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Jiang A, You L, Handley RR, Hawkins V, Reid SJ, Jacobsen JC, Patassini S, Rudiger SR, Mclaughlan CJ, Kelly JM, Verma PJ, Bawden CS, Gusella JF, MacDonald ME, Waldvogel HJ, Faull RLM, Lehnert K, Snell RG. Single nuclei RNA-seq reveals a medium spiny neuron glutamate excitotoxicity signature prior to the onset of neuronal death in an ovine Huntington's disease model. Hum Mol Genet 2024; 33:1524-1539. [PMID: 38776957 PMCID: PMC11336116 DOI: 10.1093/hmg/ddae087] [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: 03/07/2024] [Revised: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Huntington's disease (HD) is a neurodegenerative genetic disorder caused by an expansion in the CAG repeat tract of the huntingtin (HTT) gene resulting in behavioural, cognitive, and motor defects. Current knowledge of disease pathogenesis remains incomplete, and no disease course-modifying interventions are in clinical use. We have previously reported the development and characterisation of the OVT73 transgenic sheep model of HD. The 73 polyglutamine repeat is somatically stable and therefore likely captures a prodromal phase of the disease with an absence of motor symptomatology even at 5-years of age and no detectable striatal cell loss. To better understand the disease-initiating events we have undertaken a single nuclei transcriptome study of the striatum of an extensively studied cohort of 5-year-old OVT73 HD sheep and age matched wild-type controls. We have identified transcriptional upregulation of genes encoding N-methyl-D-aspartate (NMDA), α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and kainate receptors in medium spiny neurons, the cell type preferentially lost early in HD. Further, we observed an upregulation of astrocytic glutamate uptake transporters and medium spiny neuron GABAA receptors, which may maintain glutamate homeostasis. Taken together, these observations support the glutamate excitotoxicity hypothesis as an early neurodegeneration cascade-initiating process but the threshold of toxicity may be regulated by several protective mechanisms. Addressing this biochemical defect early may prevent neuronal loss and avoid the more complex secondary consequences precipitated by cell death.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, 131 Dong'an Road, Shanghai 200032, China
- Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, 130 Dong'an Road, Shanghai 200032, China
| | - Renee R Handley
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Victoria Hawkins
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Suzanne J Reid
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Jessie C Jacobsen
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Stefano Patassini
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Skye R Rudiger
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - Clive J Mclaughlan
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - Jennifer M Kelly
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - Paul J Verma
- Aquatic and Livestock Sciences, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - C Simon Bawden
- Molecular Biology and Reproductive Technology Laboratories, South Australian Research and Development Institute, 129 Holland Road, Adelaide, SA 5350, Australia
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, United States
- Department of Neurology, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, United States
| | - Henry J Waldvogel
- Department of Anatomy and Medical Imaging, Centre for Brain Research, Faculty of Medical and Health Science, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
| | - Richard L M Faull
- Department of Anatomy and Medical Imaging, Centre for Brain Research, Faculty of Medical and Health Science, The University of Auckland, 85 Park Road, Auckland 1023, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
| | - Russell G Snell
- Applied Translational Genetics Group, Centre for Brain Research, School of Biological Sciences, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
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2
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Said I, Barbash DA, Clark AG. The Structure of Simple Satellite Variation in the Human Genome and Its Correlation With Centromere Ancestry. Genome Biol Evol 2024; 16:evae153. [PMID: 39018452 PMCID: PMC11305138 DOI: 10.1093/gbe/evae153] [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: 12/14/2023] [Revised: 06/21/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024] Open
Abstract
Although repetitive DNA forms much of the human genome, its study is challenging due to limitations in assembly and alignment of repetitive short-reads. We have deployed k-Seek, software that detects tandem repeats embedded in single reads, on 2,504 human genomes from the 1,000 Genomes Project to quantify the variation and abundance of simple satellites (repeat units <20 bp). We find that the ancestral monomer of Human Satellite 3 makes up the largest portion of simple satellite content in humans (mean of ∼8 Mb). We discovered ∼50,000 rare tandem repeats that are not detected in the T2T-CHM13v2.0 assembly, including undescribed variants of telomericand pericentromeric repeats. We find broad homogeneity of the most abundant repeats across populations, except for AG-rich repeats which are more abundant in African individuals. We also find cliques of highly similar AG- and AT-rich satellites that are interspersed and form higher-order structures that covary in copy number across individuals, likely through concerted amplification via unequal exchange. Finally, we use pericentromeric polymorphisms to estimate centromeric genetic relatedness between individuals and find a strong predictive relationship between centromeric lineages and pericentromeric simple satellite abundances. In particular, ancestral monomers of Human Satellite 2 and Human Satellite 3 abundances correlate with clusters of centromeric ancestry on chromosome 16 and chromosome 9, with some clusters structured by population. These results provide new descriptions of the population dynamics that underlie the evolution of simple satellites in humans.
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Affiliation(s)
- Iskander Said
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel A Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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3
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Wang N, Zhang S, Langfelder P, Ramanathan L, Plascencia M, Gao F, Vaca R, Gu X, Deng L, Dionisio LE, Prasad BC, Vogt T, Horvath S, Aaronson JS, Rosinski J, Yang XW. Msh3 and Pms1 Set Neuronal CAG-repeat Migration Rate to Drive Selective Striatal and Cortical Pathogenesis in HD Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602815. [PMID: 39026894 PMCID: PMC11257559 DOI: 10.1101/2024.07.09.602815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Modifiers of Huntington's disease (HD) include mismatch repair (MMR) genes; however, their underlying disease-altering mechanisms remain unresolved. Knockout (KO) alleles for 9 HD GWAS modifiers/MMR genes were crossed to the Q140 Huntingtin (mHtt) knock-in mice to probe such mechanisms. Four KO mice strongly ( Msh3 and Pms1 ) or moderately ( Msh2 and Mlh1 ) rescue a triad of adult-onset, striatal medium-spiny-neuron (MSN)-selective phenotypes: somatic Htt DNA CAG-repeat expansion, transcriptionopathy, and mHtt protein aggregation. Comparatively, Q140 cortex also exhibits an analogous, but later-onset, pathogenic triad that is Msh3 -dependent. Remarkably, Q140/homozygous Msh3-KO lacks visible mHtt aggregates in the brain, even at advanced ages (20-months). Moreover, Msh3 -deficiency prevents striatal synaptic marker loss, astrogliosis, and locomotor impairment in HD mice. Purified Q140 MSN nuclei exhibit highly linear age-dependent mHtt DNA repeat expansion (i.e. repeat migration), with modal-CAG increasing at +8.8 repeats/month (R 2 =0.98). This linear rate is reduced to 2.3 and 0.3 repeats/month in Q140 with Msh3 heterozygous and homozygous alleles, respectively. Our study defines somatic Htt CAG-repeat thresholds below which there are no detectable mHtt nuclear or neuropil aggregates. Mild transcriptionopathy can still occur in Q140 mice with stabilized Htt 140-CAG repeats, but the majority of transcriptomic changes are due to somatic repeat expansion. Our analysis reveals 479 genes with expression levels highly correlated with modal-CAG length in MSNs. Thus, our study mechanistically connects HD GWAS genes to selective neuronal vulnerability in HD, in which Msh3 and Pms1 set the linear rate of neuronal mHtt CAG-repeat migration to drive repeat-length dependent pathogenesis; and provides a preclinical platform for targeting these genes for HD suppression across brain regions. One Sentence Summary Msh3 and Pms1 are genetic drivers of sequential striatal and cortical pathogenesis in Q140 mice by mediating selective CAG-repeat migration in HD vulnerable neurons.
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4
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Pellerin D, Méreaux JL, Boluda S, Danzi MC, Dicaire MJ, Davoine CS, Genis D, Spurdens G, Ashton C, Hammond JM, Gerhart BJ, Chelban V, Le PU, Safisamghabadi M, Yanick C, Lee H, Nageshwaran SK, Matos-Rodrigues G, Jaunmuktane Z, Petrecca K, Akbarian S, Nussenzweig A, Usdin K, Renaud M, Bonnet C, Ravenscroft G, Saporta MA, Napierala JS, Houlden H, Deveson IW, Napierala M, Brice A, Molina Porcel L, Seilhean D, Zuchner S, Durr A, Brais B. Somatic instability of the FGF14 -SCA27B GAA•TTC repeat reveals a marked expansion bias in the cerebellum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.01.24309777. [PMID: 39006414 PMCID: PMC11245061 DOI: 10.1101/2024.07.01.24309777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Spinocerebellar ataxia 27B (SCA27B) is a common autosomal dominant ataxia caused by an intronic GAA•TTC repeat expansion in FGF14 . Neuropathological studies have shown that neuronal loss is largely restricted to the cerebellum. Although the repeat locus is highly unstable during intergenerational transmission, it remains unknown whether it exhibits cerebral mosaicism and progressive instability throughout life. We conducted an analysis of the FGF14 GAA•TTC repeat somatic instability across 156 serial blood samples from 69 individuals, fibroblasts, induced pluripotent stem cells, and post-mortem brain tissues from six controls and six patients with SCA27B, alongside methylation profiling using targeted long-read sequencing. Peripheral tissues exhibited minimal somatic instability, which did not significantly change over periods of more than 20 years. In post-mortem brains, the GAA•TTC repeat was remarkably stable across all regions, except in the cerebellar hemispheres and vermis. The levels of somatic expansion in the cerebellar hemispheres and vermis were, on average, 3.15 and 2.72 times greater relative to other examined brain regions, respectively. Additionally, levels of somatic expansion in the brain increased with repeat length and tissue expression of FGF14 . We found no significant difference in methylation of wild-type and expanded FGF14 alleles in post-mortem cerebellar hemispheres between patients and controls. In conclusion, our study revealed that the FGF14 GAA•TTC repeat exhibits a cerebellar-specific expansion bias, which may explain the pure and late-onset cerebellar involvement in SCA27B.
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5
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Mroczek M. Comment on: "Somatic CAG repeat instability in intermediate alleles of the HTT gene and its potential association with a clinical phenotype" by Ruiz de Sabando et al. Eur J Hum Genet 2024; 32:745-746. [PMID: 38448560 PMCID: PMC11219756 DOI: 10.1038/s41431-024-01587-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Affiliation(s)
- Magdalena Mroczek
- Department of Neurology, University Hospital Basel, University of Basel, Basel, Switzerland.
- European Society of Human Genetics-Young Committee, Vienna, Austria.
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6
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Ruiz de Sabando A, Ciosi M, Galbete A, Cumming SA, Monckton DG, Ramos-Arroyo MA. Somatic CAG repeat instability in intermediate alleles of the HTT gene and its potential association with a clinical phenotype. Eur J Hum Genet 2024; 32:770-778. [PMID: 38433266 PMCID: PMC11220145 DOI: 10.1038/s41431-024-01546-6] [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: 08/16/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 03/05/2024] Open
Abstract
Huntington disease (HD) is a neurodegenerative disorder caused by ≥36 CAGs in the HTT gene. Intermediate alleles (IAs) (27-35 CAGs) are not considered HD-causing, but their potential association with neurocognitive symptoms remains controversial. As HTT somatic CAG expansion influences HD onset, we hypothesised that IAs are somatically unstable, and that somatic CAG expansion may drive phenotypic presentation in some IA carriers. We quantified HTT somatic CAG expansions by MiSeq sequencing in the blood DNA of 164 HD subjects and 191 IA (symptomatic and control) carriers, and in the brain DNA of a symptomatic 33 CAG carrier. We also performed genotype-phenotype analysis. The phenotype of symptomatic IA carriers was characterised by motor (85%), cognitive (27%) and/or behavioural (29%) signs, with a late (58.7 ± 18.6 years), but not CAG-dependent, age at onset. IAs displayed somatic expansion that were CAG and age-dependent in blood DNA, with 0.4% and 0.01% of DNA molecules expanding by CAG and year, respectively. Somatic expansions of +1 and +2 CAGs were detected in the brain of the individual with 33 CAGs, with the highest expansion frequency in the putamen (10.3%) and the lowest in the cerebellum (4.8%). Somatic expansion in blood DNA was not different in symptomatic vs. control IA carriers. In conclusion, we show that HTT IAs are somatically unstable, but we found no association with HD-like phenotypes. It is plausible, however, that some IAs, close to the HD pathological threshold and with a predisposing genetic background, could manifest with neurocognitive symptoms.
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Affiliation(s)
- Ainara Ruiz de Sabando
- Department of Medical Genetics, Hospital Universitario de Navarra, IdiSNA, 31008, Pamplona, Spain
- Department of Health Sciences, Universidad Pública de Navarra, IdiSNA, 31008, Pamplona, Spain
- Fundación Miguel Servet-Navarrabiomed, IdiSNA, 31008, Pamplona, Spain
| | - Marc Ciosi
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Arkaitz Galbete
- Department of Statistics, Informatics and Mathematics, Universidad Pública de Navarra, IdiSNA, 31006, Pamplona, Spain
| | - Sarah A Cumming
- 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
| | - Maria A Ramos-Arroyo
- Department of Medical Genetics, Hospital Universitario de Navarra, IdiSNA, 31008, Pamplona, Spain.
- Fundación Miguel Servet-Navarrabiomed, IdiSNA, 31008, Pamplona, Spain.
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7
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Choi DE, Shin JW, Zeng S, Hong EP, Jang JH, Loupe JM, Wheeler VC, Stutzman HE, Kleinstiver B, Lee JM. Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington's disease. eLife 2024; 12:RP89782. [PMID: 38869243 PMCID: PMC11175616 DOI: 10.7554/elife.89782] [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] [Indexed: 06/14/2024] Open
Abstract
An expanded CAG repeat in the huntingtin gene (HTT) causes Huntington's disease (HD). Since the length of uninterrupted CAG repeat, not polyglutamine, determines the age-at-onset in HD, base editing strategies to convert CAG to CAA are anticipated to delay onset by shortening the uninterrupted CAG repeat. Here, we developed base editing strategies to convert CAG in the repeat to CAA and determined their molecular outcomes and effects on relevant disease phenotypes. Base editing strategies employing combinations of cytosine base editors and guide RNAs (gRNAs) efficiently converted CAG to CAA at various sites in the CAG repeat without generating significant indels, off-target edits, or transcriptome alterations, demonstrating their feasibility and specificity. Candidate BE strategies converted CAG to CAA on both expanded and non-expanded CAG repeats without altering HTT mRNA and protein levels. In addition, somatic CAG repeat expansion, which is the major disease driver in HD, was significantly decreased in the liver by a candidate BE strategy treatment in HD knock-in mice carrying canonical CAG repeats. Notably, CAG repeat expansion was abolished entirely in HD knock-in mice carrying CAA-interrupted repeats, supporting the therapeutic potential of CAG-to-CAA conversion strategies in HD and potentially other repeat expansion disorders.
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Affiliation(s)
- Doo Eun Choi
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Jun Wan Shin
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Sophia Zeng
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
| | - Eun Pyo Hong
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
- Medical and Population Genetics Program, The Broad Institute of MIT and HarvardCambridgeUnited States
| | - Jae-Hyun Jang
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Jacob M Loupe
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Vanessa C Wheeler
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Hannah E Stutzman
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Massachusetts General HospitalBostonUnited States
| | - Ben Kleinstiver
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
| | - Jong-Min Lee
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
- Medical and Population Genetics Program, The Broad Institute of MIT and HarvardCambridgeUnited States
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8
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Ferguson R, Goold R, Coupland L, Flower M, Tabrizi SJ. Therapeutic validation of MMR-associated genetic modifiers in a human ex vivo model of Huntington disease. Am J Hum Genet 2024; 111:1165-1183. [PMID: 38749429 PMCID: PMC11179424 DOI: 10.1016/j.ajhg.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 06/09/2024] Open
Abstract
The pathological huntingtin (HTT) trinucleotide repeat underlying Huntington disease (HD) continues to expand throughout life. Repeat length correlates both with earlier age at onset (AaO) and faster progression, making slowing its expansion an attractive therapeutic approach. Genome-wide association studies have identified candidate variants associated with altered AaO and progression, with many found in DNA mismatch repair (MMR)-associated genes. We examine whether lowering expression of these genes affects the rate of repeat expansion in human ex vivo models using HD iPSCs and HD iPSC-derived striatal medium spiny neuron-enriched cultures. We have generated a stable CRISPR interference HD iPSC line in which we can specifically and efficiently lower gene expression from a donor carrying over 125 CAG repeats. Lowering expression of each member of the MMR complexes MutS (MSH2, MSH3, and MSH6), MutL (MLH1, PMS1, PMS2, and MLH3), and LIG1 resulted in characteristic MMR deficiencies. Reduced MSH2, MSH3, and MLH1 slowed repeat expansion to the largest degree, while lowering either PMS1, PMS2, or MLH3 slowed it to a lesser degree. These effects were recapitulated in iPSC-derived striatal cultures where MutL factor expression was lowered. CRISPRi-mediated lowering of key MMR factor expression to levels feasibly achievable by current therapeutic approaches was able to effectively slow the expansion of the HTT CAG tract. We highlight members of the MutL family as potential targets to slow pathogenic repeat expansion with the aim to delay onset and progression of HD and potentially other repeat expansion disorders exhibiting somatic instability.
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Affiliation(s)
- Ross Ferguson
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Robert Goold
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Lucy Coupland
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Michael Flower
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Sarah J Tabrizi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK.
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9
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Jiraanont P, Zafarullah M, Sulaiman N, Espinal GM, Randol JL, Durbin-Johnson B, Schneider A, Hagerman RJ, Hagerman PJ, Tassone F. FMR1 Protein Expression Correlates with Intelligence Quotient in Both Peripheral Blood Mononuclear Cells and Fibroblasts from Individuals with an FMR1 Mutation. J Mol Diagn 2024; 26:498-509. [PMID: 38522837 DOI: 10.1016/j.jmoldx.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
Fragile X syndrome (FXS) is the most common heritable form of intellectual disability and is caused by CGG repeat expansions exceeding 200 (full mutation). Such expansions lead to hypermethylation and transcriptional silencing of the fragile X messenger ribonucleoprotein 1 (FMR1) gene. As a consequence, little or no FMR1 protein (FMRP) is produced; absence of the protein, which normally is responsible for neuronal development and maintenance, causes the syndrome. Previous studies have demonstrated the causal relationship between FMRP levels and cognitive abilities in peripheral blood mononuclear cells (PBMCs) and dermal fibroblast cell lines of patients with FXS. However, it is arguable whether PBMCs or fibroblasts would be the preferred surrogate for measuring molecular markers, particularly FMRP, to represent the cognitive impairment, a core symptom of FXS. To address this concern, CGG repeats, methylation status, FMR1 mRNA, and FMRP levels were measured in both PBMCs and fibroblasts derived from 66 individuals. The findings indicated a strong association between FMR1 mRNA expression levels and CGG repeat numbers in PBMCs of premutation males after correcting for methylation status. Moreover, FMRP expression levels from both PBMCs and fibroblasts of male participants with a hypermethylated full mutation and with mosaicism demonstrated significant association between the intelligence quotient levels and FMRP levels, suggesting that PBMCs may be preferable for FXS clinical studies, because of their greater accessibility.
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Affiliation(s)
- Poonnada Jiraanont
- Division of Molecular and Cellular Medicine, Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Marwa Zafarullah
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, California
| | - Noor Sulaiman
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, California
| | - Glenda M Espinal
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, California
| | - Jamie L Randol
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, California
| | - Blythe Durbin-Johnson
- Division of Biostatistics, University of California, Davis, School of Medicine, Davis, California
| | - Andrea Schneider
- Department of Pediatrics, University of California, Davis, School of Medicine, Davis, California; UC Davis MIND Institute, University of California, Davis, Sacramento, California
| | - Randi J Hagerman
- Department of Pediatrics, University of California, Davis, School of Medicine, Davis, California; UC Davis MIND Institute, University of California, Davis, Sacramento, California
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, California; UC Davis MIND Institute, University of California, Davis, Sacramento, California
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, California; UC Davis MIND Institute, University of California, Davis, Sacramento, California.
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10
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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] [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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11
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Niewiadomska-Cimicka A, Fievet L, Surdyka M, Jesion E, Keime C, Singer E, Eisenmann A, Kalinowska-Poska Z, Nguyen HHP, Fiszer A, Figiel M, Trottier Y. AAV-Mediated CAG-Targeting Selectively Reduces Polyglutamine-Expanded Protein and Attenuates Disease Phenotypes in a Spinocerebellar Ataxia Mouse Model. Int J Mol Sci 2024; 25:4354. [PMID: 38673939 PMCID: PMC11050704 DOI: 10.3390/ijms25084354] [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: 03/26/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Polyglutamine (polyQ)-encoding CAG repeat expansions represent a common disease-causing mutation responsible for several dominant spinocerebellar ataxias (SCAs). PolyQ-expanded SCA proteins are toxic for cerebellar neurons, with Purkinje cells (PCs) being the most vulnerable. RNA interference (RNAi) reagents targeting transcripts with expanded CAG reduce the level of various mutant SCA proteins in an allele-selective manner in vitro and represent promising universal tools for treating multiple CAG/polyQ SCAs. However, it remains unclear whether the therapeutic targeting of CAG expansion can be achieved in vivo and if it can ameliorate cerebellar functions. Here, using a mouse model of SCA7 expressing a mutant Atxn7 allele with 140 CAGs, we examined the efficacy of short hairpin RNAs (shRNAs) targeting CAG repeats expressed from PHP.eB adeno-associated virus vectors (AAVs), which were introduced into the brain via intravascular injection. We demonstrated that shRNAs carrying various mismatches with the CAG target sequence reduced the level of polyQ-expanded ATXN7 in the cerebellum, albeit with varying degrees of allele selectivity and safety profile. An shRNA named A4 potently reduced the level of polyQ-expanded ATXN7, with no effect on normal ATXN7 levels and no adverse side effects. Furthermore, A4 shRNA treatment improved a range of motor and behavioral parameters 23 weeks after AAV injection and attenuated the disease burden of PCs by preventing the downregulation of several PC-type-specific genes. Our results show the feasibility of the selective targeting of CAG expansion in the cerebellum using a blood-brain barrier-permeable vector to attenuate the disease phenotype in an SCA mouse model. Our study represents a significant advancement in developing CAG-targeting strategies as a potential therapy for SCA7 and possibly other CAG/polyQ SCAs.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France; (L.F.); (C.K.); (A.E.)
| | - Lorraine Fievet
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France; (L.F.); (C.K.); (A.E.)
| | - Magdalena Surdyka
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (M.S.); (E.J.); (Z.K.-P.); (M.F.)
| | - Ewelina Jesion
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (M.S.); (E.J.); (Z.K.-P.); (M.F.)
| | - Céline Keime
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France; (L.F.); (C.K.); (A.E.)
| | - Elisabeth Singer
- Centre for Rare Diseases (ZSE), University of Tuebingen, 72076 Tuebingen, Germany;
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tuebingen, Germany
- Department of Human Genetics, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany;
| | - Aurélie Eisenmann
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France; (L.F.); (C.K.); (A.E.)
| | - Zaneta Kalinowska-Poska
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (M.S.); (E.J.); (Z.K.-P.); (M.F.)
| | - Hoa Huu Phuc Nguyen
- Department of Human Genetics, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany;
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Maciej Figiel
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (M.S.); (E.J.); (Z.K.-P.); (M.F.)
| | - Yvon Trottier
- Institute of Genetics and Molecular and Cellular Biology, INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France; (L.F.); (C.K.); (A.E.)
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12
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Skeens A, Siriwardhana C, Massinople SE, Wunder MM, Ellis ZL, Keith KM, Girman T, Frey SL, Legleiter J. The polyglutamine domain is the primary driver of seeding in huntingtin aggregation. PLoS One 2024; 19:e0298323. [PMID: 38483973 PMCID: PMC10939245 DOI: 10.1371/journal.pone.0298323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/22/2024] [Indexed: 03/17/2024] Open
Abstract
Huntington's Disease (HD) is a fatal, neurodegenerative disease caused by aggregation of the huntingtin protein (htt) with an expanded polyglutamine (polyQ) domain into amyloid fibrils. Htt aggregation is modified by flanking sequences surrounding the polyQ domain as well as the binding of htt to lipid membranes. Upon fibrillization, htt fibrils are able to template the aggregation of monomers into fibrils in a phenomenon known as seeding, and this process appears to play a critical role in cell-to-cell spread of HD. Here, exposure of C. elegans expressing a nonpathogenic N-terminal htt fragment (15-repeat glutamine residues) to preformed htt-exon1 fibrils induced inclusion formation and resulted in decreased viability in a dose dependent manner, demonstrating that seeding can induce toxic aggregation of nonpathogenic forms of htt. To better understand this seeding process, the impact of flanking sequences adjacent to the polyQ stretch, polyQ length, and the presence of model lipid membranes on htt seeding was investigated. Htt seeding readily occurred across polyQ lengths and was independent of flanking sequence, suggesting that the structured polyQ domain within fibrils is the key contributor to the seeding phenomenon. However, the addition of lipid vesicles modified seeding efficiency in a manner suggesting that seeding primarily occurs in bulk solution and not at the membrane interface. In addition, fibrils formed in the presence of lipid membranes displayed similar seeding efficiencies. Collectively, this suggests that the polyQ domain that forms the amyloid fibril core is the main driver of seeding in htt aggregation.
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Affiliation(s)
- Adam Skeens
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - Chathuranga Siriwardhana
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - Sophia E. Massinople
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - Michelle M. Wunder
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - Zachary L. Ellis
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - Kaitlyn M. Keith
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - Tyler Girman
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - Shelli L. Frey
- The Department of Chemistry, Gettysburg College, Gettysburg, Pennsylvania, United States of America
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, United States of America
- Rockefeller Neurosciences Institutes, West Virginia University, Morgantown, West Virginia, United States of America
- Department of Neuroscience, West Virginia University, Morgantown, West Virginia, United States of America
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13
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Sanchez-Flores M, Corral-Juan M, Gasch-Navalón E, Cirillo D, Sanchez I, Matilla-Dueñas A. Novel genotype-phenotype correlations, differential cerebellar allele-specific methylation, and a common origin of the (ATTTC) n insertion in spinocerebellar ataxia type 37. Hum Genet 2024; 143:211-232. [PMID: 38396267 PMCID: PMC11043136 DOI: 10.1007/s00439-024-02644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
Spinocerebellar ataxia subtype 37 (SCA37) is a rare disease originally identified in ataxia patients from the Iberian Peninsula with a pure cerebellar syndrome. SCA37 patients carry a pathogenic intronic (ATTTC)n repeat insertion flanked by two polymorphic (ATTTT)n repeats in the Disabled-1 (DAB1) gene leading to cerebellar dysregulation. Herein, we determine the precise configuration of the pathogenic 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n SCA37 alleles by CRISPR-Cas9 and long-read nanopore sequencing, reveal their epigenomic signatures in SCA37 lymphocytes, fibroblasts, and cerebellar samples, and establish new molecular and clinical correlations. The 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n pathogenic allele configurations revealed repeat instability and differential methylation signatures. Disease age of onset negatively correlated with the (ATTTC)n, and positively correlated with the 3'(ATTTT)n. Geographic origin and gender significantly correlated with age of onset. Furthermore, significant predictive regression models were obtained by machine learning for age of onset and disease evolution by considering gender, the (ATTTC)n, the 3'(ATTTT)n, and seven CpG positions differentially methylated in SCA37 cerebellum. A common 964-kb genomic region spanning the (ATTTC)n insertion was identified in all SCA37 patients analysed from Portugal and Spain, evidencing a common origin of the SCA37 mutation in the Iberian Peninsula originating 859 years ago (95% CI 647-1378). In conclusion, we demonstrate an accurate determination of the size and configuration of the regulatory 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n repeat tract, avoiding PCR bias amplification using CRISPR/Cas9-enrichment and nanopore long-read sequencing, resulting relevant for accurate genetic diagnosis of SCA37. Moreover, we determine novel significant genotype-phenotype correlations in SCA37 and identify differential cerebellar allele-specific methylation signatures that may underlie DAB1 pathogenic dysregulation.
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Affiliation(s)
- Marina Sanchez-Flores
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Marc Corral-Juan
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Esther Gasch-Navalón
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | | | - Ivelisse Sanchez
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Antoni Matilla-Dueñas
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain.
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14
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Handley RR, Reid SJ, Burch Z, Jacobsen JC, Gillis T, Correia K, Rudiger SR, McLaughlin CJ, Bawden CS, MacDonald ME, Wheeler VC, Snell RG. Somatic CAG Repeat Stability in a Transgenic Sheep Model of Huntington's Disease. J Huntingtons Dis 2024; 13:33-40. [PMID: 38393920 DOI: 10.3233/jhd-231516] [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] [Indexed: 02/25/2024]
Abstract
Somatic instability of the huntingtin (HTT) CAG repeat mutation modifies age-at-onset of Huntington's disease (HD). Understanding the mechanism and pathogenic consequences of instability may reveal therapeutic targets. Using small-pool PCR we analyzed CAG instability in the OVT73 sheep model which expresses a full-length human cDNA HTT transgene. Analyses of five- and ten-year old sheep revealed the transgene (CAG)69 repeat was remarkably stable in liver, striatum, and other brain tissues. As OVT73 sheep at ten years old have minimal cell death and behavioral changes, our findings support instability of the HTT expanded-CAG repeat as being required for the progression of HD.
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Affiliation(s)
- Renee R Handley
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Suzanne J Reid
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Zoe Burch
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jessie C Jacobsen
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy Gillis
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin Correia
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Skye R Rudiger
- Molecular Biology and Reproductive Technology, Laboratories, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Clive J McLaughlin
- Molecular Biology and Reproductive Technology, Laboratories, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - C Simon Bawden
- Molecular Biology and Reproductive Technology, Laboratories, South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Marcy E MacDonald
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Vanessa C Wheeler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Russell G Snell
- Centre for Brain Research, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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15
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Birnbaum R. Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities. Transl Psychiatry 2023; 13:402. [PMID: 38123544 PMCID: PMC10733427 DOI: 10.1038/s41398-023-02689-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Tandem repeats (TRs) are prevalent throughout the genome, constituting at least 3% of the genome, and often highly polymorphic. The high mutation rate of TRs, which can be orders of magnitude higher than single-nucleotide polymorphisms and indels, indicates that they are likely to make significant contributions to phenotypic variation, yet their contribution to schizophrenia has been largely ignored by recent genome-wide association studies (GWAS). Tandem repeat expansions are already known causative factors for over 50 disorders, while common tandem repeat variation is increasingly being identified as significantly associated with complex disease and gene regulation. The current review summarizes key background concepts of tandem repeat variation as pertains to disease risk, elucidating their potential for schizophrenia association. An overview of next-generation sequencing-based methods that may be applied for TR genome-wide identification is provided, and some key methodological challenges in TR analyses are delineated.
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Affiliation(s)
- Rebecca Birnbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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16
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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17
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Zhou C, Liu HB, Jahanbakhsh F, Deng L, Wu B, Ying M, Margolis RL, Li PP. Bidirectional Transcription at the PPP2R2B Gene Locus in Spinocerebellar Ataxia Type 12. Mov Disord 2023; 38:2230-2240. [PMID: 37735923 PMCID: PMC10840700 DOI: 10.1002/mds.29605] [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: 04/04/2023] [Revised: 08/12/2023] [Accepted: 08/29/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Spinocerebellar ataxia type 12 (SCA12) is a neurodegenerative disease caused by expansion of a CAG repeat in the PPP2R2B gene. OBJECTIVE In this study, we tested the hypothesis that the PPP2R2B antisense (PPP2R2B-AS1) transcript containing a CUG repeat is expressed and contributes to SCA12 pathogenesis. METHODS Expression of PPP2R2B-AS1 transcript was detected in SCA12 human induced pluripotent stem cells (iPSCs), iPSC-derived NGN2 neurons, and SCA12 knock-in mouse brains using strand-specific reverse transcription polymerase chain reaction. The tendency of expanded PPP2R2B-AS1 (expPPP2R2B-AS1) RNA to form foci, a marker of toxic processes involving mutant RNAs, was examined in SCA12 cell models by fluorescence in situ hybridization. The apoptotic effect of expPPP2R2B-AS1 transcripts on SK-N-MC neuroblastoma cells was evaluated by caspase 3/7 activity. Western blot was used to examine the expression of repeat associated non-ATG-initiated translation of expPPP2R2B-AS1 transcript in SK-N-MC cells. RESULTS The repeat region in the PPP2R2B gene locus is bidirectionally transcribed in SCA12 iPSCs, iPSC-derived NGN2 neurons, and SCA12 mouse brains. Transfected expPPP2R2B-AS1 transcripts induce apoptosis in SK-N-MC cells, and the apoptotic effect may be mediated, at least in part, by the RNA secondary structure. The expPPP2R2B-AS1 transcripts form CUG RNA foci in SK-N-MC cells. expPPP2R2B-AS1 transcript is translated in the alanine open reading frame (ORF) via repeat-associated non-ATG translation, which is diminished by single-nucleotide interruptions within the CUG repeat and MBNL1 overexpression. CONCLUSIONS These findings suggest that PPP2R2B-AS1 contributes to SCA12 pathogenesis and may therefore provide a novel therapeutic target for the disease. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Chengqian Zhou
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hans B. Liu
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fatemeh Jahanbakhsh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Leon Deng
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mingyao Ying
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland, USA
| | - Russell L. Margolis
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Pan P. Li
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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18
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Stöberl N, Donaldson J, Binda CS, McAllister B, Hall-Roberts H, Jones L, Massey TH, Allen ND. Mutant huntingtin confers cell-autonomous phenotypes on Huntington's disease iPSC-derived microglia. Sci Rep 2023; 13:20477. [PMID: 37993517 PMCID: PMC10665390 DOI: 10.1038/s41598-023-46852-z] [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: 08/28/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a dominantly inherited CAG repeat expansion in the huntingtin gene (HTT). Neuroinflammation and microglia have been implicated in HD pathology, however it has been unclear if mutant HTT (mHTT) expression has an adverse cell-autonomous effect on microglial function, or if they are only activated in response to the neurodegenerative brain environment in HD. To establish a human cell model of HD microglia function, we generated isogenic controls for HD patient-derived induced pluripotent stem cells (iPSC) with 109 CAG repeats (Q109). Q109 and isogenic Q22 iPSC, as well as non-isogenic Q60 and Q33 iPSC lines, were differentiated to iPSC-microglia. Our study supports a model of basal microglia dysfunction in HD leading to elevated pro-inflammatory cytokine production together with impaired phagocytosis and endocytosis capacity, in the absence of immune stimulation. These findings are consistent with early microglia activation observed in pre-manifest patients and indicate that mHTT gene expression affects microglia function in a cell-autonomous way.
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Affiliation(s)
- Nina Stöberl
- School of Biosciences, Cardiff University, Cardiff, UK.
| | - Jasmine Donaldson
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Caroline S Binda
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Branduff McAllister
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Hazel Hall-Roberts
- UK Dementia Research Institute at Cardiff, Cardiff University, Cardiff, UK
| | - Lesley Jones
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Thomas H Massey
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
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19
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Ahmad M, Ríos-Anillo MR, Acosta-López JE, Cervantes-Henríquez ML, Martínez-Banfi M, Pineda-Alhucema W, Puentes-Rozo P, Sánchez-Barros C, Pinzón A, Patel HR, Vélez JI, Villarreal-Camacho JL, Pineda DA, Arcos-Burgos M, Sánchez-Rojas M. Uncovering the Genetic and Molecular Features of Huntington's Disease in Northern Colombia. Int J Mol Sci 2023; 24:16154. [PMID: 38003344 PMCID: PMC10671691 DOI: 10.3390/ijms242216154] [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: 08/01/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Huntington's disease (HD) is a genetic disorder caused by a CAG trinucleotide expansion in the huntingtin (HTT) gene. Juan de Acosta, Atlántico, a city located on the Caribbean coast of Colombia, is home to the world's second-largest HD pedigree. Here, we include 291 descendants of this pedigree with at least one family member with HD. Blood samples were collected, and genomic DNA was extracted. We quantified the HTT CAG expansion using an amplicon sequencing protocol. The genetic heterogeneity was measured as the ratio of the mosaicism allele's read peak and the slippage ratio of the allele's read peak from our sequence data. The statistical and bioinformatic analyses were performed with a significance threshold of p < 0.05. We found that the average HTT CAG repeat length in all participants was 21.91 (SD = 8.92). Of the 291 participants, 33 (11.3%, 18 females) had a positive molecular diagnosis for HD. Most affected individuals were adults, and the most common primary and secondary alleles were 17/7 (CAG/CCG) and 17/10 (CAG/CCG), respectively. The mosaicism increased with age in the participants with HD, while the slippage analyses revealed differences by the HD allele type only for the secondary allele. The slippage tended to increase with the HTT CAG repeat length in the participants with HD, but the increase was not statistically significant. This study analyzed the genetic and molecular features of 291 participants, including 33 with HD. We found that the mosaicism increased with age in the participants with HD, particularly for the secondary allele. The most common haplotype was 17/7_17/10. The slippage for the secondary allele varied by the HD allele type, but there was no significant difference in the slippage by sex. Our findings offer valuable insights into HD and could have implications for future research and clinical management.
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Affiliation(s)
- Mostapha Ahmad
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Margarita R Ríos-Anillo
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Médica Residente de Neurología, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Johan E Acosta-López
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Facultad de Ciencias Jurídicas y Sociales, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Martha L Cervantes-Henríquez
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Facultad de Ciencias Jurídicas y Sociales, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Martha Martínez-Banfi
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Facultad de Ciencias Jurídicas y Sociales, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Wilmar Pineda-Alhucema
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Facultad de Ciencias Jurídicas y Sociales, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Pedro Puentes-Rozo
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Grupo de Neurociencias del Caribe, Universidad del Atlántico, Barranquilla 080001, Colombia
| | - Cristian Sánchez-Barros
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Life Science Research Center, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Departamento de Neurofisiología Clínica Palma de Mallorca, Hospital Juaneda Miramar, Islas Baleares, 07011 Palma, Spain
| | - Andrés Pinzón
- Bioinformatics and Systems Biology Laboratory, Institute for Genetics, Universidad Nacional de Colombia, Bogota 111321, Colombia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Jorge I Vélez
- Department of Industrial Engineering, Universidad del Norte, Barranquilla 081007, Colombia
| | - José Luis Villarreal-Camacho
- Programa de Medicina, Facultad de Ciencias de la Salud, Universidad Libre Seccional Barranquilla, Barranquilla 081007, Colombia
| | - David A Pineda
- Grupo de Investigación en Neuropsicología y Conducta, Universidad de San Buenaventura, Medellin 050010, Colombia
- Grupo de Neurociencias de Antioquia, Universidad de Antioquia, Medellin 050010, Colombia
| | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellin 050010, Colombia
| | - Manuel Sánchez-Rojas
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla 080002, Colombia
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20
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Nguyen TB, Miramontes R, Chillon-Marinas C, Maimon R, Vazquez-Sanchez S, Lau AL, McClure NR, England WE, Singha M, Stocksdale JT, Jang KH, Jung S, McKnight JI, Ho LN, Faull RLM, Steffan JS, Reidling JC, Jang C, Lee G, Cleveland DW, Lagier-Tourenne C, Spitale RC, Thompson LM. Aberrant splicing in Huntington's disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565004. [PMID: 37961595 PMCID: PMC10635028 DOI: 10.1101/2023.10.31.565004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene encoding huntingtin. Prior reports have established a correlation between CAG expanded HTT and altered gene expression. However, the mechanisms leading to disruption of RNA processing in HD remain unclear. Here, our analysis of the reported HTT protein interactome identifies interactions with known RNA-binding proteins (RBPs). Total, long-read sequencing and targeted RASL-seq of RNAs from cortex and striatum of the HD mouse model R6/2 reveals increased exon skipping which is confirmed in Q150 and Q175 knock-in mice and in HD human brain. We identify the RBP TDP-43 and the N6-methyladenosine (m6A) writer protein methyltransferase 3 (METTL3) to be upstream regulators of exon skipping in HD. Along with this novel mechanistic insight, we observe decreased nuclear localization of TDP-43 and cytoplasmic accumulation of phosphorylated TDP-43 in HD mice and human brain. In addition, TDP-43 co-localizes with HTT in human HD brain forming novel nuclear aggregate-like bodies distinct from mutant HTT inclusions or previously observed TDP-43 pathologies. Binding of TDP-43 onto RNAs encoding HD-associated differentially expressed and aberrantly spliced genes is decreased. Finally, m6A RNA modification is reduced on RNAs abnormally expressed in striatum from HD R6/2 mouse brain, including at clustered sites adjacent to TDP-43 binding sites. Our evidence supports TDP-43 loss of function coupled with altered m6A modification as a novel mechanism underlying alternative splicing/unannotated exon usage in HD and highlights the critical nature of TDP-43 function across multiple neurodegenerative diseases.
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21
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Estevez-Fraga C, Altmann A, Parker CS, Scahill RI, Costa B, Chen Z, Manzoni C, Zarkali A, Durr A, Roos RAC, Landwehrmeyer B, Leavitt BR, Rees G, Tabrizi SJ, McColgan P. Genetic topography and cortical cell loss in Huntington's disease link development and neurodegeneration. Brain 2023; 146:4532-4546. [PMID: 37587097 PMCID: PMC10629790 DOI: 10.1093/brain/awad275] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/12/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023] Open
Abstract
Cortical cell loss is a core feature of Huntington's disease (HD), beginning many years before clinical motor diagnosis, during the premanifest stage. However, it is unclear how genetic topography relates to cortical cell loss. Here, we explore the biological processes and cell types underlying this relationship and validate these using cell-specific post-mortem data. Eighty premanifest participants on average 15 years from disease onset and 71 controls were included. Using volumetric and diffusion MRI we extracted HD-specific whole brain maps where lower grey matter volume and higher grey matter mean diffusivity, relative to controls, were used as proxies of cortical cell loss. These maps were combined with gene expression data from the Allen Human Brain Atlas (AHBA) to investigate the biological processes relating genetic topography and cortical cell loss. Cortical cell loss was positively correlated with the expression of developmental genes (i.e. higher expression correlated with greater atrophy and increased diffusivity) and negatively correlated with the expression of synaptic and metabolic genes that have been implicated in neurodegeneration. These findings were consistent for diffusion MRI and volumetric HD-specific brain maps. As wild-type huntingtin is known to play a role in neurodevelopment, we explored the association between wild-type huntingtin (HTT) expression and developmental gene expression across the AHBA. Co-expression network analyses in 134 human brains free of neurodegenerative disorders were also performed. HTT expression was correlated with the expression of genes involved in neurodevelopment while co-expression network analyses also revealed that HTT expression was associated with developmental biological processes. Expression weighted cell-type enrichment (EWCE) analyses were used to explore which specific cell types were associated with HD cortical cell loss and these associations were validated using cell specific single nucleus RNAseq (snRNAseq) data from post-mortem HD brains. The developmental transcriptomic profile of cortical cell loss in preHD was enriched in astrocytes and endothelial cells, while the neurodegenerative transcriptomic profile was enriched for neuronal and microglial cells. Astrocyte-specific genes differentially expressed in HD post-mortem brains relative to controls using snRNAseq were enriched in the developmental transcriptomic profile, while neuronal and microglial-specific genes were enriched in the neurodegenerative transcriptomic profile. Our findings suggest that cortical cell loss in preHD may arise from dual pathological processes, emerging as a consequence of neurodevelopmental changes, at the beginning of life, followed by neurodegeneration in adulthood, targeting areas with reduced expression of synaptic and metabolic genes. These events result in age-related cell death across multiple brain cell types.
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Affiliation(s)
- Carlos Estevez-Fraga
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| | - Andre Altmann
- Centre for Medical Image Computing, University College London, London WC1V 6LJ, UK
| | - Christopher S Parker
- Centre for Medical Image Computing, University College London, London WC1V 6LJ, UK
| | - Rachael I Scahill
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| | - Beatrice Costa
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Zhongbo Chen
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| | - Claudia Manzoni
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Angeliki Zarkali
- Dementia Research Centre, University College London, London WC1N 3AR, UK
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute (ICM), AP-HP, Inserm, CNRS, Paris 75013, France
| | - Raymund A C Roos
- Department of Neurology, Leiden University Medical Centre, Leiden 2333, The Netherlands
| | | | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver BC V5Z 4H4Canada
- Division of Neurology, Department of Medicine, University of British Columbia Hospital, Vancouver BC V6T 2B5, Canada
| | - Geraint Rees
- Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, University College London, London WC1N 3AR, UK
| | - Sarah J Tabrizi
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
| | - Peter McColgan
- Department of Neurodegenerative Disease, University College London, London WC1B 5EH, UK
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22
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Gall-Duncan T, Luo J, Jurkovic CM, Fischer LA, Fujita K, Deshmukh AL, Harding RJ, Tran S, Mehkary M, Li V, Leib DE, Chen R, Tanaka H, Mason AG, Lévesque D, Khan M, Razzaghi M, Prasolava T, Lanni S, Sato N, Caron MC, Panigrahi GB, Wang P, Lau R, Castel AL, Masson JY, Tippett L, Turner C, Spies M, La Spada AR, Campos EI, Curtis MA, Boisvert FM, Faull RLM, Davidson BL, Nakamori M, Okazawa H, Wold MS, Pearson CE. Antagonistic roles of canonical and Alternative-RPA in disease-associated tandem CAG repeat instability. Cell 2023; 186:4898-4919.e25. [PMID: 37827155 PMCID: PMC11209935 DOI: 10.1016/j.cell.2023.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/30/2023] [Accepted: 09/09/2023] [Indexed: 10/14/2023]
Abstract
Expansions of repeat DNA tracts cause >70 diseases, and ongoing expansions in brains exacerbate disease. During expansion mutations, single-stranded DNAs (ssDNAs) form slipped-DNAs. We find the ssDNA-binding complexes canonical replication protein A (RPA1, RPA2, and RPA3) and Alternative-RPA (RPA1, RPA3, and primate-specific RPA4) are upregulated in Huntington disease and spinocerebellar ataxia type 1 (SCA1) patient brains. Protein interactomes of RPA and Alt-RPA reveal unique and shared partners, including modifiers of CAG instability and disease presentation. RPA enhances in vitro melting, FAN1 excision, and repair of slipped-CAGs and protects against CAG expansions in human cells. RPA overexpression in SCA1 mouse brains ablates expansions, coincident with decreased ATXN1 aggregation, reduced brain DNA damage, improved neuron morphology, and rescued motor phenotypes. In contrast, Alt-RPA inhibits melting, FAN1 excision, and repair of slipped-CAGs and promotes CAG expansions. These findings suggest a functional interplay between the two RPAs where Alt-RPA may antagonistically offset RPA's suppression of disease-associated repeat expansions, which may extend to other DNA processes.
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Affiliation(s)
- Terence Gall-Duncan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer Luo
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Laura A Fischer
- Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyota Fujita
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amit L Deshmukh
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephanie Tran
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mustafa Mehkary
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Vanessa Li
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - David E Leib
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Ran Chen
- Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hikari Tanaka
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Amanda G Mason
- Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Lévesque
- Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mahreen Khan
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mortezaali Razzaghi
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Tanya Prasolava
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stella Lanni
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nozomu Sato
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marie-Christine Caron
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Gagan B Panigrahi
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peixiang Wang
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rachel Lau
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec, QC, Canada
| | - Lynette Tippett
- School of Psychology, University of Auckland, Auckland, New Zealand; University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Clinton Turner
- Anatomical Pathology, LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Maria Spies
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Albert R La Spada
- Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, University of California, Irvine School of Medicine, Irvine, CA, USA; Neurobiology & Behavior, University of California, Irvine, Irvine, CA, USA; Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA
| | - Eric I Campos
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Maurice A Curtis
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | | | - Richard L M Faull
- University Research Centre for Brain Research, University of Auckland, Auckland, New Zealand; Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
| | - Beverly L Davidson
- Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Masayuki Nakamori
- Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hitoshi Okazawa
- Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Marc S Wold
- Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Christopher E Pearson
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.
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23
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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] [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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24
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Speidell A, Bin Abid N, Yano H. Brain-Derived Neurotrophic Factor Dysregulation as an Essential Pathological Feature in Huntington's Disease: Mechanisms and Potential Therapeutics. Biomedicines 2023; 11:2275. [PMID: 37626771 PMCID: PMC10452871 DOI: 10.3390/biomedicines11082275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a major neurotrophin whose loss or interruption is well established to have numerous intersections with the pathogenesis of progressive neurological disorders. There is perhaps no greater example of disease pathogenesis resulting from the dysregulation of BDNF signaling than Huntington's disease (HD)-an inherited neurodegenerative disorder characterized by motor, psychiatric, and cognitive impairments associated with basal ganglia dysfunction and the ultimate death of striatal projection neurons. Investigation of the collection of mechanisms leading to BDNF loss in HD highlights this neurotrophin's importance to neuronal viability and calls attention to opportunities for therapeutic interventions. Using electronic database searches of existing and forthcoming research, we constructed a literature review with the overarching goal of exploring the diverse set of molecular events that trigger BDNF dysregulation within HD. We highlighted research that investigated these major mechanisms in preclinical models of HD and connected these studies to those evaluating similar endpoints in human HD subjects. We also included a special focus on the growing body of literature detailing key transcriptomic and epigenetic alterations that affect BDNF abundance in HD. Finally, we offer critical evaluation of proposed neurotrophin-directed therapies and assessed clinical trials seeking to correct BDNF expression in HD individuals.
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Affiliation(s)
- Andrew Speidell
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
| | - Noman Bin Abid
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; (A.S.); (N.B.A.)
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
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Tano V, Utami KH, Yusof NABM, Bégin J, Tan WWL, Pouladi MA, Langley SR. Widespread dysregulation of mRNA splicing implicates RNA processing in the development and progression of Huntington's disease. EBioMedicine 2023; 94:104720. [PMID: 37481821 PMCID: PMC10393612 DOI: 10.1016/j.ebiom.2023.104720] [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: 02/02/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND In Huntington's disease (HD), a CAG repeat expansion mutation in the Huntingtin (HTT) gene drives a gain-of-function toxicity that disrupts mRNA processing. Although dysregulation of gene splicing has been shown in human HD post-mortem brain tissue, post-mortem analyses are likely confounded by cell type composition changes in late-stage HD, limiting the ability to identify dysregulation related to early pathogenesis. METHODS To investigate gene splicing changes in early HD, we performed alternative splicing analyses coupled with a proteogenomics approach to identify early CAG length-associated splicing changes in an established isogenic HD cell model. FINDINGS We report widespread neuronal differentiation stage- and CAG length-dependent splicing changes, and find an enrichment of RNA processing, neuronal function, and epigenetic modification-related genes with mutant HTT-associated splicing. When integrated with a proteomics dataset, we identified several of these differential splicing events at the protein level. By comparing with human post-mortem and mouse model data, we identified common patterns of altered splicing from embryonic stem cells through to post-mortem striatal tissue. INTERPRETATION We show that widespread splicing dysregulation in HD occurs in an early cell model of neuronal development. Importantly, we observe HD-associated splicing changes in our HD cell model that were also identified in human HD striatum and mouse model HD striatum, suggesting that splicing-associated pathogenesis possibly occurs early in neuronal development and persists to later stages of disease. Together, our results highlight splicing dysregulation in HD which may lead to disrupted neuronal function and neuropathology. FUNDING This research is supported by the Lee Kong Chian School of Medicine, Nanyang Technological University Singapore Nanyang Assistant Professorship Start-Up Grant, the Singapore Ministry of Education under its Singapore Ministry of Education Academic Research Fund Tier 1 (RG23/22), the BC Children's Hospital Research Institute Investigator Grant Award (IGAP), and a Scholar Award from the Michael Smith Health Research BC.
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Affiliation(s)
- Vincent Tano
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Kagistia Hana Utami
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Nur Amirah Binte Mohammad Yusof
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Jocelyn Bégin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Willy Wei Li Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore; Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore.
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Hu J, Gong X, Johnson ST, Corey DR, Mootha VV. The TCF4 Trinucleotide Repeat Expansion of Fuchs' Endothelial Corneal Dystrophy: Implications for the Anterior Segment of the Eye. Invest Ophthalmol Vis Sci 2023; 64:16. [PMID: 37204786 PMCID: PMC10204776 DOI: 10.1167/iovs.64.5.16] [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: 01/19/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023] Open
Abstract
Purpose In the United States, 70% of Fuchs' endothelial corneal dystrophy (FECD) cases are caused by an intronic trinucleotide repeat expansion in the TCF4 gene. CUG repeat RNA transcripts from this expansion accumulate as nuclear foci in the corneal endothelium. In this study, we sought to detect foci in other anterior segment cell types and assess their molecular impact. Methods We examined CUG repeat RNA foci appearance, expression of downstream affected genes, gene splicing, and TCF4 RNA expression in corneal endothelium, corneal stromal keratocytes, corneal epithelium, trabecular meshwork cells, and lens epithelium. Results CUG repeat RNA foci, the hallmark of FECD in corneal endothelium (found in 84% of endothelial cells), are less detectable in trabecular meshwork cells (41%), much less prevalent in stromal keratocytes (11%) or corneal epithelium (4%), and absent in lens epithelium. With few exceptions including mis-splicing in the trabecular meshwork, differential gene expression and splicing changes associated with the expanded repeat in corneal endothelial cells are not observed in other cell types. Expression of the TCF4 transcripts including full-length isoforms containing the repeat sequence at the 5' end is much higher in the corneal endothelium or trabecular meshwork than in the corneal stroma or corneal epithelium. Conclusions Expression of the CUG repeat containing TCF4 transcripts is higher in the corneal endothelium, likely contributing to foci formation and the large molecular and pathologic impact on those cells. Further studies are warranted to examine any glaucoma risk and impact of the observed foci in the trabecular meshwork of these patients.
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Affiliation(s)
- Jiaxin Hu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Xin Gong
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Samantha T. Johnson
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - David R. Corey
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - V. Vinod Mootha
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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27
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Aishworiya R, Hwang YH, Santos E, Hayward B, Usdin K, Durbin-Johnson B, Hagerman R, Tassone F. Clinical implications of somatic allele expansion in female FMR1 premutation carriers. Sci Rep 2023; 13:7050. [PMID: 37120588 PMCID: PMC10148869 DOI: 10.1038/s41598-023-33528-x] [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: 11/10/2022] [Accepted: 04/14/2023] [Indexed: 05/01/2023] Open
Abstract
Carriers of a premutation allele (PM) in the FMR1 gene are at risk of developing a number of Fragile X premutation asssociated disorders (FXPAC), including Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), Fragile X-associated Primary Ovarian Insufficiency (FXPOI), and Fragile X-associated neuropsychiatric disorders (FXAND). We have recently reported somatic CGG allele expansion in female PM; however, its clinical significance remains unclear. The aim of this study was to examine the potential clinical association between somatic FMR1 allele instability and PM associated disorders. Participants comprised of 424 female PM carriers age 0.3- 90 years. FMR1 molecular measures and clinical information on the presence of medical conditions, were determined for all subjects for primary analysis. Two sub-groups of participants (age ≥ 25, N = 377 and age ≥ 50, N = 134) were used in the analysis related to presence of FXPOI and FXTAS, respectively. Among all participants (N = 424), the degree of instability (expansion) was significantly higher (median 2.5 vs 2.0, P = 0.026) in participants with a diagnosis of attention deficit hyperactivity disorder (ADHD) compared to those without. FMR1 mRNA expression was significantly higher in subjects with any psychiatric disorder diagnosis (P = 0.0017); specifically, in those with ADHD (P = 0.009), and with depression (P = 0.025). Somatic FMR1 expansion was associated with the presence of ADHD in female PM and FMR1 mRNA levels were associated with the presence of mental health disorders. The findings of our research are innovative as they suggest a potential role of the CGG expansion in the clinical phenotype of PM and may potentially guide clinical prognosis and management.
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Affiliation(s)
- Ramkumar Aishworiya
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Singapore
| | - Ye Hyun Hwang
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Ellery Santos
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Department of Pediatrics, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Bruce Hayward
- Laboratory of Cell and Molecular Biology, Digestive and Kidney Diseases, National Institute of Diabetes, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, Digestive and Kidney Diseases, National Institute of Diabetes, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California, Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Randi Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA
- Department of Pediatrics, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| | - Flora Tassone
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50Th Street, Sacramento, CA, 95817, USA.
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, 4610 X St, Sacramento, CA, 95817, USA.
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28
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Choi DE, Shin JW, Zeng S, Hong EP, Jang JH, Loupe JM, Wheeler VC, Stutzman HE, Kleinstiver BP, Lee JM. Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538700. [PMID: 37162872 PMCID: PMC10168301 DOI: 10.1101/2023.04.28.538700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
An expanded CAG repeat in the huntingtin gene ( HTT ) causes Huntington's disease (HD). Since the length of uninterrupted CAG repeat, not polyglutamine, determines the age-at-onset in HD, base editing strategies to convert CAG to CAA are anticipated to delay onset by shortening the uninterrupted CAG repeat. Here, we developed base editing strategies to convert CAG in the repeat to CAA and determined their molecular outcomes and effects on relevant disease phenotypes. Base editing strategies employing combinations of cytosine base editors and gRNAs efficiently converted CAG to CAA at various sites in the CAG repeat without generating significant indels, off-target edits, or transcriptome alterations, demonstrating their feasibility and specificity. Candidate BE strategies converted CAG to CAA on both expanded and non-expanded CAG repeats without altering HTT mRNA and protein levels. In addition, somatic CAG repeat expansion, which is the major disease driver in HD, was significantly decreased by a candidate BE strategy treatment in HD knock-in mice carrying canonical CAG repeats. Notably, CAG repeat expansion was abolished entirely in HD knock-in mice carrying CAA-interrupted repeats, supporting the therapeutic potential of CAG-to-CAA conversion base editing strategies in HD and potentially other repeat expansion disorders.
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29
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Vauleon S, Schutz K, Massonnet B, Gruben N, Manchester M, Buehler A, Schick E, Boak L, Hawellek DJ. Quantifying mutant huntingtin protein in human cerebrospinal fluid to support the development of huntingtin-lowering therapies. Sci Rep 2023; 13:5332. [PMID: 37005488 PMCID: PMC10067853 DOI: 10.1038/s41598-023-32630-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/30/2023] [Indexed: 04/04/2023] Open
Abstract
Huntington's disease (HD) is caused by a cytosine adenine guanine-repeat expansion in the huntingtin gene. This results in the production of toxic mutant huntingtin protein (mHTT), which has an elongated polyglutamine (polyQ) stretch near the protein's N-terminal end. The pharmacological lowering of mHTT expression in the brain targets the underlying driver of HD and is one of the principal therapeutic strategies being pursued to slow or stop disease progression. This report describes the characterisation and validation of an assay designed to quantify mHTT in the cerebrospinal fluid of individuals with HD, for use in registrational clinical trials. The assay was optimised, and its performance was characterised with recombinant huntingtin protein (HTT) varying in overall and polyQ-repeat length. The assay was successfully validated by two independent laboratories in regulated bioanalytical environments and showed a steep signal increase as the polyQ stretch of recombinant HTTs pivoted from wild-type to mutant protein forms. Linear mixed effects modelling confirmed highly parallel concentration-response curves for HTTs, with only a minor impact of individual slopes of the concentration-response for different HTTs (typically < 5% of the overall slope). This implies an equivalent quantitative signal behaviour for HTTs with differing polyQ-repeat lengths. The reported method may be a reliable biomarker tool with relevance across the spectrum of HD mutations, which can facilitate the clinical development of HTT-lowering therapies in HD.
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Affiliation(s)
- Stephanie Vauleon
- Regulated Bioanalysis, Pharmaceutical Sciences, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Katharina Schutz
- Regulated Bioanalysis, Pharmaceutical Sciences, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Benoit Massonnet
- Regulated Bioanalysis, Pharmaceutical Sciences, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Nanda Gruben
- ICON Bioanalytical Laboratories, Assen, The Netherlands
| | - Marianne Manchester
- Pharmaceutical Sciences, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Alessandra Buehler
- Regulated Bioanalysis, Pharmaceutical Sciences, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eginhard Schick
- Regulated Bioanalysis, Pharmaceutical Sciences, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Lauren Boak
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - David J Hawellek
- Biomarkers and Translational Technologies, Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland.
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30
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Verbiest M, Maksimov M, Jin Y, Anisimova M, Gymrek M, Bilgin Sonay T. Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species. J Evol Biol 2023; 36:321-336. [PMID: 36289560 PMCID: PMC9990875 DOI: 10.1111/jeb.14106] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/29/2022] [Accepted: 08/01/2022] [Indexed: 02/03/2023]
Abstract
Short tandem repeats (STRs) are units of 1-6 bp that repeat in a tandem fashion in DNA. Along with single nucleotide polymorphisms and large structural variations, they are among the major genomic variants underlying genetic, and likely phenotypic, divergence. STRs experience mutation rates that are orders of magnitude higher than other well-studied genotypic variants. Frequent copy number changes result in a wide range of alleles, and provide unique opportunities for modulating complex phenotypes through variation in repeat length. While classical studies have identified key roles of individual STR loci, the advent of improved sequencing technology, high-quality genome assemblies for diverse species, and bioinformatics methods for genome-wide STR analysis now enable more systematic study of STR variation across wide evolutionary ranges. In this review, we explore mutation and selection processes that affect STR copy number evolution, and how these processes give rise to varying STR patterns both within and across species. Finally, we review recent examples of functional and adaptive changes linked to STRs.
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Affiliation(s)
- Max Verbiest
- Institute of Computational Life Sciences, School of Life Sciences and Facility ManagementZürich University of Applied SciencesWädenswilSwitzerland
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Mikhail Maksimov
- Department of Computer Science & EngineeringUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Ye Jin
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of BioengineeringUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Maria Anisimova
- Institute of Computational Life Sciences, School of Life Sciences and Facility ManagementZürich University of Applied SciencesWädenswilSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Melissa Gymrek
- Department of Computer Science & EngineeringUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Tugce Bilgin Sonay
- Institute of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNew YorkUSA
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31
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Zhang S, Cheng Y, Shang H. The updated development of blood-based biomarkers for Huntington's disease. J Neurol 2023; 270:2483-2503. [PMID: 36692635 PMCID: PMC9873222 DOI: 10.1007/s00415-023-11572-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
Huntington's disease is a progressive neurodegenerative disease caused by mutation of the huntingtin (HTT) gene. The identification of mutation carriers before symptom onset provides an opportunity to intervene in the early stage of the disease course. Optimal biomarkers are of great value to reflect neuropathological and clinical progression and are sensitive to potential disease-modifying treatments. Blood-based biomarkers have the merits of minimal invasiveness, low cost, easy accessibility and safety. In this review, we summarized the updated development of blood-based biomarkers for HD from six aspects, including neuronal injuries, oxidative stress, endocrine functions, immune reactions, metabolism and differentially expressed miRNAs. The blood-based biomarkers presented and discussed in this review were close to clinical applicability and might facilitate clinical design as surrogate endpoints. Exploration and validation of robust blood-based biomarkers require further standard and systemic study design in the future.
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Affiliation(s)
- Sirui Zhang
- grid.412901.f0000 0004 1770 1022Laboratory of Neurodegenerative Disorders, Department of Neurology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatric, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, 610041 China ,grid.412901.f0000 0004 1770 1022West China School of Medicine, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yangfan Cheng
- grid.412901.f0000 0004 1770 1022Laboratory of Neurodegenerative Disorders, Department of Neurology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatric, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Huifang Shang
- grid.412901.f0000 0004 1770 1022Laboratory of Neurodegenerative Disorders, Department of Neurology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatric, Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, 610041 China
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32
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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] [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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33
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Blum JA, Gitler AD. Singling out motor neurons in the age of single-cell transcriptomics. Trends Genet 2022; 38:904-919. [PMID: 35487823 PMCID: PMC9378604 DOI: 10.1016/j.tig.2022.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 01/07/2023]
Abstract
Motor neurons are a remarkably powerful cell type in the central nervous system. They innervate and control the contraction of virtually every muscle in the body and their dysfunction underlies numerous neuromuscular diseases. Some motor neurons seem resistant to degeneration whereas others are vulnerable. The intrinsic heterogeneity of motor neurons in adult organisms has remained elusive. The development of high-throughput single-cell transcriptomics has changed the paradigm, empowering rapid isolation and profiling of motor neuron nuclei, revealing remarkable transcriptional diversity within the skeletal and autonomic nervous systems. Here, we discuss emerging technologies for defining motor neuron heterogeneity in the adult motor system as well as implications for disease and spinal cord injury. We establish a roadmap for future applications of emerging techniques - such as epigenetic profiling, spatial RNA sequencing, and single-cell somatic mutational profiling to adult motor neurons, which will revolutionize our understanding of the healthy and degenerating adult motor system.
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Affiliation(s)
- Jacob A Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Neurosciences Interdepartmental Program, Stanford University School of Medicine, Stanford, CA, USA.
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Heterogeneous migration routes of DNA triplet repeat slip-outs. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 36299495 PMCID: PMC9586884 DOI: 10.1016/j.bpr.2022.100070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022]
Abstract
It is unclear how the length of a repetitive DNA tract determines the onset and progression of repeat expansion diseases, but the dynamics of secondary DNA structures formed by repeat sequences are believed to play an important role. It was recently shown that three-way DNA junctions containing slip-out hairpins of CAG or CTG repeats and contiguous triplet repeats in the adjacent duplex displayed single-molecule FRET (smFRET) dynamics that were ascribed to both local conformational motions and longer-range branch migration. Here we explore these so-called "mobile" slip-out structures through a detailed kinetic analysis of smFRET trajectories and coarse-grained modeling. Despite the apparent structural simplicity, with six FRET states resolvable, most smFRET states displayed biexponential dwell-time distributions, attributed to structural heterogeneity and overlapping FRET states. Coarse-grained modeling for a (GAC)10 repeat slip-out included trajectories that corresponded to a complete round of branch migration; the structured free energy landscape between slippage events supports the dynamical complexity observed by smFRET. A hairpin slip-out with 40 CAG repeats, which is above the repeat length required for disease in several triplet repeat disorders, displayed smFRET dwell times that were on average double those of 3WJs with 10 repeats. The rate of secondary-structure rearrangement via branch migration, relative to particular DNA processing pathways, may be an important factor in the expansion of triplet repeat expansion diseases.
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35
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Kaye J, Reisine T, Finkbeiner S. Huntington's disease iPSC models-using human patient cells to understand the pathology caused by expanded CAG repeats. Fac Rev 2022; 11:16. [PMID: 35865413 PMCID: PMC9264339 DOI: 10.12703/r/11-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A major advance in the study of Huntington's disease (HD) has been the development of human disease models employing induced pluripotent stem cells (iPSCs) derived from patients with HD. Because iPSCs provide an unlimited source of cells and can be obtained from large numbers of HD patients, they are a uniquely valuable tool for investigating disease mechanisms and for discovering potential disease-modifying therapeutics. Here, we summarize some of the important findings in HD pathophysiology that have emerged from studies of patient-derived iPSC lines. Because they retain the genome and actual disease mutations of the patient, they provide a cell source to investigate genetic contributions to the disease. iPSCs provide advantages over other disease models. While iPSC-based technology erases some epigenetic marks, newly developed transdifferentiation methods now let us investigate epigenetic factors that control expression of mutant huntingtin (mHTT). Human HD iPSC lines allow us to investigate how endogenous levels of mHTT affect cell health, in contrast to other models that often rely on overexpressing the protein. iPSCs can be differentiated into neurons and other disease-related cells such as astrocytes from different brain regions to study brain regional differences in the disease process, as well as the cell-cell dependencies involved in HD-associated neurodegeneration. They also serve as a tissue source to investigate factors that impact CAG repeat instability, which is involved in regional differences in neurodegeneration in the HD brain. Human iPSC models can serve as a powerful model system to identify genetic modifiers that may impact disease onset, progression, and symptomatology, providing novel molecular targets for drug discovery.
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Affiliation(s)
- Julia Kaye
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Terry Reisine
- Independent Scientific Consultant, Santa Cruz, CA, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA, USA
- Department of Neurology and Physiology, University of California, San Francisco, CA, USA
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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] [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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When does Huntington disease begin? Rev Neurol (Paris) 2022; 178:422-425. [PMID: 35597611 DOI: 10.1016/j.neurol.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Martí-Martínez S, Valor LM. A Glimpse of Molecular Biomarkers in Huntington's Disease. Int J Mol Sci 2022; 23:ijms23105411. [PMID: 35628221 PMCID: PMC9142992 DOI: 10.3390/ijms23105411] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022] Open
Abstract
Huntington's disease (HD) is a devastating neurodegenerative disorder that is caused by an abnormal expansion of CAG repeats in the Huntingtin (HTT) gene. Although the main symptomatology is explained by alterations at the level of the central nervous system, predominantly affecting the basal ganglia, a peripheral component of the disease is being increasingly acknowledged. Therefore, the manifestation of the disease is complex and variable among CAG expansion carriers, introducing uncertainty in the appearance of specific signs, age of onset and severity of disease. The monogenic nature of the disorder allows a precise diagnosis, but the use of biomarkers with prognostic value is still needed to achieve clinical management of the patients in an individual manner. In addition, we need tools to evaluate the patient's response to potential therapeutic approaches. In this review, we provide a succinct summary of the most interesting molecular biomarkers that have been assessed in patients, mostly obtained from body fluids such as cerebrospinal fluid, peripheral blood and saliva.
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Affiliation(s)
- Silvia Martí-Martínez
- Servicio de Neurología, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain;
| | - Luis M. Valor
- Laboratorio de Apoyo a la Investigación, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
- Correspondence: ; Tel.: +34-965-913-988
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Lee S, Lee JH. Brain somatic mutations as RNA therapeutic targets in neurological disorders. Ann N Y Acad Sci 2022; 1514:11-20. [PMID: 35527236 DOI: 10.1111/nyas.14786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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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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] [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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Karwacka M, Olejniczak M. Advances in Modeling Polyglutamine Diseases Using Genome Editing Tools. Cells 2022; 11:cells11030517. [PMID: 35159326 PMCID: PMC8834129 DOI: 10.3390/cells11030517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
Polyglutamine (polyQ) diseases, including Huntington’s disease, are a group of late-onset progressive neurological disorders caused by CAG repeat expansions. Although recently, many studies have investigated the pathological features and development of polyQ diseases, many questions remain unanswered. The advancement of new gene-editing technologies, especially the CRISPR-Cas9 technique, has undeniable value for the generation of relevant polyQ models, which substantially support the research process. Here, we review how these tools have been used to correct disease-causing mutations or create isogenic cell lines with different numbers of CAG repeats. We characterize various cellular models such as HEK 293 cells, patient-derived fibroblasts, human embryonic stem cells (hESCs), induced pluripotent stem cells (iPSCs) and animal models generated with the use of genome-editing technology.
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Ghanekar SD, Kuo SH, Staffetti JS, Zesiewicz TA. Current and Emerging Treatment Modalities for Spinocerebellar Ataxias. Expert Rev Neurother 2022; 22:101-114. [PMID: 35081319 DOI: 10.1080/14737175.2022.2029703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Spinocerebellar ataxias (SCA) are a group of rare neurodegenerative diseases that dramatically affect the lives of affected individuals and their families. Despite having a clear understanding of SCA's etiology, there are no current symptomatic or neuroprotective treatments approved by the FDA. AREAS COVERED Research efforts have greatly expanded the possibilities for potential treatments, including both pharmacological and non-pharmacological interventions. Great attention is also being given to novel therapeutics based in gene therapy, neurostimulation, and molecular targeting. This review article will address the current advances in the treatment of SCA and what potential interventions are on the horizon. EXPERT OPINION SCA is a highly complex and multifaceted disease family with the majority of research emphasizing symptomatic pharmacologic therapies. As pre-clinical trials for SCA and clinical trials for other neurodegenerative conditions illuminate the efficacy of disease modifying therapies such as AAV-mediated gene therapy and ASOs, the potential for addressing SCA at the pre-symptomatic stage is increasingly promising.
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Affiliation(s)
- Shaila D Ghanekar
- University of South Florida (USF) Department of Neurology, USF Ataxia Research Center, Tampa, Florida, USA.,James A Haley Veteran's Hospital, Tampa, Florida, USA
| | - Sheng-Han Kuo
- Department of Neurology, Columbia University, New York, New York, USA.,Initiative for Columbia Ataxia and Tremor, New York, New York, USA
| | - Joseph S Staffetti
- University of South Florida (USF) Department of Neurology, USF Ataxia Research Center, Tampa, Florida, USA.,James A Haley Veteran's Hospital, Tampa, Florida, USA
| | - Theresa A Zesiewicz
- University of South Florida (USF) Department of Neurology, USF Ataxia Research Center, Tampa, Florida, USA.,James A Haley Veteran's Hospital, Tampa, Florida, USA
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Shenoy SA, Zheng S, Liu W, Dai Y, Liu Y, Hou Z, Mori S, Tang Y, Cheng J, Duan W, Li C. A novel and accurate full-length HTT mouse model for Huntington's disease. eLife 2022; 11:e70217. [PMID: 35023827 PMCID: PMC8758142 DOI: 10.7554/elife.70217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/31/2021] [Indexed: 01/29/2023] Open
Abstract
Here, we report the generation and characterization of a novel Huntington's disease (HD) mouse model BAC226Q by using a bacterial artificial chromosome (BAC) system, expressing full-length human HTT with ~226 CAG-CAA repeats and containing endogenous human HTT promoter and regulatory elements. BAC226Q recapitulated a full-spectrum of age-dependent and progressive HD-like phenotypes without unwanted and erroneous phenotypes. BAC226Q mice developed normally, and gradually exhibited HD-like psychiatric and cognitive phenotypes at 2 months. From 3 to 4 months, BAC226Q mice showed robust progressive motor deficits. At 11 months, BAC226Q mice showed significant reduced life span, gradual weight loss and exhibited neuropathology including significant brain atrophy specific to striatum and cortex, striatal neuronal death, widespread huntingtin inclusions, and reactive pathology. Therefore, the novel BAC226Q mouse accurately recapitulating robust, age-dependent, progressive HD-like phenotypes will be a valuable tool for studying disease mechanisms, identifying biomarkers, and testing gene-targeting therapeutic approaches for HD.
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Affiliation(s)
- Sushila A Shenoy
- Department of Neuroscience, Weill Cornell Graduate School of Medical SciencesNew YorkUnited States
| | - Sushuang Zheng
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking UniversityBeijingChina
| | - Wencheng Liu
- Department of Neuroscience, Weill Cornell Graduate School of Medical SciencesNew YorkUnited States
| | - Yuanyi Dai
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking UniversityBeijingChina
| | - Yuanxiu Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking UniversityBeijingChina
| | - Zhipeng Hou
- The Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Susumu Mori
- The Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Yi Tang
- Innovation Center for Neurological Disorders, Department of Neurology, Xuanwu Hospital Capital Medical University, National Center for Neurological DisordersBeijingChina
| | - Jerry Cheng
- Department of Computer Science, New York Institute of TechnologyNew YorkUnited States
| | - Wenzhen Duan
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences; Solomon H.Snyder Department of Neuroscience, Johns Hopkins University School of medicineBaltimoreUnited States
| | - Chenjian Li
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking UniversityBeijingChina
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