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Fan J, Zhong L, Yan F, Li X, Li L, Zhao H, Han Z, Wang R, Tao Z, Zheng Y, Ma Q, Luo Y. Alteration of N6-methyladenosine modification profiles in the neutrophilic RNAs following ischemic stroke. Neuroscience 2024; 553:56-73. [PMID: 38945353 DOI: 10.1016/j.neuroscience.2024.06.014] [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: 03/20/2024] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) is one of the most extensive RNA methylation modifications in eukaryotes and participates in the pathogenesis of numerous diseases including ischemic stroke. Peripheral blood neutrophils are forerunners after ischemic brain injury and exert crucial functions. This study aims to explore the transcriptional profiles of m6A modification in neutrophils of patients with ischemic stroke. RESULTS We found that the expression levels of m6A regulators FTO and YTHDC1 were notably decreased in the neutrophils following ischemic stroke, and FTO expression was negatively correlated with neutrophil counts and neutrophil-to-lymphocyte ratio (NLR). The m6A mRNA&lncRNA epigenetic transcriptome microarray identified 416 significantly upregulated and 500 significantly downregulated mRNA peaks in neutrophils of ischemic stroke patients. Moreover, 48 mRNAs and 18 lncRNAs were hypermethylated, and 115 mRNAs and 29 lncRNAs were hypomethylated after cerebral ischemia. Gene ontology (GO) analysis identified that these m6A-modified mRNAs were primarily enriched in calcium ion transport, long-term synaptic potentiation, and base-excision repair. The signaling pathways involved were EGFR tyrosine kinase inhibitor resistance, ErbB, and base excision repair signaling pathway. MeRIP-qPCR validation results showed that NRG1 and GDPD1 were significantly hypermethylated, and LIG1, CHRND, lncRNA RP11-442J17.2, and lncRNA RP11-600P1.2 were significantly hypomethylated after cerebral ischemia. Moreover, the expression levels of major m6A regulators Mettl3, Fto, Ythdf1, and Ythdf3 were obviously declined in the brain and leukocytes of post-stroke mouse models. CONCLUSION This study explored the RNA m6A methylation pattern in the neutrophils of ischemic stroke patients, indicating that it is an intervention target of epigenetic regulation in ischemic stroke.
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Affiliation(s)
- Junfen Fan
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China; Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100053, China.
| | - Liyuan Zhong
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China
| | - Feng Yan
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China; Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100053, China
| | - Xue Li
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China
| | - Lingzhi Li
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China
| | - Haiping Zhao
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China; Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100053, China
| | - Ziping Han
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China; Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100053, China
| | - Rongliang Wang
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China; Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100053, China
| | - Zhen Tao
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China; Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100053, China
| | - Yangmin Zheng
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China; Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100053, China
| | - Qingfeng Ma
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China.
| | - Yumin Luo
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing 100053, China; Beijing Geriatric Medical Research Center and Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100053, China; Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100053, China.
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2
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Pressl C, Mätlik K, Kus L, Darnell P, Luo JD, Paul MR, Weiss AR, Liguore W, Carroll TS, Davis DA, McBride J, Heintz N. Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease. Neuron 2024; 112:924-941.e10. [PMID: 38237588 DOI: 10.1016/j.neuron.2023.12.009] [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: 06/15/2023] [Revised: 08/18/2023] [Accepted: 12/13/2023] [Indexed: 01/30/2024]
Abstract
The properties of the cell types that are selectively vulnerable in Huntington's disease (HD) cortex, the nature of somatic CAG expansions of mHTT in these cells, and their importance in CNS circuitry have not been delineated. Here, we employed serial fluorescence-activated nuclear sorting (sFANS), deep molecular profiling, and single-nucleus RNA sequencing (snRNA-seq) of motor-cortex samples from thirteen predominantly early stage, clinically diagnosed HD donors and selected samples from cingulate, visual, insular, and prefrontal cortices to demonstrate loss of layer 5a pyramidal neurons in HD. Extensive mHTT CAG expansions occur in vulnerable layer 5a pyramidal cells, and in Betz cells, layers 6a and 6b neurons that are resilient in HD. Retrograde tracing experiments in macaque brains identify layer 5a neurons as corticostriatal pyramidal cells. We propose that enhanced somatic mHTT CAG expansion and altered synaptic function act together to cause corticostriatal disconnection and selective neuronal vulnerability in HD cerebral cortex.
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Affiliation(s)
- Christina Pressl
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Kert Mätlik
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Laura Kus
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Paul Darnell
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alison R Weiss
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - William Liguore
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - David A Davis
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jodi McBride
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Nathaniel Heintz
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA.
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3
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Gall-Duncan T, Luo J, Jurkovic CM, Fischer LA, Fujita K, Deshmukh AL, Harding RJ, Tran S, Mehkary M, Li V, Leib DE, Chen R, Tanaka H, Mason AG, Lévesque D, Khan M, Razzaghi M, Prasolava T, Lanni S, Sato N, Caron MC, Panigrahi GB, Wang P, Lau R, Castel AL, Masson JY, Tippett L, Turner C, Spies M, La Spada AR, Campos EI, Curtis MA, Boisvert FM, Faull RLM, Davidson BL, Nakamori M, Okazawa H, Wold MS, Pearson CE. Antagonistic roles of canonical and Alternative-RPA in disease-associated tandem CAG repeat instability. Cell 2023; 186:4898-4919.e25. [PMID: 37827155 PMCID: PMC11209935 DOI: 10.1016/j.cell.2023.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/30/2023] [Accepted: 09/09/2023] [Indexed: 10/14/2023]
Abstract
Expansions of repeat DNA tracts cause >70 diseases, and ongoing expansions in brains exacerbate disease. During expansion mutations, single-stranded DNAs (ssDNAs) form slipped-DNAs. We find the ssDNA-binding complexes canonical replication protein A (RPA1, RPA2, and RPA3) and Alternative-RPA (RPA1, RPA3, and primate-specific RPA4) are upregulated in Huntington disease and spinocerebellar ataxia type 1 (SCA1) patient brains. Protein interactomes of RPA and Alt-RPA reveal unique and shared partners, including modifiers of CAG instability and disease presentation. RPA enhances in vitro melting, FAN1 excision, and repair of slipped-CAGs and protects against CAG expansions in human cells. RPA overexpression in SCA1 mouse brains ablates expansions, coincident with decreased ATXN1 aggregation, reduced brain DNA damage, improved neuron morphology, and rescued motor phenotypes. In contrast, Alt-RPA inhibits melting, FAN1 excision, and repair of slipped-CAGs and promotes CAG expansions. These findings suggest a functional interplay between the two RPAs where Alt-RPA may antagonistically offset RPA's suppression of disease-associated repeat expansions, which may extend to other DNA processes.
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Affiliation(s)
- Terence Gall-Duncan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer Luo
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Laura A Fischer
- Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyota Fujita
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amit L Deshmukh
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephanie Tran
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mustafa Mehkary
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Vanessa Li
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - David E Leib
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Ran Chen
- Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hikari Tanaka
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amanda G Mason
- Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Lévesque
- Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mahreen Khan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mortezaali Razzaghi
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Tanya Prasolava
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stella Lanni
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nozomu Sato
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marie-Christine Caron
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Gagan B Panigrahi
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peixiang Wang
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel Lau
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Lynette Tippett
- School of Psychology, University of Auckland, Auckland, New Zealand; University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Clinton Turner
- Anatomical Pathology, LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Maria Spies
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Albert R La Spada
- Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA, USA; Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA
| | - Eric I Campos
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Maurice A Curtis
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | | | - Richard L M Faull
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Beverly L Davidson
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Masayuki Nakamori
- Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hitoshi Okazawa
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Marc S Wold
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Christopher E Pearson
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.
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4
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Morales F, Corrales E, Vásquez M, Zhang B, Fernández H, Alvarado F, Cortés S, Santamaría-Ulloa C, Initiative-Mmdbdi MMDBD, Krahe R, Monckton DG. Individual-specific levels of CTG•CAG somatic instability are shared across multiple tissues in myotonic dystrophy type 1. Hum Mol Genet 2023; 32:621-631. [PMID: 36099027 DOI: 10.1093/hmg/ddac231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 02/07/2023] Open
Abstract
Myotonic dystrophy type 1 is a complex disease caused by a genetically unstable CTG repeat expansion in the 3'-untranslated region of the DMPK gene. Age-dependent, tissue-specific somatic instability has confounded genotype-phenotype associations, but growing evidence suggests that it also contributes directly toward disease progression. Using a well-characterized clinical cohort of DM1 patients from Costa Rica, we quantified somatic instability in blood, buccal cells, skin and skeletal muscle. Whilst skeletal muscle showed the largest expansions, modal allele lengths in skin were also very large and frequently exceeded 2000 CTG repeats. Similarly, the degree of somatic expansion in blood, muscle and skin were associated with each other. Notably, we found that the degree of somatic expansion in skin was highly predictive of that in skeletal muscle. More importantly, we established that individuals whose repeat expanded more rapidly than expected in one tissue (after correction for progenitor allele length and age) also expanded more rapidly than expected in other tissues. We also provide evidence suggesting that individuals in whom the repeat expanded more rapidly than expected in skeletal muscle have an earlier age at onset than expected (after correction for the progenitor allele length). Pyrosequencing analyses of the genomic DNA flanking the CTG repeat revealed that the degree of methylation in muscle was well predicted by the muscle modal allele length and age, but that neither methylation of the flanking DNA nor levels of DMPK sense and anti-sense transcripts could obviously explain individual- or tissue-specific patterns of somatic instability.
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Affiliation(s)
- Fernando Morales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José 2060, Costa Rica
| | - Eyleen Corrales
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José 2060, Costa Rica
| | - Melissa Vásquez
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José 2060, Costa Rica
| | - Baili Zhang
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Huberth Fernández
- Hospital Calderón Guardia/Escuela de Medicina, Universidad de Costa Rica, San José 2060, Costa Rica
| | - Fernando Alvarado
- Hospital Calderón Guardia/Escuela de Medicina, Universidad de Costa Rica, San José 2060, Costa Rica
| | - Sergio Cortés
- Hospital Calderón Guardia/Escuela de Medicina, Universidad de Costa Rica, San José 2060, Costa Rica
| | | | | | - Ralf Krahe
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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5
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Abstract
At fifteen different genomic locations, the expansion of a CAG/CTG repeat causes a neurodegenerative or neuromuscular disease, the most common being Huntington's disease and myotonic dystrophy type 1. These disorders are characterized by germline and somatic instability of the causative CAG/CTG repeat mutations. Repeat lengthening, or expansion, in the germline leads to an earlier age of onset or more severe symptoms in the next generation. In somatic cells, repeat expansion is thought to precipitate the rate of disease. The mechanisms underlying repeat instability are not well understood. Here we review the mammalian model systems that have been used to study CAG/CTG repeat instability, and the modifiers identified in these systems. Mouse models have demonstrated prominent roles for proteins in the mismatch repair pathway as critical drivers of CAG/CTG instability, which is also suggested by recent genome-wide association studies in humans. We draw attention to a network of connections between modifiers identified across several systems that might indicate pathway crosstalk in the context of repeat instability, and which could provide hypotheses for further validation or discovery. Overall, the data indicate that repeat dynamics might be modulated by altering the levels of DNA metabolic proteins, their regulation, their interaction with chromatin, or by direct perturbation of the repeat tract. Applying novel methodologies and technologies to this exciting area of research will be needed to gain deeper mechanistic insight that can be harnessed for therapies aimed at preventing repeat expansion or promoting repeat contraction.
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Affiliation(s)
- Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA,Department of Neurology, Harvard Medical School, Boston, MA, USA,Correspondence to: Vanessa C. Wheeler, Center for Genomic Medicine, Massachusetts Hospital, Boston MAA 02115, USA. E-mail: . and Vincent Dion, UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK. E-mail:
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, UK,Correspondence to: Vanessa C. Wheeler, Center for Genomic Medicine, Massachusetts Hospital, Boston MAA 02115, USA. E-mail: . and Vincent Dion, UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK. E-mail:
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6
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Mouro Pinto R, Arning L, Giordano JV, Razghandi P, Andrew MA, Gillis T, Correia K, Mysore JS, Grote Urtubey DM, Parwez CR, von Hein SM, Clark HB, Nguyen HP, Förster E, Beller A, Jayadaev S, Keene CD, Bird TD, Lucente D, Vonsattel JP, Orr H, Saft C, Petrasch-Parwez E, Wheeler VC. Patterns of CAG repeat instability in the central nervous system and periphery in Huntington's disease and in spinocerebellar ataxia type 1. Hum Mol Genet 2021; 29:2551-2567. [PMID: 32761094 PMCID: PMC7471505 DOI: 10.1093/hmg/ddaa139] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 12/23/2022] Open
Abstract
The expanded HTT CAG repeat causing Huntington’s disease (HD) exhibits somatic expansion proposed to drive the rate of disease onset by eliciting a pathological process that ultimately claims vulnerable cells. To gain insight into somatic expansion in humans, we performed comprehensive quantitative analyses of CAG expansion in ~50 central nervous system (CNS) and peripheral postmortem tissues from seven adult-onset and one juvenile-onset HD individual. We also assessed ATXN1 CAG repeat expansion in brain regions of an individual with a neurologically and pathologically distinct repeat expansion disorder, spinocerebellar ataxia type 1 (SCA1). Our findings reveal similar profiles of tissue instability in all HD individuals, which, notably, were also apparent in the SCA1 individual. CAG expansion was observed in all tissues, but to different degrees, with multiple cortical regions and neostriatum tending to have the greatest instability in the CNS, and liver in the periphery. These patterns indicate different propensities for CAG expansion contributed by disease locus-independent trans-factors and demonstrate that expansion per se is not sufficient to cause cell type or disease-specific pathology. Rather, pathology may reflect distinct toxic processes triggered by different repeat lengths across cell types and diseases. We also find that the HTT CAG length-dependent expansion propensity of an individual is reflected in all tissues and in cerebrospinal fluid. Our data indicate that peripheral cells may be a useful source to measure CAG expansion in biomarker assays for therapeutic efforts, prompting efforts to dissect underlying mechanisms of expansion that may differ between the brain and periphery.
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Affiliation(s)
- Ricardo Mouro Pinto
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Larissa Arning
- Department of Human Genetics, Ruhr-University Bochum, Bochum 44780, Germany
| | - James V Giordano
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Pedram Razghandi
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marissa A Andrew
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tammy Gillis
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin Correia
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jayalakshmi S Mysore
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Constanze R Parwez
- Department of Neuroanatomy and Molecular Brain Research, Institute of Anatomy, Ruhr-University Bochum, Bochum 44780, Germany
| | - Sarah M von Hein
- Department of Neurology, Huntington Centre NRW, St. Josef-Hospital, Ruhr-University Bochum, Bochum 44791, Germany
| | - H Brent Clark
- Department of Laboratory Medicine and Pathology, Institute of Translational Neuroscience, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr-University Bochum, Bochum 44780, Germany
| | - Eckart Förster
- Department of Neuroanatomy and Molecular Brain Research, Institute of Anatomy, Ruhr-University Bochum, Bochum 44780, Germany
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Suman Jayadaev
- Department of Neurology, University of Washington, Seattle, Washington 98195, USA
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Thomas D Bird
- Department of Neurology, University of Washington, Seattle, Washington 98195, USA.,Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,Geriatrics Research Education and Clinical Center, VA Puget Sound Medical Center, Seattle, WA 98108, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jean-Paul Vonsattel
- Department of Pathology and Cell Biology, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Harry Orr
- Department of Laboratory Medicine and Pathology, Institute of Translational Neuroscience, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Carsten Saft
- Department of Neurology, Huntington Centre NRW, St. Josef-Hospital, Ruhr-University Bochum, Bochum 44791, Germany
| | - Elisabeth Petrasch-Parwez
- Department of Neuroanatomy and Molecular Brain Research, Institute of Anatomy, Ruhr-University Bochum, Bochum 44780, Germany
| | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
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7
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Replication-independent instability of Friedreich's ataxia GAA repeats during chronological aging. Proc Natl Acad Sci U S A 2021; 118:2013080118. [PMID: 33495349 PMCID: PMC7865128 DOI: 10.1073/pnas.2013080118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The inheritance of long (GAA)n repeats in the frataxin gene causes the debilitating neurodegenerative disease Friedreich’s ataxia. Subsequent expansions of these repeats throughout a patient’s lifetime in the affected tissues, like the nervous system, may contribute to disease onset. We developed an experimental model to characterize the mechanisms of repeat instability in nondividing cells to better understand how mutations can occur as cells age chronologically. We show that repeats can expand in nondividing cells. Notably, however, large deletions are the major type of repeat-mediated genome instability in nondividing cells, implicating the loss of important genetic material with aging in the progression of Friedreich’s ataxia. Nearly 50 hereditary diseases result from the inheritance of abnormally long repetitive DNA microsatellites. While it was originally believed that the size of inherited repeats is the key factor in disease development, it has become clear that somatic instability of these repeats throughout an individual’s lifetime strongly contributes to disease onset and progression. Importantly, somatic instability is commonly observed in terminally differentiated, postmitotic cells, such as neurons. To unravel the mechanisms of repeat instability in nondividing cells, we created an experimental system to analyze the mutability of Friedreich’s ataxia (GAA)n repeats during chronological aging of quiescent Saccharomyces cerevisiae. Unexpectedly, we found that the predominant repeat-mediated mutation in nondividing cells is large-scale deletions encompassing parts, or the entirety, of the repeat and adjacent regions. These deletions are caused by breakage at the repeat mediated by mismatch repair (MMR) complexes MutSβ and MutLα and DNA endonuclease Rad1, followed by end-resection by Exo1 and repair of the resulting double-strand breaks (DSBs) via nonhomologous end joining. We also observed repeat-mediated gene conversions as a result of DSB repair via ectopic homologous recombination during chronological aging. Repeat expansions accrue during chronological aging as well—particularly in the absence of MMR-induced DSBs. These expansions depend on the processivity of DNA polymerase δ while being counteracted by Exo1 and MutSβ, implicating nick repair. Altogether, these findings show that the mechanisms and types of (GAA)n repeat instability differ dramatically between dividing and nondividing cells, suggesting that distinct repeat-mediated mutations in terminally differentiated somatic cells might influence Friedreich’s ataxia pathogenesis.
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8
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Khampang S, Parnpai R, Mahikul W, Easley CA, Cho IK, Chan AWS. CAG repeat instability in embryonic stem cells and derivative spermatogenic cells of transgenic Huntington's disease monkey. J Assist Reprod Genet 2021; 38:1215-1229. [PMID: 33611676 DOI: 10.1007/s10815-021-02106-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The expansion of CAG (glutamine; Q) trinucleotide repeats (TNRs) predominantly occurs through male lineage in Huntington's disease (HD). As a result, offspring will have larger CAG repeats compared to their fathers, which causes an earlier onset of the disease called genetic anticipation. This study aims to develop a novel in vitro model to replicate CAG repeat instability in early spermatogenesis and demonstrate the biological process of genetic anticipation by using the HD stem cell model for the first time. METHODS HD rhesus monkey embryonic stem cells (rESCs) were cultured in vitro for an extended period. Male rESCs were used to derive spermatogenic cells in vitro with a 10-day differentiation. The assessment of CAG repeat instability was performed by GeneScan and curve fit analysis. RESULTS Spermatogenic cells derived from rESCs exhibit progressive expansion of CAG repeats with high daily expansion rates compared to the extended culture of rESCs. The expansion of CAG repeats is cell type-specific and size-dependent. CONCLUSIONS Here, we report a novel stem cell model that replicates genome instability and CAG repeat expansion in in vitro derived HD monkey spermatogenic cells. The in vitro spermatogenic cell model opens a new opportunity for studying TNR instability and the underlying mechanism of genetic anticipation, not only in HD but also in other TNR diseases.
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Affiliation(s)
- Sujittra Khampang
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, USA.,Embryo Technology and Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Rangsun Parnpai
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Wiriya Mahikul
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Charles A Easley
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, USA.,Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - In Ki Cho
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, USA. .,Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
| | - Anthony W S Chan
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, USA. .,Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
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9
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Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis 2021; 10:95-122. [PMID: 33579867 PMCID: PMC7990447 DOI: 10.3233/jhd-200448] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FAN1 encodes a DNA repair nuclease. Genetic deficiencies, copy number variants, and single nucleotide variants of FAN1 have been linked to karyomegalic interstitial nephritis, 15q13.3 microdeletion/microduplication syndrome (autism, schizophrenia, and epilepsy), cancer, and most recently repeat expansion diseases. For seven CAG repeat expansion diseases (Huntington's disease (HD) and certain spinocerebellar ataxias), modification of age of onset is linked to variants of specific DNA repair proteins. FAN1 variants are the strongest modifiers. Non-coding disease-delaying FAN1 variants and coding disease-hastening variants (p.R507H and p.R377W) are known, where the former may lead to increased FAN1 levels and the latter have unknown effects upon FAN1 functions. Current thoughts are that ongoing repeat expansions in disease-vulnerable tissues, as individuals age, promote disease onset. Fan1 is required to suppress against high levels of ongoing somatic CAG and CGG repeat expansions in tissues of HD and FMR1 transgenic mice respectively, in addition to participating in DNA interstrand crosslink repair. FAN1 is also a modifier of autism, schizophrenia, and epilepsy. Coupled with the association of these diseases with repeat expansions, this suggests a common mechanism, by which FAN1 modifies repeat diseases. Yet how any of the FAN1 variants modify disease is unknown. Here, we review FAN1 variants, associated clinical effects, protein structure, and the enzyme's attributed functional roles. We highlight how variants may alter its activities in DNA damage response and/or repeat instability. A thorough awareness of the FAN1 gene and FAN1 protein functions will reveal if and how it may be targeted for clinical benefit.
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Affiliation(s)
- Amit L Deshmukh
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mohiuddin Mohiuddin
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Gagan B Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Marie-Christine Caron
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada.,Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | - Jean-Yves Masson
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada.,Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.,University of Toronto, Program of Molecular Genetics, Toronto, Ontario, Canada
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10
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Gomes-Pereira M, Monckton DG. Chronic Exposure to Cadmium and Antioxidants Does Not Affect the Dynamics of Expanded CAG•CTG Trinucleotide Repeats in a Mouse Cell Culture System of Unstable DNA. Front Cell Neurosci 2021; 14:606331. [PMID: 33603644 PMCID: PMC7884634 DOI: 10.3389/fncel.2020.606331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/29/2020] [Indexed: 12/02/2022] Open
Abstract
More than 30 human disorders are caused by the expansion of simple sequence DNA repeats, among which triplet repeats remain the most frequent. Most trinucleotide repeat expansion disorders affect primarily the nervous system, through mechanisms of neurodysfunction and/or neurodegeneration. While trinucleotide repeat tracts are short and stably transmitted in unaffected individuals, disease-associated expansions are highly dynamic in the germline and in somatic cells, with a tendency toward further expansion. Since longer repeats are associated with increasing disease severity and earlier onset of symptoms, intergenerational repeat size gains account for the phenomenon of anticipation. In turn, higher levels of age-dependent somatic expansion have been linked with increased disease severity and earlier age of onset, implicating somatic instability in the onset and progression of disease symptoms. Hence, tackling the root cause of symptoms through the control of repeat dynamics may provide therapeutic modulation of clinical manifestations. DNA repair pathways have been firmly implicated in the molecular mechanism of repeat length mutation. The demonstration that repeat expansion depends on functional DNA mismatch repair (MMR) proteins, points to MMR as a potential therapeutic target. Similarly, a role of DNA base excision repair (BER) in repeat expansion has also been suggested, particularly during the removal of oxidative lesions. Using a well-characterized mouse cell model system of an unstable CAG•CTG trinucleotide repeat, we tested if expanded repeat tracts can be stabilized by small molecules with reported roles in both pathways: cadmium (an inhibitor of MMR activity) and a variety of antioxidants (capable of neutralizing oxidative species). We found that chronic exposure to sublethal doses of cadmium and antioxidants did not result in significant reduction of the rate of trinucleotide repeat expansion. Surprisingly, manganese yielded a significant stabilization of the triplet repeat tract. We conclude that treatment with cadmium and antioxidants, at doses that do not interfere with cell survival and cell culture dynamics, is not sufficient to modify trinucleotide repeat dynamics in cell culture.
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Affiliation(s)
| | - Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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11
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Fautsch MP, Wieben ED, Baratz KH, Bhattacharyya N, Sadan AN, Hafford-Tear NJ, Tuft SJ, Davidson AE. TCF4-mediated Fuchs endothelial corneal dystrophy: Insights into a common trinucleotide repeat-associated disease. Prog Retin Eye Res 2020; 81:100883. [PMID: 32735996 PMCID: PMC7988464 DOI: 10.1016/j.preteyeres.2020.100883] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
Fuchs endothelial corneal dystrophy (FECD) is a common cause for heritable visual loss in the elderly. Since the first description of an association between FECD and common polymorphisms situated within the transcription factor 4 (TCF4) gene, genetic and molecular studies have implicated an intronic CTG trinucleotide repeat (CTG18.1) expansion as a causal variant in the majority of FECD patients. To date, several non-mutually exclusive mechanisms have been proposed that drive and/or exacerbate the onset of disease. These mechanisms include (i) TCF4 dysregulation; (ii) toxic gain-of-function from TCF4 repeat-containing RNA; (iii) toxic gain-of-function from repeat-associated non-AUG dependent (RAN) translation; and (iv) somatic instability of CTG18.1. However, the relative contribution of these proposed mechanisms in disease pathogenesis is currently unknown. In this review, we summarise research implicating the repeat expansion in disease pathogenesis, define the phenotype-genotype correlations between FECD and CTG18.1 expansion, and provide an update on research tools that are available to study FECD as a trinucleotide repeat expansion disease. Furthermore, ongoing international research efforts to develop novel CTG18.1 expansion-mediated FECD therapeutics are highlighted and we provide a forward-thinking perspective on key unanswered questions that remain in the field. FECD is a common, age-related corneal dystrophy. The majority of cases are associated with expansion of a CTG repeat (CTG18.1). FECD is the most common trinucleotide repeat expansion disease in humans. Evidence supports multiple molecular mechanisms underlying the pathophysiology. Novel CTG18.1-targeted therapeutics are in development.
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Affiliation(s)
- Michael P Fautsch
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Eric D Wieben
- Department of Biochemistry and Molecular Biology, 200 1st St SW, Mayo Clinic, Rochester, MN, USA.
| | - Keith H Baratz
- Department of Ophthalmology, 200 1st St SW, Mayo Clinic, Rochester, MN, 55905, USA.
| | | | - Amanda N Sadan
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
| | | | - Stephen J Tuft
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK.
| | - Alice E Davidson
- University College London Institute of Ophthalmology, London, ECIV 9EL, UK.
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12
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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13
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Khan H, Ullah H, Tundis R, Belwal T, Devkota HP, Daglia M, Cetin Z, Saygili EI, Campos MDG, Capanoglu E, Du M, Dar P, Xiao J. Dietary Flavonoids in the Management of Huntington’s Disease: Mechanism and Clinical Perspective. EFOOD 2020. [DOI: 10.2991/efood.k.200203.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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14
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Ates S, Deistung A, Schneider R, Prehn C, Lukas C, Reichenbach JR, Schneider-Gold C, Bellenberg B. Characterization of Iron Accumulation in Deep Gray Matter in Myotonic Dystrophy Type 1 and 2 Using Quantitative Susceptibility Mapping and R2 * Relaxometry: A Magnetic Resonance Imaging Study at 3 Tesla. Front Neurol 2019; 10:1320. [PMID: 31920940 PMCID: PMC6923271 DOI: 10.3389/fneur.2019.01320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 11/28/2019] [Indexed: 01/14/2023] Open
Abstract
Quantitative mapping of the magnetic susceptibility and the effective transverse relaxation rate (R2*) are suitable to assess the iron content in distinct brain regions. In this prospective, explorative study the iron accumulation in deep gray matter nuclei (DGM) in myotonic dystrophy type 1 (DM1) and 2 (DM2) and its clinical and neuro-cognitive relevance using susceptibility and R2* mapping was examined. Twelve classical DM1, four childhood-onset DM1 (DM1c.o.), twelve DM2 patients and twenty-nine matched healthy controls underwent MRI at 3 Tesla, neurological and neuro-cognitive tests. Susceptibility, R2* and volumes were determined for eleven DGM structures and compared between patients and controls. Twelve classical DM1, four childhood-onset DM1, and 12 DM2 patients as well as 29 matched healthy controls underwent MRI at 3 Tesla, and neurological and neuro-cognitive tests. Susceptibility, R2* and volumes were determined for 11 DGM structures and compared between patients and controls. Iron accumulation in DGM reflected by R2* or susceptibility was found in the putamen and accumbens of DM1 and in DM2, but was more widespread in DM1 (caudate, pallidum, hippocampus, subthalamic nucleus, thalamus, and substantia nigra). Opposed changes of R2* or susceptibility were detected in caudate, putamen and accumbens in the childhood-onset DM1 patients compared to classical DM1. R2* or susceptibility alterations in DGM were significantly associated with clinical symptoms including muscular weakness (DM1), daytime sleepiness (DM1), depression (DM2), and with specific cognitive deficits in DM1 and DM2.
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Affiliation(s)
- Sevda Ates
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Andreas Deistung
- Department of Radiology, University Hospital Halle (Saale), Halle (Saale), Germany.,Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital, Friedrich Schiller-University, Jena, Germany
| | - Ruth Schneider
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Christian Prehn
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Carsten Lukas
- Institute of Neuroradiology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany.,Department of Diagnostic and Interventional Radiology and Nuclear Medicine, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Jürgen R Reichenbach
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital, Friedrich Schiller-University, Jena, Germany
| | | | - Barbara Bellenberg
- Institute of Neuroradiology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany.,Department of Diagnostic and Interventional Radiology and Nuclear Medicine, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
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15
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Mollica PA, Zamponi M, Reid JA, Sharma DK, White AE, Ogle RC, Bruno RD, Sachs PC. Epigenetic alterations mediate iPSC-induced normalization of DNA repair gene expression and TNR stability in Huntington's disease cells. J Cell Sci 2018; 131:jcs.215343. [PMID: 29898922 DOI: 10.1242/jcs.215343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
Huntington's disease (HD) is a rare autosomal dominant neurodegenerative disorder caused by a cytosine-adenine-guanine (CAG) trinucleotide repeat (TNR) expansion within the HTT gene. The mechanisms underlying HD-associated cellular dysfunction in pluripotency and neurodevelopment are poorly understood. We had previously identified downregulation of selected DNA repair genes in HD fibroblasts relative to wild-type fibroblasts, as a result of promoter hypermethylation. Here, we tested the hypothesis that hypomethylation during cellular reprogramming to the induced pluripotent stem cell (iPSC) state leads to upregulation of DNA repair genes and stabilization of TNRs in HD cells. We sought to determine how the HD TNR region is affected by global epigenetic changes through cellular reprogramming and early neurodifferentiation. We find that early stage HD-affected neural stem cells (HD-NSCs) contain increased levels of global 5-hydroxymethylation (5-hmC) and normalized DNA repair gene expression. We confirm TNR stability is induced in iPSCs, and maintained in HD-NSCs. We also identify that upregulation of 5-hmC increases ten-eleven translocation 1 and 2 (TET1/2) protein levels, and show their knockdown leads to a corresponding decrease in the expression of select DNA repair genes. We further confirm decreased expression of TET1/2-regulating miR-29 family members in HD-NSCs. Our findings demonstrate that mechanisms associated with pluripotency induction lead to a recovery in the expression of select DNA repair gene and stabilize pathogenic TNRs in HD.
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Affiliation(s)
- Peter A Mollica
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA.,Molecular Diagnostics Laboratory, Sentara Norfolk General Hospital, Norfolk, VA 23507, USA
| | - Martina Zamponi
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA.,Biomedical Engineering Institute, Old Dominion University, Norfolk, VA 23529, USA
| | - John A Reid
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA.,Biomedical Engineering Institute, Old Dominion University, Norfolk, VA 23529, USA
| | - Deepak K Sharma
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Alyson E White
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Roy C Ogle
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Robert D Bruno
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Patrick C Sachs
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
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16
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McGinty RJ, Mirkin SM. Cis- and Trans-Modifiers of Repeat Expansions: Blending Model Systems with Human Genetics. Trends Genet 2018; 34:448-465. [PMID: 29567336 PMCID: PMC5959756 DOI: 10.1016/j.tig.2018.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby (cis) or physically separated from (trans) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis- and trans-modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients.
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Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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17
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McGinty RJ, Puleo F, Aksenova AY, Hisey JA, Shishkin AA, Pearson EL, Wang ET, Housman DE, Moore C, Mirkin SM. A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAA) n Repeats Associated with Friedreich's Ataxia. Cell Rep 2018; 20:2490-2500. [PMID: 28877480 DOI: 10.1016/j.celrep.2017.08.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/19/2017] [Accepted: 08/15/2017] [Indexed: 02/03/2023] Open
Abstract
Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich's ataxia. Whereas the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here, we describe a method for the rapid, genome-wide identification of trans modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1) of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAA)n repeat expansions but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal an interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach.
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Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02421, USA
| | - Franco Puleo
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Anna Y Aksenova
- Department of Biology, Tufts University, Medford, MA 02421, USA; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Julia A Hisey
- Department of Biology, Tufts University, Medford, MA 02421, USA
| | - Alexander A Shishkin
- Department of Biology, Tufts University, Medford, MA 02421, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Erika L Pearson
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Eric T Wang
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA
| | - David E Housman
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Claire Moore
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
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18
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The Chromatin Remodeler Isw1 Prevents CAG Repeat Expansions During Transcription in Saccharomyces cerevisiae. Genetics 2018; 208:963-976. [PMID: 29305386 PMCID: PMC5844344 DOI: 10.1534/genetics.117.300529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 01/02/2018] [Indexed: 12/23/2022] Open
Abstract
CAG/CTG trinucleotide repeat expansions cause several degenerative neurological and muscular diseases. Koch et al. show that the chromatin remodeling... CAG/CTG trinucleotide repeats are unstable sequences that are difficult to replicate, repair, and transcribe due to their structure-forming nature. CAG repeats strongly position nucleosomes; however, little is known about the chromatin remodeling needed to prevent repeat instability. In a Saccharomyces cerevisiae model system with CAG repeats carried on a YAC, we discovered that the chromatin remodeler Isw1 is required to prevent CAG repeat expansions during transcription. CAG repeat expansions in the absence of Isw1 were dependent on both transcription-coupled repair (TCR) and base-excision repair (BER). Furthermore, isw1∆ mutants are sensitive to methyl methanesulfonate (MMS) and exhibit synergistic MMS sensitivity when combined with BER or TCR pathway mutants. We conclude that CAG expansions in the isw1∆ mutant occur during a transcription-coupled excision repair process that involves both TCR and BER pathways. We observed increased RNA polymerase II (RNAPII) occupancy at the CAG repeat when transcription of the repeat was induced, but RNAPII binding did not change in isw1∆ mutants, ruling out a role for Isw1 remodeling in RNAPII progression. However, nucleosome occupancy over a transcribed CAG tract was altered in isw1∆ mutants. Based on the known role of Isw1 in the reestablishment of nucleosomal spacing after transcription, we suggest that a defect in this function allows DNA structures to form within repetitive DNA tracts, resulting in inappropriate excision repair and repeat-length changes. These results establish a new function for Isw1 in directly maintaining the chromatin structure at the CAG repeat, thereby limiting expansions that can occur during transcription-coupled excision repair.
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19
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Abstract
More than 40 diseases, most of which primarily affect the nervous system, are caused by expansions of simple sequence repeats dispersed throughout the human genome. Expanded trinucleotide repeat diseases were discovered first and remain the most frequent. More recently tetra-, penta-, hexa-, and even dodeca-nucleotide repeat expansions have been identified as the cause of human disease, including some of the most common genetic disorders seen by neurologists. Repeat expansion diseases include both causes of myotonic dystrophy (DM1 and DM2), the most common genetic cause of amyotrophic lateral sclerosis/frontotemporal dementia (C9ORF72), Huntington disease, and eight other polyglutamine disorders, including the most common forms of dominantly inherited ataxia, the most common recessive ataxia (Friedreich ataxia), and the most common heritable mental retardation (fragile X syndrome). Here I review distinctive features of this group of diseases that stem from the unusual, dynamic nature of the underlying mutations. These features include marked clinical heterogeneity and the phenomenon of clinical anticipation. I then discuss the diverse molecular mechanisms driving disease pathogenesis, which vary depending on the repeat sequence, size, and location within the disease gene, and whether the repeat is translated into protein. I conclude with a brief clinical and genetic description of individual repeat expansion diseases that are most relevant to neurologists.
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Affiliation(s)
- Henry Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States.
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20
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Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun 2017; 8:15855. [PMID: 28653660 PMCID: PMC5490271 DOI: 10.1038/ncomms15855] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/05/2017] [Indexed: 12/13/2022] Open
Abstract
DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5′-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5′-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5′polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via ‘phosphate steering’, basic residues energetically steer an inverted ss 5′-flap through a gateway over FEN1’s active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA)n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5′-flap specificity and catalysis, preventing genomic instability. Flap Endonuclease 1 is a DNA replication and repair enzyme indispensable for maintaining genomic stability. Here the authors provide mechanistic details on how FEN1 selects for 5′-flaps and promotes catalysis to avoid large-scale repeat expansion by a process termed ‘phosphate steering’.
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Kraus-Perrotta C, Lagalwar S. Expansion, mosaicism and interruption: mechanisms of the CAG repeat mutation in spinocerebellar ataxia type 1. CEREBELLUM & ATAXIAS 2016; 3:20. [PMID: 27895927 PMCID: PMC5118900 DOI: 10.1186/s40673-016-0058-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/03/2016] [Indexed: 11/12/2022]
Abstract
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder that primarily affects the cerebellum and brainstem. The genetic mutation is an expansion of CAG trinucleotide repeats within the coding region of the ataxin-1 gene, characterizing SCA1 as a polyglutamine expansion disease like Huntington’s. As with most polyglutamine expansion diseases, SCA1 follows the rules of genetic anticipation: the larger the expansion, the earlier and more rapid the symptoms. Unlike the majority of polyglutamine expansion diseases, the presence of histidine interruptions within the polyglutamine tract of ataxin-1 protein can prevent or mitigate disease. The present review aims to synthesize three decades of research on the ataxin-1 polyglutamine expansion mutation that causes SCA1. Data from genetic population studies and case studies is gathered along with data from manipulation studies in animal models. Specifically, we examine the molecular mechanisms that cause tract expansions and contractions, the molecular pathways that confer instability of tract length in gametic and somatic cells resulting in gametic and somatic mosaicism, the influence of maternal or paternal factors in inheritance of the expanded allele, and the effects of CAT/histidine interruptions to the ataxin-1 allele and protein product. Our review of existing data supports the following conclusions. First, polyCAG expansion of gametic alleles occur due to the failure of gap repair mechanisms for single or double strand breaks during the transition from an immature haploid spermatid to a mature haploid sperm cell. Equivalent failures were not detected in female gametic cells. Second, polyCAG expansion of somatic alleles occur due to hairpins formed on Okazaki fragments and slipped strand structures due to failures in mismatch repair and transcription-coupled nucleotide excision repair mechanisms. Third, CAT trinucleotide interruptions, which code for histidines in the translated protein, attenuate the formation of slipped strand structures which may protect the allele from the occurrence of large expansions. Many of the mechanisms of expansion identified in this review differ from those noted in Huntington’s disease indicating that gene -or sequence-specific factors may affect the behavior of the polyCAG/glutamine tract. Therefore, synthesis and review of research from the SCA1 field is valuable for future clinical and diagnostic work in the treatment and prevention of SCA1.
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Affiliation(s)
- Cara Kraus-Perrotta
- Department of Biology, Skidmore College, 815 North Broadway, Saratoga Springs, NY 12866 USA
| | - Sarita Lagalwar
- Neuroscience Program, Skidmore College, 815 North Broadway, Saratoga Springs, NY 12866 USA
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Taniguchi JB, Kondo K, Fujita K, Chen X, Homma H, Sudo T, Mao Y, Watase K, Tanaka T, Tagawa K, Tamura T, Muramatsu SI, Okazawa H. RpA1 ameliorates symptoms of mutant ataxin-1 knock-in mice and enhances DNA damage repair. Hum Mol Genet 2016; 25:4432-4447. [DOI: 10.1093/hmg/ddw272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/08/2016] [Accepted: 08/05/2016] [Indexed: 01/05/2023] Open
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Mollica PA, Reid JA, Ogle RC, Sachs PC, Bruno RD. DNA Methylation Leads to DNA Repair Gene Down-Regulation and Trinucleotide Repeat Expansion in Patient-Derived Huntington Disease Cells. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:1967-1976. [DOI: 10.1016/j.ajpath.2016.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 12/12/2022]
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Bettencourt C, Hensman‐Moss D, Flower M, Wiethoff S, Brice A, Goizet C, Stevanin G, Koutsis G, Karadima G, Panas M, Yescas‐Gómez P, García‐Velázquez LE, Alonso‐Vilatela ME, Lima M, Raposo M, Traynor B, Sweeney M, Wood N, Giunti P, Durr A, Holmans P, Houlden H, Tabrizi SJ, Jones L. DNA repair pathways underlie a common genetic mechanism modulating onset in polyglutamine diseases. Ann Neurol 2016; 79:983-90. [PMID: 27044000 PMCID: PMC4914895 DOI: 10.1002/ana.24656] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The polyglutamine diseases, including Huntington's disease (HD) and multiple spinocerebellar ataxias (SCAs), are among the commonest hereditary neurodegenerative diseases. They are caused by expanded CAG tracts, encoding glutamine, in different genes. Longer CAG repeat tracts are associated with earlier ages at onset, but this does not account for all of the difference, and the existence of additional genetic modifying factors has been suggested in these diseases. A recent genome-wide association study (GWAS) in HD found association between age at onset and genetic variants in DNA repair pathways, and we therefore tested whether the modifying effects of variants in DNA repair genes have wider effects in the polyglutamine diseases. METHODS We assembled an independent cohort of 1,462 subjects with HD and polyglutamine SCAs, and genotyped single-nucleotide polymorphisms (SNPs) selected from the most significant hits in the HD study. RESULTS In the analysis of DNA repair genes as a group, we found the most significant association with age at onset when grouping all polyglutamine diseases (HD+SCAs; p = 1.43 × 10(-5) ). In individual SNP analysis, we found significant associations for rs3512 in FAN1 with HD+SCAs (p = 1.52 × 10(-5) ) and all SCAs (p = 2.22 × 10(-4) ) and rs1805323 in PMS2 with HD+SCAs (p = 3.14 × 10(-5) ), all in the same direction as in the HD GWAS. INTERPRETATION We show that DNA repair genes significantly modify age at onset in HD and SCAs, suggesting a common pathogenic mechanism, which could operate through the observed somatic expansion of repeats that can be modulated by genetic manipulation of DNA repair in disease models. This offers novel therapeutic opportunities in multiple diseases. Ann Neurol 2016;79:983-990.
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Affiliation(s)
- Conceição Bettencourt
- Department of Molecular Neuroscience, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
- Department of Clinical and Experimental Epilepsy, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
| | - Davina Hensman‐Moss
- Department of Neurodegenerative Disease, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
| | - Michael Flower
- Department of Neurodegenerative Disease, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
| | - Sarah Wiethoff
- Department of Molecular Neuroscience, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
- Center for Neurology and Hertie Institute for Clinical Brain ResearchEberhard‐Karls‐UniversityTübingenGermany
| | - Alexis Brice
- Inserm U 1127, CNRS UMR 7225, Sorbonne UniversitésUPMC University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière (ICM)ParisFrance
- APHP, Department of GeneticsUniversity Hospital Pitié‐Salpêtrière75013 ParisFrance
| | - Cyril Goizet
- Université Bordeaux, Laboratoire Maladies Rares: Génétique et MétabolismeINSERM1211BordeauxFrance
- CHU Pellegrin, Service de Génétique Médicale, F‐33000BordeauxFrance
| | - Giovanni Stevanin
- Inserm U 1127, CNRS UMR 7225, Sorbonne UniversitésUPMC University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière (ICM)ParisFrance
- Ecole Pratique des Hautes Etudes75014 ParisFrance
| | - Georgios Koutsis
- Neurogenetics Unit, 1st Department of NeurologyUniversity of Athens Medical School, Eginition Hospital115 28 AthensGreece
| | - Georgia Karadima
- Neurogenetics Unit, 1st Department of NeurologyUniversity of Athens Medical School, Eginition Hospital115 28 AthensGreece
| | - Marios Panas
- Neurogenetics Unit, 1st Department of NeurologyUniversity of Athens Medical School, Eginition Hospital115 28 AthensGreece
| | - Petra Yescas‐Gómez
- Neurogenetics Department, National Institute of Neurology and Neurosurgery“Manuel Velasco Suárez”Mexico City CP14269Mexico
| | | | - María Elisa Alonso‐Vilatela
- Neurogenetics Department, National Institute of Neurology and Neurosurgery“Manuel Velasco Suárez”Mexico City CP14269Mexico
| | - Manuela Lima
- Department of BiologyUniversity of the Azores9500‐321 Ponta DelgadaPortugal
- Instituto de Investigação e Inovação em SaúdeUniversidade do Porto4150‐180 PortoPortugal
- Institute for Molecular and Cell Biology (IBMC)University of Porto4150‐180 PortoPortugal
| | - Mafalda Raposo
- Department of BiologyUniversity of the Azores9500‐321 Ponta DelgadaPortugal
- Instituto de Investigação e Inovação em SaúdeUniversidade do Porto4150‐180 PortoPortugal
- Institute for Molecular and Cell Biology (IBMC)University of Porto4150‐180 PortoPortugal
| | - Bryan Traynor
- Laboratory of Neurogenetics, National Institute of AgingNIHBethesdaMD 20892, USA
| | - Mary Sweeney
- Neurogenetics Unit, National Hospital for Neurology and NeurosurgeryUniversity College London HospitalsLondon WC1N 3BGUnited Kingdom
| | - Nicholas Wood
- Department of Molecular Neuroscience, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
| | - Paola Giunti
- Department of Molecular Neuroscience, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
- Ataxia Center, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
| | | | - Alexandra Durr
- Inserm U 1127, CNRS UMR 7225, Sorbonne UniversitésUPMC University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière (ICM)ParisFrance
- APHP, Department of GeneticsUniversity Hospital Pitié‐Salpêtrière75013 ParisFrance
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffCF24 4HQUnited Kingdom
| | - Henry Houlden
- Department of Molecular Neuroscience, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
- Neurogenetics Unit, National Hospital for Neurology and NeurosurgeryUniversity College London HospitalsLondon WC1N 3BGUnited Kingdom
| | - Sarah J. Tabrizi
- Department of Neurodegenerative Disease, Institute of NeurologyUniversity College LondonLondon WC1N 3BGUnited Kingdom
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical NeurosciencesCardiff UniversityCardiffCF24 4HQUnited Kingdom
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Absence of MutSβ leads to the formation of slipped-DNA for CTG/CAG contractions at primate replication forks. DNA Repair (Amst) 2016; 42:107-18. [PMID: 27155933 DOI: 10.1016/j.dnarep.2016.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/22/2022]
Abstract
Typically disease-causing CAG/CTG repeats expand, but rare affected families can display high levels of contraction of the expanded repeat amongst offspring. Understanding instability is important since arresting expansions or enhancing contractions could be clinically beneficial. The MutSβ mismatch repair complex is required for CAG/CTG expansions in mice and patients. Oddly, by unknown mechanisms MutSβ-deficient mice incur contractions instead of expansions. Replication using CTG or CAG as the lagging strand template is known to cause contractions or expansions respectively; however, the interplay between replication and repair leading to this instability remains unclear. Towards understanding how repeat contractions may arise, we performed in vitro SV40-mediated replication of repeat-containing plasmids in the presence or absence of mismatch repair. Specifically, we separated repair from replication: Replication mediated by MutSβ- and MutSα-deficient human cells or cell extracts produced slipped-DNA heteroduplexes in the contraction- but not expansion-biased replication direction. Replication in the presence of MutSβ disfavoured the retention of replication products harbouring slipped-DNA heteroduplexes. Post-replication repair of slipped-DNAs by MutSβ-proficient extracts eliminated slipped-DNAs. Thus, a MutSβ-deficiency likely enhances repeat contractions because MutSβ protects against contractions by repairing template strand slip-outs. Replication deficient in LigaseI or PCNA-interaction mutant LigaseI revealed slipped-DNA formation at lagging strands. Our results reveal that distinct mechanisms lead to expansions or contractions and support inhibition of MutSβ as a therapeutic strategy to enhance the contraction of expanded repeats.
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The Response to Oxidative DNA Damage in Neurons: Mechanisms and Disease. Neural Plast 2016; 2016:3619274. [PMID: 26942017 PMCID: PMC4752990 DOI: 10.1155/2016/3619274] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/24/2015] [Indexed: 11/26/2022] Open
Abstract
There is a growing body of evidence indicating that the mechanisms that control genome stability are of key importance in the development and function of the nervous system. The major threat for neurons is oxidative DNA damage, which is repaired by the base excision repair (BER) pathway. Functional mutations of enzymes that are involved in the processing of single-strand breaks (SSB) that are generated during BER have been causally associated with syndromes that present important neurological alterations and cognitive decline. In this review, the plasticity of BER during neurogenesis and the importance of an efficient BER for correct brain function will be specifically addressed paying particular attention to the brain region and neuron-selectivity in SSB repair-associated neurological syndromes and age-related neurodegenerative diseases.
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Schmidt MHM, Pearson CE. Disease-associated repeat instability and mismatch repair. DNA Repair (Amst) 2015; 38:117-126. [PMID: 26774442 DOI: 10.1016/j.dnarep.2015.11.008] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 11/23/2015] [Accepted: 11/30/2015] [Indexed: 12/15/2022]
Abstract
Expanded tandem repeat sequences in DNA are associated with at least 40 human genetic neurological, neurodegenerative, and neuromuscular diseases. Repeat expansion can occur during parent-to-offspring transmission, and arise at variable rates in specific tissues throughout the life of an affected individual. Since the ongoing somatic repeat expansions can affect disease age-of-onset, severity, and progression, targeting somatic expansion holds potential as a therapeutic target. Thus, understanding the factors that regulate this mutation is crucial. DNA repair, in particular mismatch repair (MMR), is the major driving force of disease-associated repeat expansions. In contrast to its anti-mutagenic roles, mammalian MMR curiously drives the expansion mutations of disease-associated (CAG)·(CTG) repeats. Recent advances have broadened our knowledge of both the MMR proteins involved in disease repeat expansions, including: MSH2, MSH3, MSH6, MLH1, PMS2, and MLH3, as well as the types of repeats affected by MMR, now including: (CAG)·(CTG), (CGG)·(CCG), and (GAA)·(TTC) repeats. Mutagenic slipped-DNA structures have been detected in patient tissues, and the size of the slip-out and their junction conformation can determine the involvement of MMR. Furthermore, the formation of other unusual DNA and R-loop structures is proposed to play a key role in MMR-mediated instability. A complex correlation is emerging between tissues showing varying amounts of repeat instability and MMR expression levels. Notably, naturally occurring polymorphic variants of DNA repair genes can have dramatic effects upon the levels of repeat instability, which may explain the variation in disease age-of-onset, progression and severity. An increasing grasp of these factors holds prognostic and therapeutic potential.
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Affiliation(s)
- Monika H M Schmidt
- Genetics & Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research & Learning, 686 Bay St., Toronto, Ontario M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Medical Sciences Bldg., 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Christopher E Pearson
- Genetics & Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research & Learning, 686 Bay St., Toronto, Ontario M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Medical Sciences Bldg., 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
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Large expansion of CTG•CAG repeats is exacerbated by MutSβ in human cells. Sci Rep 2015; 5:11020. [PMID: 26047474 PMCID: PMC4457148 DOI: 10.1038/srep11020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/12/2015] [Indexed: 11/08/2022] Open
Abstract
Trinucleotide repeat expansion disorders (TRED) are caused by genomic expansions of trinucleotide repeats, such as CTG and CAG. These expanded repeats are unstable in germline and somatic cells, with potential consequences for disease severity. Previous studies have demonstrated the involvement of DNA repair proteins in repeat instability, although the key factors affecting large repeat expansion and contraction are unclear. Here we investigated these factors in a human cell model harboring 800 CTG•CAG repeats by individually knocking down various DNA repair proteins using short interfering RNA. Knockdown of MSH2 and MSH3, which form the MutSβ heterodimer and function in mismatch repair, suppressed large repeat expansions, whereas knockdown of MSH6, which forms the MutSα heterodimer with MSH2, promoted large expansions exceeding 200 repeats by compensatory increases in MSH3 and the MutSβ complex. Knockdown of topoisomerase 1 (TOP1) and TDP1, which are involved in single-strand break repair, enhanced large repeat contractions. Furthermore, knockdown of senataxin, an RNA/DNA helicase which affects DNA:RNA hybrid formation and transcription-coupled nucleotide excision repair, exacerbated repeat instability in both directions. These results indicate that DNA repair factors, such as MutSβ play important roles in large repeat expansion and contraction, and can be an excellent therapeutic target for TRED.
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Abstract
DNA repair normally protects the genome against mutations that threaten genome integrity and thus cell viability. However, growing evidence suggests that in the case of the Repeat Expansion Diseases, disorders that result from an increase in the size of a disease-specific microsatellite, the disease-causing mutation is actually the result of aberrant DNA repair. A variety of proteins from different DNA repair pathways have thus far been implicated in this process. This review will summarize recent findings from patients and from mouse models of these diseases that shed light on how these pathways may interact to cause repeat expansion.
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Affiliation(s)
- Xiao-Nan Zhao
- Section on Genomic Structure and Function Laboratory of Cell and Molecular Biology National Institute of Diabetes, Digestive and Kidney Diseases National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Karen Usdin
- Section on Genomic Structure and Function Laboratory of Cell and Molecular Biology National Institute of Diabetes, Digestive and Kidney Diseases National Institutes of Health, Bethesda, MD 20892-0830, USA.
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Lokanga RA, Senejani AG, Sweasy JB, Usdin K. Heterozygosity for a hypomorphic Polβ mutation reduces the expansion frequency in a mouse model of the Fragile X-related disorders. PLoS Genet 2015; 11:e1005181. [PMID: 25886163 PMCID: PMC4401650 DOI: 10.1371/journal.pgen.1005181] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/27/2015] [Indexed: 11/19/2022] Open
Abstract
The Fragile X-related disorders (FXDs) are members of the Repeat Expansion Diseases, a group of human genetic conditions resulting from expansion of a specific tandem repeat. The FXDs result from expansion of a CGG/CCG repeat tract in the 5’ UTR of the FMR1 gene. While expansion in a FXD mouse model is known to require some mismatch repair (MMR) proteins, our previous work and work in mouse models of another Repeat Expansion Disease show that early events in the base excision repair (BER) pathway play a role in the expansion process. One model for repeat expansion proposes that a non-canonical MMR process makes use of the nicks generated early in BER to load the MMR machinery that then generates expansions. However, we show here that heterozygosity for a Y265C mutation in Polβ, a key polymerase in the BER pathway, is enough to significantly reduce both the number of expansions seen in paternal gametes and the extent of somatic expansion in some tissues of the FXD mouse. These data suggest that events in the BER pathway downstream of the generation of nicks are also important for repeat expansion. Somewhat surprisingly, while the number of expansions is smaller, the average size of the residual expansions is larger than that seen in WT animals. This may have interesting implications for the mechanism by which BER generates expansions. Unstable microsatellites are responsible for a number of debilitating human diseases known as the Repeat Expansion Diseases. The unstable microsatellites, which consist of tandem arrays of short repeat units, are prone to increase in length (expand) on intergenerational transmission and during the lifetime of the individual. Unlike the typical microsatellite instability seen in disorders like Lynch syndrome that arise from mutations in mismatch repair (MMR) genes, expansions of these microsatellites are abolished when MMR is lost. However, how MMR, which normally protects the genome against microsatellite instability, actually promotes microsatellite expansions in these diseases is unknown. There is evidence to suggest that a second DNA repair process, base excision repair (BER), may be involved, but whether the nicks generated early in the BER-process are subverted by an MMR-dependent pathway that generates expansions or whether some MMR proteins contribute to a BER-based expansion process is unclear. Here we show that a mutation that reduces the activity of Polβ, an essential BER enzyme, also reduces the expansion frequency. Since Polβ is essential for key events in BER downstream of the generation of nicks, our data favor a model in which expansions occur via a BER-dependent pathway in which MMR participates.
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Affiliation(s)
- Rachel Adihe Lokanga
- Section on Gene Structure and Disease, Laboratory of Cell and molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biochemistry, University of Cape Town Medical School, Cape Town, South Africa
| | - Alireza Ghodsi Senejani
- Departments of Therapeutic Radiology and Human Genetics, Yale University, School of Medicine, New Haven, Connecticut, United States of America
| | - Joann Balazs Sweasy
- Departments of Therapeutic Radiology and Human Genetics, Yale University, School of Medicine, New Haven, Connecticut, United States of America
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Age-, tissue- and length-dependent bidirectional somatic CAG•CTG repeat instability in an allelic series of R6/2 Huntington disease mice. Neurobiol Dis 2015; 76:98-111. [PMID: 25662336 DOI: 10.1016/j.nbd.2015.01.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/30/2014] [Accepted: 01/25/2015] [Indexed: 12/11/2022] Open
Abstract
The expansion of simple sequence CAG•CTG repeats is associated with a number of inherited disorders including Huntington disease (HD), myotonic dystrophy type 1 and several of the spinocerebellar ataxias. Inherited disease-associated alleles usually exceed 40 repeats and may be in excess of 1,000 repeats in some disorders. Inherited allele length is inversely proportional to age at onset, and frequent germline expansions account for the striking anticipation observed in affected families. Expanded disease associated alleles are also somatically unstable via a pathway that is age dependent and tissue specific, and also appears to be expansion biased. Somatic expansions are thought to contribute toward both tissue specificity and disease progression. Here we have examined the somatic mutational dynamics in brain and peripheral tissues from an allelic series of R6/2 HD transgenic mice inheriting from 52 to >700 CAG repeats. We found age-dependent, tissue-specific somatic instability, with particularly large expansions observed in the striatum and cortex. We also found a positive increase in somatic instability with increasing allele length. Surprisingly, however, the degree of somatic variation did not increase in a linear fashion, but leveled off with increasing allele length. Most unexpectedly, the almost exclusive bias toward the accumulation of expansions observed in mice inheriting smaller alleles was lost, and a high frequency of large somatic contractions was observed in mice inheriting very large alleles (>500 repeats). These data highlight the bidirectional nature of CAG•CTG repeat instability and the subtle balance that exists between expansion and contraction in vivo. Defining the dynamics and tissue specificity of expansion and contraction is important for understanding the role of genetic instability in pathophysiology and in particular the development of novel therapies based on suppressing expansions and/or promoting contractions.
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Usdin K, House NCM, Freudenreich CH. Repeat instability during DNA repair: Insights from model systems. Crit Rev Biochem Mol Biol 2015; 50:142-67. [PMID: 25608779 DOI: 10.3109/10409238.2014.999192] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them.
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Affiliation(s)
- Karen Usdin
- Laboratory of Cell and Molecular Biology, NIDDK, NIH , Bethesda, MD , USA
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Chatterjee A, Saha S, Chakraborty A, Silva-Fernandes A, Mandal SM, Neves-Carvalho A, Liu Y, Pandita RK, Hegde ML, Hegde PM, Boldogh I, Ashizawa T, Koeppen AH, Pandita TK, Maciel P, Sarkar PS, Hazra TK. The role of the mammalian DNA end-processing enzyme polynucleotide kinase 3'-phosphatase in spinocerebellar ataxia type 3 pathogenesis. PLoS Genet 2015; 11:e1004749. [PMID: 25633985 PMCID: PMC4310589 DOI: 10.1371/journal.pgen.1004749] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 09/11/2014] [Indexed: 01/09/2023] Open
Abstract
DNA strand-breaks (SBs) with non-ligatable ends are generated by ionizing radiation, oxidative stress, various chemotherapeutic agents, and also as base excision repair (BER) intermediates. Several neurological diseases have already been identified as being due to a deficiency in DNA end-processing activities. Two common dirty ends, 3'-P and 5'-OH, are processed by mammalian polynucleotide kinase 3'-phosphatase (PNKP), a bifunctional enzyme with 3'-phosphatase and 5'-kinase activities. We have made the unexpected observation that PNKP stably associates with Ataxin-3 (ATXN3), a polyglutamine repeat-containing protein mutated in spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph Disease (MJD). This disease is one of the most common dominantly inherited ataxias worldwide; the defect in SCA3 is due to CAG repeat expansion (from the normal 14-41 to 55-82 repeats) in the ATXN3 coding region. However, how the expanded form gains its toxic function is still not clearly understood. Here we report that purified wild-type (WT) ATXN3 stimulates, and by contrast the mutant form specifically inhibits, PNKP's 3' phosphatase activity in vitro. ATXN3-deficient cells also show decreased PNKP activity. Furthermore, transgenic mice conditionally expressing the pathological form of human ATXN3 also showed decreased 3'-phosphatase activity of PNKP, mostly in the deep cerebellar nuclei, one of the most affected regions in MJD patients' brain. Finally, long amplicon quantitative PCR analysis of human MJD patients' brain samples showed a significant accumulation of DNA strand breaks. Our results thus indicate that the accumulation of DNA strand breaks due to functional deficiency of PNKP is etiologically linked to the pathogenesis of SCA3/MJD.
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Affiliation(s)
- Arpita Chatterjee
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Saikat Saha
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Anabela Silva-Fernandes
- School of Health Sciences, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Santi M. Mandal
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Andreia Neves-Carvalho
- School of Health Sciences, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Yongping Liu
- Department of Neurology and Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Raj K. Pandita
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Muralidhar L. Hegde
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas, United States of America
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pavana M. Hegde
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas, United States of America
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Istvan Boldogh
- Department of Microbiology & Immunology; University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology, University of Florida, Gainesville, Florida, United States of America
| | - Arnulf H. Koeppen
- Department of Neurology, Albany Stratton VA Medical Center, Albany, New York, United States of America
| | - Tej K. Pandita
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Patricia Maciel
- School of Health Sciences, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Partha S. Sarkar
- Department of Neurology and Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
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Gao R, Liu Y, Silva-Fernandes A, Fang X, Paulucci-Holthauzen A, Chatterjee A, Zhang HL, Matsuura T, Choudhary S, Ashizawa T, Koeppen AH, Maciel P, Hazra TK, Sarkar PS. Inactivation of PNKP by mutant ATXN3 triggers apoptosis by activating the DNA damage-response pathway in SCA3. PLoS Genet 2015; 11:e1004834. [PMID: 25590633 PMCID: PMC4295939 DOI: 10.1371/journal.pgen.1004834] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 10/16/2014] [Indexed: 12/30/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease (MJD), is an untreatable autosomal dominant neurodegenerative disease, and the most common such inherited ataxia worldwide. The mutation in SCA3 is the expansion of a polymorphic CAG tri-nucleotide repeat sequence in the C-terminal coding region of the ATXN3 gene at chromosomal locus 14q32.1. The mutant ATXN3 protein encoding expanded glutamine (polyQ) sequences interacts with multiple proteins in vivo, and is deposited as aggregates in the SCA3 brain. A large body of literature suggests that the loss of function of the native ATNX3-interacting proteins that are deposited in the polyQ aggregates contributes to cellular toxicity, systemic neurodegeneration and the pathogenic mechanism in SCA3. Nonetheless, a significant understanding of the disease etiology of SCA3, the molecular mechanism by which the polyQ expansions in the mutant ATXN3 induce neurodegeneration in SCA3 has remained elusive. In the present study, we show that the essential DNA strand break repair enzyme PNKP (polynucleotide kinase 3'-phosphatase) interacts with, and is inactivated by, the mutant ATXN3, resulting in inefficient DNA repair, persistent accumulation of DNA damage/strand breaks, and subsequent chronic activation of the DNA damage-response ataxia telangiectasia-mutated (ATM) signaling pathway in SCA3. We report that persistent accumulation of DNA damage/strand breaks and chronic activation of the serine/threonine kinase ATM and the downstream p53 and protein kinase C-δ pro-apoptotic pathways trigger neuronal dysfunction and eventually neuronal death in SCA3. Either PNKP overexpression or pharmacological inhibition of ATM dramatically blocked mutant ATXN3-mediated cell death. Discovery of the mechanism by which mutant ATXN3 induces DNA damage and amplifies the pro-death signaling pathways provides a molecular basis for neurodegeneration due to PNKP inactivation in SCA3, and for the first time offers a possible approach to treatment.
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Affiliation(s)
- Rui Gao
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yongping Liu
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Anabela Silva-Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s PT Government Associate Laboratory, Braga/Guimarặes, Portugal
| | - Xiang Fang
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Adriana Paulucci-Holthauzen
- Department of Biomedical Engineering, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Arpita Chatterjee
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Hang L. Zhang
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tohru Matsuura
- Department of Neurology, Jichi Medical School, Shimotsuke, Japan
| | - Sanjeev Choudhary
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology and McNight Brain Research Institute, University of Florida, Gainesville, Florida, United States of America
| | - Arnulf H. Koeppen
- Department of Neurology, Albany Stratton VA Medical Center, Albany, New York, United States of America
| | - Patricia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s PT Government Associate Laboratory, Braga/Guimarặes, Portugal
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Partha S. Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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36
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Modifiers of (CAG)n instability in Machado–Joseph disease (MJD/SCA3) transmissions: an association study with DNA replication, repair and recombination genes. Hum Genet 2014; 133:1311-8. [DOI: 10.1007/s00439-014-1467-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/03/2014] [Indexed: 12/24/2022]
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Dion V. Tissue specificity in DNA repair: lessons from trinucleotide repeat instability. Trends Genet 2014; 30:220-9. [PMID: 24842550 DOI: 10.1016/j.tig.2014.04.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/14/2014] [Accepted: 04/16/2014] [Indexed: 12/13/2022]
Abstract
DNA must constantly be repaired to maintain genome stability. Although it is clear that DNA repair reactions depend on cell type and developmental stage, we know surprisingly little about the mechanisms that underlie this tissue specificity. This is due, in part, to the lack of adequate study systems. This review discusses recent progress toward understanding the mechanism leading to varying rates of instability at expanded trinucleotide repeats (TNRs) in different tissues. Although they are not DNA lesions, TNRs are hotspots for genome instability because normal DNA repair activities cause changes in repeat length. The rates of expansions and contractions are readily detectable and depend on cell identity, making TNR instability a particularly convenient model system. A better understanding of this type of genome instability will provide a foundation for studying tissue-specific DNA repair more generally, which has implications in cancer and other diseases caused by mutations in the caretakers of the genome.
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Affiliation(s)
- Vincent Dion
- University of Lausanne, Center for Integrative Genomics, Bâtiment Génopode, 1015 Lausanne, Switzerland.
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Valor LM. Transcription, epigenetics and ameliorative strategies in Huntington's Disease: a genome-wide perspective. Mol Neurobiol 2014; 51:406-23. [PMID: 24788684 PMCID: PMC4309905 DOI: 10.1007/s12035-014-8715-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/11/2014] [Indexed: 12/18/2022]
Abstract
Transcriptional dysregulation in Huntington’s disease (HD) is an early event that shapes the brain transcriptome by both the depletion and ectopic activation of gene products that eventually affect survival and neuronal functions. Disruption in the activity of gene expression regulators, such as transcription factors, chromatin-remodeling proteins, and noncoding RNAs, accounts for the expression changes observed in multiple animal and cellular models of HD and in samples from patients. Here, I review the recent advances in the study of HD transcriptional dysregulation and its causes to finally discuss the possible implications in ameliorative strategies from a genome-wide perspective. To date, the use of genome-wide approaches, predominantly based on microarray platforms, has been successful in providing an extensive catalog of differentially regulated genes, including biomarkers aimed at monitoring the progress of the pathology. Although still incipient, the introduction of combined next-generation sequencing techniques is enhancing our comprehension of the mechanisms underlying altered transcriptional dysregulation in HD by providing the first genomic landscapes associated with epigenetics and the occupancy of transcription factors. In addition, the use of genome-wide approaches is becoming more and more necessary to evaluate the efficacy and safety of ameliorative strategies and to identify novel mechanisms of amelioration that may help in the improvement of current preclinical therapeutics. Finally, the major conclusions obtained from HD transcriptomics studies have the potential to be extrapolated to other neurodegenerative disorders.
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Affiliation(s)
- Luis M Valor
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550, Alicante, Spain,
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