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Zhang J, Chen Z, Chen H, Deng Y, Li S, Jin L. Recent Advances in the Roles of MicroRNA and MicroRNA-Based Diagnosis in Neurodegenerative Diseases. BIOSENSORS 2022; 12:1074. [PMID: 36551041 PMCID: PMC9776063 DOI: 10.3390/bios12121074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Neurodegenerative diseases manifest as progressive loss of neuronal structures and their myelin sheaths and lead to substantial morbidity and mortality, especially in the elderly. Despite extensive research, there are few effective treatment options for the diseases. MicroRNAs have been shown to be involved in the developmental processes of the central nervous system. Mounting evidence suggest they play an important role in the development of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. However, there are few reviews regarding the roles of miRNAs in neurodegenerative diseases. This review summarizes the recent developments in the roles of microRNAs in neurodegenerative diseases and presents the application of microRNA-based methods in the early diagnosis of these diseases.
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2
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Palminha NM, Dos Santos Souza C, Griffin J, Liao C, Ferraiuolo L, El-Khamisy SF. Defective repair of topoisomerase I induced chromosomal damage in Huntington's disease. Cell Mol Life Sci 2022; 79:160. [PMID: 35224690 PMCID: PMC8882575 DOI: 10.1007/s00018-022-04204-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 11/30/2022]
Abstract
Topoisomerase1 (TOP1)-mediated chromosomal breaks are endogenous sources of DNA damage that affect neuronal genome stability. Whether TOP1 DNA breaks are sources of genomic instability in Huntington's disease (HD) is unknown. Here, we report defective 53BP1 recruitment in multiple HD cell models, including striatal neurons derived from HD patients. Defective 53BP1 recruitment is due to reduced H2A ubiquitination caused by the limited RNF168 activity. The reduced availability of RNF168 is caused by an increased interaction with p62, a protein involved in selective autophagy. Depletion of p62 or disruption of the interaction between RNAF168 and p62 was sufficient to restore 53BP1 enrichment and subsequent DNA repair in HD models, providing new opportunities for therapeutic interventions. These findings are reminiscent to what was described for p62 accumulation caused by C9orf72 expansion in ALS/FTD and suggest a common mechanism by which protein aggregation perturb DNA repair signaling.
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Affiliation(s)
- Nelma M Palminha
- School of Biosciences, Firth Court, Healthy Lifespan and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Cleide Dos Santos Souza
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Jon Griffin
- School of Biosciences, Firth Court, Healthy Lifespan and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Chunyan Liao
- School of Biosciences, Firth Court, Healthy Lifespan and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Sherif F El-Khamisy
- School of Biosciences, Firth Court, Healthy Lifespan and Neuroscience Institute, University of Sheffield, Sheffield, UK.
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK.
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3
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Brunet de Courssou JB, Durr A, Adams D, Corvol JC, Mariani LL. Antisense therapies in neurological diseases. Brain 2021; 145:816-831. [PMID: 35286370 DOI: 10.1093/brain/awab423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/16/2021] [Accepted: 11/01/2021] [Indexed: 12/18/2022] Open
Abstract
Advances in targeted regulation of gene expression allowed new therapeutic approaches for monogenic neurological diseases. Molecular diagnosis has paved the way to personalized medicine targeting the pathogenic roots: DNA or its RNA transcript. These antisense therapies rely on modified nucleotides sequences (single-strand DNA or RNA, both belonging to the antisense oligonucleotides family, or double-strand interfering RNA) to act specifically on pathogenic target nucleic acids, thanks to complementary base pairing. Depending on the type of molecule, chemical modifications and target, base pairing will lead alternatively to splicing modifications of primary transcript RNA or transient messenger RNA degradation or non-translation. The key to success for neurodegenerative diseases also depends on the ability to reach target cells. The most advanced antisense therapies under development in neurological disorders are presented here, at the clinical stage of development, either at phase 3 or market authorization stage, such as in spinal amyotrophy, Duchenne muscular dystrophy, transthyretin-related hereditary amyloidosis, porphyria and amyotrophic lateral sclerosis; or in earlier clinical phase 1 B, for Huntington disease, synucleinopathies and tauopathies. We also discuss antisense therapies at the preclinical stage, such as in some tauopathies, spinocerebellar ataxias or other rare neurological disorders. Each subtype of antisense therapy, antisense oligonucleotides or interfering RNA, has proved target engagement or even clinical efficacy in patients; undisputable recent advances for severe and previously untreatable neurological disorders. Antisense therapies show great promise, but many unknowns remain. Expanding the initial successes achieved in orphan or rare diseases to other disorders will be the next challenge, as shown by the recent failure in Huntington disease or due to long-term preclinical toxicity in multiple system atrophy and cystic fibrosis. This will be critical in the perspective of new planned applications to premanifest mutation carriers, or other non-genetic degenerative disorders such as multiple system atrophy or Parkinson disease.
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Affiliation(s)
- Jean-Baptiste Brunet de Courssou
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Alexandra Durr
- Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - David Adams
- Department of Neurology, Bicêtre hospital, Assistance Publique Hôpitaux de Paris, Centre de Référence National des Neuropathies Périphériques Rares, Paris Saclay University, INSERM U 1195, Le Kremlin Bicêtre, France
| | - Jean-Christophe Corvol
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France.,Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Louise-Laure Mariani
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France.,Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
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4
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Artificial miRNAs targeting CAG repeat expansion in ORFs cause rapid deadenylation and translation inhibition of mutant transcripts. Cell Mol Life Sci 2020; 78:1577-1596. [PMID: 32696070 PMCID: PMC7904544 DOI: 10.1007/s00018-020-03596-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Polyglutamine (polyQ) diseases are incurable neurological disorders caused by CAG repeat expansion in the open reading frames (ORFs) of specific genes. This type of mutation in the HTT gene is responsible for Huntington’s disease (HD). CAG repeat-targeting artificial miRNAs (art-miRNAs) were shown as attractive therapeutic approach for polyQ disorders as they caused allele-selective decrease in the level of mutant proteins. Here, using polyQ disease models, we aimed to demonstrate how miRNA-based gene expression regulation is dependent on target sequence features. We show that the silencing efficiency and selectivity of art-miRNAs is influenced by the localization of the CAG repeat tract within transcript and the specific sequence context. Furthermore, we aimed to reveal the events leading to downregulation of mutant polyQ proteins and found very rapid activation of translational repression and HTT transcript deadenylation. Slicer-activity of AGO2 was dispensable in this process, as determined in AGO2 knockout cells generated with CRISPR-Cas9 technology. We also showed highly allele-selective downregulation of huntingtin in human HD neural progenitors (NPs). Taken together, art-miRNA activity may serve as a model of the cooperative activity and targeting of ORF regions by endogenous miRNAs.
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5
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Lennox KA, Behlke MA. Chemical Modifications in RNA Interference and CRISPR/Cas Genome Editing Reagents. Methods Mol Biol 2020; 2115:23-55. [PMID: 32006393 DOI: 10.1007/978-1-0716-0290-4_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chemically modified oligonucleotides (ONs) are routinely used in the laboratory to assess gene function, and clinical advances are rapidly progressing as continual efforts are being made to optimize ON efficacy. Over the years, RNA interference (RNAi) has become one of the main tools used to inhibit RNA expression across a wide variety of species. Efforts have been made to improve the exogenous delivery of the double-stranded RNA components to the endogenous intracellular RNAi machinery to direct efficacious degradation of a user-defined RNA target. More recently, synthetic RNA ONs are being used to mimic the bacterial-derived CRISPR/Cas system to direct specific editing of the mammalian genome. Both of these techniques rely on the use of various chemical modifications to the RNA phosphate backbone or sugar in specific positions throughout the ONs to improve the desired biological outcome. Relevant chemical modifications also include conjugated targeting ligands to assist ON delivery to specific cell types. Chemical modifications are most beneficial for therapeutically relevant ONs, as they serve to enhance target binding, increase drug longevity, facilitate cell-specific targeting, improve internalization into productive intracellular compartments, and mitigate both sequence-specific as well as immune-related off-target effects (OTEs). The knowledge gained from years of optimizing RNAi reagents and characterizing the biochemical and biophysical properties of each chemical modification will hopefully accelerate the CRISPR/Cas technology into the clinic, as well as further expand the use of RNAi to treat currently undruggable diseases. This review discusses the most commonly employed chemical modifications in RNAi reagents and CRISPR/Cas guide RNAs and provides an overview of select publications that have demonstrated success in improving ON efficacy and/or mitigating undesired OTEs.
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Affiliation(s)
- Kim A Lennox
- Integrated DNA Technologies, Inc., Coralville, IA, USA.
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA
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6
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Kotowska-Zimmer A, Ostrovska Y, Olejniczak M. Universal RNAi Triggers for the Specific Inhibition of Mutant Huntingtin, Atrophin-1, Ataxin-3, and Ataxin-7 Expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 19:562-571. [PMID: 31927329 PMCID: PMC6957814 DOI: 10.1016/j.omtn.2019.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
Abstract
The expansion of CAG repeats within the coding region of associated genes is responsible for nine inherited neurodegenerative disorders including Huntington’s disease (HD), spinocerebellar ataxias (SCAs), and dentatorubral-pallidoluysian atrophy (DRPLA). Despite years of research aimed at developing an effective method of treatment, these diseases remain incurable and only their symptoms are controlled. The purpose of this study was to develop effective and allele-selective genetic tools for silencing the expression of mutated genes containing expanded CAG repeats. Here we show that repeat-targeting short hairpin RNAs preferentially reduce the levels of mutant huntingtin, atrophin-1, ataxin-3, and ataxin-7 proteins in patient-derived fibroblasts and may serve as universal allele-selective reagents for polyglutamine (polyQ) diseases.
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Affiliation(s)
- Anna Kotowska-Zimmer
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Yuliya Ostrovska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Dystrogen Gene Therapies, 1415 W 37(th) Street, Chicago, IL, USA.
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7
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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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8
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Hu J, Rigo F, Prakash TP, Corey DR. Recognition of c9orf72 Mutant RNA by Single-Stranded Silencing RNAs. Nucleic Acid Ther 2017; 27:87-94. [PMID: 28005462 PMCID: PMC5372765 DOI: 10.1089/nat.2016.0655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/15/2016] [Indexed: 01/09/2023] Open
Abstract
Mutations within the chromosome 9 open reading frame 72 (c9orf72) gene are associated with both familial amyotrophic lateral sclerosis and frontotemporal dementia. The mutation leads to an expanded GGGGCC hexanucleotide repeat within the first intron of c9orf72 and an expanded CCCCGG repeat within a corresponding antisense transcript. Both the mutant intronic and antisense RNAs have been implicated in disease. We have previously reported that duplex RNAs complementary to the repeats can recognize disease-causing RNA and block detection of nuclear foci formed by the mutant transcripts. Here, we test the hypothesis that inhibition can also be achieved by single-stranded silencing RNAs (ss-siRNAs). ss-siRNAs are single-stranded antisense oligonucleotides (ASOs) that function through RNAi interference (RNAi) to silence gene expression. ss-siRNAs can block the expanded repeats within both intronic RNA and the antisense transcripts. Inhibition is more potent than by analogous duplex RNAs. Our data suggest that the potent effects on foci are caused by a combination of mechanisms including RNAi and direct binding of the ss-siRNA to the target transcripts. These findings reinforce the suggestion that ss-siRNAs combine the favorable properties of duplex RNA and single-stranded ASOs.
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Affiliation(s)
- Jiaxin Hu
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
| | - Frank Rigo
- 3 Ionis Pharmaceuticals , Carlsbad, California
| | | | - David R Corey
- 1 Department of Pharmacology, UT Southwestern Medical Center at Dallas , Dallas, Texas
- 2 Department of Biochemistry, UT Southwestern Medical Center at Dallas , Dallas, Texas
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9
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Matsui M, Threlfall RN, Caruthers MH, Corey DR. Effect of 2'-O-methyl/thiophosphonoacetate-modified antisense oligonucleotides on huntingtin expression in patient-derived cells. ARTIFICIAL DNA, PNA & XNA 2016; 5:e1146391. [PMID: 26865404 DOI: 10.1080/1949095x.2016.1146391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Optimizing oligonucleotides as therapeutics will require exploring how chemistry can be used to enhance their effects inside cells. To achieve this goal it will be necessary to fully explore chemical space around the native DNA/RNA framework to define the potential of diverse chemical modifications. In this report we examine the potential of thiophosphonoacetate (thioPACE)-modified 2'-O-methyl oligoribonucleotides as inhibitors of human huntingtin (HTT) expression. Inhibition occurred, but was less than with analogous locked nucleic acid (LNA)-substituted oligomers lacking the thioPACE modification. These data suggest that thioPACE oligonucleotides have the potential to control gene expression inside cells. However, advantages relative to other modifications were not demonstrated. Additional modifications are likely to be necessary to fully explore any potential advantages of thioPACE substitutions.
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Affiliation(s)
- Masayuki Matsui
- a Department of Pharmacology; UT Southwestern Medical Center ; Dallas , TX USA
| | - Richard N Threlfall
- b Department of Chemistry and Biochemistry ; University of Colorado at Boulder ; Boulder , CO USA
| | - Marvin H Caruthers
- b Department of Chemistry and Biochemistry ; University of Colorado at Boulder ; Boulder , CO USA
| | - David R Corey
- a Department of Pharmacology; UT Southwestern Medical Center ; Dallas , TX USA
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10
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Bergquist H, Rocha CSJ, Álvarez-Asencio R, Nguyen CH, Rutland MW, Smith CIE, Good L, Nielsen PE, Zain R. Disruption of Higher Order DNA Structures in Friedreich's Ataxia (GAA)n Repeats by PNA or LNA Targeting. PLoS One 2016; 11:e0165788. [PMID: 27846236 PMCID: PMC5112992 DOI: 10.1371/journal.pone.0165788] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/07/2016] [Indexed: 01/08/2023] Open
Abstract
Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)4-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)5-PNA did not. We present evidence that (GAA)4-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)5-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression.
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Affiliation(s)
- Helen Bergquist
- Department of Medical Biochemistry and Microbiology, Microbiology-Immunology, Uppsala University, Uppsala, Sweden
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Cristina S. J. Rocha
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Rubén Álvarez-Asencio
- KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Stockholm, Sweden
| | - Chi-Hung Nguyen
- Laboratoire de Pharmacochimie, Institut Curie, PSL Research University, UMR 9187 – U 1196 CNRS-Institut Curie, INSERM, Centre Universitaire, Orsay, France
| | - Mark. W. Rutland
- KTH Royal Institute of Technology, School of Chemical Science and Engineering, Department of Chemistry, Stockholm, Sweden
| | - C. I. Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
| | - Liam Good
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London, United Kingdom
| | - Peter E. Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, The Panum Institute, Copenhagen, Denmark
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Sweden
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
- * E-mail:
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11
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Pendergraff HM, Debacker AJ, Watts JK. Single-Stranded Silencing RNAs: Hit Rate and Chemical Modification. Nucleic Acid Ther 2016; 26:216-22. [PMID: 27123752 DOI: 10.1089/nat.2015.0557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Single-stranded silencing RNAs (ss-siRNAs) are chemically modified single-stranded oligomers that engage the RNA interference machinery normally used by duplex RNAs to silence gene expression. ss-siRNAs have the potential to combine advantages of antisense oligonucleotides and siRNAs. Previous work has explored the chemistry of the phosphate and the oligonucleotide body. We now describe the process of attempting to develop and optimize ss-siRNAs based on five active siRNA duplexes. Three of the sequences failed to show any activity as ss-siRNAs, and in two of those cases the ss-siRNAs showed significantly increased toxicity relative to the parent duplexes. For the two sequences that did work well as ss-siRNAs, we show that the chemistry of the 3'-terminal dinucleotide also has a significant effect on the potency of ss-siRNAs. Previously published work on ss-siRNAs has been based on a 2'-O-methoxyethyl-RNA (MOE) dinucleotide at the 3'-terminus. To our surprise, oligomers containing 2'-O-Me-RNA modifications at the 3'-terminus showed significantly improved potency and activity relative to those modified with MOE at the same sites. Oligonucleotides with two locked nucleic acid units at the 3'-terminus showed improved activity over the MOE-modified analog for one sequence. Importantly, the fact that 2'-O-Me-RNA works so well makes the ss-siRNA approach accessible to a wider range of researchers since it can be achieved with inexpensive commercially available modifications.
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Affiliation(s)
- Hannah M Pendergraff
- 1 Department of Chemistry and Institute for Life Sciences, University of Southampton , United Kingdom
| | - Alexandre J Debacker
- 1 Department of Chemistry and Institute for Life Sciences, University of Southampton , United Kingdom .,2 RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts
| | - Jonathan K Watts
- 1 Department of Chemistry and Institute for Life Sciences, University of Southampton , United Kingdom .,2 RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts
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12
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Argonaute 2-dependent Regulation of Gene Expression by Single-stranded miRNA Mimics. Mol Ther 2016; 24:946-55. [PMID: 26903376 PMCID: PMC4881773 DOI: 10.1038/mt.2016.39] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 02/08/2016] [Indexed: 01/11/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding transcripts that regulate gene expression. Aberrant expression of miRNAs can affect development of cancer and other diseases. Synthetic miRNA mimics can modulate gene expression and offer an approach to therapy. Inside cells, mature miRNAs are produced as double-stranded RNAs and miRNA mimics typically retain both strands. This need for two strands has the potential to complicate drug development. Recently, synthetic chemically modified single-stranded silencing RNAs (ss-siRNA) have been shown to function through the RNAi pathway to induce gene silencing in cell culture and animals. Here, we test the hypothesis that single-stranded miRNA (ss-miRNA) can also mimic the function of miRNAs. We show that ss-miRNAs can act as miRNA mimics to silence the expression of target genes. Gene silencing requires expression of argonaute 2 (AGO2) protein and involves recruitment of AGO2 to the target transcripts. Chemically modified ss-miRNAs function effectively inside cells through endogenous RNAi pathways and broaden the options for miRNA-based oligonucleotide drug development.
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13
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Liu J, Hu J, Hicks JA, Prakash TP, Corey DR. Modulation of Splicing by Single-Stranded Silencing RNAs. Nucleic Acid Ther 2015; 25:113-20. [PMID: 25757055 DOI: 10.1089/nat.2014.0527] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Single-stranded silencing RNAs (ss-siRNAs) are chemically modified single-stranded oligonucleotides that can function through the cellular RNA interference (RNAi) machinery to modulate gene expression. Because their invention is recent, few studies have appeared describing their use and the potential of ss-siRNAs as a platform for controlling gene expression remains largely unknown. Using oligonucleotides to modulate splicing is an important area for therapeutic development and we tested the hypothesis that ss-siRNAs targeting splice sites might also be capable of directing increased production of therapeutically promising protein isoforms. Here we observe that ss-siRNAs alter splicing of dystrophin. Altered splicing requires a seed sequence complementarity to the target and expression of the RNAi factor argonaute 2. These results demonstrate that ss-siRNAs can be used to modulate splicing, providing another option for therapeutic development programs that aim to increase production of key protein isoforms. Splicing is a classical nuclear process and our data showing that it can be modulated through the action of RNA and RNAi factors offers further evidence that RNAi can take place in mammalian cell nuclei.
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Affiliation(s)
- Jing Liu
- 1Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,2Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jiaxin Hu
- 1Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,2Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jessica A Hicks
- 1Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,2Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | | | - David R Corey
- 1Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,2Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
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Eckstein F. Phosphorothioates, Essential Components of Therapeutic Oligonucleotides. Nucleic Acid Ther 2014; 24:374-87. [DOI: 10.1089/nat.2014.0506] [Citation(s) in RCA: 335] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Fritz Eckstein
- Max-Planck-Institut für Experimentelle Medizin, Göttingen, Germany
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15
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Skotte NH, Southwell AL, Østergaard ME, Carroll JB, Warby SC, Doty CN, Petoukhov E, Vaid K, Kordasiewicz H, Watt AT, Freier SM, Hung G, Seth PP, Bennett CF, Swayze EE, Hayden MR. Allele-specific suppression of mutant huntingtin using antisense oligonucleotides: providing a therapeutic option for all Huntington disease patients. PLoS One 2014; 9:e107434. [PMID: 25207939 PMCID: PMC4160241 DOI: 10.1371/journal.pone.0107434] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/11/2014] [Indexed: 01/10/2023] Open
Abstract
Huntington disease (HD) is an inherited, fatal neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene. The mutant protein causes neuronal dysfunction and degeneration resulting in motor dysfunction, cognitive decline, and psychiatric disturbances. Currently, there is no disease altering treatment, and symptomatic therapy has limited benefit. The pathogenesis of HD is complicated and multiple pathways are compromised. Addressing the problem at its genetic root by suppressing mutant huntingtin expression is a promising therapeutic strategy for HD. We have developed and evaluated antisense oligonucleotides (ASOs) targeting single nucleotide polymorphisms that are significantly enriched on HD alleles (HD-SNPs). We describe our structure-activity relationship studies for ASO design and find that adjusting the SNP position within the gap, chemical modifications of the wings, and shortening the unmodified gap are critical for potent, specific, and well tolerated silencing of mutant huntingtin. Finally, we show that using two distinct ASO drugs targeting the two allelic variants of an HD-SNP could provide a therapeutic option for all persons with HD; allele-specifically for roughly half, and non-specifically for the remainder.
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Affiliation(s)
- Niels H. Skotte
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amber L. Southwell
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jeffrey B. Carroll
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, Washington, United States of America
| | - Simon C. Warby
- Center for Advanced Research in Sleep Medicine, Department of Psychiatry, University of Montréal, Montréal, Quebec, Canada
| | - Crystal N. Doty
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eugenia Petoukhov
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kuljeet Vaid
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Andrew T. Watt
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Susan M. Freier
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Gene Hung
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Punit P. Seth
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - C. Frank Bennett
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Eric E. Swayze
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Michael R. Hayden
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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16
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Hu J, Liu J, Narayanannair KJ, Lackey JG, Kuchimanchi S, Rajeev KG, Manoharan M, Swayze EE, Lima WF, Prakash TP, Xiang Q, Martinez C, Corey DR. Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs. Biochemistry 2014; 53:4510-8. [PMID: 24981774 PMCID: PMC4108179 DOI: 10.1021/bi500610r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Dentatorubral-pallidoluysian
atrophy (DRPLA) is a progressive neurodegenerative
disorder that currently has no curative treatments. DRPLA is caused
by an expansion of a CAG trinucleotide repeat region within the protein-encoding
sequence of the atrophin-1 (ATN-1) gene. Inhibition
of mutant ATN-1 protein expression is one strategy for treating DRPLA,
and allele-selective gene silencing agents that block mutant expression
over wild-type expression would be lead compounds for therapeutic
development. Here we develop an assay for distinguishing mutant from
wild-type ATN-1 protein by gel electrophoresis. We use this assay
to evaluate duplex RNAs and single-stranded silencing RNAs (ss-siRNAs)
for allele-selective inhibition of ATN-1 protein expression. We observed
potent and allele-selective inhibition by RNA duplexes that contain
mismatched bases relative to the CAG target and have the potential
to form miRNA-like complexes. ss-siRNAs that contained mismatches
were as selective as mismatch-containing duplexes. We also report
allele-selective inhibition by duplex RNAs containing unlocked nucleic
acids or abasic substitutions, although selectivities are not as high.
Five compounds that showed >8-fold allele selectivity for mutant ATN-1 were also selective for inhibiting the expression
of two other trinucleotide repeat disease genes, ataxin-3 (ATXN-3) and huntingtin (HTT). These data
demonstrate that the expanded trinucleotide repeat within ATN-1 mRNA is a potential target for compounds designed
to achieve allele-selective inhibition of ATN-1 protein, and one agent
may allow the targeting of multiple disease genes.
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Affiliation(s)
- Jiaxin Hu
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center , 6001 Forest Park Road, Dallas, Texas 75390-9041, United States
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