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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024; 25:476-499. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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2
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Rouse WB, Tompkins VS, O’Leary CA, Moss WN. The RNA secondary structure of androgen receptor-FL and V7 transcripts reveals novel regulatory regions. Nucleic Acids Res 2024; 52:6596-6613. [PMID: 38554103 PMCID: PMC11194067 DOI: 10.1093/nar/gkae220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
The androgen receptor (AR) is a ligand-dependent nuclear transcription factor belonging to the steroid hormone nuclear receptor family. Due to its roles in regulating cell proliferation and differentiation, AR is tightly regulated to maintain proper levels of itself and the many genes it controls. AR dysregulation is a driver of many human diseases including prostate cancer. Though this dysregulation often occurs at the RNA level, there are many unknowns surrounding post-transcriptional regulation of AR mRNA, particularly the role that RNA secondary structure plays. Thus, a comprehensive analysis of AR transcript secondary structure is needed. We address this through the computational and experimental analyses of two key isoforms, full length (AR-FL) and truncated (AR-V7). Here, a combination of in-cell RNA secondary structure probing experiments (targeted DMS-MaPseq) and computational predictions were used to characterize the static structural landscape and conformational dynamics of both isoforms. Additionally, in-cell assays were used to identify functionally relevant structures in the 5' and 3' UTRs of AR-FL. A notable example is a conserved stem loop structure in the 5'UTR of AR-FL that can bind to Poly(RC) Binding Protein 2 (PCBP2). Taken together, our results reveal novel features that regulate AR expression.
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Affiliation(s)
- Warren B Rouse
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Van S Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Collin A O’Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: Departments of Biology and Chemistry, Cornell College, Mount Vernon, IA 52314, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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3
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Madhanagopal BR, Talbot H, Rodriguez A, Louis JM, Zeghal H, Vangaveti S, Reddy K, Chandrasekaran AR. The unusual structural properties and potential biological relevance of switchback DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.563609. [PMID: 38014227 PMCID: PMC10680705 DOI: 10.1101/2023.11.15.563609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Synthetic DNA motifs form the basis of nucleic acid nanotechnology, and their biochemical and biophysical properties determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.
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Affiliation(s)
| | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Jiss Maria Louis
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Hana Zeghal
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
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4
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Sanchez-Flores M, Corral-Juan M, Gasch-Navalón E, Cirillo D, Sanchez I, Matilla-Dueñas A. Novel genotype-phenotype correlations, differential cerebellar allele-specific methylation, and a common origin of the (ATTTC) n insertion in spinocerebellar ataxia type 37. Hum Genet 2024; 143:211-232. [PMID: 38396267 PMCID: PMC11043136 DOI: 10.1007/s00439-024-02644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
Spinocerebellar ataxia subtype 37 (SCA37) is a rare disease originally identified in ataxia patients from the Iberian Peninsula with a pure cerebellar syndrome. SCA37 patients carry a pathogenic intronic (ATTTC)n repeat insertion flanked by two polymorphic (ATTTT)n repeats in the Disabled-1 (DAB1) gene leading to cerebellar dysregulation. Herein, we determine the precise configuration of the pathogenic 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n SCA37 alleles by CRISPR-Cas9 and long-read nanopore sequencing, reveal their epigenomic signatures in SCA37 lymphocytes, fibroblasts, and cerebellar samples, and establish new molecular and clinical correlations. The 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n pathogenic allele configurations revealed repeat instability and differential methylation signatures. Disease age of onset negatively correlated with the (ATTTC)n, and positively correlated with the 3'(ATTTT)n. Geographic origin and gender significantly correlated with age of onset. Furthermore, significant predictive regression models were obtained by machine learning for age of onset and disease evolution by considering gender, the (ATTTC)n, the 3'(ATTTT)n, and seven CpG positions differentially methylated in SCA37 cerebellum. A common 964-kb genomic region spanning the (ATTTC)n insertion was identified in all SCA37 patients analysed from Portugal and Spain, evidencing a common origin of the SCA37 mutation in the Iberian Peninsula originating 859 years ago (95% CI 647-1378). In conclusion, we demonstrate an accurate determination of the size and configuration of the regulatory 5'(ATTTT)n-(ATTTC)n-3'(ATTTT)n repeat tract, avoiding PCR bias amplification using CRISPR/Cas9-enrichment and nanopore long-read sequencing, resulting relevant for accurate genetic diagnosis of SCA37. Moreover, we determine novel significant genotype-phenotype correlations in SCA37 and identify differential cerebellar allele-specific methylation signatures that may underlie DAB1 pathogenic dysregulation.
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Affiliation(s)
- Marina Sanchez-Flores
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Marc Corral-Juan
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Esther Gasch-Navalón
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | | | - Ivelisse Sanchez
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Antoni Matilla-Dueñas
- Neurogenetics Unit, Department of Neuroscience, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona-Can Ruti Campus, Carretera de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain.
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5
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Richardson K, Sengupta M, Sujkowski A, Libohova K, Harris AC, Wessells R, Merry DE, Todi SV. A phenotypically robust model of spinal and bulbar muscular atrophy in Drosophila. J Neurosci Res 2024; 102:e25278. [PMID: 38284836 DOI: 10.1002/jnr.25278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/14/2023] [Accepted: 11/05/2023] [Indexed: 01/30/2024]
Abstract
Spinal and bulbar muscular atrophy (SBMA) is an X-linked disorder that affects males who inherit the androgen receptor (AR) gene with an abnormal CAG triplet repeat expansion. The resulting protein contains an elongated polyglutamine (polyQ) tract and causes motor neuron degeneration in an androgen-dependent manner. The precise molecular sequelae of SBMA are unclear. To assist with its investigation and the identification of therapeutic options, we report here a new model of SBMA in Drosophila melanogaster. We generated transgenic flies that express the full-length, human AR with a wild-type or pathogenic polyQ repeat. Each transgene is inserted into the same safe harbor site on the third chromosome of the fly as a single copy and in the same orientation. Expression of pathogenic AR, but not of its wild-type variant, in neurons or muscles leads to consistent, progressive defects in longevity and motility that are concomitant with polyQ-expanded AR protein aggregation and reduced complexity in neuromuscular junctions. Additional assays show adult fly eye abnormalities associated with the pathogenic AR species. The detrimental effects of pathogenic AR are accentuated by feeding flies the androgen, dihydrotestosterone. This new, robust SBMA model can be a valuable tool toward future investigations of this incurable disease.
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Affiliation(s)
- Kristin Richardson
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Medha Sengupta
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University Sidney Kimmel Medical College, Philadelphia, Pennsylvania, USA
| | - Alyson Sujkowski
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Autumn C Harris
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Maximizing Access to Science Careers Program, Wayne State University, Detroit, Michigan, USA
| | - Robert Wessells
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Diane E Merry
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University Sidney Kimmel Medical College, Philadelphia, Pennsylvania, USA
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Maximizing Access to Science Careers Program, Wayne State University, Detroit, Michigan, USA
- Department of Neurology, Wayne State University School of Medicine, Detroit, Michigan, USA
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6
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Rafehi H, Bennett MF, Bahlo M. Detection and discovery of repeat expansions in ataxia enabled by next-generation sequencing: present and future. Emerg Top Life Sci 2023; 7:349-359. [PMID: 37733280 PMCID: PMC10754322 DOI: 10.1042/etls20230018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Hereditary cerebellar ataxias are a heterogenous group of progressive neurological disorders that are disproportionately caused by repeat expansions (REs) of short tandem repeats (STRs). Genetic diagnosis for RE disorders such as ataxias are difficult as the current gold standard for diagnosis is repeat-primed PCR assays or Southern blots, neither of which are scalable nor readily available for all STR loci. In the last five years, significant advances have been made in our ability to detect STRs and REs in short-read sequencing data, especially whole-genome sequencing. Given the increasing reliance of genomics in diagnosis of rare diseases, the use of established RE detection pipelines for RE disorders is now a highly feasible and practical first-step alternative to molecular testing methods. In addition, many new pathogenic REs have been discovered in recent years by utilising WGS data. Collectively, genomes are an important resource/platform for further advancements in both the discovery and diagnosis of REs that cause ataxia and will lead to much needed improvement in diagnostic rates for patients with hereditary ataxia.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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7
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Ikenoshita S, Matsuo K, Yabuki Y, Kawakubo K, Asamitsu S, Hori K, Usuki S, Hirose Y, Bando T, Araki K, Ueda M, Sugiyama H, Shioda N. A cyclic pyrrole-imidazole polyamide reduces pathogenic RNA in CAG/CTG triplet repeat neurological disease models. J Clin Invest 2023; 133:e164792. [PMID: 37707954 PMCID: PMC10645379 DOI: 10.1172/jci164792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Expansion of CAG and CTG (CWG) triplet repeats causes several inherited neurological diseases. The CWG repeat diseases are thought to involve complex pathogenic mechanisms through expanded CWG repeat-derived RNAs in a noncoding region and polypeptides in a coding region, respectively. However, an effective therapeutic approach has not been established for the CWG repeat diseases. Here, we show that a CWG repeat DNA-targeting compound, cyclic pyrrole-imidazole polyamide (CWG-cPIP), suppressed the pathogenesis of coding and noncoding CWG repeat diseases. CWG-cPIP bound to the hairpin form of mismatched CWG DNA, interfering with transcription elongation by RNA polymerase through a preferential activity toward repeat-expanded DNA. We found that CWG-cPIP selectively inhibited pathogenic mRNA transcripts from expanded CWG repeats, reducing CUG RNA foci and polyglutamine accumulation in cells from patients with myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Treatment with CWG-cPIP ameliorated behavioral deficits in adeno-associated virus-mediated CWG repeat-expressing mice and in a genetic mouse model of HD, without cytotoxicity or off-target effects. Together, we present a candidate compound that targets expanded CWG repeat DNA independently of its genomic location and reduces both pathogenic RNA and protein levels. CWG-cPIP may be used for the treatment of CWG repeat diseases and improvement of clinical outcomes.
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Affiliation(s)
- Susumu Ikenoshita
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Department of Neurology, Graduate School of Medical Sciences
| | - Kazuya Matsuo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
| | - Kosuke Kawakubo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
| | - Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Karin Hori
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, Japan
| | - Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis and
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Kyoto, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
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8
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Morelli KH, Wu Q, Gosztyla ML, Liu H, Yao M, Zhang C, Chen J, Marina RJ, Lee K, Jones KL, Huang MY, Li A, Smith-Geater C, Thompson LM, Duan W, Yeo GW. An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models. Nat Neurosci 2023; 26:27-38. [PMID: 36510111 PMCID: PMC9829537 DOI: 10.1038/s41593-022-01207-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 10/18/2022] [Indexed: 12/14/2022]
Abstract
Huntington's disease (HD) is a fatal, dominantly inherited neurodegenerative disorder caused by CAG trinucleotide expansion in exon 1 of the huntingtin (HTT) gene. Since the reduction of pathogenic mutant HTT messenger RNA is therapeutic, we developed a mutant allele-sensitive CAGEX RNA-targeting CRISPR-Cas13d system (Cas13d-CAGEX) that eliminates toxic CAGEX RNA in fibroblasts derived from patients with HD and induced pluripotent stem cell-derived neurons. We show that intrastriatal delivery of Cas13d-CAGEX via an adeno-associated viral vector selectively reduces mutant HTT mRNA and protein levels in the striatum of heterozygous zQ175 mice, a model of HD. This also led to improved motor coordination, attenuated striatal atrophy and reduction of mutant HTT protein aggregates. These phenotypic improvements lasted for at least eight months without adverse effects and with minimal off-target transcriptomic effects. Taken together, we demonstrate proof of principle of an RNA-targeting CRISPR-Cas13d system as a therapeutic approach for HD, a strategy with implications for the treatment of other dominantly inherited disorders.
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Affiliation(s)
- Kathryn H Morelli
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qian Wu
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hongshuai Liu
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Minmin Yao
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chuangchuang Zhang
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiaxu Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Ryan J Marina
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kari Lee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Krysten L Jones
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Megan Y Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Allison Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Charlene Smith-Geater
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - Leslie M Thompson
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Wenzhen Duan
- Division of Neurobiology, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
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The length of uninterrupted CAG repeats in stem regions of repeat disease associated hairpins determines the amount of short CAG oligonucleotides that are toxic to cells through RNA interference. Cell Death Dis 2022; 13:1078. [PMID: 36585400 PMCID: PMC9803637 DOI: 10.1038/s41419-022-05494-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/31/2022]
Abstract
Extended CAG trinucleotide repeats (TNR) in the genes huntingtin (HTT) and androgen receptor (AR) are the cause of two progressive neurodegenerative disorders: Huntington's disease (HD) and Spinal and Bulbar Muscular Atrophy (SBMA), respectively. Anyone who inherits the mutant gene in the complete penetrance range (>39 repeats for HD and 44 for SBMA) will develop the disease. An inverse correlation exists between the length of the CAG repeat and the severity and age of onset of the diseases. Growing evidence suggests that it is the length of uninterrupted CAG repeats in the mRNA rather than the length of poly glutamine (polyQ) in mutant (m)HTT protein that determines disease progression. One variant of mHTT (loss of inhibition; LOI) causes a 25 year earlier onset of HD when compared to a reference sequence, despite both coding for a protein that contains an identical number of glutamines. Short 21-22 nt CAG repeat (sCAGs)-containing RNAs can cause disease through RNA interference (RNAi). RNA hairpins (HPs) forming at the CAG TNRs are stabilized by adjacent CCG (in HD) or CUG repeats (in SBMA) making them better substrates for Dicer, the enzyme that processes CAG HPs into sCAGs. We now show that cells deficient in Dicer or unable to mediate RNAi are resistant to the toxicity of the HTT and AR derived HPs. Expression of a small HP that mimics the HD LOI variant is more stable and more toxic than a reference HP. We report that the LOI HP is processed by Dicer, loaded into the RISC more efficiently, and gives rise to a higher quantity of RISC-bound 22 nt sCAGs. Our data support the notion that RNAi contributes to the cell death seen in HD and SBMA and provide an explanation for the dramatically reduced onset of disease in HD patients that carry the LOI variant.
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10
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Childs-Disney JL, Yang X, Gibaut QMR, Tong Y, Batey RT, Disney MD. Targeting RNA structures with small molecules. Nat Rev Drug Discov 2022; 21:736-762. [PMID: 35941229 PMCID: PMC9360655 DOI: 10.1038/s41573-022-00521-4] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 01/07/2023]
Abstract
RNA adopts 3D structures that confer varied functional roles in human biology and dysfunction in disease. Approaches to therapeutically target RNA structures with small molecules are being actively pursued, aided by key advances in the field including the development of computational tools that predict evolutionarily conserved RNA structures, as well as strategies that expand mode of action and facilitate interactions with cellular machinery. Existing RNA-targeted small molecules use a range of mechanisms including directing splicing - by acting as molecular glues with cellular proteins (such as branaplam and the FDA-approved risdiplam), inhibition of translation of undruggable proteins and deactivation of functional structures in noncoding RNAs. Here, we describe strategies to identify, validate and optimize small molecules that target the functional transcriptome, laying out a roadmap to advance these agents into the next decade.
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Affiliation(s)
| | - Xueyi Yang
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | | | - Yuquan Tong
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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11
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Kurosaki T, Ashizawa T. The genetic and molecular features of the intronic pentanucleotide repeat expansion in spinocerebellar ataxia type 10. Front Genet 2022; 13:936869. [PMID: 36199580 PMCID: PMC9528567 DOI: 10.3389/fgene.2022.936869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is characterized by progressive cerebellar neurodegeneration and, in many patients, epilepsy. This disease mainly occurs in individuals with Indigenous American or East Asian ancestry, with strong evidence supporting a founder effect. The mutation causing SCA10 is a large expansion in an ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene. The ATTCT repeat is highly unstable, expanding to 280–4,500 repeats in affected patients compared with the 9–32 repeats in normal individuals, one of the largest repeat expansions causing neurological disorders identified to date. However, the underlying molecular basis of how this huge repeat expansion evolves and contributes to the SCA10 phenotype remains largely unknown. Recent progress in next-generation DNA sequencing technologies has established that the SCA10 repeat sequence has a highly heterogeneous structure. Here we summarize what is known about the structure and origin of SCA10 repeats, discuss the potential contribution of variant repeats to the SCA10 disease phenotype, and explore how this information can be exploited for therapeutic benefit.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
- Center for RNA Biology, University of Rochester, Rochester, NY, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
| | - Tetsuo Ashizawa
- Stanley H. Appel Department of Neurology, Houston Methodist Research Institute and Weil Cornell Medical College at Houston Methodist Houston, TX, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
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12
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Hou X, Li W, Liu P, Liu Z, Yuan Y, Ni J, Shen L, Tang B, Wang J. The Clinical and Ploynucleotide Repeat Expansion Analysis of ATXN2, NOP56, AR and C9orf72 in Patients With ALS From Mainland China. Front Neurol 2022; 13:811202. [PMID: 35599735 PMCID: PMC9120572 DOI: 10.3389/fneur.2022.811202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background Repeat expansions, including those in C9orf72 and ATXN2, have been implicated in amyotrophic lateral sclerosis (ALS). However, there have been few studies on the association of AR and NOP56 repeat expansion with ALS, especially in China. Accordingly, we aimed to evaluate the frequency of C9orf72 and ATXN2 repeat mutations and investigate whether NOP56 and AR repeat expansion are risk factors for ALS. Methods In this study, 736 ALS patients and several hundred healthy controls were recruited. Polymerase chain reaction (PCR) and repeat-primed PCR (RP-PCR) were performed to determine the repeat lengths in C9orf72, ATXN2, AR, and NOP56. Results GGGGCC repeats in C9orf72 were observed in six ALS patients (0.8%, 6/736) but not in any of the controls (0/365). The patients with pathogenic GGGGCC repeats showed shorter median survival times than those with a normal genotype (p = 0.006). Regarding ATXN2 CAG repeats, we identified that intermediate repeat lengths (29–34 copies) were associated with ALS (p = 0.033), and there was no difference in clinical characteristics between the groups with and without intermediate repeats (p > 0.05). Meanwhile, we observed that there was no association between the repeat size in AR and NOP56 and ALS (p > 0.05). Conclusions Our results demonstrated that pathogenetic repeats in C9orf72 are rare in China, while intermediate CAG repeats in ATXN2 are more frequent but have no effect on disease phenotypes; the repeat size in AR and NOP56 may not be a risk factor for ALS.
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Affiliation(s)
- Xiaorong Hou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Wanzhen Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Pan Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhen Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yanchun Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jie Ni
- 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 Diseases, Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- Laboratory of Medical Genetics, 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
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- Laboratory of Medical Genetics, 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
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- Laboratory of Medical Genetics, 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
- *Correspondence: Junling Wang
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13
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Barbé L, Finkbeiner S. Genetic and Epigenetic Interplay Define Disease Onset and Severity in Repeat Diseases. Front Aging Neurosci 2022; 14:750629. [PMID: 35592702 PMCID: PMC9110800 DOI: 10.3389/fnagi.2022.750629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Repeat diseases, such as fragile X syndrome, myotonic dystrophy, Friedreich ataxia, Huntington disease, spinocerebellar ataxias, and some forms of amyotrophic lateral sclerosis, are caused by repetitive DNA sequences that are expanded in affected individuals. The age at which an individual begins to experience symptoms, and the severity of disease, are partially determined by the size of the repeat. However, the epigenetic state of the area in and around the repeat also plays an important role in determining the age of disease onset and the rate of disease progression. Many repeat diseases share a common epigenetic pattern of increased methylation at CpG islands near the repeat region. CpG islands are CG-rich sequences that are tightly regulated by methylation and are often found at gene enhancer or insulator elements in the genome. Methylation of CpG islands can inhibit binding of the transcriptional regulator CTCF, resulting in a closed chromatin state and gene down regulation. The downregulation of these genes leads to some disease-specific symptoms. Additionally, a genetic and epigenetic interplay is suggested by an effect of methylation on repeat instability, a hallmark of large repeat expansions that leads to increasing disease severity in successive generations. In this review, we will discuss the common epigenetic patterns shared across repeat diseases, how the genetics and epigenetics interact, and how this could be involved in disease manifestation. We also discuss the currently available stem cell and mouse models, which frequently do not recapitulate epigenetic patterns observed in human disease, and propose alternative strategies to study the role of epigenetics in repeat diseases.
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Affiliation(s)
- Lise Barbé
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
| | - Steve Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Steve Finkbeiner,
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14
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Johnson SL, Prifti MV, Sujkowski A, Libohova K, Blount JR, Hong L, Tsou WL, Todi SV. Drosophila as a Model of Unconventional Translation in Spinocerebellar Ataxia Type 3. Cells 2022; 11:cells11071223. [PMID: 35406787 PMCID: PMC8997593 DOI: 10.3390/cells11071223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/21/2022] Open
Abstract
RNA toxicity contributes to diseases caused by anomalous nucleotide repeat expansions. Recent work demonstrated RNA-based toxicity from repeat-associated, non-AUG-initiated translation (RAN translation). RAN translation occurs around long nucleotide repeats that form hairpin loops, allowing for translation initiation in the absence of a start codon that results in potentially toxic, poly-amino acid repeat-containing proteins. Discovered in Spinocerebellar Ataxia Type (SCA) 8, RAN translation has been documented in several repeat-expansion diseases, including in the CAG repeat-dependent polyglutamine (polyQ) disorders. The ATXN3 gene, which causes SCA3, also known as Machado–Joseph Disease (MJD), contains a CAG repeat that is expanded in disease. ATXN3 mRNA possesses features linked to RAN translation. In this paper, we examined the potential contribution of RAN translation to SCA3/MJD in Drosophila by using isogenic lines that contain homomeric or interrupted CAG repeats. We did not observe unconventional translation in fly neurons or glia. However, our investigations indicate differential toxicity from ATXN3 protein-encoding mRNA that contains pure versus interrupted CAG repeats. Additional work suggests that this difference may be due in part to toxicity from homomeric CAG mRNA. We conclude that Drosophila is not suitable to model RAN translation for SCA3/MJD, but offers clues into the potential pathogenesis stemming from CAG repeat-containing mRNA in this disorder.
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Affiliation(s)
- Sean L. Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Matthew V. Prifti
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Alyson Sujkowski
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Jessica R. Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Luke Hong
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
| | - Sokol V. Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA; (S.L.J.); (M.V.P.); (A.S.); (K.L.); (J.R.B.); (L.H.); (W.-L.T.)
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Correspondence:
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15
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Perez BA, Shorrock HK, Banez‐Coronel M, Zu T, Romano LEL, Laboissonniere LA, Reid T, Ikeda Y, Reddy K, Gomez CM, Bird T, Ashizawa T, Schut LJ, Brusco A, Berglund JA, Hasholt LF, Nielsen JE, Subramony SH, Ranum LPW. CCG•CGG interruptions in high-penetrance SCA8 families increase RAN translation and protein toxicity. EMBO Mol Med 2021; 13:e14095. [PMID: 34632710 PMCID: PMC8573593 DOI: 10.15252/emmm.202114095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 12/28/2022] Open
Abstract
Spinocerebellar ataxia type 8 (SCA8), a dominantly inherited neurodegenerative disorder caused by a CTG•CAG expansion, is unusual because most individuals that carry the mutation do not develop ataxia. To understand the variable penetrance of SCA8, we studied the molecular differences between highly penetrant families and more common sporadic cases (82%) using a large cohort of SCA8 families (n = 77). We show that repeat expansion mutations from individuals with multiple affected family members have CCG•CGG interruptions at a higher frequency than sporadic SCA8 cases and that the number of CCG•CGG interruptions correlates with age at onset. At the molecular level, CCG•CGG interruptions increase RNA hairpin stability, and in cell culture experiments, increase p-eIF2α and polyAla and polySer RAN protein levels. Additionally, CCG•CGG interruptions, which encode arginine interruptions in the polyGln frame, increase toxicity of the resulting proteins. In summary, SCA8 CCG•CGG interruptions increase polyAla and polySer RAN protein levels, polyGln protein toxicity, and disease penetrance and provide novel insight into the molecular differences between SCA8 families with high vs. low disease penetrance.
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Affiliation(s)
- Barbara A Perez
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleFLUSA
| | - Hannah K Shorrock
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleFLUSA
| | - Monica Banez‐Coronel
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleFLUSA
| | - Tao Zu
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleFLUSA
| | - Lisa EL Romano
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleFLUSA
| | - Lauren A Laboissonniere
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleFLUSA
| | - Tammy Reid
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleFLUSA
| | - Yoshio Ikeda
- Department of NeurologyGunma UniversityMaebashiJapan
| | - Kaalak Reddy
- RNA InstituteUniversity at Albany–SUNYAlbanyNYUSA
| | | | - Thomas Bird
- Department of NeurologyUniversity of WashingtonSeattleWAUSA
- Geriatrics Research SectionVA Puget Sound Health Care SystemSeattleWAUSA
| | - Tetsuo Ashizawa
- Department of NeurologyHouston Methodist Research InstituteHoustonTXUSA
| | | | - Alfredo Brusco
- Department of Medical SciencesUniversity of TorinoTorinoItaly
- Medical Genetics Units“Città della Salute e della Scienza” University HospitalTorinoItaly
| | - J Andrew Berglund
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- RNA InstituteUniversity at Albany–SUNYAlbanyNYUSA
| | - Lis F Hasholt
- Institute of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Jorgen E Nielsen
- Department of NeurologyRigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | - SH Subramony
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- McKnight Brain InstituteUniversity of FloridaGainesvilleFLUSA
| | - Laura PW Ranum
- Center for NeuroGeneticsUniversity of FloridaGainesvilleFLUSA
- Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleFLUSA
- McKnight Brain InstituteUniversity of FloridaGainesvilleFLUSA
- Genetics InstituteUniversity of FloridaGainesvilleFLUSA
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16
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Li PP, Moulick R, Feng H, Sun X, Arbez N, Jin J, Marque LO, Hedglen E, Chan HE, Ross CA, Pulst SM, Margolis RL, Woodson S, Rudnicki DD. RNA Toxicity and Perturbation of rRNA Processing in Spinocerebellar Ataxia Type 2. Mov Disord 2021; 36:2519-2529. [PMID: 34390268 PMCID: PMC8884117 DOI: 10.1002/mds.28729] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/03/2021] [Accepted: 07/12/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disease caused by expansion of a CAG repeat in Ataxin-2 (ATXN2) gene. The mutant ATXN2 protein with a polyglutamine tract is known to be toxic and contributes to the SCA2 pathogenesis. OBJECTIVE Here, we tested the hypothesis that the mutant ATXN2 transcript with an expanded CAG repeat (expATXN2) is also toxic and contributes to SCA2 pathogenesis. METHODS The toxic effect of expATXN2 transcripts on SK-N-MC neuroblastoma cells and primary mouse cortical neurons was evaluated by caspase 3/7 activity and nuclear condensation assay, respectively. RNA immunoprecipitation assay was performed to identify RNA binding proteins (RBPs) that bind to expATXN2 RNA. Quantitative PCR was used to examine if ribosomal RNA (rRNA) processing is disrupted in SCA2 and Huntington's disease (HD) human brain tissue. RESULTS expATXN2 RNA induces neuronal cell death, and aberrantly interacts with RBPs involved in RNA metabolism. One of the RBPs, transducin β-like protein 3 (TBL3), involved in rRNA processing, binds to both expATXN2 and expanded huntingtin (expHTT) RNA in vitro. rRNA processing is disrupted in both SCA2 and HD human brain tissue. CONCLUSION These findings provide the first evidence of a contributory role of expATXN2 transcripts in SCA2 pathogenesis, and further support the role of expHTT transcripts in HD pathogenesis. The disruption of rRNA processing, mediated by aberrant interaction of RBPs with expATXN2 and expHTT transcripts, suggest a point of convergence in the pathogeneses of repeat expansion diseases with potential therapeutic implications. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Pan P. Li
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Roumita Moulick
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Hongxuan Feng
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Xin Sun
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Nicolas Arbez
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jing Jin
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Leonard O. Marque
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Erin Hedglen
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - H.Y. Edwin Chan
- Biochemistry Program, School of Life SciencesThe Chinese University of Hong KongHong KongChina
| | - Christopher A. Ross
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Stefan M. Pulst
- Department of NeurologyUniversity of UtahSalt Lake CityUtahUSA
| | - Russell L. Margolis
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Sarah Woodson
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Dobrila D. Rudnicki
- Department of Psychiatry and Behavioral Sciences, Division of NeurobiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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17
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Heinz A, Schilling J, van Roon-Mom W, Krauß S. The MID1 Protein: A Promising Therapeutic Target in Huntington's Disease. Front Genet 2021; 12:761714. [PMID: 34659371 PMCID: PMC8517220 DOI: 10.3389/fgene.2021.761714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Huntington's disease (HD) is caused by an expansion mutation of a CAG repeat in exon 1 of the huntingtin (HTT) gene, that encodes an expanded polyglutamine tract in the HTT protein. HD is characterized by progressive psychiatric and cognitive symptoms associated with a progressive movement disorder. HTT is ubiquitously expressed, but the pathological changes caused by the mutation are most prominent in the central nervous system. Since the mutation was discovered, research has mainly focused on the mutant HTT protein. But what if the polyglutamine protein is not the only cause of the neurotoxicity? Recent studies show that the mutant RNA transcript is also involved in cellular dysfunction. Here we discuss the abnormal interaction of the mutant HTT transcript with a protein complex containing the MID1 protein. MID1 aberrantly binds to CAG repeats and this binding increases with CAG repeat length. Since MID1 is a translation regulator, association of the MID1 complex stimulates translation of mutant HTT mRNA, resulting in an overproduction of polyglutamine protein. Thus, blocking the interaction between MID1 and mutant HTT mRNA is a promising therapeutic approach. Additionally, we show that MID1 expression in the brain of both HD patients and HD mice is aberrantly increased. This finding further supports the concept of blocking the interaction between MID1 and mutant HTT mRNA to counteract mutant HTT translation as a valuable therapeutic strategy. In line, recent studies in which either compounds affecting the assembly of the MID1 complex or molecules targeting HTT RNA, show promising results.
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Affiliation(s)
- Annika Heinz
- University of Siegen, Institute of Biology, Human Biology / Neurobiology, Siegen, Germany
| | - Judith Schilling
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Willeke van Roon-Mom
- Leiden University Medical Center, Department of Human Genetics, Leiden, Netherlands
| | - Sybille Krauß
- University of Siegen, Institute of Biology, Human Biology / Neurobiology, Siegen, Germany
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18
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McGurk L, Rifai OM, Shcherbakova O, Perlegos AE, Byrns CN, Carranza FR, Zhou HW, Kim HJ, Zhu Y, Bonini NM. Toxicity of pathogenic ataxin-2 in Drosophila shows dependence on a pure CAG repeat sequence. Hum Mol Genet 2021; 30:1797-1810. [PMID: 34077532 PMCID: PMC8444453 DOI: 10.1093/hmg/ddab148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 12/31/2022] Open
Abstract
Spinocerebellar ataxia type 2 is a polyglutamine (polyQ) disease associated with an expanded polyQ domain within the protein product of the ATXN2 gene. Interestingly, polyQ repeat expansions in ATXN2 are also associated with amyotrophic lateral sclerosis (ALS) and parkinsonism depending upon the length of the polyQ repeat expansion. The sequence encoding the polyQ repeat also varies with disease presentation: a pure CAG repeat is associated with SCA2, whereas the CAG repeat in ALS and parkinsonism is typically interrupted with the glutamine encoding CAA codon. Here, we asked if the purity of the CAG sequence encoding the polyQ repeat in ATXN2 could impact the toxicity of the ataxin-2 protein in vivo in Drosophila. We found that ataxin-2 encoded by a pure CAG repeat conferred toxicity in the retina and nervous system, whereas ataxin-2 encoded by a CAA-interrupted repeat or CAA-only repeat failed to confer toxicity, despite expression of the protein at similar levels. Furthermore, the CAG-encoded ataxin-2 protein aggregated in the fly eye, while ataxin-2 encoded by either a CAA/G or CAA repeat remained diffuse. The toxicity of the CAG-encoded ataxin-2 protein was also sensitive to the translation factor eIF4H, a known modifier of the toxic GGGGCC repeat in flies. These data indicate that ataxin-2 encoded by a pure CAG versus interrupted CAA/G polyQ repeat domain is associated with differential toxicity, indicating that mechanisms associated with the purity of the sequence of the polyQ domain contribute to disease.
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Affiliation(s)
- Leeanne McGurk
- Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Olivia M Rifai
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - China N Byrns
- Neurosciences Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
- Medical Sciences Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Faith R Carranza
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Henry W Zhou
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hyung-Jun Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yongqing Zhu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Neurosciences Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
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19
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Role and Perspective of Molecular Simulation-Based Investigation of RNA-Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding. Molecules 2021; 26:molecules26113384. [PMID: 34205049 PMCID: PMC8199858 DOI: 10.3390/molecules26113384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. Here, we focus on examples targeting RNA–protein complexes in neurodegenerative diseases and viral infections. These examples illustrate that the strategy is rather general and could be applied to different pharmacologically relevant approaches. We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy.
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20
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Cheong RY, Baldo B, Sajjad MU, Kirik D, Petersén Å. Effects of mutant huntingtin inactivation on Huntington disease-related behaviours in the BACHD mouse model. Neuropathol Appl Neurobiol 2021; 47:564-578. [PMID: 33330988 PMCID: PMC8247873 DOI: 10.1111/nan.12682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Accepted: 12/14/2020] [Indexed: 01/02/2023]
Abstract
AIMS Huntington disease (HD) is a fatal neurodegenerative disorder with no disease-modifying treatments approved so far. Ongoing clinical trials are attempting to reduce huntingtin (HTT) expression in the central nervous system (CNS) using different strategies. Yet, the distribution and timing of HTT-lowering therapies required for a beneficial clinical effect is less clear. Here, we investigated whether HD-related behaviours could be prevented by inactivating mutant HTT at different disease stages and to varying degrees in an experimental model. METHODS We generated mutant BACHD mice with either a widespread or circuit-specific inactivation of mutant HTT by using Cre recombinase (Cre) under the nestin promoter or the adenosine A2A receptor promoter respectively. We also simulated a clinical gene therapy scenario with allele-specific HTT targeting by injections of recombinant adeno-associated viral (rAAV) vectors expressing Cre into the striatum of adult BACHD mice. All mice were assessed using behavioural tests to investigate motor, metabolic and psychiatric outcome measures at 4-6 months of age. RESULTS While motor deficits, body weight changes, anxiety and depressive-like behaviours are present in BACHD mice, early widespread CNS inactivation during development significantly improves rotarod performance, body weight changes and depressive-like behaviour. However, conditional circuit-wide mutant HTT deletion from the indirect striatal pathway during development and focal striatal-specific deletion in adulthood failed to rescue any of the HD-related behaviours. CONCLUSIONS Our results indicate that widespread targeting and the timing of interventions aimed at reducing mutant HTT are important factors to consider when developing disease-modifying therapies for HD.
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Affiliation(s)
- Rachel Y. Cheong
- Translational Neuroendocrine Research UnitDepartment of Experimental Medical ScienceLund UniversityLundSweden
| | - Barbara Baldo
- Translational Neuroendocrine Research UnitDepartment of Experimental Medical ScienceLund UniversityLundSweden
- Present address:
Evotec SEHD Research and Translational SciencesHamburgGermany
| | - Muhammad U. Sajjad
- Translational Neuroendocrine Research UnitDepartment of Experimental Medical ScienceLund UniversityLundSweden
| | - Deniz Kirik
- Brain Repair and Imaging in Neural Systems UnitDepartment of Experimental Medical ScienceLund UniversityLundSweden
| | - Åsa Petersén
- Translational Neuroendocrine Research UnitDepartment of Experimental Medical ScienceLund UniversityLundSweden
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Chintalaphani SR, Pineda SS, Deveson IW, Kumar KR. An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics. Acta Neuropathol Commun 2021; 9:98. [PMID: 34034831 PMCID: PMC8145836 DOI: 10.1186/s40478-021-01201-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Short tandem repeat (STR) expansion disorders are an important cause of human neurological disease. They have an established role in more than 40 different phenotypes including the myotonic dystrophies, Fragile X syndrome, Huntington's disease, the hereditary cerebellar ataxias, amyotrophic lateral sclerosis and frontotemporal dementia. MAIN BODY STR expansions are difficult to detect and may explain unsolved diseases, as highlighted by recent findings including: the discovery of a biallelic intronic 'AAGGG' repeat in RFC1 as the cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS); and the finding of 'CGG' repeat expansions in NOTCH2NLC as the cause of neuronal intranuclear inclusion disease and a range of clinical phenotypes. However, established laboratory techniques for diagnosis of repeat expansions (repeat-primed PCR and Southern blot) are cumbersome, low-throughput and poorly suited to parallel analysis of multiple gene regions. While next generation sequencing (NGS) has been increasingly used, established short-read NGS platforms (e.g., Illumina) are unable to genotype large and/or complex repeat expansions. Long-read sequencing platforms recently developed by Oxford Nanopore Technology and Pacific Biosciences promise to overcome these limitations to deliver enhanced diagnosis of repeat expansion disorders in a rapid and cost-effective fashion. CONCLUSION We anticipate that long-read sequencing will rapidly transform the detection of short tandem repeat expansion disorders for both clinical diagnosis and gene discovery.
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Affiliation(s)
- Sanjog R. Chintalaphani
- School of Medicine, University of New South Wales, Sydney, 2052 Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Brain and Mind Centre, University of Sydney, Camperdown, NSW 2050 Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Faculty of Medicine, St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010 Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Molecular Medicine Laboratory and Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW 2137 Australia
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22
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Yang L, Dong Y, Ma Y, Ni W, Wu ZY. Genetic profile and clinical characteristics of Chinese patients with spinocerebellar ataxia type 2: A multicenter experience over 10 years. Eur J Neurol 2020; 28:955-964. [PMID: 33070405 DOI: 10.1111/ene.14601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND PURPOSE Spinocerebellar ataxia type 2 (SCA2) is the second most common type of spinocerebellar ataxia in China. However, data on the clinical and genetic features of Chinese SCA2 patients are scarce. This study aims to provide a comprehensive description of in the Chinese SCA2 cohort. METHODS A total of 135 patients with SCA2 from 92 families and 104 unrelated normal controls were recruited from three medical centers between 2008 and 2020. Sanger sequencing and TA cloning were used to determine the CAG repeat length and intrinsic structure. The clinical data of patients with SCA2, including electromyography, magnetic resonance imaging, positron-emission tomography, and clinical scale scores, were recorded. RESULTS The mean ± SD age at onset of SCA2 patients was 32.6 ± 11.9 years and the corresponding CAG repeat length was 42.1 ± 3.6. CAG repeat length accounted for 64% of the age-at-onset variance. We observed that patients had a significantly lower proportion of (CAG)8 CAA(CAG)4 CAA(CAG)8 within normal alleles than normal controls (48.8% vs. 64.9%; p = 0.003), while the distribution of the proportion of (CAG)13 CAA (CAG)8 was the opposite. Peripheral neuropathy was frequent, occurring in 75.9% of the patients. Parkinsonism was relatively common, with a frequency of 11.8%. Two patients with parkinsonism had a significantly more severe reduction in dopamine transporter levels in the bilateral striatum than the one patient with pure ataxia. An infant-onset case of SCA2 with more than 180 CAG repeats was characterized by global development delay, hypotonia and hearing impairment. CONCLUSIONS This study describes the genetic profile and clinical characteristics of the largest SCA2 cohort to date in the Chinese population and analyzes inter-population differences. Many aspects of this study population were different from other populations with SCA2.
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Affiliation(s)
- Lu Yang
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yin Ma
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Wang Ni
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,Department of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China
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23
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Johnson SL, Ranxhi B, Libohova K, Tsou WL, Todi SV. Ubiquitin-interacting motifs of ataxin-3 regulate its polyglutamine toxicity through Hsc70-4-dependent aggregation. eLife 2020; 9:60742. [PMID: 32955441 PMCID: PMC7505662 DOI: 10.7554/elife.60742] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/30/2020] [Indexed: 12/17/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) belongs to the family of polyglutamine neurodegenerations. Each disorder stems from the abnormal lengthening of a glutamine repeat in a different protein. Although caused by a similar mutation, polyglutamine disorders are distinct, implicating non-polyglutamine regions of disease proteins as regulators of pathogenesis. SCA3 is caused by polyglutamine expansion in ataxin-3. To determine the role of ataxin-3’s non-polyglutamine domains in disease, we utilized a new, allelic series of Drosophila melanogaster. We found that ataxin-3 pathogenicity is saliently controlled by polyglutamine-adjacent ubiquitin-interacting motifs (UIMs) that enhance aggregation and toxicity. UIMs function by interacting with the heat shock protein, Hsc70-4, whose reduction diminishes ataxin-3 toxicity in a UIM-dependent manner. Hsc70-4 also enhances pathogenicity of other polyglutamine proteins. Our studies provide a unique insight into the impact of ataxin-3 domains in SCA3, identify Hsc70-4 as a SCA3 enhancer, and indicate pleiotropic effects from HSP70 chaperones, which are generally thought to suppress polyglutamine degeneration.
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Affiliation(s)
- Sean L Johnson
- Department of Pharmacology, Wayne State University, Detroit, United States
| | - Bedri Ranxhi
- Department of Pharmacology, Wayne State University, Detroit, United States
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University, Detroit, United States
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University, Detroit, United States
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University, Detroit, United States.,Department of Neurology, Wayne State University, Detroit, United States
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24
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Palomino‐Hernandez O, Margreiter MA, Rossetti G. Challenges in RNA Regulation in Huntington's Disease: Insights from Computational Studies. Isr J Chem 2020. [DOI: 10.1002/ijch.202000021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Oscar Palomino‐Hernandez
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
- Computation-based Science and Technology Research CenterThe Cyprus Institute Nicosia 2121 Cyprus
- Institute of Life ScienceThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Michael A. Margreiter
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Faculty 1RWTH Aachen 52425 Aachen Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM-9)/Instute for advanced simulations (IAS-5)Forschungszentrum Juelich 52425 Jülich Germany
- Jülich Supercomputing Centre (JSC)Forschungszentrum Jülich 52425 Jülich Germany
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation University Hospital AachenRWTH Aachen University Pauwelsstraße 30 52074 Aachen Germany
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25
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Johnson SL, Blount JR, Libohova K, Ranxhi B, Paulson HL, Tsou WL, Todi SV. Differential toxicity of ataxin-3 isoforms in Drosophila models of Spinocerebellar Ataxia Type 3. Neurobiol Dis 2019; 132:104535. [PMID: 31310802 DOI: 10.1016/j.nbd.2019.104535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/28/2022] Open
Abstract
The most commonly inherited dominant ataxia, Spinocerebellar Ataxia Type 3 (SCA3), is caused by a CAG repeat expansion that encodes an abnormally long polyglutamine (polyQ) repeat in the disease protein ataxin-3, a deubiquitinase. Two major full-length isoforms of ataxin-3 exist, both of which contain the same N-terminal portion and polyQ repeat, but differ in their C-termini; one (denoted here as isoform 1) contains a motif that binds ataxin-3's substrate, ubiquitin, whereas the other (denoted here as isoform 2) has a hydrophobic tail. Most SCA3 studies have focused on isoform 1, the predominant version in mammalian brain, yet both isoforms are present in brain and a better understanding of their relative pathogenicity in vivo is needed. We took advantage of the fruit fly, Drosophila melanogaster to model SCA3 and to examine the toxicity of each ataxin-3 isoform. Our assays reveal isoform 1 to be markedly more toxic than isoform 2 in all fly tissues. Reduced toxicity from isoform 2 is due to much lower protein levels as a result of its expedited degradation. Additional studies indicate that isoform 1 is more aggregation-prone than isoform 2 and that the C-terminus of isoform 2 is critical for its enhanced proteasomal degradation. According to our results, although both full-length, pathogenic ataxin-3 isoforms are toxic, isoform 1 is likely the primary contributor to SCA3 due to its presence at higher levels. Isoform 2, as a result of rapid degradation that is dictated by its tail, is unlikely to be a key player in this disease. Our findings provide new insight into the biology of this ataxia and the cellular processing of the underlying disease protein.
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Affiliation(s)
- Sean L Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Bedri Ranxhi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Henry L Paulson
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Wei-Ling Tsou
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA.
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26
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van Cruchten RTP, Wieringa B, Wansink DG. Expanded CUG repeats in DMPK transcripts adopt diverse hairpin conformations without influencing the structure of the flanking sequences. RNA (NEW YORK, N.Y.) 2019; 25:481-495. [PMID: 30700578 PMCID: PMC6426290 DOI: 10.1261/rna.068940.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a complex neuromuscular disorder caused by expansion of a CTG repeat in the 3'-untranslated region (UTR) of the DMPK gene. Mutant DMPK transcripts form aberrant structures and anomalously associate with RNA-binding proteins (RBPs). As a first step toward better understanding of the involvement of abnormal DMPK mRNA folding in DM1 manifestation, we used SHAPE, DMS, CMCT, and RNase T1 structure probing in vitro for modeling of the topology of the DMPK 3'-UTR with normal and pathogenic repeat lengths of up to 197 CUG triplets. The resulting structural information was validated by disruption of base-pairing with LNA antisense oligonucleotides (AONs) and used for prediction of therapeutic AON accessibility and verification of DMPK knockdown efficacy in cells. Our model for DMPK RNA structure demonstrates that the hairpin formed by the CUG repeat has length-dependent conformational plasticity, with a structure that is guided by and embedded in an otherwise rigid architecture of flanking regions in the DMPK 3'-UTR. Evidence is provided that long CUG repeats may form not only single asymmetrical hairpins but also exist as branched structures. These newly identified structures have implications for DM1 pathogenic mechanisms, like sequestration of RBPs and repeat-associated non-AUG (RAN) translation.
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Affiliation(s)
- Remco T P van Cruchten
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Bé Wieringa
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
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27
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Fournier C, Anquetil V, Camuzat A, Stirati-Buron S, Sazdovitch V, Molina-Porcel L, Turbant S, Rinaldi D, Sánchez-Valle R, Barbier M, Latouche M, Stevanin G, Seilhean D, Brice A, Duyckaerts C, Le Ber I. Interrupted CAG expansions in ATXN2 gene expand the genetic spectrum of frontotemporal dementias. Acta Neuropathol Commun 2018; 6:41. [PMID: 29848387 PMCID: PMC5977499 DOI: 10.1186/s40478-018-0547-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
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28
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Martí E. RNA toxicity induced by expanded CAG repeats in Huntington's disease. Brain Pathol 2018; 26:779-786. [PMID: 27529325 DOI: 10.1111/bpa.12427] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 02/03/2023] Open
Abstract
Huntington's disease (HD) belongs to the group of inherited polyglutamine (PolyQ) diseases caused by an expanded CAG repeat in the coding region of the Huntingtin (HTT) gene that results in an elongated polyQ stretch. Abnormal function and aggregation of the mutant protein has been typically delineated as the main molecular cause underlying disease development. However, the most recent advances have revealed novel pathogenic pathways directly dependent on an RNA toxic gain-of-function. Expanded CAG repeats within exon 1 of the HTT mRNA induce toxicity through mechanisms involving, at least in part, gene expression perturbations. This has important implications not only for basic and translational research in HD, but also for other types of diseases carrying the expanded CAG in other genes, which likely share pathogenic aspects. Here I will review the evidence and mechanisms underlying RNA toxicity in CAG repeat expansions, with particular focus on HD. These comprise abnormal subcellular localization of the transcripts containing the expanded CAG repeats; sequestration of several types of proteins by the expanded CAG repeat which results in defects of alternative splicing events and gene expression; and aberrant biogenesis and detrimental activity of small CAG repeated RNAs (sCAG) that produce altered gene silencing. Although these altered pathways have been detected in HD models, their contribution to disease development and progress requires further study.
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Affiliation(s)
- Eulàlia Martí
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, 08003, Spain.,Centro de Investigacion Biomedica en Red (CIBERESP), Madrid, Spain
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29
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Zaghloul EM, Gissberg O, Moreno PMD, Siggens L, Hällbrink M, Jørgensen AS, Ekwall K, Zain R, Wengel J, Lundin KE, Smith CIE. CTG repeat-targeting oligonucleotides for down-regulating Huntingtin expression. Nucleic Acids Res 2017; 45:5153-5169. [PMID: 28334749 PMCID: PMC5435994 DOI: 10.1093/nar/gkx111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
Huntington's disease (HD) is a fatal, neurodegenerative disorder in which patients suffer from mobility, psychological and cognitive impairments. Existing therapeutics are only symptomatic and do not significantly alter the disease progression or increase life expectancy. HD is caused by expansion of the CAG trinucleotide repeat region in exon 1 of the Huntingtin gene (HTT), leading to the formation of mutant HTT transcripts (muHTT). The toxic gain-of-function of muHTT protein is a major cause of the disease. In addition, it has been suggested that the muHTT transcript contributes to the toxicity. Thus, reduction of both muHTT mRNA and protein levels would ideally be the most useful therapeutic option. We herein present a novel strategy for HD treatment using oligonucleotides (ONs) directly targeting the HTT trinucleotide repeat DNA. A partial, but significant and potentially long-term, HTT knock-down of both mRNA and protein was successfully achieved. Diminished phosphorylation of HTT gene-associated RNA-polymerase II is demonstrated, suggestive of reduced transcription downstream the ON-targeted repeat. Different backbone chemistries were found to have a strong impact on the ON efficiency. We also successfully use different delivery vehicles as well as naked uptake of the ONs, demonstrating versatility and possibly providing insights for in vivo applications.
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Affiliation(s)
- Eman M Zaghloul
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, El-Khartoum square, Azareeta, 21 521 Alexandria, Egypt
| | - Olof Gissberg
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
| | - Pedro M D Moreno
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Lee Siggens
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden, SE-141 86, Huddinge, Stockholm, Sweden
| | - Mattias Hällbrink
- Department of Neurochemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Anna S Jørgensen
- Department of Physics and Chemistry, Nucleic Acid Centre University of Southern Denmark, DK-5230 Odense, Denmark
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden, SE-141 86, Huddinge, Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Jesper Wengel
- Department of Physics and Chemistry, Nucleic Acid Centre University of Southern Denmark, DK-5230 Odense, Denmark
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
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30
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Antenora A, Rinaldi C, Roca A, Pane C, Lieto M, Saccà F, Peluso S, De Michele G, Filla A. The Multiple Faces of Spinocerebellar Ataxia type 2. Ann Clin Transl Neurol 2017; 4:687-695. [PMID: 28904990 PMCID: PMC5590519 DOI: 10.1002/acn3.437] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/09/2017] [Accepted: 06/07/2017] [Indexed: 12/13/2022] Open
Abstract
Spinocerebellar ataxia type 2 (SCA2) is among the most common forms of autosomal dominant ataxias, accounting for 15% of the total families. Occurrence is higher in specific populations such as the Cuban and Southern Italian. The disease is caused by a CAG expansion in ATXN2 gene, leading to abnormal accumulation of the mutant protein, ataxin‐2, in intracellular inclusions. The clinical picture is mainly dominated by cerebellar ataxia, although a number of other neurological signs have been described, ranging from parkinsonism to motor neuron involvement, making the diagnosis frequently challenging for neurologists, particularly when information about the family history is not available. Although the functions of ataxin‐2 have not been completely elucidated, the protein is involved in mRNA processing and control of translation. Recently, it has also been shown that the size of the CAG repeat in normal alleles represents a risk factor for ALS, suggesting that ataxin‐2 plays a fundamental role in maintenance of neuronal homeostasis.
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Affiliation(s)
- Antonella Antenora
- Department of Neurological Reproductive and Odontostomatological Sciences Federico II University Naples Italy
| | - Carlo Rinaldi
- Department of Physiology Anatomy and Genetics, University of Oxford Oxford United Kingdom
| | - Alessandro Roca
- Department of Neurological Reproductive and Odontostomatological Sciences Federico II University Naples Italy
| | - Chiara Pane
- Department of Neurological Reproductive and Odontostomatological Sciences Federico II University Naples Italy
| | - Maria Lieto
- Department of Neurological Reproductive and Odontostomatological Sciences Federico II University Naples Italy.,Department of Physiology Anatomy and Genetics, University of Oxford Oxford United Kingdom
| | - Francesco Saccà
- Department of Neurological Reproductive and Odontostomatological Sciences Federico II University Naples Italy
| | - Silvio Peluso
- Department of Neurological Reproductive and Odontostomatological Sciences Federico II University Naples Italy
| | - Giuseppe De Michele
- Department of Neurological Reproductive and Odontostomatological Sciences Federico II University Naples Italy
| | - Alessandro Filla
- Department of Neurological Reproductive and Odontostomatological Sciences Federico II University Naples Italy
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31
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Guo P, Chan HYE, Lam SL. Conformational flexibility in the RNA stem-loop structures formed by CAG repeats. FEBS Lett 2017; 591:1752-1760. [PMID: 28488797 DOI: 10.1002/1873-3468.12672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/28/2017] [Accepted: 05/05/2017] [Indexed: 11/11/2022]
Abstract
The expansion of CAG repeats has been found to be associated with at least nine human genetic disorders. In these disorders, the full-length expanded CAG RNA transcripts are cleaved into small CAG-repeated RNAs which are cytotoxic and known to be capable of forming hairpins. To better understand the RNA pathogenic mechanism, in this study we have performed high-resolution nuclear magnetic resonance structural investigations on the RNA hairpins formed by CAG repeats. Our results show the formation of a type III AGCA tetraloop and reveal the effect of stem rigidity on the loop conformational flexibility.
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Affiliation(s)
- Pei Guo
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Ho Yin Edwin Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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32
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Ciesiolka A, Jazurek M, Drazkowska K, Krzyzosiak WJ. Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions. Front Cell Neurosci 2017; 11:97. [PMID: 28442996 PMCID: PMC5387085 DOI: 10.3389/fncel.2017.00097] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions. A growing body of recent evidence revealed that the RNA structures formed by these mutant RNA repeat tracts exhibit toxic effects on cells. Therefore, in this review article, we present existing knowledge on the structural aspects of different RNA repeat tracts as revealed mainly using well-established biochemical and biophysical methods. Furthermore, in several cases, it was shown that these expanded RNA structures are potent traps for a variety of RNA-binding proteins and that the sequestration of these proteins from their normal intracellular environment causes alternative splicing aberration, inhibition of nuclear transport and export, or alteration of a microRNA biogenesis pathway. Therefore, in this review article, we also present the most studied examples of abnormal interactions that occur between mutant RNAs and their associated proteins.
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Affiliation(s)
- Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Karolina Drazkowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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Santoro M, Masciullo M, Silvestri G, Novelli G, Botta A. Myotonic dystrophy type 1: role of CCG, CTC and CGG interruptions within DMPK alleles in the pathogenesis and molecular diagnosis. Clin Genet 2017; 92:355-364. [PMID: 27991661 DOI: 10.1111/cge.12954] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/09/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystem neuromuscular disease caused by a CTG triplet expansion in the 3'-untranslated region (3'-UTR) of DMPK gene. This CTG array is usually uninterrupted in both healthy and DM1 patients, but recent studies identified pathological variant expansions containing unstable CCG, CTC and CGG interruptions with a prevalence of 3-5% of cases. In this review, we will describe the clinical, molecular and genetic issues related to the occurrence of variant expansions associated with DM1. Indeed, the identification of these complex DMPK alleles leads to practical consequences in DM1 genetic counseling and testing, because these exams can give false negative results. Moreover, DM1 patients carrying interrupted alleles can manifest either additional atypical neurological symptoms or, conversely, mild, late-onset forms. Therefore, the prognosis of the disease in these patients is difficult to determine because of the great uncertainty about the genotype-phenotype correlations. We will discuss the putative effects of the variant DM1 alleles on the pathogenic disease mechanisms, including mitotic and meiotic repeats instability and splicing alteration typical of DM1 tissues. Interruptions within the DMPK expanded alleles could also interfere with the chromatin structure, the transcriptional activity of the DM1 locus and the interaction with RNA CUG-binding proteins.
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Affiliation(s)
- M Santoro
- Department of Neuroscience, Fondazione Don Carlo Gnocchi, Milan, Italy
| | - M Masciullo
- SPInal REhabilitation Lab, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - G Silvestri
- Institute of Neurology, Fondazione Policlinico 'Gemelli', Rome, Italy
| | - G Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - A Botta
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
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Błaszczyk L, Rypniewski W, Kiliszek A. Structures of RNA repeats associated with neurological diseases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28130835 DOI: 10.1002/wrna.1412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/25/2016] [Accepted: 11/12/2016] [Indexed: 01/04/2023]
Abstract
All RNA molecules possess a 'propensity' to fold into complex secondary and tertiary structures. Although they are composed of only four types of nucleotides, they show an enormous structural richness which reflects their diverse functions in the cell. However, in some cases the folding of RNA can have deleterious consequences. Aberrantly expanded, repeated RNA sequences can exhibit gain-of-function abnormalities and become pathogenic, giving rise to many incurable neurological diseases. Most RNA repeats form long hairpin structures whose stem consists of noncanonical base pairs interspersed among Watson-Crick pairs. The expanded hairpins have an ability to sequester important proteins and form insoluble nuclear foci. The RNA pathology, common to many repeat disorders, has drawn attention to the structures of the RNA repeats. In this review, we summarize secondary structure probing and crystallographic studies of disease-related RNA repeat sequences. We discuss the unique structural features which can contribute to the pathogenic properties of the repeated runs. In addition, we present the newest reports concerning structural data linked to therapeutic approaches. WIREs RNA 2017, 8:e1412. doi: 10.1002/wrna.1412 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Kraus-Perrotta C, Lagalwar S. Expansion, mosaicism and interruption: mechanisms of the CAG repeat mutation in spinocerebellar ataxia type 1. CEREBELLUM & ATAXIAS 2016; 3:20. [PMID: 27895927 PMCID: PMC5118900 DOI: 10.1186/s40673-016-0058-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/03/2016] [Indexed: 11/12/2022]
Abstract
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder that primarily affects the cerebellum and brainstem. The genetic mutation is an expansion of CAG trinucleotide repeats within the coding region of the ataxin-1 gene, characterizing SCA1 as a polyglutamine expansion disease like Huntington’s. As with most polyglutamine expansion diseases, SCA1 follows the rules of genetic anticipation: the larger the expansion, the earlier and more rapid the symptoms. Unlike the majority of polyglutamine expansion diseases, the presence of histidine interruptions within the polyglutamine tract of ataxin-1 protein can prevent or mitigate disease. The present review aims to synthesize three decades of research on the ataxin-1 polyglutamine expansion mutation that causes SCA1. Data from genetic population studies and case studies is gathered along with data from manipulation studies in animal models. Specifically, we examine the molecular mechanisms that cause tract expansions and contractions, the molecular pathways that confer instability of tract length in gametic and somatic cells resulting in gametic and somatic mosaicism, the influence of maternal or paternal factors in inheritance of the expanded allele, and the effects of CAT/histidine interruptions to the ataxin-1 allele and protein product. Our review of existing data supports the following conclusions. First, polyCAG expansion of gametic alleles occur due to the failure of gap repair mechanisms for single or double strand breaks during the transition from an immature haploid spermatid to a mature haploid sperm cell. Equivalent failures were not detected in female gametic cells. Second, polyCAG expansion of somatic alleles occur due to hairpins formed on Okazaki fragments and slipped strand structures due to failures in mismatch repair and transcription-coupled nucleotide excision repair mechanisms. Third, CAT trinucleotide interruptions, which code for histidines in the translated protein, attenuate the formation of slipped strand structures which may protect the allele from the occurrence of large expansions. Many of the mechanisms of expansion identified in this review differ from those noted in Huntington’s disease indicating that gene -or sequence-specific factors may affect the behavior of the polyCAG/glutamine tract. Therefore, synthesis and review of research from the SCA1 field is valuable for future clinical and diagnostic work in the treatment and prevention of SCA1.
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Affiliation(s)
- Cara Kraus-Perrotta
- Department of Biology, Skidmore College, 815 North Broadway, Saratoga Springs, NY 12866 USA
| | - Sarita Lagalwar
- Neuroscience Program, Skidmore College, 815 North Broadway, Saratoga Springs, NY 12866 USA
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Griesche N, Schilling J, Weber S, Rohm M, Pesch V, Matthes F, Auburger G, Krauss S. Regulation of mRNA Translation by MID1: A Common Mechanism of Expanded CAG Repeat RNAs. Front Cell Neurosci 2016; 10:226. [PMID: 27774050 PMCID: PMC5054010 DOI: 10.3389/fncel.2016.00226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Expansion of CAG repeats, which code for the disease-causing polyglutamine protein, is a common feature in polyglutamine diseases. RNA-mediated mechanisms that contribute to neuropathology in polyglutamine diseases are important. RNA-toxicity describes a phenomenon by which the mutant CAG repeat RNA recruits RNA-binding proteins, thereby leading to aberrant function. For example the MID1 protein binds to mutant huntingtin (HTT) RNA, which is linked to Huntington's disease (HD), at its CAG repeat region and induces protein synthesis of mutant protein. But is this mechanism specific to HD or is it a common mechanism in CAG repeat expansion disorders? To answer this question, we have analyzed the interaction between MID1 and three other CAG repeat mRNAs, Ataxin2 (ATXN2), Ataxin3 (ATXN3), and Ataxin7 (ATXN7), that all differ in the sequence flanking the CAG repeat. We show that ATXN2, ATXN3, and ATXN7 bind to MID1 in a CAG repeat length-dependent manner. Furthermore, we show that functionally, in line with what we have previously observed for HTT, the binding of MID1 to ATXN2, ATXN3, and ATXN7 mRNA induces protein synthesis in a repeat length-dependent manner. Our data suggest that regulation of protein translation by the MID1 complex is a common mechanism for CAG repeat containing mRNAs.
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Affiliation(s)
| | | | | | - Marlena Rohm
- German Center for Neurodegenerative Diseases Bonn, Germany
| | - Verena Pesch
- German Center for Neurodegenerative Diseases Bonn, Germany
| | - Frank Matthes
- German Center for Neurodegenerative Diseases Bonn, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School Frankfurt, Germany
| | - Sybille Krauss
- German Center for Neurodegenerative Diseases Bonn, Germany
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Nkiliza A, Mutez E, Simonin C, Leprêtre F, Duflot A, Figeac M, Villenet C, Semaille P, Comptdaer T, Genet A, Sablonnière B, Devos D, Defebvre L, Destée A, Chartier-Harlin MC. RNA-binding disturbances as a continuum from spinocerebellar ataxia type 2 to Parkinson disease. Neurobiol Dis 2016; 96:312-322. [PMID: 27663142 DOI: 10.1016/j.nbd.2016.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/07/2016] [Accepted: 09/17/2016] [Indexed: 12/13/2022] Open
Abstract
CAG triplet expansions in Ataxin-2 gene (ATXN2) cause spinocerebellar ataxia type 2 and have a role that remains to be clarified in Parkinson's disease (PD). To study the molecular events associated with these expansions, we sequenced them and analyzed the transcriptome from blood cells of controls and three patient groups diagnosed with spinocerebellar ataxia type 2 (herein referred to as SCA2c) or PD with or without ATXN2 triplet expansions (named SCA2p). The transcriptome profiles of these 40 patients revealed three main observations: i) a specific pattern of pathways related to cellular contacts, proliferation and differentiation associated with SCA2p group, ii) similarities between the SCA2p and sporadic PD groups in genes and pathways known to be altered in PD such as Wnt, Ephrin and Leukocyte extravasation signaling iii) RNA metabolism disturbances with "RNA-binding" and "poly(A) RNA-binding" as a common feature in all groups. Remarkably, disturbances of ALS signaling were shared between SCA2p and sporadic PD suggesting common molecular dysfunctions in PD and ALS including CACNA1, hnRNP, DDX and PABPC gene family perturbations. Interestingly, the transcriptome profiles of patients with parkinsonian phenotypes were prevalently associated with alterations of translation while SCA2c and PD patients presented perturbations of splicing. While ATXN2 RNA expression was not perturbed, its protein expression in immortalized lymphoblastoid cells was significantly decreased in SCA2c and SCA2p versus control groups assuming post-transcriptional biological perturbations. In conclusion, the transcriptome data do not exclude the role of ATXN2 mutated alleles in PD but its decrease protein expression in both SCA2c and SCA2p patients suggest a potential involvement of this gene in PD. The perturbations of "RNA-binding" and "poly(A) RNA-binding" molecular functions in the three patient groups as well as gene deregulations of factors not yet described in PD but known to be deleterious in other neurological conditions, suggest the existence of RNA-binding disturbances as a continuum between spinocerebellar ataxia type 2 and Parkinson's disease.
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Affiliation(s)
- Aurore Nkiliza
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Eugénie Mutez
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Clémence Simonin
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Frédéric Leprêtre
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Aurélie Duflot
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Martin Figeac
- Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Céline Villenet
- Univ. Lille, CHU Lille, IRCL, Structural and Functional Genomics Core Facility, F-59000 Lille, France
| | - Pierre Semaille
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Thomas Comptdaer
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France
| | - Alexandre Genet
- CHU Lille, Centre de Biologie Pathologie, Unité de Neurobiologie, F-59000 Lille, France
| | - Bernard Sablonnière
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; CHU Lille, Centre de Biologie Pathologie, Unité de Neurobiologie, F-59000 Lille, France
| | - David Devos
- CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Luc Defebvre
- CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Alain Destée
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France; CHU Lille, Neurologie et Pathologie du Mouvement, F-59000 Lille, France
| | - Marie-Christine Chartier-Harlin
- Univ. Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000 Lille, France; Inserm, UMR-S 1172, Team "Early stages of Parkinson's disease", F-59000 Lille, France.
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Alaqeel AM, Abou Al-Shaar H, Shariff RK, Albakr A. The role of RNA metabolism in neurological diseases. Balkan J Med Genet 2016; 18:5-14. [PMID: 27785391 PMCID: PMC5026263 DOI: 10.1515/bjmg-2015-0080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Neurodegenerative disorders are commonly encountered in medical practices. Such diseases can lead to major morbidity and mortality among the affected individuals. The molecular pathogenesis of these disorders is not yet clear. Recent literature has revealed that mutations in RNA-binding proteins are a key cause of several human neuronal-based diseases. This review discusses the role of RNA metabolism in neurological diseases with specific emphasis on roles of RNA translation and microRNAs in neurodegeneration, RNA-mediated toxicity, repeat expansion diseases and RNA metabolism, molecular pathogenesis of amyotrophic lateral sclerosis and frontotemporal dementia, and neurobiology of survival motor neuron (SMN) and spinal muscular atrophy.
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Affiliation(s)
- A M Alaqeel
- Department of Neurosurgery, University of Calgary, Calgary, Alberta, Canada; Division of Neurosurgery, Department of Surgery, King Saud University, Riyadh, Saudi Arabia
| | - H Abou Al-Shaar
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - R K Shariff
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - A Albakr
- Division of Neurosurgery, Department of Surgery, King Saud University, Riyadh, Saudi Arabia
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Urbanek MO, Jazurek M, Switonski PM, Figura G, Krzyzosiak WJ. Nuclear speckles are detention centers for transcripts containing expanded CAG repeats. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1513-20. [PMID: 27239700 DOI: 10.1016/j.bbadis.2016.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/18/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
The human genetic disorders caused by CAG repeat expansions in the translated sequences of various genes are called polyglutamine (polyQ) diseases because of the cellular "toxicity" of the mutant proteins. The contribution of mutant transcripts to the pathogenesis of these diseases is supported by several observations obtained from cellular models of these disorders. Here, we show that the common feature of cell lines modeling polyQ diseases is the formation of nuclear CAG RNA foci. We performed qualitative and quantitative analyses of these foci in numerous cellular models endogenously and exogenously expressing mutant transcripts by fluorescence in situ hybridization (FISH). We compared the CAG RNA foci of polyQ diseases with the CUG foci of myotonic dystrophy type 1 and found substantial differences in their number and morphology. Smaller differences within the polyQ disease group were also revealed and included a positive correlation between the foci number and the CAG repeat length. We show that expanded CAA repeats, also encoding glutamine, did not trigger RNA foci formation and foci formation is independent of the presence of mutant polyglutamine protein. Using FISH combined with immunofluorescence, we demonstrated partial co-localization of CAG repeat foci with MBNL1 alternative splicing factor, which explains the mild deregulation of MBNL1-dependent genes. We also showed that foci reside within nuclear speckles in diverse cell types: fibroblasts, lymphoblasts, iPS cells and neuronal progenitors and remain dependent on integrity of these nuclear structures.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Pawel M Switonski
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Grzegorz Figura
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland.
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40
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Zhao Y, Liu X, Sun H, Wang Y, Yang W, Ma H. Contactin‑associated protein‑like 2 expression in SH‑SY5Y cells is upregulated by a FOXP2 mutant with a shortened poly‑glutamine tract. Mol Med Rep 2015; 12:8162-8. [PMID: 26497390 DOI: 10.3892/mmr.2015.4483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 09/14/2015] [Indexed: 11/06/2022] Open
Abstract
The forkhead box protein P2 (FOXP2) gene encodes an important transcription factor that contains a polyglutamine (poly‑Q) tract and a forkhead DNA binding domain. It has been observed that FOXP2 is associated with speech sound disorder (SSD), and mutations that decrease the length of the poly‑Q tract were identified in the FOXP2 gene of SSD patients. However, the exact role of poly‑Q reduction is not well understood. In the present study, constructs expressing wild‑type and poly‑Q reduction mutants of FOXP2 were generated by polymerase chain reaction (PCR) using lentiviral vectors and transfected into the SH‑SY5Y neuronal cell line. Quantitative reverse transcription (qRT)‑PCR and western blotting indicated that infected cells stably expressed high levels of FOXP2. Using this cell model, the impact of FOXP2 on the expression of contactin‑associated protein‑like 2 (CNTNAP2) were investigated, and CNTNAP2 mRNA expression levels were observed to be significantly higher in cells expressing poly‑Q‑reduced FOXP2. In addition, the expression level of CASPR2, a mammalian homolog of Drosophila Neurexin IV, was increased in cells expressing the FOXP2 mutant. Demonstration of regulation by FOXP2 indicates that CNTNAP2 may also be involved in SSD.
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Affiliation(s)
- Yunjing Zhao
- Department of Developmental Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xiaoliang Liu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Hongwei Sun
- Department of Pediatrics, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning 110024, P.R. China
| | - Yueping Wang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Wenzhu Yang
- Department of Developmental Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Hongwei Ma
- Department of Developmental Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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Bochicchio A, Rossetti G, Tabarrini O, Krauβ S, Carloni P. Molecular view of ligands specificity for CAG repeats in anti-Huntington therapy. J Chem Theory Comput 2015; 11:4911-22. [PMID: 26574279 DOI: 10.1021/acs.jctc.5b00208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Huntington's disease is a fatal and devastating neurodegenerative genetic disorder for which there is currently no cure. It is characterized by Huntingtin protein's mRNA transcripts with 36 or more CAG repeats. Inhibiting the formation of pathological complexes between these expanded transcripts and target proteins may be a valuable strategy against the disease. Yet, the rational design of molecules specifically targeting the expanded CAG repeats is limited by the lack of structural information. Here, we use well-tempered metadynamics-based free energy calculations to investigate pose and affinity of two ligands targeting CAG repeats for which affinities have been previously measured. The first consists of two 4-guanidinophenyl rings linked by an ester group. It is the most potent ligand identified so far, with Kd = 60(30) nM. The second consists of a 4-phenyl dihydroimidazole and 4-1H-indole dihydroimidazole connected by a C-C bond (Kd = 700(80) nM). Our calculations reproduce the experimental affinities and uncover the recognition pattern between ligands' and their RNA target. They also provide a molecular basis for the markedly different affinity of the two ligands for CAG repeats as observed experimentally. These findings may pave the way for a structure-based hit-to-lead optimization to further improve ligand selectivity toward CAG repeat-containing mRNAs.
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Affiliation(s)
| | - Giulia Rossetti
- Department of Oncology, Hematology and Stem Cell Transplantation, RWTH Aachen University , D-52074 Aachen, North Rhine-Westphalia, Germany
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, Università di Perugia , Via del Liceo 1, I-06123 Perugia, Perugia, Italy
| | - Sybille Krauβ
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 25, D-53127 Bonn, North Rhine-Westphalia, Germany
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42
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In Vitro Expansion of CAG, CAA, and Mixed CAG/CAA Repeats. Int J Mol Sci 2015; 16:18741-51. [PMID: 26270660 PMCID: PMC4581269 DOI: 10.3390/ijms160818741] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 12/03/2022] Open
Abstract
Polyglutamine diseases, including Huntington’s disease and a number of spinocerebellar ataxias, are caused by expanded CAG repeats that are located in translated sequences of individual, functionally-unrelated genes. Only mutant proteins containing polyglutamine expansions have long been thought to be pathogenic, but recent evidence has implicated mutant transcripts containing long CAG repeats in pathogenic processes. The presence of two pathogenic factors prompted us to attempt to distinguish the effects triggered by mutant protein from those caused by mutant RNA in cellular models of polyglutamine diseases. We used the SLIP (Synthesis of Long Iterative Polynucleotide) method to generate plasmids expressing long CAG repeats (forming a hairpin structure), CAA-interrupted CAG repeats (forming multiple unstable hairpins) or pure CAA repeats (not forming any secondary structure). We successfully modified the original SLIP protocol to generate repeats of desired length starting from constructs containing short repeat tracts. We demonstrated that the SLIP method is a time- and cost-effective approach to manipulate the lengths of expanded repeat sequences.
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Highley JR, Lorente Pons A, Cooper-Knock J, Wharton SB, Ince PG, Shaw PJ, Wood J, Kirby J. Motor neurone disease/amyotrophic lateral sclerosis associated with intermediate-length CAG repeat expansions inAtaxin-2does not have 1C2-positive polyglutamine inclusions. Neuropathol Appl Neurobiol 2015; 42:377-89. [DOI: 10.1111/nan.12254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/14/2015] [Indexed: 12/13/2022]
Affiliation(s)
- John Robin Highley
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Alejandro Lorente Pons
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Stephen B. Wharton
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Paul G. Ince
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Jon Wood
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
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Tawani A, Kumar A. Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs). PLoS One 2015; 10:e0131788. [PMID: 26148061 PMCID: PMC4493008 DOI: 10.1371/journal.pone.0131788] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 06/08/2015] [Indexed: 11/19/2022] Open
Abstract
In humans, neurodegenerative disorders such as Huntington's disease (HD) and many spinocerebellar ataxias (SCAs) have been found to be associated with CAG trinucleotide repeat expansion. An important RNA-mediated mechanism that causes these diseases involves the binding of the splicing regulator protein MBNL1 (Muscleblind-like 1 protein) to expanded r(CAG) repeats. Moreover, mutant huntingtin protein translated from expanded r(CAG) also yields toxic effects. To discern the role of mutant RNA in these diseases, it is essential to gather information about its structure. Detailed insight into the different structures and conformations adopted by these mutant transcripts is vital for developing therapeutics targeting them. Here, we report the crystal structure of an RNA model with a r(CAG) motif, which is complemented by an NMR-based solution structure obtained from restrained Molecular Dynamics (rMD) simulation studies. Crystal structure data of the RNA model resolved at 2.3 Å reveals non-canonical pairing of adenine in 5´-CAG/3´-GAC motif samples in different syn and anti conformations. The overall RNA structure has helical parameters intermediate to the A- and B-forms of nucleic acids due to the global widening of major grooves and base-pair preferences near internal AA loops. The comprehension of structural behaviour by studying the spectral features and the dynamics also supports the flexible nature of the r(CAG) motif.
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Affiliation(s)
- Arpita Tawani
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Amit Kumar
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
- * E-mail:
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Parkinsonism in spinocerebellar ataxia. BIOMED RESEARCH INTERNATIONAL 2015; 2015:125273. [PMID: 25866756 PMCID: PMC4383270 DOI: 10.1155/2015/125273] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/29/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022]
Abstract
Spinocerebellar ataxia (SCA) presents heterogeneous clinical phenotypes, and parkinsonism is reported in diverse SCA subtypes. Both levodopa responsive Parkinson disease (PD) like phenotype and atypical parkinsonism have been described especially in SCA2, SCA3, and SCA17 with geographic differences in prevalence. SCA2 is the most frequently reported subtype of SCA related to parkinsonism worldwide. Parkinsonism in SCA2 has unique genetic characteristics, such as low number of expansions and interrupted structures, which may explain the sporadic cases with low penetrance. Parkinsonism in SCA17 is more remarkable in Asian populations especially in Korea. In addition, an unclear cutoff of the pathologic range is the key issue in SCA17 related parkinsonism. SCA3 is more common in western cohorts. SCA6 and SCA8 have also been reported with a PD-like phenotype. Herein, we reviewed the epidemiologic, clinical, genetic, and pathologic features of parkinsonism in SCAs.
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Linkage analysis and whole-exome sequencing exclude extra mutations responsible for the parkinsonian phenotype of spinocerebellar ataxia-2. Neurobiol Aging 2015; 36:545.e1-7. [DOI: 10.1016/j.neurobiolaging.2014.07.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 07/27/2014] [Indexed: 12/14/2022]
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FTLD-ALS of TDP-43 type and SCA2 in a family with a full ataxin-2 polyglutamine expansion. Acta Neuropathol 2014; 128:597-604. [PMID: 24718895 DOI: 10.1007/s00401-014-1277-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/29/2014] [Indexed: 12/13/2022]
Abstract
Polyglutamine expansions in the ataxin-2 gene (ATXN2) cause autosomal dominant spinocerebellar ataxia type 2 (SCA2), but have recently also been associated with amyotrophic lateral sclerosis (ALS). We present clinical and pathological features of a family in which a pathological ATXN2 expansion led to frontotemporal lobar degeneration with ALS (FTLD-ALS) in the index case, but typical SCA2 in a son, and compare the neuropathology with a case of typical SCA2. The index case shares the molecular signature of SCA2 with prominent polyglutamine and p62-positive intranuclear neuronal inclusions mainly in the pontine nuclei, while harbouring more pronounced neocortical and spinal TDP-43 pathology. We conclude that ATXN2 mutations can cause not only ALS, but also a neuropathological overlap syndrome of SCA2 and FTLD presenting clinically as pure FTLD-ALS without ataxia. The cause of the phenotypic heterogeneity remains unexplained, but the presence of a CAA-interrupted CAG repeat in the FTLD case in this family suggests that one potential mechanism may be variation in repeat tract composition between members of the same family.
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Wojciechowska M, Olejniczak M, Galka-Marciniak P, Jazurek M, Krzyzosiak WJ. RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders. Nucleic Acids Res 2014; 42:11849-64. [PMID: 25217582 PMCID: PMC4231732 DOI: 10.1093/nar/gku794] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeat-associated disorders caused by expansions of short sequences have been classified as coding and noncoding and are thought to be caused by protein gain-of-function and RNA gain-of-function mechanisms, respectively. The boundary between such classifications has recently been blurred by the discovery of repeat-associated non-AUG (RAN) translation reported in spinocerebellar ataxia type 8, myotonic dystrophy type 1, fragile X tremor/ataxia syndrome and C9ORF72 amyotrophic lateral sclerosis and frontotemporal dementia. This noncanonical translation requires no AUG start codon and can initiate in multiple frames of CAG, CGG and GGGGCC repeats of the sense and antisense strands of disease-relevant transcripts. RNA structures formed by the repeats have been suggested as possible triggers; however, the precise mechanism of the translation initiation remains elusive. Templates containing expansions of microsatellites have also been shown to challenge translation elongation, as frameshifting has been recognized across CAG repeats in spinocerebellar ataxia type 3 and Huntington's disease. Determining the critical requirements for RAN translation and frameshifting is essential to decipher the mechanisms that govern these processes. The contribution of unusual translation products to pathogenesis needs to be better understood. In this review, we present current knowledge regarding RAN translation and frameshifting and discuss the proposed mechanisms of translational challenges imposed by simple repeat expansions.
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Affiliation(s)
- Marzena Wojciechowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marta Olejniczak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Galka-Marciniak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
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Abstract
CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date.
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Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Fiszer A, Krzyzosiak WJ. Oligonucleotide-based strategies to combat polyglutamine diseases. Nucleic Acids Res 2014; 42:6787-810. [PMID: 24848018 PMCID: PMC4066792 DOI: 10.1093/nar/gku385] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Considerable advances have been recently made in understanding the molecular aspects of pathogenesis and in developing therapeutic approaches for polyglutamine (polyQ) diseases. Studies on pathogenic mechanisms have extended our knowledge of mutant protein toxicity, confirmed the toxicity of mutant transcript and identified other toxic RNA and protein entities. One very promising therapeutic strategy is targeting the causative gene expression with oligonucleotide (ON) based tools. This straightforward approach aimed at halting the early steps in the cascade of pathogenic events has been widely tested for Huntington's disease and spinocerebellar ataxia type 3. In this review, we gather information on the use of antisense oligonucleotides and RNA interference triggers for the experimental treatment of polyQ diseases in cellular and animal models. We present studies testing non-allele-selective and allele-selective gene silencing strategies. The latter include targeting SNP variants associated with mutations or targeting the pathologically expanded CAG repeat directly. We compare gene silencing effectors of various types in a number of aspects, including their design, efficiency in cell culture experiments and pre-clinical testing. We discuss advantages, current limitations and perspectives of various ON-based strategies used to treat polyQ diseases.
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Affiliation(s)
- Agnieszka Fiszer
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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