101
|
Braun M, Shoshani S, Tabach Y. Transcriptome changes in DM1 patients’ tissues are governed by the RNA interference pathway. Front Mol Biosci 2022; 9:955753. [PMID: 36060259 PMCID: PMC9437208 DOI: 10.3389/fmolb.2022.955753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic disease caused by pathogenic expansions of CTG repeats. The expanded repeats are transcribed to long RNA and induce cellular toxicity. Recent studies suggest that the CUG repeats are processed by the RNA interference (RNAi) pathway to generate small interfering repeated RNA (siRNA). However, the effects of the CTG repeat-derived siRNAs remain unclear. We hypothesize that the RNAi machinery in DM1 patients generates distinct gene expression patterns that determine the disease phenotype in the individual patient. The abundance of genes with complementary repeats that are targeted by siRNAs in each tissue determines the way that the tissue is affected in DM1. We integrated and analyzed published transcriptome data from muscle, heart, and brain biopsies of DM1 patients, and revealed shared, characteristic changes that correlated with disease phenotype. These signatures are overrepresented by genes and transcription factors bearing endogenous CTG/CAG repeats and are governed by aberrant activity of the RNAi machinery, miRNAs, and a specific gain-of-function of the CTG repeats. Computational analysis of the DM1 transcriptome enhances our understanding of the complex pathophysiology of the disease and may reveal a path for cure.
Collapse
|
102
|
Kelley CP, Haerle MC, Wang ET. Negative autoregulation mitigates collateral RNase activity of repeat-targeting CRISPR-Cas13d in mammalian cells. Cell Rep 2022; 40:111226. [PMID: 35977479 PMCID: PMC9809062 DOI: 10.1016/j.celrep.2022.111226] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
CRISPR-Cas13 RNA endonucleases show promise for programmable RNA knockdown. However, sequence-specific binding of Cas13 unleashes non-specific bystander RNA cleavage, or collateral activity, raising concerns for experiments and therapeutic applications. Although robust in cell-free and bacterial environments, collateral activity in mammalian cells remains disputed. We investigate Cas13d collateral activity in a therapeutic context for myotonic dystrophy type 1, caused by a transcribed CTG repeat expansion. We find that, when targeting CUGn RNA in mammalian cells, Cas13d depletes endogenous and transgenic RNAs, interferes with critical cellular processes, and activates stress response and apoptosis. Collateral effects also occur when targeting abundant endogenous transcripts. To minimize collateral activity for repeat-targeting approaches, we introduce GENO, an adeno-associated virus-compatible strategy that leverages guide RNA processing to control Cas13d expression. We argue that thorough assessment of collateral activity is necessary when applying Cas13 in mammalian cells and that GENO illustrates advantages of compact regulatory systems for Cas-based gene therapies.
Collapse
Affiliation(s)
- Chase P Kelley
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL 32608, USA
| | - Maja C Haerle
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Myology Institute, University of Florida, Gainesville, FL 32608, USA.
| |
Collapse
|
103
|
Chemical interference with DSIF complex formation lowers synthesis of mutant huntingtin gene products and curtails mutant phenotypes. Proc Natl Acad Sci U S A 2022; 119:e2204779119. [PMID: 35914128 PMCID: PMC9371670 DOI: 10.1073/pnas.2204779119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Earlier work has shown that siRNA-mediated reduction of the SUPT4H or SUPT5H proteins, which interact to form the DSIF complex and facilitate transcript elongation by RNA polymerase II (RNAPII), can decrease expression of mutant gene alleles containing nucleotide repeat expansions differentially. Using luminescence and fluorescence assays, we identified chemical compounds that interfere with the SUPT4H-SUPT5H interaction and then investigated their effects on synthesis of mRNA and protein encoded by mutant alleles containing repeat expansions in the huntingtin gene (HTT), which causes the inherited neurodegenerative disorder, Huntington's Disease (HD). Here we report that such chemical interference can differentially affect expression of HTT mutant alleles, and that a prototypical chemical, 6-azauridine (6-AZA), that targets the SUPT4H-SUPT5H interaction can modify the biological response to mutant HTT gene expression. Selective and dose-dependent effects of 6-AZA on expression of HTT alleles containing nucleotide repeat expansions were seen in multiple types of cells cultured in vitro, and in a Drosophila melanogaster animal model for HD. Lowering of mutant HD protein and mitigation of the Drosophila "rough eye" phenotype associated with degeneration of photoreceptor neurons in vivo were observed. Our findings indicate that chemical interference with DSIF complex formation can decrease biochemical and phenotypic effects of nucleotide repeat expansions.
Collapse
|
104
|
Quality of Life Changes Following the Onset of Cerebellar Ataxia: Symptoms and Concerns Self-reported by Ataxia Patients and Informants. CEREBELLUM (LONDON, ENGLAND) 2022; 21:592-605. [PMID: 35334077 DOI: 10.1007/s12311-022-01393-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/29/2022]
Abstract
Semi-structured interviews of patient accounts and caregiver, or informant, perspectives are a beneficial resource for patients suffering from diseases with complex symptomatology, such as cerebellar ataxia. The aim of this study was to identify, quantify, and compare the ways in which cerebellar ataxia patients' and informants' quality of life had changed as a result of living with ataxia. Using a semi-structured interview, responses were collected from patients and informants regarding motor, cognitive, and psychosocial variables. Responses were also collected from patients and informants to open-ended questions that were subsequently categorized into 15 quality of life themes that best represented changes experienced by the patients and informants. Ataxia patients and informants agreed as to the severity of posture/gait, daily activities/fine motor tasks, speech/feeding/swallowing, and oculomotor/vision impairment. It was also demonstrated that severity ratings for specific motor-related functions strongly correlated with corresponding functions within the International Cooperative Ataxia Rating Scale (ICARS), and that this interview identified frequency associations between motor impairments and specific psychosocial difficulties, which could be useful for prognostic purposes. Overall, the information obtained from this study characterized the symptoms and challenges to ataxia patients and their caregivers, which could serve as a useful educational resource for those affected by ataxia, clinicians, and researchers.
Collapse
|
105
|
Deng N, Zhang Y, Ma Z, Lin R, Cheng TH, Tang H, Snyder M, Cohen S. DSIF modulates RNA polymerase II occupancy according to template G + C content. NAR Genom Bioinform 2022; 4:lqac054. [PMID: 35910045 PMCID: PMC9326580 DOI: 10.1093/nargab/lqac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/03/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
The DSIF complex comprising the Supt4h and Supt5h transcription elongation proteins clamps RNA polymerase II (RNAPII) onto DNA templates, facilitating polymerase processivity. Lowering DSIF components can differentially decrease expression of alleles containing nucleotide repeat expansions, suggesting that RNAPII transit through repeat expansions is dependent on DSIF functions. To globally identify sequence features that affect dependence of the polymerase on DSIF in human cells, we used ultra-deep ChIP-seq analysis and RNA-seq to investigate and quantify the genome-wide effects of Supt4h loss on template occupancy and transcript production. Our results indicate that RNAPII dependence on Supt4h varies according to G + C content. Effects of DSIF knockdown were prominent during transcription of sequences high in G + C but minimal for sequences low in G + C and were particularly evident for G + C-rich segments of long genes. Reanalysis of previously published ChIP-seq data obtained from mouse cells showed similar effects of template G + C composition on Supt5h actions. Our evidence that DSIF dependency varies globally in different template regions according to template sequence composition suggests that G + C content may have a role in the selectivity of Supt4h knockdown and Supt5h knockdown during transcription of gene alleles containing expansions of G + C-rich repeats.
Collapse
Affiliation(s)
- Ning Deng
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Yue Zhang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Richard Lin
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Tzu-Hao Cheng
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University , Taipei 112, Taiwan
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Stanley N Cohen
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| |
Collapse
|
106
|
Thaung C, Davidson AE. Fuchs endothelial corneal dystrophy: current perspectives on diagnostic pathology and genetics-Bowman Club Lecture. BMJ Open Ophthalmol 2022; 7:bmjophth-2022-001103. [PMID: 36161831 PMCID: PMC9341215 DOI: 10.1136/bmjophth-2022-001103] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 11/18/2022] Open
Abstract
Fuchs endothelial corneal dystrophy (FECD) was first described over a century ago. Since then, we have learnt much about its clinical manifestations, surgical and non-surgical treatment, microscopic appearance and pathogenesis. Over the past decade, significant advances have been made with respect to our understanding of FECD genetics. This progress now enables us to appreciate that FECD in fact describes multiple entities with distinct underlying genetic causes. For example, an early-onset and rare form of the disease has been attributed to missense mutations in the COL8A2 gene, whereas the vast majority of late-onset cases can be attributed to a non-coding repeat expansion within the TCF4 gene.FECD is one of the most common indications for corneal transplantation. In recent years, attention has turned to alternative treatment techniques that do not depend on donor tissue supply. The design and development of these non-surgical treatment approaches have benefited from increased knowledge of pathogenesis.This review will cover our current knowledge about the histology and genetics of FECD, and how combining these interdisciplinary approaches might may improve diagnostic accuracy and aid the development of therapeutics for this common and visually disabling disease.
Collapse
Affiliation(s)
- Caroline Thaung
- Moorfields Eye Hospital, London, UK .,Department of Eye Pathology, University College London Institute of Ophthalmology, London, UK
| | - Alice E Davidson
- University College London Institute of Ophthalmology, London, UK
| |
Collapse
|
107
|
Baud A, Derbis M, Tutak K, Sobczak K. Partners in crime: Proteins implicated in
RNA
repeat expansion diseases. WIRES RNA 2022; 13:e1709. [PMID: 35229468 PMCID: PMC9539487 DOI: 10.1002/wrna.1709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Baud
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Magdalena Derbis
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Katarzyna Tutak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| |
Collapse
|
108
|
Braun M, Shoshani S, Teixeira J, Mellul Shtern A, Miller M, Granot Z, Fischer SE, Garcia SMA, Tabach Y. Asymmetric inheritance of RNA toxicity in C. elegans expressing CTG repeats. iScience 2022; 25:104246. [PMID: 35494247 PMCID: PMC9051633 DOI: 10.1016/j.isci.2022.104246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/01/2022] [Accepted: 04/07/2022] [Indexed: 11/18/2022] Open
Abstract
Nucleotide repeat expansions are a hallmark of over 40 neurodegenerative diseases and cause RNA toxicity and multisystemic symptoms that worsen with age. Through an unclear mechanism, RNA toxicity can trigger severe disease manifestation in infants if the repeats are inherited from their mother. Here we use Caenorhabditis elegans bearing expanded CUG repeats to show that this asymmetric intergenerational inheritance of toxicity contributes to disease pathogenesis. In addition, we show that this mechanism is dependent on small RNA pathways with maternal repeat-derived small RNAs causing transcriptomic changes in the offspring, reduced motility, and shortened lifespan. We rescued the toxicity phenotypes in the offspring by perturbing the RNAi machinery in the affected hermaphrodites. This points to a novel mechanism linking maternal bias and the RNAi machinery and suggests that toxic RNA is transmitted to offspring, causing disease phenotypes through intergenerational epigenetic inheritance. Maternal origin of expanded CUG repeats induces RNA toxicity in Caenorhabditis elegans offspring Offspring of affected hermaphrodites show molecular and phenotypic disease phenotypes The RNAi machinery is directly related to the maternal inheritance of RNA toxicity Altering the RNAi machinery in affected hermaphrodites rescues toxicity in offspring
Collapse
Affiliation(s)
- Maya Braun
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shachar Shoshani
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Joana Teixeira
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790 Finland
| | - Anna Mellul Shtern
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Maya Miller
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Zvi Granot
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sylvia E.J. Fischer
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Susana M.D. A. Garcia
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790 Finland
- Corresponding author
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Corresponding author
| |
Collapse
|
109
|
Fakharzadeh A, Zhang J, Roland C, Sagui C. Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats. Nucleic Acids Res 2022; 50:4860-4876. [PMID: 35536254 PMCID: PMC9122592 DOI: 10.1093/nar/gkac339] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/19/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022] Open
Abstract
The expansion of d(CGG) trinucleotide repeats (TRs) lies behind several important neurodegenerative diseases. Atypical DNA secondary structures have been shown to trigger TR expansion: their characterization is important for a molecular understanding of TR disease. CD spectroscopy experiments in the last decade have unequivocally demonstrated that CGG runs adopt a left-handed Z-DNA conformation, whose features remain uncertain because it entails accommodating GG mismatches. In order to find this missing motif, we have carried out molecular dynamics (MD) simulations to explore all the possible Z-DNA helices that potentially form after the transition from B- to Z-DNA. Such helices combine either CpG or GpC Watson-Crick steps in Z-DNA form with GG-mismatch conformations set as either intrahelical or extrahelical; and participating in BZ or ZZ junctions or in alternately extruded conformations. Characterization of the stability and structural features (especially overall left-handedness, higher-temperature and steered MD simulations) identified two novel Z-DNA helices: the most stable one displays alternately extruded Gs, and is followed by a helix with symmetrically extruded ZZ junctions. The G-extrusion favors a seamless stacking of the Watson-Crick base pairs; extruded Gs favor syn conformations and display hydrogen-bonding and stacking interactions. Such conformations could have the potential to hijack the MMR complex, thus triggering further expansion.
Collapse
Affiliation(s)
- Ashkan Fakharzadeh
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| |
Collapse
|
110
|
Bioinformatics Analysis of the Interaction of miRNAs and piRNAs with Human mRNA Genes Having di- and Trinucleotide Repeats. Genes (Basel) 2022; 13:genes13050800. [PMID: 35627185 PMCID: PMC9141802 DOI: 10.3390/genes13050800] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
The variability of nucleotide repeats is considered one of the causes of diseases, but their biological function is not understood. In recent years, the interaction of miRNAs and piRNAs with the mRNAs of genes responsible for developing neurodegenerative and oncological diseases and diabetes have been actively studied. We explored candidate genes with nucleotide repeats to predict associations with miRNAs and piRNAs. The parameters of miRNAs and piRNA binding sites with mRNAs of human genes having nucleotide repeats were determined using the MirTarget program. This program defines the start of the initiation of miRNA and piRNA binding to mRNAs, the localization of miRNA and piRNA binding sites in the 5′-untranslated region (5′UTR), coding sequence (CDS) and 3′-untranslated region (3′UTR); the free energy of binding; and the schemes of nucleotide interactions of miRNAs and piRNAs with mRNAs. The characteristics of miRNAs and piRNA binding sites with mRNAs of 73 human genes were determined. The 5′UTR, 3′UTR and CDS of the mRNAs of genes are involved in the development of neurodegenerative, oncological and diabetes diseases with GU, AC dinucleotide and CCG, CAG, GCC, CGG, CGC trinucleotide repeats. The associations of miRNAs, piRNAs and candidate target genes could be recommended for developing methods for diagnosing diseases, including neurodegenerative diseases, oncological diseases and diabetes.
Collapse
|
111
|
Fang L, Liu Q, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K. DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing. Genome Biol 2022; 23:108. [PMID: 35484600 PMCID: PMC9052667 DOI: 10.1186/s13059-022-02670-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts ionic current signals into red-green-blue channels, thus transforming the repeat detection problem into an image recognition problem. DeepRepeat identifies and accurately quantifies telomeric repeats in the CHM13 cell line and achieves higher accuracy in quantifying repeats in long STRs than competing methods. We also evaluate DeepRepeat on genome-wide or candidate region datasets from seven different sources. In summary, DeepRepeat enables accurate quantification of long STRs and complements existing methods relying on basecalled reads.
Collapse
Affiliation(s)
- Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,School of Life Sciences, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA. .,Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA.
| | - Alex Mas Monteys
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pedro Gonzalez-Alegre
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
112
|
Nguyen TPN, Kumar M, Fedele E, Bonanno G, Bonifacino T. MicroRNA Alteration, Application as Biomarkers, and Therapeutic Approaches in Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23094718. [PMID: 35563107 PMCID: PMC9104163 DOI: 10.3390/ijms23094718] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 01/27/2023] Open
Abstract
MicroRNAs (miRNAs) are essential post-transcriptional gene regulators involved in various neuronal and non-neuronal cell functions and play a key role in pathological conditions. Numerous studies have demonstrated that miRNAs are dysregulated in major neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, amyotrophic lateral sclerosis, or Huntington’s disease. Hence, in the present work, we constructed a comprehensive overview of individual microRNA alterations in various models of the above neurodegenerative diseases. We also provided evidence of miRNAs as promising biomarkers for prognostic and diagnostic approaches. In addition, we summarized data from the literature about miRNA-based therapeutic applications via inhibiting or promoting miRNA expression. We finally identified the overlapping miRNA signature across the diseases, including miR-128, miR-140-5p, miR-206, miR-326, and miR-155, associated with multiple etiological cellular mechanisms. However, it remains to be established whether and to what extent miRNA-based therapies could be safely exploited in the future as effective symptomatic or disease-modifying approaches in the different human neurodegenerative disorders.
Collapse
Affiliation(s)
- T. P. Nhung Nguyen
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
| | - Mandeep Kumar
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
| | - Ernesto Fedele
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Correspondence:
| | - Giambattista Bonanno
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Tiziana Bonifacino
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), 56122 Genoa, Italy
| |
Collapse
|
113
|
Kacher R, Mounier C, Caboche J, Betuing S. Altered Cholesterol Homeostasis in Huntington’s Disease. Front Aging Neurosci 2022; 14:797220. [PMID: 35517051 PMCID: PMC9063567 DOI: 10.3389/fnagi.2022.797220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/18/2022] [Indexed: 12/25/2022] Open
Abstract
Huntington’s disease (HD) is an autosomal dominant genetic disorder caused by an expansion of the CAG repeat in the first exon of Huntingtin’s gene. The associated neurodegeneration mainly affects the striatum and the cortex at early stages and progressively spreads to other brain structures. Targeting HD at its earlier stages is under intense investigation. Numerous drugs were tested, with a rate of success of only 3.5% approved molecules used as symptomatic treatment. The restoration of cholesterol metabolism, which is central to the brain homeostasis and strongly altered in HD, could be an interesting disease-modifying strategy. Cholesterol is an essential membrane component in the central nervous system (CNS); alterations of its homeostasis have deleterious consequences on neuronal functions. The levels of several sterols, upstream of cholesterol, are markedly decreased within the striatum of HD mouse model. Transcription of cholesterol biosynthetic genes is reduced in HD cell and mouse models as well as post-mortem striatal and cortical tissues from HD patients. Since the dynamic of brain cholesterol metabolism is complex, it is essential to establish the best method to target it in HD. Cholesterol, which does not cross the blood-brain-barrier, is locally synthesized and renewed within the brain. All cell types in the CNS synthesize cholesterol during development but as they progress through adulthood, neurons down-regulate their cholesterol synthesis and turn to astrocytes for their full supply. Cellular levels of cholesterol reflect the dynamic balance between synthesis, uptake and export, all integrated into the context of the cross talk between neurons and glial cells. In this review, we describe the latest advances regarding the role of cholesterol deregulation in neuronal functions and how this could be a determinant factor in neuronal degeneration and HD progression. The pathways and major mechanisms by which cholesterol and sterols are regulated in the CNS will be described. From this overview, we discuss the main clinical strategies for manipulating cholesterol metabolism in the CNS, and how to reinstate a proper balance in HD.
Collapse
Affiliation(s)
- Radhia Kacher
- Institut du Cerveau - Paris Brain Institute (ICM), AP-HP, INSERM, CNRS, University Hospital Pitié-Salpêtrière, Sorbonne Université, Paris, France
- INSERM, U1216, Grenoble Institut Neurosciences, Université Grenoble Alpes, Grenoble, France
| | - Coline Mounier
- Neuroscience Paris Seine, Institut de Biologie Paris-Seine, Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France
- Centre National de la Recherche Scientifique, UMR 8246, Paris, France
- U1130, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Jocelyne Caboche
- Neuroscience Paris Seine, Institut de Biologie Paris-Seine, Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France
- Centre National de la Recherche Scientifique, UMR 8246, Paris, France
- U1130, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Sandrine Betuing
- Neuroscience Paris Seine, Institut de Biologie Paris-Seine, Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France
- Centre National de la Recherche Scientifique, UMR 8246, Paris, France
- U1130, Institut National de la Santé et de la Recherche Médicale, Paris, France
- *Correspondence: Sandrine Betuing,
| |
Collapse
|
114
|
Zhang S, Shen L, Jiao B. Cognitive Dysfunction in Repeat Expansion Diseases: A Review. Front Aging Neurosci 2022; 14:841711. [PMID: 35478698 PMCID: PMC9036481 DOI: 10.3389/fnagi.2022.841711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/24/2022] [Indexed: 11/16/2022] Open
Abstract
With the development of the sequencing technique, more than 40 repeat expansion diseases (REDs) have been identified during the past two decades. Moreover, the clinical features of these diseases show some commonality, and the nervous system, especially the cognitive function was affected in part by these diseases. However, the specific cognitive domains impaired in different diseases were inconsistent. Here, we survey literature on the cognitive consequences of the following disorders presenting cognitive dysfunction and summarizing the pathogenic genes, epidemiology, and different domains affected by these diseases. We found that the cognitive domains affected in neuronal intranuclear inclusion disease (NIID) were widespread including the executive function, memory, information processing speed, attention, visuospatial function, and language. Patients with C9ORF72-frontotemporal dementia (FTD) showed impairment in executive function, memory, language, and visuospatial function. While in Huntington's disease (HD), the executive function, memory, and information processing speed were affected, in the fragile X-associated tremor/ataxia syndrome (FXTAS), executive function, memory, information processing speed, and attention were impaired. Moreover, the spinocerebellar ataxias showed broad damage in almost all the cognitive domains except for the relatively intact language ability. Some other diseases with relatively rare clinical data also indicated cognitive dysfunction, such as myotonic dystrophy type 1 (DM1), progressive myoclonus epilepsy (PME), Friedreich ataxia (FRDA), Huntington disease like-2 (HDL2), and cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS). We drew a cognitive function landscape of the related REDs that might provide an aspect for differential diagnosis through cognitive domains and effective non-specific interventions for these diseases.
Collapse
Affiliation(s)
- Sizhe Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- *Correspondence: Bin Jiao
| |
Collapse
|
115
|
Austin-Tse CA, Jobanputra V, Perry DL, Bick D, Taft RJ, Venner E, Gibbs RA, Young T, Barnett S, Belmont JW, Boczek N, Chowdhury S, Ellsworth KA, Guha S, Kulkarni S, Marcou C, Meng L, Murdock DR, Rehman AU, Spiteri E, Thomas-Wilson A, Kearney HM, Rehm HL. Best practices for the interpretation and reporting of clinical whole genome sequencing. NPJ Genom Med 2022; 7:27. [PMID: 35395838 PMCID: PMC8993917 DOI: 10.1038/s41525-022-00295-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/17/2022] [Indexed: 01/19/2023] Open
Abstract
Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
Collapse
Affiliation(s)
- Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Vaidehi Jobanputra
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ted Young
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Nicole Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Saurav Guha
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Shashikant Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cherisse Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linyan Meng
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Atteeq U Rehman
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Elizabeth Spiteri
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA, USA
| | | | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | |
Collapse
|
116
|
Goswami R, Bello AI, Bean J, Costanzo KM, Omer B, Cornelio-Parra D, Odah R, Ahluwalia A, Allan SK, Nguyen N, Shores T, Aziz NA, Mohan RD. The Molecular Basis of Spinocerebellar Ataxia Type 7. Front Neurosci 2022; 16:818757. [PMID: 35401096 PMCID: PMC8987156 DOI: 10.3389/fnins.2022.818757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/07/2022] [Indexed: 11/19/2022] Open
Abstract
Spinocerebellar ataxia (SCA) type 7 (SCA7) is caused by a CAG trinucleotide repeat expansion in the ataxin 7 (ATXN7) gene, which results in polyglutamine expansion at the amino terminus of the ATXN7 protein. Although ATXN7 is expressed widely, the best characterized symptoms of SCA7 are remarkably tissue specific, including blindness and degeneration of the brain and spinal cord. While it is well established that ATXN7 functions as a subunit of the Spt Ada Gcn5 acetyltransferase (SAGA) chromatin modifying complex, the mechanisms underlying SCA7 remain elusive. Here, we review the symptoms of SCA7 and examine functions of ATXN7 that may provide further insights into its pathogenesis. We also examine phenotypes associated with polyglutamine expanded ATXN7 that are not considered symptoms of SCA7.
Collapse
Affiliation(s)
- Rituparna Goswami
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Abudu I. Bello
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Joe Bean
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Kara M. Costanzo
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Bwaar Omer
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Dayanne Cornelio-Parra
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Revan Odah
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Amit Ahluwalia
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Shefaa K. Allan
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Nghi Nguyen
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Taylor Shores
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
| | - N. Ahmad Aziz
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ryan D. Mohan
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO, United States
- *Correspondence: Ryan D. Mohan,
| |
Collapse
|
117
|
Yu J, Shan J, Yu M, Di L, Xie Z, Zhang W, Lv H, Meng L, Zheng Y, Zhao Y, Gang Q, Guo X, Wang Y, Xi J, Zhu W, Da Y, Hong D, Yuan Y, Yan C, Wang Z, Deng J. The CGG repeat expansion in RILPL1 is associated with oculopharyngodistal myopathy type 4. Am J Hum Genet 2022; 109:533-541. [PMID: 35148830 DOI: 10.1016/j.ajhg.2022.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/20/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies indicate that CGG repeat expansions in LRP12, GIPC1, and NOTCH2NLC are associated with oculopharyngodistal myopathy (OPDM) types 1, 2, and 3, respectively. However, some clinicopathologically confirmed OPDM cases continue to have unknown genetic causes. Here, through a combination of long-read whole-genome sequencing (LRS), repeat-primed polymerase chain reaction (RP-PCR), and fluorescence amplicon length analysis PCR (AL-PCR), we found that a CGG repeat expansion in the 5' UTR of RILPL1 is associated with familial and simplex OPDM type 4 (OPDM4). The number of repeats ranged from 139 to 197. Methylation analysis indicates that the methylation levels in RILPL1 were unaltered in OPDM4 individuals. Analyses of muscle biopsies suggested that the expanded CGG repeat might be translated into a toxic poly-glycine protein that co-localizes with p62 in intranuclear inclusions. Moreover, analyses suggest that the toxic RNA gain-of-function effects also contributed to the pathogenesis of this disease. Intriguingly, all four types of OPDM have been found to be associated with the CGG repeat expansions located in 5' UTRs. This finding suggests that a common pathogenic mechanism, driven by the CGG repeat expansion, might underlie all cases of OPDM.
Collapse
|
118
|
Ibañez K, Polke J, Hagelstrom RT, Dolzhenko E, Pasko D, Thomas ERA, Daugherty LC, Kasperaviciute D, Smith KR, Deans ZC, Hill S, Fowler T, Scott RH, Hardy J, Chinnery PF, Houlden H, Rendon A, Caulfield MJ, Eberle MA, Taft RJ, Tucci A. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study. Lancet Neurol 2022; 21:234-245. [PMID: 35182509 PMCID: PMC8850201 DOI: 10.1016/s1474-4422(21)00462-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 11/09/2021] [Accepted: 12/14/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Repeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who have atypical clinical presentations, especially in paediatric patients without a previous positive family history. Whole genome sequencing is increasingly used as a first-line test for other rare genetic disorders, and we aimed to assess its performance in the diagnosis of patients with neurological repeat expansion disorders. METHODS We retrospectively assessed the diagnostic accuracy of whole genome sequencing to detect the most common repeat expansion loci associated with neurological outcomes (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) using samples obtained within the National Health Service in England from patients who were suspected of having neurological disorders; previous PCR test results were used as the reference standard. The clinical accuracy of whole genome sequencing to detect repeat expansions was prospectively examined in previously genetically tested and undiagnosed patients recruited in 2013-17 to the 100 000 Genomes Project in the UK, who were suspected of having a genetic neurological disorder (familial or early-onset forms of ataxia, neuropathy, spastic paraplegia, dementia, motor neuron disease, parkinsonian movement disorders, intellectual disability, or neuromuscular disorders). If a repeat expansion call was made using whole genome sequencing, PCR was used to confirm the result. FINDINGS The diagnostic accuracy of whole genome sequencing to detect repeat expansions was evaluated against 793 PCR tests previously performed within the NHS from 404 patients. Whole genome sequencing correctly classified 215 of 221 expanded alleles and 1316 of 1321 non-expanded alleles, showing 97·3% sensitivity (95% CI 94·2-99·0) and 99·6% specificity (99·1-99·9) across the 13 disease-associated loci when compared with PCR test results. In samples from 11 631 patients in the 100 000 Genomes Project, whole genome sequencing identified 81 repeat expansions, which were also tested by PCR: 68 were confirmed as repeat expansions in the full pathogenic range, 11 were non-pathogenic intermediate expansions or premutations, and two were non-expanded repeats (16% false discovery rate). INTERPRETATION In our study, whole genome sequencing for the detection of repeat expansions showed high sensitivity and specificity, and it led to identification of neurological repeat expansion disorders in previously undiagnosed patients. These findings support implementation of whole genome sequencing in clinical laboratories for diagnosis of patients who have a neurological presentation consistent with a repeat expansion disorder. FUNDING Medical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, and Illumina.
Collapse
Affiliation(s)
- Kristina Ibañez
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - James Polke
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, UK
| | | | | | - Dorota Pasko
- Genomics England, Queen Mary University of London, London, UK
| | | | - Louise C Daugherty
- Genomics England, Queen Mary University of London, London, UK; Healx, Cambridge, UK
| | - Dalia Kasperaviciute
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Katherine R Smith
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Zandra C Deans
- Genomics Quality Assessment, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK; NHS England and NHS Improvement, London, UK
| | - Sue Hill
- NHS England and NHS Improvement, London, UK
| | - Tom Fowler
- Genomics England, Queen Mary University of London, London, UK
| | - Richard H Scott
- Genomics England, Queen Mary University of London, London, UK; Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - John Hardy
- Department of Neurodegenerative Disorders, Institute of Neurology, University College London, London, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit and Department of ClinicalNeurosciences, University of Cambridge, Cambridge, UK
| | - Henry Houlden
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, UK; Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, UK
| | - Augusto Rendon
- Genomics England, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | | | - Arianna Tucci
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK.
| |
Collapse
|
119
|
Ibañez K, Polke J, Hagelstrom RT, Dolzhenko E, Pasko D, Thomas ERA, Daugherty LC, Kasperaviciute D, Smith KR, Deans ZC, Hill S, Fowler T, Scott RH, Hardy J, Chinnery PF, Houlden H, Rendon A, Caulfield MJ, Eberle MA, Taft RJ, Tucci A. Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study. Lancet Neurol 2022. [PMID: 35182509 DOI: 10.1101/2020.11.06.371716v1.abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Repeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who have atypical clinical presentations, especially in paediatric patients without a previous positive family history. Whole genome sequencing is increasingly used as a first-line test for other rare genetic disorders, and we aimed to assess its performance in the diagnosis of patients with neurological repeat expansion disorders. METHODS We retrospectively assessed the diagnostic accuracy of whole genome sequencing to detect the most common repeat expansion loci associated with neurological outcomes (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) using samples obtained within the National Health Service in England from patients who were suspected of having neurological disorders; previous PCR test results were used as the reference standard. The clinical accuracy of whole genome sequencing to detect repeat expansions was prospectively examined in previously genetically tested and undiagnosed patients recruited in 2013-17 to the 100 000 Genomes Project in the UK, who were suspected of having a genetic neurological disorder (familial or early-onset forms of ataxia, neuropathy, spastic paraplegia, dementia, motor neuron disease, parkinsonian movement disorders, intellectual disability, or neuromuscular disorders). If a repeat expansion call was made using whole genome sequencing, PCR was used to confirm the result. FINDINGS The diagnostic accuracy of whole genome sequencing to detect repeat expansions was evaluated against 793 PCR tests previously performed within the NHS from 404 patients. Whole genome sequencing correctly classified 215 of 221 expanded alleles and 1316 of 1321 non-expanded alleles, showing 97·3% sensitivity (95% CI 94·2-99·0) and 99·6% specificity (99·1-99·9) across the 13 disease-associated loci when compared with PCR test results. In samples from 11 631 patients in the 100 000 Genomes Project, whole genome sequencing identified 81 repeat expansions, which were also tested by PCR: 68 were confirmed as repeat expansions in the full pathogenic range, 11 were non-pathogenic intermediate expansions or premutations, and two were non-expanded repeats (16% false discovery rate). INTERPRETATION In our study, whole genome sequencing for the detection of repeat expansions showed high sensitivity and specificity, and it led to identification of neurological repeat expansion disorders in previously undiagnosed patients. These findings support implementation of whole genome sequencing in clinical laboratories for diagnosis of patients who have a neurological presentation consistent with a repeat expansion disorder. FUNDING Medical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, and Illumina.
Collapse
Affiliation(s)
- Kristina Ibañez
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - James Polke
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, UK
| | | | | | - Dorota Pasko
- Genomics England, Queen Mary University of London, London, UK
| | | | - Louise C Daugherty
- Genomics England, Queen Mary University of London, London, UK; Healx, Cambridge, UK
| | - Dalia Kasperaviciute
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Katherine R Smith
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Zandra C Deans
- Genomics Quality Assessment, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK; NHS England and NHS Improvement, London, UK
| | - Sue Hill
- NHS England and NHS Improvement, London, UK
| | - Tom Fowler
- Genomics England, Queen Mary University of London, London, UK
| | - Richard H Scott
- Genomics England, Queen Mary University of London, London, UK; Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - John Hardy
- Department of Neurodegenerative Disorders, Institute of Neurology, University College London, London, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit and Department of ClinicalNeurosciences, University of Cambridge, Cambridge, UK
| | - Henry Houlden
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, UK; Department of Neuromuscular Diseases, Institute of Neurology, University College London, London, UK
| | - Augusto Rendon
- Genomics England, Queen Mary University of London, London, UK
| | - Mark J Caulfield
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | | | - Arianna Tucci
- Genomics England, Queen Mary University of London, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK.
| | | |
Collapse
|
120
|
Lockhart PJ. Advancing the diagnosis of repeat expansion disorders. Lancet Neurol 2022; 21:205-207. [DOI: 10.1016/s1474-4422(22)00033-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
|
121
|
Implications of Poly(A) Tail Processing in Repeat Expansion Diseases. Cells 2022; 11:cells11040677. [PMID: 35203324 PMCID: PMC8870147 DOI: 10.3390/cells11040677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/21/2022] Open
Abstract
Repeat expansion diseases are a group of more than 40 disorders that affect mainly the nervous and/or muscular system and include myotonic dystrophies, Huntington’s disease, and fragile X syndrome. The mutation-driven expanded repeat tract occurs in specific genes and is composed of tri- to dodeca-nucleotide-long units. Mutant mRNA is a pathogenic factor or important contributor to the disease and has great potential as a therapeutic target. Although repeat expansion diseases are quite well known, there are limited studies concerning polyadenylation events for implicated transcripts that could have profound effects on transcript stability, localization, and translation efficiency. In this review, we briefly present polyadenylation and alternative polyadenylation (APA) mechanisms and discuss their role in the pathogenesis of selected diseases. We also discuss several methods for poly(A) tail measurement (both transcript-specific and transcriptome-wide analyses) and APA site identification—the further development and use of which may contribute to a better understanding of the correlation between APA events and repeat expansion diseases. Finally, we point out some future perspectives on the research into repeat expansion diseases, as well as APA studies.
Collapse
|
122
|
Fourier A, Quadrio I. Proteinopathies associated to repeat expansion disorders. J Neural Transm (Vienna) 2022; 129:173-185. [DOI: 10.1007/s00702-021-02454-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022]
|
123
|
Neurodegenerative diseases associated with non-coding CGG tandem repeat expansions. Nat Rev Neurol 2022; 18:145-157. [PMID: 35022573 DOI: 10.1038/s41582-021-00612-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 02/07/2023]
Abstract
Non-coding CGG repeat expansions cause multiple neurodegenerative disorders, including fragile X-associated tremor/ataxia syndrome, neuronal intranuclear inclusion disease, oculopharyngeal myopathy with leukodystrophy, and oculopharyngodistal myopathy. The underlying genetic causes of several of these diseases have been identified only in the past 2-3 years. These expansion disorders have substantial overlapping clinical, neuroimaging and histopathological features. The shared features suggest common mechanisms that could have implications for the development of therapies for this group of diseases - similar therapeutic strategies or drugs may be effective for various neurodegenerative disorders induced by non-coding CGG expansions. In this Review, we provide an overview of clinical and pathological features of these CGG repeat expansion diseases and consider the likely pathological mechanisms, including RNA toxicity, CGG repeat-associated non-AUG-initiated translation, protein aggregation and mitochondrial impairment. We then discuss future research needed to improve the identification and diagnosis of CGG repeat expansion diseases, to improve modelling of these diseases and to understand their pathogenesis. We also consider possible therapeutic strategies. Finally, we propose that CGG repeat expansion diseases may represent manifestations of a single underlying neuromyodegenerative syndrome in which different organs are affected to different extents depending on the gene location of the repeat expansion.
Collapse
|
124
|
|
125
|
Wang S, Sun S. Measuring Repeat-Associated Non-AUG (RAN) Translation. Methods Mol Biol 2022; 2428:113-132. [PMID: 35171477 DOI: 10.1007/978-1-0716-1975-9_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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Expansions of short nucleotide repeats account for more than 50 neurological or neuromuscular diseases. Many repeat expansion-containing RNAs can generate toxic repeat proteins through repeat-associated non-AUG (RAN) translation in all the reading frames. Understanding how RAN translation occurs and what cellular factors regulate this process will help decipher the basic mechanism of the molecular process and disease pathogenesis. Using reporter systems to quantitatively measure RAN translation provides a platform to examine candidate genes/pathways and screen for modifiers of this non-canonical pathway. In this chapter, we describe the dual-luciferase reporter system to measure RAN translation using C9ORF72 GGGGCCexp as an example, which is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD).
Collapse
Affiliation(s)
- Shaopeng Wang
- Department of Pathology, Physiology, Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shuying Sun
- Department of Pathology, Physiology, Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
126
|
Nikitina M, Bragina E, Nazarenko M, Alifirova V. The role of alleles with an intermediate number of trinucleotide repeats in Parkinson’s disease and other neurodegenerative disorders. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:42-50. [DOI: 10.17116/jnevro202212207142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
127
|
Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
Collapse
Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| |
Collapse
|
128
|
The molecular pathogenesis of repeat expansion diseases. Biochem Soc Trans 2021; 50:119-134. [PMID: 34940797 DOI: 10.1042/bst20200143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022]
Abstract
Expanded short tandem repeats in the genome cause various monogenic diseases, particularly neurological disorders. Since the discovery of a CGG repeat expansion in the FMR1 gene in 1991, more than 40 repeat expansion diseases have been identified to date. In the coding repeat expansion diseases, in which the expanded repeat sequence is located in the coding regions of genes, the toxicity of repeat polypeptides, particularly misfolding and aggregation of proteins containing an expanded polyglutamine tract, have been the focus of investigation. On the other hand, in the non-coding repeat expansion diseases, in which the expanded repeat sequence is located in introns or untranslated regions, the toxicity of repeat RNAs has been the focus of investigation. Recently, these repeat RNAs were demonstrated to be translated into repeat polypeptides by the novel mechanism of repeat-associated non-AUG translation, which has extended the research direction of the pathological mechanisms of this disease entity to include polypeptide toxicity. Thus, a common pathogenesis has been suggested for both coding and non-coding repeat expansion diseases. In this review, we briefly outline the major pathogenic mechanisms of repeat expansion diseases, including a loss-of-function mechanism caused by repeat expansion, repeat RNA toxicity caused by RNA foci formation and protein sequestration, and toxicity by repeat polypeptides. We also discuss perturbation of the physiological liquid-liquid phase separation state caused by these repeat RNAs and repeat polypeptides, as well as potential therapeutic approaches against repeat expansion diseases.
Collapse
|
129
|
de Pontual L, Gourdon G, Tomé S. [Identification of new factors inducing CTG.CAG repeat contractions in Myotonic Dystrophy type 1]. Med Sci (Paris) 2021; 37 Hors série n° 1:6-10. [PMID: 34878385 DOI: 10.1051/medsci/2021182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic neuromuscular disease caused by an abnormal CTG repeat expansion in the 3'UTR region of the DMPK gene. In patients, the CTG repeat size varies from fifty to thousands CTG and usually increases across generations (intergenerational instability) and over time in tissues (somatic instability). Larger expansions are associated with more severe symptoms and a decreasing age of onset. Thus, the larger expansions are often associated with the most severe clinical form of DM1 (congenital form). Our PhD project is to identify new genetic and chemical factors reducing the number of repeats and to better understand the mechanisms underlying instability. To this end, genetic and pharmacological screenings are carried out in a HEK293 cell model allowing the rapid detection of expansions (increase in CTG repeat number) and contractions (decrease in CTG repeat number). The effects of different genes and chemical factors, selected during the screening, on the dynamics of the CTG repeat instability will be studied in a DM1 cell model. The results of our work will provide a better understanding of the mechanisms behind contractions. In addition, the identification of new pharmacological compounds promoting CTG contractions and thus reducing or even reversing the progression of disease will offer new therapeutic prospects for DM1 but also for other triplet repeat diseases.
Collapse
Affiliation(s)
- Laure de Pontual
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Geneviève Gourdon
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Stéphanie Tomé
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| |
Collapse
|
130
|
Arning L, Nguyen HP. Huntington disease update: new insights into the role of repeat instability in disease pathogenesis. MED GENET-BERLIN 2021; 33:293-300. [PMID: 38835439 PMCID: PMC11006308 DOI: 10.1515/medgen-2021-2101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/16/2021] [Indexed: 06/06/2024]
Abstract
The causative mutation for Huntington disease (HD), an expanded trinucleotide repeat sequence in the first exon of the huntingtin gene (HTT) is naturally polymorphic and inevitably associated with disease symptoms above 39 CAG repeats. Although symptomatic medical therapies for HD can improve the motor and non-motor symptoms for affected patients, these drugs do not stop the ongoing neurodegeneration and progression of the disease, which results in severe motor and cognitive disability and death. To date, there is still an urgent need for the development of effective disease-modifying therapies to slow or even stop the progression of HD. The increasing ability to intervene directly at the roots of the disease, namely HTT transcription and translation of its mRNA, makes it necessary to understand the pathogenesis of HD as precisely as possible. In addition to the long-postulated toxicity of the polyglutamine-expanded mutant HTT protein, there is increasing evidence that the CAG repeat-containing RNA might also be directly involved in toxicity. Recent studies have identified cis- (DNA repair genes) and trans- (loss/duplication of CAA interruption) acting variants as major modifiers of age at onset (AO) and disease progression. More and more extensive data indicate that somatic instability functions as a driver for AO as well as disease progression and severity, not only in HD but also in other polyglutamine diseases. Thus, somatic expansions of repetitive DNA sequences may be essential to promote respective repeat lengths to reach a threshold leading to the overt neurodegenerative symptoms of trinucleotide diseases. These findings support somatic expansion as a potential therapeutic target in HD and related repeat expansion disorders.
Collapse
Affiliation(s)
- Larissa Arning
- Department of Human Genetics, Medical Faculty, Ruhr-University Bochum, Bochum 44780, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Medical Faculty, Ruhr-University Bochum, Bochum 44780, Germany
| |
Collapse
|
131
|
Yefimova MG, Béré E, Cantereau-Becq A, Meunier-Balandre AC, Merceron B, Burel A, Merienne K, Ravel C, Becq F, Bourmeyster N. Myelinosome Organelles in the Retina of R6/1 Huntington Disease (HD) Mice: Ubiquitous Distribution and Possible Role in Disease Spreading. Int J Mol Sci 2021; 22:ijms222312771. [PMID: 34884576 PMCID: PMC8657466 DOI: 10.3390/ijms222312771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Visual deficit is one of the complications of Huntington disease (HD), a fatal neurological disorder caused by CAG trinucleotide expansions in the Huntingtin gene, leading to the production of mutant Huntingtin (mHTT) protein. Transgenic HD R6/1 mice expressing human HTT exon1 with 115 CAG repeats recapitulate major features of the human pathology and exhibit a degeneration of the retina. Our aim was to gain insight into the ultrastructure of the pathological HD R6/1 retina by electron microscopy (EM). We show that the HD R6/1 retina is enriched with unusual organelles myelinosomes, produced by retinal neurons and glia. Myelinosomes are present in all nuclear and plexiform layers, in the synaptic terminals of photoreceptors, in the processes of retinal neurons and glial cells, and in the subretinal space. In vitro study shows that myelinosomes secreted by human retinal glial Müller MIO-M1 cells transfected with EGFP-mHTT-exon1 carry EGFP-mHTT-exon1 protein, as revealed by immuno-EM and Western-blotting. Myelinosomes loaded with mHTT-exon1 are incorporated by naive neuronal/neuroblastoma SH-SY5Y cells. This results in the emergence of mHTT-exon1 in recipient cells. This process is blocked by membrane fusion inhibitor MDL 28170. Conclusion: Incorporation of myelinosomes carrying mHTT-exon1 in recipient cells may contribute to HD spreading in the retina. Exploring ocular fluids for myelinosome presence could bring an additional biomarker for HD diagnostics.
Collapse
Affiliation(s)
- Marina G. Yefimova
- Laboratoire Signalisation et Transports Ioniques Membranaires, Université de Poitiers/CNRS, 1 Rue Georges Bonnet, 86022 Poitiers, France; (A.C.-B.); (A.-C.M.-B.); (F.B.); (N.B.)
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Pr. Thorez, 194233 St. Petersburg, Russia
- Laboratoire de Biologie de la Reproduction-CECOS, Hopital SUD, 16 Bd de Bulgarie, CEDEX, 35000 Rennes, France;
- Correspondence:
| | - Emile Béré
- Plateforme IMAGE-UP, 1 Rue Georges Bonnet, 86022 Poitiers, France; (E.B.); (B.M.)
| | - Anne Cantereau-Becq
- Laboratoire Signalisation et Transports Ioniques Membranaires, Université de Poitiers/CNRS, 1 Rue Georges Bonnet, 86022 Poitiers, France; (A.C.-B.); (A.-C.M.-B.); (F.B.); (N.B.)
- Plateforme IMAGE-UP, 1 Rue Georges Bonnet, 86022 Poitiers, France; (E.B.); (B.M.)
| | - Annie-Claire Meunier-Balandre
- Laboratoire Signalisation et Transports Ioniques Membranaires, Université de Poitiers/CNRS, 1 Rue Georges Bonnet, 86022 Poitiers, France; (A.C.-B.); (A.-C.M.-B.); (F.B.); (N.B.)
| | - Bruno Merceron
- Plateforme IMAGE-UP, 1 Rue Georges Bonnet, 86022 Poitiers, France; (E.B.); (B.M.)
| | - Agnès Burel
- Plateforme Mric TEM, BIOSIT UMS 34 80, Université de Rennes 1, 2 Av. Pr. Léon Bernard, CEDEX, 35043 Rennes, France;
| | - Karine Merienne
- Laboratory of Cognitive and Adaptive Neurosciences (LNCA), University of Strasbourg, 67000 Strasbourg, France;
- CNRS UMR 7364, 67000 Strasbourg, France
| | - Célia Ravel
- Laboratoire de Biologie de la Reproduction-CECOS, Hopital SUD, 16 Bd de Bulgarie, CEDEX, 35000 Rennes, France;
| | - Frédéric Becq
- Laboratoire Signalisation et Transports Ioniques Membranaires, Université de Poitiers/CNRS, 1 Rue Georges Bonnet, 86022 Poitiers, France; (A.C.-B.); (A.-C.M.-B.); (F.B.); (N.B.)
| | - Nicolas Bourmeyster
- Laboratoire Signalisation et Transports Ioniques Membranaires, Université de Poitiers/CNRS, 1 Rue Georges Bonnet, 86022 Poitiers, France; (A.C.-B.); (A.-C.M.-B.); (F.B.); (N.B.)
- Service de Biochimie, CHU de Poitiers, 1, Rue de la Milétrie, 86021 Poitiers, France
| |
Collapse
|
132
|
Zhao X, Lu H, Usdin K. FAN1's protection against CGG repeat expansion requires its nuclease activity and is FANCD2-independent. Nucleic Acids Res 2021; 49:11643-11652. [PMID: 34718701 PMCID: PMC8599916 DOI: 10.1093/nar/gkab899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/20/2021] [Accepted: 10/12/2021] [Indexed: 12/21/2022] Open
Abstract
The Repeat Expansion Diseases, a large group of human diseases that includes the fragile X-related disorders (FXDs) and Huntington's disease (HD), all result from expansion of a disease-specific microsatellite via a mechanism that is not fully understood. We have previously shown that mismatch repair (MMR) proteins are required for expansion in a mouse model of the FXDs, but that the FANCD2 and FANCI associated nuclease 1 (FAN1), a component of the Fanconi anemia (FA) DNA repair pathway, is protective. FAN1's nuclease activity has been reported to be dispensable for protection against expansion in an HD cell model. However, we show here that in a FXD mouse model a point mutation in the nuclease domain of FAN1 has the same effect on expansion as a null mutation. Furthermore, we show that FAN1 and another nuclease, EXO1, have an additive effect in protecting against MSH3-dependent expansions. Lastly, we show that the loss of FANCD2, a vital component of the Fanconi anemia DNA repair pathway, has no effect on expansions. Thus, FAN1 protects against MSH3-dependent expansions without diverting the expansion intermediates into the canonical FA pathway and this protection depends on FAN1 having an intact nuclease domain.
Collapse
Affiliation(s)
- Xiaonan Zhao
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Huiyan Lu
- Laboratory Animal Sciences section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
133
|
McIntosh CS, Li D, Wilton SD, Aung-Htut MT. Polyglutamine Ataxias: Our Current Molecular Understanding and What the Future Holds for Antisense Therapies. Biomedicines 2021; 9:1499. [PMID: 34829728 PMCID: PMC8615177 DOI: 10.3390/biomedicines9111499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Polyglutamine (polyQ) ataxias are a heterogenous group of neurological disorders all caused by an expanded CAG trinucleotide repeat located in the coding region of each unique causative gene. To date, polyQ ataxias encompass six disorders: spinocerebellar ataxia types 1, 2, 3, 6, 7, and 17 and account for a larger group of disorders simply known as polyglutamine disorders, which also includes Huntington's disease. These diseases are typically characterised by progressive ataxia, speech and swallowing difficulties, lack of coordination and gait, and are unfortunately fatal in nature, with the exception of SCA6. All the polyQ spinocerebellar ataxias have a hallmark feature of neuronal aggregations and share many common pathogenic mechanisms, such as mitochondrial dysfunction, impaired proteasomal function, and autophagy impairment. Currently, therapeutic options are limited, with no available treatments that slow or halt disease progression. Here, we discuss the common molecular and clinical presentations of polyQ spinocerebellar ataxias. We will also discuss the promising antisense oligonucleotide therapeutics being developed as treatments for these devastating diseases. With recent advancements and therapeutic approvals of various antisense therapies, it is envisioned that some of the studies reviewed may progress into clinical trials and beyond.
Collapse
Affiliation(s)
- Craig S. McIntosh
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Dunhui Li
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Steve D. Wilton
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| | - May T. Aung-Htut
- Molecular Therapy Laboratory, Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute Murdoch University, Discovery Way, Murdoch, WA 6150, Australia; (C.S.M.); (D.L.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, WA 6009, Australia
| |
Collapse
|
134
|
Berdnikova DV. Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy. Chem Commun (Camb) 2021; 57:10819-10826. [PMID: 34585681 DOI: 10.1039/d1cc04241f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an emerging drug target that opens new perspectives in the treatment of viral and bacterial infections, cancer and a range of so far incurable genetic diseases. Among the various strategies towards the design and development of selective and efficient ligands for targeting and detection of therapeutically relevant RNA, photoswitchable RNA binders represent a very promising approach due to the possibility to control the ligand-RNA and protein-RNA interactions by light with high spatiotemporal resolution. However, the field of photoswitchable RNA binders still remains underexplored due to challenging design of lead structures that should combine high RNA binding selectivity with efficient photochemical performance. The aim of this highlight article is to describe the development of photoswitchable noncovalent RNA binders and to outline the current situation and perspectives of this emerging interdisciplinary field.
Collapse
Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
| |
Collapse
|
135
|
Hayward BE, Usdin K. Mechanisms of Genome Instability in the Fragile X-Related Disorders. Genes (Basel) 2021; 12:genes12101633. [PMID: 34681027 PMCID: PMC8536109 DOI: 10.3390/genes12101633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/17/2022] Open
Abstract
The Fragile X-related disorders (FXDs), which include the intellectual disability fragile X syndrome (FXS), are disorders caused by expansion of a CGG-repeat tract in the 5′ UTR of the X-linked FMR1 gene. These disorders are named for FRAXA, the folate-sensitive fragile site that localizes with the CGG-repeat in individuals with FXS. Two pathological FMR1 allele size classes are distinguished. Premutation (PM) alleles have 54–200 repeats and confer the risk of fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI). PM alleles are prone to both somatic and germline expansion, with female PM carriers being at risk of having a child with >200+ repeats. Inheritance of such full mutation (FM) alleles causes FXS. Contractions of PM and FM alleles can also occur. As a result, many carriers are mosaic for different sized alleles, with the clinical presentation depending on the proportions of these alleles in affected tissues. Furthermore, it has become apparent that the chromosomal fragility of FXS individuals reflects an underlying problem that can lead to chromosomal numerical and structural abnormalities. Thus, large numbers of CGG-repeats in the FMR1 gene predisposes individuals to multiple forms of genome instability. This review will discuss our current understanding of these processes.
Collapse
|
136
|
Gold MA, Whalen JM, Freon K, Hong Z, Iraqui I, Lambert SAE, Freudenreich CH. Restarted replication forks are error-prone and cause CAG repeat expansions and contractions. PLoS Genet 2021; 17:e1009863. [PMID: 34673780 PMCID: PMC8562783 DOI: 10.1371/journal.pgen.1009863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 11/02/2021] [Accepted: 10/06/2021] [Indexed: 12/16/2022] Open
Abstract
Disease-associated trinucleotide repeats form secondary DNA structures that interfere with replication and repair. Replication has been implicated as a mechanism that can cause repeat expansions and contractions. However, because structure-forming repeats are also replication barriers, it has been unclear whether the instability occurs due to slippage during normal replication progression through the repeat, slippage or misalignment at a replication stall caused by the repeat, or during subsequent replication of the repeat by a restarted fork that has altered properties. In this study, we have specifically addressed the fidelity of a restarted fork as it replicates through a CAG/CTG repeat tract and its effect on repeat instability. To do this, we used a well-characterized site-specific replication fork barrier (RFB) system in fission yeast that creates an inducible and highly efficient stall that is known to restart by recombination-dependent replication (RDR), in combination with long CAG repeat tracts inserted at various distances and orientations with respect to the RFB. We find that replication by the restarted fork exhibits low fidelity through repeat sequences placed 2-7 kb from the RFB, exhibiting elevated levels of Rad52- and Rad8ScRad5/HsHLTF-dependent instability. CAG expansions and contractions are not elevated to the same degree when the tract is just in front or behind the barrier, suggesting that the long-traveling Polδ-Polδ restarted fork, rather than fork reversal or initial D-loop synthesis through the repeat during stalling and restart, is the greatest source of repeat instability. The switch in replication direction that occurs due to replication from a converging fork while the stalled fork is held at the barrier is also a significant contributor to the repeat instability profile. Our results shed light on a long-standing question of how fork stalling and RDR contribute to expansions and contractions of structure-forming trinucleotide repeats, and reveal that tolerance to replication stress by fork restart comes at the cost of increased instability of repetitive sequences.
Collapse
Affiliation(s)
- Michaela A. Gold
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Jenna M. Whalen
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Karine Freon
- Institut Curie, Université PSL, Orsay, France
- Université Paris-Saclay, Orsay, France
| | - Zixin Hong
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Ismail Iraqui
- Institut Curie, Université PSL, Orsay, France
- Université Paris-Saclay, Orsay, France
| | - Sarah A. E. Lambert
- Institut Curie, Université PSL, Orsay, France
- Université Paris-Saclay, Orsay, France
- Equipes Labélisées Ligue Nationale Contre Le Cancer, Orsay, France
| | | |
Collapse
|
137
|
Lokanga RA, Kumari D, Usdin K. Common Threads: Aphidicolin-Inducible and Folate-Sensitive Fragile Sites in the Human Genome. Front Genet 2021; 12:708860. [PMID: 34567068 PMCID: PMC8456018 DOI: 10.3389/fgene.2021.708860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
The human genome has many chromosomal regions that are fragile, demonstrating chromatin breaks, gaps, or constrictions on exposure to replication stress. Common fragile sites (CFSs) are found widely distributed in the population, with the largest subset of these sites being induced by aphidicolin (APH). Other fragile sites are only found in a subset of the population. One group of these so-called rare fragile sites (RFSs) is induced by folate stress. APH-inducible CFSs are generally located in large transcriptionally active genes that are A + T rich and often enriched for tracts of AT-dinucleotide repeats. In contrast, all the folate-sensitive sites mapped to date consist of transcriptionally silenced CGG microsatellites. Thus, all the folate-sensitive fragile sites may have a very similar molecular basis that differs in key ways from that of the APH CFSs. The folate-sensitive FSs include FRAXA that is associated with Fragile X syndrome (FXS), the most common heritable form of intellectual disability. Both CFSs and RFSs can cause chromosomal abnormalities. Recent work suggests that both APH-inducible fragile sites and FRAXA undergo Mitotic DNA synthesis (MiDAS) when exposed to APH or folate stress, respectively. Interestingly, blocking MiDAS in both cases prevents chromosome fragility but increases the risk of chromosome mis-segregation. MiDAS of both APH-inducible and FRAXA involves conservative DNA replication and POLD3, an accessory subunit of the replicative polymerase Pol δ that is essential for break-induced replication (BIR). Thus, MiDAS is thought to proceed via some form of BIR-like process. This review will discuss the recent work that highlights the similarities and differences between these two groups of fragile sites and the growing evidence for the presence of many more novel fragile sites in the human genome.
Collapse
Affiliation(s)
| | - Daman Kumari
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
138
|
Gkekas I, Gioran A, Boziki MK, Grigoriadis N, Chondrogianni N, Petrakis S. Oxidative Stress and Neurodegeneration: Interconnected Processes in PolyQ Diseases. Antioxidants (Basel) 2021; 10:antiox10091450. [PMID: 34573082 PMCID: PMC8471619 DOI: 10.3390/antiox10091450] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/16/2022] Open
Abstract
Neurodegenerative polyglutamine (polyQ) disorders are caused by trinucleotide repeat expansions within the coding region of disease-causing genes. PolyQ-expanded proteins undergo conformational changes leading to the formation of protein inclusions which are associated with selective neuronal degeneration. Several lines of evidence indicate that these mutant proteins are associated with oxidative stress, proteasome impairment and microglia activation. These events may correlate with the induction of inflammation in the nervous system and disease progression. Here, we review the effect of polyQ-induced oxidative stress in cellular and animal models of polyQ diseases. Furthermore, we discuss the interplay between oxidative stress, neurodegeneration and neuroinflammation using as an example the well-known neuroinflammatory disease, Multiple Sclerosis. Finally, we review some of the pharmaceutical interventions which may delay the onset and progression of polyQ disorders by targeting disease-associated mechanisms.
Collapse
Affiliation(s)
- Ioannis Gkekas
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece;
| | - Anna Gioran
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece; (A.G.); (N.C.)
| | - Marina Kleopatra Boziki
- 2nd Neurological Department, AHEPA University General Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (M.K.B.); (N.G.)
| | - Nikolaos Grigoriadis
- 2nd Neurological Department, AHEPA University General Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (M.K.B.); (N.G.)
| | - Niki Chondrogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece; (A.G.); (N.C.)
| | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece;
- Correspondence: ; Tel.: +30-2311257525
| |
Collapse
|
139
|
Krausz C, Cioppi F. Genetic Factors of Non-Obstructive Azoospermia: Consequences on Patients' and Offspring Health. J Clin Med 2021; 10:jcm10174009. [PMID: 34501457 PMCID: PMC8432470 DOI: 10.3390/jcm10174009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/20/2022] Open
Abstract
Non-Obstructive Azoospermia (NOA) affects about 1% of men in the general population and is characterized by clinical heterogeneity implying the involvement of several different acquired and genetic factors. NOA men are at higher risk to be carriers of known genetic anomalies such as karyotype abnormalities and Y-chromosome microdeletions in respect to oligo-normozoospermic men. In recent years, a growing number of novel monogenic causes have been identified through Whole Exome Sequencing (WES). Genetic testing is useful for diagnostic and pre-TESE prognostic purposes as well as for its potential relevance for general health. Several epidemiological observations show a link between azoospermia and higher morbidity and mortality rate, suggesting a common etiology for NOA and some chronic diseases, including cancer. Since on average 50% of NOA patients has a positive TESE outcome, the identification of genetic factors in NOA patients has relevance also to the offspring's health. Although still debated, the observed increased risk of certain neurodevelopmental disorders, as well as impaired cardiometabolic and reproductive health profile in children conceived with ICSI from NOA fathers may indicate the involvement of transmissible genetic factors. This review provides an update on the reproductive and general health consequences of known genetic factors causing NOA, including offspring's health.
Collapse
|
140
|
Malik I, Kelley CP, Wang ET, Todd PK. Molecular mechanisms underlying nucleotide repeat expansion disorders. Nat Rev Mol Cell Biol 2021; 22:589-607. [PMID: 34140671 PMCID: PMC9612635 DOI: 10.1038/s41580-021-00382-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 02/05/2023]
Abstract
The human genome contains over one million short tandem repeats. Expansion of a subset of these repeat tracts underlies over fifty human disorders, including common genetic causes of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (C9orf72), polyglutamine-associated ataxias and Huntington disease, myotonic dystrophy, and intellectual disability disorders such as Fragile X syndrome. In this Review, we discuss the four major mechanisms by which expansion of short tandem repeats causes disease: loss of function through transcription repression, RNA-mediated gain of function through gelation and sequestration of RNA-binding proteins, gain of function of canonically translated repeat-harbouring proteins, and repeat-associated non-AUG translation of toxic repeat peptides. Somatic repeat instability amplifies these mechanisms and influences both disease age of onset and tissue specificity of pathogenic features. We focus on the crosstalk between these disease mechanisms, and argue that they often synergize to drive pathogenesis. We also discuss the emerging native functions of repeat elements and how their dynamics might contribute to disease at a larger scale than currently appreciated. Lastly, we propose that lynchpins tying these disease mechanisms and native functions together offer promising therapeutic targets with potential shared applications across this class of human disorders.
Collapse
Affiliation(s)
- Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Chase P Kelley
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
- Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
| |
Collapse
|
141
|
Zhao X, Usdin K. (Dys)function Follows Form: Nucleic Acid Structure, Repeat Expansion, and Disease Pathology in FMR1 Disorders. Int J Mol Sci 2021; 22:ijms22179167. [PMID: 34502075 PMCID: PMC8431139 DOI: 10.3390/ijms22179167] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
Fragile X-related disorders (FXDs), also known as FMR1 disorders, are examples of repeat expansion diseases (REDs), clinical conditions that arise from an increase in the number of repeats in a disease-specific microsatellite. In the case of FXDs, the repeat unit is CGG/CCG and the repeat tract is located in the 5' UTR of the X-linked FMR1 gene. Expansion can result in neurodegeneration, ovarian dysfunction, or intellectual disability depending on the number of repeats in the expanded allele. A growing body of evidence suggests that the mutational mechanisms responsible for many REDs share several common features. It is also increasingly apparent that in some of these diseases the pathologic consequences of expansion may arise in similar ways. It has long been known that many of the disease-associated repeats form unusual DNA and RNA structures. This review will focus on what is known about these structures, the proteins with which they interact, and how they may be related to the causative mutation and disease pathology in the FMR1 disorders.
Collapse
Affiliation(s)
- Xiaonan Zhao
- Correspondence: (X.Z.); (K.U.); Tel.: +1-301-451-6322 (X.Z.); +1-301-496-2189 (K.U.)
| | - Karen Usdin
- Correspondence: (X.Z.); (K.U.); Tel.: +1-301-451-6322 (X.Z.); +1-301-496-2189 (K.U.)
| |
Collapse
|
142
|
Godley LA. Anticipation in hematopoietic malignancies: biology, bias, or both? Leuk Lymphoma 2021; 62:3070-3072. [PMID: 34405775 DOI: 10.1080/10428194.2021.1966789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lucy A Godley
- Departments of Medicine and Human Genetics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL, USA
| |
Collapse
|
143
|
Chiu R, Rajan-Babu IS, Friedman JM, Birol I. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol 2021; 22:224. [PMID: 34389037 PMCID: PMC8361843 DOI: 10.1186/s13059-021-02447-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing.
Collapse
Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| |
Collapse
|
144
|
Nuclear export and translation of circular repeat-containing intronic RNA in C9ORF72-ALS/FTD. Nat Commun 2021; 12:4908. [PMID: 34389711 PMCID: PMC8363653 DOI: 10.1038/s41467-021-25082-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 07/16/2021] [Indexed: 12/14/2022] Open
Abstract
C9ORF72 hexanucleotide GGGGCC repeat expansion is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat-containing RNA mediates toxicity through nuclear granules and dipeptide repeat (DPR) proteins produced by repeat-associated non-AUG translation. However, it remains unclear how the intron-localized repeats are exported and translated in the cytoplasm. We use single molecule imaging approach to examine the molecular identity and spatiotemporal dynamics of the repeat RNA. We demonstrate that the spliced intron with G-rich repeats is stabilized in a circular form due to defective lariat debranching. The spliced circular intron, instead of pre-mRNA, serves as the translation template. The NXF1-NXT1 pathway plays an important role in the nuclear export of the circular intron and modulates toxic DPR production. This study reveals an uncharacterized disease-causing RNA species mediated by repeat expansion and demonstrates the importance of RNA spatial localization to understand disease etiology. Hexanucleotide repeat expansion in the intron 1 of the C9ORF72 gene can cause amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). Here the authors use single molecule imaging to show nuclear export and translation of circular repeat-containing C9ORF72 intronic RNA.
Collapse
|
145
|
Rajan-Babu IS, Peng JJ, Chiu R, Li C, Mohajeri A, Dolzhenko E, Eberle MA, Birol I, Friedman JM. Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions. Genome Med 2021; 13:126. [PMID: 34372915 PMCID: PMC8351082 DOI: 10.1186/s13073-021-00932-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/05/2021] [Indexed: 02/01/2023] Open
Abstract
Background Screening for short tandem repeat (STR) expansions in next-generation sequencing data can enable diagnosis, optimal clinical management/treatment, and accurate genetic counseling of patients with repeat expansion disorders. We aimed to develop an efficient computational workflow for reliable detection of STR expansions in next-generation sequencing data and demonstrate its clinical utility. Methods We characterized the performance of eight STR analysis methods (lobSTR, HipSTR, RepeatSeq, ExpansionHunter, TREDPARSE, GangSTR, STRetch, and exSTRa) on next-generation sequencing datasets of samples with known disease-causing full-mutation STR expansions and genomes simulated to harbor repeat expansions at selected loci and optimized their sensitivity. We then used a machine learning decision tree classifier to identify an optimal combination of methods for full-mutation detection. In Burrows-Wheeler Aligner (BWA)-aligned genomes, the ensemble approach of using ExpansionHunter, STRetch, and exSTRa performed the best (precision = 82%, recall = 100%, F1-score = 90%). We applied this pipeline to screen 301 families of children with suspected genetic disorders. Results We identified 10 individuals with full-mutations in the AR, ATXN1, ATXN8, DMPK, FXN, or HTT disease STR locus in the analyzed families. Additional candidates identified in our analysis include two probands with borderline ATXN2 expansions between the established repeat size range for reduced-penetrance and full-penetrance full-mutation and seven individuals with FMR1 CGG repeats in the intermediate/premutation repeat size range. In 67 probands with a prior negative clinical PCR test for the FMR1, FXN, or DMPK disease STR locus, or the spinocerebellar ataxia disease STR panel, our pipeline did not falsely identify aberrant expansion. We performed clinical PCR tests on seven (out of 10) full-mutation samples identified by our pipeline and confirmed the expansion status in all, showing absolute concordance between our bioinformatics and molecular findings. Conclusions We have successfully demonstrated the application of a well-optimized bioinformatics pipeline that promotes the utility of genome-wide sequencing as a first-tier screening test to detect expansions of known disease STRs. Interrogating clinical next-generation sequencing data for pathogenic STR expansions using our ensemble pipeline can improve diagnostic yield and enhance clinical outcomes for patients with repeat expansion disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00932-9.
Collapse
Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada. .,Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK.
| | - Junran J Peng
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada
| | | | | | - Chenkai Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada.,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, V6T1Z4, Canada
| | - Arezoo Mohajeri
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
| | | | | | - Inanc Birol
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z4S6, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia and Children's & Women's Hospital, Vancouver, BC, V6H3N1, Canada
| |
Collapse
|
146
|
Anticipation Can Be More Common in Hereditary Spastic Paraplegia with SPAST Mutations Than It Appears. Can J Neurol Sci 2021; 49:651-661. [PMID: 34353391 DOI: 10.1017/cjn.2021.188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND OBJECTIVE Hereditary spastic paraplegia (HSP) is a heterogeneous neurodegenerative disorder with lower-limb spasticity and weakness. Different patterns of inheritance have been identified in HSP. Most autosomal-dominant HSPs (AD-HSPs) are associated with mutations of the SPAST gene (SPG4), leading to a pure form of HSP with variable age-at-onset (AAO). Anticipation, an earlier onset of disease, as well as aggravation of symptoms in successive generations, may be correlated to SPG4. Herein, we suggested that anticipation might be a relatively common finding in SPG4 families. METHODS Whole-exome sequencing was done on DNA of 14 unrelated Iranian AD-HSP probands. Data were analyzed, and candidate variants were PCR-amplified and sequenced by the Sanger method, subsequently checked in family members to co-segregation analysis. Multiplex ligation-dependent probe amplification (MLPA) was done for seven probands. Clinical features of the probands were recorded, and the probable anticipation was checked in these families. Other previous reported SPG4 families were investigated to anticipation. RESULTS Our findings showed that SPG4 was the common subtype of HSP; three families carried variants in the KIF5A, ATL1, and MFN2 genes, while five families harbored mutations in the SPAST gene. Clinical features of only SPG4 families indicated decreasing AAO in affected individuals of the successive generations, and this difference was significant (p-value <0.05). CONCLUSION It seems SPAST will be the first candidate gene in families that manifests a pure form of AD-HSP and anticipation. Therefore, it may be a powerful situation of genotype-phenotype correlation. However, the underlying mechanism of anticipation in these families is not clear yet.
Collapse
|
147
|
C9orf72-G 4C 2 Intermediate Repeats and Parkinson's Disease; A Data-Driven Hypothesis. Genes (Basel) 2021; 12:genes12081210. [PMID: 34440384 PMCID: PMC8391122 DOI: 10.3390/genes12081210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 11/30/2022] Open
Abstract
Pathogenic C9orf72-G4C2 repeat expansions are associated with ALS/FTD, but not with Parkinson’s disease (PD); yet the possible link between intermediate repeat lengths and PD remains inconclusive. We aim to study the potential involvement of these repeats in PD. The number of C9orf72-repeats were determined by flanking and repeat-primed PCR assays, and the risk-haplotype was determined by SNP-array. Their association with PD was assessed in a stratified manner: in PD-patients-carriers of mutations in LRRK2, GBA, or SMPD1 genes (n = 388), and in PD-non-carriers (NC, n = 718). Allelic distribution was significantly different only in PD-NC compared to 600 controls when looking both at the allele with higher repeat’s size (p = 0.034) and at the combined number of repeats from both alleles (p = 0.023). Intermediate repeats (20–60 repeats) were associated with PD in PD-NC patients (p = 0.041; OR = 3.684 (CI 1.05–13.0)) but not in PD-carriers (p = 0.684). The C9orf72 risk-haplotype, determined in a subgroup of 588 PDs and 126 controls, was observed in higher frequency in PD-NC (dominant model, OR = 1.71, CI 1.04–2.81, p = 0.0356). All 19 alleles within the risk-haplotype were associated with higher C9orf72 RNA levels according to the GTEx database. Based on our data, we suggest a model in which intermediate repeats are a risk factor for PD in non-carriers, driven not only by the number of repeats but also by the variants’ genotypes within the risk-haplotype. Further studies are needed to elucidate this possible role of C9orf72 in PD pathogenesis.
Collapse
|
148
|
Bush JA, Williams CC, Meyer SM, Tong Y, Haniff HS, Childs-Disney JL, Disney MD. Systematically Studying the Effect of Small Molecules Interacting with RNA in Cellular and Preclinical Models. ACS Chem Biol 2021; 16:1111-1127. [PMID: 34166593 PMCID: PMC8867596 DOI: 10.1021/acschembio.1c00014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interrogation and manipulation of biological systems by small molecules is a powerful approach in chemical biology. Ideal compounds selectively engage a target and mediate a downstream phenotypic response. Although historically small molecule drug discovery has focused on proteins and enzymes, targeting RNA is an attractive therapeutic alternative, as many disease-causing or -associated RNAs have been identified through genome-wide association studies. As the field of RNA chemical biology emerges, the systematic evaluation of target validation and modulation of target-associated pathways is of paramount importance. In this Review, through an examination of case studies, we outline the experimental characterization, including methods and tools, to evaluate comprehensively the impact of small molecules that target RNA on cellular phenotype.
Collapse
Affiliation(s)
- Jessica A Bush
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Christopher C Williams
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Samantha M Meyer
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| |
Collapse
|
149
|
Kumutpongpanich T, Ogasawara M, Ozaki A, Ishiura H, Tsuji S, Minami N, Hayashi S, Noguchi S, Iida A, Nishino I, Mori-Yoshimura M, Oya Y, Ono K, Shimizu T, Kawata A, Shimohama S, Toyooka K, Endo K, Toru S, Sasaki O, Isahaya K, Takahashi MP, Iwasa K, Kira JI, Yamamoto T, Kawamoto M, Hamano T, Sugie K, Eura N, Shiota T, Koide M, Sekiya K, Kishi H, Hideyama T, Kawai S, Yanagimoto S, Sato H, Arahata H, Murayama S, Saito K, Hara H, Kanda T, Yaguchi H, Imai N, Kawagashira Y, Sanada M, Obara K, Kaido M, Furuta M, Kurashige T, Hara W, Kuzume D, Yamamoto M, Tsugawa J, Kishida H, Ishizuka N, Morimoto K, Tsuji Y, Tsuneyama A, Matsuno A, Sasaki R, Tamakoshi D, Abe E, Yamada S, Uzawa A. Clinicopathologic Features of Oculopharyngodistal Myopathy With LRP12 CGG Repeat Expansions Compared With Other Oculopharyngodistal Myopathy Subtypes. JAMA Neurol 2021; 78:853-863. [PMID: 34047774 DOI: 10.1001/jamaneurol.2021.1509] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Repeat expansion of CGG in LRP12 has been identified as the causative variation of oculopharyngodistal myopathy (OPDM). However, to our knowledge, the clinicopathologic features of OPDM with CGG repeat expansion in LRP12 (hereafter referred to as OPDM_LRP12) remain unknown. Objective To identify and characterize the clinicopathologic features of patients with OPDM_LRP12. Design, Setting, and Participants This case series included 208 patients with a clinical or clinicopathologic diagnosis of oculopharyngeal muscular dystrophy (OPDM) from January 1, 1978, to December 31, 2020. Patients with GCN repeat expansions in PABPN1 were excluded from the study. Repeat expansions of CGG in LRP12 were screened by repeat primed polymerase chain reaction and/or Southern blot. Main Outcomes and Measures Clinical information, muscle imaging data obtained by either computed tomography or magnetic resonance imaging, and muscle pathologic characteristics. Results Sixty-five Japanese patients with OPDM (40 men [62%]; mean [SD] age at onset, 41.0 [10.1] years) from 59 families with CGG repeat expansions in LRP12 were identified. This represents the most common OPDM subtype among all patients in Japan with genetically diagnosed OPDM. The expansions ranged from 85 to 289 repeats. A negative correlation was observed between the repeat size and the age at onset (r2 = 0.188, P = .001). The most common initial symptoms were ptosis and muscle weakness, present in 24 patients (37%). Limb muscle weakness was predominantly distal in 53 of 64 patients (83%), but 2 of 64 patients (3%) had predominantly proximal muscle weakness. Ptosis was observed in 62 of 64 patients (97%), and dysphagia or dysarthria was observed in 63 of 64 patients (98%). A total of 21 of 64 patients (33%) had asymmetric muscle weakness. Aspiration pneumonia was seen in 11 of 64 patients (17%), and 5 of 64 patients (8%) required mechanical ventilation. Seven of 64 patients (11%) developed cardiac abnormalities, and 5 of 64 patients (8%) developed neurologic abnormalities. Asymmetric muscle involvement was detected on computed tomography scans in 6 of 27 patients (22%) and on magnetic resonance imaging scans in 4 of 15 patients (27%), with the soleus and the medial head of the gastrocnemius being the worst affected. All 42 muscle biopsy samples showed rimmed vacuoles. Intranuclear tubulofilamentous inclusions were observed in only 1 of 5 patients. Conclusions and Relevance This study suggests that OPDM_LRP12 is the most frequent OPDM subtype in Japan and is characterized by oculopharyngeal weakness, distal myopathy that especially affects the soleus and gastrocnemius muscles, and rimmed vacuoles in muscle biopsy.
Collapse
Affiliation(s)
- Theerawat Kumutpongpanich
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Masashi Ogasawara
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Ayami Ozaki
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, The University of Tokyo Hospital, Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, The University of Tokyo Hospital, Tokyo, Japan
| | - Narihiro Minami
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Shinichiro Hayashi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Aritoshi Iida
- Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | | | - Madoka Mori-Yoshimura
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yasushi Oya
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Kenjiro Ono
- Division of Neurology, Department of Internal Medicine, Showa University School of Medicine, Shinagawa, Tokyo, Japan
| | - Toshio Shimizu
- Department of Neurology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Akihiro Kawata
- Department of Neurology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Shun Shimohama
- Department of Neurology, Sapporo Medical University, Sapporo, Japan
| | - Keiko Toyooka
- Department of Neurology, Osaka Toneyama Medical Center, Osaka, Japan
| | - Kaoru Endo
- Department of Neurology, Tohoku University School of Medicine, Miyagi, Japan
| | - Shuta Toru
- Department of Neurology, Nitobe Memorial Nakano General Hospital, Tokyo, Japan
| | - Oga Sasaki
- Division of Neurology, Department of Internal Medicine, St Marianna University School of Medicine, Kanagawa, Japan
| | - Kenji Isahaya
- Division of Neurology, Department of Internal Medicine, St Marianna University School of Medicine, Kanagawa, Japan
| | - Masanori P Takahashi
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazuo Iwasa
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Jun-Ichi Kira
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuya Yamamoto
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Michi Kawamoto
- Department of Neurology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Tadanori Hamano
- Second Department of Internal Medicine, Division of Neurology, Department of Aging and Dementia, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Kazuma Sugie
- Department of Neurology, Nara Medical University, Nara, Japan
| | - Nobuyuki Eura
- Department of Neurology, Nara Medical University, Nara, Japan
| | - Tomo Shiota
- Department of Neurology, Nara Medical University, Nara, Japan
| | - Mizuho Koide
- Department of Neurology, Chiba-East National Hospital, Chiba, Japan
| | - Kanako Sekiya
- Department of Neurology, Niigata City General Hospital, Niigata, Japan
| | - Hideaki Kishi
- Department of Neurology, Asahikawa Medical Center, Asahikawa, Japan
| | - Takuto Hideyama
- Department of Neurology, Tokyo Medical University, Tokyo, Japan
| | - Shigeru Kawai
- Department of Neurology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Satoshi Yanagimoto
- Department of Neurology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Hiroyasu Sato
- Department of Neurology, Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Hajime Arahata
- Department of Neurology, National Hospital Organization Omuta National Hospital, Omuta, Japan
| | - Shigeo Murayama
- Department of Neurology and Neuropathology (the Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital, Institute of Gerontology, Tokyo, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Hideo Hara
- Division of Neurology, Department of Internal Medicine, Saga University Faculty of Medicine, Saga, Japan
| | - Takashi Kanda
- Department of Neurology and Clinical Neuroscience, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Hiroshi Yaguchi
- Department of Neurology, The Jikei University Kashiwa Hospital, Kashiwa, Japan
| | - Noboru Imai
- Department of Neurology, Japanese Red Cross Shizuoka Hospital, Shizuoka, Japan
| | | | - Mitsuru Sanada
- Department of Neurology, Kanazawa Medical University Hospital, Ishikawa, Japan
| | - Kazuki Obara
- Department of Neurology, Anjo Kosei Hospital, Aichi, Japan
| | - Misako Kaido
- Department of Neurology, Sakai City Medical Center, Osaka, Japan
| | - Minori Furuta
- Department of Neurology, Gunma University, Maebashi, Japan
| | - Takashi Kurashige
- Department of Neurology, National Hospital Organization Kure Medical Center, Chugoku Cancer Center, Kure, Japan
| | - Wataru Hara
- Department of Neurology, Saitama Medical Center, Saitama, Japan
| | - Daisuke Kuzume
- Department of Neurology, Chikamori Hospital, Kochi, Japan
| | | | - Jun Tsugawa
- Department of Neurology, Fukuoka University, Fukuoka, Japan
| | - Hitaru Kishida
- Department of Neurology, Yokohama City University Medical Center, Yokohama, Japan
| | - Naoki Ishizuka
- Division of Neurology and Gerontology, Department of Internal Medicine, School of Medicine, Iwate Medical University, Iwate, Japan
| | | | - Yukio Tsuji
- Department of Neurology, Kobe University, Kobe, Japan
| | - Atsuko Tsuneyama
- Department of Neurology, Narita Red Cross Hospital, Chiba, Japan
| | - Atsuhiro Matsuno
- Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
| | - Ryo Sasaki
- Department of Neurology, Okayama University, Okayama, Japan
| | | | - Erika Abe
- Department of Neurology, National Hospital Organization Akita Hospital, Akita, Japan
| | - Shinichiro Yamada
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akiyuki Uzawa
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| |
Collapse
|
150
|
Baisden JT, Childs-Disney JL, Ryan LS, Disney MD. Affecting RNA biology genome-wide by binding small molecules and chemically induced proximity. Curr Opin Chem Biol 2021; 62:119-129. [PMID: 34118759 PMCID: PMC9264282 DOI: 10.1016/j.cbpa.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/08/2023]
Abstract
The ENCODE and genome-wide association projects have shown that much of the genome is transcribed into RNA and much less is translated into protein. These and other functional studies suggest that the druggable transcriptome is much larger than the druggable proteome. This review highlights approaches to define druggable RNA targets and structure-activity relationships across genomic RNA. Binding compounds can be identified and optimized into structure-specific ligands by using sequence-based design with various modes of action, for example, inhibiting translation or directing pre-mRNA splicing outcomes. In addition, strategies to direct protein activity against an RNA of interest via chemically induced proximity is a burgeoning area that has been validated both in cells and in preclinical animal models, and we describe that it may allow rapid access to new avenues to affect RNA biology. These approaches and the unique modes of action suggest that more RNAs are potentially amenable to targeting than proteins.
Collapse
Affiliation(s)
- Jared T Baisden
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Lucas S Ryan
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA.
| |
Collapse
|