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Lyu F, Hakariya H, Hiraoka H, Li Z, Matsubara N, Soo Y, Hashiya F, Abe N, Shu Z, Nakamoto K, Kimura Y, Abe H. Intracellular Delivery of Antisense Oligonucleotides by Tri-Branched Cyclic Disulfide Units. ChemMedChem 2024:e202400472. [PMID: 38957922 DOI: 10.1002/cmdc.202400472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
Therapeutic oligonucleotides, such as antisense DNA, show promise in treating previously untreatable diseases. However, their applications are still hindered by the poor membrane permeability of naked oligonucleotides. Therefore, it is necessary to develop efficient methods for intracellular oligonucleotide delivery. Previously, our group successfully developed disulfide-based Membrane Permeable Oligonucleotides (MPON), which achieved enhanced cellular uptake and gene silencing effects through an endocytosis-free uptake mechanism. Herein, we report a new molecular design for the next generation of MPON, called trimer MPON. The trimer MPON consists of a tri-branched backbone, three α-lipoic acid units, and a spacer linker between the oligonucleotides and tri-branched cyclic disulfide unit. We describe the design, synthesis, and functional evaluation of the trimer MPON, offering new insights into the molecular design for efficient oligonucleotide delivery.
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Affiliation(s)
- Fangjie Lyu
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Hayase Hakariya
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Haruka Hiraoka
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Zhenmin Li
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Noriaki Matsubara
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Yonghao Soo
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Zhaoma Shu
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Kosuke Nakamoto
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, 464-8601, Japan
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2
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Moreira L, Guimarães NM, Santos RS, Loureiro JA, Pereira MC, Azevedo NF. Promising strategies employing nucleic acids as antimicrobial drugs. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102122. [PMID: 38333674 PMCID: PMC10850860 DOI: 10.1016/j.omtn.2024.102122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Antimicrobial resistance (AMR) is a growing concern because it causes microorganisms to develop resistance to drugs commonly used to treat infections. This results in increased difficulty in treating infections, leading to higher mortality rates and significant economic effects. Investing in new antimicrobial agents is, therefore, necessary to prevent and control AMR. Antimicrobial nucleic acids have arisen as potential key players in novel therapies for AMR infections. They have been designed to serve as antimicrobials and to act as adjuvants to conventional antibiotics or to inhibit virulent mechanisms. This new category of antimicrobial drugs consists of antisense oligonucleotides and oligomers, DNAzymes, and transcription factor decoys, differing in terms of structure, target molecules, and mechanisms of action. They are synthesized using nucleic acid analogs to enhance their resistance to nucleases. Because bacterial envelopes are generally impermeable to oligonucleotides, delivery into the cytoplasm typically requires the assistance of nanocarriers, which can affect their therapeutic potency. Given that numerous factors contribute to the success of these antimicrobial drugs, this review aims to provide a summary of the key advancements in the use of oligonucleotides for treating bacterial infections. Their mechanisms of action and the impact of factors such as nucleic acid design, target sequence, and nanocarriers on the antimicrobial potency are discussed.
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Affiliation(s)
- Luís Moreira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno M. Guimarães
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Rita S. Santos
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana A. Loureiro
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Maria C. Pereira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Terada C, Oh K, Tsubaki R, Chan B, Aibara N, Ohyama K, Shibata MA, Wada T, Harada-Shiba M, Yamayoshi A, Yamamoto T. Dynamic and static control of the off-target interactions of antisense oligonucleotides using toehold chemistry. Nat Commun 2023; 14:7972. [PMID: 38042877 PMCID: PMC10693639 DOI: 10.1038/s41467-023-43714-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Off-target interactions between antisense oligonucleotides (ASOs) with state-of-the-art modifications and biological components still pose clinical safety liabilities. To mitigate a broad spectrum of off-target interactions and enhance the safety profile of ASO drugs, we here devise a nanoarchitecture named BRace On a THERapeutic aSo (BROTHERS or BRO), which is composed of a standard gapmer ASO paired with a partially complementary peptide nucleic acid (PNA) strand. We show that these non-canonical ASO/PNA hybrids have reduced non-specific protein-binding capacity. The optimization of the structural and thermodynamic characteristics of this duplex system enables the operation of an in vivo toehold-mediated strand displacement (TMSD) reaction, effectively reducing hybridization with RNA off-targets. The optimized BROs dramatically mitigate hepatotoxicity while maintaining the on-target knockdown activity of their parent ASOs in vivo. This technique not only introduces a BRO class of drugs that could have a transformative impact on the extrahepatic delivery of ASOs, but can also help uncover the toxicity mechanism of ASOs.
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Affiliation(s)
- Chisato Terada
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- JSPS Research Fellow (DC1), Japan Society for the Promotion of Science, Tokyo, Japan
| | - Kaho Oh
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Ryutaro Tsubaki
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, Japan
| | - Nozomi Aibara
- Department of Pharmacy Practice, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kaname Ohyama
- Department of Molecular Pathochemistry, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masa-Aki Shibata
- Department of Anatomy and Cell Biology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, Sendai, Miyagi, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
- Cardiovascular Center, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Asako Yamayoshi
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Tsuyoshi Yamamoto
- Department of Chemistry of Biofunctional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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4
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Iyer AK, Schoch KM, Verbeck A, Galasso G, Chen H, Smith S, Oldenborg A, Miller TM, Karch CM, Bonni A. Targeted ASO-mediated Atp1a2 knockdown in astrocytes reduces SOD1 aggregation and accelerates disease onset in mutant SOD1 mice. PLoS One 2023; 18:e0294731. [PMID: 38015828 PMCID: PMC10683999 DOI: 10.1371/journal.pone.0294731] [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: 07/22/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023] Open
Abstract
Astrocyte-specific ion pump α2-Na+/K+-ATPase plays a critical role in the pathogenesis of amyotrophic lateral sclerosis (ALS). Here, we test the effect of Atp1a2 mRNA-specific antisense oligonucleotides (ASOs) to induce α2-Na+/K+-ATPase knockdown in the widely used ALS animal model, SOD1*G93A mice. Two ASOs led to efficient Atp1a2 knockdown and significantly reduced SOD1 aggregation in vivo. Although Atp1a2 ASO-treated mice displayed no off-target or systemic toxicity, the ASO-treated mice exhibited an accelerated disease onset and shorter lifespan than control mice. Transcriptomics studies reveal downregulation of genes involved in oxidative response, metabolic pathways, trans-synaptic signaling, and upregulation of genes involved in glutamate receptor signaling and complement activation, suggesting a potential role for these molecular pathways in de-coupling SOD1 aggregation from survival in Atp1a2 ASO-treated mice. Together, these results reveal a role for α2-Na+/K+-ATPase in SOD1 aggregation and highlight the critical effect of temporal modulation of genetically validated therapeutic targets in neurodegenerative diseases.
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Affiliation(s)
- Abhirami K. Iyer
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kathleen M. Schoch
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Anthony Verbeck
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Grant Galasso
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Hao Chen
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sarah Smith
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Anna Oldenborg
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Timothy M. Miller
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Celeste M. Karch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Azad Bonni
- Neuroscience and Rare Diseases, Roche Pharma Research and Early Development (pRED), Roche Innovation Centre Basel, Basel, Switzerland
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5
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Yu Y, Schneider WM, Kass MA, Michailidis E, Acevedo A, Pamplona Mosimann AL, Bordignon J, Koenig A, Livingston CM, van Gijzel H, Ni Y, Ambrose PM, Freije CA, Zhang M, Zou C, Kabbani M, Quirk C, Jahan C, Wu X, Urban S, You S, Shlomai A, de Jong YP, Rice CM. An RNA-based system to study hepatitis B virus replication and evaluate antivirals. SCIENCE ADVANCES 2023; 9:eadg6265. [PMID: 37043562 PMCID: PMC10096565 DOI: 10.1126/sciadv.adg6265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Hepatitis B virus (HBV) chronically infects an estimated 300 million people, and standard treatments are rarely curative. Infection increases the risk of liver cirrhosis and hepatocellular carcinoma, and consequently, nearly 1 million people die each year from chronic hepatitis B. Tools and approaches that bring insights into HBV biology and facilitate the discovery and evaluation of antiviral drugs are in demand. Here, we describe a method to initiate the replication of HBV, a DNA virus, using synthetic RNA. This approach eliminates contaminating background signals from input virus or plasmid DNA that plagues existing systems and can be used to study multiple stages of HBV replication. We further demonstrate that this method can be uniquely applied to identify sequence variants that confer resistance to antiviral drugs.
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Affiliation(s)
- Yingpu Yu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - William M. Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Maximilian A. Kass
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Ashley Acevedo
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Ana L. Pamplona Mosimann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Juliano Bordignon
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alexander Koenig
- Infectious Diseases Research Unit, GSK, Upper Providence, PA 19426, USA
| | | | | | - Yi Ni
- German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Pradeep M. Ambrose
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Catherine A. Freije
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Mengyin Zhang
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Chenhui Zou
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mohammad Kabbani
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Corrine Quirk
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Cyprien Jahan
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Xianfang Wu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Shihyun You
- Infectious Diseases Research Unit, GSK, Upper Providence, PA 19426, USA
| | - Amir Shlomai
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Ype P. de Jong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
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6
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Sakurai Y, Yamaguchi T, Yoshida T, Horiba M, Inoue T, Obika S. Synthesis and Properties of Nucleobase-Sugar Dual Modified Nucleic Acids: 2 '-OMe-RNA and scpBNA Bearing a 5-Hydroxycytosine Nucleobase. J Org Chem 2023; 88:154-162. [PMID: 36520114 DOI: 10.1021/acs.joc.2c02038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Naturally occurring 5-hydroxycytosine (5-OHCyt), which is associated with DNA damage, was recently found to reduce the hepatotoxicity of antisense oligonucleotides (ASOs) without compromising its antisense activity when used as a replacement for cytosine (Cyt). Additionally, sugar-modified nucleic acids, such as 2'-O-methylribonucleic acid (2'-OMe-RNA) and 2'-O,4'-C-spirocyclopropylene-bridged nucleic acid (scpBNA), have emerged as useful antisense materials. Herein, we aimed to combine these two advantages by designing dual modified nucleic acids 2'-OMe-RNA-5-OHCyt and scpBNA-5-OHCyt bearing the 5-OHCyt nucleobase to develop efficient and safe ASOs. We describe the synthesis of 2'-OMe-RNA-5-OHCyt and scpBNA-5-OHCyt phosphoramidites and their incorporation into oligonucleotides (ONs). The duplex-forming ability and base discrimination properties of 2'-OMe-RNA-5-OHCyt- and scpBNA-5-OHCyt-modified ONs were similar to those of 2'-OMe-RNA-Cyt- and scpBNA-mCyt-modified ONs, respectively. We also synthesized two 2'-OMe-RNA-5-OHCyt-modified ASOs, and one of the two was found to exhibit reduced hepatotoxicity while retaining target mRNA knockdown activity in in vivo experiments.
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Affiliation(s)
- Yota Sakurai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tokuyuki Yoshida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Masahiko Horiba
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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7
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Nasseri S, Sharifi M, Mehrzad V. Effects of hsa-piR-32877 Suppression with Antisense LNA GapmeRs on the Proliferation and Apoptosis of Human Acute Myeloid Leukemia Cells. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2023; 12:18-29. [PMID: 37942262 PMCID: PMC10629728 DOI: 10.22088/ijmcm.bums.12.1.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 11/10/2023]
Abstract
Acute myeloid leukemia (AML) is an invasive form of hematologic malignancies which results in the overproduction of myeloid cells in the bone marrow. Aberrant expression of piwi-interacting RNAs (piRNAs) which belong to small non-coding RNAs, play important roles in different cancer cells' progress. hsa- piR- 32877 is up-regulated in AML. Down regulation of hsa-piR-32877 by antisense LNA GapmeRs could be potential for suppression of myeloid cell proliferation and induce myeloid cell apoptosis. We have blocked the expression of hsa-piR-32877 by antisense LNA GapmeRs in human bone marrow blast cells, and the M-07e cell line. Samples were transfected with antisense LNA GapmeRs at 24, 48, and 72 hours. The Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) was performed to investigate the expression of hsa-piR-32877, CASP3, and CASP9. Both CASP3 and CASP9 play important roles in apoptosis. Cell proliferation was studied via CFSE (carboxyfluorescein diacetate succinimidyl ester) assay. Results showed that hsa-piR-32877 was down-regulated by antisense LNA GapmeRs in the patient and cell line samples. Also, after transfection, cell proliferation and apoptosis decreased and increased, respectively. Our data suggested that hsa-piR-32877 suppression may act as a novel therapeutic method for the inhibition of human leukemic cells proliferation in AML.
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Affiliation(s)
- Sepideh Nasseri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mohammadreza Sharifi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Valiollah Mehrzad
- Department of Internal Medicine, Division of Hematology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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8
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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9
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Lu K, Fan Q, Zou X. Antisense oligonucleotide is a promising intervention for liver diseases. Front Pharmacol 2022; 13:1061842. [PMID: 36569303 PMCID: PMC9780395 DOI: 10.3389/fphar.2022.1061842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
As the body's critical metabolic organ, the liver plays an essential role in maintaining proper body homeostasis. However, as people's living standards have improved and the number of unhealthy lifestyles has increased, the liver has become overburdened. These have made liver disease one of the leading causes of death worldwide. Under the influence of adverse factors, liver disease progresses from simple steatosis to hepatitis, to liver fibrosis, and finally to cirrhosis and cancer, followed by increased mortality. Until now, there has been a lack of accepted effective treatments for liver disease. Based on current research, antisense oligonucleotide (ASO), as an alternative intervention for liver diseases, is expected to be an effective treatment due to its high efficiency, low toxicity, low dosage, strong specificity, and additional positive characteristics. In this review, we will first introduce the design, modification, delivery, and the mechanisms of ASO, and then summarize the application of ASO in liver disease treatment, including in non-alcoholic fatty liver disease (NAFLD), hepatitis, liver fibrosis, and liver cancer. Finally, we discuss challenges and perspectives on the transfer of ASO drugs into clinical use. This review provides a current and comprehensive understanding of the integrative and systematic functions of ASO for its use in liver disease.
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Affiliation(s)
- Kailing Lu
- College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Qijing Fan
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Xiaoju Zou
- College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan, China,*Correspondence: Xiaoju Zou,
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10
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Terada C, Kawamoto S, Yamayoshi A, Yamamoto T. Chemistry of Therapeutic Oligonucleotides That Drives Interactions with Biomolecules. Pharmaceutics 2022; 14:pharmaceutics14122647. [PMID: 36559141 PMCID: PMC9781680 DOI: 10.3390/pharmaceutics14122647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Oligonucleotide therapeutics that can modulate gene expression have been gradually developed for clinical applications over several decades. However, rapid advances have been made in recent years. Artificial nucleic acid technology has overcome many challenges, such as (1) poor target affinity and selectivity, (2) low in vivo stability, and (3) classical side effects, such as immune responses; thus, its application in a wide range of disorders has been extensively examined. However, even highly optimized oligonucleotides exhibit side effects, which limits the general use of this class of agents. In this review, we discuss the physicochemical characteristics that aid interactions between drugs and molecules that belong to living organisms. By systematically organizing the related data, we hope to explore avenues for symbiotic engineering of oligonucleotide therapeutics that will result in more effective and safer drugs.
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11
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Lee JW, Choi J, Choi Y, Kim K, Yang Y, Kim SH, Yoon HY, Kwon IC. Molecularly engineered siRNA conjugates for tumor-targeted RNAi therapy. J Control Release 2022; 351:713-726. [DOI: 10.1016/j.jconrel.2022.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/28/2022]
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12
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Sarli SL, Watts JK. Harnessing nucleic acid technologies for human health on earth and in space. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:113-126. [PMID: 36336357 DOI: 10.1016/j.lssr.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid therapeutics are a versatile class of sequence-programmable drugs that offer a robust and clinically viable strategy to modulate expression or correct genetic defects contributing to disease. The majority of drugs currently on the market target proteins; however, proteins only represent a subset of possible disease targets. Nucleic acid therapeutics allow intuitive engagement with genome sequences providing a more direct way to target many diseases at their genetic root cause. Their clinical success depends on platform technologies which can support durable and well tolerated pharmacological activity in a given tissue. Nucleic acid drugs possess a potent combination of target specificity and adaptability required to advance drug development for many diseases. As these therapeutic technologies mature, their clinical applications can also expand access to personalized therapies for patients with rare or solo genetic diseases. Spaceflight crew members exposed to the unique hazards of spaceflight, especially those related to galactic cosmic radiation (GCR) exposure, represent another patient subset who may also benefit from nucleic acid drugs as countermeasures. In this review, we will discuss the various classes of RNA- and DNA-targeted nucleic acid drugs, provide an overview of their present-day clinical applications, and describe major strategies to improve their delivery, safety, and overall efficacy.
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Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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13
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Nedorezova DD, Dubovichenko MV, Belyaeva EP, Grigorieva ED, Peresadina AV, Kolpashchikov DM. Specificity of oligonucleotide gene therapy (OGT) agents. Theranostics 2022; 12:7132-7157. [PMID: 36276652 PMCID: PMC9576606 DOI: 10.7150/thno.77830] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/11/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotide gene therapy (OGT) agents (e. g. antisense, deoxyribozymes, siRNA and CRISPR/Cas) are promising therapeutic tools. Despite extensive efforts, only few OGT drugs have been approved for clinical use. Besides the problem of efficient delivery to targeted cells, hybridization specificity is a potential limitation of OGT agents. To ensure tight binding, a typical OGT agent hybridizes to the stretch of 15-25 nucleotides of a unique targeted sequence. However, hybrids of such lengths tolerate one or more mismatches under physiological conditions, the problem known as the affinity/specificity dilemma. Here, we assess the scale of this problem by analyzing OGT hybridization-dependent off-target effects (HD OTE) in vitro, in animal models and clinical studies. All OGT agents except deoxyribozymes exhibit HD OTE in vitro, with most thorough evidence of poor specificity reported for siRNA and CRISPR/Cas9. Notably, siRNA suppress non-targeted genes due to (1) the partial complementarity to mRNA 3'-untranslated regions (3'-UTR), and (2) the antisense activity of the sense strand. CRISPR/Cas9 system can cause hundreds of non-intended dsDNA breaks due to low specificity of the guide RNA, which can limit therapeutic applications of CRISPR/Cas9 by ex-vivo formats. Contribution of this effects to the observed in vivo toxicity of OGT agents is unclear and requires further investigation. Locked or peptide nucleic acids improve OGT nuclease resistance but not specificity. Approaches that use RNA marker dependent (conditional) activation of OGT agents may improve specificity but require additional validation in cell culture and in vivo.
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Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Mikhail V. Dubovichenko
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina P. Belyaeva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina D. Grigorieva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Arina V. Peresadina
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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14
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Vaillant A. Oligonucleotide-Based Therapies for Chronic HBV Infection: A Primer on Biochemistry, Mechanisms and Antiviral Effects. Viruses 2022; 14:v14092052. [PMID: 36146858 PMCID: PMC9502277 DOI: 10.3390/v14092052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/21/2022] Open
Abstract
Three types of oligonucleotide-based medicines are under clinical development for the treatment of chronic HBV infection. Antisense oligonucleotides (ASOs) and synthetic interfering RNA (siRNA) are designed to degrade HBV mRNA, and nucleic acid polymers (NAPs) stop the assembly and secretion of HBV subviral particles. Extensive clinical development of ASOs and siRNA for a variety of liver diseases has established a solid understanding of their pharmacodynamics, accumulation in different tissue types in the liver, pharmacological effects, off-target effects and how chemical modifications and delivery approaches affect these parameters. These effects are highly conserved for all ASO and siRNA used in human studies to date. The clinical assessment of several ASO and siRNA compounds in chronic HBV infection in recent years is complicated by the different delivery approaches used. Moreover, these assessments have not considered the large clinical database of ASO/siRNA function in other liver diseases and known off target effects in other viral infections. The goal of this review is to summarize the current understanding of ASO/siRNA/NAP pharmacology and integrate these concepts into current clinical results for these compounds in the treatment of chronic HBV infection.
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Affiliation(s)
- Andrew Vaillant
- Replicor Inc., 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
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15
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Sabry R, Williams M, Werry N, LaMarre J, Favetta LA. BPA Decreases PDCD4 in Bovine Granulosa Cells Independently of miR-21 Inhibition. Int J Mol Sci 2022; 23:ijms23158276. [PMID: 35955412 PMCID: PMC9368835 DOI: 10.3390/ijms23158276] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 02/01/2023] Open
Abstract
microRNAs (miRNAs) are susceptible to environmental factors that might affect cellular function and impose negative effects on female reproduction. miR-21 is the most abundant miRNA in bovine granulosa cells and is widely reported as affected by Bisphenol A (BPA) exposure, yet the cause and consequences are not entirely elucidated. BPA is a synthetic endocrine disruptor associated with poor fertility. miR-21 function in bovine granulosa cells is investigated utilizing locked nucleic acid (LNA) oligonucleotides to suppress miR-21. Before measuring apoptosis and quantifying miR-21 apoptotic targets PDCD4 and PTEN, transfection was optimized and validated. BPA was introduced to see how it affects miR-21 regulation and which BPA-mediated effects are influenced by miR-21. miR-21 knockdown and specificity against additional miRNAs were confirmed. miR-21 was found to have antiapoptotic effects, which could be explained by its effect on the proapoptotic target PDCD4, but not PTEN. Previous findings of miR-21 overexpression were validated using BPA treatments, and the temporal influence of BPA on miR-21 levels was addressed. Finally, BPA effects on upstream regulators, such as VMP1 and STAT3, explain the BPA-dependent upregulation of miR-21 expression. Overall, this research enhances our understanding of miR-21 function in granulosa cells and the mechanisms of BPA-induced reproductive impairment.
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16
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Zhang L, Bernardo KD, Vickers TA, Tian J, Liang XH, Crooke ST. NAT10 and DDX21 Proteins Interact with RNase H1 and Affect the Performance of Phosphorothioate Oligonucleotides. Nucleic Acid Ther 2022; 32:280-299. [PMID: 35852833 PMCID: PMC9416547 DOI: 10.1089/nat.2021.0107] [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] [Indexed: 11/19/2022] Open
Abstract
RNase H1-dependent phosphorothioate oligonucleotides (PS-ASOs) have been developed to treat various diseases through specific degradation of target RNAs. Although many factors or features of RNA and PS-ASOs have been demonstrated to affect antisense activity of PS-ASOs, little is known regarding the roles of RNase H1-associated proteins in PS-ASO performance. In this study, we report that two nucleolar proteins, NAT10 and DDX21, interact with RNase H1 and affect the potency and safety of PS-ASOs. The interactions of these two proteins with RNase H1 were determined using BioID proximity labeling in cells and confirmed biochemically. Reduction of NAT10 and DDX21 decreased PS-ASO activity in cells, and purified NAT10 and DDX21 proteins enhanced RNase H1 cleavage rates, indicating that these two proteins facilitate RNase H1 endoribonuclease activity. Consistently, reduction of these proteins increased the levels of R-loops, and impaired pre-rRNA processing. In addition, reduction of the two proteins increased the cytotoxicity of toxic PS-ASOs, and treatment of toxic PS-ASOs also altered the localization of these proteins. Together, this study shows for the first time that NAT10 and DDX21 interact with RNase H1 protein and enhance its enzymatic activity, contributing to the potency and safety of PS-ASOs.
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Affiliation(s)
- Lingdi Zhang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Karla D. Bernardo
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Timothy A. Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Jun Tian
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Xue-hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T. Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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17
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Yoshida T, Morihiro K, Naito Y, Mikami A, Kasahara Y, Inoue T, Obika S. Identification of nucleobase chemical modifications that reduce the hepatotoxicity of gapmer antisense oligonucleotides. Nucleic Acids Res 2022; 50:7224-7234. [PMID: 35801870 PMCID: PMC9303313 DOI: 10.1093/nar/gkac562] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 12/26/2022] Open
Abstract
Currently, gapmer antisense oligonucleotide (ASO) therapeutics are under clinical development for the treatment of various diseases, including previously intractable human disorders; however, they have the potential to induce hepatotoxicity. Although several groups have reported the reduced hepatotoxicity of gapmer ASOs following chemical modifications of sugar residues or internucleotide linkages, only few studies have described nucleobase modifications to reduce hepatotoxicity. In this study, we introduced single or multiple combinations of 17 nucleobase derivatives, including four novel derivatives, into hepatotoxic locked nucleic acid gapmer ASOs and examined their effects on hepatotoxicity. The results demonstrated successful identification of chemical modifications that strongly reduced the hepatotoxicity of gapmer ASOs. This approach expands the ability to design gapmer ASOs with optimal therapeutic profiles.
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Affiliation(s)
- Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Yuki Naito
- Database Center for Life Science (DBCLS), 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Mikami
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
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18
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Boros BD, Schoch KM, Kreple CJ, Miller TM. Antisense Oligonucleotides for the Study and Treatment of ALS. Neurotherapeutics 2022; 19:1145-1158. [PMID: 35653060 PMCID: PMC9587169 DOI: 10.1007/s13311-022-01247-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 10/18/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by motor neuron loss. ALS is now associated with mutations in numerous genes, many of which cause disease in part through toxic gain-of-function mechanisms. Antisense oligonucleotides (ASOs) are small sequences of DNA that can reduce expression of a target gene at the post-transcriptional level, making them attractive for neutralizing mutant or toxic gene products. Advancements in the medicinal chemistries of ASOs have improved their pharmacodynamic profile to allow safe and effective delivery to the central nervous system. ASO therapies for ALS have rapidly developed over the last two decades, and ASOs that target SOD1, C9orf72, FUS, and ATXN2 are now in clinical trials for familial or sporadic forms of ALS. This review discusses the current state of ASO therapies for ALS, outlining their successes from preclinical development to early clinical trials.
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Affiliation(s)
- Benjamin D Boros
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, Box 8111, 115 Biotechnology Bldg, 660 S. Euclid Ave, MO, 63110, St. Louis, USA
| | - Kathleen M Schoch
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, Box 8111, 115 Biotechnology Bldg, 660 S. Euclid Ave, MO, 63110, St. Louis, USA
| | - Collin J Kreple
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, Box 8111, 115 Biotechnology Bldg, 660 S. Euclid Ave, MO, 63110, St. Louis, USA
| | - Timothy M Miller
- Department of Neurology, Hope Center for Neurological Disorders, Washington University School of Medicine, Box 8111, 115 Biotechnology Bldg, 660 S. Euclid Ave, MO, 63110, St. Louis, USA.
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19
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Katsuzaki Y, Tsukimura R, Chandela A, Chano T, Ueno Y. 4'-C-Aminoethoxy-Modified DNAs Exhibit Increased Nuclease Resistance, Sustained RNase H Activity, and Inhibition of KRAS Gene Expression. Chem Biodivers 2022; 19:e202200125. [PMID: 35773240 DOI: 10.1002/cbdv.202200125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
The linear synthesis of 4'-C-aminoethoxy thymidine (AEoT) nucleoside phosphoramidite was accomplished using deoxythymidine as the starting material. This analog was incorporated into several oligonucleotides, the applicability of which as antisense oligonucleotides (ASOs) was then evaluated. The AEoT-modified DNA/RNA duplex exhibited improved thermal stability compared to unmodified and 4'-C-aminoethyl thymidine (4'-AET) modified heteroduplexes. The serum stability of AEoT-modified DNA was notably increased by several-folds compared to that of unmodified DNA. Furthermore, RNase H-dependent cleavage of the modified-DNA/RNA hybrids was found to be sustained. In addition, the modified antisense and unmodified oligonucleotides also displayed relatively comparable inhibition of the KRAS gene in human lung cancer cells. This study strengthens our understanding of the potential application of 4'-C-aminoethoxy-modified nucleotides as ASO therapeutics.
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Affiliation(s)
- Yuki Katsuzaki
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Ryo Tsukimura
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Akash Chandela
- Faculty of Applied Biological Sciences, Gifu University, Japan
| | - Tokuhiro Chano
- Department of Medical Genetics, Shiga University of Medical, Tsukinowa-cho, Seta, Otsu, Shiga, 520-2192, Japan
| | - Yoshihito Ueno
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.,Faculty of Applied Biological Sciences, Gifu University, Japan.,Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Japan
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20
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Editorial: In vitro mechanistic evaluation of nucleic acid polymers: A cautionary tale. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:168-174. [PMID: 35402067 PMCID: PMC8956958 DOI: 10.1016/j.omtn.2022.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Hagedorn PH, Brown JM, Easton A, Pierdomenico M, Jones K, Olson RE, Mercer SE, Li D, Loy J, Høg AM, Jensen ML, Gill M, Cacace AM. Acute Neurotoxicity of Antisense Oligonucleotides After Intracerebroventricular Injection Into Mouse Brain Can Be Predicted from Sequence Features. Nucleic Acid Ther 2022; 32:151-162. [PMID: 35166597 PMCID: PMC9221153 DOI: 10.1089/nat.2021.0071] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antisense oligonucleotides are a relatively new therapeutic modality and safety evaluation is still a developing area of research. We have observed that some oligonucleotides can produce acute, nonhybridization dependent, neurobehavioral side effects after intracerebroventricular (ICV) dosing in mice. In this study, we use a combination of in vitro, in vivo, and bioinformatics approaches to identify a sequence design algorithm, which can reduce the number of acutely toxic molecules synthesized and tested in mice. We find a cellular assay measuring spontaneous calcium oscillations in neuronal cells can predict the behavioral side effects after ICV dosing, and may provide a mechanistic explanation for these observations. We identify sequence features that are overrepresented or underrepresented among oligonucleotides causing these reductions in calcium oscillations. A weighted linear combination of the five most informative sequence features predicts the outcome of ICV dosing with >80% accuracy. From this, we develop a bioinformatics tool that allows oligonucleotide designs with acceptable acute neurotoxic potential to be identified, thereby reducing the number of toxic molecules entering drug discovery pipelines. The informative sequence features we identified also suggest areas in which to focus future medicinal chemistry efforts.
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Affiliation(s)
- Peter H Hagedorn
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Jeffrey M Brown
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - Amy Easton
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - Maria Pierdomenico
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - Kelli Jones
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - Richard E Olson
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - Stephen E Mercer
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - Dong Li
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - James Loy
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - Anja M Høg
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Marianne L Jensen
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Martin Gill
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
| | - Angela M Cacace
- Bristol Myers Squibb Research and Development, Princeton, New Jersey, USA
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22
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Yasuhara H, Yoshida T, Sasaki K, Obika S, Inoue T. Reduction of Off-Target Effects of Gapmer Antisense Oligonucleotides by Oligonucleotide Extension. Mol Diagn Ther 2022; 26:117-127. [PMID: 34994962 PMCID: PMC8766371 DOI: 10.1007/s40291-021-00573-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2021] [Indexed: 12/03/2022]
Abstract
Aim Antisense oligonucleotide (ASO) has the potential to induce off-target effects by inadvertent binding of ASOs to unintended RNAs that have a sequence similar to the target RNA. In the present study, we focused on the association between oligonucleotide length and off-target effects. Oligonucleotide extension is assumed to have bilateral effects on hybridization-dependent changes in gene expression, i.e., one is the decrease of off-target effects based on the reduced number of off-target candidate genes with perfect matches, and the other is the increase of off-target effects based on the increased binding affinity between the ASO and the complementary RNAs that leads to better tolerability for mismatches. Methods To determine the effects of oligonucleotide extension of gapmer ASOs on off-target effects, an extensive microarray analysis was performed using human cells treated with a 14-mer gapmer ASO and the extended 18-mer derivatives with the same core 14-mer region. Results and Discussion Our data indicated that change in gene expression in the cells treated with 18-mer ASOs was significantly smaller than those with a 14-mer ASO, showing the decrease of off-target effects by oligonucleotide extension. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-021-00573-z.
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Affiliation(s)
- Hidenori Yasuhara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Tokuyuki Yoshida
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kiyomi Sasaki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
| | - Takao Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
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23
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Abstract
This introduction charts the history of the development of the major chemical modifications that have influenced the development of nucleic acids therapeutics focusing in particular on antisense oligonucleotide analogues carrying modifications in the backbone and sugar. Brief mention is made of siRNA development and other applications that have by and large utilized the same modifications. We also point out the pitfalls of the use of nucleic acids as drugs, such as their unwanted interactions with pattern recognition receptors, which can be mitigated by chemical modification or used as immunotherapeutic agents.
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24
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Bouwman LF, den Hamer B, van den Heuvel A, Franken M, Jackson M, Dwyer CA, Tapscott SJ, Rigo F, van der Maarel SM, de Greef JC. Systemic delivery of a DUX4-targeting antisense oligonucleotide to treat facioscapulohumeral muscular dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:813-827. [PMID: 34729250 PMCID: PMC8526479 DOI: 10.1016/j.omtn.2021.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 09/17/2021] [Indexed: 01/16/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most prevalent skeletal muscle dystrophies. Skeletal muscle pathology in individuals with FSHD is caused by inappropriate expression of the transcription factor DUX4, which activates different myotoxic pathways. At the moment there is no molecular therapy that can delay or prevent skeletal muscle wasting in FSHD. In this study, a systemically delivered antisense oligonucleotide (ASO) targeting the DUX4 transcript was tested in vivo in ACTA1-MCM;FLExDUX4 mice that express DUX4 in skeletal muscles. We show that the DUX4 ASO was well tolerated and repressed the DUX4 transcript, DUX4 protein, and mouse DUX4 target gene expression in skeletal muscles. In addition, the DUX4 ASO alleviated the severity of skeletal muscle pathology and partially prevented the dysregulation of inflammatory and extracellular matrix genes. DUX4 ASO-treated ACTA1-MCM;FLExDUX4 mice performed better on a treadmill; however, the hanging grid and four-limb grip strength tests were not improved compared to control ASO-treated ACTA1-MCM;FLExDUX4 mice. This study shows that systemic delivery of ASOs targeting DUX4 is a promising therapeutic strategy for FSHD and strategies that further improve the ASO efficacy in skeletal muscle are warranted.
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Affiliation(s)
- Linde F. Bouwman
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Anita van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Marnix Franken
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Michaela Jackson
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Chrissa A. Dwyer
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stephen J. Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Neurology, University of Washington, Seattle, WA 98105, USA
| | - Frank Rigo
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Silvère M. van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Jessica C. de Greef
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
- Corresponding author Jessica C. de Greef, Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
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25
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Wada F, Yamamoto T, Kobayashi T, Tachibana K, Ito KR, Hamasaki M, Kayaba Y, Terada C, Yamayoshi A, Obika S, Harada-Shiba M. Drug discovery and development scheme for liver-targeting bridged nucleic acid antisense oligonucleotides. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:957-969. [PMID: 34760338 PMCID: PMC8560717 DOI: 10.1016/j.omtn.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/15/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022]
Abstract
Antisense oligonucleotides (ASOs) containing bridged nucleic acids (BNAs) have been proven to be very powerful. However, ensuring a reliable discovery and translational development scheme for this class of ASOs with wider therapeutic windows remains a fundamental challenge. We here demonstrate the robustness of our scheme in the context of the selection of ASOs having two different BNA chemistries (2,′4′-BNA/locked nucleic acid [LNA] and amido-bridged nucleic acid [AmNA]) targeting human proprotein convertase subtilisin/kexin type 9 (PCSK9). The scheme features a two-step process, including (1) a unique and sensitive in vitro screening approach, called Ca2+ enrichment of medium (CEM) transfection, and (2) a ligand-targeted drug delivery approach to better reach target tissues, averting unintended accumulation of ASOs. Using CEM screening, we identified a candidate ASO that shows >70% cholesterol-lowering action in monkeys. An N-acetylgalactosamine (GalNAc) ligand then was appended to the candidate ASO to further broaden the therapeutic margin by altering the molecule’s pharmacokinetics. The GalNAc conjugate, HsPCSK9-1811-LNA, was found to be at least ten times more potent in non-human primates (compared with the unconjugated counterpart), with reduced nephrotoxicity in rats. Overall, we successfully showed that our drug development scheme is better suited for selecting clinically relevant BNA-based ASOs, especially for the treatment of liver-associated diseases.
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Affiliation(s)
- Fumito Wada
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Tadayuki Kobayashi
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Tachibana
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kosuke Ramon Ito
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mayumi Hamasaki
- Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
| | - Yukina Kayaba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8131, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan.,Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center Research Institute, 6-1 Kishibe-shinmachi, Suita, Osaka 564-8565, Japan
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26
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Bockstahler M, Salbach C, Müller AM, Kübler A, Müller OJ, Katus HA, Frey N, Kaya Z. LNA oligonucleotide mediates an anti-inflammatory effect in autoimmune myocarditis via targeting lactate dehydrogenase B. Immunology 2021; 165:158-170. [PMID: 34606637 PMCID: PMC9426621 DOI: 10.1111/imm.13421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 08/18/2021] [Accepted: 09/14/2021] [Indexed: 11/29/2022] Open
Abstract
Treatment of myocarditis is often limited to symptomatic treatment due to unknown pathomechanisms. In order to identify new therapeutic approaches, the contribution of locked nucleic acid antisense oligonucleotides (LNA ASOs) in autoimmune myocarditis was investigated. Hence, A/J mice were immunized with cardiac troponin I (TnI) to induce experimental autoimmune myocarditis (EAM) and treated with LNA ASOs. The results showed an unexpected anti‐inflammatory effect for one administered LNA ASO MB_1114 by reducing cardiac inflammation and fibrosis. The target sequence of MB_1114 was identified as lactate dehydrogenase B (mLDHB). For further analysis, mice received mLdhb‐specific GapmeR during induction of EAM. Here, mice receiving the mLdhb‐specific GapmeR showed increased protein levels of cardiac mLDHB and a reduced cardiac inflammation and fibrosis. The effect of increased cardiac mLDHB protein level was associated with a downregulation of genes of reactive oxygen species (ROS)‐associated proteins, indicating a reduction in ROS. Here, the suppression of murine pro‐apoptotic Bcl‐2‐associated X protein (mBax) was also observed. In our study, an unexpected anti‐inflammatory effect of LNA ASO MB_1114 and mLdhb‐specific GapmeR during induction of EAM could be demonstrated in vivo. This effect was associated with increased protein levels of cardiac mLDHB, mBax suppression and reduced ROS activation. Thus, LDHB and LNA ASOs may be considered as a promising target for directed therapy of myocarditis. Nevertheless, further investigations are necessary to clarify the mechanism of action of anti‐inflammatory LDHB‐triggered effects.
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Affiliation(s)
- Mariella Bockstahler
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Christian Salbach
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Anna-Maria Müller
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Andrea Kübler
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Oliver J Müller
- Department of Internal Medicine III, University of Kiel, Kiel, Germany
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Norbert Frey
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Ziya Kaya
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Heidelberg, Germany
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27
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Greenberg DS, Tzur Y, Soreq H. The Use of Gapmers for In Vivo Suppression of Hepatic mRNA Targets. Methods Mol Biol 2021; 2176:177-184. [PMID: 32865791 DOI: 10.1007/978-1-0716-0771-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This chapter describes the use of locked nucleic acid (LNA) GapmeRs for the in vivo knockdown of specific mRNAs in the mouse liver and phenotype analysis. LNA GapmeRs may be tested for efficacy by transfection in cultured cells. They are delivered into mice in vivo by intravenous tail injection .
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Affiliation(s)
- David S Greenberg
- The Life Sciences Institute and The Edmond and Lili Safra Center of Brain Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonat Tzur
- The Life Sciences Institute and The Edmond and Lili Safra Center of Brain Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hermona Soreq
- The Life Sciences Institute and The Edmond and Lili Safra Center of Brain Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
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28
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Scharner J, Aznarez I. Clinical Applications of Single-Stranded Oligonucleotides: Current Landscape of Approved and In-Development Therapeutics. Mol Ther 2020; 29:540-554. [PMID: 33359792 PMCID: PMC7854307 DOI: 10.1016/j.ymthe.2020.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/19/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded oligonucleotides have been explored as a therapeutic modality for more than 20 years. Only during the last 5 years have single-stranded oligonucleotides become a modality of choice in the fields of precision medicine and targeted therapeutics. Recently, there have been a number of development efforts involving this modality that have led to treatments for genetic diseases that were once untreatable. This review highlights key applications of single-stranded oligonucleotides that function in a sequence-dependent manner when applied to modulate precursor (pre-)mRNA splicing, gene expression, and immune pathways. These applications have been used to address diseases that range from neurological to muscular to metabolic, as well as to develop vaccines. The wide range of applications denotes the versatility of single-stranded oligonucleotides as a robust therapeutic platform. The focus of this review is centered on approved single-stranded oligonucleotide therapies and the evolution of oligonucleotide therapeutics into novel applications currently in clinical development.
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29
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Zhang N, Bewick B, Xia G, Furling D, Ashizawa T. A CRISPR-Cas13a Based Strategy That Tracks and Degrades Toxic RNA in Myotonic Dystrophy Type 1. Front Genet 2020; 11:594576. [PMID: 33362853 PMCID: PMC7758406 DOI: 10.3389/fgene.2020.594576] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/23/2020] [Indexed: 12/18/2022] Open
Abstract
Cas13a, an effector of type VI CRISPR-Cas systems, is an RNA guided RNase with multiplexing and therapeutic potential. This study employs the Leptotrichia shahii (Lsh) Cas13a and a repeat-based CRISPR RNA (crRNA) to track and eliminate toxic RNA aggregates in myotonic dystrophy type 1 (DM1) – a neuromuscular disease caused by CTG expansion in the DMPK gene. We demonstrate that LshCas13a cleaves CUG repeat RNA in biochemical assays and reduces toxic RNA load in patient-derived myoblasts. As a result, LshCas13a reverses the characteristic adult-to-embryonic missplicing events in several key genes that contribute to DM1 phenotype. The deactivated LshCas13a can further be repurposed to track RNA-rich organelles within cells. Our data highlights the reprogrammability of LshCas13a and the possible use of Cas13a to target expanded repeat sequences in microsatellite expansion diseases.
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Affiliation(s)
- Nan Zhang
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, United States
| | - Brittani Bewick
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, United States
| | - Guangbin Xia
- Indiana University School of Medicine, Fort Wayne, IN, United States
| | - Denis Furling
- Institut National de la Sante et de la Recherche Medicale (INSERM), Centre de Recherche en Myologie (CRM), Association Institut de Myologie, Sorbonne Université, Paris, France
| | - Tetsuo Ashizawa
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, United States
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30
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Kajino R, Ueno Y. (S)-5'-C-Aminopropyl-2'-O-methyl nucleosides enhance antisense activity in cultured cells and binding affinity to complementary single-stranded RNA. Bioorg Med Chem 2020; 30:115925. [PMID: 33310631 DOI: 10.1016/j.bmc.2020.115925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022]
Abstract
Antisense oligonucleotides (ASOs) are a promising clinical tool that could be applied for unmet medical needs, but there are several limitations for their therapeutic application. Here, we designed and synthesized (S)-5'-C-aminopropyl-2'-O-methylcytidine, and oligonucleotides containing (S)-5'-C-aminopropyl-2'-O-methyluridine and -methylcytidine. We then investigated the properties of ASOs containing these nucleoside analogs. (S)-5'-C-Aminopropyl modifications enhanced the thermal stability of DNA/RNA duplexes when compared to other commercially available 2'-O-methyl modifications. This suggested that the terminal ammonium cation on the alkyl side chains neutralized the negative charge of the phosphates in the duplex. Additionally, the overall conformation of ASO/RNA duplexes was retained with the modified ASOs. Thus, these duplexes exhibited the ability to elicit RNase H activity. Furthermore, we found that ASOs containing the (S)-5'-C-aminopropyl modification exhibited higher antisense potency than those containing the 2'-O-methyl modification in cultured cells. Therefore, the (S)-5'-C-aminopropyl-2'-O-methyl nucleosides synthesized in this study are promising candidates for developing antisense therapeutics.
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Affiliation(s)
- Ryohei Kajino
- United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan; Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan; Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Yanagido 1-1, Gifu 501-1193, Japan.
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31
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Tessier Y, Achanzar W, Mihalcik L, Amuzie C, Andersson P, Parry JD, Moggs J, Whiteley LO. Outcomes of the European Federation of Pharmaceutical Industries and Associations Oligonucleotide Working Group Survey on Nonclinical Practices and Regulatory Expectations for Therapeutic Oligonucleotide Safety Assessment. Nucleic Acid Ther 2020; 31:7-20. [PMID: 33054599 DOI: 10.1089/nat.2020.0892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Oligonucleotide Working Group of the European Federation of Pharmaceutical Industries and Associations (EFPIA) conducted a survey of companies to understand the trends in nonclinical practices and regulatory expectations for oligonucleotide drug safety assessment. Twenty-two companies of different types, with varying oligonucleotide experience levels in the field, participated. The survey identified key regulatory challenges and areas of perceived health authority (HA) concern regarding nonclinical safety strategies for oligonucleotides, such as the choice of toxicology species, approaches to dose setting in toxicity studies, dose scaling from animals to humans, the implementation (and regulatory acceptability) of lean packages, and methods for dealing with impurities and human-specific off-targets. The perceived oligonucleotide experience of HAs and the relevance of guidance to oligonucleotide development were also assessed. The results showed a general lack of consensus on nonclinical safety assessment approaches being used for this growing class of medicines and highlight the need for continuing collaboration between sponsors and HAs to better define best practices.
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Affiliation(s)
- Yann Tessier
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - William Achanzar
- Drug Safety Evaluation, Bristol Myers Squibb Company, New Brunswick, New Jersey, USA
| | - Lauren Mihalcik
- Amgen Research, Translational Safety & Bioanalytical Sciences, South San Francisco, California, USA
| | - Chidozie Amuzie
- Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania, USA
| | - Patrik Andersson
- Respiratory and Immunology Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Joel D Parry
- Nonclinical Safety, GSK R&D, David Jack Centre for R&D, Ware, United Kingdom
| | - Jonathan Moggs
- Preclinical Safety, Translational Medicine, Novartis Institutes for BioMedical Research, Basel, Switzerland
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32
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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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33
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Doxakis E. Therapeutic antisense oligonucleotides for movement disorders. Med Res Rev 2020; 41:2656-2688. [PMID: 32656818 DOI: 10.1002/med.21706] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/11/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022]
Abstract
Movement disorders are a group of neurological conditions characterized by abnormalities of movement and posture. They are broadly divided into akinetic and hyperkinetic syndromes. Until now, no effective symptomatic or disease-modifying therapies have been available. However, since many of these disorders are monogenic or have some well-defined genetic component, they represent strong candidates for antisense oligonucleotide (ASO) therapies. ASO therapies are based on the use of short synthetic single-stranded ASOs that bind to disease-related target RNAs via Watson-Crick base-pairing and pleiotropically modulate their function. With information arising from the RNA sequence alone, it is possible to design ASOs that not only alter the expression levels but also the splicing defects of any protein, far exceeding the intervention repertoire of traditional small molecule approaches. Following the regulatory approval of ASO therapies for spinal muscular atrophy and Duchenne muscular dystrophy in 2016, there has been tremendous momentum in testing such therapies for other neurological disorders. This review article initially focuses on the chemical modifications aimed at improving ASO effectiveness, the mechanisms by which ASOs can interfere with RNA function, delivery systems and pharmacokinetics, and the common set of toxicities associated with their application. It, then, describes the pathophysiology and the latest information on preclinical and clinical trials utilizing ASOs for the treatment of Parkinson's disease, Huntington's disease, and ataxias 1, 2, 3, and 7. It concludes with issues that require special attention to realize the full potential of ASO-based therapies.
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Affiliation(s)
- Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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34
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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: 45] [Impact Index Per Article: 11.3] [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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35
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An Overview of Non-coding RNAs and Cardiovascular System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:3-45. [PMID: 32285403 DOI: 10.1007/978-981-15-1671-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cardiovascular disease management and timely diagnosis remain a major dilemma. Delineating molecular mechanisms of cardiovascular diseases is opening horizon in the field of molecular medicines and in the development of early diagnostic markers. Non-coding RNAs are the highly functional and vibrant nucleic acids and are known to be involved in the regulation of endothelial cells, vascular and smooth muscles cells, cardiac metabolism, ischemia, inflammation and many processes in cardiovascular system. This chapter is comprehensively focusing on the overview of the non-coding RNAs including their discovery, generation, classification and functional regulation. In addition, overview regarding different non-coding RNAs as long non-coding, siRNAs and miRNAs involvement in the cardiovascular diseases is also addressed. Detailed functional analysis of this vast group of highly regulatory molecules will be promising for shaping future drug discoveries.
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36
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Raval N, Jogi H, Gondaliya P, Kalia K, Tekade RK. Cyclo-RGD Truncated Polymeric Nanoconstruct with Dendrimeric Templates for Targeted HDAC4 Gene Silencing in a Diabetic Nephropathy Mouse Model. Mol Pharm 2020; 18:641-666. [PMID: 32453574 DOI: 10.1021/acs.molpharmaceut.0c00094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diabetic nephropathy (DN), a chronic progressive kidney disease, is a significant complication of diabetes mellitus. Dysregulation of the histone deacetylases (HDACs) gene has been implicated in the pathogenesis of DN. Hence, the HDAC-inhibitors have emerged as a critical class of therapeutic agents in DN; however, the currently available HDAC4-inhibitors are mostly nonselective in nature as well as inhibit multiple HDACs. RNA interference of HDAC4 (HDAC4 siRNA) has shown immense promise, but the clinical translation has been impeded due to lack of a targeted, specific, and in vivo applicable delivery modality. In the present investigation, we examined Cyclo(RGDfC) (cRGD) truncated polymeric nanoplex with dendrimeric templates for targeted HDAC4 Gene Silencing. The developed nanoplex exhibited enhanced encapsulation of siRNA and offered superior protection against serum RNase nucleases degradation. The nanoplex was tested on podocytes (in vitro), wherein it showed selective binding to the αvβ3 integrin receptor, active cellular uptake, and significant in vitro gene silencing. The in vivo experiments showed remarkable suppression of the HDAC4 and inhibition in the progression of renal fibrosis in the Streptozotocin (STZ) induced DN C57BL/6 mice model. Histopathological and toxicological studies revealed nonsignificant abnormality/toxicity with the nanoplex. Conclusively, nanoplex was found as a promising tactic for targeted therapy of podocytes and could be extended for other kidney-related ailments.
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Affiliation(s)
- Nidhi Raval
- National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj (An Institute of National Importance), Opposite Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Hardi Jogi
- National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj (An Institute of National Importance), Opposite Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Piyush Gondaliya
- National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj (An Institute of National Importance), Opposite Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Kiran Kalia
- National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj (An Institute of National Importance), Opposite Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Rakesh K Tekade
- National Institute of Pharmaceutical Education and Research (NIPER) - Ahmedabad, Palaj (An Institute of National Importance), Opposite Air Force Station, Gandhinagar 382355, Gujarat, India
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37
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Danielsen MB, Lou C, Lisowiec-Wachnicka J, Pasternak A, Jørgensen PT, Wengel J. Gapmer Antisense Oligonucleotides Containing 2',3'-Dideoxy-2'-fluoro-3'-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing. Chemistry 2020; 26:1368-1379. [PMID: 31682037 DOI: 10.1002/chem.201904540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Indexed: 01/14/2023]
Abstract
Off-target effects remain a significant challenge in the therapeutic use of gapmer antisense oligonucleotides (AONs). Over the years various modifications have been synthesized and incorporated into AONs, however, precise control of RNase H-induced cleavage and target sequence selectivity has yet to be realized. Herein, the synthesis of the uracil and cytosine derivatives of a novel class of 2'-deoxy-2'-fluoro-3'-C-hydroxymethyl-β-d-lyxo-configured nucleotides has been accomplished and the target molecules have been incorporated into AONs. Experiments on exonuclease degradation showed improved nucleolytic stability relative to the unmodified control. Upon the introduction of one or two of the novel 2'-fluoro-3'-C-hydroxymethyl nucleotides as modifications in the gap region of a gapmer AON was associated with efficient RNase H-mediated cleavage of the RNA strand of the corresponding AON:RNA duplex. Notably, a tailored single cleavage event could be engineered depending on the positioning of a single modification. The effect of single mismatched base pairs was scanned along the full gap region demonstrating that the modification enables a remarkable specificity of RNase H cleavage. A cell-based model system was used to demonstrate the potential of gapmer AONs containing the novel modification to mediate gene silencing.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Chenguang Lou
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Anna Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Per T Jørgensen
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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38
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Abstract
Gapmers are antisense oligonucleotides composed of a central DNA segment flanked by nucleotides of modified chemistry. Hybridizing with transcripts by sequence complementarity, gapmers recruit ribonuclease H and induce target RNA degradation. Since its concept first emerged in the 1980s, much work has gone into developing gapmers for use in basic research and therapy. These include improvements in gapmer chemistry, delivery, and therapeutic safety. Gapmers have also successfully entered clinical trials for various genetic disorders, with two already approved by the U.S. Food and Drug Administration for the treatment of familial hypercholesterolemia and transthyretin amyloidosis-associated polyneuropathy. Here, we review the events surrounding the early development of gapmers, from conception to their maturity, and briefly conclude with perspectives on their use in therapy.
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Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- The Friends of Garrett Cumming Research and Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB, Canada.
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39
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Zaw K, Greer K, Aung-Htut MT, Mitrpant C, Veedu RN, Fletcher S, Wilton SD. Consequences of Making the Inactive Active Through Changes in Antisense Oligonucleotide Chemistries. Front Genet 2019; 10:1249. [PMID: 31956327 PMCID: PMC6951410 DOI: 10.3389/fgene.2019.01249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/13/2019] [Indexed: 01/02/2023] Open
Abstract
Antisense oligonucleotides are short, single-stranded nucleic acid analogues that can interfere with pre-messenger RNA (pre-mRNA) processing and induce excision of a targeted exon from the mature transcript. When developing a panel of antisense oligonucleotides to skip every dystrophin exon, we found great variation in splice switching efficiencies, with some antisense oligonucleotides ineffective, even when directed to canonical splice sites and transfected into cells at high concentrations. In this study, we re-evaluated some of these ineffective antisense oligonucleotide sequences after incorporation of locked nucleic acid residues to increase annealing potential. Antisense oligonucleotides targeting exons 16, 23, and 51 of human DMD transcripts were synthesized as two different chemistries, 2′-O-methyl modified bases on a phosphorothioate backbone or mixmers containing several locked nucleic acid residues, which were then transfected into primary human myotubes, and DMD transcripts were analyzed for exon skipping. The ineffective 2′-O-methyl modified antisense oligonucleotides induced no detectable exon skipping, while all corresponding mixmers did induce excision of the targeted exons. Interestingly, the mixmer targeting exon 51 induced two unexpected transcripts arising from partial skipping of exon 51 with retention of 95 or 188 bases from the 5′ region of exon 51. These results indicated that locked nucleic acid/2′-O-methyl mixmers are more effective at inducing exon skipping, however, this improvement may come at the cost of activating alternative cryptic splice sites and off-target effects on gene expression.
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Affiliation(s)
- Khine Zaw
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kane Greer
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science and Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science and Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Chalermchai Mitrpant
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Perron Institute for Neurological and Translational Science and Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science and Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science and Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science and Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, WA, Australia
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40
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Aupy P, Echevarría L, Relizani K, Zarrouki F, Haeberli A, Komisarski M, Tensorer T, Jouvion G, Svinartchouk F, Garcia L, Goyenvalle A. Identifying and Avoiding tcDNA-ASO Sequence-Specific Toxicity for the Development of DMD Exon 51 Skipping Therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 19:371-383. [PMID: 31881528 PMCID: PMC7063478 DOI: 10.1016/j.omtn.2019.11.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/27/2022]
Abstract
Tricyclo-DNA (tcDNA) antisense oligonucleotides (ASOs) hold promise for therapeutic splice-switching applications and the treatment of Duchenne muscular dystrophy (DMD) in particular. We have previously reported the therapeutic potential of tcDNA-ASO in mouse models of DMD, highlighting their unique pharmaceutical properties and unprecedented uptake in many tissues after systemic delivery, including the heart and central nervous system. Following these encouraging results, we developed phosphorothioate (PS)-modified tcDNA-ASOs targeting the human dystrophin exon 51 (H51). Preliminary evaluation of H51 PS-tcDNA in mice resulted in unexpected acute toxicity following intravenous administration of the selected candidate. In vivo and in vitro assays revealed complement activation, prolonged coagulation times, and platelet activation, correlating with the observed toxicity. In this study, we identify a novel PS-tcDNA sequence-specific toxicity induced by the formation of homodimer-like structures and investigate the therapeutic potential of a detoxified PS-tcDNA targeting exon 51. Modification of the H51-PS-tcDNA sequence, while maintaining target specificity through wobble pairing, abolished the observed toxicity by preventing homodimer formation. The resulting detoxified wobble-tcDNA candidate did not affect coagulation or complement pathways any longer nor activated platelets in vitro and was well tolerated in vivo in mice, confirming the possibility to detoxify specific tcDNA-ASO candidates successfully.
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Affiliation(s)
- Philippine Aupy
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | - Lucía Echevarría
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; SQY Therapeutics, 78180 Montigny le Bretonneux, France
| | - Karima Relizani
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; SQY Therapeutics, 78180 Montigny le Bretonneux, France
| | - Faouzi Zarrouki
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France
| | | | | | | | - Grégory Jouvion
- Sorbonne Université, INSERM, Pathophysiology of Pediatric Genetic Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Armand-Trousseau, UF Génétique Moléculaire, 75012 Paris, France; Institut Pasteur, Experimental Neuropathology Unit, 75015 Paris, France
| | - Fedor Svinartchouk
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; SQY Therapeutics, 78180 Montigny le Bretonneux, France
| | - Luis Garcia
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; LIA BAHN, Centre Scientifique de Monaco, 98000 Monaco
| | - Aurélie Goyenvalle
- Université Paris-Saclay, UVSQ, Inserm, END-ICAP, 78000 Versailles, France; LIA BAHN, Centre Scientifique de Monaco, 98000 Monaco.
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41
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Yoshida T, Naito Y, Yasuhara H, Sasaki K, Kawaji H, Kawai J, Naito M, Okuda H, Obika S, Inoue T. Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells. Genes Cells 2019; 24:827-835. [PMID: 31637814 PMCID: PMC6915909 DOI: 10.1111/gtc.12730] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/30/2019] [Accepted: 10/18/2019] [Indexed: 12/21/2022]
Abstract
Antisense oligonucleotide (ASO) has the potential to induce off‐target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. Conventional animal studies cannot be used to assess toxicity induced by off‐target effects because of differences in the genome sequence between humans and other animals. Consequently, the assessment of off‐target effects with in silico analysis using a human RNA database and/or in vitro expression analysis using human cells has been proposed. Our previous study showed that the number of complementary regions of ASOs with mismatches in the human RNA sequences increases dramatically as the number of tolerated mismatches increases. However, to what extent the expression of genes with mismatches is affected by off‐target effects at the cellular level is not clear. In this study, we evaluated off‐target effects of gapmer ASOs, which cleave the target RNA in an RNase H‐dependent manner, by introducing the ASO into human cells and performing microarray analysis. Our data indicate that gapmer ASOs induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also propose a scheme for the assessment of off‐target effects of gapmer ASOs.
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Affiliation(s)
- Tokuyuki Yoshida
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yuki Naito
- Database Center for Life Science (DBCLS), Mishima, Shizuoka, Japan.,National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hidenori Yasuhara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kiyomi Sasaki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Hideya Kawaji
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Setagaya-ku, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jun Kawai
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa, Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Haruhiro Okuda
- National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
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42
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Method and its Composition for encapsulation, stabilization, and delivery of siRNA in Anionic polymeric nanoplex: An In vitro- In vivo Assessment. Sci Rep 2019; 9:16047. [PMID: 31690769 PMCID: PMC6831632 DOI: 10.1038/s41598-019-52390-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/12/2019] [Indexed: 12/13/2022] Open
Abstract
Small interfering RNA (siRNA) are synthetic RNA duplex designed to specifically knockdown the abnormal gene to treat a disease at cellular and molecular levels. In spite of their high potency, specificity, and therapeutic potential, the full-fledged utility of siRNA is predominantly limited to in vitro set-up. Till date, Onpattro is the only USFDA approved siRNA therapeutics available in the clinic. The lack of a reliable in vivo siRNA delivery carrier remains a foremost obstacle towards the clinical translation of siRNA therapeutics. To address the obstacles associated with siRNA delivery, we tested a dendrimer-templated polymeric approach involving a USFDA approved carrier (albumin) for in vitro as well as in vivo delivery of siRNA. The developed approach is simple in application, enhances the serum stability, avoids in vivo RNase-degradation and mediates cytosolic delivery of siRNA following the endosomal escape process. The successful in vitro and in vivo delivery of siRNA, as well as targeted gene knockdown potential, was demonstrated by HDAC4 inhibition in vitro diabetic nephropathy (DN) podocyte model as well as in vivo DN C57BL/6 mice model. The developed approach has been tested using HDAC4 siRNA as a model therapeutics, while the application can also be extended to other gene therapeutics including micro RNA (miRNA), plasmids oligonucleotides, etc.
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43
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Yamamoto T, Sawamura M, Terada C, Kashiwada K, Wada F, Yamayoshi A, Obika S, Harada-Shiba M. Effect of modular conjugation strategy for N-acetylgalactosamine-targeted antisense oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:109-118. [PMID: 31617782 DOI: 10.1080/15257770.2019.1677911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The asialoglycoprotein receptor (ASGPr) and N-acetylgalactosamine (GalNAc) is one of the most reliable receptor-ligand combinations for delivering antisense oligonucleotides (ASOs) to the liver. Here, we show that a modular GalNAc conjugation strategy allows us to reinforce the activity of the parent, naked 2',4'-BNA/LNA gapmer targeting apolipoprotein B. The conjugation partly reduced a possible hepatotoxicity of the parent ASO. The structure-activity study revealed the significance of the metabolic susceptibility of the GalNAc moiety to nucleolytic cleavage that results in exposure of the parent gapmer. The broad usefulness of our delivery strategy of ASOs to the liver has been demonstrated.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Motoki Sawamura
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan.,Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Chisato Terada
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Koki Kashiwada
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Fumito Wada
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Mariko Harada-Shiba
- Department of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
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44
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Bosgra S, Sipkens J, de Kimpe S, den Besten C, Datson N, van Deutekom J. The Pharmacokinetics of 2'- O-Methyl Phosphorothioate Antisense Oligonucleotides: Experiences from Developing Exon Skipping Therapies for Duchenne Muscular Dystrophy. Nucleic Acid Ther 2019; 29:305-322. [PMID: 31429628 DOI: 10.1089/nat.2019.0805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Delivery to the target site and adversities related to off-target exposure have made the road to clinical success and approval of antisense oligonucleotide (AON) therapies challenging. Various classes of AONs have distinct chemical features and pharmacological properties. Understanding the similarities and differences in pharmacokinetics (PKs) among AON classes is important to make future development more efficient and may facilitate regulatory guidance of AON development programs. For the class of 2'-O-methyl phosphorothioate (2OMe PS) RNA AONs, most nonclinical and clinical PK data available today are derived from development of exon skipping therapies for Duchenne muscular dystrophy (DMD). While some publications have featured PK aspects of these AONs, no comprehensive overview is available to date. This article presents a detailed review of absorption, distribution, metabolism, and excretion of 2OMe PS AONs, compiled from publicly available data and previously unpublished internal data on drisapersen and related exon skipping candidates in preclinical species and DMD patients. Considerations regarding drug-drug interactions, toxicokinetics, and pharmacodynamics are also discussed. From the data presented, the picture emerges of consistent PK properties within the 2OMe PS class, predictable behavior across species, and a considerable overlap with other single-stranded PS AONs. A level of detail on muscle as a target tissue is provided, which was not previously available. Furthermore, muscle biopsy samples taken in DMD clinical trials allowed confirmation of the applicability of interspecies scaling approaches commonly applied in the absence of clinical target tissue data.
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45
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Hagedorn PH, Pontoppidan M, Bisgaard TS, Berrera M, Dieckmann A, Ebeling M, Møller MR, Hudlebusch H, Jensen ML, Hansen HF, Koch T, Lindow M. Identifying and avoiding off-target effects of RNase H-dependent antisense oligonucleotides in mice. Nucleic Acids Res 2019; 46:5366-5380. [PMID: 29790953 PMCID: PMC6009603 DOI: 10.1093/nar/gky397] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Antisense oligonucleotides that are dependent on RNase H for cleavage and subsequent degradation of complementary RNA are being developed as therapeutics. Besides the intended RNA target, such oligonucleotides may also cause degradation of unintended RNA off-targets by binding to partially complementary target sites. Here, we characterized the global effects on the mouse liver transcriptome of four oligonucleotides designed as gapmers, two targeting Apob and two targeting Pcsk9, all in different regions on their respective intended targets. This study design allowed separation of intended- and off-target effects on the transcriptome for each gapmer. Next, we used sequence analysis to identify possible partially complementary binding sites among the potential off-targets, and validated these by measurements of melting temperature and RNase H-cleavage rates. Generally, our observations were as expected in that fewer mismatches or bulges in the gapmer/transcript duplexes resulted in a higher chance of those duplexes being effective substrates for RNase H. Follow-up experiments in mice and cells show, that off-target effects can be mitigated by ensuring that gapmers have minimal sequence complementarity to any RNA besides the intended target, and that they do not have exaggerated binding affinity to the intended target.
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Affiliation(s)
- Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Malene Pontoppidan
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark.,Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Tina S Bisgaard
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Marco Berrera
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Andreas Dieckmann
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Martin Ebeling
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Marianne R Møller
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Heidi Hudlebusch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Marianne L Jensen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Henrik F Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Troels Koch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
| | - Morten Lindow
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark
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46
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Shen W, De Hoyos CL, Sun H, Vickers TA, Liang XH, Crooke ST. Acute hepatotoxicity of 2' fluoro-modified 5-10-5 gapmer phosphorothioate oligonucleotides in mice correlates with intracellular protein binding and the loss of DBHS proteins. Nucleic Acids Res 2019; 46:2204-2217. [PMID: 29390093 PMCID: PMC5861398 DOI: 10.1093/nar/gky060] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 01/23/2018] [Indexed: 01/06/2023] Open
Abstract
We reported previously that a 2′ fluoro-modified (2′ F) phosphorothioate (PS) antisense oligonucleotides (ASOs) with 5–10–5 gapmer configuration interacted with proteins from Drosophila behavior/human splicing (DBHS) family with higher affinity than PS-ASOs modified with 2′-O-(2-methoxyethyl) (2′ MOE) or 2′,4′-constrained 2′-O-ethyl (cEt) did. Rapid degradation of these proteins and cytotoxicity were observed in cells treated with 2′ F PS-ASO. Here, we report that 2′ F gapmer PS-ASOs of different sequences caused reduction in levels of DBHS proteins and hepatotoxicity in mice. 2′ F PS-ASOs induced activation of the P53 pathway and downregulation of metabolic pathways. Altered levels of RNA and protein markers for hepatotoxicity, liver necrosis, and apoptosis were observed as early as 24 to 48 hours after a single administration of the 2′ F PS-ASO. The observed effects were not likely due to the hybridization-dependent RNase H1 cleavage of on- or potential off-target RNAs, or due to potential toxicity of 2′ F nucleoside metabolites. Instead, we found that 2′ F PS-ASO associated with more intra-cellular proteins including proteins from DBHS family. Our results suggest that protein-binding correlates positively with the 2′ F modification-dependent loss of DBHS proteins and the toxicity of gapmer 2′ F PS-ASO in vivo.
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Affiliation(s)
- Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cheryl L De Hoyos
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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47
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Soler-Bistué A, Zorreguieta A, Tolmasky ME. Bridged Nucleic Acids Reloaded. Molecules 2019; 24:E2297. [PMID: 31234313 PMCID: PMC6630285 DOI: 10.3390/molecules24122297] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Oligonucleotides are key compounds widely used for research, diagnostics, and therapeutics. The rapid increase in oligonucleotide-based applications, together with the progress in nucleic acids research, has led to the design of nucleotide analogs that, when part of these oligomers, enhance their efficiency, bioavailability, or stability. One of the most useful nucleotide analogs is the first-generation bridged nucleic acids (BNA), also known as locked nucleic acids (LNA), which were used in combination with ribonucleotides, deoxyribonucleotides, or other analogs to construct oligomers with diverse applications. However, there is still room to improve their efficiency, bioavailability, stability, and, importantly, toxicity. A second-generation BNA, BNANC (2'-O,4'-aminoethylene bridged nucleic acid), has been recently made available. Oligomers containing these analogs not only showed less toxicity when compared to LNA-containing compounds but, in some cases, also exhibited higher specificity. Although there are still few applications where BNANC-containing compounds have been researched, the promising results warrant more effort in incorporating these analogs for other applications. Furthermore, newer BNA compounds will be introduced in the near future, offering great hope to oligonucleotide-based fields of research and applications.
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Affiliation(s)
- Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Instituto Tecnológico de Chascomús, CONICET, Universidad Nacional de San Martín, San Martín 1650, Argentina.
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires C1405BWE, Argentina.
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA.
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48
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Shen W, De Hoyos CL, Migawa MT, Vickers TA, Sun H, Low A, Bell TA, Rahdar M, Mukhopadhyay S, Hart CE, Bell M, Riney S, Murray SF, Greenlee S, Crooke RM, Liang XH, Seth PP, Crooke ST. Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index. Nat Biotechnol 2019; 37:640-650. [PMID: 31036929 DOI: 10.1038/s41587-019-0106-2] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/15/2019] [Indexed: 12/13/2022]
Abstract
The molecular mechanisms of toxicity of chemically modified phosphorothioate antisense oligonucleotides (PS-ASOs) are not fully understood. Here, we report that toxic gapmer PS-ASOs containing modifications such as constrained ethyl (cEt), locked nucleic acid (LNA) and 2'-O-methoxyethyl (2'-MOE) bind many cellular proteins with high avidity, altering their function, localization and stability. We show that RNase H1-dependent delocalization of paraspeckle proteins to nucleoli is an early event in PS-ASO toxicity, followed by nucleolar stress, p53 activation and apoptotic cell death. Introduction of a single 2'-O-methyl (2'-OMe) modification at gap position 2 reduced protein-binding, substantially decreasing hepatotoxicity and improving the therapeutic index with minimal impairment of antisense activity. We validated the ability of this modification to generally mitigate PS-ASO toxicity with more than 300 sequences. Our findings will guide the design of PS-ASOs with optimal therapeutic profiles.
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Affiliation(s)
- Wen Shen
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | | | | | | | - Hong Sun
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Audrey Low
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | | | | | | | | | | | - Stan Riney
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
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49
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Tips to Design Effective Splice-Switching Antisense Oligonucleotides for Exon Skipping and Exon Inclusion. Methods Mol Biol 2019; 1828:79-90. [PMID: 30171536 DOI: 10.1007/978-1-4939-8651-4_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Antisense-mediated exon skipping and exon inclusion have proven to be powerful tools for treating neuromuscular diseases. The approval of Exondys 51 (eteplirsen) and Spinraza (nusinersen) for the treatment of patients with Duchenne muscular dystrophy (DMD) and spinal muscular atrophy (SMA) was the most noteworthy accomplishment in 2016. Exon skipping uses short DNA-like molecules called antisense oligonucleotides (AONs) to correct the disrupted reading frame, allowing the production of functional quasi-dystrophin proteins, and ameliorate the progression of the disease. Exon inclusion for SMA employs an AON targeting an intronic splice silencer site to include an exon which is otherwise spliced out. Recently, these strategies have also been explored in many other genetic disorders, including dysferlin-deficient muscular dystrophy (e.g., Miyoshi myopathy; MM, limb-girdle muscular dystrophy type 2B; LGMD2B, and distal myopathy with anterior tibial onset; DMAT), laminin α2 chain (merosin)-deficient congenital muscular dystrophy (MDC1A), sarcoglycanopathy (e.g., limb-girdle muscular dystrophy type 2C; LGMD2C), and Fukuyama congenital muscular dystrophy (FCMD). A major challenge in exon skipping and exon inclusion is the difficulty in designing effective AONs. The mechanism of mRNA splicing is highly complex, and the efficacy of AONs is often unpredictable. We will discuss the design of effective AONs for exon skipping and exon inclusion in this chapter.
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50
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Scoles DR, Minikel EV, Pulst SM. Antisense oligonucleotides: A primer. NEUROLOGY-GENETICS 2019; 5:e323. [PMID: 31119194 PMCID: PMC6501637 DOI: 10.1212/nxg.0000000000000323] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/14/2019] [Indexed: 12/13/2022]
Abstract
There are few disease-modifying therapeutics for neurodegenerative diseases, but successes on the development of antisense oligonucleotide (ASO) therapeutics for spinal muscular atrophy and Duchenne muscular dystrophy predict a robust future for ASOs in medicine. Indeed, existing pipelines for the development of ASO therapies for spinocerebellar ataxias, Huntington disease, Alzheimer disease, amyotrophic lateral sclerosis, Parkinson disease, and others, and increased focus by the pharmaceutical industry on ASO development, strengthen the outlook for using ASOs for neurodegenerative diseases. Perhaps the most significant advantage to ASO therapeutics over other small molecule approaches is that acquisition of the target sequence provides immediate knowledge of putative complementary oligonucleotide therapeutics. In this review, we describe the various types of ASOs, how they are used therapeutically, and the present efforts to develop new ASO therapies that will contribute to a forthcoming toolkit for treating multiple neurodegenerative diseases.
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Affiliation(s)
- Daniel R Scoles
- Department of Neurology (D.R.S., S.M.P.), University of Utah, Salt Lake City, UT; and Center for the Science of Therapeutics (E.V.M.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Eric V Minikel
- Department of Neurology (D.R.S., S.M.P.), University of Utah, Salt Lake City, UT; and Center for the Science of Therapeutics (E.V.M.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Stefan M Pulst
- Department of Neurology (D.R.S., S.M.P.), University of Utah, Salt Lake City, UT; and Center for the Science of Therapeutics (E.V.M.), Broad Institute of MIT and Harvard, Cambridge, MA
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