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Kacher R, Lejeune FX, David I, Boluda S, Coarelli G, Leclere-Turbant S, Heinzmann A, Marelli C, Charles P, Goizet C, Kabir N, Hilab R, Jornea L, Six J, Dommergues M, Fauret AL, Brice A, Humbert S, Durr A. CAG repeat mosaicism is gene specific in spinocerebellar ataxias. Am J Hum Genet 2024; 111:913-926. [PMID: 38626762 PMCID: PMC11080609 DOI: 10.1016/j.ajhg.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024] Open
Abstract
Expanded CAG repeats in coding regions of different genes are the most common cause of dominantly inherited spinocerebellar ataxias (SCAs). These repeats are unstable through the germline, and larger repeats lead to earlier onset. We measured somatic expansion in blood samples collected from 30 SCA1, 50 SCA2, 74 SCA3, and 30 SCA7 individuals over a mean interval of 8.5 years, along with postmortem tissues and fetal tissues from SCA1, SCA3, and SCA7 individuals to examine somatic expansion at different stages of life. We showed that somatic mosaicism in the blood increases over time. Expansion levels are significantly different among SCAs and correlate with CAG repeat lengths. The level of expansion is greater in individuals with SCA7 who manifest disease compared to that of those who do not yet display symptoms. Brain tissues from SCA individuals have larger expansions compared to the blood. The cerebellum has the lowest mosaicism among the studied brain regions, along with a high expression of ATXNs and DNA repair genes. This was the opposite in cortices, with the highest mosaicism and lower expression of ATXNs and DNA repair genes. Fetal cortices did not show repeat instability. This study shows that CAG repeats are increasingly unstable during life in the blood and the brain of SCA individuals, with gene- and tissue-specific patterns.
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Affiliation(s)
- Radhia Kacher
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - François-Xavier Lejeune
- Sorbonne Université, Paris Brain Institute's Data Analysis Core Facility, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Isabelle David
- Sorbonne Université, Department of Genetics, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Susana Boluda
- Sorbonne Université, Department of Neuropathology Raymond Escourolle, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Giulia Coarelli
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Sabrina Leclere-Turbant
- Sorbonne Université, Biobank Neuro-CEB Biological Resource Platform, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Anna Heinzmann
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Cecilia Marelli
- MMDN, Université Montpellier, EPHE, INSERM, Montpellier, France; Expert Center for Neurogenetic Diseases, CHU, Montpellier, France
| | - Perrine Charles
- Sorbonne Université, Department of Genetics, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Cyril Goizet
- Université Bordeaux, Equipe « Neurogénétique Translationnelle - NRGEN », INCIA CNRS UMR5287 Université Bordeaux and Centre de Reference Maladies Rares « Neurogénétique », Service de Génétique Médicale, Bordeaux University Hospital (CHU Bordeaux), Bordeaux, France
| | - Nisha Kabir
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Rania Hilab
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Ludmila Jornea
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Julie Six
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Marc Dommergues
- Sorbonne Université, Service de Gynécologie Obstetrique, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Anne-Laure Fauret
- Sorbonne Université, Department of Genetics, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Sandrine Humbert
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hopital de la Pitié-Salpêtrière, Paris, France.
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Kim KH, Hong EP, Lee Y, McLean ZL, Elezi E, Lee R, Kwak S, McAllister B, Massey TH, Lobanov S, Holmans P, Orth M, Ciosi M, Monckton DG, Long JD, Lucente D, Wheeler VC, MacDonald ME, Gusella JF, Lee JM. Posttranscriptional regulation of FAN1 by miR-124-3p at rs3512 underlies onset-delaying genetic modification in Huntington's disease. Proc Natl Acad Sci U S A 2024; 121:e2322924121. [PMID: 38607933 PMCID: PMC11032436 DOI: 10.1073/pnas.2322924121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 04/14/2024] Open
Abstract
Many Mendelian disorders, such as Huntington's disease (HD) and spinocerebellar ataxias, arise from expansions of CAG trinucleotide repeats. Despite the clear genetic causes, additional genetic factors may influence the rate of those monogenic disorders. Notably, genome-wide association studies discovered somewhat expected modifiers, particularly mismatch repair genes involved in the CAG repeat instability, impacting age at onset of HD. Strikingly, FAN1, previously unrelated to repeat instability, produced the strongest HD modification signals. Diverse FAN1 haplotypes independently modify HD, with rare genetic variants diminishing DNA binding or nuclease activity of the FAN1 protein, hastening HD onset. However, the mechanism behind the frequent and the most significant onset-delaying FAN1 haplotype lacking missense variations has remained elusive. Here, we illustrated that a microRNA acting on 3'-UTR (untranslated region) SNP rs3512, rather than transcriptional regulation, is responsible for the significant FAN1 expression quantitative trait loci signal and allelic imbalance in FAN1 messenger ribonucleic acid (mRNA), accounting for the most significant and frequent onset-delaying modifier haplotype in HD. Specifically, miR-124-3p selectively targets the reference allele at rs3512, diminishing the stability of FAN1 mRNA harboring that allele and consequently reducing its levels. Subsequent validation analyses, including the use of antagomir and 3'-UTR reporter vectors with swapped alleles, confirmed the specificity of miR-124-3p at rs3512. Together, these findings indicate that the alternative allele at rs3512 renders the FAN1 mRNA less susceptible to miR-124-3p-mediated posttranscriptional regulation, resulting in increased FAN1 levels and a subsequent delay in HD onset by mitigating CAG repeat instability.
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Affiliation(s)
- Kyung-Hee Kim
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Eun Pyo Hong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Yukyeong Lee
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Zachariah L. McLean
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Department of Neurology, Harvard Medical School, Boston, MA02115
- Medical and Population Genetics Program, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - Emanuela Elezi
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
| | | | | | - Branduff McAllister
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, CardiffCF24 4HQ, United Kingdom
| | - Thomas H. Massey
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, CardiffCF24 4HQ, United Kingdom
| | - Sergey Lobanov
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, CardiffCF24 4HQ, United Kingdom
| | - Peter Holmans
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, CardiffCF24 4HQ, United Kingdom
| | - Michael Orth
- University Hospital of Old Age Psychiatry and Psychotherapy, Bern University, CH-3000Bern 60, Switzerland
| | - Marc Ciosi
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, GlasgowG12 8QQ, United Kingdom
| | - Darren G. Monckton
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, GlasgowG12 8QQ, United Kingdom
| | - Jeffrey D. Long
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA52242
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA52242
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
| | - Vanessa C. Wheeler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Department of Neurology, Harvard Medical School, Boston, MA02115
| | - Marcy E. MacDonald
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Department of Neurology, Harvard Medical School, Boston, MA02115
- Medical and Population Genetics Program, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - James F. Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Medical and Population Genetics Program, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Jong-Min Lee
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114
- Department of Neurology, Harvard Medical School, Boston, MA02115
- Medical and Population Genetics Program, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
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3
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Dalene Skarping K, Arning L, Petersén Å, Nguyen HP, Gebre-Medhin S. Attenuated huntingtin gene CAG nucleotide repeat size in individuals with Lynch syndrome. Sci Rep 2024; 14:4300. [PMID: 38383663 PMCID: PMC10881568 DOI: 10.1038/s41598-024-54277-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/10/2024] [Indexed: 02/23/2024] Open
Abstract
DNA mismatch repair (MMR) is thought to contribute to the onset and progression of Huntington disease (HD) by promoting somatic expansion of the pathogenic CAG nucleotide repeat in the huntingtin gene (HTT). Here we have studied constitutional HTT CAG repeat size in two cohorts of individuals with Lynch syndrome (LS) carrying heterozygous loss-of-function variants in the MMR genes MLH1 (n = 12/60; Lund cohort/Bochum cohort, respectively), MSH2 (n = 15/88), MSH6 (n = 21/23), and controls (n = 19/559). The sum of CAG repeats for both HTT alleles in each individual was calculated due to unknown segregation with the LS allele. In the larger Bochum cohort, the sum of CAG repeats was lower in the MLH1 subgroup compared to controls (MLH1 35.40 CAG repeats ± 3.6 vs. controls 36.89 CAG repeats ± 4.5; p = 0.014). All LS genetic subgroups in the Bochum cohort displayed lower frequencies of unstable HTT intermediate alleles and lower HTT somatic CAG repeat expansion index values compared to controls. Collectively, our results indicate that MMR gene haploinsufficiency could have a restraining impact on constitutional HTT CAG repeat size and support the notion that the MMR pathway is a driver of nucleotide repeat expansion diseases.
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Affiliation(s)
- Karin Dalene Skarping
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics and Pathology, Office for Medical Service, 221 85, Lund, Sweden
- Translational Neuroendocrine Research Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Larissa Arning
- Department of Human Genetics, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Åsa Petersén
- Translational Neuroendocrine Research Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Huu Phuc Nguyen
- Department of Human Genetics, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Samuel Gebre-Medhin
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.
- Department of Clinical Genetics and Pathology, Office for Medical Service, 221 85, Lund, Sweden.
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4
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Hong EP, Ramos EM, Aziz NA, Massey TH, McAllister B, Lobanov S, Jones L, Holmans P, Kwak S, Orth M, Ciosi M, Lomeikaite V, Monckton DG, Long JD, Lucente D, Wheeler VC, Gillis T, MacDonald ME, Sequeiros J, Gusella JF, Lee JM. Modification of Huntington's disease by short tandem repeats. Brain Commun 2024; 6:fcae016. [PMID: 38449714 PMCID: PMC10917446 DOI: 10.1093/braincomms/fcae016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/20/2023] [Accepted: 01/22/2024] [Indexed: 03/08/2024] Open
Abstract
Expansions of glutamine-coding CAG trinucleotide repeats cause a number of neurodegenerative diseases, including Huntington's disease and several of spinocerebellar ataxias. In general, age-at-onset of the polyglutamine diseases is inversely correlated with the size of the respective inherited expanded CAG repeat. Expanded CAG repeats are also somatically unstable in certain tissues, and age-at-onset of Huntington's disease corrected for individual HTT CAG repeat length (i.e. residual age-at-onset), is modified by repeat instability-related DNA maintenance/repair genes as demonstrated by recent genome-wide association studies. Modification of one polyglutamine disease (e.g. Huntington's disease) by the repeat length of another (e.g. ATXN3, CAG expansions in which cause spinocerebellar ataxia 3) has also been hypothesized. Consequently, we determined whether age-at-onset in Huntington's disease is modified by the CAG repeats of other polyglutamine disease genes. We found that the CAG measured repeat sizes of other polyglutamine disease genes that were polymorphic in Huntington's disease participants but did not influence Huntington's disease age-at-onset. Additional analysis focusing specifically on ATXN3 in a larger sample set (n = 1388) confirmed the lack of association between Huntington's disease residual age-at-onset and ATXN3 CAG repeat length. Additionally, neither our Huntington's disease onset modifier genome-wide association studies single nucleotide polymorphism data nor imputed short tandem repeat data supported the involvement of other polyglutamine disease genes in modifying Huntington's disease. By contrast, our genome-wide association studies based on imputed short tandem repeats revealed significant modification signals for other genomic regions. Together, our short tandem repeat genome-wide association studies show that modification of Huntington's disease is associated with short tandem repeats that do not involve other polyglutamine disease-causing genes, refining the landscape of Huntington's disease modification and highlighting the importance of rigorous data analysis, especially in genetic studies testing candidate modifiers.
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Affiliation(s)
- Eun Pyo Hong
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Eliana Marisa Ramos
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - N Ahmad Aziz
- Population & Clinical Neuroepidemiology, German Center for Neurodegenerative Diseases, 53127 Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn D-53113, Germany
| | - Thomas H Massey
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Branduff McAllister
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Sergey Lobanov
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Lesley Jones
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Peter Holmans
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Seung Kwak
- Molecular System Biology, CHDI Foundation, Princeton, NJ 08540, USA
| | - Michael Orth
- University Hospital of Old Age Psychiatry and Psychotherapy, Bern University, CH-3000 Bern 60, Switzerland
| | - Marc Ciosi
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Vilija Lomeikaite
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Darren G Monckton
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Jeffrey D Long
- Department of Psychiatry, Carver College of Medicine and Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - 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
| | - Tammy Gillis
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Jorge Sequeiros
- UnIGENe, IBMC—Institute for Molecular and Cell Biology, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 420-135, Portugal
- ICBAS School of Medicine and Biomedical Sciences, University of Porto, Porto 420-135, Portugal
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
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Chen Q, Yamada T, Miyagawa K, Murata A, Shoji M, Nakatani K. A new small molecule DoNA binding to CAG repeat RNA. Bioorg Med Chem 2024; 98:117580. [PMID: 38194737 DOI: 10.1016/j.bmc.2023.117580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/23/2023] [Accepted: 12/24/2023] [Indexed: 01/11/2024]
Abstract
We here report a new molecule DoNA binding to a CAG repeat RNA. DoNA is a dimer of the NA molecule that we previously reported. NA binds with high affinity to a CAG repeat DNA but not significantly to a CAG repeat RNA. Binding analyses using SPR and CSI-TOF MS indicated a significant increase in the affinity of DoNA to a single stranded CAG repeat RNA compared to NA. Systematic investigation of the RNA motifs bound by DoNA using hairpin RNA models revealed that DoNA binds to the CAG units at overhang and terminal positions, and notably, it binds to the structurally flexible internal and hairpin loop region.
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Affiliation(s)
- Qingwen Chen
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeshi Yamada
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; Current address: Nucleotide and Peptide Drug Discovery Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Asako Murata
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; Current address: Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Kazuhiko Nakatani
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Makeeva VS, Dyrkheeva NS, Lavrik OI, Zakian SM, Malakhova AA. Mutant-Huntingtin Molecular Pathways Elucidate New Targets for Drug Repurposing. Int J Mol Sci 2023; 24:16798. [PMID: 38069121 PMCID: PMC10706709 DOI: 10.3390/ijms242316798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The spectrum of neurodegenerative diseases known today is quite extensive. The complexities of their research and treatment lie not only in their diversity. Even many years of struggle and narrowly focused research on common pathologies such as Alzheimer's, Parkinson's, and other brain diseases have not brought cures for these illnesses. What can be said about orphan diseases? In particular, Huntington's disease (HD), despite affecting a smaller part of the human population, still attracts many researchers. This disorder is known to result from a mutation in the HTT gene, but having this information still does not simplify the task of drug development and studying the mechanisms of disease progression. Nonetheless, the data accumulated over the years and their analysis provide a good basis for further research. Here, we review studies devoted to understanding the mechanisms of HD. We analyze genes and molecular pathways involved in HD pathogenesis to describe the action of repurposed drugs and try to find new therapeutic targets.
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Affiliation(s)
- Vladlena S. Makeeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia; (V.S.M.); (S.M.Z.); (A.A.M.)
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia;
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia;
| | - Suren M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia; (V.S.M.); (S.M.Z.); (A.A.M.)
| | - Anastasia A. Malakhova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia; (V.S.M.); (S.M.Z.); (A.A.M.)
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8
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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 DOI: 10.1016/j.cell.2023.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Raposo M, Hübener-Schmid J, Ferreira AF, Vieira Melo AR, Vasconcelos J, Pires P, Kay T, Garcia-Moreno H, Giunti P, Santana MM, Pereira de Almeida L, Infante J, van de Warrenburg BP, de Vries JJ, Faber J, Klockgether T, Casadei N, Admard J, Schöls L, Riess O, Lima M. Blood transcriptome sequencing identifies biomarkers able to track disease stages in spinocerebellar ataxia type 3. Brain 2023; 146:4132-4143. [PMID: 37071051 DOI: 10.1093/brain/awad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/19/2022] [Accepted: 03/27/2023] [Indexed: 04/19/2023] Open
Abstract
Transcriptional dysregulation has been described in spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD), an autosomal dominant ataxia caused by a polyglutamine expansion in the ataxin-3 protein. As ataxin-3 is ubiquitously expressed, transcriptional alterations in blood may reflect early changes that start before clinical onset and might serve as peripheral biomarkers in clinical and research settings. Our goal was to describe enriched pathways and report dysregulated genes, which can track disease onset, severity or progression in carriers of the ATXN3 mutation (pre-ataxic subjects and patients). Global dysregulation patterns were identified by RNA sequencing of blood samples from 40 carriers of ATXN3 mutation and 20 controls and further compared with transcriptomic data from post-mortem cerebellum samples of MJD patients and controls. Ten genes-ABCA1, CEP72, PTGDS, SAFB2, SFSWAP, CCDC88C, SH2B1, LTBP4, MEG3 and TSPOAP1-whose expression in blood was altered in the pre-ataxic stage and simultaneously, correlated with ataxia severity in the overt disease stage, were analysed by quantitative real-time PCR in blood samples from an independent set of 170 SCA3/MJD subjects and 57 controls. Pathway enrichment analysis indicated the Gαi signalling and the oestrogen receptor signalling to be similarly affected in blood and cerebellum. SAFB2, SFSWAP and LTBP4 were consistently dysregulated in pre-ataxic subjects compared to controls, displaying a combined discriminatory ability of 79%. In patients, ataxia severity was associated with higher levels of MEG3 and TSPOAP1. We propose expression levels of SAFB2, SFSWAP and LTBP4 as well as MEG3 and TSPOAP1 as stratification markers of SCA3/MJD progression, deserving further validation in longitudinal studies and in independent cohorts.
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Affiliation(s)
- Mafalda Raposo
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Jeannette Hübener-Schmid
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, 72072 Tübingen, Germany
| | - Ana F Ferreira
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Ana Rosa Vieira Melo
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - João Vasconcelos
- Serviço de Neurologia, Hospital do Divino Espírito Santo, 9500-370 Ponta Delgada, Portugal
| | - Paula Pires
- Serviço de Neurologia, Hospital do Santo Espírito da Ilha Terceira, 9700-049 Angra do Heroísmo, Portugal
| | - Teresa Kay
- Serviço de Genética Clínica, Hospital D. Estefânia, 1169-045 Lisboa, Portugal
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Department of Neurogenetics, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London WC1N 3BG, UK
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Department of Neurogenetics, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London WC1N 3BG, UK
| | - Magda M Santana
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, 3000-075, Portugal
| | - Luis Pereira de Almeida
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, 3000-075, Portugal
| | - Jon Infante
- Neurology Service, University Hospital Marqués de Valdecilla-IDIVAL, Universidad de Cantabria, Centro de Investigación en Red de Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
| | - Bart P van de Warrenburg
- Radboud University Medical Centre, Donders Institute for Brain, Cognition and Behaviour, Department of Neurology, 6525 EN Nijmegen, The Netherlands
| | - Jeroen J de Vries
- Department of Neurology, University of Groningen, University Medical Center Groningen, 9700 AD Groningen, The Netherlands
| | - Jennifer Faber
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Thomas Klockgether
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen, 72016 Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen, 72016 Tübingen, Germany
| | - Ludger Schöls
- Department for Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center for Neurology, University of Tübingen, 72016 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72016 Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, 72072 Tübingen, Germany
- NGS Competence Center Tübingen, 72016 Tübingen, Germany
| | - Manuela Lima
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
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10
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Phadte AS, Bhatia M, Ebert H, Abdullah H, Elrazaq EA, Komolov KE, Pluciennik A. FAN1 removes triplet repeat extrusions via a PCNA- and RFC-dependent mechanism. Proc Natl Acad Sci U S A 2023; 120:e2302103120. [PMID: 37549289 PMCID: PMC10438374 DOI: 10.1073/pnas.2302103120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/22/2023] [Indexed: 08/09/2023] Open
Abstract
Human genome-wide association studies have identified FAN1 and several DNA mismatch repair (MMR) genes as modifiers of Huntington's disease age of onset. In animal models, FAN1 prevents somatic expansion of CAG triplet repeats, whereas MMR proteins promote this process. To understand the molecular basis of these opposing effects, we evaluated FAN1 nuclease function on DNA extrahelical extrusions that represent key intermediates in triplet repeat expansion. Here, we describe a strand-directed, extrusion-provoked nuclease function of FAN1 that is activated by RFC, PCNA, and ATP at physiological ionic strength. Activation of FAN1 in this manner results in DNA cleavage in the vicinity of triplet repeat extrahelical extrusions thereby leading to their removal in human cell extracts. The role of PCNA and RFC is to confer strand directionality to the FAN1 nuclease, and this reaction requires a physical interaction between PCNA and FAN1. Using cell extracts, we show that FAN1-dependent CAG extrusion removal relies on a very short patch excision-repair mechanism that competes with MutSβ-dependent MMR which is characterized by longer excision tracts. These results provide a mechanistic basis for the role of FAN1 in preventing repeat expansion and could explain the antagonistic effects of MMR and FAN1 in disease onset/progression.
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Affiliation(s)
- Ashutosh S. Phadte
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Mayuri Bhatia
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Hope Ebert
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Haaris Abdullah
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Essam Abed Elrazaq
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Konstantin E. Komolov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
| | - Anna Pluciennik
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA19107
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11
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Santana MM, Gaspar LS, Pinto MM, Silva P, Adão D, Pereira D, Ribeiro JA, Cunha I, Huebener‐Schmid J, Raposo M, Ferreira AF, Faber J, Kuhs S, Garcia‐Moreno H, Reetz K, Thieme A, Infante J, van de Warrenburg BPC, Giunti P, Riess O, Schöls L, Lima M, Klockgether T, Januário C, de Almeida LP. A standardised protocol for blood and cerebrospinal fluid collection and processing for biomarker research in ataxia. Neuropathol Appl Neurobiol 2023; 49:e12892. [PMID: 36798010 PMCID: PMC10947376 DOI: 10.1111/nan.12892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023]
Abstract
The European Spinocerebellar Ataxia Type 3/Machado-Joseph Disease Initiative (ESMI) is a consortium established with the ambition to set up the largest European longitudinal trial-ready cohort of Spinocerebellar Ataxia Type 3/Machado-Joseph Disease (SCA3/MJD), the most common autosomal dominantly inherited ataxia worldwide. A major focus of ESMI has been the identification of SCA3/MJD biomarkers to enable future interventional studies. As biosample collection and processing variables significantly impact the outcomes of biomarkers studies, biosampling procedures standardisation was done previously to study visit initiation. Here, we describe the ESMI consensus biosampling protocol, developed within the scope of ESMI, that ultimately might be translated to other neurodegenerative disorders, particularly ataxias, being the first step to protocol harmonisation in the field.
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Affiliation(s)
- Magda M. Santana
- Center for Neuroscience and Cell Biology (CNC)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Institute for Interdisciplinary ResearchUniversity of Coimbra (IIIUC)CoimbraPortugal
| | - Laetitia S. Gaspar
- Center for Neuroscience and Cell Biology (CNC)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Institute for Interdisciplinary ResearchUniversity of Coimbra (IIIUC)CoimbraPortugal
| | - Maria M. Pinto
- Center for Neuroscience and Cell Biology (CNC)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Faculty of PharmacyUniversity of Coimbra (FFUC)CoimbraPortugal
| | - Patrick Silva
- Center for Neuroscience and Cell Biology (CNC)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Institute for Interdisciplinary ResearchUniversity of Coimbra (IIIUC)CoimbraPortugal
- Faculty of PharmacyUniversity of Coimbra (FFUC)CoimbraPortugal
| | - Diana Adão
- Center for Neuroscience and Cell Biology (CNC)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Dina Pereira
- Center for Neuroscience and Cell Biology (CNC)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Institute for Interdisciplinary ResearchUniversity of Coimbra (IIIUC)CoimbraPortugal
| | - Joana Afonso Ribeiro
- Neurology Department, Child Development CentreCoimbra's Hospital and University Centre (CHUC)CoimbraPortugal
| | - Inês Cunha
- Department of NeurologyCoimbra University Hospital Center (CHUC)CoimbraPortugal
| | - Jeannette Huebener‐Schmid
- Institute of Medical Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
- Centre for Rare DiseasesUniversity of TübingenTübingenGermany
| | - Mafalda Raposo
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
- Faculdade de Ciências e Tecnologia (FCT)Universidade dos Açores (UAc)Ponta DelgadaPortugal
| | - Ana F. Ferreira
- Faculdade de Ciências e Tecnologia (FCT)Universidade dos Açores (UAc)Ponta DelgadaPortugal
| | - Jennifer Faber
- DZNE, German Center for Neurodegenerative DiseasesBonnGermany
- Department of NeurologyUniversity Hospital BonnBonnGermany
| | - Sandra Kuhs
- DZNE, German Center for Neurodegenerative DiseasesBonnGermany
| | - Hector Garcia‐Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neurogenetics, National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
| | - Kathrin Reetz
- Department of NeurologyRWTH Aachen UniversityAachenGermany
- JARA‐BRAIN Institute Molecular Neuroscience and NeuroimagingForschungszentrum Jülich GmbH and RWTH Aachen UniversityAachenGermany
| | - Andreas Thieme
- Department of NeurologyEssen University HospitalEssenGermany
- Center for Translational Neuro‐ and Behavioral Sciences (C‐TNBS), Essen University HospitalUniversity of Duisburg‐EssenEssenGermany
| | - Jon Infante
- Service of NeurologyUniversity Hospital Marqués de Valdecilla (IDIVAL), University of Cantabria (UC), Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)SantanderSpain
| | - Bart P. C. van de Warrenburg
- Department of Neurology, Radboud University Medical CentreDonders Institute for Brain, Cognition and BehaviourNijmegenThe Netherlands
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neurogenetics, National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
| | - Olaf Riess
- Institute of Medical Genetics and Applied GenomicsUniversity of TübingenTübingenGermany
- Centre for Rare DiseasesUniversity of TübingenTübingenGermany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases and Hertie‐Institute for Clinical Brain ResearchUniversity of TübingenTübingenGermany
- German Centre for Neurodegenerative Diseases (DZNE)TübingenGermany
| | - Manuela Lima
- Faculdade de Ciências e Tecnologia (FCT)Universidade dos Açores (UAc)Ponta DelgadaPortugal
| | - Thomas Klockgether
- DZNE, German Center for Neurodegenerative DiseasesBonnGermany
- Department of NeurologyUniversity Hospital BonnBonnGermany
| | - Cristina Januário
- Department of NeurologyCoimbra University Hospital Center (CHUC)CoimbraPortugal
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC)University of CoimbraCoimbraPortugal
- Center for Innovative Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Faculty of PharmacyUniversity of Coimbra (FFUC)CoimbraPortugal
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12
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Sturchio A, Duker AP, Muñoz-Sanjuan I, Espay AJ. Subtyping monogenic disorders: Huntington disease. Handb Clin Neurol 2023; 193:171-184. [PMID: 36803810 DOI: 10.1016/b978-0-323-85555-6.00003-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Huntington disease is a highly disabling neurodegenerative disease characterized by psychiatric, cognitive, and motor deficits. The causal genetic mutation in huntingtin (Htt, also known as IT15), located on chromosome 4p16.3, leads to an expansion of a triplet coding for polyglutamine. The expansion is invariably associated with the disease when >39 repeats. Htt encodes for the protein huntingtin (HTT), which carries out many essential biological functions in the cell, in particular in the nervous system. The precise mechanism of toxicity is not known. Based on a one-gene-one-disease framework, the prevailing hypothesis ascribes toxicity to the universal aggregation of HTT. However, the aggregation process into mutant huntingtin (mHTT) is associated with a reduction of the levels of wild-type HTT. A loss of wild-type HTT may plausibly be pathogenic, contributing to the disease onset and progressive neurodegeneration. Moreover, many other biological pathways are altered in Huntington disease, such as in the autophagic system, mitochondria, and essential proteins beyond HTT, potentially explaining biological and clinical differences among affected individuals. As one gene does not mean one disease, future efforts at identifying specific Huntington subtypes are important to design biologically tailored therapeutic approaches that correct the corresponding biological pathways-rather than continuing to exclusively target the common denominator of HTT aggregation for elimination.
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Affiliation(s)
- Andrea Sturchio
- James J. and Joan A. Gardner Family Center for Parkinson's disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States; Department of Clinical Neuroscience, Neuro Svenningsson, Karolinska Institutet, Stockholm, Sweden.
| | - Andrew P Duker
- James J. and Joan A. Gardner Family Center for Parkinson's disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | | | - Alberto J Espay
- James J. and Joan A. Gardner Family Center for Parkinson's disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States.
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13
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Melo ARV, Raposo M, Ventura M, Martins S, Pavão S, Alonso I, Bettencourt C, Lima M. Genetic Variation in ATXN3 (Ataxin-3) 3'UTR: Insights into the Downstream Regulatory Elements of the Causative Gene of Machado-Joseph Disease/Spinocerebellar Ataxia Type 3. Cerebellum 2023; 22:37-45. [PMID: 35034258 DOI: 10.1007/s12311-021-01358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 02/01/2023]
Abstract
Untranslated regions are involved in the regulation of transcriptional and post-transcriptional processes. Characterization of these regions remains poorly explored for ATXN3, the causative gene of Machado-Joseph disease (MJD). Although a few genetic modifiers have been identified for MJD age at onset (AO), they only explain a small fraction of the AO variance. Our aim was to analyse variation at the 3'UTR of ATXN3 in MJD patients, analyse its impact on AO and attempt to build haplotypes that might discriminate between normal and expanded alleles.After assessing ATXN3 3'UTR variants in molecularly confirmed MJD patients, an in silico analysis was conducted to predict their functional impact (e.g. their effect on miRNA-binding sites). Alleles in cis with the expanded (CAG)n were inferred from family data, and haplotypes were built. The effect of the alternative alleles on the AO and on SARA and NESSCA ataxia scales was tested.Nine variants, all previously described, were found. For eight variants, in silico analyses predicted (a) deleterious effects (rs10151135; rs55966267); (b) changes on miRNA-binding sites (rs11628764; rs55966267; rs709930) and (c) alterations of RNA-binding protein (RBP)-binding sites (rs1055996; rs910369; rs709930; rs10151135; rs3092822; rs7158733). Patients harbouring the alternative allele at rs10151135 had significantly higher SARA Axial subscores (p = 0.023), comparatively with those homozygous for the reference allele. Ten different haplotypes were obtained, one of which was exclusively found in cis with the expanded and four with the normal allele. These findings, which are relevant for the design of allele-specific therapies, warrant further investigation in independent MJD cohorts.
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14
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Jin X, Tanaka H, Jin M, Fujita K, Homma H, Inotsume M, Yong H, Umeda K, Kodera N, Ando T, Okazawa H. PQBP5/NOL10 maintains and anchors the nucleolus under physiological and osmotic stress conditions. Nat Commun 2023; 14:9. [PMID: 36599853 PMCID: PMC9813255 DOI: 10.1038/s41467-022-35602-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Polyglutamine binding protein 5 (PQBP5), also called nucleolar protein 10 (NOL10), binds to polyglutamine tract sequences and is expressed in the nucleolus. Using dynamic imaging of high-speed atomic force microscopy, we show that PQBP5/NOL10 is an intrinsically disordered protein. Super-resolution microscopy and correlative light and electron microscopy method show that PQBP5/NOL10 makes up the skeletal structure of the nucleolus, constituting the granule meshwork in the granular component area, which is distinct from other nucleolar substructures, such as the fibrillar center and dense fibrillar component. In contrast to other nucleolar proteins, which disperse to the nucleoplasm under osmotic stress conditions, PQBP5/NOL10 remains in the nucleolus and functions as an anchor for reassembly of other nucleolar proteins. Droplet and thermal shift assays show that the biophysical features of PQBP5/NOL10 remain stable under stress conditions, explaining the spatial role of this protein. PQBP5/NOL10 can be functionally depleted by sequestration with polyglutamine disease proteins in vitro and in vivo, leading to the pathological deformity or disappearance of the nucleolus. Taken together, these findings indicate that PQBP5/NOL10 is an essential protein needed to maintain the structure of the nucleolus.
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Affiliation(s)
- Xiaocen Jin
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hikari Tanaka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Meihua Jin
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kyota Fujita
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hidenori Homma
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Maiko Inotsume
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Huang Yong
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kenichi Umeda
- Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Hitoshi Okazawa
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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15
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Rosser A, Tabrizi S. Lesley Jones: In Memoriam. J Huntingtons Dis 2022; 11:349-350. [PMID: 36565129 DOI: 10.3233/jhd-229007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Taylor A, Barros D, Gobet N, Schuepbach T, McAllister B, Aeschbach L, Randall E, Trofimenko E, Heuchan E, Barszcz P, Ciosi M, Morgan J, Hafford-Tear N, Davidson A, Massey T, Monckton D, Jones L, network REGISTRYH, Xenarios I, Dion V. Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing. NAR Genom Bioinform 2022; 4:lqac089. [PMID: 36478959 PMCID: PMC9719798 DOI: 10.1093/nargab/lqac089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 12/07/2022] Open
Abstract
Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and preclinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. Interrupted alleles are sometimes present within repeats and can alter disease manifestation. Determining repeat size mosaicism and identifying interruptions in targeted sequencing datasets remains a major challenge. This is in part because standard alignment tools are ill-suited for repetitive and unstable sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington's disease and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 blood-derived samples from Huntington's disease individuals and did not require prior knowledge of the flanking sequences. Furthermore, RD can be used to identify alleles with interruptions and provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and in the development of novel therapies.
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Affiliation(s)
- Alysha S Taylor
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Dinis Barros
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Nastassia Gobet
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Thierry Schuepbach
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Newbiologix, Ch. De la corniche 6-8, 1066 Epalinges, Switzerland
| | - Branduff McAllister
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lorene Aeschbach
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Emma L Randall
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Evgeniya Trofimenko
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005 Paris, France
| | - Eleanor R Heuchan
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Paula Barszcz
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
| | - Marc Ciosi
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Joanne Morgan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | | | - Alice E Davidson
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
| | - Thomas H Massey
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Darren G Monckton
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | | | - Ioannis Xenarios
- Centre for Integrative Genomics, University of Lausanne, Bâtiment Génopode, 1015 Lausanne, Switzerland
- Health2030 Genome Center, Ch des Mines 14, 1202 Genève, Switzerland
| | - Vincent Dion
- UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
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17
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Koval I, Dighiero-Brecht T, Tobin AJ, Tabrizi SJ, Scahill RI, Tezenas du Montcel S, Durrleman S, Durr A. Forecasting individual progression trajectories in Huntington disease enables more powered clinical trials. Sci Rep 2022; 12:18928. [PMID: 36344508 PMCID: PMC9640581 DOI: 10.1038/s41598-022-18848-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
Variability in neurodegenerative disease progression poses great challenges for the evaluation of potential treatments. Identifying the persons who will experience significant progression in the short term is key for the implementation of trials with smaller sample sizes. We apply here disease course mapping to forecast biomarker progression for individual carriers of the pathological CAG repeat expansions responsible for Huntington disease. We used data from two longitudinal studies (TRACK-HD and TRACK-ON) to synchronize temporal progression of 15 clinical and imaging biomarkers from 290 participants with Huntington disease. We used then the resulting HD COURSE MAP to forecast clinical endpoints from the baseline data of 11,510 participants from ENROLL-HD, an external validation cohort. We used such forecasts to select participants at risk for progression and compute the power of trials for such an enriched population. HD COURSE MAP forecasts biomarkers 5 years after the baseline measures with a maximum mean absolute error of 10 points for the total motor score and 2.15 for the total functional capacity. This allowed reducing sample sizes in trial up to 50% including participants with a higher risk for progression ensuring a more homogeneous group of participants.
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Affiliation(s)
- Igor Koval
- Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié Salpêtrière, Sorbonne Université, 75013, Paris, France
| | - Thomas Dighiero-Brecht
- Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié Salpêtrière, Sorbonne Université, 75013, Paris, France
| | - Allan J Tobin
- Biological Adaptation and Ageing, Sorbonne Université, Paris, France
- Brain Research Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Sarah J Tabrizi
- UCL Queen Square Institute of Neurology, University College London, Queen Square, London, UK
| | - Rachael I Scahill
- UCL Queen Square Institute of Neurology, University College London, Queen Square, London, UK
| | - Sophie Tezenas du Montcel
- Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié Salpêtrière, Sorbonne Université, 75013, Paris, France
| | - Stanley Durrleman
- Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié Salpêtrière, Sorbonne Université, 75013, Paris, France.
| | - Alexandra Durr
- Department of Neurology, DMU Neurosciences, Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inserm, AP-HP, Hôpital de la Pitié Salpêtrière, 75013, Paris, France.
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18
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Papoutsi M, Flower M, Hensman Moss DJ, Holmans P, Estevez-Fraga C, Johnson EB, Scahill RI, Rees G, Langbehn D, Tabrizi SJ. Intellectual enrichment and genetic modifiers of cognition and brain volume in Huntington's disease. Brain Commun 2022; 4:fcac279. [PMID: 36519153 PMCID: PMC9732861 DOI: 10.1093/braincomms/fcac279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/22/2022] [Accepted: 10/27/2022] [Indexed: 12/14/2022] Open
Abstract
An important step towards the development of treatments for cognitive impairment in ageing and neurodegenerative diseases is to identify genetic and environmental modifiers of cognitive function and understand the mechanism by which they exert an effect. In Huntington's disease, the most common autosomal dominant dementia, a small number of studies have identified intellectual enrichment, i.e. a cognitively stimulating lifestyle and genetic polymorphisms as potential modifiers of cognitive function. The aim of our study was to further investigate the relationship and interaction between genetic factors and intellectual enrichment on cognitive function and brain atrophy in Huntington's disease. For this purpose, we analysed data from Track-HD, a multi-centre longitudinal study in Huntington's disease gene carriers and focused on the role of intellectual enrichment (estimated at baseline) and the genes FAN1, MSH3, BDNF, COMT and MAPT in predicting cognitive decline and brain atrophy. We found that carrying the 3a allele in the MSH3 gene had a positive effect on global cognitive function and brain atrophy in multiple cortical regions, such that 3a allele carriers had a slower rate of cognitive decline and atrophy compared with non-carriers, in agreement with its role in somatic instability. No other genetic predictor had a significant effect on cognitive function and the effect of MSH3 was independent of intellectual enrichment. Intellectual enrichment also had a positive effect on cognitive function; participants with higher intellectual enrichment, i.e. those who were better educated, had higher verbal intelligence and performed an occupation that was intellectually engaging, had better cognitive function overall, in agreement with previous studies in Huntington's disease and other dementias. We also found that intellectual enrichment interacted with the BDNF gene, such that the positive effect of intellectual enrichment was greater in Met66 allele carriers than non-carriers. A similar relationship was also identified for changes in whole brain and caudate volume; the positive effect of intellectual enrichment was greater for Met66 allele carriers, rather than for non-carriers. In summary, our study provides additional evidence for the beneficial role of intellectual enrichment and carrying the 3a allele in MSH3 in cognitive function in Huntington's disease and their effect on brain structure.
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Affiliation(s)
- Marina Papoutsi
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
- Ixico plc, London, UK
| | - Michael Flower
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Davina J Hensman Moss
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Carlos Estevez-Fraga
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Eileanoir B Johnson
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Rachael I Scahill
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
| | - Geraint Rees
- Wellcome Centre for Human Neuroimaging, Queen Square Institute of Neurology, University College London, London, UK
- Institute of Cognitive Neuroscience, University College London, London, UK
| | - Douglas Langbehn
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sarah J Tabrizi
- UCL Huntington’s Disease Centre, Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute at University College London, London, UK
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19
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Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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20
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Cho IK, Easley CA 4th, Chan AWS. Suppression of trinucleotide repeat expansion in spermatogenic cells in Huntington's disease. J Assist Reprod Genet 2022. [PMID: 36066723 DOI: 10.1007/s10815-022-02594-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Trinucleotide repeats (TNRs) are dispersed throughout the human genome. About 20 loci are related to human diseases, such as Huntington’s disease (HD). A larger TNR instability is predominantly observed in the paternal germ cells in some TNR disorders. Suppressing the expansion during spermatogenesis can provide a unique opportunity to end the vicious cycle of genetic anticipation. Here, using an in vitro differentiation method to derive advanced spermatogenic cells, we investigated the efficacy of two therapeutic agents, araC (cytarabine) and aspirin, on stabilizing TNRs in spermatogenic cells. Two WT patient-derived induced pluripotent stem cell (iPSC) lines and two HD hiPSC lines, with 44 Q and 180 Q, were differentiated into spermatogonial stem cell-like cells (SSCLCs). Both HD cell lines showed CAG tract expansion in SSCLC. When treated with araC and aspirin, HD1 showed moderate but not statistically significant stabilization of TNR. In HD2, 10 nM of aspirin and araC showed significant stabilization of TNR. All cell lines showed increased DNA damage response (DDR) gene expression in SSCLCs while more genes were significantly induced in HD SSCLC. In HD1, araC and aspirin treatment showed general suppression of DNA damage response genes. In HD2, only FAN1, OGG1, and PCNA showed significant suppression. When the methylation profile of HD cells was analyzed, FAN1 and OGG1 showed significant hypermethylation after the aspirin and araC treatment in SSCLC compared to the control. This study underscores the utility of our in vitro spermatogenesis model to study and develop therapies for TNR disorders such as HD.
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21
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Abstract
Roughly 3% of the human genome consists of microsatellites or tracts of short tandem repeats (STRs). These STRs are often unstable, undergoing high-frequency expansions (increases) or contractions (decreases) in the number of repeat units. Some microsatellite instability (MSI) is seen at multiple STRs within a single cell and is associated with certain types of cancer. A second form of MSI is characterised by expansion of a single gene-specific STR and such expansions are responsible for a group of 40+ human genetic disorders known as the repeat expansion diseases (REDs). While the mismatch repair (MMR) pathway prevents genome-wide MSI, emerging evidence suggests that some MMR factors are directly involved in generating expansions in the REDs. Thus, MMR suppresses some forms of expansion while some MMR factors promote expansion in other contexts. This review will cover what is known about the paradoxical effect of MMR on microsatellite expansion in mammalian cells.
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22
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Ru D, Li J, Xie O, Peng L, Jiang H, Qiu R. Explainable artificial intelligence based on feature optimization for age at onset prediction of spinocerebellar ataxia type 3. Front Neuroinform 2022; 16:978630. [PMID: 36110986 PMCID: PMC9468717 DOI: 10.3389/fninf.2022.978630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Existing treatments can only delay the progression of spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) after onset, so the prediction of the age at onset (AAO) can facilitate early intervention and follow-up to improve treatment efficacy. The objective of this study was to develop an explainable artificial intelligence (XAI) based on feature optimization to provide an interpretable and more accurate AAO prediction. A total of 1,008 affected SCA3/MJD subjects from mainland China were analyzed. The expanded cytosine-adenine-guanine (CAG) trinucleotide repeats of 10 polyQ-related genes were genotyped and included in related models as potential AAO modifiers. The performance of 4 feature optimization methods and 10 machine learning (ML) algorithms were compared, followed by building the XAI based on the SHapley Additive exPlanations (SHAP). The model constructed with an artificial neural network (ANN) and feature optimization of Crossing-Correlation-StepSVM performed best and achieved a coefficient of determination (R2) of 0.653 and mean absolute error (MAE), root mean square error (RMSE), and median absolute error (MedianAE) of 4.544, 6.090, and 3.236 years, respectively. The XAI explained the predicted results, which suggests that the factors affecting the AAO were complex and associated with gene interactions. An XAI based on feature optimization can improve the accuracy of AAO prediction and provide interpretable and personalized prediction.
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Affiliation(s)
- Danlei Ru
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ouyi Xie
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Linliu Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong Jiang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
- *Correspondence: Rong Qiu
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23
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Tabrizi SJ, Estevez-Fraga C, van Roon-Mom WMC, Flower MD, Scahill RI, Wild EJ, Muñoz-Sanjuan I, Sampaio C, Rosser AE, Leavitt BR. Potential disease-modifying therapies for Huntington's disease: lessons learned and future opportunities. Lancet Neurol 2022; 21:645-658. [PMID: 35716694 PMCID: PMC7613206 DOI: 10.1016/s1474-4422(22)00121-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 01/03/2023]
Abstract
Huntington's disease is the most frequent autosomal dominant neurodegenerative disorder; however, no disease-modifying interventions are available for patients with this disease. The molecular pathogenesis of Huntington's disease is complex, with toxicity that arises from full-length expanded huntingtin and N-terminal fragments of huntingtin, which are both prone to misfolding due to proteolysis; aberrant intron-1 splicing of the HTT gene; and somatic expansion of the CAG repeat in the HTT gene. Potential interventions for Huntington's disease include therapies targeting huntingtin DNA and RNA, clearance of huntingtin protein, DNA repair pathways, and other treatment strategies targeting inflammation and cell replacement. The early termination of trials of the antisense oligonucleotide tominersen suggest that it is time to reflect on lessons learned, where the field stands now, and the challenges and opportunities for the future.
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Affiliation(s)
- Sarah J Tabrizi
- Huntington's Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK.
| | - Carlos Estevez-Fraga
- Huntington's Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | | | - Michael D Flower
- Huntington's Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Rachael I Scahill
- Huntington's Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Edward J Wild
- Huntington's Disease Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | | | - Cristina Sampaio
- CHDI Management, CHDI Foundation Los Angeles, CA, USA; Laboratory of Clinical Pharmacology, Faculdade de Medicina de Lisboa, Lisbon, Portugal
| | - Anne E Rosser
- BRAIN unit, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Blair R Leavitt
- Centre for Huntington's disease, University of British Columbia, Vancouver, BC, Canada
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24
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Li X, Cao G, Liu X, Tang TS, Guo C, Liu H. Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases. Front Cell Neurosci 2022; 16:852002. [PMID: 35846567 PMCID: PMC9279898 DOI: 10.3389/fncel.2022.852002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/23/2022] [Indexed: 12/22/2022] Open
Abstract
Most of the neurodegenerative diseases and aging are associated with reactive oxygen species (ROS) or other intracellular damaging agents that challenge the genome integrity of the neurons. As most of the mature neurons stay in G0/G1 phase, replication-uncoupled DNA repair pathways including BER, NER, SSBR, and NHEJ, are pivotal, efficient, and economic mechanisms to maintain genomic stability without reactivating cell cycle. In these progresses, polymerases are prominent, not only because they are responsible for both sensing and repairing damages, but also for their more diversified roles depending on the cell cycle phase and damage types. In this review, we summarized recent knowledge on the structural and biochemical properties of distinct polymerases, including DNA and RNA polymerases, which are known to be expressed and active in nervous system; the biological relevance of these polymerases and their interactors with neuronal degeneration would be most graphically illustrated by the neurological abnormalities observed in patients with hereditary diseases associated with defects in DNA repair; furthermore, the vicious cycle of the trinucleotide repeat (TNR) and impaired DNA repair pathway is also discussed. Unraveling the mechanisms and contextual basis of the role of the polymerases in DNA damage response and repair will promote our understanding about how long-lived postmitotic cells cope with DNA lesions, and why disrupted DNA repair contributes to disease origin, despite the diversity of mutations in genes. This knowledge may lead to new insight into the development of targeted intervention for neurodegenerative diseases.
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Affiliation(s)
- Xiaoling Li
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Xiaoling Li
| | - Guanghui Cao
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Xiaokang Liu
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Caixia Guo
- Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- *Correspondence: Caixia Guo
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Hongmei Liu
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Hwang YH, Hayward BE, Zafarullah M, Kumar J, Durbin Johnson B, Holmans P, Usdin K, Tassone F. Both cis and trans-acting genetic factors drive somatic instability in female carriers of the FMR1 premutation. Sci Rep 2022; 12:10419. [PMID: 35729184 PMCID: PMC9213438 DOI: 10.1038/s41598-022-14183-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
The fragile X mental retardation (FMR1) gene contains an expansion-prone CGG repeat within its 5' UTR. Alleles with 55-200 repeats are known as premutation (PM) alleles and confer risk for one or more of the FMR1 premutation (PM) disorders that include Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), Fragile X-associated Primary Ovarian Insufficiency (FXPOI), and Fragile X-Associated Neuropsychiatric Disorders (FXAND). PM alleles expand on intergenerational transmission, with the children of PM mothers being at risk of inheriting alleles with > 200 CGG repeats (full mutation FM) alleles) and thus developing Fragile X Syndrome (FXS). PM alleles can be somatically unstable. This can lead to individuals being mosaic for multiple size alleles. Here, we describe a detailed evaluation of somatic mosaicism in a large cohort of female PM carriers and show that 94% display some evidence of somatic instability with the presence of a series of expanded alleles that differ from the next allele by a single repeat unit. Using two different metrics for instability that we have developed, we show that, as with intergenerational instability, there is a direct relationship between the extent of somatic expansion and the number of CGG repeats in the originally inherited allele and an inverse relationship with the number of AGG interruptions. Expansions are progressive as evidenced by a positive correlation with age and by examination of blood samples from the same individual taken at different time points. Our data also suggests the existence of other genetic or environmental factors that affect the extent of somatic expansion. Importantly, the analysis of candidate single nucleotide polymorphisms (SNPs) suggests that two DNA repair factors, FAN1 and MSH3, may be modifiers of somatic expansion risk in the PM population as observed in other repeat expansion disorders.
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Affiliation(s)
- Ye Hyun Hwang
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Bruce Eliot Hayward
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marwa Zafarullah
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Jay Kumar
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Blythe Durbin Johnson
- Department of Public Health Sciences, University of California, Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurology, School of Medicine, Cardiff University, Cardiff, UK
| | - Karen Usdin
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, 95817, USA. .,MIND Institute, University of California Davis Medical Center, Sacramento, CA, 95817, USA.
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26
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Welch G, Tsai LH. Mechanisms of DNA damage-mediated neurotoxicity in neurodegenerative disease. EMBO Rep 2022; 23:e54217. [PMID: 35499251 PMCID: PMC9171412 DOI: 10.15252/embr.202154217] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/18/2022] [Accepted: 04/19/2022] [Indexed: 12/26/2022] Open
Abstract
Neurons are highly susceptible to DNA damage accumulation due to their large energy requirements, elevated transcriptional activity, and long lifespan. While newer research has shown that DNA breaks and mutations may facilitate neuron diversity during development and neuronal function throughout life, a wealth of evidence indicates deficient DNA damage repair underlies many neurological disorders, especially age-associated neurodegenerative diseases. Recently, efforts to clarify the molecular link between DNA damage and neurodegeneration have improved our understanding of how the genomic location of DNA damage and defunct repair proteins impact neuron health. Additionally, work establishing a role for senescence in the aging and diseased brain reveals DNA damage may play a central role in neuroinflammation associated with neurodegenerative disease.
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Affiliation(s)
- Gwyneth Welch
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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27
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Durr A, Humbert S. When does Huntington disease begin? Rev Neurol (Paris) 2022:S0035-3787(22)00570-7. [PMID: 35597611 DOI: 10.1016/j.neurol.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
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Tabolacci E, Nobile V, Pucci C, Chiurazzi P. Mechanisms of the FMR1 Repeat Instability: How Does the CGG Sequence Expand? Int J Mol Sci 2022; 23:ijms23105425. [PMID: 35628235 PMCID: PMC9141726 DOI: 10.3390/ijms23105425] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Abstract
A dynamic mutation in exon 1 of the FMR1 gene causes Fragile X-related Disorders (FXDs), due to the expansion of an unstable CGG repeat sequence. Based on the CGG sequence size, two types of FMR1 alleles are possible: “premutation” (PM, with 56-200 CGGs) and “full mutation” (FM, with >200 triplets). Premutated females are at risk of transmitting a FM allele that, when methylated, epigenetically silences FMR1 and causes Fragile X syndrome (FXS), a very common form of inherited intellectual disability (ID). Expansions events of the CGG sequence are predominant over contractions and are responsible for meiotic and mitotic instability. The CGG repeat usually includes one or more AGG interspersed triplets that influence allele stability and the risk of transmitting FM to children through maternal meiosis. A unique mechanism responsible for repeat instability has not been identified, but several processes are under investigations using cellular and animal models. The formation of unusual secondary DNA structures at the expanded repeats are likely to occur and contribute to the CGG expansion. This review will focus on the current knowledge about CGG repeat instability addressing the CGG sequence expands.
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Affiliation(s)
- Elisabetta Tabolacci
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.T.); (V.N.); (C.P.)
| | - Veronica Nobile
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.T.); (V.N.); (C.P.)
| | - Cecilia Pucci
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.T.); (V.N.); (C.P.)
| | - Pietro Chiurazzi
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.T.); (V.N.); (C.P.)
- UOC Genetica Medica, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy
- Correspondence: ; Tel.: +39-06-3015-4606
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Abstract
Research into the genetic etiology of a neurological disorder can provide directions for genetic diagnosis and targeted therapy. In the past, germline mutations, which are transmitted from parents or newly arise from parental germ cells, were considered as major genetic causes of neurological disorders. However, recent evidence has shown that somatic mutations in the brain, which can arise from neural stem cells during development or over aging, account for a significant number of brain disorders, ranging from neurodevelopmental, neurodegenerative, and neuropsychiatric to neoplastic disease. Moreover, the identification of disease-causing somatic mutations or mutated genes has provided new insights into molecular pathogenesis and unveiled potential therapeutic targets for treating neurological disorders that have few, or no, therapeutic options. RNA therapeutics, including antisense oligonucleotide (ASO) and small interfering RNA (siRNA), are emerging as promising therapeutic tools for treating genetic neurological disorders. As the number of approved and investigational ASO and siRNA drugs for neurological disorders associated with germline mutations increases, they may also prove to be attractive modalities for treating neurologic disorders resulting from somatic mutations. In this perspective, we highlight several neurological diseases caused by brain somatic mutations and discuss the potential role of RNA therapeutics in these conditions.
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Affiliation(s)
- Sungyul Lee
- SoVarGen Co., Ltd., Daejeon, Republic of Korea
| | - Jeong Ho Lee
- SoVarGen Co., Ltd., Daejeon, Republic of Korea.,Graduate School of Medical Science and Engineering, Korea Advanced Institute Science and Technology (KAIST), KAIST BioMedical Research Center, Daejeon, Republic of Korea
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30
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Barbé L, Finkbeiner S. Genetic and Epigenetic Interplay Define Disease Onset and Severity in Repeat Diseases. Front Aging Neurosci 2022; 14:750629. [PMID: 35592702 PMCID: PMC9110800 DOI: 10.3389/fnagi.2022.750629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Repeat diseases, such as fragile X syndrome, myotonic dystrophy, Friedreich ataxia, Huntington disease, spinocerebellar ataxias, and some forms of amyotrophic lateral sclerosis, are caused by repetitive DNA sequences that are expanded in affected individuals. The age at which an individual begins to experience symptoms, and the severity of disease, are partially determined by the size of the repeat. However, the epigenetic state of the area in and around the repeat also plays an important role in determining the age of disease onset and the rate of disease progression. Many repeat diseases share a common epigenetic pattern of increased methylation at CpG islands near the repeat region. CpG islands are CG-rich sequences that are tightly regulated by methylation and are often found at gene enhancer or insulator elements in the genome. Methylation of CpG islands can inhibit binding of the transcriptional regulator CTCF, resulting in a closed chromatin state and gene down regulation. The downregulation of these genes leads to some disease-specific symptoms. Additionally, a genetic and epigenetic interplay is suggested by an effect of methylation on repeat instability, a hallmark of large repeat expansions that leads to increasing disease severity in successive generations. In this review, we will discuss the common epigenetic patterns shared across repeat diseases, how the genetics and epigenetics interact, and how this could be involved in disease manifestation. We also discuss the currently available stem cell and mouse models, which frequently do not recapitulate epigenetic patterns observed in human disease, and propose alternative strategies to study the role of epigenetics in repeat diseases.
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Affiliation(s)
- Lise Barbé
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
| | - Steve Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Steve Finkbeiner,
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31
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Zhao X, McHugh C, Coffey SR, Jimenez DA, Adams E, Carroll JB, Usdin K. Stool is a sensitive and noninvasive source of DNA for monitoring expansion in repeat expansion disease mouse models. Dis Model Mech 2022; 15:275011. [PMID: 35403689 PMCID: PMC9118036 DOI: 10.1242/dmm.049453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/05/2022] [Indexed: 11/27/2022] Open
Abstract
Repeat expansion diseases are a large group of human genetic disorders caused by expansion of a specific short tandem repeat tract. Expansion in somatic cells affects age of onset and disease severity in some of these disorders. However, alleles in DNA derived from blood, a commonly used source of DNA, usually show much less expansion than disease-relevant cells in the central nervous system in both humans and mouse models. Here we examined the extent of expansion in different DNA sources from mouse models of the fragile X-related disorders, Huntington's disease, spinocerebellar ataxia type 1 and spinocerebellar ataxia type 2. We found that DNA isolated from stool is a much better indicator of somatic expansion than DNA from blood. As stool is a sensitive and noninvasive source of DNA, it can be useful for studies of factors affecting the risk of expansion, or the monitoring of treatments aimed at reducing expansion in preclinical trials, as it would allow expansions to be examined longitudinally in the same animal and allow significant changes in expansion to be observed much earlier than is possible with other DNA sources. Summary: Stool is a readily available, noninvasive and sensitive source of DNA for monitoring repeat expansion in mouse models of four different repeat expansion diseases.
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Affiliation(s)
- Xiaonan Zhao
- 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, MD 20892, USA
| | - Cassandra McHugh
- Behavioral Neuroscience Program, Psychology Department, Western Washington University, Bellingham, WA 98225, USA
| | - Sydney R Coffey
- Behavioral Neuroscience Program, Psychology Department, Western Washington University, Bellingham, WA 98225, USA
| | - Diego Antonio Jimenez
- 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, MD 20892, USA
| | - Elizabeth Adams
- Behavioral Neuroscience Program, Psychology Department, Western Washington University, Bellingham, WA 98225, USA
| | - Jeffrey B Carroll
- Behavioral Neuroscience Program, Psychology Department, Western Washington University, Bellingham, WA 98225, USA
| | - 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, MD 20892, USA
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32
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Campion LN, Mejia Maza A, Yadav R, Penney EB, Murcar MG, Correia K, Gillis T, Fernandez-Cerado C, Velasco-Andrada MS, Legarda GP, Ganza-Bautista NG, Lagarde JBB, Acuña PJ, Multhaupt-Buell T, Aldykiewicz G, Supnet ML, De Guzman JK, Go C, Sharma N, Munoz EL, Ang MC, Diesta CCE, Bragg DC, Ozelius LJ, Wheeler VC. Tissue-specific and repeat length-dependent somatic instability of the X-linked dystonia parkinsonism-associated CCCTCT repeat. Acta Neuropathol Commun 2022; 10:49. [PMID: 35395816 PMCID: PMC8994295 DOI: 10.1186/s40478-022-01349-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/14/2022] [Indexed: 12/17/2022] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a progressive adult-onset neurodegenerative disorder caused by insertion of a SINE-VNTR-Alu (SVA) retrotransposon in the TAF1 gene. The SVA retrotransposon contains a CCCTCT hexameric repeat tract of variable length, whose length is inversely correlated with age at onset. This places XDP in a broader class of repeat expansion diseases, characterized by the instability of their causative repeat mutations. Here, we observe similar inverse correlations between CCCTCT repeat length with age at onset and age at death and no obvious correlation with disease duration. To gain insight into repeat instability in XDP we performed comprehensive quantitative analyses of somatic instability of the XDP CCCTCT repeat in blood and in seventeen brain regions from affected males. Our findings reveal repeat length-dependent and expansion-based instability of the XDP CCCTCT repeat, with greater levels of expansion in brain than in blood. The brain exhibits regional-specific patterns of instability that are broadly similar across individuals, with cerebellum exhibiting low instability and cortical regions exhibiting relatively high instability. The spectrum of somatic instability in the brain includes a high proportion of moderate repeat length changes of up to 5 repeats, as well as expansions of ~ 20- > 100 repeats and contractions of ~ 20–40 repeats at lower frequencies. Comparison with HTT CAG repeat instability in postmortem Huntington’s disease brains reveals similar brain region-specific profiles, indicating common trans-acting factors that contribute to the instability of both repeats. Analyses in XDP brains of expansion of a different SVA-associated CCCTCT located in the LIPG gene, and not known to be disease-associated, reveals repeat length-dependent expansion at overall lower levels relative to the XDP CCCTCT repeat, suggesting that expansion propensity may be modified by local chromatin structure. Together, the data support a role for repeat length-dependent somatic expansion in the process(es) driving the onset of XDP and prompt further investigation into repeat dynamics and the relationship to disease.
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33
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McAllister B, Donaldson J, Binda CS, Powell S, Chughtai U, Edwards G, Stone J, Lobanov S, Elliston L, Schuhmacher LN, Rees E, Menzies G, Ciosi M, Maxwell A, Chao MJ, Hong EP, Lucente D, Wheeler V, Lee JM, MacDonald ME, Long JD, Aylward EH, Landwehrmeyer GB, Rosser AE, Paulsen JS, Williams NM, Gusella JF, Monckton DG, Allen ND, Holmans P, Jones L, Massey TH; REGISTRY Investigators of the European Huntington’s disease network, PREDICT-HD Investigators of the Huntington Study Group. Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset. Nat Neurosci 2022; 25:446-57. [PMID: 35379994 DOI: 10.1038/s41593-022-01033-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
The age at onset of motor symptoms in Huntington's disease (HD) is driven by HTT CAG repeat length but modified by other genes. In this study, we used exome sequencing of 683 patients with HD with extremes of onset or phenotype relative to CAG length to identify rare variants associated with clinical effect. We discovered damaging coding variants in candidate modifier genes identified in previous genome-wide association studies associated with altered HD onset or severity. Variants in FAN1 clustered in its DNA-binding and nuclease domains and were associated predominantly with earlier-onset HD. Nuclease activities of purified variants in vitro correlated with residual age at motor onset of HD. Mutating endogenous FAN1 to a nuclease-inactive form in an induced pluripotent stem cell model of HD led to rates of CAG expansion similar to those observed with complete FAN1 knockout. Together, these data implicate FAN1 nuclease activity in slowing somatic repeat expansion and hence onset of HD.
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34
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Abstract
Polyglutamine diseases are a collection of nine CAG trinucleotide expansion disorders, presenting with a spectrum of neurological and clinical phenotypes. Recent human, mouse and cell studies of Huntington's disease have highlighted the role of DNA repair genes in somatic expansion of the CAG repeat region, modifying disease pathogenesis. Incomplete splicing of the HTT gene has also been shown to occur in humans, with the resulting exon 1 fragment most probably contributing to the Huntington's disease phenotype. In the spinocerebellar ataxias, studies have converged on transcriptional dysregulation of ion channels as a key disease modifier. In addition, advances have been made in understanding how increased levels of toxic, polyglutamine-expanded proteins can arise in the spinocerebellar ataxias through post-transcriptional and -translational modifications and autophagic mechanisms. Recent studies in spinal and bulbar muscular atrophy implicate similar pathogenic pathways to the more common polyglutamine diseases, highlighting autophagy stimulation as a potential therapeutic target. Finally, the therapeutic use of antisense oligonucleotides in several polyglutamine diseases has shown preclinical benefits and serves as potential future therapies in humans.
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Affiliation(s)
- Emma L Bunting
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Joseph Hamilton
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK; UK Dementia Research Institute, University College London, London, WC1N 3BG, UK.
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35
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Gall-Duncan T, Sato N, Yuen RKC, Pearson CE. Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. Genome Res 2022; 32:1-27. [PMID: 34965938 PMCID: PMC8744678 DOI: 10.1101/gr.269530.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/29/2021] [Indexed: 11/25/2022]
Abstract
Expansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans. TRs are a common form of genetic variation with biological consequences, observed, so far, in humans, dogs, plants, oysters, and yeast. Repeat diseases show atypical clinical features, genetic anticipation, and multiple and partially penetrant phenotypes among family members. Discovery of disease-causing repeat expansion loci accelerated through technological advances in DNA sequencing and computational analyses. Between 2019 and 2021, 17 new disease-causing TR expansions were reported, totaling 63 TR loci (>69 diseases), with a likelihood of more discoveries, and in more organisms. Recent and historical lessons reveal that properly assessed clinical presentations, coupled with genetic and biological awareness, can guide discovery of disease-causing unstable TRs. We highlight critical but underrecognized aspects of TR mutations. Repeat motifs may not be present in current reference genomes but will be in forthcoming gapless long-read references. Repeat motif size can be a single nucleotide to kilobases/unit. At a given locus, repeat motif sequence purity can vary with consequence. Pathogenic repeats can be "insertions" within nonpathogenic TRs. Expansions, contractions, and somatic length variations of TRs can have clinical/biological consequences. TR instabilities occur in humans and other organisms. TRs can be epigenetically modified and/or chromosomal fragile sites. We discuss the expanding field of disease-associated TR instabilities, highlighting prospects, clinical and genetic clues, tools, and challenges for further discoveries of disease-causing TR instabilities and understanding their biological and pathological impacts-a vista that is about to expand.
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Affiliation(s)
- Terence Gall-Duncan
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nozomu Sato
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Ryan K C Yuen
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christopher E Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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36
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Hasuike Y, Tanaka H, Gall-Duncan T, Mehkary M, Nakatani K, Pearson CE, Tsuji S, Mochizuki H, Nakamori M. CAG repeat-binding small molecule improves motor coordination impairment in a mouse model of Dentatorubral-pallidoluysian atrophy. Neurobiol Dis 2021; 163:105604. [PMID: 34968706 DOI: 10.1016/j.nbd.2021.105604] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/06/2021] [Accepted: 12/26/2021] [Indexed: 11/22/2022] Open
Abstract
Dentatorubral-pallidoluysian atrophy (DRPLA) is a devastating genetic disease presenting myoclonus, epilepsy, ataxia, and dementia. DRPLA is caused by the expansion of a CAG repeat in the ATN1 gene. Aggregation of the polyglutamine-expanded ATN1 protein causes neuro-degeneration of the dentatorubral and pallidoluysian systems. The expanded CAG repeats are unstable, and ongoing repeat expansions contribute to disease onset, progression, and severity. Inducing contractions of expanded repeats can be a means to treat DRPLA, for which no disease-modifying or curative therapies exist at present. Previously, we characterized a small molecule, naphthyridine-azaquinolone (NA), which binds to CAG slip-out structures and induces repeat contraction in Huntington's disease mice. Here, we demonstrate that long-term intracerebroventricular infusion of NA leads to repeat contraction, reductions in mutant ATN1 aggregation, and improved motor phenotype in a murine model of DRPLA. Furthermore, NA-induced contraction resulted in the modification of repeat-length-dependent dysregulation of gene expression profiles in DRPLA mice. Our study reveals the therapeutic potential of repeat contracting small molecules for repeat expansion disorders, such as DRPLA.
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37
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Raposo M, Bettencourt C, Melo ARV, Ferreira AF, Alonso I, Silva P, Vasconcelos J, Kay T, Saraiva-Pereira ML, Costa MD, Vilasboas-Campos D, Bettencourt BF, Bruges-Armas J, Houlden H, Heutink P, Jardim LB, Sequeiros J, Maciel P, Lima M. Novel Machado-Joseph disease-modifying genes and pathways identified by whole-exome sequencing. Neurobiol Dis 2021; 162:105578. [PMID: 34871736 DOI: 10.1016/j.nbd.2021.105578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/08/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Machado-Joseph disease (MJD/SCA3) is a neurodegenerative polyglutamine disorder exhibiting a wide spectrum of phenotypes. The abnormal size of the (CAG)n at ATXN3 explains ~55% of the age at onset variance, suggesting the involvement of other factors, namely genetic modifiers, whose identification remains limited. Our aim was to find novel genetic modifiers, analyse their epistatic effects and identify disease-modifying pathways contributing to MJD variable expressivity. We performed whole-exome sequencing in a discovery sample of four age at onset concordant and four discordant first-degree relative pairs of Azorean patients, to identify candidate variants which genotypes differed for each discordant pair but were shared in each concordant pair. Variants identified by this approach were then tested in an independent multi-origin cohort of 282 MJD patients. Whole-exome sequencing identified 233 candidate variants, from which 82 variants in 53 genes were prioritized for downstream analysis. Eighteen disease-modifying pathways were identified; two of the most enriched pathways were relevant for the nervous system, namely the neuregulin signaling and the agrin interactions at neuromuscular junction. Variants at PARD3, NFKB1, CHD5, ACTG1, CFAP57, DLGAP2, ITGB1, DIDO1 and CERS4 modulate age at onset in MJD, with those identified in CFAP57, ACTG1 and DIDO1 showing consistent effects across cohorts of different geographical origins. Network analyses of the nine novel MJD modifiers highlighted several important molecular interactions, including genes/proteins previously related with MJD pathogenesis, namely between ACTG1/APOE and VCP/ITGB1. We describe novel pathways, modifiers, and their interaction partners, providing a broad molecular portrait of age at onset modulation to be further exploited as new disease-modifying targets for MJD and related diseases.
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Affiliation(s)
- Mafalda Raposo
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal.
| | - Conceição Bettencourt
- Department of Neurodegenerative Disease and Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.
| | - Ana Rosa Vieira Melo
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
| | - Ana F Ferreira
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal.
| | - Isabel Alonso
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Paulo Silva
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.
| | - João Vasconcelos
- Departamento de Neurologia, Hospital do Divino Espírito Santo, Ponta Delgada, Portugal
| | - Teresa Kay
- Departamento de Genética Clínica, Hospital D. Estefânia, Lisboa, Portugal
| | - Maria Luiza Saraiva-Pereira
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Brazil; Serviço de Genética Médica/Centro de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
| | - Marta D Costa
- Instituto de Investigação em Ciências da Vida e Saúde (ICVS), Escola de Medicina, Universidade do Minho, Braga, Portugal; ICVS/3B's - Laboratório Associado, Braga/Guimarães, Portugal.
| | - Daniela Vilasboas-Campos
- Instituto de Investigação em Ciências da Vida e Saúde (ICVS), Escola de Medicina, Universidade do Minho, Braga, Portugal; ICVS/3B's - Laboratório Associado, Braga/Guimarães, Portugal
| | - Bruno Filipe Bettencourt
- Serviço Especializado de Epidemiologia e Biologia Molecular (SEEBMO), Hospital de Santo Espírito da Ilha Terceira (HSEIT), Angra do Heroísmo, Azores, Portugal
| | - Jácome Bruges-Armas
- Serviço Especializado de Epidemiologia e Biologia Molecular (SEEBMO), Hospital de Santo Espírito da Ilha Terceira (HSEIT), Angra do Heroísmo, Azores, Portugal; CHRC - Comprehensive Health Research Centre, Faculdade de Ciências Médicas & CEDOC - Chronic Diseases Research Center, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Henry Houlden
- Department of Molecular Neuroscience, Institute of Neurology, University College London and Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, University College London Hospitals, London, United Kingdom, London.
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
| | - Laura Bannach Jardim
- Departamento de Medicina Interna, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Serviço de Genética Médica/Centro de Pesquisa Clínica e Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
| | - Jorge Sequeiros
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.
| | - Patrícia Maciel
- Instituto de Investigação em Ciências da Vida e Saúde (ICVS), Escola de Medicina, Universidade do Minho, Braga, Portugal; ICVS/3B's - Laboratório Associado, Braga/Guimarães, Portugal.
| | - Manuela Lima
- Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal.
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Switonski PM, Delaney JR, Bartelt LC, Niu C, Ramos-Zapatero M, Spann NJ, Alaghatta A, Chen T, Griffin EN, Bapat J, Sopher BL, La Spada AR. Altered H3 histone acetylation impairs high-fidelity DNA repair to promote cerebellar degeneration in spinocerebellar ataxia type 7. Cell Rep 2021; 37:110062. [PMID: 34852229 PMCID: PMC8710427 DOI: 10.1016/j.celrep.2021.110062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 10/11/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022] Open
Abstract
A common mechanism in inherited ataxia is a vulnerability of DNA damage. Spinocerebellar ataxia type 7 (SCA7) is a CAG-polyglutamine-repeat disorder characterized by cerebellar and retinal degeneration. Polyglutamine-expanded ataxin-7 protein incorporates into STAGA co-activator complex and interferes with transcription by altering histone acetylation. We performed chromatic immunoprecipitation sequencing ChIP-seq on cerebellum from SCA7 mice and observed increased H3K9-promoter acetylation in DNA repair genes, resulting in increased expression. After detecting increased DNA damage in SCA7 cells, mouse primary cerebellar neurons, and patient stem-cell-derived neurons, we documented reduced homology-directed repair (HDR) and single-strand annealing (SSA). To evaluate repair at endogenous DNA in native chromosome context, we modified linear amplification-mediated high-throughput genome-wide translocation sequencing and found that DNA translocations are less frequent in SCA7 models, consistent with decreased HDR and SSA. Altered DNA repair function in SCA7 may predispose the subject to excessive DNA damage, leading to neuron demise and highlights DNA repair as a therapy target. Switonski et al. performed ChIP-seq on cerebellar DNA from SCA7 mice and detect increased histone H3-promoter acetylation in DNA repair genes. They document DNA damage in SCA7 models and patient stem-cell-derived neurons. Using in vitro assays and genome-wide translocation sequencing, they observe altered DNA repair in SCA7.
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Affiliation(s)
- Pawel M Switonski
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Joe R Delaney
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Luke C Bartelt
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chenchen Niu
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Maria Ramos-Zapatero
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathanael J Spann
- Department of Cellular & Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Akshay Alaghatta
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Toby Chen
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Emily N Griffin
- Department of Cellular & Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jaidev Bapat
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bryce L Sopher
- Department of Neurology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Albert R La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; UCI Institute for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
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Zhao X, Lu H, Usdin K. FAN1's protection against CGG repeat expansion requires its nuclease activity and is FANCD2-independent. Nucleic Acids Res 2021; 49:11643-11652. [PMID: 34718701 PMCID: PMC8599916 DOI: 10.1093/nar/gkab899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/20/2021] [Accepted: 10/12/2021] [Indexed: 12/21/2022] Open
Abstract
The Repeat Expansion Diseases, a large group of human diseases that includes the fragile X-related disorders (FXDs) and Huntington's disease (HD), all result from expansion of a disease-specific microsatellite via a mechanism that is not fully understood. We have previously shown that mismatch repair (MMR) proteins are required for expansion in a mouse model of the FXDs, but that the FANCD2 and FANCI associated nuclease 1 (FAN1), a component of the Fanconi anemia (FA) DNA repair pathway, is protective. FAN1's nuclease activity has been reported to be dispensable for protection against expansion in an HD cell model. However, we show here that in a FXD mouse model a point mutation in the nuclease domain of FAN1 has the same effect on expansion as a null mutation. Furthermore, we show that FAN1 and another nuclease, EXO1, have an additive effect in protecting against MSH3-dependent expansions. Lastly, we show that the loss of FANCD2, a vital component of the Fanconi anemia DNA repair pathway, has no effect on expansions. Thus, FAN1 protects against MSH3-dependent expansions without diverting the expansion intermediates into the canonical FA pathway and this protection depends on FAN1 having an intact nuclease domain.
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Affiliation(s)
- Xiaonan Zhao
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Huiyan Lu
- Laboratory Animal Sciences section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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40
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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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41
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McIntosh CS, Li D, Wilton SD, Aung-Htut MT. Polyglutamine Ataxias: Our Current Molecular Understanding and What the Future Holds for Antisense Therapies. Biomedicines 2021; 9:1499. [PMID: 34829728 PMCID: PMC8615177 DOI: 10.3390/biomedicines9111499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Polyglutamine (polyQ) ataxias are a heterogenous group of neurological disorders all caused by an expanded CAG trinucleotide repeat located in the coding region of each unique causative gene. To date, polyQ ataxias encompass six disorders: spinocerebellar ataxia types 1, 2, 3, 6, 7, and 17 and account for a larger group of disorders simply known as polyglutamine disorders, which also includes Huntington's disease. These diseases are typically characterised by progressive ataxia, speech and swallowing difficulties, lack of coordination and gait, and are unfortunately fatal in nature, with the exception of SCA6. All the polyQ spinocerebellar ataxias have a hallmark feature of neuronal aggregations and share many common pathogenic mechanisms, such as mitochondrial dysfunction, impaired proteasomal function, and autophagy impairment. Currently, therapeutic options are limited, with no available treatments that slow or halt disease progression. Here, we discuss the common molecular and clinical presentations of polyQ spinocerebellar ataxias. We will also discuss the promising antisense oligonucleotide therapeutics being developed as treatments for these devastating diseases. With recent advancements and therapeutic approvals of various antisense therapies, it is envisioned that some of the studies reviewed may progress into clinical trials and beyond.
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Affiliation(s)
- Craig S. McIntosh
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Dunhui Li
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Steve D. Wilton
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - May T. Aung-Htut
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
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Tanaka H, Kondo K, Fujita K, Homma H, Tagawa K, Jin X, Jin M, Yoshioka Y, Takayama S, Masuda H, Tokuyama R, Nakazaki Y, Saito T, Saido T, Murayama S, Ikura T, Ito N, Yamamori Y, Tomii K, Bianchi ME, Okazawa H. HMGB1 signaling phosphorylates Ku70 and impairs DNA damage repair in Alzheimer's disease pathology. Commun Biol 2021; 4:1175. [PMID: 34635772 DOI: 10.1038/s42003-021-02671-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
DNA damage is increased in Alzheimer's disease (AD), while the underlying mechanisms are unknown. Here, we employ comprehensive phosphoproteome analysis, and identify abnormal phosphorylation of 70 kDa subunit of Ku antigen (Ku70) at Ser77/78, which prevents Ku70-DNA interaction, in human AD postmortem brains. The abnormal phosphorylation inhibits accumulation of Ku70 to the foci of DNA double strand break (DSB), impairs DNA damage repair and eventually causes transcriptional repression-induced atypical cell death (TRIAD). Cells under TRIAD necrosis reveal senescence phenotypes. Extracellular high mobility group box 1 (HMGB1) protein, which is released from necrotic or hyper-activated neurons in AD, binds to toll-like receptor 4 (TLR4) of neighboring neurons, and activates protein kinase C alpha (PKCα) that executes Ku70 phosphorylation at Ser77/78. Administration of human monoclonal anti-HMGB1 antibody to post-symptomatic AD model mice decreases neuronal DSBs, suppresses secondary TRIAD necrosis of neurons, prevents escalation of neurodegeneration, and ameliorates cognitive symptoms. TRIAD shares multiple features with senescence. These results discover the HMGB1-Ku70 axis that accounts for the increase of neuronal DNA damage and secondary enhancement of TRIAD, the cell death phenotype of senescence, in AD.
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Gusella JF, Lee JM, MacDonald ME. Huntington's disease: nearly four decades of human molecular genetics. Hum Mol Genet 2021; 30:R254-R263. [PMID: 34169318 PMCID: PMC8490011 DOI: 10.1093/hmg/ddab170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Huntington's disease (HD) is a devastating neurogenetic disorder whose familial nature and progressive course were first described in the 19th century but for which no disease-modifying treatment is yet available. Through the active participation of HD families, this disorder has acted as a flagship for the application of human molecular genetic strategies to identify disease genes, understand pathogenesis and identify rational targets for development of therapies.
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Affiliation(s)
- James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
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44
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Abstract
The human genome contains over one million short tandem repeats. Expansion of a subset of these repeat tracts underlies over fifty human disorders, including common genetic causes of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (C9orf72), polyglutamine-associated ataxias and Huntington disease, myotonic dystrophy, and intellectual disability disorders such as Fragile X syndrome. In this Review, we discuss the four major mechanisms by which expansion of short tandem repeats causes disease: loss of function through transcription repression, RNA-mediated gain of function through gelation and sequestration of RNA-binding proteins, gain of function of canonically translated repeat-harbouring proteins, and repeat-associated non-AUG translation of toxic repeat peptides. Somatic repeat instability amplifies these mechanisms and influences both disease age of onset and tissue specificity of pathogenic features. We focus on the crosstalk between these disease mechanisms, and argue that they often synergize to drive pathogenesis. We also discuss the emerging native functions of repeat elements and how their dynamics might contribute to disease at a larger scale than currently appreciated. Lastly, we propose that lynchpins tying these disease mechanisms and native functions together offer promising therapeutic targets with potential shared applications across this class of human disorders.
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Affiliation(s)
- Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Chase P Kelley
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
- Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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45
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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: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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46
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Wright GEB, Caron NS, Ng B, Casal L, Casazza W, Xu X, Ooi J, Pouladi MA, Mostafavi S, Ross CJD, Hayden MR. Gene expression profiles complement the analysis of genomic modifiers of the clinical onset of Huntington disease. Hum Mol Genet 2021; 29:2788-2802. [PMID: 32898862 PMCID: PMC7530525 DOI: 10.1093/hmg/ddaa184] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder that is caused by a CAG repeat expansion in HTT. The length of this repeat, however, only explains a proportion of the variability in age of onset in patients. Genome-wide association studies have identified modifiers that contribute toward a proportion of the observed variance. By incorporating tissue-specific transcriptomic information with these results, additional modifiers can be identified. We performed a transcriptome-wide association study assessing heritable differences in genetically determined expression in diverse tissues, with genome-wide data from over 4000 patients. Functional validation of prioritized genes was undertaken in isogenic HD stem cells and patient brains. Enrichment analyses were performed with biologically relevant gene sets to identify the core pathways. HD-associated gene coexpression modules were assessed for associations with neurological phenotypes in an independent cohort and to guide drug repurposing analyses. Transcriptomic analyses identified genes that were associated with age of HD onset and displayed colocalization with gene expression signals in brain tissue (FAN1, GPR161, PMS2, SUMF2), with supporting evidence from functional experiments. This included genes involved in DNA repair, as well as novel-candidate modifier genes that have been associated with other neurological conditions. Further, cortical coexpression modules were also associated with cognitive decline and HD-related traits in a longitudinal cohort. In summary, the combination of population-scale gene expression information with HD patient genomic data identified novel modifier genes for the disorder. Further, these analyses expanded the pathways potentially involved in modifying HD onset and prioritized candidate therapeutics for future study.
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Affiliation(s)
- Galen E B Wright
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Nicholas S Caron
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Bernard Ng
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Department of Statistics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Lorenzo Casal
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - William Casazza
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Department of Statistics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Xiaohong Xu
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Jolene Ooi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), Singapore 138648, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Sara Mostafavi
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Department of Statistics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Colin J D Ross
- BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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47
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Loupe JM, Pinto RM, Kim KH, Gillis T, Mysore JS, Andrew MA, Kovalenko M, Murtha R, Seong I, Gusella JF, Kwak S, Howland D, Lee R, Lee JM, Wheeler VC, MacDonald ME. Promotion of somatic CAG repeat expansion by Fan1 knock-out in Huntington's disease knock-in mice is blocked by Mlh1 knock-out. Hum Mol Genet 2021; 29:3044-3053. [PMID: 32876667 PMCID: PMC7645713 DOI: 10.1093/hmg/ddaa196] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/20/2020] [Accepted: 08/27/2020] [Indexed: 12/13/2022] Open
Abstract
Recent genome-wide association studies of age-at-onset in Huntington’s disease (HD) point to distinct modes of potential disease modification: altering the rate of somatic expansion of the HTT CAG repeat or altering the resulting CAG threshold length-triggered toxicity process. Here, we evaluated the mouse orthologs of two HD age-at-onset modifier genes, FAN1 and RRM2B, for an influence on somatic instability of the expanded CAG repeat in Htt CAG knock-in mice. Fan1 knock-out increased somatic expansion of Htt CAG repeats, in the juvenile- and the adult-onset HD ranges, whereas knock-out of Rrm2b did not greatly alter somatic Htt CAG repeat instability. Simultaneous knock-out of Mlh1, the ortholog of a third HD age-at-onset modifier gene (MLH1), which suppresses somatic expansion of the Htt knock-in CAG repeat, blocked the Fan1 knock-out-induced acceleration of somatic CAG expansion. This genetic interaction indicates that functional MLH1 is required for the CAG repeat destabilizing effect of FAN1 loss. Thus, in HD, it is uncertain whether the RRM2B modifier effect on timing of onset may be due to a DNA instability mechanism. In contrast, the FAN1 modifier effects reveal that functional FAN1 acts to suppress somatic CAG repeat expansion, likely in genetic interaction with other DNA instability modifiers whose combined effects can hasten or delay onset and other CAG repeat length-driven phenotypes.
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Affiliation(s)
- Jacob M Loupe
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - 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
| | - Kyung-Hee Kim
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Tammy Gillis
- 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
| | - Marissa A Andrew
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marina Kovalenko
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ryan Murtha
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - IhnSik Seong
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Seung Kwak
- CHDI Foundation, Princeton, NJ 08540, USA
| | | | - Ramee Lee
- CHDI Foundation, Princeton, NJ 08540, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - 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
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.,Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
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48
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Zhao X, Usdin K. (Dys)function Follows Form: Nucleic Acid Structure, Repeat Expansion, and Disease Pathology in FMR1 Disorders. Int J Mol Sci 2021; 22:ijms22179167. [PMID: 34502075 PMCID: PMC8431139 DOI: 10.3390/ijms22179167] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
Fragile X-related disorders (FXDs), also known as FMR1 disorders, are examples of repeat expansion diseases (REDs), clinical conditions that arise from an increase in the number of repeats in a disease-specific microsatellite. In the case of FXDs, the repeat unit is CGG/CCG and the repeat tract is located in the 5' UTR of the X-linked FMR1 gene. Expansion can result in neurodegeneration, ovarian dysfunction, or intellectual disability depending on the number of repeats in the expanded allele. A growing body of evidence suggests that the mutational mechanisms responsible for many REDs share several common features. It is also increasingly apparent that in some of these diseases the pathologic consequences of expansion may arise in similar ways. It has long been known that many of the disease-associated repeats form unusual DNA and RNA structures. This review will focus on what is known about these structures, the proteins with which they interact, and how they may be related to the causative mutation and disease pathology in the FMR1 disorders.
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Affiliation(s)
- Xiaonan Zhao
- Correspondence: (X.Z.); (K.U.); Tel.: +1-301-451-6322 (X.Z.); +1-301-496-2189 (K.U.)
| | - Karen Usdin
- Correspondence: (X.Z.); (K.U.); Tel.: +1-301-451-6322 (X.Z.); +1-301-496-2189 (K.U.)
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49
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Murthy M, Cheng YY, Holton JL, Bettencourt C. Neurodegenerative movement disorders: An epigenetics perspective and promise for the future. Neuropathol Appl Neurobiol 2021; 47:897-909. [PMID: 34318515 PMCID: PMC9291277 DOI: 10.1111/nan.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 02/02/2023]
Abstract
Neurodegenerative movement disorders (NMDs) are age‐dependent disorders that are characterised by the degeneration and loss of neurons, typically accompanied by pathological accumulation of different protein aggregates in the brain, which lead to motor symptoms. NMDs include Parkinson's disease, multiple system atrophy, progressive supranuclear palsy, and Huntington's disease, among others. Epigenetic modifications are responsible for functional gene regulation during development, adult life and ageing and have progressively been implicated in complex diseases such as cancer and more recently in neurodegenerative diseases, such as NMDs. DNA methylation is by far the most widely studied epigenetic modification and consists of the reversible addition of a methyl group to the DNA without changing the DNA sequence. Although this research field is still in its infancy in relation to NMDs, an increasing number of studies point towards a role for DNA methylation in disease processes. This review addresses recent advances in epigenetic and epigenomic research in NMDs, with a focus on human brain DNA methylation studies. We discuss the current understanding of the DNA methylation changes underlying these disorders, the potential for use of these DNA modifications in peripheral tissues as biomarkers in early disease detection, classification and progression as well as a promising role in future disease management and therapy.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Yun Yung Cheng
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
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50
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Costantino I, Nicodemus J, Chun J. Genomic Mosaicism Formed by Somatic Variation in the Aging and Diseased Brain. Genes (Basel) 2021; 12:1071. [PMID: 34356087 DOI: 10.3390/genes12071071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
Over the past 20 years, analyses of single brain cell genomes have revealed that the brain is composed of cells with myriad distinct genomes: the brain is a genomic mosaic, generated by a host of DNA sequence-altering processes that occur somatically and do not affect the germline. As such, these sequence changes are not heritable. Some processes appear to occur during neurogenesis, when cells are mitotic, whereas others may also function in post-mitotic cells. Here, we review multiple forms of DNA sequence alterations that have now been documented: aneuploidies and aneusomies, smaller copy number variations (CNVs), somatic repeat expansions, retrotransposons, genomic cDNAs (gencDNAs) associated with somatic gene recombination (SGR), and single nucleotide variations (SNVs). A catch-all term of DNA content variation (DCV) has also been used to describe the overall phenomenon, which can include multiple forms within a single cell’s genome. A requisite step in the analyses of genomic mosaicism is ongoing technology development, which is also discussed. Genomic mosaicism alters one of the most stable biological molecules, DNA, which may have many repercussions, ranging from normal functions including effects of aging, to creating dysfunction that occurs in neurodegenerative and other brain diseases, most of which show sporadic presentation, unlinked to causal, heritable genes.
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