1
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Mao EYC, Yen HY, Wu CC. Structural basis of how MGME1 processes DNA 5' ends to maintain mitochondrial genome integrity. Nucleic Acids Res 2024; 52:4067-4078. [PMID: 38471810 DOI: 10.1093/nar/gkae186] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
Mitochondrial genome maintenance exonuclease 1 (MGME1) helps to ensure mitochondrial DNA (mtDNA) integrity by serving as an ancillary 5'-exonuclease for DNA polymerase γ. Curiously, MGME1 exhibits unique bidirectionality in vitro, being capable of degrading DNA from either the 5' or 3' end. The structural basis of this bidirectionally and, particularly, how it processes DNA from the 5' end to assist in mtDNA maintenance remain unclear. Here, we present a crystal structure of human MGME1 in complex with a 5'-overhang DNA, revealing that MGME1 functions as a rigid DNA clamp equipped with a single-strand (ss)-selective arch, allowing it to slide on single-stranded DNA in either the 5'-to-3' or 3'-to-5' direction. Using a nuclease activity assay, we have dissected the structural basis of MGME1-derived DNA cleavage patterns in which the arch serves as a ruler to determine the cleavage site. We also reveal that MGME1 displays partial DNA-unwinding ability that helps it to better resolve 5'-DNA flaps, providing insights into MGME1-mediated 5'-end processing of nascent mtDNA. Our study builds on previously solved MGME1-DNA complex structures, finally providing the comprehensive functional mechanism of this bidirectional, ss-specific exonuclease.
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Affiliation(s)
- Eric Y C Mao
- Department of Chemistry, College of Science, National Cheng Kung University, Tainan City 701, Taiwan
| | - Han-Yi Yen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City 701, Taiwan
| | - Chyuan-Chuan Wu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City 701, Taiwan
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2
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Jaiswal AS, Dutta A, Srinivasan G, Yuan Y, Zhou D, Shaheen M, Sadideen D, Kirby A, Williamson E, Gupta Y, Olsen SK, Xu M, Loranc E, Mukhopadhyay P, Pertsemlidis A, Bishop AR, Sung P, Nickoloff J, Hromas R. TATDN2 resolution of R-loops is required for survival of BRCA1-mutant cancer cells. Nucleic Acids Res 2023; 51:12224-12241. [PMID: 37953292 PMCID: PMC10711561 DOI: 10.1093/nar/gkad952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
BRCA1-deficient cells have increased IRE1 RNase, which degrades multiple microRNAs. Reconstituting expression of one of these, miR-4638-5p, resulted in synthetic lethality in BRCA1-deficient cancer cells. We found that miR-4638-5p represses expression of TATDN2, a poorly characterized member of the TATD nuclease family. We discovered that human TATDN2 has RNA 3' exonuclease and endonuclease activity on double-stranded hairpin RNA structures. Given the cleavage of hairpin RNA by TATDN2, and that BRCA1-deficient cells have difficulty resolving R-loops, we tested whether TATDN2 could resolve R-loops. Using in vitro biochemical reconstitution assays, we found TATDN2 bound to R-loops and degraded the RNA strand but not DNA of multiple forms of R-loops in vitro in a Mg2+-dependent manner. Mutations in amino acids E593 and E705 predicted by Alphafold-2 to chelate an essential Mg2+ cation completely abrogated this R-loop resolution activity. Depleting TATDN2 increased cellular R-loops, DNA damage and chromosomal instability. Loss of TATDN2 resulted in poor replication fork progression in the presence of increased R-loops. Significantly, we found that TATDN2 is essential for survival of BRCA1-deficient cancer cells, but much less so for cognate BRCA1-repleted cancer cells. Thus, we propose that TATDN2 is a novel target for therapy of BRCA1-deficient cancers.
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Affiliation(s)
- Aruna S Jaiswal
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Gayathri Srinivasan
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Montaser Shaheen
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Doraid T Sadideen
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Austin Kirby
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Elizabeth A Williamson
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yogesh K Gupta
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Shaun K Olsen
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Mingjiang Xu
- Department of Molecular Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Eva Loranc
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Pramiti Mukhopadhyay
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Alexander Pertsemlidis
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
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3
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Mortberg MA, Gentile JE, Nadaf N, Vanderburg C, Simmons S, Dubinsky D, Slamin A, Maldonado S, Petersen C, Jones N, Kordasiewicz H, Zhao H, Vallabh S, Minikel E. A single-cell map of antisense oligonucleotide activity in the brain. Nucleic Acids Res 2023; 51:7109-7124. [PMID: 37188501 PMCID: PMC10415122 DOI: 10.1093/nar/gkad371] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
Antisense oligonucleotides (ASOs) dosed into cerebrospinal fluid (CSF) distribute broadly throughout the central nervous system (CNS). By modulating RNA, they hold the promise of targeting root molecular causes of disease and hold potential to treat myriad CNS disorders. Realization of this potential requires that ASOs must be active in the disease-relevant cells, and ideally, that monitorable biomarkers also reflect ASO activity in these cells. The biodistribution and activity of such centrally delivered ASOs have been deeply characterized in rodent and non-human primate (NHP) models, but usually only in bulk tissue, limiting our understanding of the distribution of ASO activity across individual cells and across diverse CNS cell types. Moreover, in human clinical trials, target engagement is usually monitorable only in a single compartment, CSF. We sought a deeper understanding of how individual cells and cell types contribute to bulk tissue signal in the CNS, and how these are linked to CSF biomarker outcomes. We employed single nucleus transcriptomics on tissue from mice treated with RNase H1 ASOs against Prnp and Malat1 and NHPs treated with an ASO against PRNP. Pharmacologic activity was observed in every cell type, though sometimes with substantial differences in magnitude. Single cell RNA count distributions implied target RNA suppression in every single sequenced cell, rather than intense knockdown in only some cells. Duration of action up to 12 weeks post-dose differed across cell types, being shorter in microglia than in neurons. Suppression in neurons was generally similar to, or more robust than, the bulk tissue. In macaques, PrP in CSF was lowered 40% in conjunction with PRNP knockdown across all cell types including neurons, arguing that a CSF biomarker readout is likely to reflect ASO pharmacodynamic effect in disease-relevant cells in a neuronal disorder. Our results provide a reference dataset for ASO activity distribution in the CNS and establish single nucleus sequencing as a method for evaluating cell type specificity of oligonucleotide therapeutics and other modalities.
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Affiliation(s)
- Meredith A Mortberg
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Juliana E Gentile
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Naeem M Nadaf
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Charles Vanderburg
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sean Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dan Dubinsky
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Adam Slamin
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Salome Maldonado
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Caroline L Petersen
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Nichole Jones
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Hien T Zhao
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Sonia M Vallabh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA02115, USA
- Prion Alliance, Cambridge, MA 02139, USA
| | - Eric Vallabh Minikel
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA02115, USA
- Prion Alliance, Cambridge, MA 02139, USA
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4
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Mortberg MA, Gentile JE, Nadaf N, Vanderburg C, Simmons S, Dubinsky D, Slamin A, Maldonado S, Petersen CL, Jones N, Kordasiewicz HB, Zhao HT, Vallabh SM, Minikel EV. A single-cell map of antisense oligonucleotide activity in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528473. [PMID: 36824749 PMCID: PMC9948956 DOI: 10.1101/2023.02.14.528473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Antisense oligonucleotides (ASOs) dosed into cerebrospinal fluid (CSF) distribute broadly throughout the brain and hold the promise of treating myriad brain diseases by modulating RNA. CNS tissue is not routinely biopsied in living individuals, leading to reliance on CSF biomarkers to inform on drug target engagement. Animal models can link CSF biomarkers to brain parenchyma, but our understanding of how individual cells contribute to bulk tissue signal is limited. Here we employed single nucleus transcriptomics on tissue from mice treated with RNase H1 ASOs against Prnp and Malat1 and macaques treated with an ASO against PRNP . Activity was observed in every cell type, though sometimes with substantial differences in magnitude. Single cell RNA count distributions implied target suppression in every single sequenced cell, rather than intense knockdown in only some cells. Duration of action up to 12 weeks post-dose differed across cell types, being shorter in microglia than in neurons. Suppression in neurons was generally similar to, or more robust than, the bulk tissue. In macaques, PrP in CSF was lowered 40% in conjunction with PRNP knockdown across all cell types including neurons, arguing that a CSF biomarker readout is likely to reflect disease-relevant cells in a neuronal disorder.
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Affiliation(s)
- Meredith A Mortberg
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
| | - Juliana E Gentile
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
| | - Naeem Nadaf
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
| | - Charles Vanderburg
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
| | - Sean Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
| | - Dan Dubinsky
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Adam Slamin
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Salome Maldonado
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Caroline L Petersen
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Nichole Jones
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | | | - Hien T Zhao
- Ionis Pharmaceuticals, Carlsbad, CA, 92010, USA
| | - Sonia M Vallabh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts GeneralHospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Prion Alliance, Cambridge, MA, 02139, USA
| | - Eric Vallabh Minikel
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard,Cambridge, MA, 02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts GeneralHospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Prion Alliance, Cambridge, MA, 02139, USA
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5
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Robillard KN, de Vrieze E, van Wijk E, Lentz JJ. Altering gene expression using antisense oligonucleotide therapy for hearing loss. Hear Res 2022; 426:108523. [PMID: 35649738 DOI: 10.1016/j.heares.2022.108523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 04/20/2022] [Accepted: 05/14/2022] [Indexed: 12/12/2022]
Abstract
Hearing loss affects more than 430 million people, worldwide, and is the third most common chronic physical condition in the United States and Europe (GBD Hearing Loss Collaborators, 2021; NIOSH, 2021; WHO, 2021). The loss of hearing significantly impacts motor and cognitive development, communication, education, employment, and overall quality of life. The inner ear houses the sensory organs for both hearing and balance and provides an accessible target for therapeutic delivery. Antisense oligonucleotides (ASOs) use various mechanisms to manipulate gene expression and can be tailor-made to treat disorders with defined genetic targets. In this review, we discuss the preclinical advancements within the field of the highly promising ASO-based therapies for hereditary hearing loss disorders. Particular focus is on ASO mechanisms of action, preclinical studies on ASO treatments of hearing loss, timing of therapeutic intervention, and delivery routes to the inner ear.
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Affiliation(s)
| | - Erik de Vrieze
- Department of Otorhinolaryngology, RUMC, Geert Grooteplein 10, Route 855, GA, Nijmegen 6525, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, RUMC, Nijmegen, NL
| | - Erwin van Wijk
- Department of Otorhinolaryngology, RUMC, Geert Grooteplein 10, Route 855, GA, Nijmegen 6525, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, RUMC, Nijmegen, NL.
| | - Jennifer J Lentz
- Neuroscience Center of Excellence, LSUHSC, New Orleans, LA, USA; Department of Otorhinolaryngology, LSUHSC, 2020 Gravier Street, Lions Building, Room 795, New Orleans, LA, USA.
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6
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Pang J, Guo Q, Lu Z. The catalytic mechanism, metal dependence, substrate specificity, and biodiversity of ribonuclease H. Front Microbiol 2022; 13:1034811. [PMID: 36478866 PMCID: PMC9719913 DOI: 10.3389/fmicb.2022.1034811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2023] Open
Abstract
Ribonucleoside monophosphates are inevitably misincorporated into the DNA genome inside cells, and they need to be excised to avoid chromosome instability. Ribonucleases H (RNases H) are enzymes that specifically hydrolyze the RNA strand of RNA/DNA hybrids or the RNA moiety from DNA containing a stretch of RNA, they therefore are required for DNA integrity. Extensive studies have drawn a mostly clear picture of the mechanisms of RNase H catalysis, but some questions are still lacking definitive answers. This review summarizes three alternative models of RNase H catalysis. The two-metal model is prevalent, but a three-metal model suggests the involvement of a third cation in catalysis. Apparently, the mechanisms underlying metal-dependent hydrolyzation are more complicated than initially thought. We also discuss the metal choices of RNases H and analyze how chemically similar cations function differently. Substrate and cleavage-site specificities vary among RNases H, and this is explicated in detail. An intriguing phenomenon is that organisms have diverse RNase H combinations, which may provide important hints to how rnh genes were transferred during evolution. Whether RNase H is essential for cellular growth, a key question in the study of in vivo functions, is also discussed. This article may aid in understanding the mechanisms underlying RNase H and in developing potentially promising applications of it.
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Affiliation(s)
| | | | - Zheng Lu
- Department of Biology, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
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7
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Karlowicz A, Dubiel AB, Czerwinska J, Bledea A, Purzycki P, Grzelewska M, McAuley RJ, Szczesny RJ, Brzuska G, Krol E, Szczesny B, Szymanski MR. In vitro reconstitution reveals a key role of human mitochondrial EXOG in RNA primer processing. Nucleic Acids Res 2022; 50:7991-8007. [PMID: 35819194 PMCID: PMC9371904 DOI: 10.1093/nar/gkac581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/01/2022] [Accepted: 06/24/2022] [Indexed: 11/12/2022] Open
Abstract
The removal of RNA primers is essential for mitochondrial DNA (mtDNA) replication. Several nucleases have been implicated in RNA primer removal in human mitochondria, however, no conclusive mechanism has been elucidated. Here, we reconstituted minimal in vitro system capable of processing RNA primers into ligatable DNA ends. We show that human 5'-3' exonuclease, EXOG, plays a fundamental role in removal of the RNA primer. EXOG cleaves short and long RNA-containing flaps but also in cooperation with RNase H1, processes non-flap RNA-containing intermediates. Our data indicate that the enzymatic activity of both enzymes is necessary to process non-flap RNA-containing intermediates and that regardless of the pathway, EXOG-mediated RNA cleavage is necessary prior to ligation by DNA Ligase III. We also show that upregulation of EXOG levels in mitochondria increases ligation efficiency of RNA-containing substrates and discover physical interactions, both in vitro and in cellulo, between RNase H1 and EXOG, Pol γA, Pol γB and Lig III but not FEN1, which we demonstrate to be absent from mitochondria of human lung epithelial cells. Together, using human mtDNA replication enzymes, we reconstitute for the first time RNA primer removal reaction and propose a novel model for RNA primer processing in human mitochondria.
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Affiliation(s)
- Anna Karlowicz
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Andrzej B Dubiel
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Jolanta Czerwinska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, ul. Pawinskiego 5A, 02-106 Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Adela Bledea
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Piotr Purzycki
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Marta Grzelewska
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Ryan J McAuley
- Department of Ophthalmology and Visual Sciences, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, ul. Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Gabriela Brzuska
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Ewelina Krol
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Bartosz Szczesny
- Department of Ophthalmology and Visual Sciences, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Michal R Szymanski
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
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8
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Crooke ST, Liang XH, Baker BF, Crooke RM. Antisense technology: A review. J Biol Chem 2021; 296:100416. [PMID: 33600796 PMCID: PMC8005817 DOI: 10.1016/j.jbc.2021.100416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Antisense technology is beginning to deliver on the broad promise of the technology. Ten RNA-targeted drugs including eight single-strand antisense drugs (ASOs) and two double-strand ASOs (siRNAs) have now been approved for commercial use, and the ASOs in phase 2/3 trials are innovative, delivered by multiple routes of administration and focused on both rare and common diseases. In fact, two ASOs are used in cardiovascular outcome studies and several others in very large trials. Interest in the technology continues to grow, and the field has been subject to a significant number of reviews. In this review, we focus on the molecular events that result in the effects observed and use recent clinical results involving several different ASOs to exemplify specific molecular mechanisms and specific issues. We conclude with the prospective on the technology.
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Affiliation(s)
- Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA.
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Brenda F Baker
- Development Communication, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Rosanne M Crooke
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
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9
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Liang XH, Nichols JG, De Hoyos CL, Crooke ST. Some ASOs that bind in the coding region of mRNAs and induce RNase H1 cleavage can cause increases in the pre-mRNAs that may blunt total activity. Nucleic Acids Res 2020; 48:9840-9858. [PMID: 32870273 PMCID: PMC7515700 DOI: 10.1093/nar/gkaa715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 01/06/2023] Open
Abstract
Antisense oligonucleotide (ASO) drugs that trigger RNase H1 cleavage of target RNAs have been developed to treat various diseases. Basic pharmacological principles suggest that the development of tolerance is a common response to pharmacological interventions. In this manuscript, for the first time we report a molecular mechanism of tolerance that occurs with some ASOs. Two observations stimulated our interest: some RNA targets are difficult to reduce with RNase H1 activating ASOs and some ASOs display a shorter duration of activity than the prolonged target reduction typically observed. We found that certain ASOs targeting the coding region of some mRNAs that initially reduce target mRNAs can surprisingly increase the levels of the corresponding pre-mRNAs. The increase in pre-mRNA is delayed and due to enhanced transcription and likely also slower processing. This process requires that the ASOs bind in the coding region and reduce the target mRNA by RNase H1 while the mRNA resides in the ribosomes. The pre-mRNA increase is dependent on UPF3A and independent of the NMD pathway or the XRN1-CNOT pathway. The response is consistent in multiple cell lines and independent of the methods used to introduce ASOs into cells.
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Affiliation(s)
- Xue-hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cheryl L De Hoyos
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
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10
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Falkenberg M, Gustafsson CM. Mammalian mitochondrial DNA replication and mechanisms of deletion formation. Crit Rev Biochem Mol Biol 2020; 55:509-524. [DOI: 10.1080/10409238.2020.1818684] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Claes M. Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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11
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Fathi Dizaji B. Strategies to target long non-coding RNAs in cancer treatment: progress and challenges. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00074-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Long non-coding RNAs are important regulators of gene expression and diverse biological processes. Their aberrant expression contributes to a verity of diseases including cancer development and progression, providing them with great potential to be diagnostic and prognostic biomarkers and therapeutic targets. Therefore, they can have a key role in personalized cancer medicine.
This review aims at introducing possible strategies to target long ncRNAs therapeutically in cancer. Also, chemical modification of nucleic acid-based therapeutics to improve their pharmacological properties is explained. Then, approaches for the systematic delivery of reagents into the tumor cells or organs are briefly discussed, followed by describing obstacles to the expansion of the therapeutics.
Main text
Long ncRNAs function as oncogenes or tumor suppressors, whose activity can modulate all hallmarks of cancer. They are expressed in a very restricted spatial and temporal pattern and can be easily detected in the cells or biological fluids of patients. These properties make them excellent targets for the development of anticancer drugs. Targeting methods aim to attenuate oncogenic lncRNAs or interfere with lncRNA functions to prevent carcinogenesis. Numerous strategies including suppression of oncogenic long ncRNAs, alternation of their epigenetic effects, interfering with their function, restoration of downregulated or lost long ncRNAs, and recruitment of long ncRNAs regulatory elements and expression patterns are recommended for targeting long ncRNAs therapeutically in cancer. These approaches have shown inhibitory effects on malignancy. In this regard, proliferation, migration, and invasion of tumor cells have been inhibited and apoptosis has been induced in different cancer cells in vitro and in vivo. Downregulation of oncogenic long ncRNAs and upregulation of some growth factors (e.g., neurotrophic factor) have been achieved.
Conclusions
Targeting long non-coding RNAs therapeutically in cancer and efficient and safe delivery of the reagents have been rarely addressed. Only one clinical trial involving lncRNAs has been reported. Among different technologies, RNAi is the most commonly used and effective tool to target lncRNAs. However, other technologies need to be examined and further research is essential to put lncRNAs into clinical practice.
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12
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Song Z, Jia R, Tang M, Xia F, Xu H, Li Z, Huang C. Antisense oligonucleotide technology can be used to investigate a circular but not linear RNA-mediated function for its encoded gene locus. SCIENCE CHINA-LIFE SCIENCES 2020; 64:784-794. [PMID: 32815066 DOI: 10.1007/s11427-020-1743-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023]
Abstract
As a class of powerful molecular tool, antisense oligonucleotides (ASOs) are not only broadly used in protein and RNA biology, but also a highly selective therapeutic strategy for many diseases. Although the concept that ASO reagents only reduce expression of the targeted gene in a post-transcriptional manner has long been established, the effect and mechanism of ASO reagents on RNA polymerase II (Pol II) transcription are largely unknown. This raised question is particularly important for the appropriate use of ASOs and the valid interpretation of ASO-mediated experiments. In this study, our results show that linear RNA ASO attenuates transcription of nascent transcripts by inducing premature transcription termination which is combinatorially controlled by Integrator, exosome, and Rat1 in Drosophila. However, circular RNA (circRNA) ASO transfection does not affect transcription activity of the encoded gene. These data suggest that the ASO technique can be applied to study a circRNA-mediated but not linear RNA-mediated function for its encoded gene locus.
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Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Mingfeng Tang
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Fei Xia
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Haiyang Xu
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 400044, China. .,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 400044, China.
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13
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Antisense drug discovery and development technology considered in a pharmacological context. Biochem Pharmacol 2020; 189:114196. [PMID: 32800852 DOI: 10.1016/j.bcp.2020.114196] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
When coined, the term "antisense" included oligonucleotides of any structure, with any chemical modification and designed to work through any post-RNA hybridization mechanism. However, in practice the term "antisense" has been used to describe single stranded oligonucleotides (ss ASOs) designed to hybridize to RNAswhile the term "siRNA" has come to mean double stranded oligonucleotides designed to activate Ago2. However, the two approaches share many common features. The medicinal chemistry developed for ASOs greatly facilitated the development of siRNA technology and remains the chemical basis for both approaches. Many of challenges faced and solutions achieved share many common features. In fact, because ss ASOs can be designed to activate Ago2, the two approaches intersect at this remarkably important protein. There are also meaningful differences. The pharmacokinetic properties are quite different and thus potential routes of delivery differ. ASOs may be designedto use a variety of post-RNA binding mechanismswhile siRNAs depend solely on the robust activity of Ago2. However, siRNAs and ASOs are both used for therapeutic purposes and both must be and can be understood in a pharmacological context. Thus, the goals of this review are to put ASOs in pharmacological context and compare their behavior as pharmacological agents to the those of siRNAs.
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14
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Silva AC, Lobo DD, Martins IM, Lopes SM, Henriques C, Duarte SP, Dodart JC, Nobre RJ, Pereira de Almeida L. Antisense oligonucleotide therapeutics in neurodegenerative diseases: the case of polyglutamine disorders. Brain 2020; 143:407-429. [PMID: 31738395 DOI: 10.1093/brain/awz328] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/09/2019] [Accepted: 08/22/2019] [Indexed: 12/20/2022] Open
Abstract
Polyglutamine (polyQ) disorders are a group of nine neurodegenerative diseases that share a common genetic cause, which is an expansion of CAG repeats in the coding region of the causative genes that are otherwise unrelated. The trinucleotide expansion encodes for an expanded polyQ tract in the respective proteins, resulting in toxic gain-of-function and eventually in neurodegeneration. Currently, no disease-modifying therapies are available for this group of disorders. Nevertheless, given their monogenic nature, polyQ disorders are ideal candidates for therapies that target specifically the gene transcripts. Antisense oligonucleotides (ASOs) have been under intense investigation over recent years as gene silencing tools. ASOs are small synthetic single-stranded chains of nucleic acids that target specific RNA transcripts through several mechanisms. ASOs can reduce the levels of mutant proteins by breaking down the targeted transcript, inhibit mRNA translation or alter the maturation of the pre-mRNA via splicing correction. Over the years, chemical optimization of ASO molecules has allowed significant improvement of their pharmacological properties, which has in turn made this class of therapeutics a very promising strategy to treat a variety of neurodegenerative diseases. Indeed, preclinical and clinical strategies have been developed in recent years for some polyQ disorders using ASO therapeutics. The success of ASOs in several animal models, as well as encouraging results in the clinic for Huntington's disease, points towards a promising future regarding the application of ASO-based therapies for polyQ disorders in humans, offering new opportunities to address unmet medical needs for this class of disorders. This review aims to present a brief overview of key chemical modifications, mechanisms of action and routes of administration that have been described for ASO-based therapies. Moreover, it presents a review of the most recent and relevant preclinical and clinical trials that have tested ASO therapeutics in polyQ disorders.
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Affiliation(s)
- Ana C Silva
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Diana D Lobo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Inês M Martins
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Sara M Lopes
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Carina Henriques
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,ViraVector, Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal
| | - Sónia P Duarte
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | | | - Rui Jorge Nobre
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.,ViraVector, Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal
| | - Luis Pereira de Almeida
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,ViraVector, Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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15
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Kuciński J, Chamera S, Kmera A, Rowley MJ, Fujii S, Khurana P, Nowotny M, Wierzbicki AT. Evolutionary History and Activity of RNase H1-Like Proteins in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2020; 61:1107-1119. [PMID: 32191307 PMCID: PMC7295395 DOI: 10.1093/pcp/pcaa040] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/14/2020] [Indexed: 06/01/2023]
Abstract
RNase H1 is an endonuclease specific toward the RNA strand of RNA:DNA hybrids. Members of this protein family are present in most living organisms and are essential for removing RNA that base pairs with DNA. It prevents detrimental effects of RNA:DNA hybrids and is involved in several biological processes. Arabidopsis thaliana has been previously shown to contain three genes encoding RNase H1 proteins that localize to three distinct cellular compartments. We show that these genes originate from two gene duplication events. One occurred in the common ancestor of dicots and produced nuclear and organellar RNase H1 paralogs. Second duplication occurred in the common ancestor of Brassicaceae and produced mitochondrial- and plastid-localized proteins. These proteins have the canonical RNase H1 activity, which requires at least four ribonucleotides for endonucleolytic digestion. Analysis of mutants in the RNase H1 genes revealed that the nuclear RNH1A and mitochondrial RNH1B are dispensable for development under normal growth conditions. However, the presence of at least one organellar RNase H1 (RNH1B or RNH1C) is required for embryonic development. The plastid-localized RNH1C affects plastid DNA copy number and sensitivity to replicative stress. Our results present the evolutionary history of RNH1 proteins in A. thaliana, demonstrate their canonical RNase H1 activity and indicate their role in early embryonic development.
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Affiliation(s)
- Jan Kuciński
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sebastian Chamera
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Aleksandra Kmera
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - M Jordan Rowley
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sho Fujii
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Pragya Khurana
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej T Wierzbicki
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
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16
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Østergaard ME, De Hoyos CL, Wan WB, Shen W, Low A, Berdeja A, Vasquez G, Murray S, Migawa MT, Liang XH, Swayze EE, Crooke ST, Seth PP. Understanding the effect of controlling phosphorothioate chirality in the DNA gap on the potency and safety of gapmer antisense oligonucleotides. Nucleic Acids Res 2020; 48:1691-1700. [PMID: 31980820 PMCID: PMC7038945 DOI: 10.1093/nar/gkaa031] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/07/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023] Open
Abstract
Therapeutic oligonucleotides are often modified using the phosphorothioate (PS) backbone modification which enhances stability from nuclease mediated degradation. However, substituting oxygen in the phosphodiester backbone with sulfur introduce chirality into the backbone such that a full PS 16-mer oligonucleotide is comprised of 215 distinct stereoisomers. As a result, the role of PS chirality on the performance of antisense oligonucleotides (ASOs) has been a subject of debate for over two decades. We carried out a systematic analysis to determine if controlling PS chirality in the DNA gap region can enhance the potency and safety of gapmer ASOs modified with high-affinity constrained Ethyl (cEt) nucleotides in the flanks. As part of this effort, we examined the effect of systematically controlling PS chirality on RNase H1 cleavage patterns, protein mislocalization phenotypes, activity and toxicity in cells and in mice. We found that while controlling PS chirality can dramatically modulate interactions with RNase H1 as evidenced by changes in RNA cleavage patterns, these were insufficient to improve the overall therapeutic profile. We also found that controlling PS chirality of only two PS linkages in the DNA gap was sufficient to modulate RNase H1 cleavage patterns and combining these designs with simple modifications such as 2'-OMe to the DNA gap resulted in dramatic improvements in therapeutic index. However, we were unable to demonstrate improved potency relative to the stereorandom parent ASO or improved safety over the 2'-OMe gap-modified stereorandom parent ASO. Overall, our work shows that while controlling PS chirality can modulate RNase H1 cleavage patterns, ASO sequence and design are the primary drivers which determine the pharmacological and toxicological properties of gapmer ASOs.
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Affiliation(s)
| | - Cheryl L De Hoyos
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - W Brad Wan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Wen Shen
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Andres Berdeja
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Guillermo Vasquez
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Susan Murray
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael T Migawa
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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17
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Scharner J, Ma WK, Zhang Q, Lin KT, Rigo F, Bennett CF, Krainer AR. Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides. Nucleic Acids Res 2020; 48:802-816. [PMID: 31802121 PMCID: PMC6954394 DOI: 10.1093/nar/gkz1132] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/03/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022] Open
Abstract
Splice-switching antisense oligonucleotides (ASOs), which bind specific RNA-target sequences and modulate pre-mRNA splicing by sterically blocking the binding of splicing factors to the pre-mRNA, are a promising therapeutic modality to treat a range of genetic diseases. ASOs are typically 15–25 nt long and considered to be highly specific towards their intended target sequence, typically elements that control exon definition and/or splice-site recognition. However, whether or not splice-modulating ASOs also induce hybridization-dependent mis-splicing of unintended targets has not been systematically studied. Here, we tested the in vitro effects of splice-modulating ASOs on 108 potential off-targets predicted on the basis of sequence complementarity, and identified 17 mis-splicing events for one of the ASOs tested. Based on analysis of data from two overlapping ASO sequences, we conclude that off-target effects are difficult to predict, and the choice of ASO chemistry influences the extent of off-target activity. The off-target events caused by the uniformly modified ASOs tested in this study were significantly reduced with mixed-chemistry ASOs of the same sequence. Furthermore, using shorter ASOs, combining two ASOs, and delivering ASOs by free uptake also reduced off-target activity. Finally, ASOs with strategically placed mismatches can be used to reduce unwanted off-target splicing events.
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Affiliation(s)
| | - Wai Kit Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
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18
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Reyes A, Rusecka J, Tońska K, Zeviani M. RNase H1 Regulates Mitochondrial Transcription and Translation via the Degradation of 7S RNA. Front Genet 2020; 10:1393. [PMID: 32082360 PMCID: PMC7006045 DOI: 10.3389/fgene.2019.01393] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/19/2019] [Indexed: 02/02/2023] Open
Abstract
RNase H1 is able to recognize DNA/RNA heteroduplexes and to degrade their RNA component. As a consequence, it has been implicated in different aspects of mtDNA replication such as primer formation, primer removal, and replication termination, and significant differences have been reported between control and mutant RNASEH1 skin fibroblasts from patients. However, neither mtDNA depletion nor the presence of deletions have been described in skin fibroblasts while still presenting signs of mitochondrial dysfunction (lower mitochondrial membrane potential, reduced oxygen consumption, slow growth in galactose). Here, we show that RNase H1 has an effect on mtDNA transcripts, most likely through the regulation of 7S RNA and other R-loops. The observed effect on both mitochondrial mRNAs and 16S rRNA results in decreased mitochondrial translation and subsequently mitochondrial dysfunction in cells carrying mutations in RNASEH1.
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Affiliation(s)
- Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Aurelio Reyes, ; Massimo Zeviani,
| | - Joanna Rusecka
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Katarzyna Tońska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Aurelio Reyes, ; Massimo Zeviani,
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19
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Reidenbach AG, Minikel EV, Zhao HT, Guzman SG, Leed AJ, Mesleh MF, Kordasiewicz HB, Schreiber SL, Vallabh SM. Characterization of the Prion Protein Binding Properties of Antisense Oligonucleotides. Biomolecules 2019; 10:E1. [PMID: 31861275 PMCID: PMC7022474 DOI: 10.3390/biom10010001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 01/08/2023] Open
Abstract
Antisense oligonucleotides (ASOs) designed to lower prion protein (PrP) expression in the brain through RNase H1-mediated degradation of PrP RNA are in development as prion disease therapeutics. ASOs were previously reported to sequence-independently interact with PrP and inhibit prion accumulation in cell culture, yet in vivo studies using a new generation of ASOs found that only PrP-lowering sequences were effective at extending survival. Cerebrospinal fluid (CSF) PrP has been proposed as a pharmacodynamic biomarker for trials of such ASOs, but is only interpretable if PrP lowering is indeed the relevant mechanism of action in vivo and if measurement of PrP is unconfounded by any PrP-ASO interaction. Here, we examine the PrP-binding and antiprion properties of ASOs in vitro and in cell culture. Binding parameters determined by isothermal titration calorimetry were similar across all ASOs tested, indicating that ASOs of various chemistries bind full-length recombinant PrP with low- to mid-nanomolar affinity in a sequence-independent manner. Nuclear magnetic resonance, dynamic light scattering, and visual inspection of ASO-PrP mixtures suggested, however, that this interaction is characterized by the formation of large aggregates, a conclusion further supported by the salt dependence of the affinity measured by isothermal titration calorimetry. Sequence-independent inhibition of prion accumulation in cell culture was observed. The inefficacy of non-PrP-lowering ASOs against prion disease in vivo may be because their apparent activity in vitro is an artifact of aggregation, or because the concentration of ASOs in relevant compartments within the central nervous system (CNS) quickly drops below the effective concentration for sequence-independent antiprion activity after bolus dosing into CSF. Measurements of PrP concentration in human CSF were not impacted by the addition of ASO. These findings support the further development of PrP-lowering ASOs and of CSF PrP as a pharmacodynamic biomarker.
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Affiliation(s)
- Andrew G. Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (A.G.R.); (E.V.M.); (S.G.G.); (S.L.S.)
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric Vallabh Minikel
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (A.G.R.); (E.V.M.); (S.G.G.); (S.L.S.)
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Prion Alliance, Cambridge, MA 02139, USA
| | - Hien T. Zhao
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA; (H.T.Z.); (H.B.K.)
| | - Stacy G. Guzman
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (A.G.R.); (E.V.M.); (S.G.G.); (S.L.S.)
- Exceptional Research Opportunities Program (EXROP), Howard Hughes Medical Institute (HHMI), Chevy Chase, MD 20815, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alison J. Leed
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (A.J.L.); (M.F.M.)
| | - Michael F. Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (A.J.L.); (M.F.M.)
| | | | - Stuart L. Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (A.G.R.); (E.V.M.); (S.G.G.); (S.L.S.)
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sonia M. Vallabh
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; (A.G.R.); (E.V.M.); (S.G.G.); (S.L.S.)
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Prion Alliance, Cambridge, MA 02139, USA
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20
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Wu CC, Lin JL, Yang-Yen HF, Yuan HS. A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication. Nucleic Acids Res 2019; 47:5405-5419. [PMID: 30949702 PMCID: PMC6547421 DOI: 10.1093/nar/gkz241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/13/2019] [Accepted: 03/25/2019] [Indexed: 01/01/2023] Open
Abstract
Replication of sufficient mitochondrial DNA (mtDNA) is essential for maintaining mitochondrial functions in mammalian cells. During mtDNA replication, RNA primers must be removed before the nascent circular DNA strands rejoin. This process involves mitochondrial RNase H1, which removes most of the RNA primers but leaves two ribonucleotides attached to the 5′ end of nascent DNA. A subsequent 5′-exonuclease is required to remove the residual ribonucleotides, however, it remains unknown if any mitochondrial 5′-exonuclease could remove two RNA nucleotides from a hybrid duplex DNA. Here, we report that human mitochondrial Exonuclease G (ExoG) may participate in this particular process by efficiently cleaving at RNA–DNA junctions to remove the 5′-end RNA dinucleotide in an RNA/DNA hybrid duplex. Crystal structures of human ExoG bound respectively with DNA, RNA/DNA hybrid and RNA–DNA chimeric duplexes uncover the underlying structural mechanism of how ExoG specifically recognizes and cleaves at RNA–DNA junctions of a hybrid duplex with an A-form conformation. This study hence establishes the molecular basis of ExoG functioning as a unique 5′-exonuclease to mediate the flap-independent RNA primer removal process during mtDNA replication to maintain mitochondrial genome integrity.
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Affiliation(s)
- Chyuan-Chuan Wu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Jason L J Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hsin-Fang Yang-Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan 10048, ROC
- To whom correspondence should be addressed. Tel: +886 2 27884151;
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21
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Klim JR, Vance C, Scotter EL. Antisense oligonucleotide therapies for Amyotrophic Lateral Sclerosis: Existing and emerging targets. Int J Biochem Cell Biol 2019; 110:149-153. [PMID: 30904737 DOI: 10.1016/j.biocel.2019.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/04/2019] [Accepted: 03/20/2019] [Indexed: 12/14/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a disease with highly heterogenous causes, most of which remain unknown, a multitude of possible disease mechanisms, and no therapy currently available that can halt disease progression. However, recent advances in antisense oligonucleotides have made them a viable option for targeted therapeutics for patients. These molecules offer a method of targeting RNA that is highly specific, adaptable, and does not require viral delivery. Antisense oligonucleotides are therefore being developed for several genetic causes of ALS. Furthermore, biological pathways involved in the pathogenesis of disease also offer tantalizing targets for intervention using antisense oligonucleotides. Here we detail existing and potential targets for antisense oligonucleotides in ALS and briefly examine the requirements for these drugs to reach and be effective in clinic.
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Affiliation(s)
- Joseph R Klim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Caroline Vance
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RX, United Kingdom
| | - Emma L Scotter
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, 85 Park Rd, Grafton, Auckland, New Zealand.
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22
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Seth PP, Swayze EE. The Medicinal Chemistry of RNase H-activating Antisense Oligonucleotides. ADVANCES IN NUCLEIC ACID THERAPEUTICS 2019. [DOI: 10.1039/9781788015714-00032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review focuses on the properties that an RNase H-activating antisense oligonucleotide (ASO) drug must have to function effectively in animals, as well as on medicinal chemistry strategies to achieve these properties. The biochemistry and structural requirements for activating RNase H are briefly summarized, as well as chemical modifications that can effect activation of RNase H when an ASO is bound to target RNA. The key modifications available to the medicinal chemist to engineer desired properties of the ASO are briefly reviewed, as are ASO design strategies to achieve optimal activity in animal systems. Lastly, the interactions of ASOs with proteins and strategies to control these interactions to improve the profile of ASOs are discussed.
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Affiliation(s)
- Punit P. Seth
- Ionis Pharmaceuticals 2855 Gazelle Court Carlsbad CA 92010 USA
| | - Eric E. Swayze
- Ionis Pharmaceuticals 2855 Gazelle Court Carlsbad CA 92010 USA
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Posse V, Al-Behadili A, Uhler JP, Clausen AR, Reyes A, Zeviani M, Falkenberg M, Gustafsson CM. RNase H1 directs origin-specific initiation of DNA replication in human mitochondria. PLoS Genet 2019; 15:e1007781. [PMID: 30605451 PMCID: PMC6317783 DOI: 10.1371/journal.pgen.1007781] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/23/2018] [Indexed: 11/21/2022] Open
Abstract
Human mitochondrial DNA (mtDNA) replication is first initiated at the origin of H-strand replication. The initiation depends on RNA primers generated by transcription from an upstream promoter (LSP). Here we reconstitute this process in vitro using purified transcription and replication factors. The majority of all transcription events from LSP are prematurely terminated after ~120 nucleotides, forming stable R-loops. These nascent R-loops cannot directly prime mtDNA synthesis, but must first be processed by RNase H1 to generate 3′-ends that can be used by DNA polymerase γ to initiate DNA synthesis. Our findings are consistent with recent studies of a knockout mouse model, which demonstrated that RNase H1 is required for R-loop processing and mtDNA maintenance in vivo. Both R-loop formation and DNA replication initiation are stimulated by the mitochondrial single-stranded DNA binding protein. In an RNase H1 deficient patient cell line, the precise initiation of mtDNA replication is lost and DNA synthesis is initiated from multiple sites throughout the mitochondrial control region. In combination with previously published in vivo data, the findings presented here suggest a model, in which R-loop processing by RNase H1 directs origin-specific initiation of DNA replication in human mitochondria. Human mitochondria contain a double-stranded DNA genome that codes for key components of the oxidative phosphorylation system. The mitochondrial DNA (mtDNA) is replicated by a replication machinery distinct from that operating in the nucleus and mutations affecting individual replication factors have been associated with an array of rare, human diseases. In the present work, we demonstrate that RNase H1 directs origin-specific initiation of DNA replication in human mitochondria and that disease-causing mutations may impair this process. A unique feature of mtDNA replication is that primers required for initiation of leading-strand DNA replication are produced by the mitochondrial transcription machinery. A substantial fraction of all transcription events is prematurely terminated about 120 nucleotides downstream of the promoter and the RNA remains firmly associated with the genome, forming R-loops. Interestingly, the free 3′-end of these R-loops cannot directly prime initiation of DNA synthesis, but must first be processed by RNase H1. The process is stimulated by the mitochondrial single-stranded DNA binding protein and faithfully reconstitutes replication events mapped in vivo. In combination with mapping of replication events in fibroblasts derived from patients with mutations in RNASEH1, our findings point to a possible model for replication initiation in human mitochondria similar to that previously described in the E. coli plasmid, ColE1.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders R Clausen
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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24
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Al-Behadili A, Uhler JP, Berglund AK, Peter B, Doimo M, Reyes A, Wanrooij S, Zeviani M, Falkenberg M. A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL. Nucleic Acids Res 2018; 46:9471-9483. [PMID: 30102370 PMCID: PMC6182146 DOI: 10.1093/nar/gky708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/21/2018] [Accepted: 07/24/2018] [Indexed: 11/12/2022] Open
Abstract
The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates. The process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. We find that RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation, a conclusion which is supported by analysis of RNase H1-deficient patient cells. A second nuclease is therefore required to remove the last ribonucleotides and we demonstrate that Flap endonuclease 1 (FEN1) can execute this function in vitro. Removal of RNA primers at OriL thus depends on a two-nuclease model, which in addition to RNase H1 requires FEN1 or a FEN1-like activity. These findings define the role of RNase H1 at OriL and help to explain the pathogenic consequences of disease causing mutations in RNase H1.
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Affiliation(s)
- Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Anna-Karin Berglund
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Aurelio Reyes
- MRC-Mitochondrial Biology Unit, University of Cambridge, MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
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25
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Influence of mismatched and bulged nucleotides on SNP-preferential RNase H cleavage of RNA-antisense gapmer heteroduplexes. Sci Rep 2017; 7:12532. [PMID: 28970564 PMCID: PMC5624880 DOI: 10.1038/s41598-017-12844-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/11/2017] [Indexed: 12/15/2022] Open
Abstract
This study focused on determining design rules for gapmer-type antisense oligonucleotides (ASOs), that can differentiate cleavability of two SNP variants of RNA in the presence of ribonuclease H based on the mismatch type and position in the heteroduplex. We describe the influence of structural motifs formed by several arrangements of multiple mismatches (various types of mismatches and their position within the ASO/target RNA duplex) on RNase H cleavage selectivity of five different SNP types. The targets were mRNA fragments of APP, SCA3, SNCA and SOD1 genes, carrying C-to-G, G-to-C, G-to-A, A-to-G and C-to-U substitutions. The results show that certain arrangements of mismatches enhance discrimination between wild type and mutant SNP alleles of RNA in vitro as well as in HeLa cells. Among the over 120 gapmers tested, we found two gapmers that caused preferential degradation of the mutant allele APP 692 G and one that led to preferential cleavage of the mutant SNCA 53 A allele, both in vitro and in cells. However, several gapmers promoted selective cleavage of mRNA mutant alleles in in vitro experiments only.
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26
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Iwamoto N, Butler DCD, Svrzikapa N, Mohapatra S, Zlatev I, Sah DWY, Meena, Standley SM, Lu G, Apponi LH, Frank-Kamenetsky M, Zhang JJ, Vargeese C, Verdine GL. Control of phosphorothioate stereochemistry substantially increases the efficacy of antisense oligonucleotides. Nat Biotechnol 2017; 35:845-851. [PMID: 28829437 DOI: 10.1038/nbt.3948] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/26/2017] [Indexed: 12/26/2022]
Abstract
Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to separate the individual stereoisomers, nor to synthesize stereochemically pure ASOs. Here we report the development of a scalable synthetic process that yields therapeutic ASOs having high stereochemical and chemical purity. Using this method, we synthesized rationally designed stereopure components of mipomersen, a drug comprising 524,288 stereoisomers. We demonstrate that phosphorothioate (PS) stereochemistry substantially affects the pharmacologic properties of ASOs. We report that Sp-configured PS linkages are stabilized relative to Rp, providing stereochemical protection from pharmacologic inactivation of the drug. Further, we elucidated a triplet stereochemical code in the stereopure ASOs, 3'-SpSpRp, that promotes target RNA cleavage by RNase H1 in vitro and provides a more durable response in mice than stereorandom ASOs.
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Affiliation(s)
| | | | | | | | - Ivan Zlatev
- Wave Life Sciences, Cambridge, Massachusetts, USA
| | | | - Meena
- Wave Life Sciences, Cambridge, Massachusetts, USA
| | | | - Genliang Lu
- Wave Life Sciences, Cambridge, Massachusetts, USA
| | | | | | | | | | - Gregory L Verdine
- Wave Life Sciences, Cambridge, Massachusetts, USA.,Department of Stem Cell and Regenerative Biology, Department of Chemistry and Chemical Biology, Harvard University and Harvard Medical School, Cambridge, Massachusetts, USA
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27
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Hagedorn PH, Hansen BR, Koch T, Lindow M. Managing the sequence-specificity of antisense oligonucleotides in drug discovery. Nucleic Acids Res 2017; 45:2262-2282. [PMID: 28426096 PMCID: PMC5389529 DOI: 10.1093/nar/gkx056] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 01/21/2017] [Indexed: 01/06/2023] Open
Abstract
All drugs perturb the expression of many genes in the cells that are exposed to them. These gene expression changes can be divided into effects resulting from engaging the intended target and effects resulting from engaging unintended targets. For antisense oligonucleotides, developments in bioinformatics algorithms, and the quality of sequence databases, allow oligonucleotide sequences to be analyzed computationally, in terms of the predictability of their interactions with intended and unintended RNA targets. Applying these tools enables selection of sequence-specific oligonucleotides where no- or only few unintended RNA targets are expected. To evaluate oligonucleotide sequence-specificity experimentally, we recommend a transcriptomics protocol where two or more oligonucleotides targeting the same RNA molecule, but with entirely different sequences, are evaluated together. This helps to clarify which changes in cellular RNA levels result from downstream processes of engaging the intended target, and which are likely to be related to engaging unintended targets. As required for all classes of drugs, the toxic potential of oligonucleotides must be evaluated in cell- and animal models before clinical testing. Since potential adverse effects related to unintended targeting are sequence-dependent and therefore species-specific, in vitro toxicology assays in human cells are especially relevant in oligonucleotide drug discovery.
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Affiliation(s)
- Peter H Hagedorn
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Bo R Hansen
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Troels Koch
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark
| | - Morten Lindow
- Roche Pharmaceutical Discovery and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm 2970, Denmark.,Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark.,The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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28
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Patro LPP, Kumar A, Kolimi N, Rathinavelan T. 3D-NuS: A Web Server for Automated Modeling and Visualization of Non-Canonical 3-Dimensional Nucleic Acid Structures. J Mol Biol 2017; 429:2438-2448. [PMID: 28652006 DOI: 10.1016/j.jmb.2017.06.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 06/15/2017] [Accepted: 06/15/2017] [Indexed: 10/19/2022]
Abstract
The inherent conformational flexibility of nucleic acids facilitates the formation of a range of conformations such as duplex, triplex, quadruplex, etc. that play crucial roles in biological processes. Elucidation of the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand the mismatch repair, misregulation of alternative splicing mechanisms and the sequence-dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information. Furthermore, structural insights about nucleic acid triplexes, which are generally not tractable to structure determination by X-ray crystallography or NMR techniques, are essential to establish their biological function(s). A web server, namely 3D-NuS (http://iith.ac.in/3dnus/), has been developed to generate energy-minimized models of 80 different types of triplexes, 64 types of G-quadruplexes, left-handed Z-DNA/RNA duplexes, and RNA-DNA hybrid duplex along with inter- and intramolecular DNA or RNA duplexes comprising a variety of mismatches and their chimeric forms for any user-defined sequence and length. It also generates an ensemble of conformations corresponding to the modeled structure. These structures may serve as good starting models for docking proteins and small molecules with nucleic acids, NMR structure determination, cryo-electron microscope modeling, DNA/RNA nanotechnology applications and molecular dynamics simulation studies.
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Affiliation(s)
- L Ponoop Prasad Patro
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Abhishek Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
| | - Narendar Kolimi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State 502285, India
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29
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Islam MA, Waki R, Fujisaka A, Ito KR, Obika S. In vitro and in vivo biophysical properties of oligonucleotides containing 5'-thio nucleosides. Drug Discov Ther 2017; 10:263-270. [PMID: 27890900 DOI: 10.5582/ddt.2016.01055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Phosphorothioate modification is one of the most widely investigated and promising chemical modifications in oligonucleotide (ON) based therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which a 5'-bridging oxygen is replaced with a sulfur atom, are gaining importance for ON-based research. Several reports have been published describing the synthesis of 5'-thio-modified ONs but no detailed in vitro and in vivo data are available. Here, we report the synthesis of 5'-thio-modified 2'-deoxy-5-methylcytidine. 5'-Thio-modified thymidine and 2'-deoxy-5-methylcytidine were incorporated into target ONs, then we evaluated their binding affinity, nuclease stability, RNase H mediated scission, stability in blood serum, and in vitro and in vivo activity. This is the first report showing the influence of 5'-thio-modified antisense ONs in in vitro and in vivo experiments.
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Affiliation(s)
- Md Ariful Islam
- Graduate School of Pharmaceutical Sciences, Osaka University
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30
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Crooke ST. Molecular Mechanisms of Antisense Oligonucleotides. Nucleic Acid Ther 2017; 27:70-77. [PMID: 28080221 PMCID: PMC5372764 DOI: 10.1089/nat.2016.0656] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/14/2016] [Indexed: 12/12/2022] Open
Abstract
In 1987, when I became interested in the notion of antisense technology, I returned to my roots in RNA biochemistry and began work to understand how oligonucleotides behave in biological systems. Since 1989, my research has focused primarily on this topic, although I have been involved in most areas of research in antisense technology. I believe that the art of excellent science is to frame large important questions that are perhaps not immediately answerable with existing knowledge and methods, and then conceive a long-term (multiyear) research strategy that begins by answering the most pressing answerable questions on the path to the long-term goals. Then, a step-by-step research pathway that will address the strategic questions posed must be implemented, adjusting the plan as new things are learned. This is the approach we have taken at Ionis. Obviously, to create antisense technology, we have had to address a wide array of strategic questions, for example, the medicinal chemistry of oligonucleotides, manufacturing and analytical methods, pharmacokinetics and toxicology, as well as questions about the molecular pharmacology of antisense oligonucleotides (ASOs). Each of these endeavors has consumed nearly three decades of scientific effort, is still very much a work-in-progress, and has resulted in hundreds of publications. As a recipient of the Lifetime Achievement Award 2016 granted by the Oligonucleotide Therapeutic Society, in this note, my goal is to summarize the contributions of my group to the efforts to understand the molecular mechanisms of ASOs.
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Affiliation(s)
- Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. , Carlsbad, California
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31
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Modified Antisense Oligonucleotides and Their Analogs in Therapy of Neuromuscular Diseases. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-34175-0_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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32
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Ribonuclease H1-dependent hepatotoxicity caused by locked nucleic acid-modified gapmer antisense oligonucleotides. Sci Rep 2016; 6:30377. [PMID: 27461380 PMCID: PMC4961955 DOI: 10.1038/srep30377] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/30/2016] [Indexed: 12/16/2022] Open
Abstract
Gapmer antisense oligonucleotides cleave target RNA effectively in vivo, and is considered as promising therapeutics. Especially, gapmers modified with locked nucleic acid (LNA) shows potent knockdown activity; however, they also cause hepatotoxic side effects. For developing safe and effective gapmer drugs, a deeper understanding of the mechanisms of hepatotoxicity is required. Here, we investigated the cause of hepatotoxicity derived from LNA-modified gapmers. Chemical modification of gapmer’s gap region completely suppressed both knockdown activity and hepatotoxicity, indicating that the root cause of hepatotoxicity is related to intracellular gapmer activity. Gene silencing of hepatic ribonuclease H1 (RNaseH1), which catalyses gapmer-mediated RNA knockdown, strongly supressed hepatotoxic effects. Small interfering RNA (siRNA)-mediated knockdown of a target mRNA did not result in any hepatotoxic effects, while the gapmer targeting the same position on mRNA as does the siRNA showed acute toxicity. Microarray analysis revealed that several pre-mRNAs containing a sequence similar to the gapmer target were also knocked down. These results suggest that hepatotoxicity of LNA gapmer is caused by RNAseH1 activity, presumably because of off-target cleavage of RNAs inside nuclei.
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33
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Uhler JP, Thörn C, Nicholls TJ, Matic S, Milenkovic D, Gustafsson CM, Falkenberg M. MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication. Nucleic Acids Res 2016; 44:5861-71. [PMID: 27220468 PMCID: PMC4937333 DOI: 10.1093/nar/gkw468] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 12/17/2022] Open
Abstract
Recently, MGME1 was identified as a mitochondrial DNA nuclease with preference for single-stranded DNA (ssDNA) substrates. Loss-of-function mutations in patients lead to mitochondrial disease with DNA depletion, deletions, duplications and rearrangements. Here, we assess the biochemical role of MGME1 in the processing of flap intermediates during mitochondrial DNA replication using reconstituted systems. We show that MGME1 can cleave flaps to enable efficient ligation of newly replicated DNA strands in combination with POLγ. MGME1 generates a pool of imprecisely cut products (short flaps, nicks and gaps) that are converted to ligatable nicks by POLγ through extension or excision of the 3'-end strand. This is dependent on the 3'-5' exonuclease activity of POLγ which limits strand displacement activity and enables POLγ to back up to the nick by 3'-5' degradation. We also demonstrate that POLγ-driven strand displacement is sufficient to generate DNA- but not RNA-flap substrates suitable for MGME1 cleavage and ligation during replication. Our findings have implications for RNA primer removal models, the 5'-end processing of nascent DNA at OriH, and DNA repair.
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Affiliation(s)
- Jay P Uhler
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Christian Thörn
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Thomas J Nicholls
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Stanka Matic
- Max Planck Institute for Biology of Ageing, 50391 Cologne, Germany
| | | | - Claes M Gustafsson
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Maria Falkenberg
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
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34
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Burel SA, Hart CE, Cauntay P, Hsiao J, Machemer T, Katz M, Watt A, Bui HH, Younis H, Sabripour M, Freier SM, Hung G, Dan A, Prakash TP, Seth PP, Swayze EE, Bennett CF, Crooke ST, Henry SP. Hepatotoxicity of high affinity gapmer antisense oligonucleotides is mediated by RNase H1 dependent promiscuous reduction of very long pre-mRNA transcripts. Nucleic Acids Res 2015; 44:2093-109. [PMID: 26553810 PMCID: PMC4797265 DOI: 10.1093/nar/gkv1210] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/27/2015] [Indexed: 12/24/2022] Open
Abstract
High affinity antisense oligonucleotides (ASOs) containing bicylic modifications (BNA) such as locked nucleic acid (LNA) designed to induce target RNA cleavage have been shown to have enhanced potency along with a higher propensity to cause hepatotoxicity. In order to understand the mechanism of this hepatotoxicity, transcriptional profiles were collected from the livers of mice treated with a panel of highly efficacious hepatotoxic or non-hepatotoxic LNA ASOs. We observed highly selective transcript knockdown in mice treated with non-hepatotoxic LNA ASOs, while the levels of many unintended transcripts were reduced in mice treated with hepatotoxic LNA ASOs. This transcriptional signature was concurrent with on-target RNA reduction and preceded transaminitis. Remarkably, the mRNA transcripts commonly reduced by toxic LNA ASOs were generally not strongly associated with any particular biological process, cellular component or functional group. However, they tended to have much longer pre-mRNA transcripts. We also demonstrate that the off-target RNA knockdown and hepatotoxicity is attenuated by RNase H1 knockdown, and that this effect can be generalized to high affinity modifications beyond LNA. This suggests that for a certain set of ASOs containing high affinity modifications such as LNA, hepatotoxicity can occur as a result of unintended off-target RNase H1 dependent RNA degradation.
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Affiliation(s)
| | | | | | - Jill Hsiao
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | | | | | - Andy Watt
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | | | | | | | | | - Gene Hung
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | - Amy Dan
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
| | - T P Prakash
- Isis Pharmaceuticals, Carlsbad, CA 921010, USA
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35
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Zong X, Huang L, Tripathi V, Peralta R, Freier SM, Guo S, Prasanth KV. Knockdown of nuclear-retained long noncoding RNAs using modified DNA antisense oligonucleotides. Methods Mol Biol 2015; 1262:321-31. [PMID: 25555591 DOI: 10.1007/978-1-4939-2253-6_20] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Long noncoding RNAs (lncRNAs) have recently emerged as important players in diverse cellular processes. Among them, a large fraction of lncRNAs are localized within cell nucleus. And several of these nuclear-retained lncRNAs have been found to regulate key nuclear processes, which brings up the requirement of effective genetic tools to explore the functions of this "dark matter" inside the nucleus. While siRNAs and shRNAs are widely used tools in loss-of-function studies, their general efficiency in depleting nuclear-retained lncRNAs is limited, due to the fact that the RNAi machinery is located mainly in the cytoplasm of mammalian cells. Here, we describe the usage of chemically modified chimeric DNA antisense oligonucleotides (ASO) in effective knockdown of nuclear-retained lncRNAs, with a focus on the detailed workflow from the design and synthesis of ASOs, to in vitro and in vivo delivery methods.
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Affiliation(s)
- Xinying Zong
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Room, C426, Chem. and Life Sci. Building, 601S Goodwin Avenue, Urbana-Champaign, IL, 61801, USA
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36
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Primer removal during mammalian mitochondrial DNA replication. DNA Repair (Amst) 2015; 34:28-38. [PMID: 26303841 DOI: 10.1016/j.dnarep.2015.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 12/17/2022]
Abstract
The small circular mitochondrial genome in mammalian cells is replicated by a dedicated replisome, defects in which can cause mitochondrial disease in humans. A fundamental step in mitochondrial DNA (mtDNA) replication and maintenance is the removal of the RNA primers needed for replication initiation. The nucleases RNase H1, FEN1, DNA2, and MGME1 have been implicated in this process. Here we review the role of these nucleases in the light of primer removal pathways in mitochondria, highlight associations with disease, as well as consider the implications for mtDNA replication initiation.
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37
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Nishina K, Piao W, Yoshida-Tanaka K, Sujino Y, Nishina T, Yamamoto T, Nitta K, Yoshioka K, Kuwahara H, Yasuhara H, Baba T, Ono F, Miyata K, Miyake K, Seth PP, Low A, Yoshida M, Bennett CF, Kataoka K, Mizusawa H, Obika S, Yokota T. DNA/RNA heteroduplex oligonucleotide for highly efficient gene silencing. Nat Commun 2015; 6:7969. [PMID: 26258894 PMCID: PMC4918363 DOI: 10.1038/ncomms8969] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 07/01/2015] [Indexed: 12/13/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are recognized therapeutic agents for the modulation of specific genes at the post-transcriptional level. Similar to any medical drugs, there are opportunities to improve their efficacy and safety. Here we develop a short DNA/RNA heteroduplex oligonucleotide (HDO) with a structure different from double-stranded RNA used for short interfering RNA and single-stranded DNA used for ASO. A DNA/locked nucleotide acid gapmer duplex with an α-tocopherol-conjugated complementary RNA (Toc-HDO) is significantly more potent at reducing the expression of the targeted mRNA in liver compared with the parent single-stranded gapmer ASO. Toc-HDO also improves the phenotype in disease models more effectively. In addition, the high potency of Toc-HDO results in a reduction of liver dysfunction observed in the parent ASO at a similar silencing effect. HDO technology offers a novel concept of therapeutic oligonucleotides, and the development of this molecular design opens a new therapeutic field.
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Affiliation(s)
- Kazutaka Nishina
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Wenying Piao
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yumiko Sujino
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Tomoko Nishina
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Tsuyoshi Yamamoto
- Bioorganic Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Keiko Nitta
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Hiroya Kuwahara
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Hidenori Yasuhara
- Bioorganic Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Takeshi Baba
- Bioorganic Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Fumiko Ono
- The Corporation for Production and Research of Laboratory Primates, 1-16-2 Sakura, Tsukuba-shi, Ibaraki 305-0003, Japan
| | - Kanjiro Miyata
- Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koichi Miyake
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
| | - Punit P. Seth
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, USA
| | - Audrey Low
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, USA
| | - Masayuki Yoshida
- Department of Life Science and Medical Ethics, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - C. Frank Bennett
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, USA
| | - Kazunori Kataoka
- Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hidehiro Mizusawa
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Satoshi Obika
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
- Bioorganic Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
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38
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Rukov JL, Hagedorn PH, Høy IB, Feng Y, Lindow M, Vinther J. Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs. Nucleic Acids Res 2015. [PMID: 26220183 PMCID: PMC4787823 DOI: 10.1093/nar/gkv759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Processing and post-transcriptional regulation of RNA often depend on binding of regulatory molecules to short motifs in RNA. The effects of such interactions are difficult to study, because most regulatory molecules recognize partially degenerate RNA motifs, embedded in a sequence context specific for each RNA. Here, we describe Library Sequencing (LibSeq), an accurate massively parallel reporter method for completely characterizing the regulatory potential of thousands of short RNA sequences in a specific context. By sequencing cDNA derived from a plasmid library expressing identical reporter genes except for a degenerate 7mer subsequence in the 3′UTR, the regulatory effects of each 7mer can be determined. We show that LibSeq identifies regulatory motifs used by RNA-binding proteins and microRNAs. We furthermore apply the method to cells transfected with RNase H recruiting oligonucleotides to obtain quantitative information for >15000 potential target sequences in parallel. These comprehensive datasets provide insights into the specificity requirements of RNase H and allow a specificity measure to be calculated for each tested oligonucleotide. Moreover, we show that inclusion of chemical modifications in the central part of an RNase H recruiting oligonucleotide can increase its sequence-specificity.
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Affiliation(s)
- Jakob Lewin Rukov
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Peter H Hagedorn
- Roche Pharmaceutical Discovery and Early Development, Roche Innovation Center Copenhagen A/S, Fremtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Isabel Bro Høy
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Yanping Feng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, P.R. China
| | - Morten Lindow
- Roche Pharmaceutical Discovery and Early Development, Roche Innovation Center Copenhagen A/S, Fremtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Jeppe Vinther
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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39
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Østergaard ME, Thomas G, Koller E, Southwell AL, Hayden MR, Seth PP. Biophysical and biological characterization of hairpin and molecular beacon RNase H active antisense oligonucleotides. ACS Chem Biol 2015; 10:1227-33. [PMID: 25654188 DOI: 10.1021/cb500880f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Antisense oligonucleotides (ASOs) are single stranded, backbone modified nucleic acids, which mediate cleavage of complementary RNA by directing RNase H cleavage in cell culture and in animals. It has generally been accepted that the single stranded state in conjunction with the phosphorothioate modified backbone is necessary for cellular uptake and transport to the active compartment. Herein, we examine the effect of using hairpin structured ASOs to (1) determine if an ASO agent requires a single stranded conformation for efficient RNA knock down, (2) use a fluorophore-quencher labeled ASO to evaluate which moieties the ASO interacts with in cells and examine if cellular distribution can be determined with such probes, and (3) evaluate if self-structured ASOs can improve allele selective silencing between closely related huntingtin alleles. We show that hairpin shaped ASOs can efficiently down-regulate RNA in vitro, but potency correlates strongly negatively with increasing stability of the hairpin structure. Furthermore, self-structured ASOs can efficiently reduce huntingtin mRNA in the central nervous system of mice.
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Affiliation(s)
| | - George Thomas
- Isis Pharmaceuticals, 2855
Gazelle Court, Carlsbad, California, United States
| | - Erich Koller
- Isis Pharmaceuticals, 2855
Gazelle Court, Carlsbad, California, United States
| | - Amber L. Southwell
- Centre
for Molecular Medicine and Therapeutics, Child and Family Research
Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Michael R. Hayden
- Centre
for Molecular Medicine and Therapeutics, Child and Family Research
Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Punit P. Seth
- Isis Pharmaceuticals, 2855
Gazelle Court, Carlsbad, California, United States
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40
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Minias AE, Brzostek AM, Korycka- Machala M, Dziadek B, Minias P, Rajagopalan M, Madiraju M, Dziadek J. RNase HI Is Essential for Survival of Mycobacterium smegmatis. PLoS One 2015; 10:e0126260. [PMID: 25965344 PMCID: PMC4429107 DOI: 10.1371/journal.pone.0126260] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 03/31/2015] [Indexed: 12/21/2022] Open
Abstract
RNases H are involved in the removal of RNA from RNA/DNA hybrids. Type I RNases H are thought to recognize and cleave the RNA/DNA duplex when at least four ribonucleotides are present. Here we investigated the importance of RNase H type I encoding genes for model organism Mycobacterium smegmatis. By performing gene replacement through homologous recombination, we demonstrate that each of the two presumable RNase H type I encoding genes, rnhA and MSMEG4305, can be removed from M. smegmatis genome without affecting the growth rate of the mutant. Further, we demonstrate that deletion of both RNases H type I encoding genes in M. smegmatis leads to synthetic lethality. Finally, we question the possibility of existence of RNase HI related alternative mode of initiation of DNA replication in M. smegmatis, the process initially discovered in Escherichia coli. We suspect that synthetic lethality of double mutant lacking RNases H type I is caused by formation of R-loops leading to collapse of replication forks. We report Mycobacterium smegmatis as the first bacterial species, where function of RNase H type I has been found essential.
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Affiliation(s)
- Alina E. Minias
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- * E-mail: (AM); (JD)
| | - Anna M. Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | | | - Bozena Dziadek
- Department of Immunoparasitology, University of Lodz, Lodz, Poland
| | - Piotr Minias
- Department of Teacher Training and Biodiversity Studies, University of Lodz, Lodz, Poland
| | - Malini Rajagopalan
- Department of Microbiology, University of Texas Health Center at Tyler, Tyler, Texas, United States of America
| | - Murty Madiraju
- Department of Microbiology, University of Texas Health Center at Tyler, Tyler, Texas, United States of America
| | - Jaroslaw Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- * E-mail: (AM); (JD)
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41
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Wan WB, Migawa MT, Vasquez G, Murray HM, Nichols JG, Gaus H, Berdeja A, Lee S, Hart CE, Lima WF, Swayze EE, Seth PP. Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages. Nucleic Acids Res 2014; 42:13456-68. [PMID: 25398895 PMCID: PMC4267618 DOI: 10.1093/nar/gku1115] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 12/19/2022] Open
Abstract
Bicyclic oxazaphospholidine monomers were used to prepare a series of phosphorothioate (PS)-modified gapmer antisense oligonucleotides (ASOs) with control of the chirality of each of the PS linkages within the 10-base gap. The stereoselectivity was determined to be 98% for each coupling. The objective of this work was to study how PS chirality influences biophysical and biological properties of the ASO including binding affinity (Tm), nuclease stability, activity in vitro and in vivo, RNase H activation and cleavage patterns (both human and E. coli) in a gapmer context. Compounds that had nine or more Sp-linkages in the gap were found to be poorly active in vitro, while compounds with uniform Rp-gaps exhibited activity very similar to that of the stereo-random parent ASOs. Conversely, when tested in vivo, the full Rp-gap compound was found to be quickly metabolized resulting in low activity. A total of 31 ASOs were prepared with control of the PS chirally of each linkage within the gap in an attempt to identify favorable Rp/Sp positions. We conclude that a mix of Rp and Sp is required to achieve a balance between good activity and nuclease stability.
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Affiliation(s)
- W Brad Wan
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Michael T Migawa
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Guillermo Vasquez
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Heather M Murray
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Josh G Nichols
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Hans Gaus
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Andres Berdeja
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Sam Lee
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | | | - Walt F Lima
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Isis Pharmaceuticals, Inc., 2855 Gazelle Ct, Carlsbad, CA 92010, USA
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42
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Antisense oligonucleotides capable of promoting specific target mRNA reduction via competing RNase H1-dependent and independent mechanisms. PLoS One 2014; 9:e108625. [PMID: 25299183 PMCID: PMC4191969 DOI: 10.1371/journal.pone.0108625] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/03/2014] [Indexed: 11/19/2022] Open
Abstract
Antisense oligonucleotides (ASOs) are most commonly designed to reduce targeted RNA via RNase H1-dependent degradation. In this paper we demonstrate that cellular proteins can compete for sites targeted by RNase H1-dependent ASOs. We further show that some ASOs designed to mediate RNase H1 cleavage can, in certain instances, promote target reduction both by RNase H1-mediated cleavage and by steric inhibition of binding of splicing factors at a site required for efficient processing of the pre-mRNA. In the latter case, RNase H cleavage was prevented by binding of a second protein, HSPA8, to the ASO/pre-mRNA heteroduplex. In addition, using a precisely controlled minigene system, we directly demonstrated that activity of ASOs targeting sites in introns is strongly influenced by splicing efficiency.
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43
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Yamamoto T, Fujii N, Yasuhara H, Wada S, Wada F, Shigesada N, Harada-Shiba M, Obika S. Evaluation of multiple-turnover capability of locked nucleic acid antisense oligonucleotides in cell-free RNase H-mediated antisense reaction and in mice. Nucleic Acid Ther 2014; 24:283-90. [PMID: 24758560 DOI: 10.1089/nat.2013.0470] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The multiple-turnover ability of a series of locked nucleic acid (LNA)-based antisense oligonucleotides (AONs) in the RNase H-mediated scission reaction was estimated using a newly developed cell-free reaction system. We determined the initial reaction rates of AONs under multiple-turnover conditions and found that among 24 AONs tested, AONs with melting temperatures (Tm) of 40°C-60°C efficiently elicit multiple rounds of RNA scission. On the other hand, by measuring Tm with two 10-mer RNAs partially complementary to AONs as models of cleaved 5' and 3' fragments of mRNA, we found that AONs require adequate binding affinity for efficient turnover activities. We further demonstrated that the efficacy of a set of 13-mer AONs in mice correlated with their turnover efficiency, indicating that the intracellular situation where AONs function is similar to multiple-turnover conditions. Our methodology and findings may provide an opportunity to shed light on a previously unknown antisense mechanism, leading to further improvement of the activity and safety profiles of AONs.
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Affiliation(s)
- Tsuyoshi Yamamoto
- 1 Graduate School of Pharmaceutical Sciences, Osaka University , Suita, Osaka, Japan
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44
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Šipova H, Špringer T, Rejman D, Šimak O, Petrová M, Novák P, Rosenbergová Š, Páv O, Liboska R, Barvík I, Štěpanek J, Rosenberg I, Homola J. 5'-O-Methylphosphonate nucleic acids--new modified DNAs that increase the Escherichia coli RNase H cleavage rate of hybrid duplexes. Nucleic Acids Res 2014; 42:5378-89. [PMID: 24523351 PMCID: PMC4005664 DOI: 10.1093/nar/gku125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Several oligothymidylates containing various ratios of phosphodiester and isopolar 5'-hydroxyphosphonate, 5'-O-methylphosphonate and 3'-O-methylphosphonate internucleotide linkages were examined with respect to their hybridization properties with oligoriboadenylates and their ability to induce RNA cleavage by ribonuclease H (RNase H). The results demonstrated that the increasing number of 5'-hydroxyphosphonate or 5'-O-methylphosphonate units in antisense oligonucleotides (AOs) significantly stabilizes the heteroduplexes, whereas 3'-O-methylphosphonate AOs cause strong destabilization of the heteroduplexes. Only the heteroduplexes with 5'-O-methylphosphonate units in the antisense strand exhibited a significant increase in Escherichia coli RNase H cleavage activity by up to 3-fold (depending on the ratio of phosphodiester and phosphonate linkages) in comparison with the natural heteroduplex. A similar increase in RNase H cleavage activity was also observed for heteroduplexes composed of miRNA191 and complementary AOs containing 5'-O-methylphosphonate units. We propose for this type of AOs, working via the RNase H mechanism, the abbreviation MEPNA (MEthylPhosphonate Nucleic Acid).
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Affiliation(s)
- Hana Šipova
- Institute of Photonics and Electronics AS CR, v.v.i., Chaberská 57, 182 51 Prague, Czech Republic, Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2., 166 10 Prague, Czech Republic and Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague, Czech Republic
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45
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Therapeutic applications of anti-sense mechanisms for the treatment of cancer. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.085] [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] Open
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46
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Hu Y, Cheng X, Cao F, Huang A, Tavis JE. β-Thujaplicinol inhibits hepatitis B virus replication by blocking the viral ribonuclease H activity. Antiviral Res 2013; 99:221-9. [DOI: 10.1016/j.antiviral.2013.06.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 12/16/2022]
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47
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Østergaard ME, Southwell AL, Kordasiewicz H, Watt AT, Skotte NH, Doty CN, Vaid K, Villanueva EB, Swayze EE, Bennett CF, Hayden MR, Seth PP. Rational design of antisense oligonucleotides targeting single nucleotide polymorphisms for potent and allele selective suppression of mutant Huntingtin in the CNS. Nucleic Acids Res 2013; 41:9634-50. [PMID: 23963702 PMCID: PMC3834808 DOI: 10.1093/nar/gkt725] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Autosomal dominant diseases such as Huntington’s disease (HD) are caused by a gain of function mutant protein and/or RNA. An ideal treatment for these diseases is to selectively suppress expression of the mutant allele while preserving expression of the wild-type variant. RNase H active antisense oligonucleotides (ASOs) or small interfering RNAs can achieve allele selective suppression of gene expression by targeting single nucleotide polymorphisms (SNPs) associated with the repeat expansion. ASOs have been previously shown to discriminate single nucleotide changes in targeted RNAs with ∼5-fold selectivity. Based on RNase H enzymology, we enhanced single nucleotide discrimination by positional incorporation of chemical modifications within the oligonucleotide to limit RNase H cleavage of the non-targeted transcript. The resulting oligonucleotides demonstrate >100-fold discrimination for a single nucleotide change at an SNP site in the disease causing huntingtin mRNA, in patient cells and in a completely humanized mouse model of HD. The modified ASOs were also well tolerated after injection into the central nervous system of wild-type animals, suggesting that their tolerability profile is suitable for advancement as potential allele-selective HD therapeutics. Our findings lay the foundation for efficient allele-selective downregulation of gene expression using ASOs—an outcome with broad application to HD and other dominant genetic disorders.
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Affiliation(s)
- Michael E Østergaard
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA and Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, V5Z 4H4, Canada
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48
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Abstract
Adequate therapies are lacking for Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and other neurodegenerative diseases. The ability to use antisense oligonucleotides (ASOs) to target disease-associated genes by means of RNA may offer a potent approach for the treatment of these, and other, neurodegenerative disorders. In modifying the basic backbone chemistry, chemical groups, and target sequence, ASOs can act through numerous mechanisms to decrease or increase total protein levels, preferentially shift splicing patterns, and inhibit microRNAs, all at the level of the RNA molecule. Here, we discuss many of the more commonly used ASO chemistries, as well as the different mechanisms of action that can result from these specific chemical modifications. When applied to multiple neurodegenerative mouse models, ASOs that specifically target the detrimental transgenes have been shown to rescue disease associated phenotypes in vivo. These supporting mouse model data have moved the ASOs from the bench to the clinic, with two neuro-focused human clinical trials now underway and several more being proposed. Although still early in development, translating ASOs into human patients for neurodegeneration appears promising.
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Affiliation(s)
- Sarah L. DeVos
- Department of Neurology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
| | - Timothy M. Miller
- Department of Neurology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110 USA
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49
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Wahlestedt C. Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov 2013; 12:433-46. [DOI: 10.1038/nrd4018] [Citation(s) in RCA: 396] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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50
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The hepatitis B virus ribonuclease H is sensitive to inhibitors of the human immunodeficiency virus ribonuclease H and integrase enzymes. PLoS Pathog 2013; 9:e1003125. [PMID: 23349632 PMCID: PMC3551811 DOI: 10.1371/journal.ppat.1003125] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 11/27/2012] [Indexed: 12/26/2022] Open
Abstract
Nucleos(t)ide analog therapy blocks DNA synthesis by the hepatitis B virus (HBV) reverse transcriptase and can control the infection, but treatment is life-long and has high costs and unpredictable long-term side effects. The profound suppression of HBV by the nucleos(t)ide analogs and their ability to cure some patients indicates that they can push HBV to the brink of extinction. Consequently, more patients could be cured by suppressing HBV replication further using a new drug in combination with the nucleos(t)ide analogs. The HBV ribonuclease H (RNAseH) is a logical drug target because it is the second of only two viral enzymes that are essential for viral replication, but it has not been exploited, primarily because it is very difficult to produce active enzyme. To address this difficulty, we expressed HBV genotype D and H RNAseHs in E. coli and enriched the enzymes by nickel-affinity chromatography. HBV RNAseH activity in the enriched lysates was characterized in preparation for drug screening. Twenty-one candidate HBV RNAseH inhibitors were identified using chemical structure-activity analyses based on inhibitors of the HIV RNAseH and integrase. Twelve anti-RNAseH and anti-integrase compounds inhibited the HBV RNAseH at 10 µM, the best compounds had low micromolar IC50 values against the RNAseH, and one compound inhibited HBV replication in tissue culture at 10 µM. Recombinant HBV genotype D RNAseH was more sensitive to inhibition than genotype H. This study demonstrates that recombinant HBV RNAseH suitable for low-throughput antiviral drug screening has been produced. The high percentage of compounds developed against the HIV RNAseH and integrase that were active against the HBV RNAseH indicates that the extensive drug design efforts against these HIV enzymes can guide anti-HBV RNAseH drug discovery. Finally, differential inhibition of HBV genotype D and H RNAseHs indicates that viral genetic variability will be a factor during drug development. Current therapy for HBV blocks DNA synthesis by the viral reverse transcriptase and can control the infection indefinitely, but treatment rarely cures patients. More patients could be cured by suppressing HBV replication further using a new drug in combination with the existing ones. The HBV RNAseH is a logical drug target because it is the second of only two viral enzymes that are essential for viral replication, but it has not been exploited, primarily because it is very difficult to produce active enzyme. We expressed active recombinant HBV RNAseHs and demonstrated that it was suitable for antiviral drug screening. Twenty-one candidate HBV RNAseH inhibitors were identified based on antagonists of the HIV RNAseH and integrase enzymes. Twelve of these compounds inhibited the HBV RNAseH in enzymatic assays, and one inhibited HBV replication in cell-based assays. The high percentage of compounds developed against the HIV RNAseH and integrase that were also active against the HBV RNAseH indicates that the extensive drug design efforts against these HIV enzymes can be used to guide anti-HBV RNAseH drug discovery.
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