1
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Kojak N, Kuno J, Fittipaldi KE, Khan A, Wenger D, Glasser M, Donnianni RA, Tang Y, Zhang J, Huling K, Ally R, Mujica AO, Turner T, Magardino G, Huang PY, Kerk SY, Droguett G, Prissette M, Rojas J, Gomez T, Gagliardi A, Hunt C, Rabinowitz JS, Gong G, Poueymirou W, Chiao E, Zambrowicz B, Siao CJ, Kajimura D. Somatic and intergenerational G4C2 hexanucleotide repeat instability in a human C9orf72 knock-in mouse model. Nucleic Acids Res 2024; 52:5732-5755. [PMID: 38597682 PMCID: PMC11162798 DOI: 10.1093/nar/gkae250] [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: 06/12/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
Expansion of a G4C2 repeat in the C9orf72 gene is associated with familial Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). To investigate the underlying mechanisms of repeat instability, which occurs both somatically and intergenerationally, we created a novel mouse model of familial ALS/FTD that harbors 96 copies of G4C2 repeats at a humanized C9orf72 locus. In mouse embryonic stem cells, we observed two modes of repeat expansion. First, we noted minor increases in repeat length per expansion event, which was dependent on a mismatch repair pathway protein Msh2. Second, we found major increases in repeat length per event when a DNA double- or single-strand break (DSB/SSB) was artificially introduced proximal to the repeats, and which was dependent on the homology-directed repair (HDR) pathway. In mice, the first mode primarily drove somatic repeat expansion. Major changes in repeat length, including expansion, were observed when SSB was introduced in one-cell embryos, or intergenerationally without DSB/SSB introduction if G4C2 repeats exceeded 400 copies, although spontaneous HDR-mediated expansion has yet to be identified. These findings provide a novel strategy to model repeat expansion in a non-human genome and offer insights into the mechanism behind C9orf72 G4C2 repeat instability.
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Affiliation(s)
- Nada Kojak
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Junko Kuno
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - David Wenger
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Yajun Tang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Jade Zhang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Katie Huling
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Roxanne Ally
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | - Pei Yi Huang
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Sze Yen Kerk
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | - Jose Rojas
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | - Guochun Gong
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | - Eric Chiao
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
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2
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Ferguson R, Goold R, Coupland L, Flower M, Tabrizi SJ. Therapeutic validation of MMR-associated genetic modifiers in a human ex vivo model of Huntington disease. Am J Hum Genet 2024; 111:1165-1183. [PMID: 38749429 PMCID: PMC11179424 DOI: 10.1016/j.ajhg.2024.04.015] [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: 11/30/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 06/09/2024] Open
Abstract
The pathological huntingtin (HTT) trinucleotide repeat underlying Huntington disease (HD) continues to expand throughout life. Repeat length correlates both with earlier age at onset (AaO) and faster progression, making slowing its expansion an attractive therapeutic approach. Genome-wide association studies have identified candidate variants associated with altered AaO and progression, with many found in DNA mismatch repair (MMR)-associated genes. We examine whether lowering expression of these genes affects the rate of repeat expansion in human ex vivo models using HD iPSCs and HD iPSC-derived striatal medium spiny neuron-enriched cultures. We have generated a stable CRISPR interference HD iPSC line in which we can specifically and efficiently lower gene expression from a donor carrying over 125 CAG repeats. Lowering expression of each member of the MMR complexes MutS (MSH2, MSH3, and MSH6), MutL (MLH1, PMS1, PMS2, and MLH3), and LIG1 resulted in characteristic MMR deficiencies. Reduced MSH2, MSH3, and MLH1 slowed repeat expansion to the largest degree, while lowering either PMS1, PMS2, or MLH3 slowed it to a lesser degree. These effects were recapitulated in iPSC-derived striatal cultures where MutL factor expression was lowered. CRISPRi-mediated lowering of key MMR factor expression to levels feasibly achievable by current therapeutic approaches was able to effectively slow the expansion of the HTT CAG tract. We highlight members of the MutL family as potential targets to slow pathogenic repeat expansion with the aim to delay onset and progression of HD and potentially other repeat expansion disorders exhibiting somatic instability.
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Affiliation(s)
- Ross Ferguson
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Robert Goold
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Lucy Coupland
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Michael Flower
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Sarah J Tabrizi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK.
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3
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Rajagopal S, Donaldson J, Flower M, Hensman Moss DJ, Tabrizi SJ. Genetic modifiers of repeat expansion disorders. Emerg Top Life Sci 2023; 7:325-337. [PMID: 37861103 PMCID: PMC10754329 DOI: 10.1042/etls20230015] [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: 05/19/2023] [Revised: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Repeat expansion disorders (REDs) are monogenic diseases caused by a sequence of repetitive DNA expanding above a pathogenic threshold. A common feature of the REDs is a strong genotype-phenotype correlation in which a major determinant of age at onset (AAO) and disease progression is the length of the inherited repeat tract. Over a disease-gene carrier's life, the length of the repeat can expand in somatic cells, through the process of somatic expansion which is hypothesised to drive disease progression. Despite being monogenic, individual REDs are phenotypically variable, and exploring what genetic modifying factors drive this phenotypic variability has illuminated key pathogenic mechanisms that are common to this group of diseases. Disease phenotypes are affected by the cognate gene in which the expansion is found, the location of the repeat sequence in coding or non-coding regions and by the presence of repeat sequence interruptions. Human genetic data, mouse models and in vitro models have implicated the disease-modifying effect of DNA repair pathways via the mechanisms of somatic mutation of the repeat tract. As such, developing an understanding of these pathways in the context of expanded repeats could lead to future disease-modifying therapies for REDs.
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Affiliation(s)
- Sangeerthana Rajagopal
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Jasmine Donaldson
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Michael Flower
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Davina J Hensman Moss
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
- St George's University of London, London SW17 0RE, U.K
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
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4
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Masnovo C, Lobo AF, Mirkin SM. Replication dependent and independent mechanisms of GAA repeat instability. DNA Repair (Amst) 2022; 118:103385. [PMID: 35952488 PMCID: PMC9675320 DOI: 10.1016/j.dnarep.2022.103385] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 11/20/2022]
Abstract
Trinucleotide repeat instability is a driver of human disease. Large expansions of (GAA)n repeats in the first intron of the FXN gene are the cause Friedreich's ataxia (FRDA), a progressive degenerative disorder which cannot yet be prevented or treated. (GAA)n repeat instability arises during both replication-dependent processes, such as cell division and intergenerational transmission, as well as in terminally differentiated somatic tissues. Here, we provide a brief historical overview on the discovery of (GAA)n repeat expansions and their association to FRDA, followed by recent advances in the identification of triplex H-DNA formation and replication fork stalling. The main body of this review focuses on the last decade of progress in understanding the mechanism of (GAA)n repeat instability during DNA replication and/or DNA repair. We propose that the discovery of additional mechanisms of (GAA)n repeat instability can be achieved via both comparative approaches to other repeat expansion diseases and genome-wide association studies. Finally, we discuss the advances towards FRDA prevention or amelioration that specifically target (GAA)n repeat expansions.
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Affiliation(s)
- Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Ayesha F Lobo
- 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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5
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Wipf P, Polyzos AA, McMurray CT. A Double-Pronged Sword: XJB-5-131 Is a Suppressor of Somatic Instability and Toxicity in Huntington's Disease. J Huntingtons Dis 2022; 11:3-15. [PMID: 34924397 PMCID: PMC9028625 DOI: 10.3233/jhd-210510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Due to large increases in the elderly populations across the world, age-related diseases are expected to expand dramatically in the coming years. Among these, neurodegenerative diseases will be among the most devastating in terms of their emotional and economic impact on patients, their families, and associated subsidized health costs. There is no currently available cure or rescue for dying brain cells. Viable therapeutics for any of these disorders would be a breakthrough and provide relief for the large number of affected patients and their families. Neurodegeneration is accompanied by elevated oxidative damage and inflammation. While natural antioxidants have largely failed in clinical trials, preclinical phenotyping of the unnatural, mitochondrial targeted nitroxide, XJB-5-131, bodes well for further translational development in advanced animal models or in humans. Here we consider the usefulness of synthetic antioxidants for the treatment of Huntington's disease. The mitochondrial targeting properties of XJB-5-131 have great promise. It is both an electron scavenger and an antioxidant, reducing both somatic expansion and toxicity simultaneously through the same redox mechanism. By quenching reactive oxygen species, XJB-5-131 breaks the cycle between the rise in oxidative damage during disease progression and the somatic growth of the CAG repeat which depends on oxidation.
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Affiliation(s)
- Pater Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aris A. Polyzos
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cynthia T. McMurray
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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6
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Roy JCL, Vitalo A, Andrew MA, Mota-Silva E, Kovalenko M, Burch Z, Nhu AM, Cohen PE, Grabczyk E, Wheeler VC, Mouro Pinto R. Somatic CAG expansion in Huntington's disease is dependent on the MLH3 endonuclease domain, which can be excluded via splice redirection. Nucleic Acids Res 2021; 49:3907-3918. [PMID: 33751106 PMCID: PMC8053082 DOI: 10.1093/nar/gkab152] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 11/18/2022] Open
Abstract
Somatic expansion of the CAG repeat tract that causes Huntington's disease (HD) is thought to contribute to the rate of disease pathogenesis. Therefore, factors influencing repeat expansion are potential therapeutic targets. Genes in the DNA mismatch repair pathway are critical drivers of somatic expansion in HD mouse models. Here, we have tested, using genetic and pharmacological approaches, the role of the endonuclease domain of the mismatch repair protein MLH3 in somatic CAG expansion in HD mice and patient cells. A point mutation in the MLH3 endonuclease domain completely eliminated CAG expansion in the brain and peripheral tissues of a HD knock-in mouse model (HttQ111). To test whether the MLH3 endonuclease could be manipulated pharmacologically, we delivered splice switching oligonucleotides in mice to redirect Mlh3 splicing to exclude the endonuclease domain. Splice redirection to an isoform lacking the endonuclease domain was associated with reduced CAG expansion. Finally, CAG expansion in HD patient-derived primary fibroblasts was also significantly reduced by redirecting MLH3 splicing to the endogenous endonuclease domain-lacking isoform. These data indicate the potential of targeting the MLH3 endonuclease domain to slow somatic CAG repeat expansion in HD, a therapeutic strategy that may be applicable across multiple repeat expansion disorders.
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Affiliation(s)
- Jennie C L Roy
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Antonia Vitalo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Marissa A Andrew
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eduarda Mota-Silva
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marina Kovalenko
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zoe Burch
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anh M Nhu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.,Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA
| | - Ed Grabczyk
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Vanessa C Wheeler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Ricardo Mouro Pinto
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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7
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A Variation in FGF14 Is Associated with Downbeat Nystagmus in a Genome-Wide Association Study. THE CEREBELLUM 2021; 19:348-357. [PMID: 32157568 PMCID: PMC7198638 DOI: 10.1007/s12311-020-01113-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Downbeat nystagmus (DBN) is a frequent form of acquired persisting central fixation nystagmus, often associated with other cerebellar ocular signs, such as saccadic smooth pursuit or gaze-holding deficits. Despite its distinct clinical features, the underlying etiology of DBN often remains unclear. Therefore, a genome-wide association study (GWAS) was conducted in 106 patients and 2609 healthy controls of European ancestry to identify genetic variants associated with DBN. A genome-wide significant association (p < 5 × 10-8) with DBN was found for a variation on chromosome 13 located within the fibroblast growth factor 14 gene (FGF14). FGF14 is expressed in Purkinje cells (PCs) and a reduction leads to a decreased spontaneous firing rate and excitability of PCs, compatible with the pathophysiology of DBN. In addition, mutations in the FGF14 gene cause spinocerebellar ataxia type 27. Suggestive associations (p < 1 × 10-05) could be detected for 15 additional LD-independent loci, one of which is also located in the FGF14 gene. An association of a region containing the dihydrofolate reductase (DHFR) and MutS Homolog 3 (MSH3) genes on chromosome 5 was slightly below the genome-wide significance threshold. DHFR is relevant for neuronal regulation, and a dysfunction is known to induce cerebellar damage. Among the remaining twelve suggestive associations, four genes (MAST4, TPPP, FTMT, and IDS) seem to be involved in cerebral pathological processes. Thus, this GWAS analysis has identified a potential genetic contribution to idiopathic DBN, including suggestive associations to several genes involved in postulated pathological mechanisms of DBN (i.e., impaired function of cerebellar PCs).
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8
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Zhao X, Kumari D, Miller CJ, Kim GY, Hayward B, Vitalo AG, Pinto RM, Usdin K. Modifiers of Somatic Repeat Instability in Mouse Models of Friedreich Ataxia and the Fragile X-Related Disorders: Implications for the Mechanism of Somatic Expansion in Huntington's Disease. J Huntingtons Dis 2021; 10:149-163. [PMID: 33579860 PMCID: PMC7990428 DOI: 10.3233/jhd-200423] [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: 12/18/2022]
Abstract
Huntington's disease (HD) is one of a large group of human disorders that are caused by expanded DNA repeats. These repeat expansion disorders can have repeat units of different size and sequence that can be located in any part of the gene and, while the pathological consequences of the expansion can differ widely, there is evidence to suggest that the underlying mutational mechanism may be similar. In the case of HD, the expanded repeat unit is a CAG trinucleotide located in exon 1 of the huntingtin (HTT) gene, resulting in an expanded polyglutamine tract in the huntingtin protein. Expansion results in neuronal cell death, particularly in the striatum. Emerging evidence suggests that somatic CAG expansion, specifically expansion occurring in the brain during the lifetime of an individual, contributes to an earlier disease onset and increased severity. In this review we will discuss mouse models of two non-CAG repeat expansion diseases, specifically the Fragile X-related disorders (FXDs) and Friedreich ataxia (FRDA). We will compare and contrast these models with mouse and patient-derived cell models of various other repeat expansion disorders and the relevance of these findings for somatic expansion in HD. We will also describe additional genetic factors and pathways that modify somatic expansion in the FXD mouse model for which no comparable data yet exists in HD mice or humans. These additional factors expand the potential druggable space for diseases like HD where somatic expansion is a significant contributor to disease impact.
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Affiliation(s)
- Xiaonan Zhao
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daman Kumari
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carson J Miller
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Geum-Yi Kim
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bruce Hayward
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Antonia G Vitalo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ricardo Mouro Pinto
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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9
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Monckton DG. The Contribution of Somatic Expansion of the CAG Repeat to Symptomatic Development in Huntington's Disease: A Historical Perspective. J Huntingtons Dis 2021; 10:7-33. [PMID: 33579863 PMCID: PMC7990401 DOI: 10.3233/jhd-200429] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery in the early 1990s of the expansion of unstable simple sequence repeats as the causative mutation for a number of inherited human disorders, including Huntington's disease (HD), opened up a new era of human genetics and provided explanations for some old problems. In particular, an inverse association between the number of repeats inherited and age at onset, and unprecedented levels of germline instability, biased toward further expansion, provided an explanation for the wide symptomatic variability and anticipation observed in HD and many of these disorders. The repeats were also revealed to be somatically unstable in a process that is expansion-biased, age-dependent and tissue-specific, features that are now increasingly recognised as contributory to the age-dependence, progressive nature and tissue specificity of the symptoms of HD, and at least some related disorders. With much of the data deriving from affected individuals, and model systems, somatic expansions have been revealed to arise in a cell division-independent manner in critical target tissues via a mechanism involving key components of the DNA mismatch repair pathway. These insights have opened new approaches to thinking about how the disease could be treated by suppressing somatic expansion and revealed novel protein targets for intervention. Exciting times lie ahead in turning these insights into novel therapies for HD and related disorders.
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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, UK
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10
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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: 160] [Impact Index Per Article: 40.0] [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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11
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Large-scale contractions of Friedreich's ataxia GAA repeats in yeast occur during DNA replication due to their triplex-forming ability. Proc Natl Acad Sci U S A 2020; 117:1628-1637. [PMID: 31911468 PMCID: PMC6983365 DOI: 10.1073/pnas.1913416117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Expansions of GAA repeats cause a severe hereditary neurodegenerative disease, Friedreich’s ataxia. In this study, we characterized the mechanisms of GAA repeat contractions in a yeast experimental system. These mechanisms might, in the long run, aid development of a therapy for this currently incurable disease. We show that GAA repeats contract during DNA replication, which can explain the high level of somatic instability of this repeat in patient tissues. We also provided evidence that a triple-stranded DNA structure is at the heart of GAA repeat instability. This discovery highlights the role of triplex DNA in genome instability and human disease. Friedreich’s ataxia (FRDA) is a human hereditary disease caused by the presence of expanded (GAA)n repeats in the first intron of the FXN gene [V. Campuzano et al., Science 271, 1423–1427 (1996)]. In somatic tissues of FRDA patients, (GAA)n repeat tracts are highly unstable, with contractions more common than expansions [R. Sharma et al., Hum. Mol. Genet. 11, 2175–2187 (2002)]. Here we describe an experimental system to characterize GAA repeat contractions in yeast and to conduct a genetic analysis of this process. We found that large-scale contraction is a one-step process, resulting in a median loss of ∼60 triplet repeats. Our genetic analysis revealed that contractions occur during DNA replication, rather than by various DNA repair pathways. Repeats contract in the course of lagging-strand synthesis: The processivity subunit of DNA polymerase δ, Pol32, and the catalytic domain of Rev1, a translesion polymerase, act together in the same pathway to counteract contractions. Accumulation of single-stranded DNA (ssDNA) in the lagging-strand template greatly increases the probability that (GAA)n repeats contract, which in turn promotes repeat instability in rfa1, rad27, and dna2 mutants. Finally, by comparing contraction rates for homopurine-homopyrimidine repeats differing in their mirror symmetry, we found that contractions depend on a repeat’s triplex-forming ability. We propose that accumulation of ssDNA in the lagging-strand template fosters the formation of a triplex between the nascent and fold-back template strands of the repeat. Occasional jumps of DNA polymerase through this triplex hurdle, result in repeat contractions in the nascent lagging strand.
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12
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13
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Guo J, Chen L, Li GM. DNA mismatch repair in trinucleotide repeat instability. SCIENCE CHINA. LIFE SCIENCES 2017; 60:1087-1092. [PMID: 29075942 DOI: 10.1007/s11427-017-9186-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 09/30/2017] [Indexed: 11/29/2022]
Abstract
Trinucleotide repeat expansions cause over 30 severe neuromuscular and neurodegenerative disorders, including Huntington's disease, myotonic dystrophy type 1, and fragile X syndrome. Although previous studies have substantially advanced the understanding of the disease biology, many key features remain unknown. DNA mismatch repair (MMR) plays a critical role in genome maintenance by removing DNA mismatches generated during DNA replication. However, MMR components, particularly mismatch recognition protein MutSβ and its interacting factors MutLα and MutLγ, have been implicated in trinucleotide repeat instability. In this review, we will discuss the roles of these key MMR proteins in promoting trinucleotide repeat instability.
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Affiliation(s)
- Jinzhen Guo
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Luping Chen
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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Polyzos AA, McMurray CT. Close encounters: Moving along bumps, breaks, and bubbles on expanded trinucleotide tracts. DNA Repair (Amst) 2017; 56:144-155. [PMID: 28690053 PMCID: PMC5558859 DOI: 10.1016/j.dnarep.2017.06.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Expansion of simple triplet repeats (TNR) underlies more than 30 severe degenerative diseases. There is a good understanding of the major pathways generating an expansion, and the associated polymerases that operate during gap filling synthesis at these "difficult to copy" sequences. However, the mechanism by which a TNR is repaired depends on the type of lesion, the structural features imposed by the lesion, the assembled replication/repair complex, and the polymerase that encounters it. The relationships among these parameters are exceptionally complex and how they direct pathway choice is poorly understood. In this review, we consider the properties of polymerases, and how encounters with GC-rich or abnormal structures might influence polymerase choice and the success of replication and repair. Insights over the last three years have highlighted new mechanisms that provide interesting choices to consider in protecting genome stability.
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Affiliation(s)
- Aris A Polyzos
- MBIB Division, Lawrence Berkeley Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, United States
| | - Cynthia T McMurray
- MBIB Division, Lawrence Berkeley Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, United States.
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15
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Genetic Contributors to Intergenerational CAG Repeat Instability in Huntington's Disease Knock-In Mice. Genetics 2016; 205:503-516. [PMID: 27913616 PMCID: PMC5289832 DOI: 10.1534/genetics.116.195578] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/12/2016] [Indexed: 12/11/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by the expansion of a CAG trinucleotide repeat in exon 1 of the HTT gene. Longer repeat sizes are associated with increased disease penetrance and earlier ages of onset. Intergenerationally unstable transmissions are common in HD families, partly underlying the genetic anticipation seen in this disorder. HD CAG knock-in mouse models also exhibit a propensity for intergenerational repeat size changes. In this work, we examine intergenerational instability of the CAG repeat in over 20,000 transmissions in the largest HD knock-in mouse model breeding datasets reported to date. We confirmed previous observations that parental sex drives the relative ratio of expansions and contractions. The large datasets further allowed us to distinguish effects of paternal CAG repeat length on the magnitude and frequency of expansions and contractions, as well as the identification of large repeat size jumps in the knock-in models. Distinct degrees of intergenerational instability were observed between knock-in mice of six background strains, indicating the occurrence of trans-acting genetic modifiers. We also found that lines harboring a neomycin resistance cassette upstream of Htt showed reduced expansion frequency, indicative of a contributing role for sequences in cis, with the expanded repeat as modifiers of intergenerational instability. These results provide a basis for further understanding of the mechanisms underlying intergenerational repeat instability.
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16
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Lai Y, Budworth H, Beaver JM, Chan NLS, Zhang Z, McMurray CT, Liu Y. Crosstalk between MSH2-MSH3 and polβ promotes trinucleotide repeat expansion during base excision repair. Nat Commun 2016; 7:12465. [PMID: 27546332 PMCID: PMC4996945 DOI: 10.1038/ncomms12465] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/06/2016] [Indexed: 01/07/2023] Open
Abstract
Studies in knockout mice provide evidence that MSH2-MSH3 and the BER machinery promote trinucleotide repeat (TNR) expansion, yet how these two different repair pathways cause the mutation is unknown. Here we report the first molecular crosstalk mechanism, in which MSH2-MSH3 is used as a component of the BER machinery to cause expansion. On its own, pol β fails to copy TNRs during DNA synthesis, and bypasses them on the template strand to cause deletion. Remarkably, MSH2-MSH3 not only stimulates pol β to copy through the repeats but also enhances formation of the flap precursor for expansion. Our results provide direct evidence that MMR and BER, operating together, form a novel hybrid pathway that changes the outcome of TNR instability from deletion to expansion during the removal of oxidized bases. We propose that cells implement crosstalk strategies and share machinery when a canonical pathway is ineffective in removing a difficult lesion.
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Affiliation(s)
- Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, USA
| | - Helen Budworth
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 33R249, Berkeley, California 94720, USA
| | - Jill M. Beaver
- Biochemistry Ph.D. Program, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, USA
| | - Nelson L. S. Chan
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 33R249, Berkeley, California 94720, USA
| | - Zunzhen Zhang
- Department of Occupational and Environmental Health, Sichuan University West China School of Public Health, 16#, Section 3, Renmin Nan Lu, Chengdu, Sichuan 610041, China
| | - Cynthia T. McMurray
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 33R249, Berkeley, California 94720, USA
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, USA
- Biochemistry Ph.D. Program, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, USA
- Biomolecular Sciences Institute, School of Integrated Sciences and Humanity, Florida International University, 11200 SW 8th Street, Miami, Florida 33199, USA
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17
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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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18
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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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19
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Koeppen AH, Ramirez L, Becker AB, Feustel PJ, Mazurkiewicz JE. Friedreich ataxia: failure of GABA-ergic and glycinergic synaptic transmission in the dentate nucleus. J Neuropathol Exp Neurol 2015; 74:166-76. [PMID: 25575136 PMCID: PMC4294979 DOI: 10.1097/nen.0000000000000160] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Atrophy of large neurons in the dentate nucleus (DN) is an important pathologic correlate of neurologic disability in patients with Friedreich ataxia (FA). Thinning of the DN was quantified in 29 autopsy cases of FA and 2 carriers by measuring the thickness of the gray matter ribbon on stains with anti-glutamic acid decarboxylase, the rate-limiting enzyme in the biosynthesis of γ-amino-butyric acid (GABA). The DN was thinner than normal in all cases of FA, and atrophy correlated inversely with disease duration but not with age at onset or length of the homozygous guanine-adenine-adenine trinucleotide expansions. In 13 of the FA cases, frozen DN tissue was available for assay of frataxin. Dentate nucleus atrophy was more severe when frataxin was very low. Immunohistochemical staining for glutamic acid decarboxylase revealed grumose reaction and preservation of small GABA-ergic neurons in the DN of FA patients. Residual small DN neurons and varicose axons also contained the glycine transporter 2, identifying them as glycinergic. Immunohistochemistry also confirmed severe loss of GABA-A and glycine receptors in the DN with comparable depletion of the receptor-anchoring protein gephyrin. Thus, loss of gephyrin and failure to position GABA-A and glycine receptors correctly may reduce trophic support of large DN neurons and contribute to their atrophy. By contrast, Purkinje cells may escape retrograde atrophy in FA by issuing new axonal sprouts to small surviving DN neurons where they form reparative grumose clusters.
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Affiliation(s)
- Arnulf H. Koeppen
- Research Service, VA Medical Center, Albany, New York
- Department of Neurology, Albany Medical College, Albany, New York
- Department of Pathology, Albany Medical College, Albany, New York
| | - Liane Ramirez
- Research Service, VA Medical Center, Albany, New York
| | | | - Paul J. Feustel
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, New York
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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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21
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Abstract
DNA mismatch repair is a conserved antimutagenic pathway that maintains genomic stability through rectification of DNA replication errors and attenuation of chromosomal rearrangements. Paradoxically, mutagenic action of mismatch repair has been implicated as a cause of triplet repeat expansions that cause neurological diseases such as Huntington disease and myotonic dystrophy. This mutagenic process requires the mismatch recognition factor MutSβ and the MutLα (and/or possibly MutLγ) endonuclease, and is thought to be triggered by the transient formation of unusual DNA structures within the expanded triplet repeat element. This review summarizes the current knowledge of DNA mismatch repair involvement in triplet repeat expansion, which encompasses in vitro biochemical findings, cellular studies, and various in vivo transgenic animal model experiments. We present current mechanistic hypotheses regarding mismatch repair protein function in mediating triplet repeat expansions and discuss potential therapeutic approaches targeting the mismatch repair pathway.
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Affiliation(s)
- Ravi R Iyer
- Teva Branded Pharmaceutical Products R&D, Inc., West Chester, Pennsylvania 19380;
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