MJD participants n = 24 participated in a semi-attended, ambulatory diagnostic sleep study to capture polysomnography, actigraphy and sleep diary data. Self-report measures collected were the Pittsburgh Sleep Quality Index (PSQI), STOP-BANG Questionnaire for Obstructive Sleep Apnoea (OSA), International Restless Legs Syndrome Study Group rating scale (IRLS), Kessler-5 (K5) and EuroQoL-5 Dimension (EQ5D). Caregivers (n = 22) reported EQ-5D, K5 and bed partners’ sleep behaviour (Mayo Sleep Questionnaire-Informant). Environmental factors were measured. Results We observed Nocturia, Sleep Related Leg Cramps, OSA, REM Behaviour Disorder, and RLS, respectively in 100%, 71%, 47%, 43%, and 33% of participants with a significant positive correlation between Body mass index (BMI) and Apnoea hypopnea index (AHI). The majority of sleep was spent in non-rapid eye movement sleep (NREM)-N2 stage (77.8% (67.7, 81.6)). Overcrowding (92%) and overnight care needs (42%) interrupted sleep. MJD participants and caregivers reported high psychological distress (K5 median 12.5 IQR 7, 16.5 & 8 IQR 6, 12 respectively). Conclusion Poor sleep quality and sleep disturbances are prevalent among this cohort. Disease manifestations and environmental factors are driving factors. Larger sample sizes are required to predict risk factors and confirm observed associations. Aboriginal People living with MJD in Australia experience numerous sleep disorders. Majority of sleep was spent in non-rapid eye movement sleep. Overcrowding and overnight care needs interrupt sleep. MJD participants and caregivers reported high psychological distress.
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Affiliation(s)
- Desireé LaGrappe
- Centre for Disease Control, Public Health Unit, Northern Territory Government Department of Health, O'Keefe House, Katherine Hospital, George Rd, Katherine, Northern Territory, 0850, Australia
- Judith Lumley Centre, School of Nursing and Midwifery, La Trobe University, Level 3, George Sinclair Building, Bundoora, Victoria, 3086, Australia
| | - Libby Massey
- MJD Foundation, PO Box 414, Alyangula, Northern Territory, 0885, Australia
- College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Bebegu Yumba, Douglas Campus, 1 James Cook Drive, QLD, 4814, Australia
- Corresponding author. MJD Foundation Ltd, PO Box 414, Alyangula, Northern Territory, 0885, Australia.
| | - Anuk Kruavit
- Adelaide Respiratory, Level 5, Calvary Adelaide Hospital, Adelaide, South Australia, 5000, Australia
- Department of Respiratory and Sleep Medicine, Royal Darwin Hospital, 105 Rocklands Drive, Tiwi, Northern Territory, 0810, Australia
| | - Timothy Howarth
- College of Health and Human Sciences, Charles Darwin University, Ellengowan Drive, Casuarina, Northern Territory, 0810, Australia
- Darwin Respiratory and Sleep Health, Darwin Private Hospital, Tiwi, Darwin, Northern Territory, Australia
| | - Gayangwa Lalara
- MJD Foundation, PO Box 414, Alyangula, Northern Territory, 0885, Australia
| | - Bronwyn Daniels
- MJD Foundation, PO Box 414, Alyangula, Northern Territory, 0885, Australia
| | | | - Kimberley Flavell
- College of Medicine and Public Health, Flinders University, Sturt Rd, Bedford Park, Adelaide, South Australia, Australia
| | - Ruth Barker
- College of Healthcare Sciences, James Cook University, Box 6811, Cairns, 4870, Townsville, QLD, Australia
| | - Howard Flavell
- Department of Rehabilitation Medicine, Palmerston Regional Hospital, Linco Rd, Holtze, Northern Territory, 0829, Australia
| | - Subash S. Heraganahally
- Department of Respiratory and Sleep Medicine, Royal Darwin Hospital, 105 Rocklands Drive, Tiwi, Northern Territory, 0810, Australia
- Darwin Respiratory and Sleep Health, Darwin Private Hospital, Tiwi, Darwin, Northern Territory, Australia
- College of Medicine and Public Health, Flinders University, Sturt Rd, Bedford Park, Adelaide, South Australia, Australia
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Sena LS, Dos Santos Pinheiro J, Hasan A, Saraiva-Pereira ML, Jardim LB. Spinocerebellar ataxia type 2 from an evolutionary perspective: Systematic review and meta-analysis. Clin Genet 2021; 100:258-267. [PMID: 33960424 DOI: 10.1111/cge.13978] [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: 03/02/2021] [Revised: 04/19/2021] [Accepted: 05/05/2021] [Indexed: 01/27/2023]
Abstract
Dominant diseases due to expanded CAG repeat tracts, such as spinocerebellar ataxia type 2 (SCA2), are prone to anticipation and worsening of clinical picture in subsequent generations. There is insufficient data about selective forces acting on the maintenance of these diseases in populations. We made a systematic review and meta-analysis on the effect of the CAG length over age at onset, instability of transmissions, anticipation, de novo or sporadic cases, fitness, segregation of alleles, and ancestral haplotypes. The correlation between CAG expanded and age at onset was r2 = 0.577, and transmission of the mutant allele was associated with an increase of 2.42 CAG repeats in the next generation and an anticipation of 14.62 years per generation, on average. One de novo and 18 sporadic cases were detected. Affected SCA2 individuals seem to have more children than controls. The expanded allele was less segregated than the 22-repeat allele in children of SCA2 subjects. Several ancestral SCA2 haplotypes were published. Data suggest that SCA2 lineages may tend to disappear eventually, due to strong anticipation phenomena. Whether or not the novel cases come from common haplotypes associated with a predisposition to further expansions is a question that needs to be addressed by future studies.
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Affiliation(s)
- Lucas Schenatto Sena
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Jordânia Dos Santos Pinheiro
- Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ali Hasan
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Maria Luiza Saraiva-Pereira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Instituto de Genética Médica Populacional, Porto Alegre, Brazil.,Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Laura Bannach Jardim
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Centros de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Instituto de Genética Médica Populacional, Porto Alegre, Brazil.,Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Departamento de Medicina Interna, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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