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Aldous SG, Smith EJ, Landles C, Osborne GF, Cañibano-Pico M, Nita IM, Phillips J, Zhang Y, Jin B, Hirst MB, Benn CL, Bond BC, Edelmann W, Greene JR, Bates GP. A CAG repeat threshold for therapeutics targeting somatic instability in Huntington's disease. Brain 2024; 147:1784-1798. [PMID: 38387080 PMCID: PMC11068328 DOI: 10.1093/brain/awae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
The Huntington's disease mutation is a CAG repeat expansion in the huntingtin gene that results in an expanded polyglutamine tract in the huntingtin protein. The CAG repeat is unstable and expansions of hundreds of CAGs have been detected in Huntington's disease post-mortem brains. The age of disease onset can be predicted partially from the length of the CAG repeat as measured in blood. Onset age is also determined by genetic modifiers, which in six cases involve variation in DNA mismatch repair pathways genes. Knocking-out specific mismatch repair genes in mouse models of Huntington's disease prevents somatic CAG repeat expansion. Taken together, these results have led to the hypothesis that somatic CAG repeat expansion in Huntington's disease brains is required for pathogenesis. Therefore, the pathogenic repeat threshold in brain is longer than (CAG)40, as measured in blood, and is currently unknown. The mismatch repair gene MSH3 has become a major focus for therapeutic development, as unlike other mismatch repair genes, nullizygosity for MSH3 does not cause malignancies associated with mismatch repair deficiency. Potential treatments targeting MSH3 currently under development include gene therapy, biologics and small molecules, which will be assessed for efficacy in mouse models of Huntington's disease. The zQ175 knock-in model carries a mutation of approximately (CAG)185 and develops early molecular and pathological phenotypes that have been extensively characterized. Therefore, we crossed the mutant huntingtin allele onto heterozygous and homozygous Msh3 knockout backgrounds to determine the maximum benefit of targeting Msh3 in this model. Ablation of Msh3 prevented somatic expansion throughout the brain and periphery, and reduction of Msh3 by 50% decreased the rate of expansion. This had no effect on the deposition of huntingtin aggregation in the nuclei of striatal neurons, nor on the dysregulated striatal transcriptional profile. This contrasts with ablating Msh3 in knock-in models with shorter CAG repeat expansions. Therefore, further expansion of a (CAG)185 repeat in striatal neurons does not accelerate the onset of molecular and neuropathological phenotypes. It is striking that highly expanded CAG repeats of a similar size in humans cause disease onset before 2 years of age, indicating that somatic CAG repeat expansion in the brain is not required for pathogenesis. Given that the trajectory for somatic CAG expansion in the brains of Huntington's disease mutation carriers is unknown, our study underlines the importance of administering treatments targeting somatic instability as early as possible.
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Affiliation(s)
- Sarah G Aldous
- Huntington's Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Edward J Smith
- Huntington's Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Christian Landles
- Huntington's Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Georgina F Osborne
- Huntington's Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Maria Cañibano-Pico
- Huntington's Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Iulia M Nita
- Huntington's Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Jemima Phillips
- Huntington's Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Yongwei Zhang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Bo Jin
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | | | - Caroline L Benn
- LoQus23 Therapeutics, Riverside, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Brian C Bond
- Prism Training and Consultancy Limited, St John's Innovation Centre, Cambridge, CB4 0WS, UK
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | | | - Gillian P Bates
- Huntington's Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
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Pressl C, Mätlik K, Kus L, Darnell P, Luo JD, Paul MR, Weiss AR, Liguore W, Carroll TS, Davis DA, McBride J, Heintz N. Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease. Neuron 2024; 112:924-941.e10. [PMID: 38237588 DOI: 10.1016/j.neuron.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/18/2023] [Accepted: 12/13/2023] [Indexed: 01/30/2024]
Abstract
The properties of the cell types that are selectively vulnerable in Huntington's disease (HD) cortex, the nature of somatic CAG expansions of mHTT in these cells, and their importance in CNS circuitry have not been delineated. Here, we employed serial fluorescence-activated nuclear sorting (sFANS), deep molecular profiling, and single-nucleus RNA sequencing (snRNA-seq) of motor-cortex samples from thirteen predominantly early stage, clinically diagnosed HD donors and selected samples from cingulate, visual, insular, and prefrontal cortices to demonstrate loss of layer 5a pyramidal neurons in HD. Extensive mHTT CAG expansions occur in vulnerable layer 5a pyramidal cells, and in Betz cells, layers 6a and 6b neurons that are resilient in HD. Retrograde tracing experiments in macaque brains identify layer 5a neurons as corticostriatal pyramidal cells. We propose that enhanced somatic mHTT CAG expansion and altered synaptic function act together to cause corticostriatal disconnection and selective neuronal vulnerability in HD cerebral cortex.
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Affiliation(s)
- Christina Pressl
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Kert Mätlik
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Laura Kus
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Paul Darnell
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alison R Weiss
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - William Liguore
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - David A Davis
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jodi McBride
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Nathaniel Heintz
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA.
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McClellan JM, Zoghbi AW, Buxbaum JD, Cappi C, Crowley JJ, Flint J, Grice DE, Gulsuner S, Iyegbe C, Jain S, Kuo PH, Lattig MC, Passos-Bueno MR, Purushottam M, Stein DJ, Sunshine AB, Susser ES, Walsh CA, Wootton O, King MC. An evolutionary perspective on complex neuropsychiatric disease. Neuron 2024; 112:7-24. [PMID: 38016473 PMCID: PMC10842497 DOI: 10.1016/j.neuron.2023.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
The forces of evolution-mutation, selection, migration, and genetic drift-shape the genetic architecture of human traits, including the genetic architecture of complex neuropsychiatric illnesses. Studying these illnesses in populations that are diverse in genetic ancestry, historical demography, and cultural history can reveal how evolutionary forces have guided adaptation over time and place. A fundamental truth of shared human biology is that an allele responsible for a disease in anyone, anywhere, reveals a gene critical to the normal biology underlying that condition in everyone, everywhere. Understanding the genetic causes of neuropsychiatric disease in the widest possible range of human populations thus yields the greatest possible range of insight into genes critical to human brain development. In this perspective, we explore some of the relationships between genes, adaptation, and history that can be illuminated by an evolutionary perspective on studies of complex neuropsychiatric disease in diverse populations.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anthony W Zoghbi
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Flint
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Conrad Iyegbe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | | | | | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Anna B Sunshine
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ezra S Susser
- Department of Epidemiology, Mailman School of Public Health, and New York State Psychiatric Institute, Columbia University, New York, NY 10032, USA
| | - Christopher A Walsh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Wootton
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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Pressl C, Mätlik K, Kus L, Darnell P, Luo JD, Paul MR, Weiss AR, Liguore W, Carroll TS, Davis DA, McBride J, Heintz N. Selective Vulnerability of Layer 5a Corticostriatal Neurons in Huntington's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538096. [PMID: 37162977 PMCID: PMC10168234 DOI: 10.1101/2023.04.24.538096] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The properties of the cell types that are selectively vulnerable in Huntington's disease (HD) cortex, the nature of somatic CAG expansions of mHTT in these cells, and their importance in CNS circuitry have not been delineated. Here we employed serial fluorescence activated nuclear sorting (sFANS), deep molecular profiling, and single nucleus RNA sequencing (snRNAseq) to demonstrate that layer 5a pyramidal neurons are vulnerable in primary motor cortex and other cortical areas of HD donors. Extensive mHTT -CAG expansions occur in vulnerable layer 5a pyramidal cells, and in Betz cells, layer 6a, layer 6b neurons that are resilient in HD. Retrograde tracing experiments in macaque brains identify the vulnerable layer 5a neurons as corticostriatal pyramidal cells. We propose that enhanced somatic mHTT -CAG expansion and altered synaptic function act together to cause corticostriatal disconnection and selective neuronal vulnerability in the HD cerebral cortex.
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Murley AG, Nie Y, Golder Z, Keogh MJ, Smith C, Ironside JW, Chinnery PF. High-Depth PRNP Sequencing in Brains With Sporadic Creutzfeldt-Jakob Disease. Neurol Genet 2023; 9:e200054. [PMID: 36686280 PMCID: PMC9853313 DOI: 10.1212/nxg.0000000000200054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/23/2022] [Indexed: 01/20/2023]
Abstract
Background and Objectives Sporadic Creutzfeldt-Jakob disease (sCJD) has established genetic risk factors, but, in contrast to genetic and acquired CJD, the initial trigger for misfolded prion aggregation and spread is not known. In this study, we tested the hypotheses that pathologic somatic variants in the prion gene PRNP are increased in sCJD, potentially leading to the seeding of misfolded prion protein. Methods High-depth amplicon-based short read sequencing of the PRNP coding region was performed on postmortem brain tissue from patients with a clinical and neuropathologic diagnosis of sCJD (n = 142), Alzheimer disease (AD) (n = 51) and controls with no clinical or neuropathologic diagnosis of a neurodegenerative disease (n = 71). Each DNA sample was sequenced twice, including independent PCR amplification, library preparation, and sequencing. We used RePlow to call somatic variants with high sensitivity and specificity and optimal sequence kernel association test to compare variant burden between groups. Results Two sCJD cases had somatic (variant allele frequency 0.5-1%) PRNP variants not previously identified, but with high in silico predicated pathogenicity. However, the pathogenicity of these variants is uncertain, as both located in the octapeptide repeat region where no point variations have previously been associated with sCJD. There was no overall difference in burden somatic PRNP in sCJD compared with controls and a lower burden compared with Alzheimer disease. Discussion Somatic variants in PRNP are unlikely to play a major role in sCJD but may contribute to the disease mechanism in a minority of cases.
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Affiliation(s)
- Alexander G Murley
- Department of Clinical Neurosciences (A.G.M., Y.N., Z.G., M.J.K., C.), School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus; Medical Research Council Mitochondrial Biology Unit (Y.N., Z.G.), University of Cambridge, Cambridge Biomedical Campus; Translational and Clinical Research Institute (M.J.K., P.F.C.), Newcastle University, Newcastle Upon Tyne; and Centre for Clinical Brain Sciences (C.S., J.W.I.), University of Edinburgh, Cambridge, UK
| | - Yu Nie
- Department of Clinical Neurosciences (A.G.M., Y.N., Z.G., M.J.K., C.), School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus; Medical Research Council Mitochondrial Biology Unit (Y.N., Z.G.), University of Cambridge, Cambridge Biomedical Campus; Translational and Clinical Research Institute (M.J.K., P.F.C.), Newcastle University, Newcastle Upon Tyne; and Centre for Clinical Brain Sciences (C.S., J.W.I.), University of Edinburgh, Cambridge, UK
| | - Zoe Golder
- Department of Clinical Neurosciences (A.G.M., Y.N., Z.G., M.J.K., C.), School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus; Medical Research Council Mitochondrial Biology Unit (Y.N., Z.G.), University of Cambridge, Cambridge Biomedical Campus; Translational and Clinical Research Institute (M.J.K., P.F.C.), Newcastle University, Newcastle Upon Tyne; and Centre for Clinical Brain Sciences (C.S., J.W.I.), University of Edinburgh, Cambridge, UK
| | - Michael John Keogh
- Department of Clinical Neurosciences (A.G.M., Y.N., Z.G., M.J.K., C.), School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus; Medical Research Council Mitochondrial Biology Unit (Y.N., Z.G.), University of Cambridge, Cambridge Biomedical Campus; Translational and Clinical Research Institute (M.J.K., P.F.C.), Newcastle University, Newcastle Upon Tyne; and Centre for Clinical Brain Sciences (C.S., J.W.I.), University of Edinburgh, Cambridge, UK
| | - Colin Smith
- Department of Clinical Neurosciences (A.G.M., Y.N., Z.G., M.J.K., C.), School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus; Medical Research Council Mitochondrial Biology Unit (Y.N., Z.G.), University of Cambridge, Cambridge Biomedical Campus; Translational and Clinical Research Institute (M.J.K., P.F.C.), Newcastle University, Newcastle Upon Tyne; and Centre for Clinical Brain Sciences (C.S., J.W.I.), University of Edinburgh, Cambridge, UK
| | - James W Ironside
- Department of Clinical Neurosciences (A.G.M., Y.N., Z.G., M.J.K., C.), School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus; Medical Research Council Mitochondrial Biology Unit (Y.N., Z.G.), University of Cambridge, Cambridge Biomedical Campus; Translational and Clinical Research Institute (M.J.K., P.F.C.), Newcastle University, Newcastle Upon Tyne; and Centre for Clinical Brain Sciences (C.S., J.W.I.), University of Edinburgh, Cambridge, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences (A.G.M., Y.N., Z.G., M.J.K., C.), School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus; Medical Research Council Mitochondrial Biology Unit (Y.N., Z.G.), University of Cambridge, Cambridge Biomedical Campus; Translational and Clinical Research Institute (M.J.K., P.F.C.), Newcastle University, Newcastle Upon Tyne; and Centre for Clinical Brain Sciences (C.S., J.W.I.), University of Edinburgh, Cambridge, UK
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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] [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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7
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Alfano M, De Antoni L, Centofanti F, Visconti VV, Maestri S, Degli Esposti C, Massa R, D'Apice MR, Novelli G, Delledonne M, Botta A, Rossato M. Characterization of full-length CNBP expanded alleles in myotonic dystrophy type 2 patients by Cas9-mediated enrichment and nanopore sequencing. eLife 2022; 11:80229. [PMID: 36018009 PMCID: PMC9462847 DOI: 10.7554/elife.80229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/25/2022] [Indexed: 11/30/2022] Open
Abstract
Myotonic dystrophy type 2 (DM2) is caused by CCTG repeat expansions in the CNBP gene, comprising 75 to >11,000 units and featuring extensive mosaicism, making it challenging to sequence fully expanded alleles. To overcome these limitations, we used PCR-free Cas9-mediated nanopore sequencing to characterize CNBP repeat expansions at the single-nucleotide level in nine DM2 patients. The length of normal and expanded alleles can be assessed precisely using this strategy, agreeing with traditional methods, and revealing the degree of mosaicism. We also sequenced an entire ~50 kbp expansion, which has not been achieved previously for DM2 or any other repeat-expansion disorders. Our approach precisely counted the repeats and identified the repeat pattern for both short interrupted and uninterrupted alleles. Interestingly, in the expanded alleles, only two DM2 samples featured the expected pure CCTG repeat pattern, while the other seven presented also TCTG blocks at the 3′ end, which have not been reported before in DM2 patients, but confirmed hereby with orthogonal methods. The demonstrated approach simultaneously determines repeat length, structure/motif, and the extent of somatic mosaicism, promising to improve the molecular diagnosis of DM2 and achieve more accurate genotype–phenotype correlations for the better stratification of DM2 patients in clinical trials.
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Affiliation(s)
| | - Luca De Antoni
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Federica Centofanti
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | | | - Simone Maestri
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Roberto Massa
- Department of Systems Medicine (Neurology), University of Rome Tor Vergata, Rome, Italy
| | | | - Giuseppe Novelli
- Laboratory of Medical Genetics, University of Rome Tor Vergata, Rome, Italy
| | | | - Annalisa Botta
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
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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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9
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Monckton DG. The Contribution of Somatic Expansion of the CAG Repeat to Symptomatic Development in Huntington's Disease: A Historical Perspective. J Huntingtons Dis 2021; 10:7-33. [PMID: 33579863 PMCID: PMC7990401 DOI: 10.3233/jhd-200429] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery in the early 1990s of the expansion of unstable simple sequence repeats as the causative mutation for a number of inherited human disorders, including Huntington’s disease (HD), opened up a new era of human genetics and provided explanations for some old problems. In particular, an inverse association between the number of repeats inherited and age at onset, and unprecedented levels of germline instability, biased toward further expansion, provided an explanation for the wide symptomatic variability and anticipation observed in HD and many of these disorders. The repeats were also revealed to be somatically unstable in a process that is expansion-biased, age-dependent and tissue-specific, features that are now increasingly recognised as contributory to the age-dependence, progressive nature and tissue specificity of the symptoms of HD, and at least some related disorders. With much of the data deriving from affected individuals, and model systems, somatic expansions have been revealed to arise in a cell division-independent manner in critical target tissues via a mechanism involving key components of the DNA mismatch repair pathway. These insights have opened new approaches to thinking about how the disease could be treated by suppressing somatic expansion and revealed novel protein targets for intervention. Exciting times lie ahead in turning these insights into novel therapies for HD and related disorders.
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Affiliation(s)
- Darren G Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Benn CL, Gibson KR, Reynolds DS. Drugging DNA Damage Repair Pathways for Trinucleotide Repeat Expansion Diseases. J Huntingtons Dis 2021; 10:203-220. [PMID: 32925081 PMCID: PMC7990437 DOI: 10.3233/jhd-200421] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA damage repair (DDR) mechanisms have been implicated in a number of neurodegenerative diseases (both genetically determined and sporadic). Consistent with this, recent genome-wide association studies in Huntington’s disease (HD) and other trinucleotide repeat expansion diseases have highlighted genes involved in DDR mechanisms as modifiers for age of onset, rate of progression and somatic instability. At least some clinical genetic modifiers have been shown to have a role in modulating trinucleotide repeat expansion biology and could therefore provide new disease-modifying therapeutic targets. In this review, we focus on key considerations with respect to drug discovery and development using DDR mechanisms as a target for trinucleotide repeat expansion diseases. Six areas are covered with specific reference to DDR and HD: 1) Target identification and validation; 2) Candidate selection including therapeutic modality and delivery; 3) Target drug exposure with particular focus on blood-brain barrier penetration, engagement and expression of pharmacology; 4) Safety; 5) Preclinical models as predictors of therapeutic efficacy; 6) Clinical outcome measures including biomarkers.
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Affiliation(s)
- Caroline L Benn
- LoQus23 Therapeutics, Riverside, Babraham Research Campus, Cambridge, UK
| | - Karl R Gibson
- Sandexis Medicinal Chemistry Ltd, Innovation House, Discovery Park, Sandwich, Kent, UK
| | - David S Reynolds
- LoQus23 Therapeutics, Riverside, Babraham Research Campus, Cambridge, UK
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Jones L, Wheeler VC, Pearson CE. Special Issue: DNA Repair and Somatic Repeat Expansion in Huntington's Disease. J Huntingtons Dis 2021; 10:3-5. [PMID: 33554921 PMCID: PMC7990429 DOI: 10.3233/jhd-219001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lesley Jones
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - 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
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.,University of Toronto, Program of Molecular Genetics
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12
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Donaldson J, Powell S, Rickards N, Holmans P, Jones L. What is the Pathogenic CAG Expansion Length in Huntington's Disease? J Huntingtons Dis 2021; 10:175-202. [PMID: 33579866 PMCID: PMC7990448 DOI: 10.3233/jhd-200445] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Huntington's disease (HD) (OMIM 143100) is caused by an expanded CAG repeat tract in the HTT gene. The inherited CAG length is known to expand further in somatic and germline cells in HD subjects. Age at onset of the disease is inversely correlated with the inherited CAG length, but is further modulated by a series of genetic modifiers which are most likely to act on the CAG repeat in HTT that permit it to further expand. Longer repeats are more prone to expansions, and this expansion is age dependent and tissue-specific. Given that the inherited tract expands through life and most subjects develop disease in mid-life, this implies that in cells that degenerate, the CAG length is likely to be longer than the inherited length. These findings suggest two thresholds- the inherited CAG length which permits further expansion, and the intracellular pathogenic threshold, above which cells become dysfunctional and die. This two-step mechanism has been previously proposed and modelled mathematically to give an intracellular pathogenic threshold at a tract length of 115 CAG (95% confidence intervals 70- 165 CAG). Empirically, the intracellular pathogenic threshold is difficult to determine. Clues from studies of people and models of HD, and from other diseases caused by expanded repeat tracts, place this threshold between 60- 100 CAG, most likely towards the upper part of that range. We assess this evidence and discuss how the intracellular pathogenic threshold in manifest disease might be better determined. Knowing the cellular pathogenic threshold would be informative for both understanding the mechanism in HD and deploying treatments.
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Affiliation(s)
- Jasmine Donaldson
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie Powell
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Nadia Rickards
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
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